Root: scop

Classes:

1. All alpha proteins [46456] (284)
   1. Globin-like [46457] (2)
      core: 6 helices; folded leaf, partly opened
      1. Globin-like [46458] (4)
         uperfamily
         1. Truncated hemoglobin [46459] (6)
            lack the first helix (A)
            1. Protozoan/bacterial hemoglobin [46460]
               1. Ciliate (Paramecium caudatum) [TaxId: 5885] [46461] (2)
               2. Green alga (Chlamydomonas eugametos) [TaxId: 3054] [46462] (2)
                  Globin li637
               3. Cyanobacteria (Synechocystis sp.), pcc 6803 [TaxId: 1143] [81667] (5)
                  SQ P73925
               4. Mycobacterium tuberculosis, HbN [TaxId: 1773] [63437] (4)
                  SQ Q10784
               5. Mycobacterium tuberculosis, HbO [TaxId: 1773] [88965] (1)
               6. Bacillus subtilis [TaxId: 1423] [116748] (1)
                  SQ O31607 6-124 # YjbI
         2. Nerve tissue mini-hemoglobin (neural globin) [74660] (1)
            lack the first helix but otherwise is more similar to conventional globins than the truncated ones
            1. Nerve tissue mini-hemoglobin (neural globin) [74661]
               1. Milky ribbon-worm (Cerebratulus lacteus) [TaxId: 6221] [74662] (2)
                  SQ O76242
         3. Globins [46463] (81)
            Heme-binding protein
            1. Hemoglobin I [46464]
               1. Ark clam (Scapharca inaequivalvis) [TaxId: 6561] [46465] (19)
               2. Clam (Lucina pectinata) [TaxId: 29163] [46466] (4)
            2. Trematode hemoglobin/myoglobin [63438]
               1. Paramphistomum epiclitum [TaxId: 54403] [63439] (2)
            3. Glycera globin [46467]
               1. Marine bloodworm (Glycera dibranchiata) [TaxId: 6350] [46468] (8)
            4. Myoglobin [46469]
               1. Sperm whale (Physeter catodon) [TaxId: 9755] [46470] (181)
                  SQ P02185
               2. Slug sea hare (Aplysia limacina) [TaxId: 6502] [46471] (7)
               3. Common seal (Phoca vitulina) [TaxId: 9720] [46472] (1)
               4. Pig (Sus scrofa) [TaxId: 9823] [46473] (17)
               5. Horse (Equus caballus) [TaxId: 9796] [46474] (45)
               6. Human (Homo sapiens) [TaxId: 9606] [46475] (1)
               7. Asian elephant (Elephas maximus) [TaxId: 9783] [46476] (1)
               8. Loggerhead sea turtle (Caretta caretta) [TaxId: 8467] [46477] (2)
               9. Yellowfin tuna (Thunnus albacares) [TaxId: 8236] [46478] (1)
            5. Erythrocruorin [46479]
               1. Midge (Chironomus thummi thummi), fraction III [TaxId: 7154] [46480] (4)
            6. Leghemoglobin [46481]
               1. Yellow lupin (Lupinus luteus) [TaxId: 3873] [46482] (17)
               2. Soybean (Glycine max), isoform A [TaxId: 3847] [46483] (2)
            7. Non-symbiotic plant hemoglobin [46484]
               1. Rice (Oryza sativa) [TaxId: 4530] [46485] (1)
            8. Hemoglobin, alpha-chain [46486]
               1. Human (Homo sapiens) [TaxId: 9606] [46487] (192)
                  SQ P69905 P01922 P01934 P01935
               2. Human (Homo sapiens), zeta isoform [TaxId: 9606] [68937] (1)
               3. Horse (Equus caballus) [TaxId: 9796] [46488] (19)
               4. Deer (Odocoileus virginianus) [TaxId: 9874] [46489] (1)
               5. Cow (Bos taurus) [TaxId: 9913] [46490] (11)
               6. Pig (Sus scrofa) [TaxId: 9823] [46491] (2)
               7. Maned wolf (Chrysocyon brachyurus) [TaxId: 68728] [63440] (5)
               8. Chicken (Gallus gallus) [TaxId: 9031] [46492] (1)
               9. Bar-headed goose (Anser indicus) [TaxId: 8846] [46493] (3)
               10. Graylag goose (Anser anser) [TaxId: 8843] [68938] (1)
               11. Aldabra giant tortoise (Geochelone gigantea) [TaxId: 167804] [100976] (3)
                   SQ P83134
               12. Trout (Oncorhynchus mykiss) [TaxId: 8022] [46494] (2)
               13. Emerald rockcod (Pagothenia bernacchii) [TaxId: 40690] [46495] (9)
               14. Cartilaginous fish akaei (Dasyatis akajei) [TaxId: 31902] [46496] (2)
               15. Antarctic fish (Trematomus newnesi) [TaxId: 35730] [46497] (5)
               16. Fish (Leiostomus xanthurus) [TaxId: 59837] [46498] (1)
               17. Houndshark (Mustelus griseus) [TaxId: 89020] [46499] (2)
               18. Bluefin tuna (Thunnus thynnus) [TaxId: 8237] [109623] (3)
                   SQ Q8AYM0
               19. Yellow perch (Perca flavescens) [TaxId: 8167] [116749] (1)
                   SQ P83270; 78% sequence identity
               20. Donkey (Equus asinus) [TaxId: 9793] [158217] (1)
                   SQ P01959 1-141
                   beta-chain sequences of donkey and horse hemoglobins are identical
            9. Hemoglobin, beta-chain [46500]
               1. Human (Homo sapiens) [TaxId: 9606] [46501] (195)
                  SQ P68871
               2. Human fetus (Homo sapiens), gamma-chain [TaxId: 9606] [46502] (4)
               3. Human (Homo sapiens), embryonic gower II [TaxId: 9606] [46503] (1)
               4. Horse (Equus caballus) [TaxId: 9796] [46504] (19)
               5. Donkey (Equus asinus) [TaxId: 9793] [158216] (1)
                  beta-chain sequences of donkey and horse hemoglobins are identical
               6. Deer (Odocoileus virginianus) [TaxId: 9874] [46505] (1)
               7. Cow (Bos taurus) [TaxId: 9913] [46506] (11)
               8. Pig (Sus scrofa) [TaxId: 9823] [46507] (2)
               9. Maned wolf (Chrysocyon brachyurus) [TaxId: 68728] [63441] (1)
               10. Mouse (Mus musculus) [TaxId: 10090] [68939] (1)
               11. Chicken (Gallus gallus) [TaxId: 9031] [46508] (1)
               12. Bar-headed goose (Anser indicus) [TaxId: 8846] [46509] (3)
               13. Graylag goose (Anser anser) [TaxId: 8843] [68940] (1)
               14. Aldabra giant tortoise (Geochelone gigantea) [TaxId: 167804] [100977] (3)
                   SQ P83133
               15. Trout (Oncorhynchus mykiss) [TaxId: 8022] [46510] (2)
               16. Emerald rockcod (Pagothenia bernacchii) [TaxId: 40690] [46511] (9)
               17. Cartilaginous fish akaei (Dasyatis akajei) [TaxId: 31902] [46512] (2)
               18. Antarctic fish (Trematomus newnesi) [TaxId: 35730] [46513] (5)
               19. Fish (Leiostomus xanthurus) [TaxId: 59837] [46514] (1)
               20. Houndshark (Mustelus griseus) [TaxId: 89020] [46515] (2)
               21. Bluefin tuna (Thunnus thynnus) [TaxId: 8237] [109624] (3)
                   SQ Q8AYM1
               22. Human (Homo sapiens), delta-chain [TaxId: 9606] [116750] (2)
                   SQ P02042
               23. Yellow perch (Perca flavescens) [TaxId: 8167] [116751] (7)
                   SQ P83273; 86% sequence identity
               24. Canis lupus familiaris [TaxId: 9615] [158218] (2)
            10. Chimeric hemoglobin beta-alpha [46516]
                1. Synthetic, based on Homo sapiens sequence [46517] (1)
            11. Hagfish hemoglobin [68941]
                1. Inshore hagfish (Eptatretus burgeri) [TaxId: 7764] [68942] (2)
            12. Lamprey globin [46518]
                1. Sea lamprey (Petromyzon marinus) [TaxId: 7757] [46519] (4)
                2. Lamprey (Lampetra fluviatilis) [TaxId: 7748] [88966] (1)
            13. Ascaris hemoglobin, domain 1 [46520]
                1. Pig roundworm (Ascaris suum) [TaxId: 6253] [46521] (1)
            14. Hemoglobin [46522]
                1. Innkeeper worm (Urechis caupo) [TaxId: 6431] [46523] (1)
            15. Hemoglobin, different isoforms [46524]
                1. Caudina arenicola, also known as Molpadia arenicola [TaxId: 7698] [46525] (2)
            16. Neuroglobin [100978]
                1. Human (Homo sapiens) [TaxId: 9606] [100979] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [109625] (3)
                   SQ Q9ER97
            17. Bacterial dimeric hemoglobin [46526]
                1. Vitreoscilla stercoraria [TaxId: 61] [46527] (4)
            18. Flavohemoglobin, N-terminal domain [46528]
                1. Alcaligenes eutrophus [TaxId: 106590] [46529] (1)
                2. Escherichia coli [TaxId: 562] [74663] (1)
            19. Dehaloperoxidase [46530]
                1. Amphitrite ornata [TaxId: 129555] [46531] (4)
            20. Heme-based aerotactic transducer HemAT, sensor domain [100980]
                1. Bacillus subtilis [TaxId: 1423] [100981] (2)
            21. Cytoglobin [109626]
                1. Human (Homo sapiens) [TaxId: 9606] [109627] (6)
                   SQ Q8WWM9 18-171
            22. Hypothetical protein PA3967 [109628]
                1. Pseudomonas aeruginosa [TaxId: 287] [109629] (1)
                   SQ Q9HX49
            23. Extracellular dodecameric hemoglobin (erythrocruorin), subunit IV (globin A) [116752]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [116753] (4)
                   SQ P13579
            24. Extracellular dodecameric hemoglobin (erythrocruorin), subunit II (globin B) [116754]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [116755] (4)
                   SQ P02218
            25. Extracellular dodecameric hemoglobin (erythrocruorin), subunit III (globin C) [116756]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [116757] (4)
                   SQ P11069 20-168
            26. Extracellular dodecameric hemoglobin (erythrocruorin), subunit D1 [116758]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [116759] (4)
                   SQ O61233 19-158
         4. Phycocyanin-like phycobilisome proteins [46532] (26)
            oligomers of two different types of globin-like subunits containing two extra helices at the N-terminus
            binds a bilin chromophore
            1. Phycocyanin alpha subunit [88933]
               1. Red alga (Cyanidium caldarium) [TaxId: 2771] [88934] (1)
               2. Red alga (Polysiphonia urceolata) [TaxId: 65404] [88936] (1)
               3. Cyanobacterium (Fremyella diplosiphon) [TaxId: 1197] [88937] (1)
               4. Synechococcus vulcanus [TaxId: 32053] [88938] (3)
               5. Synechococcus elongatus [TaxId: 32046] [88967] (1)
               6. Spirulina platensis [TaxId: 118562] [88939] (2)
               7. Spirulina sp. [TaxId: 1157] [158219] (12)
            2. Phycocyanin beta subunit [88940]
               1. Red alga (Cyanidium caldarium) [TaxId: 2771] [88941] (1)
               2. Red alga (Polysiphonia urceolata) [TaxId: 65404] [88942] (1)
               3. Cyanobacterium (Fremyella diplosiphon) [TaxId: 1197] [88943] (1)
               4. Synechococcus vulcanus [TaxId: 32053] [88944] (3)
               5. Synechococcus elongatus [TaxId: 32046] [88968] (1)
               6. Spirulina platensis [TaxId: 118562] [88952] (2)
            3. Allophycocyanin alpha subunit [88953]
               1. Spirulina platensis [TaxId: 118562] [88954] (1)
               2. Cyanobacterium (Mastigocladus laminosus) [TaxId: 83541] [88955] (1)
               3. Red algae (Porphyra yezoensis) [TaxId: 2788] [88956] (1)
            4. Allophycocyanin beta subunit [88957]
               1. Spirulina platensis [TaxId: 118562] [88958] (1)
               2. Cyanobacterium (Mastigocladus laminosus) [TaxId: 83541] [88959] (1)
               3. Red algae (Porphyra yezoensis) [TaxId: 2788] [88960] (1)
            5. Phycoerythrin alpha subunit [88961]
               1. Red alga (Polysiphonia urceolata) [TaxId: 65404] [88510] (1)
               2. Red alga (Griffithsia monilis) [TaxId: 42003] [88511] (1)
               3. Red algae (Gracilaria chilensis) [TaxId: 2775] [88512] (1)
            6. Phycoerythrin beta subunit [88513]
               1. Red alga (Polysiphonia urceolata) [TaxId: 65404] [88514] (1)
               2. Red alga (Griffithsia monilis) [TaxId: 42003] [88515] (1)
               3. Red algae (Gracilaria chilensis) [TaxId: 2775] [88516] (1)
               4. Cryptophyte (Rhodomonas sp. CS24) [TaxId: 79257] [46544] (3)
                  SQ P27198
      2. alpha-helical ferredoxin [46548] (2)
         contains two Fe4-S4 clusters
         uperfamily
         1. Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain [46549] (3)
            1. Succinate dehydogenase [81669]
               1. Escherichia coli [TaxId: 562] [81670] (3)
            2. Fumarate reductase [46550]
               1. Escherichia coli [TaxId: 562] [46551] (7)
               2. Wolinella succinogenes [TaxId: 844] [46552] (8)
         2. Dihydropyrimidine dehydrogenase, N-terminal domain [46553] (1)
            1. Dihydropyrimidine dehydrogenase, N-terminal domain [46554]
               includes the N-terminal tail and the linker to domain 2
               1. Pig (Sus scrofa) [TaxId: 9823] [46555] (5)
   2. Long alpha-hairpin [46556] (20)
      2 helices; antiparallel hairpin, left-handed twist
      1. GreA transcript cleavage protein, N-terminal domain [46557] (1)
         uperfamily
         1. GreA transcript cleavage protein, N-terminal domain [46558] (3)
            1. GreA transcript cleavage protein, N-terminal domain [46559]
               C-terminal domain is FKBP-like
               1. Escherichia coli [TaxId: 562] [46560] (1)
               2. Thermus aquaticus [TaxId: 271] [140098] (3)
                  SQ Q8VQD7 3-77
               3. Thermus thermophilus [TaxId: 274] [140099] (6)
                  SQ Q5SJG6 1-77! SQ Q72JT8 3-77
      2. Ribosomal protein L29 (L29p) [46561] (1)
         uperfamily
         1. Ribosomal protein L29 (L29p) [46562] (5)
            1. Ribosomal protein L29 (L29p) [46563]
               1. Archaeon Haloarcula marismortui [TaxId: 2238] [46564] (44)
                  SQ P10971
               2. Thermotoga maritima [TaxId: 2336] [109630] (1)
                  SQ P38514
               3. Thermus thermophilus [TaxId: 274] [140100] (6)
                  SQ Q5SHP6 12-62
               4. Escherichia coli [TaxId: 562] [140101] (30)
                  SQ P0A7M6 1-63
               5. Deinococcus radiodurans [TaxId: 1299] [158220] (8)
                  SQ Q9RXJ4 1-66
      3. Chaperone J-domain [46565] (1)
         uperfamily
         1. Chaperone J-domain [46566] (8)
            Pfam 00226
            1. HSC20 (HSCB), N-terminal (J) domain [46567]
               1. Escherichia coli [TaxId: 562] [46568] (1)
            2. HSP40 [46569]
               1. Human (Homo sapiens) [TaxId: 9606] [46570] (1)
            3. DnaJ chaperone, N-terminal (J) domain [46571]
               1. Escherichia coli [TaxId: 562] [46572] (3)
            4. Auxilin J-domain [88969]
               1. Cow (Bos taurus) [TaxId: 9913] [88970] (2)
            5. Hypothetical protein KIAA0730 [100982]
               1. Human (Homo sapiens) [TaxId: 9606] [100983] (1)
                  structural genomics
            6. Large T antigen, the N-terminal J domain [46573]
               1. Murine polyomavirus [TaxId: 10634] [46574] (1)
               2. Simian virus 40, Sv40 [TaxId: 10633] [68943] (1)
            7. CSL-type zinc finger-containing protein 3 (J-domain protein DjC7, 1700030a21RIK) [116760]
               1. Mouse (Mus musculus) [TaxId: 10090] [116761] (1)
                  SQ Q91ZF0 49-129
      4. Prefoldin [46579] (1)
         uperfamily
         1. Prefoldin [46580] (2)
            contains one or two beta-hairpins at the tip of alpha-hairpin
            1. Prefoldin alpha subunit [46581]
               1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [46582] (1)
            2. Prefoldin beta subunit [46583]
               1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [46584] (1)
      5. HR1 repeat [46585] (1)
         uperfamily
         1. HR1 repeat [46586] (1)
            protein kinase effector domain
            1. Protein kinase c-like 1, pkn/prk1 [46587]
               1. Human (Homo sapiens) [TaxId: 9606] [46588] (3)
      6. tRNA-binding arm [46589] (4)
         formerly a class II aminoacyl-tRNA synthetase N-domain
         uperfamily
         1. Seryl-tRNA synthetase (SerRS) [46590] (1)
            1. Seryl-tRNA synthetase (SerRS) [46591]
               1. Thermus thermophilus, strain hb27 [TaxId: 274] [46592] (4)
         2. Phenylalanyl-tRNA synthetase (PheRS) [46593] (1)
            1. Phenylalanyl-tRNA synthetase (PheRS) [46594]
               1. Thermus thermophilus [TaxId: 274] [46595] (2)
         3. Valyl-tRNA synthetase (ValRS) C-terminal domain [81635] (1)
            1. Valyl-tRNA synthetase (ValRS) C-terminal domain [81634]
               1. Thermus thermophilus [TaxId: 274] [81633] (3)
         4. Methicillin resistance protein FemA probable tRNA-binding arm [81671] (1)
            inserted in the C-terminal NAT-like domain
            1. Methicillin resistance protein FemA probable tRNA-binding arm [81672]
               proposed to bind tRNA-Gly
               1. Staphylococcus aureus [TaxId: 1280] [81673] (1)
      7. Eukaryotic DNA topoisomerase I, dispensable insert domain [46596] (1)
         uperfamily
         1. Eukaryotic DNA topoisomerase I, dispensable insert domain [46597] (1)
            1. Eukaryotic DNA topoisomerase I, dispensable insert domain [46598]
               1. Human (Homo sapiens) [TaxId: 9606] [46599] (9)
                  SQ P11387 203-767
      8. C-terminal UvrC-binding domain of UvrB [46600] (1)
         uperfamily
         1. C-terminal UvrC-binding domain of UvrB [46601] (1)
            1. C-terminal UvrC-binding domain of UvrB [46602]
               1. Escherichia coli [TaxId: 562] [46603] (2)
      9. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46604] (1)
         uperfamily
         1. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46605] (2)
            1. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46606]
               delta subunit in mitochondria
               this domain unfolds when bound to the gamma subunit
               1. Escherichia coli [TaxId: 562] [46607] (4)
               2. Cow (Bos taurus) [TaxId: 9913] [46608] (4)
      10. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46609] (1)
          uperfamily
          1. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46610] (19)
             1. Fe superoxide dismutase (FeSOD) [46611]
                1. Mycobacterium tuberculosis [TaxId: 1773] [46612] (5)
                2. Pseudomonas ovalis [TaxId: 303] [46613] (2)
                3. Escherichia coli [TaxId: 562] [46614] (13)
                4. Thermosynechococcus elongatus [TaxId: 146786] [88971] (1)
                5. Aquifex pyrophilus [TaxId: 2714] [46615] (1)
                6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [46616] (2)
                   SQ P80857
                7. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [46617] (1)
                8. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [74664] (1)
                9. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [100984] (1)
                10. Cowpea (Vigna unguiculata) [TaxId: 3917] [116762] (1)
                    SQ Q9M7R2 21-245
             2. Mn superoxide dismutase (MnSOD) [46618]
                1. Human (Homo sapiens) [TaxId: 9606] [46619] (44)
                2. Aspergillus fumigatus [TaxId: 5085] [68944] (1)
                3. Escherichia coli [TaxId: 562] [46620] (12)
                4. Thermus thermophilus [TaxId: 274] [46621] (2)
                5. Bacillus halodenitrificans [TaxId: 1482] [74665] (1)
                6. Anabaena sp. [TaxId: 1167] [74666] (1)
                7. Deinococcus radiodurans [TaxId: 1299] [116763] (3)
                   SQ Q9RUV2
             3. Cambialistic superoxide dismutase [46622]
                active with either Fe or Mn
                1. Propionibacterium shermanii [TaxId: 1752] [46623] (6)
                2. Porphyromonas gingivalis [TaxId: 837] [46624] (3)
                   SQ P19665
      11. Sporulation inhibitor Sda [100985] (1)
          uperfamily
          1. Sporulation inhibitor Sda [100986] (1)
             1. Sporulation inhibitor Sda [100987]
                1. Bacillus subtilis [TaxId: 1423] [100988] (1)
      12. Transcriptional repressor TraM [109631] (1)
          similar structure to L29p (scop_sf 46561); contains extra short helix; forms homodimer: an open bundle
          uperfamily
          1. Transcriptional repressor TraM [109632] (1)
             1. Transcriptional repressor TraM [109633]
                1. Agrobacterium tumefaciens [TaxId: 358] [109634] (3)
                   SQ Q57471
      13. DnaK suppressor protein DksA, alpha-hairpin domain [109635] (1)
          uperfamily
          1. DnaK suppressor protein DksA, alpha-hairpin domain [109636] (1)
             1. DnaK suppressor protein DksA, alpha-hairpin domain [109637]
                1. Escherichia coli [TaxId: 562] [109638] (1)
                   SQ P18274 7-151
      14. ISY1 domain-like [140102] (1)
          uperfamily
          1. ISY1 N-terminal domain-like [140103] (1)
             N-terminal region of Pfam 06246
             1. Pre-mRNA-splicing factor ISY1 homolog [140104]
                1. Mouse (Mus musculus) [TaxId: 10090] [140105] (1)
                   SQ Q69ZQ2 23-102
      15. Calcyclin-binding protein-like [140106] (1)
          uperfamily
          1. Siah interacting protein N terminal domain-like [140107] (2)
             Pfam 09032
             1. Calcyclin-binding protein, CacyBP [140108]
                1. Human (Homo sapiens) [TaxId: 9606] [140109] (3)
                   SQ Q9HB71 1-47
                2. Mouse (Mus musculus) [TaxId: 10090] [140110] (1)
                   SQ Q9CXW3 1-55
      16. Endosomal sorting complex assembly domain [140111] (3)
          forms 'fan'-like heterooligomers, in which the domains of different subunit make similar interactions at the tip of the hairpin
          uperfamily
          1. VPS23 C-terminal domain [140112] (1)
             1. Vacuolar protein sorting-associated protein 23, VPS23 [140113]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140114] (6)
                   SQ P25604 322-385! SQ P25604 325-383
          2. VPS28 N-terminal domain [140115] (1)
             includes structurally variable linker region
             1. Vacuolar protein sorting-associated protein 28, VPS28 [140116]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140117] (6)
                   SQ Q02767 15-125! SQ Q02767 23-123
          3. VPS37 C-terminal domain-like [140118] (1)
             Pfam 07200; Modifier of rudimentary, Mod(r)
             1. Vacuolar protein sorting-associated protein 37, VPS37 (SRN2) [140119]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140120] (3)
                   SQ Q99176 139-203! SQ Q99176 142-206
      17. SPy1572-like [140121] (1)
          forms homodimer: an open bundle, different from the TRAM dimer
          uperfamily
          1. SPy1572-like [140122] (1)
             1. Hypothetical protein SPy1572 [140123]
                1. Streptococcus pyogenes [TaxId: 1314] [140124] (1)
                   SQ Q99YR7 1-77
      18. Rabenosyn-5 Rab-binding domain-like [140125] (1)
          uperfamily
          1. Rabenosyn-5 Rab-binding domain-like [140126] (1)
             1. FYVE finger-containing Rab5 effector protein rabenosyn-5 [140127]
                1. Human (Homo sapiens) [TaxId: 9606] [140128] (4)
                   SQ Q9H1K0 441-501! SQ Q9H1K0 456-501! SQ Q9H1K0 734-784
      19. MxiH-like [140129] (1)
          Type III secretion system needle
          uperfamily
          1. MxiH-like [140130] (2)
             1. MxiH needle protein [140131]
                1. Shigella flexneri [TaxId: 623] [140132] (2)
                   SQ P0A223 20-78
             2. BsaL needle protein [140133]
                1. Burkholderia pseudomallei [TaxId: 28450] [140134] (1)
                   SQ Q63K18 1-84
      20. YnzC-like [158221] (1)
          1. YznC-like [158222] (1)
             Pfam 05979; DUF896
             1. Hypothetical protein YnzC [158223]
                1. Bacillus subtilis [TaxId: 1423] [158224] (1)
                   SQ O31818 1-42
   3. Type I dockerin domain [63445] (1)
      tandem repeat of two calcium-binding loop-helix motifs, distinct from the EF-hand
      1. Type I dockerin domain [63446] (1)
         uperfamily
         1. Type I dockerin domain [63447] (3)
            1. Cellulosome endoglucanase SS [63448]
               1. Clostridium thermocellum [TaxId: 1515] [63449] (2)
            2. Endo-1,4-beta-xylanase Y [100989]
               1. Clostridium thermocellum [TaxId: 1515] [100990] (3)
            3. Cellulosomal scaffolding protein A [140135]
               1. Clostridium thermocellum [TaxId: 1515] [140136] (1)
                  SQ Q06851 1793-1852
   4. LEM/SAP HeH motif [63450] (6)
      helix-extended loop-helix; parallel helices
      1. LEM domain [63451] (1)
         uperfamily
         1. LEM domain [63452] (2)
            1. Thymopoietin, LAP2 [63453]
               1. Human (Homo sapiens) [TaxId: 9606] [63454] (3)
            2. Inner nuclear membrane protein emerin [63455]
               1. Human (Homo sapiens) [TaxId: 9606] [63456] (3)
      2. SAP domain [68906] (1)
         uperfamily
         1. SAP domain [68907] (7)
            Pfam 02037
            1. DNA binding C-terminal domain of ku70 [68908]
               1. Human (Homo sapiens) [TaxId: 9606] [68909] (2)
            2. Mitochondrial resolvase ydc2 N-terminal domain [68945]
               1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [68946] (1)
            3. S/mar DNA-binding protein Tho1 [74667]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74668] (1)
            4. p53 binding domain of protein inhibitor of activated STAT protein 1, PIAS-1 [116764]
               1. Human (Homo sapiens) [TaxId: 9606] [116765] (1)
                  SQ O75925 1-65
            5. Rififylin (FYVE-RING finger protein Sakura) [116766]
               1. Human (Homo sapiens) [TaxId: 9606] [116767] (1)
                  SQ Q8WZ73 45-139
            6. Nuclear protein hcc-1 [140137]
               1. Human (Homo sapiens) [TaxId: 9606] [140138] (1)
                  SQ P82979 5-46
            7. Heterogeneous nuclear ribonucleoprotein U-like protein 1 [140139]
               1. Human (Homo sapiens) [TaxId: 9606] [140140] (1)
                  SQ Q9BUJ2 1-37
      3. Rho N-terminal domain-like [68912] (2)
         uperfamily
         1. Rho termination factor, N-terminal domain [68913] (1)
            1. Rho termination factor, N-terminal domain [68914]
               1. Escherichia coli [TaxId: 562] [50295] (14)
                  SQ P03002
         2. YqbF C-terminal domain-like [158225] (2)
            1. Hypothetical protein YqbF [158226]
               1. Bacillus subtilis [TaxId: 1423] [158227] (1)
                  SQ P45922 50-103
            2. Uncharacterized protein HI1507 in Mu-like prophage FluMu region [158228]
               1. Haemophilus influenzae [TaxId: 727] [158229] (1)
                  SQ P44229 1-38
      4. Recombination endonuclease VII, C-terminal and dimerization domains [68918] (1)
         uperfamily
         1. Recombination endonuclease VII, C-terminal and dimerization domains [68919] (1)
            1. Recombination endonuclease VII, C-terminal and dimerization domains [68920]
               1. Bacteriophage T4 [TaxId: 10665] [54074] (7)
      5. DNA-binding domain of EIN3-like [116768] (1)
         decorated with additional structures
         uperfamily
         1. DNA-binding domain of EIN3-like [116769] (1)
            middle part of Pfam 04873
            1. Ethylene insensitive 3 (EIN3)-like protein 3, EIL3 [116770]
               1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116771] (1)
                  SQ O23116 162-288
      6. PRP4-like [158230] (1)
         1. PRP4-like [158231] (1)
            Pfam 08799; pre-mRNA processing factor 4 (PRP4) like
            1. Pre-mRNA-splicing factor 18 [158232]
               1. Human (Homo sapiens) [TaxId: 9606] [158233] (1)
                  SQ Q99633 60-122
   5. SOCS box-like [158234] (1)
      helix-loop-helix motif with orthogonally packed helices
      1. SOCS box-like [158235] (1)
         1. SOCS box-like [158236] (2)
            Pfam 07525
            1. Suppressor of cytokine signaling 4, SOCS-4 [158237]
               1. Human (Homo sapiens) [TaxId: 9606] [158238] (1)
                  SQ Q8WXH5 386-429
            2. Suppressor of cytokine signaling 2, SOCS-2 [158239]
               1. Human (Homo sapiens) [TaxId: 9606] [158240] (1)
                  SQ O14508 149-198
   6. RPB6/omega subunit-like [63561] (1)
      core: 2 helices and adjacent loops
      1. RPB6/omega subunit-like [63562] (2)
         the bacterial omega and eukaryotic RPB6 subunits both function in polymerase assembly; the common core is involved in conserved interactions with other subunits
         uperfamily
         1. RNA polymerase omega subunit [63563] (3)
            4 helices; irregular array
            1. RNA polymerase omega subunit [63564]
               1. Thermus aquaticus [TaxId: 271] [63565] (3)
               2. Thermus thermophilus [TaxId: 274] [74729] (16)
                  SQ Q8RQE7; part of multichain biological unit
               3. Thermus thermophilus HB8 [TaxId: 300852] [158241] (2)
         2. RPB6 [55294] (2)
            1. RPB6 [55295]
               essential subunit of RNA polymerases I, II and III
               1. Human (Homo sapiens) [TaxId: 9606] [55296] (1)
               2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64318] (30)
                  SQ P20435; part of multichain biological unit
   7. KRAB domain (Kruppel-associated box) [109639] (1)
      2 helices: one short, one long; aromatic-rich iterface
      1. KRAB domain (Kruppel-associated box) [109640] (1)
         uperfamily
         1. KRAB domain (Kruppel-associated box) [109641] (1)
            Pfam 01352
            1. hypotheical protein 2610044O15Rik [109642]
               1. Mouse (Mus musculus) [TaxId: 10090] [109643] (1)
                  SQ Q8BG62 4-54
   8. Cytochrome c [46625] (1)
      core: 3 helices; folded leaf, opened
      1. Cytochrome c [46626] (8)
         covalently-bound heme completes the core
         uperfamily
         1. monodomain cytochrome c [46627] (44)
            1. Cytochrome c6 (synonym: cytochrome c553) [46628]
               1. Bacillus pasteurii [TaxId: 1474] [46629] (5)
               2. Monoraphidium braunii [TaxId: 34112] [46630] (3)
               3. Desulfovibrio vulgaris, different strains [TaxId: 881] [46631] (2)
               4. Desulfovibrio desulfuricans [TaxId: 876] [46632] (1)
               5. Chlamydomonas reinhardtii [TaxId: 3055] [46633] (2)
               6. Cyanobacterium (Synechococcus elongatus) [TaxId: 32046] [46634] (1)
               7. Arthrospira maxima [TaxId: 129910] [63457] (2)
               8. Green alga (Scenedesmus obliquus) [TaxId: 3088] [46635] (2)
               9. Red alga (Porphyra yezoensis) [TaxId: 2788] [63458] (1)
               10. Green alga (Cladophora glomerata) [TaxId: 162068] [81674] (1)
            2. Cytochrome c552 [46636]
               1. Thermus thermophilus [TaxId: 274] [46637] (6)
                  SQ P04164
               2. Pseudomonas nautica [TaxId: 2743] [46638] (1)
               3. Paracoccus denitrificans [TaxId: 266] [46639] (5)
               4. Hydrogenobacter thermophilus [TaxId: 940] [46640] (6)
               5. Nitrosomonas europaea [TaxId: 915] [46641] (2)
            3. Photosystem II associated cytochrome c549 [63459]
               1. Synechocystis sp., pcc 6803 [TaxId: 1143] [63460] (1)
               2. Arthrospira maxima [TaxId: 129910] [63461] (1)
            4. Cytochrome c550 [100991]
               1. Thermosynechococcus elongatus [TaxId: 146786] [100992] (2)
            5. Mitochondrial cytochrome c [46642]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46643] (45)
                  SQ P00044
               2. Horse (Equus caballus) [TaxId: 9796] [46644] (16)
                  SQ P00004
               3. Rice embryos (Oryza sativa) [TaxId: 4530] [46645] (1)
               4. Bluefin tuna (Thunnus thynnus) [TaxId: 8237] [46646] (5)
                  identical sequence to Thunnus alalunga, TaxId: 8235
               5. Bonito (Katsuwonus pelamis) [TaxId: 8226] [46647] (2)
               6. Human (Homo sapiens) [TaxId: 9606] [109644] (1)
                  SQ P99999
            6. Cytochrome ch [46648]
               1. Methylobacterium extorquens [TaxId: 408] [46649] (1)
            7. Cytochrome c2 [46650]
               1. Rhodospirillum rubrum [TaxId: 1085] [46651] (2)
               2. Rhodobacter capsulatus [TaxId: 1061] [46652] (3)
                  SQ P00094
               3. Rhodobacter sphaeroides [TaxId: 1063] [46653] (5)
               4. Rhodopseudomonas viridis [TaxId: 1079] [46654] (3)
               5. Rhodopseudomonas palustris [TaxId: 1076] [46655] (4)
               6. Rhodopila globiformis [TaxId: 1071] [46656] (1)
               7. Paracoccus denitrificans [TaxId: 266] [46657] (2)
               8. Rhodospirillum centenum [TaxId: 34018] [68947] (1)
            8. Mono-heme c-type cytochrome SoxX [81675]
               1. Rhodovulum sulfidophilum [TaxId: 35806] [81676] (7)
            9. Cytochrome c5 [46658]
               1. Azotobacter vinelandii [TaxId: 354] [46659] (1)
            10. Mono-heme c-type cytochrome ScyA [68948]
                1. Shewanella putrefaciens [TaxId: 24] [68949] (2)
            11. Cytochrome c551 [46660]
                1. Pseudomonas stutzeri [TaxId: 316] [46661] (3)
                2. Pseudomonas aeruginosa [TaxId: 287] [46662] (4)
                3. Paracoccus denitrificans [TaxId: 266] [46663] (11)
                4. Ectothiorhodospira halophila [TaxId: 1053] [46664] (1)
            12. SHP, an oxygen binding cytochrome c [46667]
                1. Rhodobacter sphaeroides [TaxId: 1063] [46668] (4)
            13. Cytochrome c'' [68950]
                close homologue of SHP
                1. Methylophilus methylotrophus, strain w3a1 [TaxId: 17] [68951] (3)
            14. p-Cresol methylhydroxylase, cytochrome c subunit [46669]
                the other subunit is a flavoprotein
                1. Pseudomonas putida [TaxId: 303] [46670] (4)
            15. Cytochrome c-L (MoxG) [109645]
                1. Methylobacterium extorquens [TaxId: 408] [109646] (1)
                   SQ P14774 49-197
         2. N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [46671] (3)
            1. N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [46672]
               the C-terminal domain is a 8-bladed beta-propeller
               1. Paracoccus pantotrophus [TaxId: 82367] [46673] (11)
                  formerly Thiosphaera pantotropha
               2. Pseudomonas aeruginosa [TaxId: 287] [46674] (9)
               3. Paracoccus denitrificans [TaxId: 266] [46675] (2)
         3. Quinoprotein alcohol dehydrogenase, C-terminal domain [68952] (2)
            1. Quinoprotein alcohol dehydrogenase, C-terminal domain [68953]
               1. Comamonas testosteroni [TaxId: 285] [68954] (1)
               2. Pseudomonas putida, hk5 [TaxId: 303] [74669] (1)
         4. Cytochrome bc1 domain [46676] (3)
            1. Cytochrome bc1 domain [46677]
               1. Cow (Bos taurus) [TaxId: 9913] [46678] (19)
                  SQ P00125
               2. Chicken (Gallus gallus) [TaxId: 9031] [46679] (3)
               3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63462] (9)
         5. Two-domain cytochrome c [46680] (3)
            duplication: consists of two cytochrome c type domains
            1. Cytochrome c4 [46681]
               1. Pseudomonas stutzeri [TaxId: 316] [46682] (3)
               2. Thiobacillus ferrooxidans [TaxId: 920] [88972] (1)
            2. Flavocytochrome c sulfide dehydrogenase, FCSD, cytochrome subunit [46683]
               1. Purple phototrophic bacterium (Chromatium vinosum) [TaxId: 1049] [46684] (1)
         6. Di-heme cytochrome c SoxA [81677] (1)
            two-domain cytochrome c with novel domain arrangement
            1. Di-heme cytochrome c SoxA [81678]
               cysteine persulfide(cys sulfane) heme coordination
               1. Rhodovulum sulfidophilum [TaxId: 35806] [81679] (11)
         7. Di-heme cytochrome c peroxidase [46685] (3)
            duplication: contains two cytochrome c-type domains
            1. Di-heme cytochrome c peroxidase [46686]
               1. Pseudomonas aeruginosa [TaxId: 287] [46687] (5)
               2. Pseudomonas nautica [TaxId: 2743] [100993] (3)
                  SQ P83787
               3. Nitrosomonas europaea [TaxId: 915] [68955] (1)
         8. Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [68956] (2)
            1. Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [68957]
               duplication: tandem repeat of two cytochrome c-like domains
               1. Paracoccus denitrificans [TaxId: 266] [68958] (2)
               2. Pseudomonas putida [TaxId: 303] [68959] (2)
   9. DNA/RNA-binding 3-helical bundle [46688] (14)
      core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
      1. Homeodomain-like [46689] (19)
         consists only of helices
         uperfamily
         1. Homeodomain [46690] (42)
            Pfam 00046
            1. Engrailed Homeodomain [46691]
               1. Drosophila melanogaster [TaxId: 7227] [46692] (10)
            2. Mating type protein A1 Homeodomain [46693]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46694] (6)
            3. mat alpha2 Homeodomain [46695]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46696] (6)
            4. Hepatocyte nuclear factor 1a (LFB1/HNF1) [46697]
               atypical Homeodomain with a large insertion into HTH motif
               1. Rat (Rattus rattus) [TaxId: 10117] [46698] (2)
               2. Human (Homo sapiens) [TaxId: 9606] [81680] (1)
            5. Oct-1 POU Homeodomain [46699]
               1. Human (Homo sapiens) [TaxId: 9606] [46700] (7)
            6. Pit-1 POU homeodomain [46701]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [46702] (1)
            7. Thyroid transcription factor 1 homeodomain [46703]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [46704] (1)
            8. Oct-2 POU Homeodomain [46705]
               1. Human (Homo sapiens) [TaxId: 9606] [46706] (1)
            9. Oct-3 POU Homeodomain [46707]
               1. Mouse (Mus musculus) [TaxId: 10090] [46708] (1)
            10. Homeobox protein hox-b1 [46709]
                1. Human (Homo sapiens) [TaxId: 9606] [46710] (1)
            11. Homeobox protein hox-a9 [100994]
                1. Mouse (Mus musculus) [TaxId: 10090] [100995] (1)
            12. pbx1 [46711]
                1. Human (Homo sapiens) [TaxId: 9606] [46712] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [46713] (2)
            13. Insulin gene enhancer protein isl-1 [46714]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [46715] (1)
            14. Msx-1 homeodomain [63463]
                1. Mouse (Mus musculus) [TaxId: 10090] [63464] (1)
            15. Antennapedia Homeodomain [46716]
                1. Drosophila melanogaster [TaxId: 7227] [46717] (5)
            16. Ultrabithorax (ubx) homeodomain [46718]
                1. Drosophila melanogaster [TaxId: 7227] [46719] (1)
            17. Extradenticle (exd) homeodomain [46720]
                1. Drosophila melanogaster [TaxId: 7227] [46721] (3)
            18. Even-skipped homeodomain [63465]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63466] (1)
            19. Fushi Tarazu protein [46722]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46723] (1)
            20. VND/NK-2 protein [46724]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46725] (4)
            21. Paired protein [46726]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46727] (1)
            22. Homeo-prospero domain of Prospero protein [81681]
                single domain composed of a homeodomain-homology N-terminal region (1245-1295) and the prospero-specific C-terminal region (1296-1396) that forms a 4-helical bundle
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [81682] (2)
            23. Homeodomain-only protein, Hop [109647]
                1. Mouse (Mus musculus) [TaxId: 10090] [109648] (2)
                   SQ Q8R1H0
            24. ZF-HD homeobox protein At5g65410 [116772]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116773] (1)
                   SQ Q9FKP8 182-248
            25. ZF-HD homeobox protein At4g24660 [116774]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116775] (1)
                   SQ Q9SB61 148-215
            26. DNA-binding protein SATB2 [116776]
                1. Human (Homo sapiens) [TaxId: 9606] [116777] (1)
                   SQ Q9UPW6 615-672 # the structure of the 1st CUT domain (350-437) is also known: 1WIZ
            27. Homeobox-leucine zipper protein Homez [116778]
                1. Human (Homo sapiens) [TaxId: 9606] [116779] (1)
                   SQ Q8IX15 337-399
                   Structural genomics target
            28. Hepatocyte nuclear factor 6 [116780]
                1. Mouse (Mus musculus) [TaxId: 10090] [116781] (1)
                   SQ O08755 291-437
            29. LAG1 longevity assurance homolog 5, LASS5 [140141]
                1. Mouse (Mus musculus) [TaxId: 10090] [140142] (1)
                   SQ Q9D6K9 77-135
            30. Paired box protein pax6 [140143]
                1. Human (Homo sapiens) [TaxId: 9606] [140144] (1)
                   SQ P26367 211-278
            31. Transcriptional adaptor 2-like, TADA2L, isoform b [140145]
                1. Human (Homo sapiens) [TaxId: 9606] [140146] (1)
                   SQ Q9BVJ0 72-118
            32. Lag1 longevity assurance homolog 6, LASS6 [140147]
                1. Mouse (Mus musculus) [TaxId: 10090] [140148] (1)
                   SQ Q8C172 76-127
            33. Homeobox protein prh [140149]
                1. Human (Homo sapiens) [TaxId: 9606] [140150] (1)
                   SQ Q03014 138-194
            34. Pituitary homeobox 2 [140151]
                1. Human (Homo sapiens) [TaxId: 9606] [140152] (1)
                   SQ Q99697 85-144
            35. Homeobox protein pknox1 [140153]
                1. Human (Homo sapiens) [TaxId: 9606] [140154] (1)
                   SQ P55347 257-318
            36. Homeotic bicoid protein [140155]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140156] (1)
                   SQ P09081 97-163
            37. Hypothetical protein 4930532d21rik [140157]
                1. Mouse (Mus musculus) [TaxId: 10090] [140158] (1)
                   SQ Q8C0V1 712-760
            38. Homeobox-containing protein 1, HMBOX1 (Flj21616) [140159]
                1. Human (Homo sapiens) [TaxId: 9606] [140160] (1)
                   SQ Q6NT76 268-350
            39. Homeobox protein hox-b13 [140161]
                1. Human (Homo sapiens) [TaxId: 9606] [140162] (1)
                   SQ Q92826 216-273
            40. Zinc fingers and homeoboxes protein 1, ZHX1 [158242]
                1. Human (Homo sapiens) [TaxId: 9606] [158243] (1)
                   SQ Q9UKY1 565-640
         2. Recombinase DNA-binding domain [46728] (5)
            1. HIN recombinase (DNA-binding domain) [46729]
               1. Synthetic [46730] (8)
            2. gamma,delta resolvase (C-terminal domain) [46731]
               1. Escherichia coli [TaxId: 562] [46732] (11)
            3. Transposase tc3a1-65 [46733]
               1. Caenorhabditis elegans [TaxId: 6239] [46734] (2)
                  SQ P34257 2-104
            4. Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase [46735]
               contains additional helix at each terminus
               1. Bacteriophage mu [TaxId: 10677] [46736] (2)
            5. Transposase [46737]
               1. Bacteriophage mu [TaxId: 10677] [46738] (2)
         3. Myb/SANT domain [46739] (15)
            1. c-Myb, DNA-binding domain [46740]
               duplication
               1. Mouse (Mus musculus) [TaxId: 10090] [46742] (16)
            2. b-Myb DNA binding domain [46743]
               1. Chicken (Gallus gallus) [TaxId: 9031] [46744] (1)
            3. v-Myb [68960]
               1. Avian myeloblastosis virus [TaxId: 11866] [68961] (1)
            4. Rap1 [63467]
               1. Human (Homo sapiens) [TaxId: 9606] [63468] (1)
            5. SANT domain of the nucleosome remodeling ATPase ISWI [100996]
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [100997] (1)
            6. 2610100b20rik gene product [109649]
               1. Mouse (Mus musculus) [TaxId: 10090] [109650] (1)
                  SQ Q80TB4 1951-2032
            7. Hypothetical protein C14orf106 (KIAA1903) [116782]
               1. Human (Homo sapiens) [TaxId: 9606] [116783] (1)
                  SQ Q6P0N0 877-936
            8. Metastasis associated protein MTA3 [140163]
               1. Mouse (Mus musculus) [TaxId: 10090] [140164] (1)
                  SQ Q924K8 267-323
            9. REST corepressor 1, CoREST [140165]
               1. Human (Homo sapiens) [TaxId: 9606] [140166] (2)
                  SQ Q9UKL0 376-440
            10. Radialis [140167]
                stand-alone Myb/SANT domain
                1. Garden snapdragon (Antirrhinum majus) [TaxId: 4151] [140168] (1)
                   SQ Q58FS3 8-70
            11. DnaJ homolog subfamily C member 1 [140169]
                1. Human (Homo sapiens) [TaxId: 9606] [140170] (2)
                   SQ Q96KC8 327-385! SQ Q96KC8 484-543
            12. Nuclear receptor corepressor 2 [140171]
                1. Human (Homo sapiens) [TaxId: 9606] [140172] (1)
                   SQ Q9Y618 413-480
            13. MYSM1 (KIAA1915) [140173]
                1. Human (Homo sapiens) [TaxId: 9606] [140174] (1)
                   SQ Q5VVJ2 117-181
            14. Telomere binding protein TBP1 [158244]
                1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [158245] (3)
                   SQ Q84ZU4 578-660
            15. Telomere repeat-binding protein [158246]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [158247] (1)
                   SQ Q9LTI6 464-560
         4. SLIDE domain [100998] (1)
            myb-related probable DNA-binding motif
            1. SLIDE domain of the nucleosome remodeling ATPase ISWI [100999]
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101000] (1)
         5. GARP response regulators [81683] (1)
            plant myb-related DNA-binding motif
            1. Arr10-B [81684]
               1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [81685] (1)
         6. DNA-binding domain of telomeric protein [46745] (2)
            part of Pfam 00249 (Myb/SANT domain)
            1. DNA-binding domain of human telomeric protein, hTRF1 [46746]
               1. Human (Homo sapiens) [TaxId: 9606] [46747] (4)
                  SQ P54274 379-430 # structure of dimerisation domain (62-265) is also known (scop_sp 63603)
            2. Telomeric repeat binding factor 2, TRF2 [116784]
               1. Human (Homo sapiens) [TaxId: 9606] [116785] (4)
                  SQ Q15554 446-500 # structure of dimerisation domain (43-245) is also known (scop_sp 63605)
         7. Paired domain [46748] (3)
            duplication: consists of two domains of this fold
            1. Pax-5 [68962]
               1. Human (Homo sapiens) [TaxId: 9606] [68963] (2)
            2. Pax-6 [68936]
               1. Human (Homo sapiens) [TaxId: 9606] [46750] (1)
            3. Paired protein (prd) [46751]
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46752] (1)
         8. DNA-binding domain of rap1 [46753] (1)
            duplication: consist of two domains of this fold
            1. DNA-binding domain of rap1 [46754]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46755] (1)
         9. Centromere-binding [46756] (2)
            duplication: tandem repeat of two similar domains
            1. DNA-binding domain of centromere binding protein B (CENP-B) [46757]
               1. Human (Homo sapiens) [TaxId: 9606] [46758] (2)
            2. Ars-binding protein 1, ABP1 [74670]
               1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [74671] (1)
         10. FIS-like [100918] (4)
             1. FIS protein [48285]
                includes N-terminal dimerisation subdomain
                1. Escherichia coli [TaxId: 562] [48286] (12)
             2. DNA-binding domain of NTRC [48287]
                includes N-terminal dimerisation subdomain
                1. Salmonella typhimurium [TaxId: 90371] [48288] (1)
             3. Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain [101001]
                1. Rhodobacter sphaeroides [TaxId: 1063] [101002] (1)
             4. Transcriptional regulator TyrR, C-terminal domain [63470]
                1. Haemophilus influenzae [TaxId: 727] [63471] (1)
         11. AraC type transcriptional activator [46759] (2)
             duplication: consists of two structural repeats bipartite HTH protein
             1. MarA [46760]
                1. Escherichia coli [TaxId: 562] [46761] (1)
             2. Rob transcription factor, N-terminal domain [46762]
                1. Escherichia coli [TaxId: 562] [46763] (1)
         12. Tetracyclin repressor-like, N-terminal domain [46764] (34)
             1. Tetracyclin repressor (Tet-repressor, TetR) [46765]
                1. Escherichia coli [TaxId: 562] [46766] (13)
             2. Multidrug binding protein QacR [68964]
                1. Staphylococcus aureus [TaxId: 1280] [68965] (47)
                   SQ P23217
             3. Hypothetical transcriptional regulator YcdC [88973]
                1. Escherichia coli [TaxId: 562] [88974] (1)
             4. Hypothetical transcriptional regulator YsiA [101003]
                1. Bacillus subtilis [TaxId: 1423] [101004] (1)
             5. Hypothetical transcriptional regulator YfiR [101005]
                1. Bacillus subtilis [TaxId: 1423] [101006] (1)
             6. Ethr repressor [109651]
                1. Mycobacterium tuberculosis [TaxId: 1773] [109652] (3)
                   SQ P96222 22-215
             7. A-factor receptor homolog CprB [109653]
                gamma-butyrolactone receptor
                1. Streptomyces coelicolor [TaxId: 1902] [109654] (2)
                   SQ O66122
             8. Putative transcriptional repressor YbiH [109655]
                1. Salmonella typhimurium [TaxId: 90371] [109656] (1)
                   SQ Q8ZQN9
             9. Putative transcriptional regulator YxaF [109657]
                1. Bacillus subtilis [TaxId: 1423] [109658] (1)
                   SQ P42105
             10. Transcriptional regulator BC3163 [140175]
                 1. Bacillus cereus [TaxId: 1396] [140176] (1)
                    SQ Q81BJ4 9-77
             11. Putative transcriptional regulator [140177]
                 1. Rhodococcus sp. rha1 [TaxId: 101510] [140178] (2)
             12. Putative transcriptional regulator SCO5951 [140179]
                 1. Streptomyces coelicolor [TaxId: 1902] [140180] (2)
                    SQ O54180 13-80
             13. Transcriptional regulator Cgl2612 [140181]
                 1. Corynebacterium glutamicum [TaxId: 1718] [140182] (4)
                    SQ Q8NMG3 1-174
             14. Transcriptional regulator EF0787 [140183]
                 1. Enterococcus faecalis [TaxId: 1351] [140184] (2)
                    SQ Q837P6 4-71
             15. Putative transcriptional regulator RHA1_ro09068 [140185]
                 1. Rhodococcus sp. [TaxId: 1831] [140186] (2)
                    SQ Q0RX74 10-78
             16. Probable transcriptional regulator PA3133 [140187]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140188] (1)
                    SQ Q9HZ91 1-76
             17. Transcriptional regulator RHA1_ro04179 [140189]
                 1. Rhodococcus sp. [TaxId: 1831] [140190] (4)
                    SQ Q0S914 9-77
             18. Transcriptional regulator BC5000 [140191]
                 1. Bacillus cereus [TaxId: 1396] [140192] (2)
                    SQ Q815X4 6-77
             19. Probable transcriptional regulator RHA1_ro04631 [140193]
                 1. Rhodococcus sp. rha1 [TaxId: 101510] [140194] (2)
                    SQ Q0S7R9 4-80
             20. Putative transcriptional regulator Rha04620 [140195]
                 1. Rhodococcus sp. rha1 [TaxId: 101510] [140196] (1)
             21. Hemolysin II regulatory protein, HlyIIR [140197]
                 1. Bacillus cereus [TaxId: 1396] [140198] (1)
                    SQ Q7X506 4-76
             22. Putative transcriptional regulator SCO7704 [140199]
                 1. Streptomyces coelicolor [TaxId: 1902] [140200] (1)
                    SQ Q93JG8 16-83
             23. Probable transcriptional regulator PA1836 [140201]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140202] (1)
                    SQ Q9I2Q9 6-75
             24. Putative regulator SCO4008 [140203]
                 1. Streptomyces coelicolor [TaxId: 1902] [140204] (2)
                    SQ Q9ADP7 7-74
             25. Transcriptional regulator PsrA [140205]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140206] (1)
                    SQ Q9HZJ9 2-80
             26. Putative transcriptional regulator SCO0857 [140207]
                 1. Streptomyces coelicolor [TaxId: 1902] [140208] (2)
                    SQ Q9RCV4 35-99
             27. Transcriptional regulator TM1030 [140209]
                 1. Thermotoga maritima [TaxId: 2336] [140210] (5)
                    SQ Q9X0C0 1-75! SQ Q9X0C0 2-75
             28. Putative transcriptional regulator Atu0279 [140211]
                 1. Agrobacterium tumefaciens [TaxId: 358] [140212] (1)
                    SQ Q8UIL4 3-76
             29. Transcriptional activator DhaS [158248]
                 1. Lactococcus lactis [TaxId: 1358] [158249] (2)
                    SQ Q9CIV9 8-78
             30. Putative transcriptional regulator SCO4940 [158250]
                 1. Streptomyces coelicolor [TaxId: 1902] [158251] (1)
                    SQ Q8CJS4 8-82
             31. Putative transcriptional regulator RHA1_ro03468 [158252]
                 1. Rhodococcus sp. RHA1 [TaxId: 101510] [158253] (2)
                    SQ Q0SB15 18-87
             32. Putative regulatory protein Sco4313 [158254]
                 1. Streptomyces coelicolor [TaxId: 1902] [158255] (1)
                    SQ Q9KXS8 8-86
             33. Transcriptional regulator Cgl1640/Cg1846 [158256]
                 1. Corynebacterium glutamicum [TaxId: 1718] [158257] (1)
                    SQ Q8NQ14 1-78
             34. Putative transcriptional regulator SCO4850 [158258]
                 1. Streptomyces coelicolor [TaxId: 1902] [158259] (1)
                    SQ Q9KZ96 15-89
         13. Middle operon regulator, Mor [109659] (1)
             contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
             1. Middle operon regulator, Mor [109660]
                1. Bacteriophage Mu [TaxId: 10677] [109661] (1)
                   SQ P23848 27-120
         14. Psq domain [140213] (1)
             Pfam 05225
             1. Ligand-dependent corepressor (LCoR) [140214]
                1. Human (Homo sapiens) [TaxId: 9606] [140215] (1)
                   SQ Q96JN0 343-405
         15. Alr1493-like [140216] (1)
             Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
             1. Hypothetical protein Ava_0674 (Alr1493 orthologue) [140217]
                1. Anabaena variabilis [TaxId: 1172] [140218] (2)
                   SQ Q3MFD8 1-102
         16. Nanomeric phage protein-like [140219] (1)
             contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
             1. Phage protein BC1890 [140220]
                1. Bacillus cereus [TaxId: 1396] [140221] (6)
                   SQ Q81ES4 13-132
                   host bacterium
         17. SWIRM domain [140222] (3)
             Pfam 04433; contains extra N-terminal helix
             1. Transcription regulatory protein swi3 [140223]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140224] (1)
                   SQ P32591 311-395
             2. Transcriptional adaptor 2-like, TADA2L [140225]
                1. Mouse (Mus musculus) [TaxId: 10090] [140226] (3)
                   SQ Q8CHV6 343-443! SQ Q8CHV6 355-443
             3. Lysine-specific histone demethylase 1, LSD1 [140227]
                1. Human (Homo sapiens) [TaxId: 9606] [140228] (9)
                   SQ O60341 169-279
         18. Cgl2762-like [158260] (1)
             Pfam 01527; Transposase 8
             1. Uncharacterized protein Cgl2762 [158261]
                1. Corynebacterium glutamicum [TaxId: 1718] [158262] (1)
                   SQ Q8NM20 1-89
         19. RpiR-like [158263] (1)
             Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
             1. Putative transcriptional regulator YbbH [158264]
                1. Bacillus subtilis [TaxId: 1423] [158265] (3)
                   SQ Q45581 1-83
      2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
         uperfamily
         1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3)
            1. Ada DNA repair protein [46769]
               1. Escherichia coli [TaxId: 562] [46770] (1)
            2. O6-alkylguanine-DNA alkyltransferase [46771]
               1. Human (Homo sapiens) [TaxId: 9606] [46772] (9)
                  SQ P16455 6-176
               2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [46773] (1)
      3. ARID-like [46774] (1)
         contains extra helices at both N- and C-termini
         uperfamily
         1. ARID domain [46775] (4)
            1. DNA-binding domain from the dead ringer protein [46776]
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46777] (2)
            2. MRF-2 DNA-binding domain [46779]
               1. Human (Homo sapiens) [TaxId: 9606] [46780] (2)
            3. Transcription regulator Adr6 (Swi1) [74672]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74673] (2)
            4. SWI-SNF complex protein p270, SMARCF1 [109662]
               1. Human (Homo sapiens) [TaxId: 9606] [109663] (1)
                  SQ O14497 617-736
      4. "Winged helix" DNA-binding domain [46785] (84)
         contains a small beta-sheet (wing)
         uperfamily
         1. Biotin repressor-like [46786] (2)
            1. Biotin repressor, N-terminal domain [46787]
               the middle domain is an alpha+beta fold somewhat similar to the SH2 fold
               C-terminal domain has SH3-like common fold
               1. Escherichia coli [TaxId: 562] [46788] (5)
            2. Putative transcriptional regulator TM1602, N-terminal domain [74674]
               1. Thermotoga maritima [TaxId: 2336] [74675] (1)
         2. LexA repressor, N-terminal DNA-binding domain [46789] (1)
            1. LexA repressor, N-terminal DNA-binding domain [46790]
               1. Escherichia coli [TaxId: 562] [46791] (4)
         3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
            1. Arginine repressor (ArgR), N-terminal DNA-binding domain [46793]
               1. Escherichia coli [TaxId: 562] [46794] (1)
               2. Bacillus stearothermophilus [TaxId: 1422] [46795] (1)
               3. Bacillus subtilis [TaxId: 1423] [68966] (6)
         4. Transcriptional repressor Rex, N-terminal domain [101007] (1)
            1. Transcriptional repressor Rex, N-terminal domain [101008]
               AT-rich DNA-binding protein p25
               1. Thermus aquaticus [TaxId: 271] [101009] (3)
                  SQ Q9X2V5; # CASP5
         5. CAP C-terminal domain-like [46796] (9)
            1. Catabolite gene activator protein (CAP), C-terminal domain [46797]
               N-terminal domain has double beta-helix fold
               1. Escherichia coli [TaxId: 562] [46798] (26)
            2. CO-sensing protein CooA, C-terminal domain [46799]
               1. Rhodospirillum rubrum [TaxId: 1085] [46800] (1)
            3. Listeriolysin regulatory protein PrfA, C-terminal domain [88975]
               1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [88976] (11)
            4. Transcriptional regulator PG0396, C-terminal domain [140229]
               1. Porphyromonas gingivalis [TaxId: 837] [140230] (1)
                  SQ Q7MAW7 152-232
            5. Probable transcription regulator BT4300, C-terminal domain [140231]
               1. Bacteroides thetaiotaomicron [TaxId: 818] [140232] (1)
                  SQ Q89ZS6 148-220
            6. Transcriptional regulator TTHA1359, C-terminal domain [140233]
               1. Thermus thermophilus [TaxId: 274] [140234] (1)
                  SQ Q5SIL0 118-199
            7. Cyclic AMP receptor-like protein Vfr [158266]
               1. Pseudomonas aeruginosa [TaxId: 287] [158267] (1)
                  SQ P55222 143-213
            8. Chlorophenol reduction protein CprK [158268]
               1. Desulfitobacterium dehalogenans [TaxId: 36854] [158269] (2)
                  SQ Q9LAS2 148-226
               2. Desulfitobacterium hafniense [TaxId: 49338] [158270] (7)
                  SQ Q18R04 148-227! SQ Q18R04 148-229
         6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
            Swapped dimer with the "wing" C-terminal strands
            1. LprA [68968]
               1. Archaeon Pyrococcus furiosus [TaxId: 2261] [68969] (1)
            2. Putative transcriptional regulator PH1519 [101010]
               archaeal feast/famine regulatory protein
               1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101011] (3)
                  identical sequence to Pyrococcus sp. ot3 protein
            3. Regulatory protein AsnC [140235]
               1. Escherichia coli [TaxId: 562] [140236] (2)
                  SQ P0ACI6 4-66
            4. Transcriptional regulator LrpC [140237]
               1. Bacillus subtilis [TaxId: 1423] [140238] (8)
                  SQ P96582 1-63
         7. ArsR-like transcriptional regulators [46801] (4)
            The N- and C-terminal helical extensions to the common fold form the dimer interface
            1. SmtB repressor [46802]
               1. Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129] [46803] (4)
                  SQ P30340
            2. Metal-sensing transcriptional repressor CzrA [109664]
               1. Staphylococcus aureus [TaxId: 1280] [109665] (2)
                  SQ O85142
            3. Putative arsenical resistance operon repressor AF0168 [116786]
               lacks the extra C-terminal helix
               1. Archaeoglobus fulgidus [TaxId: 2234] [116787] (1)
                  SQ O30069
            4. Cadmium efflux system accessory protein CadC [140239]
               1. Staphylococcus aureus [TaxId: 1280] [140240] (4)
                  SQ P20047 12-119
         8. Transcriptional regulator IclR, N-terminal domain [74676] (1)
            1. Transcriptional regulator IclR, N-terminal domain [74677]
               1. Thermotoga maritima [TaxId: 2336] [74678] (1)
         9. MarR-like transcriptional regulators [63379] (20)
            The N- and C-terminal helical extensions to the common fold form the dimer interface
            1. Multiple antibiotic resistance repressor, MarR [68970]
               1. Escherichia coli [TaxId: 562] [68971] (1)
            2. MexR repressor [81686]
               1. Pseudomonas aeruginosa [TaxId: 287] [81687] (1)
            3. Transcriptional regulator SlyA [81688]
               1. Enterococcus faecalis [TaxId: 1351] [81689] (1)
               2. Salmonella typhimurium [TaxId: 90371] [158271] (2)
                  SQ P40676 1-140
            4. Staphylococcal accessory regulator A homolog, SarR [63472]
               1. Staphylococcus aureus [TaxId: 1280] [63473] (1)
            5. Staphylococcal accessory regulator A homolog, SarS [88977]
               duplication: tandem repeat of two SarR-like domains assembled together as in the SarR dimer
               1. Staphylococcus aureus [TaxId: 1280] [88978] (1)
            6. Pleiotropic regulator of virulence genes, SarA [48292]
               closely related to SarR but adopts a different fold; possible experimental artifact?
               1. Staphylococcus aureus [TaxId: 1280] [48293] (5)
            7. Putative transcriptional regulator YusO [101012]
               1. Bacillus subtilis [TaxId: 1423] [101013] (1)
            8. Hypothetical protein PH1061 [101014]
               1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101015] (1)
            9. Putative transcriptional regulator TM0816 [140241]
               1. Thermotoga maritima [TaxId: 2336] [140242] (2)
                  SQ Q9WZS3 1-140
            10. Probable transcriptional regulator PA3067 [140243]
                1. Pseudomonas aeruginosa [TaxId: 287] [140244] (4)
                   SQ Q9HZE1 2-146
            11. Probable transcriptional regulator PA4135 [140245]
                1. Pseudomonas aeruginosa [TaxId: 287] [140246] (1)
                   SQ Q9HWP6 5-140
            12. Organic hydroperoxide resistance transcriptional regulator OhrR [140247]
                1. Bacillus subtilis [TaxId: 1423] [140248] (7)
                   SQ O34777 8-144
            13. Transcriptional regulator PA3341 [140249]
                1. Pseudomonas aeruginosa [TaxId: 287] [140250] (1)
                   SQ Q9HYQ4 8-144
            14. Protease production regulatory protein Hpr [140251]
                1. Bacillus subtilis [TaxId: 1423] [140252] (4)
                   SQ P11065 6-167
            15. Transcriptional regulator TM0710 [140253]
                1. Thermotoga maritima [TaxId: 2336] [140254] (4)
                   SQ Q9WZG9 5-143
            16. Transcriptional regulator DR1159 [140255]
                1. Deinococcus radiodurans [TaxId: 1299] [140256] (2)
                   SQ Q9RV71 8-179
            17. Transcriptional regulator MgrA [158272]
                1. Staphylococcus aureus [TaxId: 1280] [158273] (1)
                   SQ Q7A1J9 6-141
            18. Ta1064 (RFK), N-terminal domain [158274]
                1. Thermoplasma acidophilum [TaxId: 2303] [158275] (1)
                   SQ Q9HJA6 5-89
            19. Transcriptional regulator OEOE1854 [158276]
                1. Oenococcus oeni [TaxId: 1247] [158277] (4)
                   SQ Q04CY6 3-137
         10. DNA-binding protein Mj223 [81690] (1)
             homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold
             1. DNA-binding protein Mj223 [81691]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [81692] (1)
         11. Penicillinase repressor [101016] (4)
             homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
             1. Methicillin resistance regulatory protein MecI [101017]
                1. Staphylococcus aureus [TaxId: 1280] [101018] (8)
             2. Penicillinase repressor BlaI [101019]
                1. Bacillus licheniformis [TaxId: 1402] [101020] (2)
                2. Staphylococcus aureus [TaxId: 1280] [109666] (2)
                   SQ Q9K4N1
             3. Hypothetical protein Rv1846c [158278]
                MT1894
                1. Mycobacterium tuberculosis [TaxId: 1773] [158279] (2)
                   SQ P95163 3-124
         12. GntR-like transcriptional regulators [46804] (4)
             1. Fatty acid responsive transcription factor FadR, N-terminal domain [46805]
                1. Escherichia coli [TaxId: 562] [46806] (5)
             2. Transcriptional repressor TraR, N-terminal domain [140257]
                1. Streptomyces sp. [TaxId: 1931] [140258] (1)
                   SQ Q54677 1-99
                   78% identity to the UniProt entry species
             3. Transcriptional regulator YydK [158280]
                1. Bacillus subtilis [TaxId: 1423] [158281] (3)
                   SQ Q45591 5-82
             4. Putative transcriptional regulator RHA1_ro03477 [158282]
                1. Rhodococcus sp. RHA1 [TaxId: 101510] [158283] (1)
                   SQ Q0SB06 25-93
         13. N-terminal domain of Bacillus PurR [101021] (1)
             1. N-terminal domain of Bacillus PurR [101022]
                1. Bacillus subtilis [TaxId: 1423] [101023] (2)
         14. Replication terminator protein (RTP) [46807] (1)
             1. Replication terminator protein (RTP) [46808]
                contains long helix in the C-terminal extension; forms dimer similar to the LysR-like dimer
                1. Bacillus subtilis [TaxId: 1423] [46809] (10)
         15. LysR-like transcriptional regulators [88979] (2)
             contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
             1. LysR-type regulatory protein CbnR [88980]
                1. Ralstonia eutropha [TaxId: 106590] [88981] (2)
             2. Probable LysR-type transcriptional regulator PA0477 [140259]
                1. Pseudomonas aeruginosa [TaxId: 287] [140260] (4)
                   SQ Q9I641 3-91
         16. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
             contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
             1. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46811]
                1. Escherichia coli [TaxId: 562] [46812] (3)
         17. Transcription factor MotA, activation domain [46813] (1)
             The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
             1. Transcription factor MotA, activation domain [46814]
                1. Bacteriophage T4 [TaxId: 10665] [46815] (2)
         18. Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
             contains extra N-terminal helix
             1. Transcription factor E/IIe-alpha, N-terminal domain [101025]
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101026] (1)
         19. FUR-like [101027] (1)
             contains extra N-terminal helix and an alpha+beta dimerisation subdomain
             1. Ferric uptake regulation protein, FUR [101028]
                1. Pseudomonas aeruginosa [TaxId: 287] [101029] (1)
         20. Replication initiation protein [46816] (3)
             duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
             1. RepE54 [46817]
                1. Escherichia coli, mini-F plasmid [TaxId: 562] [46818] (5)
             2. Replication protein A, repA [88982]
                1. Pseudomonas syringae pv. savastanoi [TaxId: 29438] [88983] (1)
             3. Replication initiation protein PI [158284]
                1. Escherichia coli [TaxId: 562] [158285] (2)
                   SQ P03067 152-268! SQ P03067 9-151
         21. Helicase DNA-binding domain [46819] (5)
             follows the extended AAA-ATPase domain
             1. Holliday junction helicase RuvB [46820]
                1. Thermus thermophilus [TaxId: 274] [46821] (3)
                2. Thermotoga maritima [TaxId: 2336] [63474] (6)
             2. CDC6, C-terminal domain [46822]
                contains the N- and C-terminal helical extensions to the common fold
                1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [46823] (1)
             3. CDC6-like protein APE0152, C-terminal domain [116788]
                1. Aeropyrum pernix [TaxId: 56636] [116789] (2)
                   SQ Q9YFU8
             4. Hypothetical protein SSO1545, C-terminal domain [140261]
                1. Sulfolobus solfataricus [TaxId: 2287] [140262] (2)
                   SQ Q97Y08 284-356
         22. RecQ helicase DNA-binding domain-like [101030] (3)
             follows the tandem AAA-ATPase domain
             1. DNA helicase RecQ DNA-binding domain [101031]
                1. Escherichia coli [TaxId: 562] [101032] (2)
             2. Werner syndrome ATP-dependent helicase WRN [140263]
                1. Human (Homo sapiens) [TaxId: 9606] [140264] (1)
                   SQ Q14191 949-1092
             3. Hel308 helicase [158286]
                1. Archaeoglobus fulgidus [TaxId: 2234] [158287] (2)
         23. SCF ubiquitin ligase complex WHB domain [74679] (4)
             1. Anaphase promoting complex (APC) [74680]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74681] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [74682] (3)
                   SQ Q13616 17-776
             2. Cullin-3 homologue [101033]
                1. Mouse (Mus musculus) [TaxId: 10090] [101034] (1)
             3. Cullin-4A [158288]
                1. Human (Homo sapiens) [TaxId: 9606] [158289] (1)
                   SQ Q13619 676-759
         24. C-terminal fragment of elongation factor SelB [74683] (1)
             1. C-terminal fragment of elongation factor SelB [74684]
                duplication: tandem repeat of four "winged helix" domains
                1. Moorella thermoacetica [TaxId: 1525] [74685] (21)
         25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
             1. Restriction endonuclease FokI, N-terminal (recognition) domain [46825]
                duplication: consists of three elaborated "winged helix" domains
                1. Flavobacterium okeanokoites [TaxId: 244] [46826] (2)
         26. TnsA endonuclease, C-terminal domain [46782] (1)
             1. TnsA endonuclease, C-terminal domain [46783]
                1. Escherichia coli [TaxId: 562] [46784] (2)
                   SQ P13988
         27. Plant O-methyltransferase, N-terminal domain [63475] (5)
             unknown function
             1. Chalcone O-methyltransferase [63476]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [63477] (2)
             2. Isoflavone O-methyltransferase [63478]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [63479] (2)
             3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [74686]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [74687] (2)
             4. Aclacinomycin-10-hydroxylase RdmB [101035]
                evolved a different function; binds SAM and SAH
                1. Streptomyces purpurascens [TaxId: 1924] [101036] (4)
                   SQ Q54527
             5. Carminomycin 4-O-methyltransferase [109667]
                1. Streptomyces peucetius [TaxId: 1950] [109668] (2)
                   SQ Q06528
         28. Linker histone H1/H5 [46827] (3)
             1. Histone H5, globular domain [46828]
                1. Chicken (Gallus gallus) [TaxId: 9031] [46829] (1)
             2. Histone H1, globular domain [46830]
                1. Chicken (Gallus gallus) [TaxId: 9031] [46831] (1)
             3. Histone H1 homologue Hho1p [101037]
                duplication: contains two similar globular domains
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101038] (4)
         29. Forkhead DNA-binding domain [46832] (6)
             1. Afx (Foxo4) [46833]
                1. Human (Homo sapiens) [TaxId: 9606] [46834] (2)
             2. Adipocyte-transcription factor FREAC-11 (s12, fkh-14) [46835]
                1. Human (Homo sapiens) [TaxId: 9606] [46836] (1)
             3. Interleukin enhancer binding factor [88984]
                1. Human (Homo sapiens) [TaxId: 9606] [88985] (3)
             4. Genesis [46837]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [46838] (2)
             5. HFH-1 (HNF-3 forkhead homolog-1) [46839]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [46840] (1)
             6. Forkhead box protein P2, FOXP2 [140265]
                1. Human (Homo sapiens) [TaxId: 9606] [140266] (8)
                   SQ O15409 503-584
         30. DNA-binding domain from rap30 [46841] (1)
             1. DNA-binding domain from rap30 [46842]
                1. Human (Homo sapiens) [TaxId: 9606] [46843] (2)
         31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
             1. C-terminal domain of the rap74 subunit of TFIIF [63481]
                peptide-recognition motif
                1. Human (Homo sapiens) [TaxId: 9606] [63482] (4)
         32. C-terminal domain of RPA32 [46844] (1)
             1. C-terminal domain of RPA32 [46845]
                peptide-recognition motif
                1. Human (Homo sapiens) [TaxId: 9606] [46846] (2)
         33. DEP domain [63483] (5)
             membrane-binding domain
             1. Segment polarity protein Dishevelled-1 [63484]
                1. Mouse (Mus musculus) [TaxId: 10090] [63485] (1)
             2. Regulatory domain of epac2, domain 2 [81693]
                1. Mouse (Mus musculus) [TaxId: 10090] [81694] (1)
             3. Pleckstrin [101039]
                1. Mouse (Mus musculus) [TaxId: 10090] [101040] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [116790] (2)
                   SQ P08567 125-219 # structure of the N-terminal PH domain (1-105) is also known (scop_sp 50741)
             4. Pleckstrin 2 [101041]
                1. Mouse (Mus musculus) [TaxId: 10090] [101042] (1)
         34. Cell cycle transcription factor e2f-dp [46847] (2)
             heterodimer of two homologous chains
             1. Cell cycle transcription factor E2F-4 [88652]
                1. Human (Homo sapiens) [TaxId: 9606] [88653] (1)
             2. Cell cycle transcription factor DP-2 [88654]
                1. Human (Homo sapiens) [TaxId: 9606] [88655] (1)
         35. The central core domain of TFIIE beta [46850] (1)
             1. The central core domain of TFIIE beta [46851]
                1. Human (Homo sapiens) [TaxId: 9606] [46852] (2)
         36. Z-DNA binding domain [46853] (4)
             Pfam 02295
             1. Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 [46854]
                1. Human (Homo sapiens) [TaxId: 9606] [46855] (9)
             2. Dlm-1 [63486]
                1. Mouse (Mus musculus) [TaxId: 10090] [63487] (1)
             3. dsRNA-binding protein E3 (E3L) [101043]
                1. Vaccinia virus [TaxId: 10245] [101044] (1)
             4. 34L [109669]
                1. Yaba-like disease virus, YLDV [TaxId: 132475] [109670] (1)
                   SQ Q9DHS8 1-75
         37. P4 origin-binding domain-like [46856] (2)
             C-terminus passes through the first loop
             1. Class II MHC transcription factor RFX1 [46857]
                1. Human (Homo sapiens) [TaxId: 9606] [46858] (1)
             2. P4 origin-binding domain [74688]
                1. Bacteriophage P4 [TaxId: 10680] [74689] (1)
         38. ets domain [46859] (9)
             1. Fli-1 [46860]
                1. Human (Homo sapiens) [TaxId: 9606] [46861] (1)
             2. ETS-1 transcription factor, residues 331-440 [46862]
                1. Mouse (Mus musculus) [TaxId: 10090] [46863] (6)
                   SQ P27577 301-440
                2. Human (Homo sapiens) [TaxId: 9606] [46864] (3)
             3. Transcription factor PU.1, residues 171-259 [46865]
                1. Mouse (Mus musculus) [TaxId: 10090] [46866] (1)
             4. GA binding protein (GABP) alpha [46867]
                1. Mouse (Mus musculus) [TaxId: 10090] [46868] (1)
             5. Serum response factor accessory protein 1a, SAP-1 [46869]
                1. Human (Homo sapiens) [TaxId: 9606] [46870] (4)
             6. Elk-1 [46871]
                1. Human (Homo sapiens) [TaxId: 9606] [46872] (1)
             7. Sam pointed domain containing ets transcription SPDEF [140267]
                1. Human (Homo sapiens) [TaxId: 9606] [140268] (1)
                   SQ O95238 247-334
             8. E74-like factor 5 ese-2b [140269]
                1. Human (Homo sapiens) [TaxId: 9606] [140270] (1)
                   SQ Q9UKW6 173-265
         39. Heat-shock transcription factor [46873] (2)
             1. Heat-shock transcription factor [46874]
                1. Drosophila melanogaster [TaxId: 7227] [46875] (2)
                2. Milk yeast (Kluyveromyces lactis) [TaxId: 28985] [46876] (9)
         40. Interferon regulatory factor [46877] (3)
             Pfam 00605
             1. Interferon regulatory factor 1 (IRF-1) [46878]
                1. Mouse (Mus musculus) [TaxId: 10090] [46879] (1)
             2. Interferon regulatory factor-2, IRF-2 [46880]
                1. Mouse (Mus musculus) [TaxId: 10090] [46881] (3)
             3. Interferon regulatory factor 3, IRF-3 [116791]
                1. Human (Homo sapiens) [TaxId: 9606] [116792] (9)
                   SQ Q14653 3-112
         41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
             1. 39 kda initiator binding protein, IBP39, N-terminal domain [101046]
                1. Trichomonas vaginalis [TaxId: 5722] [101047] (2)
         42. Iron-dependent repressor protein [46882] (3)
             1. Diphtheria toxin repressor (DtxR) [46883]
                1. Corynebacterium diphtheriae [TaxId: 1717] [46884] (17)
                   SQ P33120
             2. Iron-dependent regulator IdeR [46885]
                1. Mycobacterium tuberculosis [TaxId: 1773] [46886] (13)
                   SQ Q50495
             3. Manganese transport regulator MntR [88986]
                1. Bacillus subtilis [TaxId: 1423] [88987] (20)
         43. Dissimilatory sulfite reductase DsvD [101048] (1)
             1. Dissimilatory sulfite reductase DsvD [101049]
                1. Desulfovibrio vulgaris [TaxId: 881] [101050] (3)
         44. La domain [101051] (3)
             Pfam 05383; RNA-binding domain
             1. Lupus La autoantigen N-terminal domain [101052]
                1. Human (Homo sapiens) [TaxId: 9606] [101053] (12)
                2. Trypanosoma brucei [TaxId: 5691] [101054] (1)
             2. La-related protein 4 LARP4 [140271]
                C-mpl binding protein
                1. Human (Homo sapiens) [TaxId: 9606] [140272] (1)
                   SQ Q71RC2 112-199
         45. Methionine aminopeptidase, insert domain [46887] (2)
             circularly permuted version of the "winged helix" fold
             1. Methionine aminopeptidase, insert domain [46888]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [46889] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [46890] (18)
                   SQ P50579 110-478
         46. PCI domain (PINT motif) [109671] (2)
             Pfam 01399
             1. COP9 signalosome complex subunit 4, GSN4 [109672]
                1. Mouse (Mus musculus) [TaxId: 10090] [109673] (1)
                   SQ O88544 296-366
             2. Hypothetical protein C20orf116 homolog [116793]
                1. Mouse (Mus musculus) [TaxId: 10090] [116794] (1)
                   SQ Q80WW9 216-274
         47. F93-like [109674] (3)
             contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
             1. Hypothetical protein F93 [109675]
                1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [109676] (1)
                   SQ P20222
             2. Uncharacterized protein APE0880.1 [158290]
                1. Aeropyrum pernix [TaxId: 56636] [158291] (2)
                   SQ Q9YDN4 1-92
             3. STIV F93 [158292]
                different dimerization mode than SSV1 F93
                1. Sulfolobus turreted icosahedral virus [TaxId: 269145] [158293] (2)
                   SQ Q6Q0J9 5-93
         48. Archaeal DNA-binding protein [109677] (1)
             contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
             1. Sso10a (SSO10449) [109678]
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [109679] (3)
                   SQ Q5W1E8
         49. TrmB-like [109680] (2)
             The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
             1. Hypothetical protein AF2008 [109681]
                1. Archaeoglobus fulgidus [TaxId: 2234] [109682] (1)
                   SQ O28271
             2. Hypothetical transcriptional regulator ST1889 [140273]
                1. Sulfolobus tokodaii [TaxId: 111955] [140274] (2)
                   SQ Q96ZE4 1-109
         50. Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
             similar domain organization to the transcriptional regulator IclR
             1. Heat-inducible transcription repressor HrcA, N-terminal domain [109684]
                1. Thermotoga maritima [TaxId: 2336] [109685] (1)
                   SQ Q9WZV5
         51. DNA replication factor Cdt1 [109686] (1)
             1. DNA replication factor Cdt1 [109687]
                1. Mouse (Mus musculus) [TaxId: 10090] [109688] (1)
                   SQ Q8R4E9 179-365
         52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
             C-terminal part of Pfam 06272
             1. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109690]
                1. Human (Homo sapiens) [TaxId: 9606] [109691] (1)
                   SQ Q9UBQ5
         53. Vacuolar sorting protein domain [109692] (3)
             duplication: tandem repeat of two "winged-helix" domains
             1. Vacuolar sorting protein SNF8 [109693]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109694] (2)
                   SQ Q12483 20-232
             2. Vacuolar protein sorting-associated protein VPS36 [109695]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109696] (2)
                   SQ Q06696 396-566
             3. Vacuolar protein sorting-associated protein VPS25 [109697]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109698] (10)
                   SQ P47142
         54. Transcriptional regulator Rrf2 [109699] (2)
             Pfam 02082
             1. Hypothetical protein ywnA [109700]
                1. Bacillus subtilis [TaxId: 1423] [109701] (1)
                   SQ P71036 4-130
             2. Hypothetical protein BC1842 [140275]
                1. Bacillus cereus [TaxId: 1396] [140276] (3)
                   SQ Q81EX1 5-142
         55. Rio2 serine protein kinase N-terminal domain [109702] (1)
             1. Rio2 serine protein kinase N-terminal domain [109703]
                1. Archaeoglobus fulgidus [TaxId: 2234] [109704] (5)
                   SQ O30245 # AF2426
         56. Rad21/Rec8-like [116795] (1)
             Pfam 04824
             1. Sister chromatid cohesion protein 1 (SCC1), C-terminal domain [116796]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116797] (1)
                   SQ Q12158 483-561
         57. Hypothetical protein PH1932 [116798] (1)
             contains new dimerisation all-alpha C-terminal subdomain
             1. Hypothetical protein PH1932 [116799]
                1. Pyrococcus horikoshii [TaxId: 53953] [116800] (2)
                   SQ O59595
         58. An Obfc1 domain [116801] (1)
             helix-loop insertion in the HTH motif
             1. OB fold-containing protein 1, Obfc1 [116802]
                1. Mouse (Mus musculus) [TaxId: 10090] [116803] (1)
                   SQ Q8K2X3 198-304
         59. ScpB/YpuH-like [116804] (1)
             Pfam 04079
             duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
             1. Segregation and condensation protein B, ScpB [116805]
                1. Chlorobium tepidum [TaxId: 1097] [116806] (1)
                   SQ Q8KF54 1-162
         60. PadR-like [116807] (3)
             Pfam 03551; related to the MarR-like family (Pfam 01047)
             1. Predicted transcriptional regulator [116808]
                monomeric
                1. Clostridium thermocellum [TaxId: 1515] [116809] (1)
                   SQ Q4CEJ8 4-106
             2. Hypothetical protein AphA [116810]
                contains extra C-terminal dimerisation domain
                1. Vibrio cholerae [TaxId: 666] [116811] (1)
                   SQ Q9X399 # "winged helix" domain: 1-87, dimerisation domain: 91-179
             3. Hypothetical protein TM0937 [140277]
                1. Thermotoga maritima [TaxId: 2336] [140278] (1)
                   SQ Q9X035 4-117
         61. Hypothetical protein YhgG [116812] (1)
             1. Hypothetical protein YhgG [116813]
                1. Escherichia coli [TaxId: 562] [116814] (1)
                   SQ P64638
         62. ROK associated domain [140279] (3)
             found N-terminal to ROK domain in some proteins
             1. Mlc protein N-terminal domain [140280]
                1. Escherichia coli [TaxId: 562] [140281] (6)
                   SQ P50456 12-81
             2. N-acetylglucosamine kinase [140282]
                Transcriptional regulator, XylR-related
                1. Thermotoga maritima [TaxId: 2336] [140283] (1)
                   SQ Q9X0V1 10-71
             3. Transcriptional regulator VC2007 N-terminal domain [140284]
                1. Vibrio cholerae [TaxId: 666] [140285] (1)
                   SQ Q9KQJ1 10-80
         63. PF1790-like [140286] (1)
             sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil
             1. Transcriptional regulatory protein PF1790 [140287]
                1. Pyrococcus furiosus [TaxId: 2261] [140288] (2)
                   SQ Q8U030 1-194
         64. MukF N-terminal domain-like [140289] (1)
             N-terminal part of Pfam 03882
             1. Chromosome partition protein MukF (KicB), N-terminal domain [140290]
                1. Escherichia coli [TaxId: 562] [140291] (2)
                   SQ P60293 8-118
         65. CodY HTH domain [140292] (1)
             Pfam 08222
             1. GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain [140293]
                1. Bacillus subtilis [TaxId: 1423] [140294] (3)
                   SQ P39779 167-257
         66. FtsK C-terminal domain-like [140295] (2)
             PfamB 000224
             1. DNA translocase FtsK [140296]
                1. Escherichia coli [TaxId: 562] [140297] (1)
                   SQ P46889 1261-1329
                2. Pseudomonas aeruginosa [TaxId: 287] [140298] (15)
                   SQ Q9I0M3 742-811
         67. Nudix-associated domain [140299] (2)
             PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
             1. Hypothetical protein BT0354, C-terminal domain [140300]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [140301] (4)
                   SQ Q8AAV8 150-225
             2. Hypothetical protein EF2700, C-terminal domain [140302]
                1. Enterococcus faecalis [TaxId: 1351] [140303] (2)
                   SQ Q830S2 205-268
         68. HxlR-like [140304] (5)
             Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
             1. Hypothetical protein PG0823 [140305]
                1. Porphyromonas gingivalis [TaxId: 837] [140306] (2)
                   SQ Q7M7B7 3-104
             2. Hypothetical protein PA1607 [140307]
                includes extra C-terminal SH3-like subdomain, which is segment-swapped in the dimer
                1. Pseudomonas aeruginosa [TaxId: 287] [140308] (2)
                   SQ Q9I3B4 5-146
             3. Hypothetical protein EF0647 [140309]
                1. Enterococcus faecalis [TaxId: 1351] [140310] (2)
                   SQ Q838C3 1-108
             4. Putative transcriptional regulator YtfH [140311]
                1. Salmonella typhimurium [TaxId: 90371] [140312] (2)
                   SQ Q7CP90 9-122
             5. Putative transcriptional regulator YtcD [158294]
                1. Bacillus subtilis [TaxId: 1423] [158295] (4)
                   SQ O34533 10-104
         69. Marine metagenome family WH1 [158296] (1)
             1. Hypothetical protein GOS_3836187 [158297]
                1. Environmental samples [158298] (1)
                   marine metagenome
         70. ReutB4095-like [158299] (1)
             probable biological unit is a homohexamer
             1. Putative DNA-binding protein ReutB4095 [158300]
                1. Ralstonia eutropha [TaxId: 106590] [158301] (2)
                   SQ Q46TT3 12-92
         71. PH0730 N-terminal domain-like [158302] (1)
             1. Hypothetical protein PH0730 [158303]
                1. Pyrococcus horikoshii [TaxId: 53953] [158304] (1)
                   SQ O58461 28-96
         72. FaeA-like [158305] (1)
             Pfam 04703
             1. P fimbrial regulatory protein PapI [158306]
                KS71A
                1. Escherichia coli [TaxId: 562] [158307] (1)
                   SQ P62584 5-77
         73. STY4665 C-terminal domain-like [158308] (1)
             Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
             1. Hypothetical protein STY4665 [158309]
                1. Salmonella typhi [TaxId: 90370] [158310] (1)
                   SQ Q8Z1C5 396-528
         74. PSPTO2686-like [158311] (1)
             Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
             1. Hypothetical protein PSPTO2686 [158312]
                1. Pseudomonas syringae pv. tomato [TaxId: 323] [158313] (2)
                   SQ Q882E2 13-96! SQ Q882E2 97-180
         75. RHA1_ro06458-like [158314] (1)
             1. Hypothetical protein RHA1_ro06458 [158315]
                1. Rhodococcus sp. RHA1 [TaxId: 101510] [158316] (1)
                   SQ Q0S2K3 1-85
         76. YjcQ-like [158317] (1)
             Pfam 09639
             1. Uncharacterized protein YjcQ [158318]
                1. Bacillus subtilis [TaxId: 1423] [158319] (1)
                   SQ O31639 5-82
         77. F112-like [158320] (1)
             1. F-112 [158321]
                1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [158322] (1)
                   SQ P20220 4-73
         78. MerB N-terminal domain-like [158323] (1)
             1. Alkylmercury lyase MerB [158324]
                1. Escherichia coli [TaxId: 562] [158325] (1)
                   SQ P77072 21-80
         79. CED-4 C-terminal domain-like [158326] (1)
             similar domain architecture to AAA+ helicases
             1. Cell death protein 4, CED-4 [158327]
                1. Caenorhabditis elegans [TaxId: 6239] [158328] (1)
                   SQ P30429 386-543
         80. ELL N2 domain-like [158329] (1)
             PfamB 026212; includes recent PDB entry 2e5n
             1. RNA polymerase II elongation factor ELL [158330]
                1. Human (Homo sapiens) [TaxId: 9606] [158331] (1)
                   SQ P55199 197-297
         81. PF0610-like [158332] (1)
             PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
             1. Hypothetical protein PF0610 [158333]
                1. Pyrococcus furiosus [TaxId: 2261] [158334] (1)
                   SQ Q8U362 1-105
         82. Rv2827c N-terminal domain-like [158335] (1)
             ~80 N-terminal residues of Pfam 09407' DUF2005
             1. Hypothetical protein Rv2827c [158336]
                1. Mycobacterium tuberculosis [TaxId: 1773] [158337] (2)
                   SQ P71625 1-82
         83. Rps19E-like [158338] (1)
             Pfam 01090; local sequence similarity to members of the GntR-like family
             1. Ribosomal protein S19e [158339]
                1. Pyrococcus abyssi [TaxId: 29292] [158340] (1)
                   SQ Q9V0G8 2-150
         84. RPO3F domain-like [158341] (2)
             middle region of Pfam 05158
             1. DNA-directed RNA polymerase III subunit RPC6, RPO3F [158342]
                1. Mouse (Mus musculus) [TaxId: 10090] [158343] (1)
                   SQ Q921X6 11-79
                2. Human (Homo sapiens) [TaxId: 9606] [158344] (1)
                   SQ Q9H1D9 78-155
      5. C-terminal effector domain of the bipartite response regulators [46894] (3)
         binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
         uperfamily
         1. PhoB-like [46895] (6)
            contains 4-stranded meander beta-sheet in the N-terminal extension
            1. OmpR [46896]
               1. Escherichia coli [TaxId: 562] [46897] (3)
            2. PhoB [46898]
               1. Thermotoga maritima [TaxId: 2336] [68972] (1)
               2. Escherichia coli [TaxId: 562] [46899] (4)
            3. Response regulator DrrB [88988]
               1. Thermotoga maritima [TaxId: 2336] [88989] (1)
            4. Probable regulatory protein EmbR [140313]
               N-terminal domain, unlike the other members
               1. Mycobacterium tuberculosis [TaxId: 1773] [140314] (3)
                  SQ P66799 10-104
            5. Transcriptional regulatory protein PrrA [140315]
               1. Mycobacterium tuberculosis [TaxId: 1773] [140316] (4)
                  SQ P0A5Z6 128-233
         2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5)
            contains additional, fourth helix in the C-terminal extension
            1. Germination protein GerE [63488]
               single-domain protein homologous to the C-terminal domain of NarL
               1. Bacillus subtilis [TaxId: 1423] [63489] (1)
            2. Quorum-sensing transcription factor TraR, C-terminal domain [74690]
               1. Agrobacterium tumefaciens [TaxId: 358] [74691] (2)
            3. Nitrate/nitrite response regulator (NarL) [46901]
               1. Escherichia coli [TaxId: 562] [46902] (11)
            4. Transcriptional regulator RcsB [88990]
               1. Erwinia amylovora [TaxId: 552] [88991] (1)
            5. Response regulatory protein StyR, C-terminal domain [140317]
               1. Pseudomonas fluorescens [TaxId: 294] [140318] (2)
                  SQ O30989 131-200
         3. Spo0A [46903] (2)
            elaborated with additional helices
            1. Spo0A [46904]
               1. Bacillus stearothermophilus [TaxId: 1422] [46905] (1)
               2. Bacillus subtilis [TaxId: 1423] [74692] (1)
      6. TrpR-like [48295] (3)
         contains an extra shared helix after the HTH motif
         uperfamily
         1. Trp repressor, TrpR [48296] (1)
            intertwined dimer of identical 6-helical subunits
            1. Trp repressor, TrpR [48297]
               1. Escherichia coli [TaxId: 562] [48298] (16)
         2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2)
            monomeric; contains additional N-terminal helices
            1. Chromosomal replication initiation factor DnaA C-terminal domain IV [81696]
               1. Aquifex aeolicus [TaxId: 63363] [81697] (5)
               2. Escherichia coli [TaxId: 562] [88992] (1)
         3. SPO1678-like [158345] (1)
            Pfam 06627; DUF1153
            1. Uncharacterized protein SPO1678 [158346]
               1. Silicibacter pomeroyi [TaxId: 89184] [158347] (1)
                  SQ Q5LST8 1-93
      7. Ribosomal protein L11, C-terminal domain [46906] (1)
         uperfamily
         1. Ribosomal protein L11, C-terminal domain [46907] (6)
            1. Ribosomal protein L11, C-terminal domain [46908]
               1. Bacillus stearothermophilus [TaxId: 1422] [46909] (9)
               2. Thermotoga maritima [TaxId: 2336] [46910] (6)
               3. Archaeon Haloarcula marismortui [TaxId: 2238] [109705] (39)
                  SQ P14122 67-136
               4. Deinococcus radiodurans [TaxId: 1299] [158348] (4)
                  SQ Q9RSS7 72-144
               5. Escherichia coli [TaxId: 562] [158349] (29)
                  SQ P0A7J7 73-141
               6. Thermus thermophilus [TaxId: 274] [158350] (16)
                  SQ P36238 70-139! SQ P36238 71-137
      8. Ribosomal protein S18 [46911] (1)
         uperfamily
         1. Ribosomal protein S18 [46912] (2)
            1. Ribosomal protein S18 [46913]
               1. Thermus thermophilus [TaxId: 274] [46914] (47)
                  SQ P80382
               2. Escherichia coli [TaxId: 562] [158351] (24)
                  SQ P0A7T7 19-73
      9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
         uperfamily
         1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2)
            1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46917]
               links two duplicated two-domain units formed by domains 1-2 and 4-5
               1. Streptomyces antibioticus [TaxId: 1890] [46918] (2)
               2. Mouse (Mus musculus) [TaxId: 10090] [116815] (1)
                  SQ Q8K1R3 273-363
      10. N-terminal Zn binding domain of HIV integrase [46919] (1)
          uperfamily
          1. N-terminal Zn binding domain of HIV integrase [46920] (2)
             Zn-binding site is near the C-terminus
             1. N-terminal Zn binding domain of HIV integrase [46921]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [46922] (7)
                2. Human immunodeficiency virus type 2 [TaxId: 11709] [46923] (1)
      11. RNA polymerase subunit RPB10 [46924] (1)
          uperfamily
          1. RNA polymerase subunit RPB10 [46925] (2)
             Zn-binding site is near the N-terminus
             1. RNA polymerase subunit RPB10 [46926]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [46927] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63490] (30)
                   SQ P22139; part of multichain biological unit
      12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
          uperfamily
          1. Sigma3 domain [88660] (3)
             1. Sigma70 [88661]
                1. Thermus thermophilus [TaxId: 274] [88662] (16)
                   SQ Q9WX78
             2. Sigma factor SigA [88663]
                1. Thermus aquaticus [TaxId: 271] [88664] (1)
             3. Sigma factor sigma-28 (FliA) [101055]
                1. Aquifex aeolicus [TaxId: 63363] [101056] (2)
          2. Sigma4 domain [88665] (7)
             1. Sigma70 (SigA, RpoD) [88666]
                1. Thermus thermophilus [TaxId: 274] [88667] (16)
                   SQ Q9WX78
                2. Escherichia coli [TaxId: 562] [116816] (2)
                   SQ P00579 546-613
                3. Thermotoga maritima [TaxId: 2336] [116817] (1)
                   SQ P77994 313-399
                4. Thermus aquaticus [TaxId: 271] [88669] (3)
             2. SigmaE factor (RpoE) [88993]
                1. Escherichia coli [TaxId: 562] [88994] (3)
             3. SigmaF [74769]
                1. Bacillus stearothermophilus [TaxId: 1422] [74770] (1)
             4. Sigma factor sigma-28 (FliA) [101057]
                1. Aquifex aeolicus [TaxId: 63363] [101058] (2)
          3. YlxM/p13-like [109706] (2)
             Pfam 04297; UPF0122
             structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers
             1. Hypothetical protein SPy1201 [109707]
                1. Streptococcus pyogenes [TaxId: 1314] [109708] (1)
                   SQ P67253
             2. Hypothetical protein SAV1236 [116818]
                1. Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280] [116819] (1)
                   SQ P67248
      13. KorB DNA-binding domain-like [109709] (1)
          contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
          uperfamily
          1. KorB DNA-binding domain-like [109710] (2)
             [N-terminal half of Pfam 06613]
             1. Transcriptional repressor protein KorB DNA-binding domain [109711]
                1. Escherichia coli [TaxId: 562] [109712] (1)
                   SQ P07674 137-252 # structure of the C-terminal domain (297-358) is determined separately; scop_sp 69244
             2. Putative partitioning protein ParB/Spo0J [109713]
                1. Thermus thermophilus [TaxId: 274] [109714] (1)
                   SQ Q9LCY0 # Fragment
      14. Rps17e-like [116820] (1)
          uperfamily
          1. Rps17e-like [116821] (1)
             Pfam 00833
             1. ribosomal protein S17e [116822]
                1. Methanobacterium thermoautotrophicum [TaxId: 145262] [116823] (1)
                   SQ O26894; MTH803
   10. Another 3-helical bundle [81602] (5)
       topologically similar to the DNA/RNA-binding bundles; distinct packing
       1. FF domain [81698] (1)
          uperfamily
          1. FF domain [81699] (3)
             1. Hypa/FBP11 [81700]
                1. Human (Homo sapiens) [TaxId: 9606] [81701] (2)
                   Flj21157
             2. Transcription elongation regulator 1 [158352]
                1. Human (Homo sapiens) [TaxId: 9606] [158353] (3)
                   SQ O14776 651-719! SQ O14776 784-853! SQ O14776 888-959
             3. Pre-mRNA-processing protein PRP40 [158354]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [158355] (1)
                   SQ P33203 134-189
       2. Protein serine/threonine phosphatase 2C, C-terminal domain [81601] (1)
          uperfamily
          1. Protein serine/threonine phosphatase 2C, C-terminal domain [81600] (1)
             1. Protein serine/threonine phosphatase 2C, C-terminal domain [81599]
                1. Human (Homo sapiens) [TaxId: 9606] [81598] (1)
       3. B-form DNA mimic Ocr [101059] (1)
          uperfamily
          1. B-form DNA mimic Ocr [101060] (1)
             1. B-form DNA mimic Ocr [101061]
                Gene 0.3 protein; active form is a dimer
                1. Bacteriophage T7 [TaxId: 10760] [101062] (1)
       4. DEK C-terminal domain [109715] (1)
          uperfamily
          1. DEK C-terminal domain [109716] (1)
             1. DEK C-terminal domain [109717]
                1. Human (Homo sapiens) [TaxId: 9606] [109718] (1)
                   SQ P35659 309-375
       5. IscX-like [140319] (1)
          uperfamily
          1. IscX-like [140320] (1)
             Pfam 04384; DUF528
             1. Iron-sulfur cluster assembly protein IscX [140321]
                formerly hypothetical protein YfhJ
                1. Escherichia coli [TaxId: 562] [140322] (1)
                   SQ P0C0L9 2-65
   11. RuvA C-terminal domain-like [46928] (9)
       3 helices; bundle, right-handed twist
       1. DNA helicase RuvA subunit, C-terminal domain [46929] (1)
          possibly related to UBA-like domains
          uperfamily
          1. DNA helicase RuvA subunit, C-terminal domain [46930] (3)
             1. DNA helicase RuvA subunit, C-terminal domain [46931]
                tetramer; binds Holliday junction
                1. Escherichia coli [TaxId: 562] [46932] (4)
                2. Mycobacterium leprae [TaxId: 1769] [46933] (1)
                3. Thermus thermophilus [TaxId: 274] [81702] (2)
       2. UBA-like [46934] (4)
          uperfamily
          1. UBA domain [46935] (24)
             1. DNA repair protein Hhr23a [46936]
                1. Human (Homo sapiens) [TaxId: 9606] [46937] (5)
             2. Sequestosome 1 (Sqstm1) [101063]
                ubiquitin-binding protein p62
                1. Human (Homo sapiens) [TaxId: 9606] [101064] (4)
             3. Auxilin-like protein Swa2p [101065]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101066] (1)
             4. Ubiquitin-protein ligase ubc1 [109719]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109720] (1)
                   SQ P21734
             5. Ubiquitin carboxyl-terminal hydrolase 25 [109721]
                1. Mouse (Mus musculus) [TaxId: 10090] [109722] (1)
                   SQ P57080 1-67
             6. NEDD8 ultimate buster-1 (Nub1) [116824]
                1. Mouse (Mus musculus) [TaxId: 10090] [116825] (1)
                   SQ P54729 469-540
             7. Ubiquitin isopeptidase T [116826]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116827] (2)
                   SQ Q9LJT6 594-665; Q8L6Y1 651-710
             8. Rhomboid family protein At3g58460 [116828]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116829] (1)
                   SQ Q8LB17 342-401
             9. Ubiquitin-associated protein 1, UBAP1 [116830]
                1. Human (Homo sapiens) [TaxId: 9606] [116831] (1)
                   SQ Q9NZ09 381-430
             10. UBA/UBX 33.3 kDa protein [116832]
                 1. Mouse (Mus musculus) [TaxId: 10090] [116833] (1)
                    SQ Q922Y1 2-52
             11. Tudor domain containing protein 3, TDRD3 [116834]
                 1. Human (Homo sapiens) [TaxId: 9606] [116835] (1)
                    SQ Q9H7E2 194-243
             12. DSK2 [140323]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140324] (28)
                    SQ P48510 328-371! SQ P48510 328-373
             13. Ubiquilin-3 [140325]
                 1. Human (Homo sapiens) [TaxId: 9606] [140326] (1)
                    SQ Q9H347 615-655
             14. Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain [140327]
                 1. Human (Homo sapiens) [TaxId: 9606] [140328] (5)
                    SQ P61086 157-198
             15. Cbl-interacting protein p70, STS1 [140329]
                 1. Human (Homo sapiens) [TaxId: 9606] [140330] (1)
                    SQ Q8TF42 26-76
             16. Ubiquitin-associated protein 2-like Ubap2l [140331]
                 RSGI ruh-015
                 1. Mouse (Mus musculus) [TaxId: 10090] [140332] (1)
                    SQ Q80X50 19-109
             17. Trinucleotide repeat containing 6c protein, TNRC6C [140333]
                 1. Human (Homo sapiens) [TaxId: 9606] [140334] (1)
                    SQ Q86UE5 197-268
             18. Suppressor of T-cell receptor signaling 2 (STS-2) [140335]
                 1. Human (Homo sapiens) [TaxId: 9606] [140336] (1)
                    SQ P57075 20-70
             19. Migration-inducing protein 19 NBR1 [140337]
                 Next to Brca1 gene 1
                 1. Human (Homo sapiens) [TaxId: 9606] [140338] (1)
                    SQ Q14596 916-956
             20. Ubiquilin-like protein Ubqlnl [140339]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140340] (1)
                    SQ Q14DL0 561-610
             21. Serine/threonine protein kinase LATS2 [140341]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140342] (1)
                    SQ Q7TSJ6 98-138
             22. 4931431F19Rik [140343]
                 Riken cDNA clone 4931431f19
                 1. Mouse (Mus musculus) [TaxId: 10090] [140344] (1)
                    SQ Q9D4I8 447-507
             23. UBA-domain protein mud1 [158356]
                 1. Schizosaccharomyces pombe [TaxId: 4896] [158357] (2)
                    SQ Q10256 295-332
             24. Endocytic protein Ede1, YBL047C [158358]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [158359] (1)
                    SQ P34216 1339-1381
          2. TS-N domain [63423] (4)
             1. Elongation factor Ts (EF-Ts), N-terminal domain [63424]
                1. Escherichia coli [TaxId: 562] [63425] (1)
                2. Thermus thermophilus [TaxId: 274] [63426] (1)
                3. Cow (Bos taurus), mitochondrial [TaxId: 9913] [116836] (1)
                   SQ P43896 56-331
                4. Human (Homo sapiens), mitochondrial [TaxId: 9606] [140345] (1)
                   SQ P43897 45-95
          3. TAP-C domain-like [68973] (2)
             1. FG-binding, C-terminal domain of TAP [68974]
                1. Human (Homo sapiens) [TaxId: 9606] [68975] (2)
             2. NSFL1 (p97 ATPase) cofactor p47, UBA-like domain [101067]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [101068] (1)
          4. CUE domain [88995] (4)
             Pfam 02845
             1. Vacuolar protein sorting-associated protein vps9 [88996]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88997] (2)
             2. Protein Cue2 (hypothetical protein YKL090W) [88998]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88999] (1)
             3. Toll-interacting protein [116837]
                1. Human (Homo sapiens) [TaxId: 9606] [116838] (1)
                   SQ Q9H0E2 229-274
             4. Activating signal cointegrator 1 complex subunit 2 [140346]
                1. Human (Homo sapiens) [TaxId: 9606] [140347] (1)
                   SQ Q9H1I8 463-525
       3. post-HMGL domain-like [89000] (2)
          uperfamily
          1. DmpG/LeuA communication domain-like [89001] (2)
             1. 4-hydroxy-2-oxovalerate aldolase DmpG, communication domain [89002]
                1. Pseudomonas sp. [TaxId: 306] [89003] (1)
                   gene product DmpG
             2. 2-isopropylmalate synthase LeuA, communication domain [109723]
                1. Mycobacterium tuberculosis [TaxId: 1773] [109724] (1)
                   SQ P96420
          2. Conserved carboxylase domain [109725] (1)
             Pfam 02436
             duplication: contains two domains of this fold, connected with a helical linker
             1. Transcarboxylase 5S subunit, C-terminal domain [109726]
                1. Propionibacterium freudenreichii shermanii [TaxId: 1752] [109727] (6)
                   SQ Q70AC7 3-474; d1: 307-367; d2: 416-459
       4. CRAL/TRIO N-terminal domain [46938] (1)
          uperfamily
          1. CRAL/TRIO N-terminal domain [46939] (3)
             1. N-terminal domain of phosphatidylinositol transfer protein sec14p [46940]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46941] (1)
             2. Alpha-tocopherol transfer protein [101069]
                1. Human (Homo sapiens) [TaxId: 9606] [101070] (3)
             3. Supernatant protein factor (SPF), N-terminal domain [101071]
                Sec14-like protein 2; contains extra C-terminal beta-sandwich domain
                1. Human (Homo sapiens) [TaxId: 9606] [101072] (2)
                   SQ O76054
       5. Elongation factor TFIIS domain 2 [46942] (1)
          uperfamily
          1. Elongation factor TFIIS domain 2 [46943] (1)
             1. Elongation factor TFIIS domain 2 [46944]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46945] (1)
       6. Double-stranded DNA-binding domain [46950] (1)
          uperfamily
          1. Double-stranded DNA-binding domain [46951] (2)
             1. Hypothetical protein MTH1615 [46952]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [46953] (1)
             2. Programmed cell death protein 5 [140348]
                1. Human (Homo sapiens) [TaxId: 9606] [140349] (1)
                   SQ O14737 8-112
       7. Hypothetical protein AF0491, middle domain [109728] (1)
          uperfamily
          1. Hypothetical protein AF0491, middle domain [109729] (1)
             1. Hypothetical protein AF0491, middle domain [109730]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [109731] (2)
                   SQ O29759
       8. HBS1-like domain [109732] (1)
          possibly related to UBA-like domains
          uperfamily
          1. HBS1-like domain [109733] (1)
             1. HBS1-like protein [109734]
                1. Mouse (Mus musculus) [TaxId: 10090] [109735] (1)
                   SQ Q69ZS7 51-120
       9. FGAM synthase PurL, linker domain [109736] (1)
          uperfamily
          1. FGAM synthase PurL, linker domain [109737] (1)
             1. FGAM synthase PurL, linker domain [109738]
                1. Salmonella typhimurium [TaxId: 90371] [109739] (1)
                   SQ P74881
   12. S13-like H2TH domain [81297] (1)
       core: 3-4 helices
       1. S13-like H2TH domain [46946] (3)
          contains a helix-two turns-helix (H2TH) motif
          uperfamily
          1. Ribosomal protein S13 [46947] (2)
             contains 3 helices and a beta-hairpin in the core and a non-globular C-terminal extension
             1. Ribosomal protein S13 [46948]
                1. Thermus thermophilus [TaxId: 274] [46949] (44)
                   SQ P80377
                2. Escherichia coli [TaxId: 562] [158360] (26)
                   SQ P0A7S9 1-114
          2. Middle domain of MutM-like DNA repair proteins [81626] (6)
             contains 4 helices in the core
             1. DNA repair protein MutM (Fpg) [81620]
                1. Thermus thermophilus [TaxId: 274] [81608] (1)
                2. Bacillus stearothermophilus [TaxId: 1422] [81611] (9)
                3. Escherichia coli [TaxId: 562] [81614] (1)
                4. Lactococcus lactis [TaxId: 1358] [81615] (7)
                   SQ P42371
             2. Endonuclease VIII [81703]
                1. Escherichia coli [TaxId: 562] [81704] (9)
                   SQ P50465
             3. Endonuclease VIII-like 1 (NEIL1) [109740]
                1. Human (Homo sapiens) [TaxId: 9606] [109741] (1)
                   SQ Q96FI4 1-333
          3. Topoisomerase VI-B subunit middle domain [81705] (1)
             1. Topoisomerase VI-B subunit middle domain [81706]
                1. Archaeon Sulfolobus shibatae [TaxId: 2286] [81707] (10)
   13. Putative DNA-binding domain [46954] (1)
       core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
       1. Putative DNA-binding domain [46955] (7)
          uperfamily
          1. Domains B1 and B5 of PheRS-beta, PheT [46956] (1)
             duplication: contains two such domains related by pseudo dyad
             1. Domains B1 and B5 of PheRS-beta, PheT [46957]
                1. Thermus thermophilus [TaxId: 274] [46958] (13)
                   identical sequence to Thermus aquaticus, TaxId: 271
          2. DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [46959] (1)
             1. DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [46960]
                1. Human (Homo sapiens) [TaxId: 9606] [46961] (2)
          3. Dachshund-homology domain [74693] (2)
             Pfam 02437
             1. Retinal determination protein Dachshund [74694]
                1. Human (Homo sapiens) [TaxId: 9606] [74695] (1)
             2. Ski oncogene [109742]
                1. Human (Homo sapiens) [TaxId: 9606] [109743] (1)
                   SQ P12755 91-192
          4. DNA-binding N-terminal domain of transcription activators [46962] (4)
             includes a dimerisation, antiparallel coiled-coil subdomain
             1. Transcription activator BmrR [46963]
                followed by long alpha-helical linker
                1. Bacillus subtilis [TaxId: 1423] [46964] (7)
                   SQ P39075
             2. Multidrug transporter activator MtaN [68976]
                1. Bacillus subtilis [TaxId: 1423] [68977] (2)
                   SQ P71039 1-109
             3. Transcriptional regulator CueR [101073]
                copper efflux regulator
                1. Escherichia coli [TaxId: 562] [101074] (3)
             4. Transcriptional regulator ZntR [101075]
                Zn(II)-responsive regulator of ZntA
                1. Escherichia coli [TaxId: 562] [101076] (3)
          5. Terminase gpNU1 subunit domain [74696] (1)
             1. Terminase gpNU1 subunit domain [74697]
                1. Bacteriophage lambda [TaxId: 10710] [74698] (1)
          6. Excisionase-like [46891] (2)
             kinked C-terminal helix
             1. mu transposase, DNA-binding domain [46892]
                1. Bacteriophage mu [TaxId: 10677] [46893] (4)
             2. Excisionase Xis [89004]
                1. Bacteriophage lambda [TaxId: 10710] [89005] (8)
                   SQ P03699 1-55
          7. N-terminal subdomain of bacterial translation initiation factor IF2 [89006] (1)
             1. N-terminal subdomain of bacterial translation initiation factor IF2 [89007]
                1. Escherichia coli [TaxId: 562] [89008] (1)
   14. Spectrin repeat-like [46965] (16)
       3 helices; bundle, closed, left-handed twist; up-and-down
       1. Spectrin repeat [46966] (1)
          uperfamily
          1. Spectrin repeat [46967] (5)
             1. Spectrin alpha chain [46968]
                1. Drosophila sp. [TaxId: 7242] [46969] (1)
                2. Chicken (Gallus gallus) [TaxId: 9031] [46970] (4)
                   SQ P07751 1662-1981
                3. Human (Homo sapiens) [TaxId: 9606] [101077] (1)
             2. Spectrin beta chain [101078]
                1. Human (Homo sapiens) [TaxId: 9606] [101079] (1)
             3. alpha-actinin [46971]
                1. Human (Homo sapiens) [TaxId: 9606] [46972] (2)
       2. Enzyme IIa from lactose specific PTS, IIa-lac [46973] (1)
          uperfamily
          1. Enzyme IIa from lactose specific PTS, IIa-lac [46974] (1)
             form trimers with 9 helices in a bundle
             1. Enzyme IIa from lactose specific PTS, IIa-lac [46975]
                1. Lactococcus lactis [TaxId: 1358] [46976] (2)
       3. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46977] (1)
          uperfamily
          1. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46978] (5)
             1. L-aspartate oxidase [46979]
                1. Escherichia coli [TaxId: 562] [46980] (3)
             2. Succinate dehydogenase [81708]
                1. Escherichia coli [TaxId: 562] [81709] (2)
             3. Fumarate reductase [46981]
                1. Escherichia coli [TaxId: 562] [46982] (7)
                2. Wolinella succinogenes [TaxId: 844] [46983] (8)
             4. Adenylylsulfate reductase A subunit [68978]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [68979] (2)
       4. Smac/diablo [46984] (1)
          uperfamily
          1. Smac/diablo [46985] (1)
             1. Smac/diablo [46986]
                1. Human (Homo sapiens) [TaxId: 9606] [46987] (2)
       5. BAG domain [63491] (1)
          uperfamily
          1. BAG domain [63492] (6)
             Pfam 02179
             1. BAG-family molecular chaperon regulator-1, BAG1 [63493]
                1. Human (Homo sapiens) [TaxId: 9606] [63494] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [63495] (1)
                3. Nematode (Caenorhabditis elegans) [TaxId: 6239] [109744] (1)
                   SQ O44739 74-210
             2. Silencer of death domains, Sodd (Bag4) [74699]
                1. Human (Homo sapiens) [TaxId: 9606] [74700] (2)
             3. BAG-family molecular chaperone regulator-3 [101080]
                Bcl2-associated athanogene 3
                1. Mouse (Mus musculus) [TaxId: 10090] [101081] (1)
             4. BAG-family molecular chaperone regulator-5, BAG-5 [109745]
                1. Mouse (Mus musculus) [TaxId: 10090] [109746] (1)
                   SQ Q8CI32 1-86
       6. GAT-like domain [89009] (2)
          uperfamily
          1. GAT domain [89010] (3)
             1. ADP-ribosylation factor binding protein Gga1 [89011]
                1. Human (Homo sapiens) [TaxId: 9606] [89012] (6)
                   SQ Q9UJY5 211-299
             2. Target of Myb protein 1, TOM1 [158361]
                1. Human (Homo sapiens) [TaxId: 9606] [158362] (1)
                   SQ O60784 215-307
             3. ADP-ribosylation factor binding protein Gga3 [158363]
                1. Human (Homo sapiens) [TaxId: 9606] [158364] (6)
                   SQ Q9NZ52 208-299! SQ Q9NZ52 211-300
          2. Phosphoinositide-binding clathrin adaptor, domain 2 [100929] (2)
             this domain is associated with the N-terminal ENTH-like domain
             1. Clathrin assembly lymphoid myeloid leukaemia protein, Calm [100930]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [100931] (4)
             2. AP180 (Lap) [100932]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [100933] (1)
       7. Tubulin chaperone cofactor A [46988] (1)
          uperfamily
          1. Tubulin chaperone cofactor A [46989] (2)
             the C-terminal helix is shorter that the other two helices
             1. Tubulin chaperone cofactor A [46990]
                1. Baker's yeast (Saccharomyces cerevisiae), Rbl2p [TaxId: 4932] [46991] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [74701] (1)
       8. Ribosomal protein S20 [46992] (1)
          uperfamily
          1. Ribosomal protein S20 [46993] (2)
             1. Ribosomal protein S20 [46994]
                1. Thermus thermophilus [TaxId: 274] [46995] (45)
                   SQ P80380
                2. Escherichia coli [TaxId: 562] [158365] (26)
                   SQ P0A7U7 2-86
       9. Glycogen synthesis protein GlgS [109747] (1)
          uperfamily
          1. Glycogen synthesis protein GlgS [109748] (1)
             1. Glycogen synthesis protein GlgS [109749]
                1. Escherichia coli [TaxId: 562] [109750] (1)
                   SQ P26649
       10. Alpha-hemoglobin stabilizing protein AHSP [109751] (1)
           the bundle twist angle is close to zero (small positive value); similar to the RRF alpha-helical bundle, scop_sf 55194
           uperfamily
           1. Alpha-hemoglobin stabilizing protein AHSP [109752] (1)
              1. Alpha-hemoglobin stabilizing protein AHSP [109753]
                 1. Human (Homo sapiens) [TaxId: 9606] [109754] (7)
                    SQ Q9NZD4 1-94
       11. PhoU-like [109755] (1)
           duplication: consists of two sequence each repeats adopting this fold
           uperfamily
           1. PhoU-like [109756] (4)
              Pfam 01895
              1. PhoU homolog TM1734 [109757]
                 1. Thermotoga maritima [TaxId: 2336] [109758] (1)
                    SQ Q9X256
              2. Phosphate transport system protein PhoU [116839]
                 1. Aquifex aeolicus [TaxId: 63363] [116840] (2)
                    SQ O67053 1-209
                 2. Bacillus stearothermophilus [TaxId: 1422] [116841] (1)
                    SQ Q818I8; 49% sequence identity
              3. Hypothetical protein PH0236, N-terminal domain [140350]
                 form dimers of dimers, similar to PhoU subunits and dimers, respectively
                 1. Pyrococcus horikoshii [TaxId: 53953] [140351] (4)
                    SQ O57975 9-107
       12. XseB-like [116842] (1)
           helix-swapped homodimer
           uperfamily
           1. XseB-like [116843] (1)
              Pfam 02609
              1. Exonuclease VII small subunit XseB [116844]
                 1. Bordetella pertussis [TaxId: 520] [116845] (1)
                    SQ Q7VV85 13-80
       13. MIT domain [116846] (1)
           uperfamily
           1. MIT domain [116847] (3)
              Pfam 04212
              1. Hypothetical protein 1500032H18Rik [116848]
                 1. Mouse (Mus musculus) [TaxId: 10090] [116849] (1)
                    SQ Q8VDV8 6-87
              2. Vacuolar protein sorting factor 4a (VPS4A, SKD2) [140352]
                 1. Human (Homo sapiens) [TaxId: 9606] [140353] (2)
                    SQ Q9UN37 1-77
              3. Vacuolar sorting protein 4b (VPS4B, SKD1 protein) [140354]
                 1. Human (Homo sapiens) [TaxId: 9606] [140355] (4)
                    SQ O75351 1-104! SQ O75351 1-77
       14. PPK N-terminal domain-like [140356] (1)
           uperfamily
           1. PPK N-terminal domain-like [140357] (2)
              N-terminal part of Pfam 02503
              1. Polyphosphate kinase, PPK [140358]
                 1. Escherichia coli [TaxId: 562] [140359] (4)
                    SQ P0A7B1 2-106
                 2. Porphyromonas gingivalis [TaxId: 837] [140360] (2)
                    SQ Q7MTR1 4-112
       15. MIT domain-like [140361] (1)
           uperfamily
           1. MIT domain [140362] (1)
              1. Nuclear receptor binding factor 2, NRBF2, N-terminal domain [140363]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140364] (1)
                    SQ Q8VCQ3 4-86
       16. Efb C-domain-like [158366] (1)
           1. Efb C-domain-like [158367] (2)
              PfamB 008033
              1. Fibrinogen-binding protein Efb (Fib) [158368]
                 1. Staphylococcus aureus [TaxId: 1280] [158369] (8)
                    SQ A6QG59 101-165! SQ P68798 105-165! SQ P68799 101-165
              2. Uncharacterized protein SAV1155 [158370]
                 1. Staphylococcus aureus [TaxId: 1280] [158371] (4)
                    SQ Q99UV2 52-109
   15. immunoglobulin/albumin-binding domain-like [46996] (11)
       3 helices; bundle, closed, left-handed twist; up-and-down; mirror topology to the spectrin-like fold
       1. Bacterial immunoglobulin/albumin-binding domains [46997] (2)
          uperfamily
          1. Immunoglobulin-binding protein A modules [46998] (1)
             1. Immunoglobulin-binding protein A modules [46999]
                1. Staphylococcus aureus [TaxId: 1280] [47000] (14)
          2. GA module, an albumin-binding domain [47001] (3)
             Pfam 01468; also includes FIVAR module, Pfam 07554
             1. PAB [47002]
                1. Peptostreptococcus magnus [TaxId: 1260] [47003] (6)
                   SQ Q51911 213-265
             2. IgG binding protein G [63496]
                1. Streptococcus sp., group G [TaxId: 1306] [63497] (2)
             3. Ebh protein [116850]
                1. Staphylococcus aureus [TaxId: 1280] [116851] (1)
                   SQ Q8NWQ6 3912-4037
       2. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81710] (1)
          uperfamily
          1. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81711] (1)
             dimeric
             1. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81712]
                1. Streptococcus pyogenes [TaxId: 1314] [81713] (1)
       3. Families 57/38 glycoside transferase middle domain [88688] (3)
          uperfamily
          1. 4-alpha-glucanotransferase, domain 2 [89013] (1)
             family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
             1. 4-alpha-glucanotransferase, domain 2 [89014]
                1. Archaeon Thermococcus litoralis [TaxId: 2265] [89015] (3)
          2. alpha-mannosidase, domain 2 [88693] (2)
             family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
             1. Golgi alpha-mannosidase II [88694]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [88695] (46)
                   SQ Q24451 94-1107
             2. Lysosomal alpha-mannosidase [89016]
                the single-chain precursor is processed into 5 peptides; heavily glycosylated
                1. Cow (Bos taurus) [TaxId: 9913] [89017] (1)
          3. AmyC C-terminal domain-like [101086] (2)
             1. Hypothetical protein TT1467, domain 2 [101087]
                1. Thermus thermophilus [TaxId: 274] [101088] (1)
             2. Alpha-amylase AmyC [140365]
                1. Thermotoga maritima [TaxId: 2336] [140366] (1)
                   SQ A1GKL6 415-528
       4. Phosphoprotein XD domain [101089] (1)
          uperfamily
          1. Phosphoprotein XD domain [101090] (2)
             1. RNA polymerase alpha subunit [101091]
                1. Measles virus [TaxId: 11234] [101092] (2)
                   SQ Q89728 459-507
                2. Sendai virus [TaxId: 11191] [101093] (1)
       5. Staphylocoagulase [101094] (1)
          duplication: consists of two domains of this fold
          uperfamily
          1. Staphylocoagulase [101095] (1)
             1. Staphylocoagulase [101096]
                1. Staphylococcus aureus [TaxId: 1280] [101097] (2)
       6. Heat shock protein 70kD (HSP70), C-terminal subdomain [100934] (1)
          uperfamily
          1. Heat shock protein 70kD (HSP70), C-terminal subdomain [100935] (3)
             1. DnaK [100936]
                1. Escherichia coli [TaxId: 562] [100937] (3)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [101098] (1)
             2. Chaperone protein hscA (Hsc66) [116852]
                1. Escherichia coli [TaxId: 562] [116853] (1)
                   SQ P0A6Z1 390-615
       7. Typo IV secretion system protein TraC [101082] (1)
          uperfamily
          1. Typo IV secretion system protein TraC [101083] (1)
             1. Typo IV secretion system protein TraC [101084]
                1. Escherichia coli [TaxId: 562] [101085] (1)
       8. Avirulence protein AvrPto [116854] (1)
          uperfamily
          1. Avirulence protein AvrPto [116855] (1)
             1. Avirulence protein AvrPto [116856]
                1. Pseudomonas syringae [TaxId: 317] [116857] (2)
                   SQ Q08242 29-133
       9. Coronavirus NSP7-like [140367] (1)
          uperfamily
          1. Coronavirus NSP7-like [140368] (1)
             1. Nonstructural protein 7, NSP7 [140369]
                1. SARS coronavirus [TaxId: 227859] [140370] (5)
                   SQ P59641 3837-3909! SQ P59641 3837-3919
       10. Vng1086c-like [140371] (1)
           homotetramer; comprises two dimers similar to the antidote epsilon subunit dimer
           uperfamily
           1. Vng1086c-like [140372] (1)
              Pfam 01893; UPF0058
              1. Nypothetical protein Vng1086c [140373]
                 1. Halobacterium salinarium [TaxId: 2242] [140374] (1)
                    SQ Q9HQM9 1-89
                    also Halobacterium halobium
       11. AF1782-like [158372] (1)
           1. AF1782-like [158373] (2)
              Pfam 04010; DUF357
              1. Hypothetical protein AF1782 [158374]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [158375] (1)
                    SQ O28492 1-75
              2. Uncharacterized protein MTH1690 [158376]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [158377] (1)
                    SQ O27725 3-77
   16. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47004] (1)
       3 helices; bundle, closed, right-handed twist; up-and-down
       1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47005] (1)
          uperfamily
          1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47006] (3)
             1. E3-binding domain of dihydrolipoamide acetyltransferase [47007]
                1. Bacillus stearothermophilus [TaxId: 1422] [47008] (1)
             2. E3-binding domain of dihydrolipoamide succinyltransferase [47009]
                1. Escherichia coli [TaxId: 562] [47010] (4)
             3. E3/E1 binding domain of dihydrolipoyl acetyltransferase [47011]
                1. Bacillus stearothermophilus [TaxId: 1422] [47012] (5)
                   SQ P11961 118-170
                   SQ Q8VV74 128-169
   17. ChaB-like [140375] (1)
       3 helices, the first one is shorter than the other two; bundle, capped by a small, C-terminal beta-hairpin
       1. ChaB-like [140376] (1)
          uperfamily
          1. ChaB-like [140377] (1)
             Pfam 06150
             1. Putative cation transport regulator ChaB [140378]
                1. Escherichia coli [TaxId: 562] [140379] (1)
                   SQ P0AE63 2-76
   18. Protozoan pheromone-like [47013] (2)
       3 helices; bundle, closed, left-handed twist, up-and-down
       1. Protozoan pheromone proteins [47014] (1)
          uperfamily
          1. Protozoan pheromone proteins [47015] (5)
             1. ER-1 [47016]
                1. Euplotes raikovi [TaxId: 5938] [47017] (2)
             2. ER-2 [47018]
                1. Euplotes raikovi [TaxId: 5938] [47019] (1)
             3. ER-10 [47020]
                1. Euplotes raikovi [TaxId: 5938] [47021] (1)
             4. ER-11 [47022]
                1. Euplotes raikovi [TaxId: 5938] [47023] (1)
             5. ER-22 [47024]
                1. Euplotes raikovi [TaxId: 5938] [47025] (1)
       2. Hypothetical membrane protein Ta0354, soluble domain [116858] (1)
          uperfamily
          1. Hypothetical membrane protein Ta0354, soluble domain [116859] (1)
             1. Hypothetical membrane protein Ta0354, soluble domain [116860]
                1. Thermoplasma acidophilum [TaxId: 2303] [116861] (1)
                   SQ Q9HL76 69-121
   19. Acyl-CoA binding protein-like [47026] (2)
       core: 3 helices; bundle, closed, left-handed twist; up-and-down
       1. Acyl-CoA binding protein [47027] (1)
          uperfamily
          1. Acyl-CoA binding protein [47028] (2)
             1. Acyl-CoA binding protein [47029]
                1. Cow (Bos taurus) [TaxId: 9913] [47030] (6)
                   SQ P07107
                2. Plasmodium falciparum [TaxId: 5833] [63498] (1)
       2. Second domain of FERM [47031] (1)
          uperfamily
          1. Second domain of FERM [47032] (9)
             1. Moesin [47033]
                1. Human (Homo sapiens) [TaxId: 9606] [47034] (3)
                   SQ P26038 4-297
             2. Radixin [47035]
                1. Mouse (Mus musculus) [TaxId: 10090] [47036] (20)
             3. Ezrin [81714]
                1. Human (Homo sapiens) [TaxId: 9606] [81715] (1)
             4. Erythroid membrane protein 4.1R [47037]
                1. Human (Homo sapiens) [TaxId: 9606] [47038] (1)
             5. Merlin [68980]
                the neurofibromatosis 2 tumor suppressor protein
                1. Human (Homo sapiens) [TaxId: 9606] [68981] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [74702] (1)
             6. Talin [81716]
                1. Chicken (Gallus gallus) [TaxId: 9031] [81717] (5)
             7. Talin-1 [116862]
                1. Mouse (Mus musculus) [TaxId: 10090] [116863] (1)
                   SQ P26039 209-410
             8. Focal adhesion kinase 1 [140380]
                1. Chicken (Gallus gallus) [TaxId: 9031] [140381] (5)
                   SQ Q00944 131-253
   20. YqgQ-like [158378] (1)
       3 helices, bundle, left-handed twist, extended overside connection between the first and second helices
       1. YqgQ-like [158379] (1)
          1. YqgQ-like [158380] (1)
             Pfam 06014; DUF910
             1. Hypothetical protein YqgQ [158381]
                1. Bacillus subtilis [TaxId: 1423] [158382] (3)
                   SQ P54494 1-62
   21. Kix domain of CBP (creb binding protein) [47039] (1)
       3 helices; bundle, partly opened
       1. Kix domain of CBP (creb binding protein) [47040] (1)
          uperfamily
          1. Kix domain of CBP (creb binding protein) [47041] (1)
             1. Kix domain of CBP (creb binding protein) [47042]
                1. Mouse (Mus musculus) [TaxId: 10090] [47043] (3)
   22. RAP domain-like [47044] (1)
       3 helices, the first one is shorter than the other two; bundle, partly opened
       1. RAP domain-like [47045] (1)
          uperfamily
          1. RAP domain [47046] (1)
             1. alpha-2-Macroglobulin receptor associated protein (RAP) [47047]
                1. Human (Homo sapiens) [TaxId: 9606] [47048] (7)
   23. VHP, Villin headpiece domain [47049] (1)
       3 short helices; irregular array
       1. VHP, Villin headpiece domain [47050] (1)
          uperfamily
          1. VHP, Villin headpiece domain [47051] (5)
             1. Villin [47052]
                1. Chicken (Gallus gallus) [TaxId: 9031] [47053] (6)
                2. Human (Homo sapiens) [TaxId: 9606] [109759] (1)
                   SQ P09327 792-826
             2. Dematin [101099]
                1. Human (Homo sapiens) [TaxId: 9606] [101100] (1)
             3. Actin-binding LIM protein homologue KIAA0843 [101101]
                1. Human (Homo sapiens) [TaxId: 9606] [101102] (1)
             4. Advillin [109760]
                1. Human (Homo sapiens) [TaxId: 9606] [109761] (1)
                   SQ O75366 784-819
   24. BSD domain-like [140382] (1)
       core: 3 helices; triangular array; the extra N-terminal and C-terminal helices form a coiled coil structure
       1. BSD domain-like [140383] (1)
          uperfamily
          1. BSD domain [140384] (2)
             Pfam 03909
             1. TFIIH basal transcription factor complex p62 subunit, BTF2 [140385]
                1. Human (Homo sapiens) [TaxId: 9606] [140386] (1)
                   SQ P32780 103-150
             2. Synapse associated protein 1, SYAP1 [140387]
                1. Human (Homo sapiens) [TaxId: 9606] [140388] (1)
                   SQ Q96A49 130-216
   25. TAF(II)230 TBP-binding fragment [47054] (1)
       3 short helices; irregular array
       1. TAF(II)230 TBP-binding fragment [47055] (1)
          uperfamily
          1. TAF(II)230 TBP-binding fragment [47056] (1)
             1. TAF(II)230 TBP-binding fragment [47057]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [47058] (1)
   26. S15/NS1 RNA-binding domain [47059] (1)
       3 helices; irregular array
       1. S15/NS1 RNA-binding domain [47060] (3)
          uperfamily
          1. N-terminal, RNA-binding domain of nonstructural protein NS1 [47061] (2)
             1. N-terminal, RNA-binding domain of nonstructural protein NS1 [47062]
                1. Influenza A virus [TaxId: 11320] [47063] (2)
                2. Influenza B virus [TaxId: 11520] [140389] (1)
                   SQ P03502 15-103
          2. Ribosomal protein S15 [47064] (3)
             contains additional N-terminal helix that forms a separate unit
             1. Ribosomal protein S15 [47065]
                1. Bacillus stearothermophilus [TaxId: 1422] [47066] (1)
                2. Thermus thermophilus [TaxId: 274] [47067] (42)
                   SQ P80378
                3. Escherichia coli [TaxId: 562] [158383] (10)
                   SQ Q8X9M2 2-89
          3. a tRNA synthase domain [47068] (3)
             1. Multifunctional Glu-Pro-tRNA synthase (EPRS) second repeated element [47069]
                1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [47070] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [63499] (1)
             2. N-terminal domain of eukaryotic tryptophanyl-tRNA synthetase (TrpRS) [101103]
                1. Human (Homo sapiens) [TaxId: 9606] [101104] (1)
   27. Frizzled cysteine-rich domain [63500] (1)
       Core: 3 helices; irregular array; disulfide-rich
       1. Frizzled cysteine-rich domain [63501] (1)
          uperfamily
          1. Frizzled cysteine-rich domain [63502] (2)
             1. Secreted Frizzled-related protein 3 (SFRP-3;fzb) [63503]
                1. Mouse (Mus musculus) [TaxId: 10090] [63504] (1)
             2. Frizzled 8 (FZ8) [63505]
                1. Mouse (Mus musculus) [TaxId: 10090] [63506] (1)
   28. T4 endonuclease V [47076] (1)
       3 helices; irregular array
       1. T4 endonuclease V [47077] (1)
          uperfamily
          1. T4 endonuclease V [47078] (1)
             1. T4 endonuclease V [47079]
                1. Bacteriophage T4 [TaxId: 10665] [47080] (7)
   29. Fertilization protein [47081] (1)
       core: 3 helices; bundle, closed, right-handed twist; up-and-down
       1. Fertilization protein [47082] (1)
          uperfamily
          1. Fertilization protein [47083] (3)
             1. Lysin [47084]
                1. Red abalone (Haliotis rufescens) [TaxId: 6454] [47085] (4)
                2. Green abalone (Haliotis fulgens) [TaxId: 6456] [47086] (1)
             2. SP18 [47087]
                1. Green abalone (Haliotis fulgens) [TaxId: 6456] [47088] (1)
   30. PGBD-like [47089] (1)
       core: 3 helices; bundle, closed, left-handed twist; parallel
       1. PGBD-like [47090] (2)
          uperfamily
          1. Peptidoglycan binding domain, PGBD [47091] (2)
             1. Zn2+ DD-carboxypeptidase, N-terminal domain [47092]
                probable peptidoglycan-binding domain
                1. Streptomyces albus G [TaxId: 1962] [47093] (1)
             2. Probable N-acetylmuramoyl-L-alanine amidase YbjR, C-terminal domain [140390]
                1. Escherichia coli [TaxId: 562] [140391] (2)
                   SQ P75820 195-275
          2. MMP N-terminal domain [63427] (4)
             1. Fibroblast collagenase (MMP-1) [116864]
                1. Human (Homo sapiens) [TaxId: 9606] [116865] (1)
                   SQ P03956 32-466
             2. Gelatinase A (MMP-2) [63428]
                1. Human (Homo sapiens) [TaxId: 9606] [63430] (3)
             3. Stromelysin-1 (MMP-3) [63429]
                1. Human (Homo sapiens), fibroblast [TaxId: 9606] [63431] (1)
             4. Gelatinase B (MMP-9) [74703]
                1. Human (Homo sapiens) [TaxId: 9606] [74704] (1)
   31. HMG-box [47094] (1)
       3 helices; irregular array
       1. HMG-box [47095] (1)
          uperfamily
          1. HMG-box [47096] (12)
             1. High mobility group protein 1, HMG1 [47097]
                duplication: contains HMG-box domains
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47098] (4)
                2. Hamster (Cricetulus griseus) [TaxId: 10029] [47099] (5)
             2. High mobility group protein 2, HMG2 [109762]
                1. Pig (Sus scrofa) [TaxId: 9823] [109763] (3)
                   SQ P17741 1-77, 89-163
             3. HMG-D [47100]
                1. Drosophila melanogaster [TaxId: 7227] [47101] (3)
             4. NHP6a [47102]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47103] (3)
             5. SRY [47104]
                1. Human (Homo sapiens) [TaxId: 9606] [47105] (5)
             6. Sox-5 [47106]
                1. Mouse (Mus musculus) [TaxId: 10090] [47107] (1)
             7. Sox-2 [81718]
                1. Mouse (Mus musculus) [TaxId: 10090] [81719] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [101105] (1)
             8. Lymphoid enhancer-binding factor, LEF1 [47110]
                1. Mouse (Mus musculus) [TaxId: 10090] [47111] (1)
             9. Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) [68982]
                Contains 6 HMG-box domains
                1. Human (Homo sapiens) [TaxId: 9606] [68983] (3)
                2. Mouse (Mus musculus) [TaxId: 10090] [109764] (3)
                   SQ P25976 388-383, 392-470, 567-655
   32. Histone-fold [47112] (1)
       core: 3 helices; long middle helix is flanked at each end with shorter ones
       1. Histone-fold [47113] (4)
          uperfamily
          1. Nucleosome core histones [47114] (23)
             form octamers composed of two copies of each of the four histones
             1. Histone H2A [47115]
                1. Chicken (Gallus gallus), erythrocytes [TaxId: 9031] [47116] (7)
                   SQ P02263
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [47117] (29)
                3. Human (Homo sapiens), variant H2A.Z [TaxId: 9606] [47118] (1)
                4. Baker's yeast (Saccharomyces cerevisiae), H2A.1 [TaxId: 4932] [68984] (2)
                5. Human (Homo sapiens), H2A.a [TaxId: 9606] [140392] (2)
                   SQ P28001 11-118
                6. Mouse (Mus musculus), H2A.1 [TaxId: 10090] [158384] (1)
                   SQ P22752 14-118
             2. Histone H2B [47119]
                1. Chicken (Gallus gallus), erythrocytes [TaxId: 9031] [47120] (7)
                   SQ P02279
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [47121] (32)
                3. Baker's yeast (Saccharomyces cerevisiae), H2B.2 [TaxId: 4932] [68985] (2)
                4. Mouse (Mus musculus), H2Ba [TaxId: 10090] [140393] (3)
                   SQ Q9D2U9 34-126
                5. Human (Homo sapiens), H2B.k [TaxId: 9606] [140394] (2)
                   SQ O60814 30-125
                6. Xenopus (Silurana) tropicalis [TaxId: 8364] [158385] (4)
             3. Histone H3 [47122]
                1. Chicken (Gallus gallus), erythrocytes [TaxId: 9031] [47123] (9)
                   SQ P84229
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [47124] (34)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [68986] (1)
                4. Mouse(Mus musculus), H3.1 [TaxId: 10090] [140395] (4)
                   SQ P68433 38-135
                5. fruit fly (Drosophila melanogaster) [TaxId: 7227] [158386] (4)
             4. Histone H4 [47125]
                1. Chicken (Gallus gallus), erythrocytes [TaxId: 9031] [47126] (5)
                   SQ P62801
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [47127] (45)
                3. Mouse (Mus musculus) [TaxId: 10090] [47128] (1)
                4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [68987] (1)
                5. fruit fly (Drosophila melanogaster) [TaxId: 7227] [158387] (4)
             5. macro-H2A.1, histone domain [140396]
                1. Human (Homo sapiens) [TaxId: 9606] [140397] (3)
                   SQ O75367 11-116
          2. Archaeal histone [47129] (4)
             1. Archaeal histone [68897]
                1. Archaeon Methanothermus fervidus, histone A [TaxId: 2180] [68895] (2)
                2. Archaeon Methanothermus fervidus, histone B [TaxId: 2180] [68896] (3)
                3. Archaeon Methanopyrus kandleri [TaxId: 2320] [68988] (1)
                4. Archaeon (Pyrococcus horikoshii) [TaxId: 53953] [101106] (1)
          3. TBP-associated factors, TAFs [47134] (13)
             1. TAF(II)42 [47135]
                TAFii42 and TAFii62 form heterotetramer similar to (H3-H4)2
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [47136] (1)
             2. TAF(II)62 [47137]
                TAFii42 and TAFii62 form heterotetramer similar to (H3-H4)2
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [47138] (1)
             3. TAF(II)18 [47139]
                1. Human (Homo sapiens) [TaxId: 9606] [47140] (2)
             4. TAF(II)28 [47141]
                1. Human (Homo sapiens) [TaxId: 9606] [47142] (2)
             5. TAF(II)-135, (TAF(II)-130, hTAF4), histone fold domain [81720]
                lacks the third helix, forms a heterodimer with TAF(II)-20 similar to H2A-H2B
                1. Human (Homo sapiens) [TaxId: 9606] [81721] (1)
             6. TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain [81722]
                forms a heterodimer with TAF(II)-135 similar to H2A-H2B
                1. Human (Homo sapiens) [TaxId: 9606] [81723] (1)
             7. Negative cofactor 2, NC2, alpha chain [63507]
                1. Human (Homo sapiens) [TaxId: 9606] [63508] (1)
             8. Negative cofactor 2, NC2, beta chain [63509]
                1. Human (Homo sapiens) [TaxId: 9606] [63510] (1)
             9. Nuclear transcription factor Y subunit beta (Nf-Yb3) [81724]
                forms a heterodimer with Nf-Yc2 similar to H2A/H2B
                1. Human (Homo sapiens) [TaxId: 9606] [81725] (1)
             10. Nuclear transcription factor Y subunit gamma (Nf-Yc2) [81726]
                 forms a heterodimer with Nf-Yb3 similar to H2A/H2B
                 1. Human (Homo sapiens) [TaxId: 9606] [81727] (1)
             11. Histone domain of Son of sevenless protein [101107]
                 1. Human (Homo sapiens) [TaxId: 9606] [101108] (1)
             12. Chrac-14 [140398]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140399] (4)
                    SQ Q9V444 11-99
             13. Chrac-16 [140400]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140401] (4)
                    SQ Q9V452 29-100
          4. Bacterial histone-fold protein [101318] (2)
             duplication: two repeats of histone fold are arranged as subunits in the archael histone dimer; new structure from Thermus thermophilus (1wws) comprised of dimers similar the to the H3-H4 tetramer
             1. Hypothetical protein Aq_328 [101319]
                1. Aquifex aeolicus [TaxId: 63363] [101320] (1)
             2. Hypothetical protein TTHA1479 [140402]
                1. Thermus thermophilus [TaxId: 274] [140403] (9)
                   SQ Q5SI95 1-148
   33. Open three-helical up-and-down bundle [47143] (7)
       core: 3 helices; bundle, open
       1. HSC20 (HSCB), C-terminal oligomerisation domain [47144] (1)
          uperfamily
          1. HSC20 (HSCB), C-terminal oligomerisation domain [47145] (1)
             1. HSC20 (HSCB), C-terminal oligomerisation domain [47146]
                1. Escherichia coli [TaxId: 562] [47147] (1)
       2. Diol dehydratase, gamma subunit [47148] (1)
          contains irregular N-terminal subdomain
          uperfamily
          1. Diol dehydratase, gamma subunit [47149] (2)
             1. Diol dehydratase, gamma subunit [47150]
                1. Klebsiella oxytoca [TaxId: 571] [47151] (7)
                2. Klebsiella pneumoniae [TaxId: 573] [81728] (2)
       3. Methane monooxygenase hydrolase, gamma subunit [47152] (1)
          duplication: consists of two domains of this fold
          uperfamily
          1. Methane monooxygenase hydrolase, gamma subunit [47153] (2)
             1. Methane monooxygenase hydrolase, gamma subunit [47154]
                1. Methylococcus capsulatus [TaxId: 414] [47155] (37)
                2. Methylosinus trichosporium [TaxId: 426] [47156] (2)
       4. Mitochondrial import receptor subunit Tom20 [47157] (1)
          uperfamily
          1. Mitochondrial import receptor subunit Tom20 [47158] (1)
             1. Mitochondrial import receptor subunit Tom20 [47159]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47160] (1)
       5. Hemolysin expression modulating protein HHA [68989] (1)
          uperfamily
          1. Hemolysin expression modulating protein HHA [68990] (1)
             1. Hemolysin expression modulating protein HHA [68991]
                1. Escherichia coli [TaxId: 562] [68992] (1)
       6. EF2458-like [140404] (1)
          N-terminal helix swapped dimer; interrupted antiparallel coiled coil
          uperfamily
          1. EF2458-like [140405] (1)
             Pfam 07408; DUF1507
             1. Hypothetical protein EF2458 [140406]
                1. Enterococcus faecalis [TaxId: 1351] [140407] (2)
                   SQ Q831P3 1-82
       7. YvfG-like [158388] (1)
          1. YvfG-like [158389] (1)
             Pfam 09628
             1. Hypothetical protein YvfG [158390]
                1. Bacillus subtilis [TaxId: 1423] [158391] (4)
                   SQ P71066 3-69
   34. beta-catenin-interacting protein ICAT [81729] (1)
       core: 3 helices; irregular array
       1. beta-catenin-interacting protein ICAT [81730] (1)
          uperfamily
          1. beta-catenin-interacting protein ICAT [81731] (1)
             1. beta-catenin-interacting protein ICAT [81732]
                consists of a globular N-domain and extended C-terminal tail
                1. Human (Homo sapiens) [TaxId: 9606] [81733] (3)
                   SQ Q9NSA3 8-53
   35. DNA polymerase III theta subunit-like [116730] (1)
       3 helices; irregular array
       1. DNA polymerase III theta subunit-like [46575] (1)
          uperfamily
          1. DNA polymerase III theta subunit-like [46576] (2)
             Pfam 06440
             independent solution structure determinations of different members resulted in similar secondary structures but different folds
             1. Theta subunit of DNA polymerase III [46577]
                1. Escherichia coli [TaxId: 562] [46578] (3)
             2. Homolog of theta (HOT) [116866]
                1. Bacteriophage P1 [TaxId: 10678] [116867] (3)
                   SQ Q71T70
   36. Four-helical up-and-down bundle [47161] (28)
       core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
       1. Apolipoprotein [47162] (1)
          uperfamily
          1. Apolipoprotein [47163] (3)
             Can exist in a coiled-coil oligomeric form, see PDB entry 1AV1
             family may also include the five-helical bundle protein Apolipophorin-III
             1. Apolipoprotein E [88703]
                1. Human (Homo sapiens), E3 [TaxId: 9606] [47165] (7)
                2. Human (Homo sapiens), E2 [TaxId: 9606] [47167] (2)
                3. Human (Homo sapiens), E4 [TaxId: 9606] [47169] (3)
       2. Aspartate receptor, ligand-binding domain [47170] (1)
          uperfamily
          1. Aspartate receptor, ligand-binding domain [47171] (2)
             1. Aspartate receptor, ligand-binding domain [47172]
                1. Escherichia coli [TaxId: 562] [47173] (1)
                2. Salmonella typhimurium [TaxId: 90371] [47174] (7)
       3. Cytochromes [47175] (2)
          Heme-containing proteins
          uperfamily
          1. Cytochrome b562 [47176] (1)
             1. Cytochrome b562 [47177]
                1. Escherichia coli [TaxId: 562] [47178] (6)
          2. Cytochrome c'-like [47179] (9)
             1. Cytochrome c' [47180]
                1. Rhodospirillum molischianum [TaxId: 1083] [47181] (1)
                2. Chromatium vinosum [TaxId: 1049] [47182] (1)
                3. Alcaligenes denitrificans [TaxId: 32002] [47183] (1)
                4. Alcaligenes sp. [TaxId: 512] [47184] (5)
                5. Rhodocyclus gelatinosus [TaxId: 28068] [47185] (5)
                6. Rhodobacter capsulatus [TaxId: 1061] [47186] (4)
                7. Rhodobacter sphaeroides [TaxId: 1063] [81734] (1)
                8. Rhodopseudomonas palustris [TaxId: 1076] [47187] (2)
             2. Cytochrome c-556 [101109]
                1. Rhodopseudomonas palustris [TaxId: 1076] [101110] (1)
       4. Hemerythrin-like [47188] (1)
          uperfamily
          1. Hemerythrin-like [47189] (3)
             Iron-binding proteins
             1. Hemerythrin [47190]
                1. Sipunculid worm (Themiste dyscritum) [TaxId: 6436] [47191] (4)
                2. Phascolopsis gouldii [TaxId: 6442] [47192] (4)
             2. Myohemerythin [47193]
                1. Sipunculan worm (Themiste zostericola) [TaxId: 6437] [47194] (3)
       5. TMV-like viral coat proteins [47195] (1)
          uperfamily
          1. TMV-like viral coat proteins [47196] (3)
             1. Tobacco mosaic virus coat protein [47197]
                1. Tobacco mosaic virus, vulgare strain [TaxId: 12242] [47198] (4)
             2. Cucumber green mottle mosaic virus [47199]
                1. Cucumber green mottle mosaic virus, strain watermelon [TaxId: 12235] [47200] (1)
             3. Ribgrass mosaic virus [47201]
                1. Ribgrass mosaic virus [TaxId: 51680] [47202] (1)
       6. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47212] (1)
          uperfamily
          1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47213] (1)
             1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47214]
                1. Human (Homo sapiens) [TaxId: 9606] [47215] (7)
       7. Proteasome activator [47216] (1)
          uperfamily
          1. Proteasome activator [47217] (2)
             1. Proteasome activator reg(alpha) [47218]
                The structure of the proteasome complex with this protein from (Trypanosoma brucei) is available (1fnt); however, PDB entry 1FNT designates protein chains by both upper case and lower case letters creating problems with its processing and presentation; the proteasome activator pa26 chains are designated by lower case letters (c;d;e;f;g;h;i;j;k;l;m;n;o;p)
                1. Human (Homo sapiens) [TaxId: 9606] [47219] (1)
             2. Proteasome activator protein PA26 [158392]
                1. Trypanosoma brucei [TaxId: 5691] [158393] (21)
                   SQ Q9U8G2 4-231
       8. alpha-catenin/vinculin-like [47220] (2)
          uperfamily
          1. alpha-catenin/vinculin [47221] (4)
             possible duplication: contains several domains of this fold
             The listed PDB entries contain different large fragments but not the whole proteins
             1. alpha-catenin [47222]
                1. Mouse (Mus musculus) [TaxId: 10090] [47223] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [63511] (2)
             2. Vinculin [47224]
                1. Chicken (Gallus gallus) [TaxId: 9031] [47225] (3)
                   SQ P12003
                2. Human (Homo sapiens) [TaxId: 9606] [101111] (4)
                   SQ P18206 1-257
          2. VBS domain [140408] (1)
             Pfam 08913; Vinculin Binding Site
             1. Talin 1 [140409]
                1. Mouse (Mus musculus) [TaxId: 10090] [140410] (1)
                   SQ P26039 1838-1973
       9. FAT domain of focal adhesion kinase [68993] (1)
          uperfamily
          1. FAT domain of focal adhesion kinase [68994] (3)
             1. FAT domain of focal adhesion kinase [68995]
                1. Human (Homo sapiens) [TaxId: 9606] [68996] (9)
                2. Mouse (Mus musculus) [TaxId: 10090] [68997] (1)
                3. Chicken (Gallus gallus) [TaxId: 9031] [81735] (3)
                   SQ Q00944 RE 920-1053
       10. Oxygen-evolving enhancer protein 3, [101112] (1)
           uperfamily
           1. Oxygen-evolving enhancer protein 3, [101113] (1)
              1. Oxygen-evolving enhancer protein 3, [101114]
                 PsbQ protein of photosystem II
                 1. Spinach (Spinacia oleracea) [TaxId: 3562] [101115] (1)
       11. Histidine-containing phosphotransfer domain, HPT domain [47226] (6)
           contains additional, fifth helix at the N-terminus
           uperfamily
           1. Aerobic respiration control sensor protein, ArcB [47227] (1)
              1. Aerobic respiration control sensor protein, ArcB [47228]
                 1. Escherichia coli [TaxId: 562] [47229] (4)
           2. Phosphorelay protein-like [47230] (3)
              1. Phosphorelay protein ypd1 [47231]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47232] (6)
              2. Histidine-containing phosphotransfer protein HP2 [140411]
                 1. Maize (Zea mays) [TaxId: 4577] [140412] (4)
                    SQ Q9SLX1 9-139
              3. Histidine-containing phosphotransfer protein HP1 [140413]
                 1. Rice (Oryza sativa) [TaxId: 4530] [140414] (4)
                    SQ Q6VAK4 2-143
           3. Chemotaxis protein CheA P1 domain [63512] (2)
              1. Chemotaxis protein CheA P1 domain [63513]
                 1. Salmonella typhimurium [TaxId: 90371] [63514] (1)
                 2. Thermotoga maritima [TaxId: 2336] [109765] (1)
                    SQ Q56310 4-104
           4. Sensor-like histidine kinase YojN, C-terminal domain [116868] (1)
              1. Sensor-like histidine kinase YojN, C-terminal domain [116869]
                 1. Escherichia coli [TaxId: 562] [116870] (1)
                    SQ P39838 775-890
           5. Phosphorelay protein luxU [116871] (1)
              1. Phosphorelay protein luxU [116872]
                 1. Vibrio harveyi [TaxId: 669] [116873] (1)
                    SQ Q9ZBB6
           6. SphA-like [158394] (1)
              1. Histidine phosphotransferase ShpA [158395]
                 1. Caulobacter crescentus [TaxId: 155892] [158396] (2)
                    SQ A0EJF9 8-111
       12. Bacterial GAP domain [47233] (1)
           contains extra helices in the loops at one end of the bundle
           uperfamily
           1. Bacterial GAP domain [47234] (3)
              1. ExoS toxin [47235]
                 1. Pseudomonas aeruginosa [TaxId: 287] [47236] (2)
              2. SptP tyrosine phosphatase [47237]
                 1. Salmonella typhimurium [TaxId: 90371] [47238] (2)
              3. YopE [68998]
                 1. Yersinia pestis [TaxId: 632] [68999] (1)
       13. Outer surface protein C (OspC) [63515] (1)
           uperfamily
           1. Outer surface protein C (OspC) [63516] (1)
              1. Outer surface protein C (OspC) [63517]
                 1. Lyme disease spirochete (Borrelia burgdorferi), different strains [TaxId: 139] [63518] (3)
       14. Flagellar export chaperone FliS [101116] (1)
           can form closed, open and helix-swapped bundles
           uperfamily
           1. Flagellar export chaperone FliS [101117] (2)
              1. Flagellar export chaperone FliS [101118]
                 1. Aquifex aeolicus [TaxId: 63363] [101119] (2)
                 2. Bacillus subtilis [TaxId: 1423] [101120] (1)
       15. Domain of the SRP/SRP receptor G-proteins [47364] (1)
           uperfamily
           1. Domain of the SRP/SRP receptor G-proteins [47365] (7)
              1. Signal sequence recognition protein Ffh [47366]
                 1. Thermus aquaticus [TaxId: 271] [47367] (25)
                 2. Archaeon Acidianus ambivalens [TaxId: 2283] [63538] (2)
                 3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101121] (2)
              2. Signal recognition particle receptor, FtsY [47368]
                 1. Escherichia coli [TaxId: 562] [47369] (2)
                 2. Thermus aquaticus [TaxId: 271] [101122] (8)
                 3. Thermotoga maritima [TaxId: 2336] [109766] (1)
                    SQ Q9WZ40
              3. Signal recognition particle 54 kDa protein, SRP54 [116874]
                 1. Mouse (Mus musculus) [TaxId: 10090] [116875] (1)
                    SQ P14576 4-85
       16. FAD-dependent thiol oxidase [69000] (1)
           uperfamily
           1. FAD-dependent thiol oxidase [69001] (2)
              1. Thiol oxidase Erv2p [69002]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69003] (2)
              2. Augmenter of liver regeneration [89018]
                 a mammalian FAD-dependent sulfhydryl oxidase
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [89019] (1)
       17. Group V grass pollen allergen [81736] (1)
           uperfamily
           1. Group V grass pollen allergen [81737] (2)
              1. Pollen allergen Phl P 6 [81738]
                 1. Timothy grass (Phleum pratense) [TaxId: 15957] [81739] (1)
              2. Functional domain of pollen allergen Phl P 5b [89020]
                 1. Timothy grass (Phleum pratense) [TaxId: 15957] [89021] (1)
       18. Nucleotidyltransferase substrate binding subunit/domain [81593] (4)
           uperfamily
           1. Family 1 bi-partite nucleotidyltransferase subunit [81740] (2)
              1. Hypothetical protein HI0074 [81741]
                 function unknown; form complex with putative catalytic subunit HI0073 (see 1no5)
                 1. Haemophilus influenzae [TaxId: 727] [81742] (1)
              2. Probable nucleotidyltransferase subunit TTHA0048 [116876]
                 1. Thermus thermophilus [TaxId: 274] [116877] (5)
                    SQ Q5SM95
                    Structural genomics target
           2. HEPN domain [89022] (2)
              1. Hypothetical protein TM0613 [89023]
                 Family 5 probable bi-partite nucleotidyltransferase subunit; predicted partner is putative catalytic subunit TM0614
                 1. Thermotoga maritima [TaxId: 2336] [89024] (1)
              2. Hypothetical protein TT1696 [101123]
                 1. Thermus thermophilus [TaxId: 274] [101124] (1)
           3. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81592] (1)
              N-terminal catalytic domain is followed by an all-alpha domain
              1. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81591]
                 1. Staphylococcus aureus [TaxId: 1280] [81590] (2)
           4. Glutamine synthase adenylyltransferase GlnE, domain 2 [109767] (1)
              1. Glutamine synthase adenylyltransferase GlnE, domain 2 [109768]
                 1. Escherichia coli [TaxId: 562] [109769] (1)
                    SQ P30870 1-437
       19. RecG, N-terminal domain [69008] (1)
           uperfamily
           1. RecG, N-terminal domain [69009] (1)
              1. RecG, N-terminal domain [69010]
                 1. Thermotoga maritima [TaxId: 2336] [69011] (1)
       20. Colicin D immunity protein [101125] (1)
           uperfamily
           1. Colicin D immunity protein [101126] (1)
              1. Colicin D immunity protein [101127]
                 tRNA-mimic
                 1. Escherichia coli [TaxId: 562] [101128] (3)
       21. Nickel-containing superoxide dismutase, NiSOD [109770] (1)
           uperfamily
           1. Nickel-containing superoxide dismutase, NiSOD [109771] (2)
              1. Nickel-containing superoxide dismutase, NiSOD [109772]
                 1. Streptomyces seoulensis [TaxId: 73044] [109773] (5)
                    SQ P80734
                 2. Streptomyces coelicolor [TaxId: 1902] [109774] (3)
                    SQ P80735
       22. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109775] (1)
           contains extra alpha+beta subdomain formed by the N- and C-termini.
           uperfamily
           1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109776] (1)
              1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109777]
                 1. Mouse (Mus musculus) [TaxId: 10090] [109778] (1)
                    SQ Q9DBG5 206-431
       23. Domain from hypothetical 2610208m17rik protein [109779] (1)
           uperfamily
           1. Domain from hypothetical 2610208m17rik protein [109780] (1)
              1. Domain from hypothetical 2610208m17rik protein [109781]
                 1. Mouse (Mus musculus) [TaxId: 10090] [109782] (1)
                    SQ Q8C4Q6 1-115
       24. TrmE connector domain [116878] (1)
           uperfamily
           1. TrmE connector domain [116879] (1)
              1. TrmE connector domain [116880]
                 1. Thermotoga maritima [TaxId: 2336] [116881] (2)
                    SQ Q9WYA4
       25. YppE-like [140415] (1)
           flattened bundle at one end with helices 2 and coming in contact and separating helices 1 and 3
           uperfamily
           1. YppE-like [140416] (3)
              Pfam 08807; DUF1798
              1. Hypothetical protein Lin2004 [140417]
                 1. Listeria innocua [TaxId: 1642] [140418] (1)
                    SQ Q92AB8 1-120
              2. Hypothetical protein MW1337 [140419]
                 SA1281 ortholog
                 1. Staphylococcus aureus [TaxId: 1280] [140420] (1)
                    SQ Q8NWP7 1-110
              3. Hypothetical protein YppE [140421]
                 1. Bacillus subtilis [TaxId: 1423] [140422] (3)
                    SQ P50833 1-123
       26. MW0975(SA0943)-like [140423] (1)
           open bundle; there is a long groove between helices 1 and 4
           uperfamily
           1. MW0975(SA0943)-like [140424] (1)
              1. Hypothetical protein MW0975 (SA0943) [140425]
                 1. Staphylococcus aureus [TaxId: 1280] [140426] (1)
                    SQ Q8NX77 21-205
       27. VPS28 C-terminal domain-like [140427] (1)
           uperfamily
           1. VPS28 C-terminal domain-like [140428] (1)
              C-terminal part of Pfam 03997
              1. Vacuolar protein sorting-associated protein 28, VPS28 [140429]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140430] (10)
                    SQ Q02767 148-241
       28. TM1646-like [158397] (1)
           1. TM1646-like [158398] (1)
              Pfam 03885; DUF327
              1. Hypothetical protein TM1646 [158399]
                 1. Thermotoga maritima [TaxId: 2336] [158400] (1)
                    SQ Q9X1X9 34-152
   37. PTS-regulatory domain, PRD [63519] (1)
       core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection
       1. PTS-regulatory domain, PRD [63520] (1)
          duplication: consists of two domains of this fold
          uperfamily
          1. PTS-regulatory domain, PRD [63521] (1)
             1. Transcriptional antiterminator LicT [63522]
                1. Bacillus subtilis [TaxId: 1423] [63523] (3)
   38. Ferritin-like [47239] (6)
       core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
       1. Ferritin-like [47240] (9)
          contains bimetal-ion centre in the middle of the bundle
          uperfamily
          1. Ferritin [47241] (34)
             1. Rubrerythrin, N-terminal domain [47242]
                1. Desulfovibrio vulgaris [TaxId: 881] [47243] (10)
                   SQ P24931
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [101129] (3)
             2. Hypothetical rubrerythrin [101130]
                1. Archaeon Sulfolobus tokodaii [TaxId: 111955] [101131] (1)
             3. Hypothetical protein TM1526 [101132]
                1. Thermotoga maritima [TaxId: 2336] [101133] (1)
             4. Bacterioferritin (cytochrome b1) [47244]
                binds heme between two subunits; 24-mer
                1. Escherichia coli [TaxId: 562] [47245] (20)
                2. Rhodobacter capsulatus [TaxId: 1061] [69004] (1)
                3. Desulfovibrio desulfuricans [TaxId: 876] [89025] (3)
                4. Azotobacter vinelandii [TaxId: 354] [140431] (24)
                   SQ P22759 1-155
             5. Non-hem ferritin [63524]
                1. Escherichia coli, FtnA [TaxId: 562] [63525] (1)
                2. Campylobacter jejuni [TaxId: 197] [69005] (1)
                3. Thermotoga maritima [TaxId: 2336] [109783] (1)
                   SQ Q9X0L2
                4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [140432] (24)
                   SQ O29424 3-164
             6. Dodecameric ferritin homolog [47250]
                1. Escherichia coli, Dps [TaxId: 562] [47251] (7)
                   ferritin homolog that binds to and protects DNA
                2. Listeria innocua [TaxId: 1642] [47252] (43)
                3. Bacillus anthracis, Dlp-1 [TaxId: 1392] [74705] (1)
                4. Bacillus anthracis, Dlp-2 [TaxId: 1392] [74706] (1)
                5. Bacillus brevis, Dps [TaxId: 1393] [89026] (1)
                6. Agrobacterium tumefaciens, Dps [TaxId: 358] [89027] (1)
                7. Helicobacter pylori, Nap [TaxId: 210] [81743] (1)
                8. Streptococcus suis [TaxId: 1307] [101134] (37)
                9. Archaeon Halobacterium salinarum [TaxId: 2242] [101135] (5)
                   SQ Q9HMP7
                10. Mycobacterium smegmatis [TaxId: 1772] [109784] (20)
                    SQ Q8VP75
                11. Lactococcus lactis, DpsB [TaxId: 1358] [140433] (12)
                    SQ A2RJ45 3-173
                12. Lactococcus lactis, DpsA [TaxId: 1358] [140434] (4)
                    SQ A2RLG8 6-173
                13. Treponema pallidum, TpF1 [TaxId: 160] [140435] (16)
                    SQ P16665 26-176
             7. (Apo)ferritin [47246]
                1. Human (Homo sapiens), H chain [TaxId: 9606] [47247] (3)
                2. Horse (Equus caballus), L chain [TaxId: 9796] [47248] (20)
                3. Mouse (Mus musculus) [TaxId: 10090] [63526] (2)
                4. Bullfrog (Rana catesbeiana) [TaxId: 8400] [47249] (7)
                5. Human (Homo sapiens), mitocondial isoform [TaxId: 9606] [109785] (1)
                   SQ Q8N4E7
                6. Cabbage looper(Trichoplusia ni), L chain [TaxId: 7111] [140436] (12)
                   SQ Q52SA8 1-200
                7. Cabbage looper(Trichoplusia ni), H chain [TaxId: 7111] [140437] (12)
                   SQ Q8WQX3 21-211
             8. Hypothetical protein PF1190 [140438]
                significant sequence similarity to the half-ferritin family
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [140439] (2)
                   SQ Q8U1L6 9-166
             9. Nigerythrin, N-terminal domain [140440]
                1. Desulfovibrio vulgaris [TaxId: 881] [140441] (6)
                   SQ P30820 1-166
          2. Ribonucleotide reductase-like [47253] (18)
             1. Methane monooxygenase hydrolase alpha subunit [88789]
                1. Methylococcus capsulatus [TaxId: 414] [88790] (43)
                2. Methylosinus trichosporium [TaxId: 426] [88791] (2)
             2. Methane monooxygenase hydrolase beta subunit [88792]
                1. Methylococcus capsulatus [TaxId: 414] [88793] (31)
                2. Methylosinus trichosporium [TaxId: 426] [88794] (2)
             3. Ribonucleotide reductase R2 [47257]
                1. Escherichia coli [TaxId: 562] [47258] (24)
                2. Salmonella typhimurium [TaxId: 90371] [47259] (4)
                3. Corynebacterium ammoniagenes [TaxId: 1697] [69006] (6)
                4. Mouse (Mus musculus) [TaxId: 10090] [47260] (5)
                   SQ P11157
                5. Baker's yeast (Saccharomyces cerevisiae), Y2 [TaxId: 4932] [88795] (2)
                   SQ P09938
                6. Baker's yeast (Saccharomyces cerevisiae), Y4 [TaxId: 4932] [88796] (2)
                   SQ P49723
                7. Chlamydia trachomatis [TaxId: 813] [109786] (1)
                   SQ O84835
                8. Mycobacterium tuberculosis [TaxId: 1773] [109787] (1)
                   SQ Q50549 10-291
                9. Human (Homo sapiens), RRM2 [TaxId: 9606] [158401] (1)
                   SQ P31350 66-350
             4. delta 9-stearoyl-acyl carrier protein desaturase [47261]
                1. Castor bean (Ricinus communis) [TaxId: 3988] [47262] (5)
             5. Phenylacetic acid degradation protein PaaC [101136]
                1. Escherichia coli [TaxId: 562] [101137] (1)
             6. Toluene, o-xylene monooxygenase oxygenase subunit TouA [109788]
                contains the TouB(TmoB)-binding YHS (sub)domain (Pfam 04945) in the C-terminal part (401-450)
                1. Pseudomonas stutzeri [TaxId: 316] [109789] (5)
                   SQ O87798
             7. Toluene, o-xylene monooxygenase oxygenase subunit TouE [109790]
                1. Pseudomonas stutzeri [TaxId: 316] [109791] (6)
                   SQ O87802
             8. Possible acyl-[acyl-carrier protein] desaturase [140442]
                1. Mycobacterium tuberculosis [TaxId: 1773] [140443] (1)
                   SQ O53442 8-274
          3. Manganese catalase (T-catalase) [100951] (2)
             1. Manganese catalase (T-catalase) [47263]
                1. Lactobacillus plantarum [TaxId: 1590] [74707] (3)
                2. Thermus thermophilus [TaxId: 274] [140444] (2)
                   SQ Q5SM21 1-299
          4. YciF-like [140445] (2)
             Pfam 05974; DUF892
             1. Hypothetical ptotein RPA3308 [140446]
                putative structural protein
                1. Rhodopseudomonas palustris [TaxId: 1076] [140447] (2)
                   SQ Q6N4M9 1-160
             2. Hypothetical protein YciF [140448]
                1. Escherichia coli [TaxId: 562] [140449] (2)
                   SQ P21362 3-161
          5. half-ferritin [140450] (1)
             comprise of alpha-hairpin subunits forming the ferritin-like four-helical bundle; assembles further in a homodecamer
             1. Hypothetical protein NE0167 [140451]
                1. Nitrosomonas europaea [TaxId: 915] [140452] (10)
                   SQ Q82XT5 4-94
          6. PMT1231-like [158402] (1)
             PfamB 016165
             1. Hypothetical protein PMT1231 [158403]
                1. Prochlorococcus marinus [TaxId: 1219] [158404] (1)
                   SQ Q7V6D4 20-241
          7. MiaE-like [158405] (1)
             Pfam 06175; tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
             1. Putative tRNA-(Ms(2)io(6)a)-hydroxylase PP2188 [158406]
                1. Pseudomonas putida [TaxId: 303] [158407] (2)
                   SQ Q88KV1 3-201
          8. AMB4284-like [158408] (1)
             possible rubrerythrin
             1. Uncharacterized protein AMB4284 homologue [158409]
                1. Magnetospirillum magnetotacticum ms-1 [TaxId: 272627] [158410] (1)
                   SQ Q2VZ87 3-154
          9. Rv2844-like [158411] (1)
             PfamB 061364
             1. Hypothetical protein Rv2844 [158412]
                1. Mycobacterium tuberculosis [TaxId: 1773] [158413] (1)
                   SQ O05815 17-158
       2. Cobalamin adenosyltransferase-like [89028] (2)
          crossover loop goes across a different side of the 4-helical bundle; no internal metal-binding site
          uperfamily
          1. Cobalamin adenosyltransferase [89032] (2)
             1. Putative ATP-binding cobalamin adenosyltransferase YvqK [101138]
                1. Bacillus subtilis [TaxId: 1423] [101139] (1)
             2. Hypothetical protein Ta0546 [89033]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89034] (1)
          2. Hypothetical protein Ta1238 [89029] (1)
             1. Hypothetical protein Ta1238 [89030]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89031] (1)
       3. EsxAB dimer-like [140453] (1)
          (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
          uperfamily
          1. ESAT-6 like [140454] (2)
             Pfam 06013; the conserwed WxG motif makes the turn at the alpha-hairpin tip
             1. ESAT-6 like protein EsxB [140455]
                1. Mycobacterium tuberculosis [TaxId: 1773] [140456] (1)
                   SQ P0A566 1-99
             2. ESAT-6, EsxA [140457]
                6 kDa early secretory antigenic target
                1. Mycobacterium tuberculosis [TaxId: 1773] [140458] (1)
                   SQ P0A564 1-94
       4. PE/PPE dimer-like [140459] (2)
          (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals inside the bundle
          uperfamily
          1. PE [140460] (1)
             Pfam 00934; pairs with with the N-terminal hairpin of PPE
             1. PE25 [140461]
                1. Mycobacterium tuberculosis [TaxId: 1773] [140462] (2)
                   SQ Q7D756 8-84
          2. PPE [140463] (1)
             Pfam 00823; contains extra C-terminal alpha-hairpin, unlike the PE family subunit
             1. PPE41 [140464]
                1. Mycobacterium tuberculosis [TaxId: 1773] [140465] (2)
                   SQ Q79FE1 2-174
       5. HP0062-like [158414] (1)
          (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
          1. HP0062-like [158415] (1)
             Pfam 09647
             1. Hypothetical protein HP0062 [158416]
                1. Helicobacter pylori [TaxId: 210] [158417] (1)
                   SQ O24902 4-80
       6. SO2669-like [158418] (1)
          (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
          1. SO2669-like [158419] (1)
             1. Hypothetical protein SO2669 [158420]
                1. Shewanella oneidensis [TaxId: 70863] [158421] (8)
                   SQ Q8EDS4 1-64
   39. 4-helical cytokines [47265] (1)
       core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
       1. 4-helical cytokines [47266] (3)
          there are two different topoisomers of this fold with different entanglements of the two crossover connections
          uperfamily
          1. Long-chain cytokines [47267] (14)
             1. Granulocyte-colony stimulating factor (G-CSF) [47268]
                1. Human (Homo sapiens) [TaxId: 9606] [47269] (5)
                2. Cow (Bos taurus) [TaxId: 9913] [47270] (1)
                3. Dog (Canis familiaris) [TaxId: 9615] [47271] (2)
             2. Interleukin-6 [47272]
                1. Human (Homo sapiens) [TaxId: 9606] [47273] (4)
                2. Human herpesvirus 8, Kaposi's sarcoma herpes-virus [TaxId: 37296] [63528] (1)
             3. Leukemia inhibitory factor (LIF) [47274]
                1. Mouse (Mus musculus) [TaxId: 10090] [47275] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [63529] (4)
             4. Growth hormone, somatotropin [47276]
                1. Human (Homo sapiens) [TaxId: 9606] [47277] (9)
             5. Prolactin (placental lactogen) [47278]
                1. Sheep (Ovis aries) [TaxId: 9940] [47279] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [89035] (2)
             6. Ciliary neurotrophic factor (CNTF) [47280]
                1. Human (Homo sapiens) [TaxId: 9606] [47281] (1)
             7. Leptin (obesity protein) [47282]
                1. Human (Homo sapiens) [TaxId: 9606] [47283] (1)
             8. Oncostatin M [47284]
                1. Human (Homo sapiens) [TaxId: 9606] [47285] (1)
             9. Heterodimeric interleukin-12 alpha chain [63530]
                1. Human (Homo sapiens) [TaxId: 9606] [63531] (1)
          2. Short-chain cytokines [47286] (14)
             1. Erythropoietin [47287]
                long chain cytokine with a short-chain cytokine topology
                1. Human (Homo sapiens) [TaxId: 9606] [47288] (3)
             2. Thrombopoietin [101140]
                long chain cytokine with a short-chain cytokine topology
                1. Human (Homo sapiens) [TaxId: 9606] [101141] (2)
             3. Granulocyte-macrophage colony-stimulating factor (GM-CSF) [47289]
                1. Human (Homo sapiens) [TaxId: 9606] [47290] (3)
             4. Interleukin-4 (IL-4) [47291]
                1. Human (Homo sapiens) [TaxId: 9606] [47292] (16)
             5. Interleukin-5 [47293]
                intertwined dimer
                1. Human (Homo sapiens) [TaxId: 9606] [47294] (1)
             6. Macrophage colony-stimulating factor (M-CSF) [47295]
                forms dimer similar to the Flt3 ligand and SCF dimers
                1. Human (Homo sapiens) [TaxId: 9606] [47296] (1)
             7. Flt3 ligand [47297]
                forms dimer similar to the M-CSF and SCF dimers
                1. Human (Homo sapiens) [TaxId: 9606] [47298] (1)
             8. Stem cell factor, SCF [47299]
                forms dimer similar to the M-CSF and Flt3 ligand dimers
                1. Human (Homo sapiens) [TaxId: 9606] [47300] (3)
             9. Interleukin-2 (IL-2) [47301]
                1. Human (Homo sapiens) [TaxId: 9606] [47302] (15)
             10. Interleukin-3 (IL-3) [47303]
                 1. Human (Homo sapiens) [TaxId: 9606] [47304] (1)
             11. Interleukin-13 (IL-13) [63532]
                 1. Human (Homo sapiens) [TaxId: 9606] [63533] (3)
             12. Interleukin-15 (IL-15) [158422]
                 1. Human (Homo sapiens) [TaxId: 9606] [158423] (10)
                    SQ P40933 49-162
                 2. Mouse (Mus musculus) [TaxId: 10090] [158424] (2)
                    SQ P48346 49-162
             13. Interleukin-21 (IL-21) [158425]
                 1. Human (Homo sapiens) [TaxId: 9606] [158426] (1)
                    SQ Q9HBE4 23-155
          3. Interferons/interleukin-10 (IL-10) [47305] (13)
             contains an additional helix in one of the crossover connections
             1. Interleukin-10 (cytokine synthesis inhibitory factor, CSIF) [47306]
                intertwined dimer, similar to interferon-gamma
                1. Human (Homo sapiens) [TaxId: 9606] [47307] (7)
                2. Epstein-Barr virus [TaxId: 10376] [47308] (3)
                3. Human herpesvirus 5 [TaxId: 10359] [74708] (1)
             2. Interleukin-19 [81744]
                1. Human (Homo sapiens) [TaxId: 9606] [81745] (1)
             3. Interferon-beta [47309]
                1. Human (Homo sapiens) [TaxId: 9606] [47310] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [47311] (2)
                   SQ P01575 22-182
                   CA-atoms only
             4. Interleukin-22 (IL-22) [89036]
                1. Human (Homo sapiens) [TaxId: 9606] [89037] (8)
             5. Interferon-alpha 2b [47312]
                1. Human (Homo sapiens) [TaxId: 9606] [47313] (1)
             6. Interferon-alpha 2a [47314]
                1. Human (Homo sapiens) [TaxId: 9606] [47315] (2)
             7. Interferon-tau [47316]
                1. Sheep (Ovis aries) [TaxId: 9940] [47317] (1)
             8. Interferon-gamma [47318]
                intertwined dimer
                1. Cow (Bos taurus) [TaxId: 9913] [47319] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [47320] (5)
                3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [47321] (1)
   40. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47322] (1)
       core: 4 helices; bundle; one loop crosses over one side of the bundle
       1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47323] (1)
          uperfamily
          1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47324] (10)
             1. Methionyl-tRNA synthetase (MetRS) [47325]
                this domain follows the Rossmann-fold catalytic domain of class I aaRS
                1. Thermus thermophilus [TaxId: 274] [47326] (4)
                2. Escherichia coli [TaxId: 562] [47327] (9)
                3. Pyrococcus abyssi [TaxId: 29292] [109792] (1)
                   SQ Q9V011 1-606 # C-domain 616-722 is solved separately: 1MKH
             2. Cysteinyl-tRNA synthetase (CysRS) [74709]
                contains extra C-terminal alpha+beta subdomain: [alpha(2)-beta(2)], ordered in the complex with tRNA
                1. Escherichia coli [TaxId: 562] [74710] (3)
                   SQ P21888; extra C-terminal subdomain: 407-461
             3. Isoleucyl-tRNA synthetase (IleRS) [47328]
                1. Thermus thermophilus [TaxId: 274] [47329] (3)
                2. Staphylococcus aureus [TaxId: 1280] [47330] (3)
                   contains additional alpha+beta and Zn-binding domains in the C-terminal extension
             4. Valyl-tRNA synthetase (ValRS) [47331]
                includes additional alpha+beta (sub)domain at the C-terminus
                1. Thermus thermophilus [TaxId: 274] [47332] (3)
             5. Arginyl-tRNA synthetase (ArgRS) [47333]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47334] (3)
                2. Thermus thermophilus [TaxId: 274] [69007] (1)
             6. Leucyl-tRNA synthetase (LeuRS) [81746]
                1. Thermus thermophilus [TaxId: 274] [81747] (3)
   41. Acyl carrier protein-like [47335] (3)
       4 helices, bundle; helix 3 is shorter than others; up-and-down
       1. ACP-like [47336] (3)
          uperfamily
          1. Acyl-carrier protein (ACP) [47337] (9)
             1. Acyl carrier protein [47338]
                1. Escherichia coli [TaxId: 562] [47339] (23)
                   SQ P02901
                2. Bacillus subtilis [TaxId: 1423] [63534] (2)
                3. Mycobacterium tuberculosis [TaxId: 1773] [74711] (1)
                4. Thermotoga maritima [TaxId: 2336] [109793] (1)
                   SQ Q9WY19
             2. Actinorhodin polyketide synthase acyl carrier protein, ACT ACP [47340]
                1. Streptomyces coelicolor, A3(2) [TaxId: 1902] [47341] (2)
             3. Frenolicin polyketide synthase acyl carrier protein, Fren ACP [89038]
                1. Streptomyces roseofulvus [TaxId: 33902] [89039] (1)
             4. Oxytetracycline polyketide synthase acyl carrier [101142]
                1. Streptomyces rimosus [TaxId: 1927] [101143] (1)
             5. Type I fatty acid synthase ACP domain [89040]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [89041] (1)
             6. Hypothetical protein Atu2571 [158427]
                1. Agrobacterium tumefaciens [TaxId: 358] [158428] (1)
                   SQ Q8UCC7 1-83
          2. Peptidyl carrier domain [47342] (1)
             1. Peptidyl carrier protein (PCP), thioester domain [47343]
                1. Bacillus brevis [TaxId: 1393] [47344] (4)
          3. apo-D-alanyl carrier protein [63535] (1)
             1. apo-D-alanyl carrier protein [63536]
                1. Lactobacillus casei [TaxId: 1582] [63537] (2)
       2. Colicin E immunity proteins [47345] (1)
          uperfamily
          1. Colicin E immunity proteins [47346] (3)
             1. ImmE7 protein (Im7) [47347]
                1. Escherichia coli [TaxId: 562] [47348] (13)
             2. ImmE8 (Im8) [47349]
                1. Escherichia coli [TaxId: 562] [47350] (2)
             3. ImmE9 protein (Im9) [47351]
                1. Escherichia coli [TaxId: 562] [47352] (14)
       3. Retrovirus capsid dimerization domain-like [47353] (2)
          uperfamily
          1. Retrovirus capsid protein C-terminal domain [47354] (4)
             1. EIAV capsid protein p26 [47355]
                1. Equine infectious anemia virus [TaxId: 11665] [47356] (2)
             2. HTLV-I capsid protein [47357]
                1. Human T-cell leukemia virus type 1 [TaxId: 11908] [47358] (1)
             3. HIV capsid protein, dimerisation domain [47359]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [47360] (7)
             4. RSV capsid protein [47361]
                1. Rous sarcoma virus [TaxId: 11886] [47362] (2)
          2. SCAN domain [140466] (2)
             Pfam 02023; forms segment-swapped dimers compared to the retroviral capsid domain
             1. Zinc finger protein 42 [140467]
                1. Human (Homo sapiens) [TaxId: 9606] [140468] (2)
                   SQ P28698 37-128
             2. Zinc finger protein 174 [140469]
                1. Human (Homo sapiens) [TaxId: 9606] [140470] (2)
                   SQ Q15697 37-132
   42. Bromodomain-like [47363] (15)
       4 helices; bundle; minor mirror variant of up-and-down topology
       1. Bromodomain [47370] (1)
          uperfamily
          1. Bromodomain [47371] (5)
             1. GCN5 [47372]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47373] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [47374] (3)
             2. P300/CAF histone acetyltransferase bromodomain [47375]
                1. Human (Homo sapiens) [TaxId: 9606] [47376] (7)
             3. TAFII250 double bromodomain module [47377]
                1. Human (Homo sapiens) [TaxId: 9606] [47378] (1)
             4. CREB-binding protein, CBP [74712]
                1. Human (Homo sapiens) [TaxId: 9606] [74713] (5)
       2. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69012] (1)
          uperfamily
          1. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69013] (3)
             1. Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) [69014]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [69015] (3)
             2. Pyruvate dehydrogenase kinase [69016]
                1. Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116] [69017] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [158429] (8)
                   SQ Q15120 13-176
       3. Acyl-CoA dehydrogenase C-terminal domain-like [47203] (2)
          multidomain flavoprotein; N-terminal domain is all-alpha; the middle domain is open (5,8) barrel
          uperfamily
          1. Medium chain acyl-CoA dehydrogenase-like, C-terminal domain [47204] (12)
             1. Butyryl-CoA dehydrogenase, C-domain [47205]
                1. Megasphaera elsdenii [TaxId: 907] [47206] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [69018] (1)
             2. Medium chain acyl-CoA dehydrogenase, C-domain [47207]
                1. Pig (Sus scrofa) [TaxId: 9823] [47208] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [47209] (8)
                   SQ P11310 34-421
                3. Thermus thermophilus [TaxId: 274] [116882] (1)
                   SQ Q5SJ70 32-409
             3. Isovaleryl-CoA dehydrogenase, C-domain [47210]
                1. Human (Homo sapiens) [TaxId: 9606] [47211] (1)
             4. Isobutyryl-CoA dehydrogenase [101144]
                1. Human (Homo sapiens) [TaxId: 9606] [101145] (1)
             5. Protein FkbI [101146]
                involved in biosynthesis of methoxymalonyl extender unit of fk520 polyketide immunosuppressant
                1. Streptomyces hygroscopicus [TaxId: 1912] [101147] (1)
             6. Glutaryl-CoA dehydrogenase GCDH [109794]
                1. Human (Homo sapiens) [TaxId: 9606] [109795] (4)
                   SQ Q92947
             7. 4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain [116883]
                1. Clostridium aminobutyricum [TaxId: 33953] [116884] (1)
                   SQ P55792
             8. Nitroalkane oxidase [140471]
                1. Fusarium oxysporum [TaxId: 5507] [140472] (18)
                   SQ Q8X1D8 261-430
             9. Acyl-CoA dehydrogenase [140473]
                1. Thermus thermophilus [TaxId: 274] [140474] (8)
                   SQ Q5SGZ2 235-387
          2. acyl-CoA oxidase C-terminal domains [74714] (2)
             duplication: tandem repeat of this fold
             1. Peroxisomal acyl-CoA oxidase-II, domains 3 and 4 [74715]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [74716] (3)
             2. Acyl-coenzyme A oxidase 1, domains 3 and 4 [116885]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116886] (1)
                   SQ O65202
       4. Plant invertase/pectin methylesterase inhibitor [101148] (1)
          contains a short alpha-hairpin at the N-terminal extension
          uperfamily
          1. Plant invertase/pectin methylesterase inhibitor [101149] (2)
             Pfam 04043
             1. Invertase inhibitor [101150]
                1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [101151] (9)
             2. Pectin methylesterase inhibitor 1, PMEI1 [116887]
                forms dimers and trimers by swapping the extra N-terminal hairpins
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116888] (3)
                   SQ Q9LNF2 28-176
       5. Mob1/phocein [101152] (1)
          common fold is elaborated with additional short helices; contains a zinc-binding site
          uperfamily
          1. Mob1/phocein [101153] (2)
             1. Mob1a [101154]
                1. Human (Homo sapiens) [TaxId: 9606] [101155] (1)
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [109796] (1)
                   SQ Q7T1M9 33-215
       6. Bacteriocin immunity protein-like [109797] (2)
          uperfamily
          1. Carnobacteriocin B2 immunity protein [109798] (1)
             1. Carnobacteriocin B2 immunity protein [109799]
                1. Carnobacterium piscicola [TaxId: 2751] [109800] (1)
                   SQ P38582
          2. EntA-Im [140475] (1)
             1. Enterocine A immunity protein, EntA-Im [140476]
                1. Enterococcus faecium [TaxId: 1352] [140477] (3)
                   SQ Q47785 3-82
       7. LemA-like [140478] (1)
          helices 2 and 3 are shorther than helices 1 and 4
          uperfamily
          1. LemA-like [140479] (1)
             Pfam 04011
             1. Hypothetical protein TM0961 [140480]
                1. Thermotoga maritima [TaxId: 2336] [140481] (1)
                   SQ Q9X056 35-183
       8. MAST3 pre-PK domain-like [140482] (1)
          this domain precedes the Protein Kinase domain in Microtubule-associated serine/threonine-protein kinase 3 (MAST3)
          uperfamily
          1. MAST3 pre-PK domain-like [140483] (1)
             1. Microtubule-associated serine/threonine-protein kinase 3, MAST3 (KIAA0561) [140484]
                1. Human (Homo sapiens) [TaxId: 9606] [140485] (1)
                   SQ O60307 181-281
       9. PA2201 N-terminal domain-like [140486] (1)
          uperfamily
          1. PA2201 N-terminal domain-like [140487] (1)
             trimerisation domain
             1. Hypothetical protein PA2201 [140488]
                1. Pseudomonas aeruginosa [TaxId: 287] [140489] (3)
                   SQ Q9I1R6 6-129
       10. Nqo1C-terminal domain-like [140490] (1)
           contains extra C-terminal helix that caps the bundle at one end and Fe4-S4 cluster at the other end
           uperfamily
           1. Nqo1C-terminal domain-like [140491] (1)
              PfamB 000336; sequence similarity to the Fe4-S4 ferredoxins in the cluser-binding site
              1. NADH-quinone oxidoreductase chain 1, Nqo1 [140492]
                 1. Thermus thermophilus [TaxId: 274] [140493] (4)
                    SQ Q56222 334-438
       11. Bacillus cereus metalloprotein-like [158430] (1)
           Duplication: tandem repeat of two domains of this fold with similar sequences; binds a dimetal ion cluster between the repeats
           1. Bacillus cereus metalloprotein-like [158431] (2)
              1. Uncharacterized protein BCE_G9241_1042 [158432]
                 1. Bacillus cereus [TaxId: 1396] [158433] (12)
                    SQ Q4MW04 11-144! SQ Q4MW04 145-274
              2. Uncharacterized protein BCE_G9241_0798 [158434]
                 1. Bacillus cereus [TaxId: 1396] [158435] (40)
                    SQ Q4MWP8 125-259! SQ Q4MWP8 4-124
       12. Ta0600-like [158436] (1)
           1. Ta0600-like [158437] (2)
              Pfam 03685; UPF0147
              1. Uncharacterized protein MMP1188 [158438]
                 1. Methanococcus maripaludis [TaxId: 39152] [158439] (4)
                    SQ Q6LY05 4-91
              2. Uncharacterized protein Ta0600 [158440]
                 1. Thermoplasma acidophilum [TaxId: 2303] [158441] (1)
                    SQ Q9HKJ8 2-86
       13. DsbB-like [158442] (1)
           contains an extra helix in a long loop between helices 3 and 4
           1. DsbB-like [158443] (1)
              Pfam 02600
              1. Disulfide bond formation protein DsbB [158444]
                 1. Escherichia coli [TaxId: 562] [158445] (1)
                    SQ P0A6M2 14-162
       14. IVS-encoded protein-like [158446] (1)
           IVS: Intervening sequence with conserved ORF in eubacterial 23S rRNA genes; forms a homopentamer with a toroid-shaped structure containing a tapered central channel
           1. IVS-encoded protein-like [158447] (2)
              Pfam 05635
              1. Uncharacterized protein XCC0516 [158448]
                 1. Xanthomonas campestris pv. campestris [TaxId: 340] [158449] (5)
                    SQ Q8PD29 9-125
              2. Uncharacterized protein BT0352 [158450]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [158451] (5)
                    SQ Q8AAW0 1-115
       15. YqcC-like [158452] (1)
           1. YqcC-like [158453] (1)
              Pfam 04287; DUF446
              1. Hypothetical protein YqcC [158454]
                 1. Escherichia coli [TaxId: 562] [158455] (1)
                    SQ Q46919 1-109
   43. ROP-like [47379] (8)
       4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
       1. ROP protein [47380] (1)
          uperfamily
          1. ROP protein [47381] (1)
             1. ROP protein [47382]
                1. Escherichia coli [TaxId: 562] [47383] (14)
                   SQ P03051
       2. Homodimeric domain of signal transducing histidine kinase [47384] (1)
          uperfamily
          1. Homodimeric domain of signal transducing histidine kinase [47385] (3)
             1. EnvZ histidine kinase [47386]
                1. Escherichia coli [TaxId: 562] [47387] (1)
             2. Histidine kinase CheA [47388]
                1. Thermotoga maritima [TaxId: 2336] [47389] (1)
             3. Sensor histidine kinase TM0853 [140494]
                1. Thermotoga maritima [TaxId: 2336] [140495] (1)
                   SQ Q9WZV7 232-320
       3. Nonstructural protein ns2, Nep, M1-binding domain [101156] (1)
          uperfamily
          1. Nonstructural protein ns2, Nep, M1-binding domain [101157] (1)
             1. Nonstructural protein ns2, Nep, M1-binding domain [101158]
                1. Influenza A virus [TaxId: 11320] [101159] (1)
       4. Dimerisation domain of CENP-B [101160] (1)
          uperfamily
          1. Dimerisation domain of CENP-B [101161] (1)
             1. Dimerisation domain of CENP-B [101162]
                1. Human (Homo sapiens) [TaxId: 9606] [101163] (1)
       5. Hypothetical protein D-63 [109801] (1)
          uperfamily
          1. Hypothetical protein D-63 [109802] (1)
             1. Hypothetical protein D-63 [109803]
                1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [109804] (1)
                   SQ P20215
       6. HP1531-like [140496] (1)
          contains short extra helix in the loop between the two bundle-forming helices
          uperfamily
          1. HP1531-like [140497] (1)
             Small sequence family, specific to Helicobacteraceae
             1. Hypothetical protein HP1531 [140498]
                1. Helicobacter pylori [TaxId: 210] [140499] (6)
                   SQ P64665 1-79
       7. BAS1536-like [140500] (1)
          uperfamily
          1. BAS1536-like [140501] (2)
             PfamB 015565
             1. Hypothetical protein BAS1536 [140502]
                1. Bacillus anthracis [TaxId: 1392] [140503] (2)
                   SQ Q81SJ3 19-72
             2. Hypothetical protein BAS4809, C-terminal domain [140504]
                1. Bacillus anthracis [TaxId: 1392] [140505] (1)
                   SQ Q81XQ9 52-108
       8. FHV B2 protein-like [140506] (1)
          uperfamily
          1. FHV B2 protein-like [140507] (1)
             1. B2 [140508]
                1. Flock house virus, FHV [TaxId: 12287] [140509] (6)
                   SQ P68831 1-72! SQ P68831 2-71
   44. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47390] (1)
       4 helices; bundle, closed, right-handed twist
       1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47391] (1)
          dimer of identical alpha-hairpin motifs
          uperfamily
          1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47392] (2)
             1. cAMP-dependent protein kinase type II regulatory subunit [47393]
                1. Mouse (Mus musculus) [TaxId: 10090] [47394] (18)
             2. cAMP-dependent protein kinase type I-alpha regulatory subunit [140510]
                1. Cow (Bos taurus) [TaxId: 9913] [140511] (2)
                   SQ P00514 12-61
   45. Orange domain-like [158456] (1)
       4 helices; dimer of identical alpha-hairpin subunits;
       1. Orange domain-like [158457] (1)
          1. Hairy Orange domain [158458] (1)
             Pfam 07527
             1. Hairy/enhancer-of-split related with YRPW motif protein 1; HESR-1 [158459]
                1. Human (Homo sapiens) [TaxId: 9606] [158460] (2)
                   SQ Q9Y5J3 111-165
   46. Soluble domain of poliovirus core protein 3a [89042] (1)
       4 helices; bundle, closed, right-handed twist
       1. Soluble domain of poliovirus core protein 3a [89043] (1)
          dimer of identical alpha-hairpin motifs
          uperfamily
          1. Soluble domain of poliovirus core protein 3a [89044] (1)
             1. Soluble domain of poliovirus core protein 3a [89045]
                1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [89046] (1)
   47. Transcription factor IIA (TFIIA), alpha-helical domain [47395] (1)
       4 helices; bundle, closed, right-handed twist
       1. Transcription factor IIA (TFIIA), alpha-helical domain [47396] (1)
          dimer of non-identical alpha-hairpins
          uperfamily
          1. Transcription factor IIA (TFIIA), alpha-helical domain [47397] (4)
             heterodimer of two homologous chains
             1. Large chain TOA1, N-terminal domain [88833]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88834] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [101164] (1)
             2. Small chain TOA2, N-terminal domain [88835]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88836] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [101165] (1)
   48. Ectatomin subunits [47400] (1)
       4 helices; bundle, closed, left-handed twist
       1. Ectatomin subunits [47401] (1)
          disulfide-linked heterodimer of similar alpha-hairpin subunits
          uperfamily
          1. Ectatomin subunits [47402] (2)
             1. Ectatomin subunit A, EA [88837]
                1. Ant (Ectatomma tuberculatum), venom [TaxId: 39300] [88838] (1)
             2. Ectatomin subunit B, EB [88839]
                1. Ant (Ectatomma tuberculatum), venom [TaxId: 39300] [88840] (1)
   49. Dimerisation interlock [47405] (4)
       4 helices; bundle, closed, right-handed twist
       1. SinR repressor dimerisation domain-like [47406] (1)
          intertwined heterodimer of two homologous chains
          uperfamily
          1. SinR repressor dimerisation domain-like [47407] (2)
             1. SinR repressor dimerisation domain [88841]
                1. Bacillus subtilis [TaxId: 1423] [88842] (1)
             2. SinI anti-repressor [88843]
                1. Bacillus subtilis [TaxId: 1423] [88844] (1)
       2. Dimerization cofactor of HNF-1 alpha [100957] (1)
          uperfamily
          1. Dimerization cofactor of HNF-1 alpha [100958] (1)
             1. Hepatocyte nuclear factor 1 (HNF-1), N-terminal domain [47410]
                1. Mouse (Mus musculus) [TaxId: 10090] [47411] (5)
       3. Docking domain A of the erythromycin polyketide synthase (DEBS) [101166] (1)
          uperfamily
          1. Docking domain A of the erythromycin polyketide synthase (DEBS) [101167] (1)
             1. Erythronolide synthase [101168]
                1. Saccharopolyspora erythraea [TaxId: 1836] [101169] (1)
       4. Phenylalanine zipper [109805] (1)
          interlocking dimer with longer helices and aromatic-rich core
          uperfamily
          1. Adapter protein APS, dimerisation domain [109806] (1)
             1. Adapter protein APS, dimerisation domain [109807]
                1. Human (Homo sapiens) [TaxId: 9606] [109808] (1)
                   SQ O14492 21-85
   50. lambda repressor-like DNA-binding domains [47412] (1)
       core: 4 helices; folded leaf, closed
       1. lambda repressor-like DNA-binding domains [47413] (13)
          uperfamily
          1. POU-specific domain [47414] (3)
             1. Oct-1 [47415]
                canonical 4-helical fold
                1. Human (Homo sapiens) [TaxId: 9606] [47416] (7)
             2. Pit-1 [47417]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47418] (1)
             3. Hepatocyte nuclear factor 1a (LFB1/HNF1) [81748]
                atypical POU domain with extra N-terminal helix
                1. Human (Homo sapiens) [TaxId: 9606] [81749] (1)
          2. Phage repressors [47419] (7)
             consists of different sequence families of HTH repressors of phage origins
             1. lambda C1 repressor, DNA-binding domain [47420]
                1. Bacteriophage lambda [TaxId: 10710] [47421] (6)
             2. 434 C1 repressor, DNA-binding domain [47422]
                1. Bacteriophage 434 [TaxId: 10712] [47423] (8)
                   SQ P16117 10-62; contains a short additional helix at C-terminus
             3. cro 434 [47424]
                1. Bacteriophage 434 [TaxId: 10712] [47425] (3)
                   contains a short additional helix at C-terminus
             4. P22 C2 repressor, DNA-binding domain [47426]
                1. Salmonella bacteriophage P22 [TaxId: 10754] [47427] (3)
                   contains a short additional helix at C-terminus
             5. cro lambda repressor [47428]
                the fourth helix is replaced with a beta hairpin
                3 helices; folded leaf, opened
                1. Bacteriophage lambda [TaxId: 10710] [47429] (9)
             6. Ner [47430]
                1. Bacteriophage mu [TaxId: 10677] [47431] (2)
             7. cro p22 [109809]
                1. Bacteriophage p22 [TaxId: 10754] [109810] (1)
                   SQ P09964
          3. SinR domain-like [47432] (8)
             1. SinR repressor, DNA-binding domain [47433]
                1. Bacillus subtilis [TaxId: 1423] [47434] (1)
             2. Putative transcription regulator CylR2 [109811]
                1. Enterococcus faecalis [TaxId: 1351] [109812] (3)
                   SQ Q8VL32
             3. Regulatory protein C.BclI [140512]
                1. Bacillus caldolyticus [TaxId: 1394] [140513] (4)
             4. Restriction-modification controller protein C.AhdI [140514]
                1. Aeromonas hydrophila [TaxId: 644] [140515] (2)
                   SQ Q7X0F0 5-73
             5. Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain [140516]
                1. Streptomyces wedmorensis [TaxId: 43759] [140517] (20)
                   SQ Q56185 6-76
             6. Putative transcriptional regulator RHA1_ro04071 [158461]
                1. Rhodococcus sp. RHA1 [TaxId: 101510] [158462] (2)
                   SQ Q0S9B8 3-84
             7. Uncharacterized protein Atu1735 [158463]
                1. Agrobacterium tumefaciens [TaxId: 358] [158464] (1)
                   SQ Q8UEM2 30-91
             8. Antitoxin HigA [158465]
                Uncharacterized transcriptional regulator YddM
                1. Escherichia coli [TaxId: 562] [158466] (2)
                   SQ P67699 8-94
          4. Cyanase N-terminal domain [47435] (1)
             probably does not bind to DNA
             1. Cyanase N-terminal domain [47436]
                1. Escherichia coli [TaxId: 562] [47437] (22)
          5. GalR/LacI-like bacterial regulator [47438] (4)
             lacks the first helix of canonical fold
             3 helices; bundle, partly opened, right-handed twist
             1. Purine repressor (PurR), N-terminal domain [47439]
                1. Escherichia coli [TaxId: 562] [47440] (24)
             2. Lac repressor (LacR), N-terminal domain [47441]
                1. Escherichia coli [TaxId: 562] [47442] (14)
             3. Fructose repressor (FruR), N-terminal domain [47443]
                1. Escherichia coli [TaxId: 562] [47444] (2)
             4. Glucose-resistance amylase regulator CcpA, N-terminal domain [116889]
                1. Bacillus megaterium [TaxId: 1404] [116890] (5)
                   SQ P46828
          6. YdiL-like [109813] (2)
             contains extra C-terminal all-alpha dimerization subdomain; the dimer may bind DNA
             1. Putative cytoplasmic protein YdiL [109814]
                1. Salmonella typhimurium [TaxId: 90371] [109815] (1)
                   SQ Q8ZPR1
             2. Hypothetical protein SO3848 [158467]
                1. Shewanella oneidensis [TaxId: 70863] [158468] (1)
                   SQ Q8EAP9 5-166
          7. CUT domain [116891] (4)
             Pfam 02376
             1. Homeobox protein Cux-2, CUTL2 [116892]
                1. Human (Homo sapiens) [TaxId: 9606] [116893] (3)
                   SQ O14529 825-912; 966-1063
             2. DNA-binding protein SATB2 [116894]
                1. Human (Homo sapiens) [TaxId: 9606] [116895] (2)
                   SQ Q9UPW6 350-437; the structure of a homedomain (615-672) is also known: 1WI3
             3. Hepatocyte nuclear factor 6 [116896]
                1. Mouse (Mus musculus) [TaxId: 10090] [116897] (1)
                   SQ O08755 291-437
             4. DNA-binding protein SATB1 [140518]
                1. Human (Homo sapiens) [TaxId: 9606] [140519] (3)
                   SQ Q01826 368-455
          8. Probable transcriptional regulator VC1968, N-terminal domain [116898] (1)
             1. Probable transcriptional regulator VC1968, N-terminal domain [116899]
                1. Vibrio cholerae [TaxId: 666] [116900] (1)
                   SQ Q9KQN0
          9. Bacteriophage CII protein [140520] (1)
             Pfam 05269; a compact helix-swapped dimer of the canonical fold; includes the extra C-terminal teramerisation region (alpha-helix); in the tetramer-DNA complex only two of the four HTH motifs interact with DNA
             1. Regulatory protein cII [140521]
                1. Bacteriophage lambda [TaxId: 10710] [140522] (12)
                   SQ P03042 2-80! SQ P03042 4-81
          10. NE0471 C-terminal domain-like [140523] (1)
              1. Hypothetical protein NE0471 C-terminal domain [140524]
                 1. Nitrosomonas europaea [TaxId: 915] [140525] (2)
                    SQ Q82X29 88-154
          11. PrgX N-terminal domain-like [140526] (1)
              Part of Pfam 01381
              1. PrgX [140527]
                 possibly involved in pheromone-inducible conjugation
                 1. Enterococcus faecalis [TaxId: 1351] [140528] (40)
                    SQ Q04114 1-69! SQ Q04114 2-66
          12. EDF1-like [140529] (1)
              part of Pfam 01381
              1. Endothelial differentiation-related factor 1, EDF1 [140530]
                 1. Human (Homo sapiens) [TaxId: 9606] [140531] (1)
                    SQ O60869 71-148
          13. NE1354 [140532] (2)
              contains extra C-terminal dimerisation arm (beta-strand)
              1. HTH-motif protein NE1354 [140533]
                 1. Nitrosomonas europaea [TaxId: 915] [140534] (2)
                    SQ Q82UW4 1-69
              2. Hypothetical protein RPA3824 [158469]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [158470] (2)
                    SQ Q6N370 28-116
   51. Signal peptide-binding domain [47445] (1)
       4 helices; orthogonal array
       1. Signal peptide-binding domain [47446] (1)
          uperfamily
          1. Signal peptide-binding domain [47447] (4)
             1. Signal sequence binding protein Ffh [47448]
                1. Escherichia coli [TaxId: 562] [47449] (13)
                2. Thermus aquaticus [TaxId: 271] [47450] (1)
                3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101170] (2)
             2. SRP54M [47451]
                1. Human (Homo sapiens) [TaxId: 9606] [47452] (3)
   52. A DNA-binding domain in eukaryotic transcription factors [47453] (1)
       4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
       1. A DNA-binding domain in eukaryotic transcription factors [47454] (1)
          uperfamily
          1. A DNA-binding domain in eukaryotic transcription factors [47455] (2)
             1. Skn-1 [47456]
                1. Caenorhabditis elegans [TaxId: 6239] [47457] (1)
             2. Mafg [74717]
                1. Mouse (Mus musculus) [TaxId: 10090] [74718] (1)
   53. HLH-like [47458] (2)
       4-helices; bundle, closed, left-handed twist; 2 crossover connections
       1. HLH, helix-loop-helix DNA-binding domain [47459] (1)
          dimer of two identical helix-loop-helix subunits
          uperfamily
          1. HLH, helix-loop-helix DNA-binding domain [47460] (9)
             1. Max protein [47461]
                BHLHZ region; contains leucine-zipper motif
                1. Human (Homo sapiens) [TaxId: 9606] [47462] (4)
                2. Mouse (Mus musculus) [TaxId: 10090] [47463] (1)
             2. Myc proto-oncogene protein [81750]
                1. Human (Homo sapiens) [TaxId: 9606] [81751] (1)
                   BHLHZ region; contains leucine-zipper motif
             3. Mad protein [81752]
                1. Human (Homo sapiens) [TaxId: 9606] [81753] (1)
                   BHLHZ region; contains leucine-zipper motif
             4. Myod B/HLH domain [47464]
                1. Mouse (Mus musculus) [TaxId: 10090] [47465] (1)
             5. Usf B/HLH domain [47466]
                1. Human (Homo sapiens) [TaxId: 9606] [47467] (1)
             6. Pho4 B/HLH domain [47468]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47469] (1)
             7. SREBP-1a [47470]
                1. Human (Homo sapiens) [TaxId: 9606] [47471] (1)
             8. SREBP-2 [101171]
                1. Human (Homo sapiens) [TaxId: 9606] [101172] (1)
       2. Docking domain B of the erythromycin polyketide synthase (DEBS) [101173] (1)
          uperfamily
          1. Docking domain B of the erythromycin polyketide synthase (DEBS) [101174] (1)
             1. Erythronolide synthase [101175]
                1. Saccharopolyspora erythraea [TaxId: 1836] [101176] (1)
   54. HAMP domain-like [158471] (1)
       dimer of helix-loop-helix segments; distict from the HLH-like fold; parallel four-helical bundle with two overside connections
       1. HAMP domain-like [158472] (1)
          1. HAMP domain [158473] (1)
             Pfam 00672
             1. Hypothetical protein AF1503 [158474]
                C-terminal domain
                1. Archaeoglobus fulgidus [TaxId: 2234] [158475] (4)
                   SQ O28769 278-331
   55. EF Hand-like [47472] (4)
       core: 4 helices; array of 2 hairpins, opened
       1. EF-hand [47473] (11)
          Duplication: consists of two EF-hand units: each is made of two helices connected with calcium-binding loop
          uperfamily
          1. Calbindin D9K [47474] (2)
             made of two EF-hands only
             1. Calbindin D9K [47475]
                1. Cow (Bos taurus) [TaxId: 9913] [47476] (18)
                   SQ P02633
                2. Pig (Sus scrofa) [TaxId: 9823] [47477] (1)
          2. S100 proteins [47478] (17)
             dimer: subunits are made of two EF-hands
             1. Calcyclin (S100) [47479]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [47480] (6)
                2. Human (Homo sapiens), s100a6 [TaxId: 9606] [74719] (4)
                3. Human (Homo sapiens), s100a4 [TaxId: 9606] [81754] (9)
                   MTS1 protein
                4. Rat (Rattus norvegicus), s100a1 [TaxId: 10116] [69019] (5)
                5. Rat (Rattus norvegicus), s100b [TaxId: 10116] [47481] (7)
                6. Cow (Bos taurus), s100b [TaxId: 9913] [47482] (6)
                7. Human (Homo sapiens), s100b [TaxId: 9606] [47483] (12)
                8. Human (Homo sapiens), P11 s100a10, calpactin [TaxId: 9606] [47484] (2)
                   ligand of annexin II
                9. Human (Homo sapiens), psoriasin s100a7 [TaxId: 9606] [47485] (3)
                10. Pig (Sus scrofa), calgizzarin s100c (s100a11) [TaxId: 9823] [47486] (1)
                11. Rabbit (Oryctolagus cuniculus), calgizzarin s100a11 [TaxId: 9986] [89047] (1)
                12. Human (Homo sapiens), calgranulin s100a8, MRP8 [TaxId: 9606] [47487] (7)
                    Migration inhibitory factor-related protein 8
                13. Human (Homo sapiens), calgranulin C, s100a12 [TaxId: 9606] [47488] (3)
                14. Human (Homo sapiens), s100a9 (mrp14) [TaxId: 9606] [69020] (7)
                15. Human (Homo sapiens), s100a3 [TaxId: 9606] [74720] (1)
                16. Human (Homo sapiens), s100p [TaxId: 9606] [81755] (2)
                17. Human (Homo sapiens), s100a13 [TaxId: 9606] [140535] (8)
                    SQ Q99584 1-98
          3. Polcalcin [89048] (3)
             calcium-binding pollen allergen; two EF-hands per subunit
             1. Polcalcin phl p 7 [89049]
                1. Timothy grass (Phleum pratense) [TaxId: 15957] [89050] (1)
             2. Polcalcin bet v 4 [101177]
                1. White birch (Betula verrucosa) [TaxId: 3505] [101178] (1)
             3. Polcalcin Che a 3 [109816]
                1. Pigweed (Chenopodium album) [TaxId: 3559] [109817] (4)
                   SQ Q84V36
          4. Osteonectin [47489] (1)
             5 helices; two EF-hands plus one of additional helices in the N-terminal part
             1. C-terminal (EC) domain of BM-40/SPARC/osteonectin [47490]
                1. Human (Homo sapiens) [TaxId: 9606] [47491] (3)
          5. Parvalbumin [47492] (9)
             6-helices; array of 3 hairpins, closed
             made with two-helical hairpin and two EF-hands
             1. Oncomodulin [47493]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47494] (3)
             2. Parvalbumin [47495]
                1. Carp (Cyprinus carpio) [TaxId: 7962] [47496] (7)
                2. Pike (Esox lucius) [TaxId: 8010] [47497] (9)
                3. Leopard shark (Triakis semifasciata) [TaxId: 30493] [47498] (1)
                4. Whiting (Merlangius merlangus) [TaxId: 8058] [47499] (1)
                5. Silver hake (Merluccius bilinearis) [TaxId: 79698] [47500] (1)
                6. Rat (Rattus rattus) [TaxId: 10117] [47501] (4)
                   SQ P02625
                7. Human (Homo sapiens) [TaxId: 9606] [109818] (2)
                   SQ P20472
                8. Rattus norvegicus [TaxId: 10116] [158476] (1)
          6. Calmodulin-like [47502] (49)
             Duplication: made with two pairs of EF-hands
             1. Troponin C [47503]
                1. Chicken (Gallus gallus) [TaxId: 9031] [47504] (28)
                   SQ P09860
                2. Turkey (Meleagris gallopavo) [TaxId: 9103] [47505] (2)
                3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [47506] (4)
                4. Chicken (Gallus gallus), cardiac isoform [TaxId: 9031] [47507] (1)
                5. Human (Homo sapiens), cardiac isoform [TaxId: 9606] [47508] (21)
                6. Rainbow trout (Oncorhynchus mykiss) [TaxId: 8022] [109819] (2)
                   SQ Q7ZZB9 1-89
             2. Sarcoplasmic calcium-binding protein [47509]
                1. Sandworm (Nereis diversicolor) [TaxId: 126592] [47510] (2)
                   SQ P04571
                2. Amphioxus (Branchiostoma lanceolatum) [TaxId: 7740] [47511] (1)
             3. Calcium vector protein [47514]
                1. Amphioxus (Branchiostoma lanceolatum) [TaxId: 7740] [47515] (4)
             4. Calcium-regulated photoprotein [47512]
                structurally most similar to sarcoplasmic calcium-binding protein
                1. Jellyfish (Aequorea aequorea), aequorin [TaxId: 168712] [47513] (9)
                2. Hydrozoa (Obelia longissima), obelin [TaxId: 32570] [63541] (7)
                   SQ Q27709
                3. Hydrozoa (Obelia geniculata), obelin [TaxId: 185004] [63542] (1)
                4. Jellyfish (Aequorea victoria), aequorin 1 [TaxId: 6100] [116901] (1)
                   SQ P07164 16-196
             5. Calerythrin [101179]
                structurally most similar to sarcoplasmic calcium-binding protein
                1. Saccharopolyspora erythraea [TaxId: 1836] [101180] (1)
             6. EHCABP [69021]
                1. Entamoeba (Entamoeba histolytica) [TaxId: 5759] [69022] (2)
             7. Calmodulin [47516]
                1. Human (Homo sapiens) [TaxId: 9606] [47517] (60)
                   SQ P02593
                2. Cow (Bos taurus) [TaxId: 9913] [47518] (56)
                   SQ P62157
                3. Rat (Rattus rattus) [TaxId: 10117] [47519] (5)
                   SQ P62161
                4. Chicken (Gallus gallus) [TaxId: 9031] [47520] (2)
                   mutant with a two residue deletion in the central helix
                5. African frog (Xenopus laevis) [TaxId: 8355] [47521] (13)
                6. Drosophila melanogaster [TaxId: 7227] [47522] (6)
                7. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89051] (1)
                8. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89052] (3)
                9. Ciliate (Paramecium tetraurelia) [TaxId: 5888] [47523] (4)
                   SQ Q42478
                10. Potato (Solanum tuberosum) [TaxId: 4113] [109820] (1)
                11. Rattus norvegicus [TaxId: 10116] [158477] (2)
             8. Calmodulin-related protein NB-1 (CLP) [74721]
                1. Human (Homo sapiens) [TaxId: 9606] [74722] (1)
             9. Caltractin (centrin 2) [89053]
                1. Human (Homo sapiens) [TaxId: 9606] [89054] (5)
                2. Green algae (Chlamydomonas reinhardtii) [TaxId: 3055] [89055] (1)
             10. Cdc4p [63543]
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [63544] (1)
             11. Myosin Light Chain Mlc1p [81756]
                 light chain of class V myosin
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81757] (3)
             12. Myosin Essential Chain [47524]
                 1. Bay scallop (Aequipecten irradians) [TaxId: 31199] [47525] (13)
                    SQ P13543
                 2. Chicken (Gallus gallus) [TaxId: 9031] [47526] (5)
                 3. Human (Homo sapiens) [TaxId: 9606] [101181] (3)
             13. Myosin Regulatory Chain [47527]
                 1. Bay scallop (Aequipecten irradians) [TaxId: 31199] [47528] (13)
                    SQ P07291
                 2. Chicken (Gallus gallus) [TaxId: 9031] [47529] (1)
             14. Calcineurin regulatory subunit (B-chain) [47530]
                 1. Cow (Bos taurus) [TaxId: 9913] [47531] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [47532] (3)
             15. Calcineurin B-like protein 2 [101182]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101183] (2)
             16. Recoverin [47533]
                 Calcium-myristoyl switch; only one EF-hand is functional
                 1. Cow (Bos taurus) [TaxId: 9913] [47534] (11)
             17. Kchip1, Kv4 potassium channel-interacting protein [101184]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101185] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [116902] (1)
                    SQ Q9NZI2
             18. Frequenin (neuronal calcium sensor 1) [47535]
                 1. Human (Homo sapiens) [TaxId: 9606] [63545] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47536] (2)
             19. Guanylate cyclase activating protein 2, GCAP-2 [47537]
                 1. Cow (Bos taurus) [TaxId: 9913] [47538] (1)
             20. Neurocalcin [47539]
                 1. Cow (Bos taurus) [TaxId: 9913] [47540] (1)
             21. Calcium- and integrin-binding protein, CIB [47541]
                 1. Human (Homo sapiens) [TaxId: 9606] [47542] (5)
                    SQ Q99828
             22. Calcium-dependent protein kinase sk5 CLD [109821]
                 1. Soybean (Glycine max) [TaxId: 3847] [109822] (2)
                    SQ P28583 328-508
             23. Calmodulin-related protein T21P5.17 [109823]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [109824] (1)
                    SQ Q9SRP5 2-67
          7. Eps15 homology domain (EH domain) [47543] (4)
             1. Eps15 [47544]
                1. Mouse (Mus musculus) [TaxId: 10090] [47545] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [47546] (5)
             2. Pob1 [63546]
                1. Human (Homo sapiens) [TaxId: 9606] [63547] (1)
             3. Reps1 [63548]
                1. Mouse (Mus musculus) [TaxId: 10090] [63549] (1)
          8. Cbp40 (plasmodial specific CaII-binding protein LAV1-2) [81758] (1)
             4 EF-hands assembled in a compact structure like the Penta-EF-hand proteins; contains additional N-terminal all-alpha subdomain
             1. Cbp40 (plasmodial specific CaII-binding protein LAV1-2) [81759]
                1. Physarum polycephalum [TaxId: 5791] [81760] (2)
          9. Penta-EF-hand proteins [63550] (11)
             1. Apoptosis-linked protein alg-2 [63551]
                1. Mouse (Mus musculus) [TaxId: 10090] [63552] (1)
             2. Sorcin [69023]
                1. Human (Homo sapiens) [TaxId: 9606] [69024] (1)
                2. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [74723] (1)
             3. Grancalcin [47550]
                Calpain small subunit homologue
                1. Human (Homo sapiens) [TaxId: 9606] [47551] (4)
             4. Calpain small (regulatory) subunit (domain VI) [47552]
                1. Human (Homo sapiens) [TaxId: 9606] [47553] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [47554] (6)
                3. Pig (Sus scrofa) [TaxId: 9823] [47555] (6)
             5. Calpain large subunit, C-terminal domain (domain IV) [47556]
                1. Human (Homo sapiens), M-type [TaxId: 9606] [47557] (2)
                2. Rat (Rattus norvegicus), M-type [TaxId: 10116] [47558] (2)
                3. Rat (Rattus norvegicus), mu-type [TaxId: 10116] [101186] (1)
             6. Programmed cell death 6 protein-like protein [116903]
                1. Leishmania major [TaxId: 5664] [116904] (1)
                   SQ Q4QG08 53-234
          10. EF-hand modules in multidomain proteins [47547] (8)
              1. Phosphoinositide-specific phospholipase C, isozyme D1 (PLC-D!) [47548]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [47549] (10)
              2. Dystrophin [47559]
                 probably lost calcium-binding function; contains extra helices in each domain
                 1. Human (Homo sapiens) [TaxId: 9606] [47560] (2)
              3. Cbl [47561]
                 1. Human (Homo sapiens) [TaxId: 9606] [47562] (12)
              4. alpha-Actinin [63553]
                 1. Human (Homo sapiens) [TaxId: 9606] [63554] (1)
              5. Nucleobindin 1 (CALNUC) [109825]
                 1. Human (Homo sapiens) [TaxId: 9606] [109826] (1)
                    SQ Q02818 228-326
              6. Diacylglycerol kinase alpha, N-terminal domain [116905]
                 contains two pairs of EF-hands, the modified first pair (res 25-109) does not bind calcium but retains the common fold
                 1. Human (Homo sapiens) [TaxId: 9606] [116906] (1)
                    SQ O95217 P23743 1-116
              7. DJ-1-binding protein, DJBP [140536]
                 1. Human (Homo sapiens) [TaxId: 9606] [140537] (4)
                    SQ Q5THR3 1160-1242
              8. Phospholipase C-beta-2 [158478]
                 1. Human (Homo sapiens) [TaxId: 9606] [158479] (2)
                    SQ Q00722 142-311
          11. p25-alpha [140538] (2)
              Pfam 05517; comprises two degenerate EF-hands and extra C-terminal helix, packed agains the bundle end
              1. Hypothetical protein c32e8.3 [140539]
                 1. Caenorhabditis elegans [TaxId: 6239] [140540] (1)
                    SQ P91127 8-110
              2. Protein cgi-38 [140541]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140542] (1)
                    SQ Q9CRB6 1-138
       2. Insect pheromone/odorant-binding proteins [47565] (1)
          the N-terminal extension, containing a few short helices, forms a flexible lid for the binding cavity
          uperfamily
          1. Insect pheromone/odorant-binding proteins [47566] (6)
             1. Thp12-carrier protein [47567]
                1. Yellow mealworm (Tenebrio molitor) [TaxId: 7067] [47568] (2)
             2. Moth pheromone-binding protein, PBP [47569]
                1. Silk moth (Bombyx mori) [TaxId: 7091] [47570] (7)
                2. Polyphemus moth (Antheraea polyphemus) [TaxId: 7120] [101187] (3)
             3. Pheromone binding protein PBPLma [101188]
                1. Madeira cockroach (Leucophaea maderae) [TaxId: 36963] [101189] (3)
             4. Odorant binding protein LUSH [101190]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101191] (8)
             5. Pheromone-binding protein asp1 [101192]
                1. Common honeybee (Apis mellifera) [TaxId: 7460] [101193] (1)
       3. Hypothetical protein MTH865 [69025] (1)
          uperfamily
          1. Hypothetical protein MTH865 [69026] (1)
             1. Hypothetical protein MTH865 [69027]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69028] (1)
       4. Cloroperoxidase [47571] (1)
          duplication: consists of 2 similar domains composed of 2 EF hand-like motifs each
          uperfamily
          1. Cloroperoxidase [47572] (1)
             1. Cloroperoxidase [47573]
                1. Fungus (Caldariomyces fumago) [TaxId: 5474] [47574] (24)
   56. CH domain-like [47575] (3)
       core: 4 helices: bundle
       1. Calponin-homology domain, CH-domain [47576] (1)
          uperfamily
          1. Calponin-homology domain, CH-domain [47577] (12)
             Pfam 00307
             1. Calponin [69029]
                1. Chicken (Gallus gallus) [TaxId: 9031] [69030] (1)
             2. beta-spectrin [47578]
                1. Human (Homo sapiens) [TaxId: 9606] [47579] (2)
             3. Fimbrin (Plastin), actin-crosslinking domain [47580]
                duplication: tandem repeat of four CH domains
                1. Human (Homo sapiens) [TaxId: 9606] [47581] (2)
                   SQ P13797 121-375, 517-627
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [109827] (1)
                   SQ Q7G188 123-623
                3. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [109828] (1)
                   SQ O59945 108-614
             4. Utrophin [47582]
                1. Human (Homo sapiens) [TaxId: 9606] [47583] (2)
             5. Dystrophin [47584]
                duplication: consists of tandem repeat of two CH domains
                1. Human (Homo sapiens) [TaxId: 9606] [47585] (1)
             6. Actin binding domain of plectin [89056]
                duplication: consists of tandem repeat of two CH domains
                1. Human (Homo sapiens) [TaxId: 9606] [89057] (3)
                   SQ Q9QXS1 182-411
             7. Microtubule-associated protein eb1, N-terminal microtubule binding domain [101194]
                member of rp/eb family
                1. Human (Homo sapiens) [TaxId: 9606] [101195] (7)
                   SQ Q15691 2-132
                2. Mouse (Mus musculus) [TaxId: 10090] [109829] (1)
                   SQ Q61166 16-116
             8. Ras GTPase-activating-like protein rng2 [101196]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [101197] (2)
                   SQ O14188 32-190
             9. Transgelin [109830]
                1. Mouse (Mus musculus) [TaxId: 10090] [109831] (1)
                   SQ P37804 23-153
       2. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81761] (1)
          uperfamily
          1. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81762] (1)
             1. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81763]
                1. Lactococcus lactis [TaxId: 1358] [81764] (1)
       3. Hook domain [116907] (1)
          uperfamily
          1. Hook domain [116908] (1)
             N-terminal part of Pfam 05622
             1. Hook homolog 1, Hook1 [116909]
                1. Mouse (Mus musculus) [TaxId: 10090] [116910] (1)
                   SQ Q8BIL5 12-162
   57. Domain of poly(ADP-ribose) polymerase [47586] (1)
       core: 4 helices: bundle; unusual topology
       1. Domain of poly(ADP-ribose) polymerase [47587] (1)
          duplication: consists of 2 helix-loop-helix structural repeats
          uperfamily
          1. Domain of poly(ADP-ribose) polymerase [47588] (3)
             1. Domain of poly(ADP-ribose) polymerase [47589]
                1. Chicken (Gallus gallus) [TaxId: 9031] [47590] (7)
                2. Mouse (Mus musculus) [TaxId: 10090] [81765] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [101198] (8)
                   SQ P09874 661-1010
   58. SWIB/MDM2 domain [47591] (1)
       core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
       duplication: consists of two structural repeats
       1. SWIB/MDM2 domain [47592] (1)
          binds to the transactivation domain of human p53
          uperfamily
          1. SWIB/MDM2 domain [47593] (5)
             Pfam 02201
             1. MDM2 [47594]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [47595] (2)
                   SQ P56273 13-119
                2. Human (Homo sapiens) [TaxId: 9606] [47596] (7)
             2. Hypothetical protein AT5G14170 (rafl11-05-p19) [101199]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101200] (1)
             3. Hypothetical protein AT5G08430 (rafl09-47-k03) [101201]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101202] (1)
             4. SWI/SNF related regulator of chromatin (BRG1-associated factor 60a) [109832]
                1. Mouse (Mus musculus) [TaxId: 10090] [109833] (1)
                   SQ Q61466 252-331
   59. Pre-protein crosslinking domain of SecA [81766] (1)
       core: 4 helices: bundle; flanked by two short beta-hairpins
       duplication: consists of two structural repeats
       1. Pre-protein crosslinking domain of SecA [81767] (1)
          uperfamily
          1. Pre-protein crosslinking domain of SecA [81768] (2)
             1. Pre-protein crosslinking domain of SecA [81769]
                1. Bacillus subtilis [TaxId: 1423] [81770] (4)
                   SQ P28366
                2. Mycobacterium tuberculosis [TaxId: 1773] [89058] (2)
   60. Ribbon-helix-helix [47597] (1)
       core: 4 helices; array of 2 hairpins, opened
       1. Ribbon-helix-helix [47598] (11)
          formerly Met repressor-like; dimeric proteins; the N-termini form a small beta-sheet ribbon
          uperfamily
          1. Arc/Mnt-like phage repressors [47599] (2)
             1. Arc repressor [47600]
                1. Salmonella bacteriophage P22 [TaxId: 10754] [47601] (12)
             2. Mnt repressor [47602]
                1. Salmonella bacteriophage P22 [TaxId: 10754] [47603] (1)
          2. CopG-like [100970] (5)
             similar to the phage repressor family
             1. Transcriptional repressor CopG [47605]
                plasmid-encoded
                1. Streptococcus agalactiae [TaxId: 1311] [47606] (3)
             2. Plasmid partition protein ParG [101203]
                1. Salmonella enterica [TaxId: 28901] [101204] (1)
             3. Nickel responsive regulator NikR, N-terminal domain [101205]
                1. Escherichia coli [TaxId: 562] [101206] (11)
                2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [140543] (12)
                   SQ O58316 1-50
             4. Uncharacterized protein HP0222 [158480]
                1. Helicobacter pylori [TaxId: 210] [158481] (2)
                   SQ O25010 31-73
          3. Omega transcriptional repressor [100971] (1)
             plasmid-encoded, similar to the phage repressor family
             1. Omega transcriptional repressor [69031]
                1. Streptococcus pyogenes [TaxId: 1314] [69032] (13)
          4. Met repressor, MetJ (MetR) [100972] (1)
             1. Met repressor, MetJ (MetR) [47607]
                1. Escherichia coli [TaxId: 562] [47608] (10)
          5. NE0241-like [140544] (1)
             contains extra C-terminal long helix; currently consists of an orphan protein
             1. Hypothetical protein NE0241 [140545]
                1. Nitrosomonas europaea [TaxId: 915] [140546] (1)
                   SQ Q82XL7 10-95
          6. SeqA N-terminal domain-like [140547] (1)
             N-terminal part of Pfam 03925
             1. SeqA [140548]
                a negative modulator of replication initiation
                1. Escherichia coli [TaxId: 562] [140549] (4)
                   SQ P0AFY8 1-35
          7. Trafficking protein A-like [140550] (1)
             1. Trafficking protein A [140551]
                1. Neisseria gonorrhoeae [TaxId: 485] [140552] (8)
                   SQ Q5F881 2-70
          8. VCA0319-like [140553] (1)
             COG4453; extended and extra C-terminal helices; potential component of the bi-partite system also including an acetyltransferase
             1. Hypothetical protein VCA0482 (VCA0319) [140554]
                Proteins of identical sequence, VCA0482 VCA0319 are encoded by two different genes
                1. Vibrio cholerae [TaxId: 666] [140555] (2)
                   SQ Q9K2J6 3-83
          9. VirC2-like [158482] (1)
             Pfam 07181; duplicated ribbon-helix-helix motif; fold forms a trefoil knot
             1. VirC2 [158483]
                Encoded by Ti plasmid
                1. Agrobacterium tumefaciens [TaxId: 358] [158484] (1)
                   SQ P07166 82-202
          10. PutA pre-N-terminal region-like [158485] (1)
              in PutA it forms a separate ribbon-helix-helix domain connected to the N-terminal enzymatic domain by a flexible linker
              1. Bifunctional protein putA [158486]
                 1. Escherichia coli [TaxId: 562] [158487] (6)
                    SQ P09546 3-45
          11. MJ0366-like [158488] (1)
              PfamB 022101; duplicated ribbon-helix-helix motif; forms trefoil knot; predicted DNA binding
              1. Uncharacterized protein MJ0366 [158489]
                 1. Methanococcus jannaschii [TaxId: 2190] [158490] (1)
                    SQ Q57812 6-87
   61. GST C-terminal domain-like [47615] (1)
       core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
       1. GST C-terminal domain-like [47616] (2)
          this domains follows the thioredoxin-like N-terminal domain
          uperfamily
          1. Glutathione S-transferase (GST), C-terminal domain [47617] (44)
             1. Class pi GST [81347]
                1. Human (Homo sapiens) [TaxId: 9606] [47619] (49)
                2. Pig (Sus scrofa) [TaxId: 9823] [47620] (1)
                3. Mouse (Mus musculus) [TaxId: 10090] [47621] (12)
                4. Onchocerca volvulus [TaxId: 6282] [116911] (2)
                   SQ P46427
             2. Class mu GST [81348]
                1. Human (Homo sapiens) [TaxId: 9606] [47622] (29)
                   SQ P09488 P28161
                2. Rat (Rattus norvegicus) [TaxId: 10116] [47623] (16)
                3. Chicken (Gallus gallus) [TaxId: 9031] [47624] (2)
             3. Class alpha GST [81349]
                1. Human (Homo sapiens), (a1-1) [TaxId: 9606] [47625] (29)
                   SQ P08263
                2. Rat (Rattus norvegicus), (a1-1) [TaxId: 10116] [47626] (2)
                3. Mouse (Mus musculus), (a1-1) [TaxId: 10090] [47627] (2)
                4. Mouse (Mus musculus), (a1-4) [TaxId: 10090] [47628] (2)
                5. Mouse (Mus musculus), (a2-2) [TaxId: 10090] [89059] (1)
                6. Schistosoma japonicum [TaxId: 6182] [47633] (14)
                   SQ P08515
                7. Blood fluke (Schistosoma haematobium) [TaxId: 6185] [89060] (12)
                8. Fasciola hepatica [TaxId: 6192] [47634] (2)
             4. Class theta GST [81350]
                1. Human (Homo sapiens) [TaxId: 9606] [47629] (3)
             5. Class sigma GST [81351]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47630] (1)
                   synonym: hematopoietic prostaglandin D synthase
                2. Human (Homo sapiens) [TaxId: 9606] [89061] (33)
                   SQ O60760; synonym: hematopoietic prostaglandin D synthase
                3. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [81771] (1)
                4. Squid (Ommastrephes sloani pacificus) [TaxId: 6634] [47631] (2)
                5. Heligmosomoides polygyrus [TaxId: 6339] [109834] (1)
                   SQ Q9NJQ6 # Fragment
             6. Class omega GST [81352]
                1. Human (Homo sapiens) [TaxId: 9606] [47632] (1)
             7. Class zeta GST [81353]
                1. Human (Homo sapiens) [TaxId: 9606] [63555] (1)
                   maleylacetoacetate isomerase
                2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [63556] (1)
             8. Class tau GST [81354]
                1. Aegilops tauschii, also known as Triticum tauschii [TaxId: 37682] [74726] (1)
                2. Rice (Oryza sativa) [TaxId: 4530] [89062] (1)
             9. Class delta GST [81355]
                formerly a part of class theta enzymes
                1. Mosquito (Anopheles dirus b), isozyme 1-3 [TaxId: 123217] [74724] (1)
                2. Mosquito (Anopheles dirus b), isozyme 1-4 [TaxId: 123217] [74725] (1)
                3. Mosquito (Anopheles dirus b), isozyme 1-5 [TaxId: 123217] [101207] (1)
                4. Mosquito (Anopheles dirus b), isozyme 1-6 [TaxId: 123217] [101208] (1)
                5. African malaria mosquito (Anopheles gambiae), isozyme 1-6 [TaxId: 7165] [101209] (1)
             10. Class phi GST [81356]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [47635] (2)
                 2. Maize (Zea mays), type I [TaxId: 4577] [47636] (2)
                 3. Maize (Zea mays), type III [TaxId: 4577] [47637] (1)
             11. Class beta GST [81357]
                 1. Escherichia coli [TaxId: 562] [47638] (3)
                 2. Proteus mirabilis [TaxId: 584] [47639] (2)
                 3. Sphingomonas paucimobilis [TaxId: 13689] [47640] (1)
             12. Pf GST [101210]
                 cannot be assigned to any of the known GST classes
                 1. Malarial parasite (Plasmodium falciparum) [TaxId: 5833] [101211] (5)
             13. Glutaredoxin 2 [63557]
                 similar to class zeta enzymes
                 1. Escherichia coli [TaxId: 562] [63558] (1)
             14. Yeast prion protein ure2p, nitrogen regulation fragment [47641]
                 similar to class phi enzymes
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47642] (8)
             15. GST-like domain of elongation factor 1-gamma [81772]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81773] (1)
             16. Chloride intracellular channel 1 (clic1) [69033]
                 similar to class theta enzymes; the N-domain undergoes a redox-controlled structural transition
                 1. Human (Homo sapiens) [TaxId: 9606] [69034] (4)
             17. Microsomal prostaglandin E synthase-2 [140556]
                 1. Crab-eating macaque (Macaca fascicularis) [TaxId: 9541] [140557] (8)
                    SQ Q9N0A4 213-373
             18. Hypothetical protein AGR_pAT_752p/Atu5508 [140558]
                 putative glutathione S-transferase
                 1. Agrobacterium tumefaciens [TaxId: 358] [140559] (2)
                    SQ Q7D2W7 88-236
          2. Arc1p N-terminal domain-like [158491] (1)
             PfamB 021108
             1. GU4 nucleic-binding protein 1, Arc1p [158492]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [158493] (23)
                   SQ P46672 4-121
   62. Methionine synthase domain-like [47643] (3)
       4 helices; bundle, left-handed twist; right-handed superhelix
       1. Methionine synthase domain [47644] (1)
          uperfamily
          1. Methionine synthase domain [47645] (1)
             1. Methionine synthase domain [47646]
                1. Escherichia coli [TaxId: 562] [47647] (4)
       2. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47648] (1)
          uperfamily
          1. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47649] (6)
             1. Thymidine phosphorylase [47650]
                1. Escherichia coli [TaxId: 562] [47651] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [101212] (1)
             2. Pyrimidine nucleoside phosphorylase [47652]
                1. Bacillus stearothermophilus [TaxId: 1422] [47653] (1)
             3. Anthranilate phosphoribosyltransferase (TrpD) [81774]
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [81775] (14)
                2. Pectobacterium carotovorum [TaxId: 554] [81776] (2)
                3. Thermus thermophilus [TaxId: 274] [101213] (5)
       3. TM0693-like [140560] (1)
          helix-swapped dimer; in which the two last helices of this fold form a single coiled-coil helix
          uperfamily
          1. TM0693-like [140561] (1)
             1. Hypothetical protein TM0693 [140562]
                1. Thermotoga maritima [TaxId: 2336] [140563] (4)
                   SQ Q9WZF7 1-78
   63. KaiA/RbsU domain [101214] (1)
       4 helices; bundle, right-handed twist; right-handed superhelix
       1. KaiA/RbsU domain [101215] (2)
          uperfamily
          1. Circadian clock protein KaiA, C-terminal domain [101216] (3)
             1. Circadian clock protein KaiA, C-terminal domain [101217]
                1. Thermosynechococcus elongatus bp-1 [TaxId: 197221] [101218] (5)
                   SQ Q79V62 174-283
                2. Cyanobacterium (Nostoc sp. PCC 7120) [TaxId: 103690] [101219] (1)
                   KaiA from Nostoc species lacks the N-terminal CheY-like domain
                3. Synechococcus elongatus PCC 7942 [TaxId: 1140] [109835] (1)
                   SQ Q79PF6
          2. Phosphoserine phosphatase RsbU, N-terminal domain [109836] (1)
             forms a helix-swapped dimer that otherwise is similar to the KaiA domain dimer
             1. Phosphoserine phosphatase RsbU, N-terminal domain [109837]
                1. Bacillus subtilis [TaxId: 1423] [109838] (1)
                   SQ P40399 1-84
   64. STAT-like [47654] (6)
       4 long helices; bundle, left-handed twist (coiled coil); right-handed superhelix
       1. STAT [47655] (1)
          uperfamily
          1. STAT [47656] (3)
             1. STAT-1, coiled coil domain [47657]
                1. Human (Homo sapiens) [TaxId: 9606] [47658] (1)
             2. STAT3b [47659]
                1. Mouse (Mus musculus) [TaxId: 10090] [47660] (1)
             3. STAT homologue coiled coil domain [101220]
                1. Dictyostelium discoideum [TaxId: 44689] [101221] (2)
       2. t-snare proteins [47661] (1)
          uperfamily
          1. t-snare proteins [47662] (6)
             1. Syntaxin 1A N-terminal domain [47663]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [47664] (3)
                2. Longfin inshore squid (Loligo pealei) [TaxId: 6621] [101222] (1)
             2. Syntaxin 6, SNAP-25 homolog [74727]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [74728] (1)
             3. Sso1 [47665]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47666] (1)
             4. Vam3p N-terminal domain [63559]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63560] (1)
             5. Vesicle transport v-SNARE protein Vti1-like 2 [140564]
                three-helical fragment similar to spectrin repeat
                1. Mouse (Mus musculus) [TaxId: 10090] [140565] (1)
                   SQ O89116 6-94
       3. Cag-Z [109839] (1)
          four-helical bundle without significant twist
          uperfamily
          1. Cag-Z [109840] (1)
             1. Cag-Z [109841]
                1. Helicobacter pylori [TaxId: 210] [109842] (1)
                   SQ Q9JMX9
       4. CAPPD, an extracellular domain of amyloid beta A4 protein [109843] (1)
          the first three helices are longer than the fourth one and, taken separately, adopt a Spectrin repeat-like fold (scop_cf 46965)
          uperfamily
          1. CAPPD, an extracellular domain of amyloid beta A4 protein [109844] (1)
             1. CAPPD, an extracellular domain of amyloid beta A4 protein [109845]
                1. Human (Homo sapiens) [TaxId: 9606] [109846] (2)
                   SQ P05067 374-569 # structures are known for other fragments: 28-123 (scop_sp 56494); 124-189 (scop_sp 89814); 287-344 (scop_sp 57371); 681-/-711 (scop_sp 58608)
       5. FlgN-like [140566] (1)
          the last helix is shorter than the three others; a short extra helix between helices 2 an 3 fills the gap in the bundle
          uperfamily
          1. FlgN-like [140567] (1)
             Pfam 05130
             1. Hypothetical protein PA3352 [140568]
                1. Pseudomonas aeruginosa [TaxId: 287] [140569] (1)
                   SQ Q9HYP4 1-130
       6. MukF C-terminal domain-like [140570] (1)
          uperfamily
          1. MukF C-terminal domain-like [140571] (1)
             C-terminal part of Pfam 03882
             1. Chromosome partition protein MukF (KicB), C-terminal domain [140572]
                1. Escherichia coli [TaxId: 562] [140573] (2)
                   SQ P60293 119-281
   65. N-cbl like [47667] (5)
       4 helices; bundle, left-handed twist; left-handed superhelix
       1. N-terminal domain of cbl (N-cbl) [47668] (1)
          uperfamily
          1. N-terminal domain of cbl (N-cbl) [47669] (1)
             1. N-terminal domain of cbl (N-cbl) [47670]
                1. Human (Homo sapiens) [TaxId: 9606] [47671] (12)
       2. Transferrin receptor-like dimerisation domain [47672] (1)
          uperfamily
          1. Transferrin receptor-like dimerisation domain [47673] (2)
             1. Transferrin receptor ectodomain, C-terminal domain [47674]
                1. Human (Homo sapiens) [TaxId: 9606] [47675] (4)
             2. Glutamate carboxypeptidase II [140574]
                1. Human (Homo sapiens) [TaxId: 9606] [140575] (17)
                   SQ Q04609 594-750
       3. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47676] (1)
          uperfamily
          1. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47677] (2)
             Smart 00509
             1. Transcription elongation factor TFIIS N-domain [47678]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47679] (1)
             2. Transcription elongation factor S-II protein 3 [116912]
                1. Mouse (Mus musculus) [TaxId: 10090] [116913] (1)
                   SQ P23881 1-87
       4. HIV integrase-binding domain [140576] (1)
          uperfamily
          1. HIV integrase-binding domain [140577] (1)
             N-terminal part of PfamB 012949
             1. PC4 and SFRS1-interacting protein, PSIP1 [140578]
                1. Human (Homo sapiens) [TaxId: 9606] [140579] (3)
                   SQ O75475 346-426! SQ O75475 347-429
       5. PG0775 C-terminal domain-like [158494] (1)
          1. PG0775 C-terminal domain-like [158495] (1)
             PfamB 133436
             1. Uncharacterized protein PG0775 [158496]
                Acyl-CoA dehydrogenase family protein
                1. Porphyromonas gingivalis [TaxId: 837] [158497] (2)
                   SQ Q7MW70 443-564
   66. Replisome organizer (g39p helicase loader/inhibitor protein) [89063] (1)
       4 helices; bundle, right-handed twist; left-handed superhelix
       1. Replisome organizer (g39p helicase loader/inhibitor protein) [89064] (1)
          uperfamily
          1. Replisome organizer (g39p helicase loader/inhibitor protein) [89065] (1)
             1. Replisome organizer (g39p helicase loader/inhibitor protein) [89066]
                1. Bacteriophage Spp1 [TaxId: 10724] [89067] (1)
   67. Hypothetical protein YqbG [116914] (1)
       core: 4 helices; bundle, right-handed twist; left-handed superhelix
       1. Hypothetical protein YqbG [116915] (1)
          uperfamily
          1. Hypothetical protein YqbG [116916] (1)
             1. Hypothetical protein YqbG [116917]
                1. Bacillus subtilis [TaxId: 1423] [116918] (1)
                   SQ P45923
   68. DnaD domain-like [158498] (1)
       4 helices; bundle, right-handed twist; left-handed superhelix
       1. DnaD domain-like [158499] (1)
          1. DnaD domain [158500] (1)
             Pfam 04271
             1. Uncaracterized protein EF2839 [158501]
                1. Enterococcus faecalis [TaxId: 1351] [158502] (1)
                   SQ Q830E8 158-231
   69. C-terminal domain of B transposition protein [47680] (1)
       4 helices; irregular array
       1. C-terminal domain of B transposition protein [47681] (1)
          uperfamily
          1. C-terminal domain of B transposition protein [47682] (1)
             1. C-terminal domain of B transposition protein [47683]
                1. Bacteriophage mu [TaxId: 10677] [47684] (1)
   70. HAND domain of the nucleosome remodeling ATPase ISWI [101223] (1)
       4 helices; irregular array
       1. HAND domain of the nucleosome remodeling ATPase ISWI [101224] (1)
          uperfamily
          1. HAND domain of the nucleosome remodeling ATPase ISWI [101225] (1)
             1. HAND domain of the nucleosome remodeling ATPase ISWI [101226]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101227] (1)
   71. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89068] (1)
       4 helices; irregular array
       1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89069] (1)
          uperfamily
          1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89070] (1)
             1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89071]
                1. Escherichia coli [TaxId: 562] [89072] (1)
   72. Anaphylotoxins (complement system) [47685] (1)
       4 helices; irregular array, disulfide-linked
       1. Anaphylotoxins (complement system) [47686] (1)
          uperfamily
          1. Anaphylotoxins (complement system) [47687] (2)
             can be classified as disulfide-rich
             1. C5a anaphylotoxin [47688]
                1. Human (Homo sapiens) [TaxId: 9606] [47689] (2)
                2. Pig (Sus scrofa domestica) [TaxId: 9823] [47690] (1)
   73. Cytochrome c oxidase subunit h [47693] (1)
       4 helices; irregular array, disulfide-linked
       1. Cytochrome c oxidase subunit h [47694] (1)
          uperfamily
          1. Cytochrome c oxidase subunit h [47695] (1)
             1. Cytochrome c oxidase subunit h [47696]
                1. Cow (Bos taurus) [TaxId: 9913] [47697] (21)
   74. Crustacean CHH/MIH/GIH neurohormone [81777] (1)
       4 helices; irregular array, disulfide-linked
       1. Crustacean CHH/MIH/GIH neurohormone [81778] (1)
          uperfamily
          1. Crustacean CHH/MIH/GIH neurohormone [81779] (1)
             1. Mlt-inhibiting hormone (MIH) [81780]
                1. Kuruma prawn (Marsupenaeus japonicus) [TaxId: 27405] [81781] (1)
   75. C-terminal domain of DFF45/ICAD (DFF-C domain) [81782] (1)
       4 helices; folded leaf; right-handed superhelix
       1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81783] (1)
          uperfamily
          1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81784] (1)
             1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81785]
                present only in a long splicing variant of DFF45; essential for chaperone activity
                1. Human (Homo sapiens) [TaxId: 9606] [81786] (2)
   76. BH2638-like [158503] (1)
       4 helices, folded leaf, right-handed superhelix; some similarity to the DFF-C domain fold (scop_cf 81782)
       1. BH2638-like [158504] (1)
          1. BH2638-like [158505] (1)
             Pfam 05256; UPF0223
             1. Uncharacterized protein BH2638 [158506]
                1. Bacillus halodurans [TaxId: 86665] [158507] (2)
                   SQ Q9K9K7 4-88
   77. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47698] (1)
       4 helices; folded leaf; right-handed superhelix
       1. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47699] (3)
          can be classified as disulfide-rich
          uperfamily
          1. Plant lipid-transfer and hydrophobic proteins [47700] (7)
             1. Soybean hydrophobic protein [47701]
                1. Soybean (Glycine max) [TaxId: 3847] [47702] (1)
             2. Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1) [47703]
                1. Wheat (Triticum aestivum), L. seeds [TaxId: 4565] [47704] (3)
                2. Barley (Hordeum vulgare) [TaxId: 4513] [47705] (4)
                3. Maize (Zea mays) [TaxId: 4577] [47706] (11)
                4. Rice (Oryza sativa) [TaxId: 4530] [47707] (5)
                   SQ P23096 26-116
             3. Non-specific lipid-transfer protein homologue (ns-LTP2) [81787]
                different pattern for Cys-pairing compared with ns-LTP1
                1. Rice (Oryza sativa) [TaxId: 4530] [81788] (1)
                2. Triticum turgidum [TaxId: 4571] [89073] (2)
          2. Proteinase/alpha-amylase inhibitors [47708] (3)
             1. 0.19 alpha-amylase inhibitor [47709]
                1. Wheat (Triticum aestivum) [TaxId: 4565] [47710] (1)
             2. Trypsin/alpha-amylase inhibitor RBI [47711]
                1. Eleusine coracana, seeds [TaxId: 4511] [47712] (3)
             3. Hageman factor/amylase inhibitor [47713]
                1. Maize (Zea mays) [TaxId: 4577] [47714] (2)
          3. Seed storage protein, 2S albumin [47715] (3)
             two chains result from a single-chain precursor
             1. Napin BNIb [47716]
                1. Rape (Brassica napus) [TaxId: 3708] [47717] (1)
             2. 2S albumin RicC3 [101228]
                1. Castor bean (Ricinus communis) [TaxId: 3988] [101229] (1)
             3. Methionine-rich 2S protein (albumin 8) [109847]
                1. Common sunflower (Helianthus annuus) [TaxId: 4232] [109848] (1)
                   SQ P23110
   78. p53 tetramerization domain [47718] (1)
       core: 4 helices; bundle
       1. p53 tetramerization domain [47719] (1)
          homotetramer
          uperfamily
          1. p53 tetramerization domain [47720] (1)
             1. p53 tetramerization domain [47721]
                1. Human (Homo sapiens) [TaxId: 9606] [47722] (19)
   79. Bcr-Abl oncoprotein oligomerization domain [69035] (1)
       core: 4 long helices; bundle
       1. Bcr-Abl oncoprotein oligomerization domain [69036] (1)
          homotetramer
          uperfamily
          1. Bcr-Abl oncoprotein oligomerization domain [69037] (1)
             1. Bcr-Abl oncoprotein oligomerization domain [69038]
                1. Human (Homo sapiens) [TaxId: 9606] [69039] (1)
   80. Domain of early E2A DNA-binding protein, ADDBP [47723] (1)
       4 helices; bundle, partly opened
       1. Domain of early E2A DNA-binding protein, ADDBP [47724] (1)
          this domain is the first in the fragment of known structure
          uperfamily
          1. Domain of early E2A DNA-binding protein, ADDBP [47725] (1)
             1. Domain of early E2A DNA-binding protein, ADDBP [47726]
                Single-stranded DNA-binding protein
                1. Human adenovirus type 5 [TaxId: 28285] [47727] (4)
   81. IHF-like DNA-binding proteins [47728] (1)
       core: 4 helices; bundle, partly opened, capped with a beta-sheet
       1. IHF-like DNA-binding proteins [47729] (2)
          dimer of identical subunits
          uperfamily
          1. Prokaryotic DNA-bending protein [47730] (8)
             1. Integration host factor alpha subunit (IHFA) [88878]
                heterodimer of two related subunits
                1. Escherichia coli [TaxId: 562] [88879] (5)
             2. Integration host factor beta subunit (IHFB) [88880]
                heterodimer of two related subunits
                1. Escherichia coli [TaxId: 562] [88881] (5)
             3. HU protein [47735]
                1. Bacillus stearothermophilus [TaxId: 1422] [47736] (2)
                2. Thermotoga maritima [TaxId: 2336] [47737] (2)
                   SQ P36206
                3. Anabaena sp. [TaxId: 1167] [89074] (3)
                4. Escherichia coli [TaxId: 562] [101230] (2)
                5. Escherichia coli, beta-isoform [TaxId: 562] [158508] (1)
                   SQ P0ACF4 1-90
                   HupB
             4. Transcription factor 1, TF1 [47738]
                1. Bacteriophage SPO1 [TaxId: 10685] [47739] (2)
          2. DNA-binding domain (fragment?) of the TraM protein [63566] (1)
             old provisional classification awaiting the entire protein structure; structure of a different fragment of this protein (PDB 2g7o) is classified into a different superfamily
             1. DNA-binding domain (fragment?) of the TraM protein [63567]
                1. Escherichia coli [TaxId: 562] [63568] (1)
   82. TraM-like [140580] (1)
       multihelical oligomeric protein; structure of whole subunit is not known; the N-terminal part is implicated in DNA binding, the middle region forms tetrameric parallel coiled coil, surrounded by the C-terminal helices
       1. TraM-like [140581] (1)
          uperfamily
          1. TraM-like [140582] (2)
             Pfam 05261
             1. TraM [140583]
                also includes the N-terminal domain structure 1dp3, previously classified into a different family (scop_fa 63566)
                1. Escherichia coli [TaxId: 562] [140584] (2)
                   SQ P10026 50-127! SQ P10026 60-167
                2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [158509] (8)
   83. CO dehydrogenase ISP C-domain like [47740] (1)
       core: 4 helices, bundle
       1. CO dehydrogenase ISP C-domain like [47741] (1)
          contains 2Fe-2S cluster
          uperfamily
          1. CO dehydrogenase ISP C-domain like [47742] (8)
             1. Aldehyde oxidoreductase, domain 2 [47743]
                1. Desulfovibrio gigas [TaxId: 879] [47744] (3)
                   SQ Q46509
                2. Desulfovibrio desulfuricans [TaxId: 876] [47745] (1)
             2. Xanthine oxidase, domain 2 [47746]
                1. Cow (Bos taurus) [TaxId: 9913] [47747] (7)
                   SQ P80457
             3. Xanthine dehydrogenase chain A, domain 2 [69040]
                1. Rhodobacter capsulatus [TaxId: 1061] [69041] (2)
             4. Carbon monoxide (CO) dehydrogenase iron-sulfur protein, C-domain [47748]
                1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [47749] (5)
                2. Hydrogenophaga pseudoflava [TaxId: 47421] [47750] (4)
             5. Quinoline 2-oxidoreductase small subunit QorS, C-domain [109849]
                1. Pseudomonas putida [TaxId: 303] [109850] (1)
                   SQ P72223
             6. 4-hydroxybenzoyl-CoA reductase gamma subunit HrcC, C-terminal domain [116919]
                1. Thauera aromatica [TaxId: 59405] [116920] (2)
                   SQ O33818
   84. Protein HNS-dependent expression A; HdeA [47751] (1)
       4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
       1. Protein HNS-dependent expression A; HdeA [47752] (1)
          overall fold is similar to the fold of N-terminal subdomain of the GluRS anticodon-binding domain (1GLN)
          uperfamily
          1. Protein HNS-dependent expression A; HdeA [47753] (1)
             1. Protein HNS-dependent expression A; HdeA [47754]
                periplasmic protein that supports acid resistance in enteric bacteria
                1. Escherichia coli [TaxId: 562] [47755] (2)
   85. PABP domain-like [63569] (2)
       4 helices; an orthogonal array
       1. PABC (PABP) domain [63570] (1)
          uperfamily
          1. PABC (PABP) domain [63571] (4)
             1. poly(A) binding protein [63572]
                1. Human (Homo sapiens) [TaxId: 9606] [63573] (3)
                2. Protozoan (Trypanosoma cruzi) [TaxId: 5693] [101231] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74730] (1)
             2. hyperplastic discs protein [63574]
                1. Human (Homo sapiens) [TaxId: 9606] [63575] (1)
       2. Ribosomal protein L20 [74731] (1)
          uperfamily
          1. Ribosomal protein L20 [74732] (4)
             1. Ribosomal protein L20 [74733]
                1. Aquifex aeolicus [TaxId: 63363] [74734] (1)
                2. Thermus thermophilus [TaxId: 274] [158510] (11)
                   SQ P60491 1-117
                3. Escherichia coli [TaxId: 562] [158511] (29)
                   SQ P0A7L3 1-117
                4. Deinococcus radiodurans [TaxId: 1299] [158512] (10)
                   SQ Q9RSW7 2-118
   86. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47756] (1)
       4 helices; an orthogonal array
       1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47757] (1)
          uperfamily
          1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47758] (1)
             1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47759]
                1. Salmonella typhimurium [TaxId: 90371] [47760] (2)
   87. Dcp2 domain-like [140585] (1)
       4 helices; orthogonal array of two alpha hairpins
       1. Dcp2 domain-like [140586] (1)
          uperfamily
          1. Dcp2 box A domain [140587] (1)
             Pfam 05026
             1. mRNA decapping enzyme Dcp2p, N-terminal domain [140588]
                1. Schizosaccharomyces pombe [TaxId: 4896] [140589] (2)
                   SQ O13828 1-94
   88. Type III secretion system domain [140590] (1)
       core: 4 helices, orthogonal array; right-handed superhelix
       1. Type III secretion system domain [140591] (3)
          uperfamily
          1. TyeA-like [140592] (1)
             Pfam 09059
             1. TyeA [140593]
                1. Yersinia pestis [TaxId: 632] [140594] (2)
                   SQ P69968 2-92
          2. YopR Core [140595] (1)
             Pfam 09025, contains extra N-terminal helix
             1. Yop proteins translocation protein H, YscH (IcrP) [140596]
                1. Yersinia pestis [TaxId: 632] [140597] (1)
                   SQ P68590 42-145
          3. LcrE-like [140598] (1)
             Duplication; contains two domains of this fold; Pfam 07201 (HrpJ-like) covers the first domain and the N-terminal half of the second domain
             1. Outer membrane protein yopN (LcrE) [140599]
                1. Yersinia pestis [TaxId: 632] [140600] (3)
                   SQ P68640 73-269! SQ P68640 78-283
   89. YugE-like [116921] (1)
       4-helices; bundle; right-handed twist
       1. YugE-like [116922] (1)
          uperfamily
          1. YugE-like [116923] (1)
             1. hypothetical protein YugE [116924]
                1. Bacillus stearothermophilus [TaxId: 1422] [116925] (1)
                   SQ Q5KVS1; 97% sequence identity; Geobacillus kaustophilus TaxID: 1462
   90. PWI domain [101232] (1)
       4 helices; up-and-down bundle; topological similarity to the bromodomain-like and SAM domain-like folds
       1. PWI domain [101233] (1)
          uperfamily
          1. PWI domain [101234] (1)
             1. Ser/Arg-related nuclear matrix protein srm160 [101235]
                1. Human (Homo sapiens) [TaxId: 9606] [101236] (1)
   91. PAH2 domain [47761] (1)
       4 helices; open up-and-down bundle; binds alpha-helical peptides
       1. PAH2 domain [47762] (1)
          uperfamily
          1. PAH2 domain [47763] (2)
             1. Sin3B [47764]
                1. Mouse (Mus musculus) [TaxId: 10090] [47765] (3)
             2. Sin3A [47766]
                1. Mouse (Mus musculus) [TaxId: 10090] [47767] (3)
                   SQ Q96ST3 295-383
   92. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81789] (1)
       4 helices; open up-and-down bundle; flexible N-terminal tail
       1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81790] (1)
          uperfamily
          1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81791] (1)
             1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81792]
                1. Pig (Sus scrofa) [TaxId: 9823] [81793] (4)
   93. XPC-binding domain [101237] (1)
       4 helices; array
       1. XPC-binding domain [101238] (1)
          uperfamily
          1. XPC-binding domain [101239] (3)
             1. XPC-binding domain of Rad23 homolog A (Hhr23a) [101240]
                1. Human (Homo sapiens) [TaxId: 9606] [101241] (3)
                   SQ P54725 230-288
             2. XPC-binding domain of Rad23 homolog B (Hhr23b) [109851]
                1. Human (Homo sapiens) [TaxId: 9606] [109852] (3)
                   SQ P54727 275-342 # structure of the N-terminal domain (1-87) is also known (scop_sp 102778)
             3. Rad23 STI1 domain [140601]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140602] (2)
                   SQ P32628 253-309
   94. DinB/YfiT-like putative metalloenzymes [109853] (1)
       core: 4 helices; bundle, closed, left-handed twist; an unusual topology with a higher contact order
       1. DinB/YfiT-like putative metalloenzymes [109854] (4)
          contains metal-binding site on the bundle surface surrounded by loops
          uperfamily
          1. YfiT-like putative metal-dependent hydrolases [109855] (1)
             probably distantly related to the DinB family (Pfam 05163)
             1. YfiT [109856]
                1. Bacillus subtilis [TaxId: 1423] [109857] (1)
                   SQ O31562
          2. DinB-like [140603] (4)
             Pfam 05163
             1. Hypothetical protein BH3987 [140604]
                family assignment by RPS BLAST hit; similar to YfiT subunit fold and metal-binding site, but different dimerisation mode
                1. Bacillus halodurans [TaxId: 86665] [140605] (2)
                   SQ Q9RC77 1-141
             2. Hypothetical protein BCE2162 [158513]
                1. Bacillus cereus [TaxId: 1396] [158514] (2)
                   SQ Q739H9 1-142
             3. Hypothetical protein DR1065 [158515]
                1. Deinococcus radiodurans [TaxId: 1299] [158516] (1)
                   SQ Q9RVG4 2-184
             4. Hypothetical protein ExigDRAFT_2445 [158517]
                1. Exiguobacterium sibiricum 255-15 [TaxId: 262543] [158518] (1)
                   SQ Q41IB9 1-147
          3. Sden0562-like [158519] (1)
             Pfam 09351; DUF1993
             1. Hypothetical protein Sden0562 [158520]
                1. Shewanella denitrificans [TaxId: 192073] [158521] (4)
                   SQ Q12RS4 1-171
          4. Maleylpyruvate isomerase-like [158522] (1)
             1. Micothiol-dependent maleylpyruvate isomerase [158523]
                1. Corynebacterium glutamicum [TaxId: 1718] [158524] (2)
                   SQ Q8NLC1 1-160
                   Cgl3021
   95. EspA/CesA-like [116926] (1)
       4 helices; bundle, closed, left ight-handed twist; interlocked (hetero)dimer of 2-helical subunits
       1. EspA/CesA-like [116927] (2)
          secreted protein and its chaperone both adopt similar substructures in the heterodimer
          uperfamily
          1. EspA-like [116928] (1)
             Pfam 03433
             1. Secreted protein EspA [116929]
                1. Escherichia coli [TaxId: 562] [116930] (1)
                   SQ Q47184 31-190
          2. EspA chaperone CesA [116931] (1)
             1. EspA chaperone CesA [116932]
                1. Escherichia coli [TaxId: 562] [116933] (1)
                   SQ O52124 3-85
   96. NblA-like [109858] (1)
       4 helices; dimer of identical alpha-hairpin subunits; open bundle
       1. NblA-like [109859] (1)
          uperfamily
          1. NblA-like [109860] (1)
             Pfam 04485
             1. Phycobilisome degradation protein NblA [109861]
                1. Anabaena sp. PCC 7120 [TaxId: 103690] [109862] (1)
                   SQ Q8YNP7
   97. EF2947-like [140606] (1)
       4 helices; "diamond" array; duplication: N-terminal and C-terminal pairs of helices are related by pseudo dyad
       1. EF2947-like [140607] (1)
          uperfamily
          1. EF2947-like [140608] (1)
             1. Hypothetical protein EF2947 [140609]
                1. Enterococcus faecalis [TaxId: 1351] [140610] (1)
                   SQ Q82ZV0 1-132
   98. EB1 dimerisation domain-like [140611] (1)
       dimeric 4-helical bundle with a coiled coil at one end formed by the longer N-terminal helices
       1. EB1 dimerisation domain-like [140612] (1)
          uperfamily
          1. EB1 dimerisation domain-like [140613] (1)
             Pfam 03271
             1. Microtubule-associated protein EB1, C-terminal dimerization domain [140614]
                1. Human (Homo sapiens) [TaxId: 9606] [140615] (9)
                   SQ Q15691 189-249! SQ Q15691 189-254! SQ Q15691 190-248! SQ Q15691 191-254
   99. SAM domain-like [47768] (16)
       4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
       1. SAM/Pointed domain [47769] (3)
          uperfamily
          1. Pointed domain [47770] (7)
             1. Ets-1 transcription factor pointed domain [47771]
                1. Mouse (Mus musculus) [TaxId: 10090] [47772] (1)
             2. Etv6 transcription factor pointed domain (Tel SAM) [74735]
                1. Human (Homo sapiens) [TaxId: 9606] [74736] (2)
                2. Escherichia coli [TaxId: 562] [158525] (2)
             3. Ets DNA-binding protein pokkuri (Yan) [109863]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [109864] (2)
                   SQ Q01842 42-118
             4. Modulator of the activity of Ets (MAE, CG15085-PA) [109865]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [109866] (1)
                   SQ Q9I7G2 94-173
             5. GABP-alpha subunit [109867]
                1. Mouse (Mus musculus) [TaxId: 10090] [109868] (1)
                   SQ Q00422 168-254 # structure of the Ets domain (320-429) is also known (scop_sp 46868)
             6. Transcriptional regulator ERG [109869]
                1. Human (Homo sapiens) [TaxId: 9606] [109870] (1)
                   SQ P11308 115-208
          2. SAM (sterile alpha motif) domain [47773] (16)
             1. EphA4 receptor tyrosine kinases [47774]
                1. Mouse (Mus musculus) [TaxId: 10090] [47775] (1)
             2. EphB2 receptor [47776]
                1. Human (Homo sapiens) [TaxId: 9606] [47777] (2)
                2. Chicken (Gallus gallus) [TaxId: 9031] [47778] (1)
             3. C-terminal domain of p73 [47779]
                1. Human (Homo sapiens) [TaxId: 9606] [47780] (2)
             4. Polyhomeotic [74737]
                1. Drosophila melanogaster [TaxId: 7227] [74738] (3)
             5. RNA-binding protein Smaug [89075]
                1. Drosophila melanogaster [TaxId: 7227] [89076] (1)
             6. Ephrin type-A receptor 8, C-terminal domain [101242]
                1. Human (Homo sapiens) [TaxId: 9606] [101243] (1)
             7. Ste50p, N-terminal domain [101244]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101245] (2)
             8. Serine/threonine-protein kinase ste11 [101246]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101247] (3)
             9. Sam-domain protein samsn-1 [101248]
                1. Mouse (Mus musculus) [TaxId: 10090] [101249] (1)
             10. C-terminal domain of p63 [116934]
                 1. Human (Homo sapiens) [TaxId: 9606] [116935] (1)
                    SQ Q9H3D4 544-610
             11. Sh3 and multiple ankyrin repeat domains 3 (Shank3) [140616]
                 1. Rat(Rattus norvegicus) [TaxId: 10116] [140617] (6)
                    SQ Q9JLU4 1749-1815
             12. Connector enhancer of kinase suppressor of Ras 1, CNK1 [140618]
                 1. Human (Homo sapiens) [TaxId: 9606] [140619] (1)
                    SQ Q969H4 1-78
             13. Polycomb protein Scm [140620]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140621] (5)
                    SQ Q9VHA0 795-871
             14. Sphingomyelin synthase 1, SMS1 [140622]
                 Phosphatidylcholine:ceramide cholinephosphotransferase 1
                 1. Mouse (Mus musculus) [TaxId: 10090] [140623] (1)
                    SQ Q8VCQ6 1-84
             15. Centaurin-delta 1 (Arap2) [140624]
                 1. Human(Homo sapiens) [TaxId: 9606] [140625] (1)
                    SQ Q8WZ64 1-78
          3. Variant SAM domain [158526] (2)
             shares a sequence motif with Pfam 07647, but has a distinct packing of helices
             1. Deleted in Liver Cancer 2, DLC2 [158527]
                1. Human (Homo sapiens) [TaxId: 9606] [158528] (2)
                   SQ Q9Y3M8 50-120
             2. Deleted in liver cancer 1 protein, DLC-1 [158529]
                1. Human (Homo sapiens) [TaxId: 9606] [158530] (2)
                   SQ Q96QB1 1-76! SQ Q96QB1 1-78
       2. RuvA domain 2-like [47781] (7)
          duplication: contains two helix-hairpin-helix (HhH) motifs
          uperfamily
          1. DNA helicase RuvA subunit, middle domain [47782] (3)
             1. DNA helicase RuvA subunit, middle domain [47783]
                tetramer; binds Holliday junction
                1. Escherichia coli [TaxId: 562] [47784] (5)
                2. Mycobacterium leprae [TaxId: 1769] [47785] (1)
                3. Thermus thermophilus [TaxId: 274] [81794] (1)
          2. Excinuclease UvrC C-terminal domain [81795] (1)
             1. Excinuclease UvrC C-terminal domain [81796]
                1. Escherichia coli [TaxId: 562] [81797] (1)
          3. NAD+-dependent DNA ligase, domain 3 [47786] (1)
             1. NAD+-dependent DNA ligase, domain 3 [47787]
                duplication: consists of two RuvA-like domains (four HhH motifs); also contains a zinc-finger subdomain
                1. Thermus filiformis [TaxId: 276] [47788] (2)
          4. Topoisomerase V repeat domain [140626] (1)
             1. Topoisomerase V [140627]
                1. Methanopyrus kandleri [TaxId: 2320] [140628] (4)
                   SQ Q977W1 294-350! SQ Q977W1 351-409! SQ Q977W1 410-464! SQ Q977W1 465-519
          5. Hef domain-like [140629] (4)
             helicase/nuclease domain; forms homo and heterodimers; probably includes the Excinuclease UvrC C-terminal domain (scop_fa 81795, that contains a single NMR structure of a monomeric truncated domain, 1kft)
             1. DNA excision repair protein ERCC-1 [140630]
                1. Human (Homo sapiens) [TaxId: 9606] [140631] (2)
                   SQ P07992 219-296! SQ P07992 220-297
             2. ATP-dependent RNA helicase PF2015 [140632]
                1. Pyrococcus furiosus [TaxId: 2261] [140633] (2)
                   SQ Q8TZH8 694-761
             3. DNA repair endonuclease XPF [140634]
                1. Aeropyrum pernix [TaxId: 56636] [140635] (6)
                   SQ Q9YC15 160-229
                2. Human (Homo sapiens) [TaxId: 9606] [140636] (4)
                   SQ Q92889 823-905! SQ Q92889 837-898
          6. Tex HhH-containing domain-like [158531] (1)
             tandem repeat of two Ruva_2-like domains
             1. Transcriptional accessory factor Tex [158532]
                1. Pseudomonas aeruginosa [TaxId: 287] [158533] (6)
                   SQ Q9HTY8 474-563! SQ Q9HTY8 564-636
          7. ComEA-like [158534] (2)
             sequence similarity to the HhH-motif domains of the PsbU-like and Tex-like families
             1. Uncharacterized protein TTHA1967 [158535]
                1. Thermus thermophilus [TaxId: 274] [158536] (1)
                   SQ Q5SGW3 11-75
             2. KIF22, C-terminal domain [158537]
                1. Human (Homo sapiens) [TaxId: 9606] [158538] (1)
                   SQ Q14807 570-660
       3. C-terminal domain of RNA polymerase alpha subunit [47789] (1)
          contains one classic and one pseudo HhH motifs
          uperfamily
          1. C-terminal domain of RNA polymerase alpha subunit [47790] (3)
             1. C-terminal domain of RNA polymerase alpha subunit [47791]
                1. Escherichia coli [TaxId: 562] [47792] (2)
                2. Thermus thermophilus [TaxId: 274] [47793] (1)
                3. Bacillus subtilis [TaxId: 1423] [140637] (1)
                   SQ P20429 245-311
       4. Rad51 N-terminal domain-like [47794] (3)
          contains one classic and one pseudo HhH motifs
          uperfamily
          1. DNA repair protein Rad51, N-terminal domain [47795] (4)
             1. DNA repair protein Rad51, N-terminal domain [47796]
                1. Human (Homo sapiens) [TaxId: 9606] [47797] (1)
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [101250] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109871] (1)
                   SQ P25454 81-395
                4. Archaeon Methanococcus voltae [TaxId: 2188] [109872] (7)
                   SQ O73948
          2. NusA extra C-terminal domains [109873] (1)
             1. Transcription elongation protein NusA [109874]
                1. Escherichia coli [TaxId: 562] [109875] (2)
                   SQ P03003 352-419
          3. Hypothetical protein AF1548, C-terminal domain [116936] (1)
             1. Hypothetical protein AF1548, C-terminal domain [116937]
                1. Archaeoglobus fulgidus [TaxId: 2234] [116938] (1)
                   SQ 28724
       5. Barrier-to-autointegration factor, BAF [47798] (1)
          contains one classic and one pseudo HhH motifs
          uperfamily
          1. Barrier-to-autointegration factor, BAF [47799] (1)
             1. Barrier-to-autointegration factor, BAF [47800]
                1. Human (Homo sapiens) [TaxId: 9606] [47801] (8)
       6. DNA polymerase beta, N-terminal domain-like [47802] (1)
          contains one classic and one pseudo HhH motifs
          uperfamily
          1. DNA polymerase beta, N-terminal domain-like [47803] (4)
             1. DNA polymerase beta, N-terminal (8 kD)-domain [47804]
                topologically similar to the second domain
                1. Human (Homo sapiens) [TaxId: 9606] [47805] (107)
                   SQ P06746
                2. Rat (Rattus norvegicus) [TaxId: 10116] [47806] (10)
             2. Terminal deoxynucleotidyl transferase [69042]
                1. Mouse (Mus musculus) [TaxId: 10090] [69043] (3)
             3. DNA polymerase lambda [101251]
                1. Human (Homo sapiens) [TaxId: 9606] [101252] (25)
       7. PsbU/PolX domain-like [81585] (2)
          contains one classic and one pseudo HhH motifs
          uperfamily
          1. DNA polymerase beta-like, second domain [81584] (4)
             topological similarity to the N-terminal domain
             1. DNA polymerase beta [81579]
                1. Human (Homo sapiens) [TaxId: 9606] [81575] (107)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [81577] (18)
             2. Terminal deoxynucleotidyl transferase [81583]
                1. Mouse (Mus musculus) [TaxId: 10090] [81582] (3)
             3. DNA polymerase lambda [101253]
                1. Human (Homo sapiens) [TaxId: 9606] [101254] (24)
          2. PsbU-like [158539] (1)
             Pfam 06514
             1. Photosystem II 12 kDa extrinsic protein PsbU [158540]
                1. Thermosynechococcus elongatus [TaxId: 146786] [158541] (1)
                   SQ Q9F1L5 37-134
       8. 5' to 3' exonuclease, C-terminal subdomain [47807] (1)
          uperfamily
          1. 5' to 3' exonuclease, C-terminal subdomain [47808] (8)
             1. T4 RNase H [47809]
                1. Bacteriophage T4 [TaxId: 10665] [47810] (2)
             2. 5' to 3' exonuclease domain of DNA polymerase Taq [47811]
                1. Thermus aquaticus [TaxId: 271] [47812] (4)
             3. T5 5'-exonuclease [47813]
                1. Bacteriophage T5 [TaxId: 10726] [47814] (4)
             4. Flap endonuclease-1 (Fen-1 nuclease) [47815]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [47816] (2)
                2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [81798] (1)
                3. Archaeon Pyrococcus furiosus [TaxId: 2261] [47818] (1)
                4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [101255] (2)
                5. Human (Homo sapiens) [TaxId: 9606] [140638] (3)
                   SQ P39748 218-357
       9. HRDC-like [47819] (4)
          uperfamily
          1. HRDC domain from helicases [47820] (3)
             1. HRDC domain from RecQ helicase [47821]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47822] (1)
                2. Escherichia coli [TaxId: 562] [140639] (3)
                   SQ P15043 530-606
             2. Werner syndrome ATP-dependent helicase, WRN [140640]
                1. Human (Homo sapiens) [TaxId: 9606] [140641] (3)
                   SQ Q14191 1140-1239! SQ Q14191 1142-1235
          2. RNA polymerase II subunit RBP4 (RpoF) [69044] (3)
             1. RNA polymerase II subunit RBP4 (RpoF) [69045]
                includes the N-terminal heterodimerisation alpha-hairpin
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [69046] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116939] (1)
                   SQ P20433 46-221
                3. Human (Homo sapiens) [TaxId: 9606] [140642] (4)
                   SQ O15514 14-142
          3. RNase D C-terminal domains [140643] (1)
             tandem repeat of two domains of this fold, the first domain belongs to Pfam 00570
             1. Ribonuclease D [140644]
                1. Escherichia coli [TaxId: 562] [140645] (2)
                   SQ P09155 194-294! SQ P09155 295-375
          4. EXOSC10 HRDC domain-like [140646] (2)
             1. Exosome complex exonuclease RRP6 domain [140647]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140648] (4)
                   SQ Q12149 421-516
             2. Exosome component 10, EXOSC10 [140649]
                1. Human (Homo sapiens) [TaxId: 9606] [140650] (1)
                   SQ Q01780 483-595
       10. lambda integrase-like, N-terminal domain [47823] (1)
           uperfamily
           1. lambda integrase-like, N-terminal domain [47824] (3)
              1. Cre recombinase [47825]
                 1. Bacteriophage P1 [TaxId: 10678] [47826] (24)
                    SQ P06956 20-341
              2. Recombinase XerD [47827]
                 1. Escherichia coli [TaxId: 562] [47828] (1)
              3. Flp recombinase [47829]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47830] (3)
       11. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47831] (1)
           uperfamily
           1. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47832] (1)
              1. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47833]
                 inserted in the phosphohistidine domain
                 1. Escherichia coli [TaxId: 562] [47834] (11)
       12. Hypothetical protein YjbJ [69047] (1)
           uperfamily
           1. Hypothetical protein YjbJ [69048] (1)
              1. Hypothetical protein YjbJ [69049]
                 1. Escherichia coli [TaxId: 562] [69050] (1)
       13. Putative methyltransferase TM0872, insert domain [81799] (1)
           uperfamily
           1. Putative methyltransferase TM0872, insert domain [81800] (2)
              1. Putative methyltransferase TM0872, insert domain [81801]
                 1. Thermotoga maritima [TaxId: 2336] [81802] (2)
                 2. Thermus thermophilus [TaxId: 274] [116940] (1)
                    SQ Q5SJD8
       14. eIF2alpha middle domain-like [116742] (1)
           uperfamily
           1. eIF2alpha middle domain-like [116743] (3)
              1. Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 [116744]
                 1. Human (Homo sapiens) [TaxId: 9606] [116745] (2)
                    SQ P05198
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116746] (1)
                 3. Sulfolobus solfataricus [TaxId: 2287] [140651] (1)
                    SQ Q97Z79 85-175
       15. YozE-like [140652] (1)
           uperfamily
           1. YozE-like [140653] (2)
              Pfam 06855; DUF1250
              1. Hypothetical protein YozE [140654]
                 1. Bacillus subtilis [TaxId: 1423] [140655] (1)
                    SQ O31864 1-74
              2. Uncharacterized protein MW1311 [158542]
                 1. Staphylococcus aureus [TaxId: 1280] [158543] (2)
                    SQ Q7BEF3 4-73
       16. GspK insert domain-like [158544] (1)
           tandem repeat of two SAM-like domains iserted into pilin fold; domain 1 contains one classic HhH motif
           1. GspK insert domain-like [158545] (1)
              middle part of Pfam 03934
              1. Pseudopilin GspK [158546]
                 1. Escherichia coli [TaxId: 562] [158547] (2)
                    SQ A7ZRI8 103-212! SQ A7ZRI8 213-283
   100. Retroviral matrix proteins [47835] (1)
        4-5 helices; right-handed superhelix
        1. Retroviral matrix proteins [47836] (6)
           the 5th, C-terminal helix is missing in some of the member structures
           uperfamily
           1. Immunodeficiency virus matrix proteins [47837] (2)
              1. HIV-1 matrix protein (HIV-1 MA, HIVp17, p17, MA) [47838]
                 topologically similar to one subunit in the interferon-gamma intertwined dimer
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [47839] (12)
              2. SIV matrix antigen [47840]
                 1. Simian immunodeficiency virus [TaxId: 11723] [47841] (2)
           2. HTLV-II matrix protein [47842] (1)
              the C-terminal helix region is disordered(?)
              1. HTLV-II matrix protein [47843]
                 1. Human T-cell leukemia virus type 2 [TaxId: 11909] [47844] (1)
           3. Mason-Pfizer monkey virus matrix protein [47845] (1)
              the C-terminal helix region is missing(?)
              1. Mason-Pfizer monkey virus matrix protein [47846]
                 1. Simian Mason-Pfizer virus [TaxId: 11855] [47847] (2)
           4. GAG polyprotein M-domain [47848] (1)
              the C-terminal helix region is missing(?)
              1. GAG polyprotein M-domain [47849]
                 1. Rous sarcoma virus [TaxId: 11886] [47850] (1)
           5. EIAV matrix antigen [69051] (1)
              1. EIAV matrix antigen [69052]
                 1. Equine infectious anemia virus, EIAV [TaxId: 11665] [69053] (1)
           6. MMLV matrix protein-like [81803] (2)
              1. MMLV matrix protein [81804]
                 1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [81805] (1)
              2. Product of RIKEN cDNA 3110009e22 [109876]
                 1. Unclassified, murine endogenous retrovirus [TaxId: 12908] [109877] (1)
                    SQ O62708 7-98 # 73% sequence identity
   101. Flavivirus capsid protein C [101256] (1)
        core: 5 helices; right-handed superhelix; swapped dimer with the two long C-terminal helices
        1. Flavivirus capsid protein C [101257] (1)
           uperfamily
           1. Flavivirus capsid protein C [101258] (2)
              1. Flavivirus capsid protein C [101259]
                 1. Dengue virus type 2 [TaxId: 11060] [101260] (1)
                 2. Kunjin virus [TaxId: 11077] [109878] (1)
                    SQ P14335 23-98
   102. Hepatitis B viral capsid (hbcag) [47851] (1)
        5 helices; array; two long helices form a hairpin that dimerizes into a 4-helical bundle
        1. Hepatitis B viral capsid (hbcag) [47852] (1)
           uperfamily
           1. Hepatitis B viral capsid (hbcag) [47853] (1)
              1. Hepatitis B viral capsid (hbcag) [47854]
                 1. Hepatitis B virus [TaxId: 10407] [47855] (1)
   103. Apolipophorin-III [47856] (1)
        5 helices; bundle, closed, left-handed twist
        1. Apolipophorin-III [47857] (1)
           uperfamily
           1. Apolipophorin-III [47858] (2)
              1. Apolipophorin-III [47859]
                 five-helical bundle
                 probably related to four-helical (apo)lipoproteins
                 1. African locust (Locusta migratoria) [TaxId: 7004] [47860] (2)
                 2. Manduca sexta [TaxId: 7130] [69054] (1)
   104. Methenyltetrahydrofolate cyclohydrolase-like [101261] (1)
        5 helices; bundle, closed, left-handed twist
        1. Methenyltetrahydrofolate cyclohydrolase-like [101262] (1)
           uperfamily
           1. Methenyltetrahydrofolate cyclohydrolase-like [101263] (1)
              COG3404
              1. Hypothetical protein TM1560 [101264]
                 putative serine cycle enzyme
                 1. Thermotoga maritima [TaxId: 2336] [101265] (1)
   105. A middle domain of Talin 1 [109879] (1)
        5 helices; bundle, closed, left-handed twist; helices 2-5 adopt the Four-helical up-and-down bundle fold (scop_cf 47161)
        1. A middle domain of Talin 1 [109880] (1)
           uperfamily
           1. A middle domain of Talin 1 [109881] (1)
              1. A middle domain of Talin 1 [109882]
                 1. Mouse (Mus musculus) [TaxId: 10090] [109883] (2)
                    SQ P26039 486-782
   106. I/LWEQ domain [109884] (1)
        5 helices; bundle, closed, left-handed twist
        1. I/LWEQ domain [109885] (1)
           uperfamily
           1. I/LWEQ domain [109886] (2)
              Pfam 01608
              actin-binding motif that adopts different folds; possibly refolds upon binding
              1. Huntingtin interacting protein 12 [109887]
                 Hip1r thatch domain core
                 1. Human (Homo sapiens) [TaxId: 9606] [109888] (1)
                    SQ O75146 773-965
              2. Talin 1 [109889]
                 4-helical bundle of the Bromodomain-like fold (scop_cf 47363); similar to helices 2-5 of the Huntingtin interacting protein 12
                 1. Mouse (Mus musculus) [TaxId: 10090] [109890] (2)
                    SQ P26039 486-782
   107. RNA-binding protein She2p [116941] (1)
        5 helices; bundle, closed, left-handed twist; topological similarity to the middle domain of the L-aspartase-like fold (scop_cf 48556)
        1. RNA-binding protein She2p [116942] (1)
           uperfamily
           1. RNA-binding protein She2p [116943] (1)
              1. RNA-binding protein She2p [116944]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116945] (1)
                    SQ P36068 6-237
   108. Hyaluronidase domain-like [140656] (3)
        5 helices; bundle, closed, left-handed twist; up-and-down (meander) topology
        1. Hyaluronidase post-catalytic domain-like [140657] (1)
           uperfamily
           1. Hyaluronidase post-catalytic domain-like [140658] (2)
              1. Hyaluronidase, post-catalytic domain 3 [140659]
                 1. Clostridium perfringens [TaxId: 1502] [140660] (6)
                    SQ Q8XL08 496-624
              2. Glucosaminidase GH84 post-catalytic domain [140661]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [140662] (12)
                    SQ Q89ZI2 458-610! SQ Q89ZI2 458-611
        2. TTHA0068-like [140663] (1)
           uperfamily
           1. TTHA0068-like [140664] (2)
              Pfam 03745; DUF309
              1. Hypothetical protein rrnAC1037 [140665]
                 1. Haloarcula marismortui [TaxId: 2238] [140666] (1)
                    SQ Q5V3A0 15-159
              2. Hypothetical protein TTHA0068 [140667]
                 1. Thermus thermophilus [TaxId: 274] [140668] (3)
                    SQ Q5SM75 1-94
        3. FLJ32549 domain-like [158548] (1)
           1. FLJ32549 domain-like [158549] (1)
              middle part of Pfam 09404; DUF2003
              1. Hypothetical protein BC048403 [158550]
                 FLJ32549 ortholog; cDNA sequence
                 1. Mouse (Mus musculus) [TaxId: 10090] [158551] (1)
                    SQ Q6P1I3 123-294
   109. YoaC-like [140669] (1)
        5 helices; bundle, one crossover connection, the arrangement of the first four helices is similar to the KaiA/RbsU domain fold (scop_cf 101214)
        1. YoaC-like [140670] (1)
           uperfamily
           1. YoaC-like [140671] (1)
              1. Hypothetical protein YoaC [140672]
                 1. Salmonella typhimurium [TaxId: 90371] [140673] (1)
                    SQ Q8ZRJ2 11-107
                    STM0327
   110. Saposin-like [47861] (2)
        5 helices; folded leaf, closed
        1. Saposin [47862] (4)
           Lipid-binding can promote conformational changes and oligomerisation in some members
           uperfamily
           1. Saposin B [81806] (1)
              the alternative subunit conformation is an open four-helical bundle; helices 3 and 4 form a contiguous helix
              1. Saposin B [81807]
                 1. Human (Homo sapiens) [TaxId: 9606] [81808] (1)
           2. NKL-like [47863] (3)
              1. NK-lysin, NKL [47864]
                 1. Pig (Sus scrofa) [TaxId: 9823] [47865] (1)
              2. Granulysin, NKG5 protein [81809]
                 1. Human (Homo sapiens) [TaxId: 9606] [81810] (1)
              3. Saposin C [89077]
                 1. Human (Homo sapiens) [TaxId: 9606] [89078] (7)
           3. Ameobapore A [101266] (1)
              1. Ameobapore A [101267]
                 pore-forming toxin
                 1. Entamoeba histolytica [TaxId: 5759] [101268] (1)
           4. Swaposin [47866] (1)
              circularly permuted saposin domain inserted in plant acid proteases
              1. (Pro)phytepsin [47867]
                 1. Barley (Hordeum vulgare) [TaxId: 4513] [47868] (1)
        2. Bacteriocin AS-48 [47869] (1)
           uperfamily
           1. Bacteriocin AS-48 [47870] (1)
              1. Bacteriocin AS-48 [47871]
                 cyclic peptide
                 1. Enterococcus faecalis [TaxId: 1351] [47872] (4)
   111. Annexin [47873] (1)
        5 helices; folded leaf, closed
        1. Annexin [47874] (1)
           duplication: consists of four domains of the same fold
           uperfamily
           1. Annexin [47875] (14)
              1. Annexin I [47876]
                 1. Human (Homo sapiens) [TaxId: 9606] [47877] (2)
                 2. Pig (Sus scrofa) [TaxId: 9823] [47878] (2)
              2. Annexin III [47879]
                 1. Human (Homo sapiens) [TaxId: 9606] [47880] (2)
              3. Annexin IV [47881]
                 1. Cow (Bos taurus) [TaxId: 9913] [47882] (3)
              4. Annexin V [47883]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [47884] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [47885] (10)
                 3. Rat (Rattus norvegicus) [TaxId: 10116] [47886] (15)
              5. Annexin VI [47887]
                 further duplication: consists of two four-domain units
                 1. Cow (Bos taurus) [TaxId: 9913] [47888] (2)
              6. Annexin XII [47889]
                 1. Hydra (Hydra attenuata) [TaxId: 6087] [47890] (1)
                 2. Hydra vulgaris [TaxId: 6087] [47891] (1)
              7. Plant annexin-like protein [47892]
                 1. Bell pepper (Capsicum annuum) [TaxId: 4072] [47893] (1)
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116946] (3)
                    SQ Q9SYT0
              8. Annexin GH1 [89079]
                 1. Cotton (Gossypium hirsutum) [TaxId: 3635] [89080] (2)
              9. Annexin II [116947]
                 1. Human (Homo sapiens) [TaxId: 9606] [116948] (2)
                    SQ P07355
   112. TAFH domain-like [158552] (1)
        5 helices; folded leaf, closed
        1. TAFH domain-like [158553] (1)
           1. TAFH domain-like [158554] (2)
              Pfam 07531
              1. Transcription initiation factor TFIID subunit 4, TAF4 [158555]
                 1. Human (Homo sapiens) [TaxId: 9606] [158556] (1)
                    SQ O00268 583-679
              2. ETO [158557]
                 Synonyms: AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2
                 1. Human (Homo sapiens) [TaxId: 9606] [158558] (2)
                    SQ Q06455 119-225! SQ Q06455 120-222
   113. Transducin (alpha subunit), insertion domain [47894] (1)
        5 helices; folded leaf
        1. Transducin (alpha subunit), insertion domain [47895] (1)
           this domain interrupts the G-protein common fold
           uperfamily
           1. Transducin (alpha subunit), insertion domain [47896] (4)
              1. Transducin (alpha subunit), insertion domain [47897]
                 1. Cow (Bos taurus) [TaxId: 9913] [47898] (15)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [47899] (31)
                 3. Mouse (Mus musculus) [TaxId: 10090] [140674] (6)
                    SQ P21279 67-183! SQ P27600 82-203! SQ P27601 76-201
                 4. Homo sapiens [TaxId: 9606] [158559] (4)
   114. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47911] (1)
        5 helices; irregular array; left-handed superhelix
        1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47912] (1)
           uperfamily
           1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47913] (1)
              1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47914]
                 1. Human (Homo sapiens) [TaxId: 9606] [47915] (2)
                    SQ P42768 241-309
   115. Left-handed superhelix [47916] (4)
        core: 4-5 helices; bundle; left-handed superhelix
        1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47917] (1)
           uperfamily
           1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47918] (8)
              1. F1 ATP synthase alpha subunit, domain 3 [88886]
                 1. Cow (Bos taurus) [TaxId: 9913] [88893] (18)
                    SQ P19483
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [88925] (2)
                 3. Bacillus sp., strain ps3 [TaxId: 1409] [88926] (1)
                 4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88927] (2)
              2. F1 ATP synthase beta subunit, domain 3 [88928]
                 1. Cow (Bos taurus) [TaxId: 9913] [88929] (12)
                    SQ P00829
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [88930] (8)
                 3. Bacillus sp., strain ps3 [TaxId: 1409] [88931] (1)
                 4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88932] (2)
        2. Ypt/Rab-GAP domain of gyp1p [47923] (1)
           uperfamily
           1. Ypt/Rab-GAP domain of gyp1p [47924] (1)
              duplication: contains two similar domains of this fold
              1. Ypt/Rab-GAP domain of gyp1p [47925]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47926] (3)
        3. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69055] (1)
           uperfamily
           1. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69056] (2)
              1. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69057]
                 1. Escherichia coli [TaxId: 562] [69058] (12)
                    SQ P45568
                 2. Zymomonas mobilis [TaxId: 542] [109891] (2)
                    SQ Q9X5F2
        4. BH3980-like [158560] (1)
           1. BH3980-like [158561] (3)
              Pfam 06304; DUF1048
              1. Hypothetical protein BCE3448 [158562]
                 1. Bacillus cereus [TaxId: 1396] [158563] (2)
                    SQ Q734F7 14-95
              2. Uncharacterized protein BH3980 [158564]
                 1. Bacillus halodurans [TaxId: 86665] [158565] (1)
                    SQ Q9K5V7 1-112
              3. Uncharacterized protein BH3976 [158566]
                 1. Bacillus halodurans [TaxId: 86665] [158567] (1)
                    SQ Q9K5W1 16-105
   116. ATPD N-terminal domain-like [47927] (2)
        core: 5 helices; bundle
        1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47928] (1)
           uperfamily
           1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47929] (1)
              1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47930]
                 1. Escherichia coli [TaxId: 562] [47931] (2)
        2. AF1862-like [158568] (1)
           probable biological unit is a hexamer
           1. Cas Cmr5-like [158569] (1)
              Pfam 09701; CRISPR-associated protein
              1. Hypothetical protein AF1862 [158570]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [158571] (1)
                    SQ O28417 2-153
   117. ERP29 C domain-like [47932] (2)
        5 helices; bundle
        1. ERP29 C domain-like [47933] (1)
           uperfamily
           1. ERP29 C domain-like [47934] (2)
              1. Endoplasmic reticulum protein ERP29, C-terminal domain [47935]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [47936] (1)
              2. Windbeutel, C-terminal domain [101269]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101270] (8)
        2. Helical domain of Sec23/24 [81811] (1)
           uperfamily
           1. Helical domain of Sec23/24 [81812] (2)
              1. Sec23 [81813]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81814] (3)
              2. Sec24 [81815]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81816] (4)
   118. Functional domain of the splicing factor Prp18 [47937] (1)
        core: 5 helices; bundle
        1. Functional domain of the splicing factor Prp18 [47938] (1)
           uperfamily
           1. Functional domain of the splicing factor Prp18 [47939] (1)
              1. Functional domain of the splicing factor Prp18 [47940]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47941] (1)
   119. Retrovirus capsid protein, N-terminal core domain [47942] (1)
        core: 5 helices; bundle
        1. Retrovirus capsid protein, N-terminal core domain [47943] (1)
           uperfamily
           1. Retrovirus capsid protein, N-terminal core domain [47944] (5)
              1. HIV-1 capsid protein [47945]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [47946] (16)
              2. EIAV capsid protein p26 [47947]
                 1. Equine infectious anemia virus [TaxId: 11665] [47948] (2)
              3. HTLV-I capsid protein [47949]
                 1. Human T-cell leukemia virus type 1 [TaxId: 11908] [47950] (2)
              4. RSV capsid protein [47951]
                 1. Rous sarcoma virus [TaxId: 11886] [47952] (3)
              5. AKV capsid [116949]
                 1. AKV murine leukemia virus [TaxId: 11791] [116950] (1)
                    SQ P03336 215-345 # fragment of the core shell protein p30 (215-477)
   120. GINS helical bundle-like [158572] (1)
        5 helices, staggered bundle;
        1. GINS helical bundle-like [158573] (4)
           common to all subunits of the GINS complex
           1. PSF1 N-terminal domain-like [158574] (1)
              1. DNA replication complex GINS protein PSF1 [158575]
                 1. Human (Homo sapiens) [TaxId: 9606] [158576] (5)
                    SQ Q14691 1-144! SQ Q14691 1-145
           2. PSF2 C-terminal domain-like [158577] (1)
              C-terminal part of PF04128
              1. DNA replication complex GINS protein PSF2 [158578]
                 1. Human (Homo sapiens) [TaxId: 9606] [158579] (7)
                    SQ Q9Y248 62-173
           3. PSF3 C-terminal domain-like [158580] (1)
              C-terminal part of Pfam 06425
              1. GINS complex subunit 3, PSF3 [158581]
                 1. Human (Homo sapiens) [TaxId: 9606] [158582] (7)
                    SQ Q9BRX5 88-92
           4. SLD5 N-terminal domain-like [158583] (1)
              N-terminal part of Pfam 05916
              1. GINS complex subunit 4, SLD5 [158584]
                 1. Human (Homo sapiens) [TaxId: 9606] [158585] (7)
                    SQ Q9BRT9 21-165
   121. Jann4075-like [158586] (1)
        core: 5 helices; the C-terminal helix is surrounded by the others; similarity to some EF-hand domains
        1. Jann4075-like [158587] (1)
           1. Jann4075-like [158588] (1)
              1. Uncharacterized protein Jann4075 [158589]
                 1. Jannaschia sp. ccs1 [TaxId: 290400] [158590] (4)
                    SQ Q28JX0 1-113
   122. Cyclin-like [47953] (1)
        core: 5 helices; one helix is surrounded by the others
        1. Cyclin-like [47954] (3)
           duplication: consists of two domains of this fold
           uperfamily
           1. Cyclin [47955] (11)
              1. Cyclin A [47956]
                 1. Human (Homo sapiens) [TaxId: 9606] [47957] (56)
                    SQ P20248 175-432
                 2. Cow (Bos taurus) [TaxId: 9913] [47958] (97)
              2. Cyclin H (mcs2) [47959]
                 1. Human (Homo sapiens) [TaxId: 9606] [47960] (2)
              3. Viral cyclin [47961]
                 1. Herpesvirus saimiri [TaxId: 10381] [47962] (8)
                 2. Murine herpesvirus 68 [TaxId: 33708] [47963] (1)
                 3. Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] [47964] (1)
              4. CDK5 activator 1 (NCK5a, p25) [74739]
                 1. Human (Homo sapiens) [TaxId: 9606] [74740] (4)
                    SQ Q15078 145-294
              5. Cyclin K [158591]
                 1. Human (Homo sapiens) [TaxId: 9606] [158592] (2)
                    SQ O75909 14-157! SQ O75909 158-267
              6. Cyclin-T2 [158593]
                 1. Human (Homo sapiens) [TaxId: 9606] [158594] (4)
                    SQ O60583 150-262! SQ O60583 7-149
              7. Cyclin T1 [158595]
                 1. Human (Homo sapiens) [TaxId: 9606] [158596] (14)
                    SQ O60563 151-259! SQ O60563 151-263! SQ O60563 5-150! SQ O60563 8-150
              8. G1/S-specific cyclin-E1 [158597]
                 1. Human (Homo sapiens) [TaxId: 9606] [158598] (2)
                    SQ P24864 103-242! SQ P24864 243-372
           2. Transcription factor IIB (TFIIB), core domain [47965] (2)
              1. Transcription factor IIB (TFIIB), core domain [47966]
                 1. Human (Homo sapiens) [TaxId: 9606] [47967] (5)
                 2. Archaeon Pyrococcus woesei [TaxId: 2262] [47968] (2)
           3. Retinoblastoma tumor suppressor domains [47969] (1)
              1. Retinoblastoma tumor suppressor domains [47970]
                 contains an additional C-terminal helix
                 1. Human (Homo sapiens) [TaxId: 9606] [47971] (9)
   123. Arp2/3 complex 21 kDa subunit ARPC3 [69059] (1)
        5 helices; one helix is surrounded by the others
        1. Arp2/3 complex 21 kDa subunit ARPC3 [69060] (1)
           uperfamily
           1. Arp2/3 complex 21 kDa subunit ARPC3 [69061] (1)
              1. Arp2/3 complex 21 kDa subunit ARPC3 [69062]
                 1. Cow (Bos taurus) [TaxId: 9913] [69063] (10)
                    SQ O15145 # 100% sequence identity
   124. RNase III domain-like [69064] (1)
        core: 5 helices; one helix is surrounded by the others
        1. RNase III domain-like [69065] (2)
           uperfamily
           1. RNase III catalytic domain-like [69066] (3)
              Pfam 00636
              1. RNase III endonuclease catalytic domain [69067]
                 1. Thermotoga maritima [TaxId: 2336] [81817] (1)
                 2. Aquifex aeolicus [TaxId: 63363] [69068] (22)
              2. Hypothetical protein BC0111 [109892]
                 1. Bacillus cereus [TaxId: 1396] [109893] (1)
                    SQ Q81J58
           2. PF0609-like [140675] (1)
              specific to Thermococci; shares conserved carboxylic residues and similar dimerisation mode with the RNase III domain; contains integrated in the fold extra C-terminal helix, making it similar to the core fold of Ribosomal protein S7 (scop_cf 47972)
              1. Hypothetical protein PF0609 [140676]
                 SECSG target pfu-631545-001
                 1. Pyrococcus furiosus [TaxId: 2261] [140677] (2)
                    SQ Q8U363 2-125
   125. Ribosomal protein S7 [47972] (1)
        core: 5 helices; contains one more helix and a beta-hairpin outside the core
        1. Ribosomal protein S7 [47973] (1)
           uperfamily
           1. Ribosomal protein S7 [47974] (4)
              1. Ribosomal protein S7 [47975]
                 1. Bacillus stearothermophilus [TaxId: 1422] [47976] (1)
                 2. Thermus thermophilus [TaxId: 274] [47977] (47)
                    SQ P17291
                 3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [63577] (1)
                 4. Escherichia coli [TaxId: 562] [158599] (24)
                    SQ P02359 2-151
   126. post-AAA+ oligomerization domain-like [48018] (1)
        core: 5 helices: bundle
        1. post-AAA+ oligomerization domain-like [48019] (2)
           associated with N-terminal domain from the AAA+ family of P-loop hydrolases
           uperfamily
           1. DNA polymerase III clamp loader subunits, C-terminal domain [48020] (10)
              contains an extra helix
              1. gamma subunit [63578]
                 1. Escherichia coli [TaxId: 562] [63579] (3)
                    SQ P06710 5-368
                 2. Thermotoga maritima [TaxId: 2336] [140678] (1)
                    SQ Q9WZM9 209-306
              2. delta prime subunit [48021]
                 1. Escherichia coli [TaxId: 562] [48022] (4)
                    SQ P28631
              3. delta subunit [63580]
                 1. Escherichia coli [TaxId: 562] [63581] (4)
                    SQ P28630
              4. Replication factor C [63582]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [63583] (1)
              5. Replication factor C1 [109894]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109895] (1)
                    SQ P38630 295-696 # helical segment (667-696) together with unassigned C-terminal sequence forms an all-alpha subdomain
              6. Replication factor C4 [109896]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109897] (1)
                    SQ P40339
              7. Replication factor C3 [109898]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109899] (1)
                    SQ P38629
              8. Replication factor C2 [109900]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109901] (1)
                    SQ P40348
              9. Replication factor C5 [109902]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109903] (1)
                    SQ P38251
           2. MgsA/YrvN C-terminal domain-like [158600] (3)
              1. Uncharacterized protein NTHI1458 [158601]
                 1. Haemophilus influenzae [TaxId: 727] [158602] (2)
                    SQ Q4QL22 251-434
              2. Uncharacterized protein EfaeDRAFT_0938 [158603]
                 1. Enterococcus faecium [TaxId: 1352] [158604] (20)
                    SQ Q3XY27 238-423! SQ Q3XY27 241-328
              3. Uncharacterized protein YrvN [158605]
                 1. Prochlorococcus marinus [TaxId: 1219] [158606] (2)
                    SQ Q7V3J8 258-420
                    PMM0077
   127. PAP/OAS1 substrate-binding domain [81632] (1)
        core: 5-helical bundle; up-and-down; right-handed twist
        1. PAP/OAS1 substrate-binding domain [81631] (5)
           this domain follows the catalytic nucleotidyltransferase domain
           uperfamily
           1. Poly(A) polymerase, PAP, middle domain [81630] (2)
              1. Poly(A) polymerase, PAP, middle domain [81629]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81628] (7)
                 2. Cow (Bos taurus) [TaxId: 9913] [56707] (3)
                    SQ P25500 18-497
           2. 2'-5'-oligoadenylate synthetase 1, OAS1, second domain [101271] (1)
              1. 2'-5'-oligoadenylate synthetase 1, OAS1, second domain [101272]
                 1. Pig (Sus scrofa) [TaxId: 9823] [101273] (1)
           3. Archaeal tRNA CCA-adding enzyme substrate-binding domain [101274] (1)
              1. tRNA nucleotidyltransferase, second domain [101275]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [101276] (28)
                    SQ O28126
           4. RNA editing terminal uridyl transferase 2, RET2, domain 2 [140679] (1)
              1. RNA editing terminal uridyl transferase 2, TUTase 2, RET2 [140680]
                 1. Trypanosoma brucei [TaxId: 5691] [140681] (1)
                    SQ Q86MV5 289-471
           5. AadK C-terminal domain-like [158607] (1)
              C-terminal part of Pfam 04439; Streptomycin adenylyltransferase; contains extra C-terminal helix
              1. Aminoglycoside 6-adenylyltransferase AadK [158608]
                 1. Bacillus subtilis [TaxId: 1423] [158609] (1)
                    SQ P17585 138-282
   128. Anti-sigma factor AsiA [69069] (1)
        core: 5 helices: orthogonal array
        1. Anti-sigma factor AsiA [69070] (1)
           uperfamily
           1. Anti-sigma factor AsiA [69071] (1)
              1. Anti-sigma factor AsiA [69072]
                 1. Bacteriophage T4 [TaxId: 10665] [69073] (4)
                    SQ P32267
   129. Antibiotic binding domain of TipA-like multidrug resistance regulators [89081] (1)
        5 helices: orthogonal array
        1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89082] (1)
           uperfamily
           1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89083] (1)
              1. Transcriptional activator TipA-S [89084]
                 1. Streptomyces lividans [TaxId: 1916] [89085] (1)
   130. Surp module (SWAP domain) [109904] (1)
        5 helices: irregular array
        1. Surp module (SWAP domain) [109905] (1)
           uperfamily
           1. Surp module (SWAP domain) [109906] (3)
              Pfam 01805
              1. Splicing factor 4 [109907]
                 1. Mouse (Mus musculus) [TaxId: 10090] [109908] (2)
                    SQ Q8CH02 165-239
              2. Arginine/serine-rich-splicing factor 14 [158610]
                 1. Human (Homo sapiens) [TaxId: 9606] [158611] (1)
                    SQ Q8IX01 587-639
              3. Splicing factor 3 subunit 1, SF3A1 [158612]
                 1. Human (Homo sapiens) [TaxId: 9606] [158613] (2)
                    SQ Q15459 134-217! SQ Q15459 48-110
   131. YgfY-like [109909] (1)
        5 helices; array; forms a tight dimer in crystals
        1. YgfY-like [109910] (1)
           uperfamily
           1. YgfY-like [109911] (1)
              Pfam 03937; despite the Pfam annotation, this family shows no topological similarity to the TPR repeat proteins
              1. Hypothetical protein NMA1147 [109912]
                 1. Neisseria meningitidis, mc58 [TaxId: 487] [109913] (1)
                    SQ Q9JR91
   132. Hypothetical protein YhaI [109914] (1)
        core: 5 helices; orthogonal array; folding similarity to the TipA-S domain (1ny9)
        1. Hypothetical protein YhaI [109915] (1)
           oligomerizes via extra N-terminal helix forming trimeric coil-coiled
           uperfamily
           1. Hypothetical protein YhaI [109916] (1)
              1. Hypothetical protein YhaI [109917]
                 1. Bacillus subtilis [TaxId: 1423] [109918] (1)
                    SQ O07517
   133. Hypothetical protein At3g22680 [109919] (1)
        5 helices; array; probable biological unit is a homodimer
        1. Hypothetical protein At3g22680 [109920] (1)
           uperfamily
           1. Hypothetical protein At3g22680 [109921] (1)
              1. Hypothetical protein At3g22680 [109922]
                 1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [109923] (2)
                    SQ Q9LUJ3
   134. SP0561-like [140682] (1)
        5 helices; array; includes extra N-terminal and C-terminal short strands forming parrallel beta-sheet ladder
        1. SP0561-like [140683] (1)
           uperfamily
           1. SP0561-like [140684] (1)
              Pfam 08984; DUF1858
              1. Hypothetical protein SPr0485/SP0561 [140685]
                 1. Streptococcus pneumoniae [TaxId: 1313] [140686] (1)
                    SQ Q8CZ42 3-81
   135. RbcX-like [158614] (1)
        5 helices per subunit; irregular array of short and long helices; swapping of the C-terminal helices in the dimer
        1. RbcX-like [158615] (1)
           1. RbcX-like [158616] (3)
              Pfam 02341 (note typo in the Pfam name: RcbX)
              1. RuBisCo chaperone RbcX [158617]
                 1. Synechococcus sp. pcc 7002 [TaxId: 32049] [158618] (47)
                    SQ Q44177 2-111! SQ Q44177 3-109! SQ Q44177 3-111
                 2. Anabaena sp. [TaxId: 1167] [158619] (2)
                    SQ Q44212 1-115
                 3. Synechocystis sp., strain PCC 6803 [TaxId: 1143] [158620] (3)
                    SQ Q55670 4-123
   136. YheA-like [158621] (1)
        5 helices; "kinked" antiparallel coiled coil; forms flexible oligomeric assemblies via two different dimerisation interfaces
        1. YheA/YmcA-like [158622] (2)
           1. YmcA-like [158623] (1)
              N-terminal and C-terminal parts correspond to PfamB 012831 and PfamB 007043, respectively
              1. Uncharacterized protein YmcA [158624]
                 1. Bacillus subtilis [TaxId: 1423] [158625] (2)
                    SQ O31779 2-124
           2. YheA-like [158626] (3)
              Pfam 06133; DUF964
              1. Hypothetical protein YheA [158627]
                 1. Bacillus subtilis [TaxId: 1423] [158628] (2)
                    SQ O07542 3-112
              2. Hypothetical protein SP1372 [158629]
                 1. Streptococcus pneumoniae [TaxId: 1313] [158630] (4)
                    SQ Q97Q59 1-111
              3. YheA-like protein [158631]
                 1. Bacillus stearothermophilus [TaxId: 1422] [158632] (4)
                    SQ Q5L2A5 3-115
   137. RPA2825-like [158633] (1)
        5 helices, array; long flexible loop between helices 1 and 2; the remaining helices are arranged similar to the PGBD-like fold (scop_cf 47089)
        1. RPA2825-like [158634] (1)
           1. RPA2825-like [158635] (1)
              PfamB 041910
              1. Hypothetical protein RPA2825 [158636]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [158637] (1)
                    SQ Q6N5Z3 1-130
   138. ENT-like [158638] (1)
        5 helices, irregular array, right-handed superhelix
        1. ENT-like [158639] (1)
           1. Emsy N terminal (ENT) domain-like [158640] (1)
              Pfam 03735
              1. Emsy [158641]
                 1. Human (Homo sapiens) [TaxId: 9606] [158642] (5)
                    SQ Q7Z589 9-124! SQ Q8TE50 11-107
   139. YfmB-like [140687] (1)
        5 helices, array; buried N-terminal helix; some topological similarity (circular permutation?) to the Nucleotidyltransferase substrate binding subunit/domain (scop_sf 81593)
        1. YfmB-like [140688] (1)
           uperfamily
           1. YfmB-like [140689] (1)
              1. Hypothetical protein YfmB [140690]
                 1. Bacillus subtilis [TaxId: 1423] [140691] (2)
                    SQ O34626 1-113
   140. N-terminal domain of adenylylcyclase associated protein, CAP [101277] (1)
        6 helices: bundle; left-handed twist, up-and-down topology
        1. N-terminal domain of adenylylcyclase associated protein, CAP [101278] (1)
           uperfamily
           1. N-terminal domain of adenylylcyclase associated protein, CAP [101279] (1)
              1. N-terminal domain of adenylylcyclase associated protein, CAP [101280]
                 1. Dictyostelium discoideum [TaxId: 44689] [101281] (3)
   141. IpaD-like [140692] (1)
        6 helices; bundle, up-and-down; can be divided into two four-helical bundles sharing two helices (3 and 6), which are twice longer than the rest
        1. IpaD-like [140693] (1)
           uperfamily
           1. IpaD-like [140694] (2)
              Pfam 06511
              1. Invasin IpaD [140695]
                 1. Shigella flexneri [TaxId: 623] [140696] (6)
                    SQ P18013 128-320! SQ P18013 144-314! SQ P18013 39-322
              2. Putative membrane antigen BipD [140697]
                 1. Burkholderia pseudomallei [TaxId: 28450] [140698] (5)
                    SQ Q63K37 35-301
   142. Iron-dependent repressor protein, dimerization domain [47978] (1)
        6 helices, homodimer of 3-helical domains
        1. Iron-dependent repressor protein, dimerization domain [47979] (1)
           uperfamily
           1. Iron-dependent repressor protein, dimerization domain [47980] (3)
              1. Diphtheria toxin repressor (DtxR) [47981]
                 1. Corynebacterium diphtheriae [TaxId: 1717] [47982] (17)
                    SQ P33120
              2. Iron-dependent regulator [47983]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [47984] (13)
                    SQ Q50495
              3. Manganese transport regulator MntR [89086]
                 1. Bacillus subtilis [TaxId: 1423] [89087] (20)
   143. Glutamyl tRNA-reductase dimerization domain [69074] (1)
        6 helices, homodimer of 3-helical domains
        1. Glutamyl tRNA-reductase dimerization domain [69075] (1)
           uperfamily
           1. Glutamyl tRNA-reductase dimerization domain [69076] (1)
              1. Glutamyl tRNA-reductase dimerization domain [69077]
                 includes the long 'spinal' helix
                 1. Archaeon Methanopyrus kandleri [TaxId: 2320] [69078] (1)
   144. GRIP domain [101282] (1)
        6 helices, homodimer of 3-helical domains
        1. GRIP domain [101283] (1)
           uperfamily
           1. GRIP domain [101284] (1)
              1. Golgi autoantigen, golgin-245 [101285]
                 1. Human (Homo sapiens) [TaxId: 9606] [101286] (2)
   145. BAR/IMD domain-like [116747] (1)
        6 helices, homodimer of 3-helical domains
        1. BAR/IMD domain-like [103657] (4)
           core: dimeric six-helical bundle; protuding long helices form aniparallel coiled coils at both bundle ends
           uperfamily
           1. BAR domain [103658] (5)
              sensor of membrane curvature
              1. Amphiphysin [103659]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103660] (1)
              2. Endophilin-1 [140699]
                 SH3-containing GRB2-like protein 2
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [140700] (1)
                    SQ Q62420 25-247
                    UniProt sequence of Rat species, O35179, is a fragment that does not cover the entire domain
                 2. Human (Homo sapiens) [TaxId: 9606] [140701] (6)
                    SQ Q99962 11-247! SQ Q99962 26-247
                 3. Mouse (Mus musculus) [TaxId: 10090] [140702] (2)
                    SQ Q62420 27-246
              3. DCC-interacting protein 13-alpha, APPL1 [158643]
                 1. Human (Homo sapiens) [TaxId: 9606] [158644] (1)
                    SQ Q9UKG1 6-273
           2. Arfaptin, Rac-binding fragment [64599] (1)
              1. Arfaptin, Rac-binding fragment [64600]
                 active form is a dimer
                 1. Human (Homo sapiens) [TaxId: 9606] [64601] (4)
           3. IMD domain [140703] (1)
              Pfam 08397
              1. BAP2/IRSp53 N-terminal domain [140704]
                 1. Human (Homo sapiens) [TaxId: 9606] [140705] (4)
                    SQ Q9UQB8 1-248! SQ Q9UQB8 2-228
           4. FCH domain [158645] (2)
              Pfam 00611; Fes/CIP4 homology domain
              1. Formin-binding protein 1, FNBP1 [158646]
                 1. Human (Homo sapiens) [TaxId: 9606] [158647] (1)
                    SQ Q96RU3 1-288
              2. CDC42-interacting protein 4, CIP4 [158648]
                 1. Human (Homo sapiens) [TaxId: 9606] [158649] (1)
                    SQ Q15642 10-288
   146. L27 domain [101287] (1)
        6 helices, heterodimer of 3-helical domains
        1. L27 domain [101288] (1)
           uperfamily
           1. L27 domain [101289] (9)
              1. Associated tight junction protein Pals-1 [101290]
                 1. Human (Homo sapiens) [TaxId: 9606] [101291] (1)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [140706] (2)
                    SQ Q63ZW7 4-65
                    identical sequence to mouse domain
              2. Maguk p55 subfamily member 5, Patj [101292]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101293] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [140707] (2)
                    SQ Q8N3R9 118-177
              3. Presynaptic protein sap97 [101294]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101295] (1)
              4. Peripheral plasma membrane protein cask [101296]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101297] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [140708] (3)
                    SQ O14936 403-456
              5. Lin-7 [140709]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140710] (2)
                    SQ O88951 8-64
                    homolog B
                 2. Caenorhabditis elegans [TaxId: 6239] [140711] (1)
                    SQ Q9U245 116-165
   147. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109924] (1)
        dimer of 3-helical segments; consists of two subdomains: 4-helical bundle and coiled coil
        1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109925] (1)
           uperfamily
           1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109926] (1)
              1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109927]
                 1. Mouse (Mus musculus) [TaxId: 10090] [109928] (1)
                    SQ P43035 1-85
   148. Phage replication organizer domain [140712] (1)
        6 helices, homodimer of 3-helical domains
        1. Phage replication organizer domain [140713] (1)
           DNA binding induces further oligomerization
           uperfamily
           1. Phage replication organizer domain [140714] (1)
              Pfam 06720
              1. Early protein gp16.7 [140715]
                 1. Bacteriophage phi-29 [TaxId: 10756] [140716] (10)
                    SQ P16517 67-130
   149. YejL-like [158650] (1)
        6 helices; intertwined homodimer of three-helical subunits, bundle
        1. YejL-like [158651] (1)
           1. YejL-like [158652] (5)
              Pfam 07208; DUF1414
              1. Hypothetical protein CPS2611 [158653]
                 1. Colwellia psychrerythraea [TaxId: 28229] [158654] (4)
                    SQ Q481E4 7-68
              2. Uncharacterized protein HI0840 [158655]
                 1. Haemophilus influenzae [TaxId: 727] [158656] (2)
                    SQ P44897 1-72
              3. Hypothetical protein VP2129 [158657]
                 1. Vibrio parahaemolyticus [TaxId: 670] [158658] (2)
                    SQ Q87MV2 1-75
              4. Uncharacterized protein YejL [158659]
                 1. Escherichia coli [TaxId: 562] [158660] (2)
                    SQ P0AD24 1-75
              5. Uncharacterized protein SO2176 [158661]
                 1. Shewanella oneidensis [TaxId: 70863] [158662] (3)
                    SQ Q8EF26 1-72
   150. Mediator hinge subcomplex-like [140717] (1)
        6 helices; heterodimer of structurally similar subunits; the N-terminal hairpins form a four-helical bundle, whereas the C-terminal helices form coiled coil structure
        1. Mediator hinge subcomplex-like [140718] (2)
           uperfamily
           1. CSE2-like [140719] (1)
              Pfam 07544
              1. RNA polymerase II holoenzyme component SRB7 (MED21) [140720]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140721] (3)
                    SQ P47822 2-130! SQ P47822 3-133
           2. MED7 hinge region [140722] (1)
              C-terminal part of Pfam 05983
              1. RNA polymerase II mediator complex protein MED7 [140723]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140724] (3)
                    SQ Q08278 108-205
   151. DEATH domain [47985] (1)
        6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
        1. DEATH domain [47986] (4)
           uperfamily
           1. DEATH domain, DD [81312] (9)
              Pfam 00531
              1. p75 low affinity neurotrophin receptor [47988]
                 residues 334-418
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [47989] (1)
              2. Fas [47990]
                 1. Human (Homo sapiens) [TaxId: 9606] [47991] (1)
              3. FADD (Mort1) [47992]
                 contains two domains of this superfamily: DED and DD, in this order
                 1. Human (Homo sapiens) [TaxId: 9606] [47993] (3)
                 2. Mouse (Mus musculus) [TaxId: 10090] [47994] (1)
              4. Pelle death domain [48003]
                 1. Drosophila melanogaster [TaxId: 7227] [48004] (3)
              5. Tube death domain [48005]
                 complexed with Pelle death domain
                 1. Drosophila melanogaster [TaxId: 7227] [48006] (1)
              6. Tumor necrosis factor receptor-1 death domain [74741]
                 1. Human (Homo sapiens) [TaxId: 9606] [74742] (1)
              7. Interleukin-1 receptor-associated kinase 4, IRAK4 [116951]
                 1. Mouse (Mus musculus) [TaxId: 10090] [116952] (1)
                    SQ Q8R4K2 1-114
              8. Netrin receptor UNC5B [116953]
                 1. Mouse (Mus musculus) [TaxId: 10090] [116954] (1)
                    SQ Q8K1S3 854-943
           2. DEATH effector domain, DED [81388] (2)
              1. FADD (Mort1) [81387]
                 contains two domains of this superfamily: DED and DD, in this order
                 1. Human (Homo sapiens) [TaxId: 9606] [81386] (3)
              2. PEA-15 (phosphoprotein enriched in astrocytes 15 kDa) [81818]
                 DED is followed by an irregular C-terminal tail
                 1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [81819] (1)
           3. Caspase recruitment domain, CARD [81313] (5)
              1. Raidd CARD domain [47995]
                 1. Human (Homo sapiens) [TaxId: 9606] [47996] (1)
              2. Apoptotic protease activating factor 1, APAF-1 [47997]
                 1. Human (Homo sapiens) [TaxId: 9606] [47998] (6)
              3. Procaspase 9 prodomain [47999]
                 1. Human (Homo sapiens) [TaxId: 9606] [48000] (1)
              4. Iceberg [48001]
                 an inhibitor of interleukin-1beta generation
                 1. Human (Homo sapiens) [TaxId: 9606] [48002] (1)
              5. Cell death protein 4, CED-4 [158663]
                 1. Caenorhabditis elegans [TaxId: 6239] [158664] (1)
                    SQ P30429 1-108
           4. Pyrin domain, PYD [101298] (2)
              1. Apoptosis-associated speck-like protein Asc [101299]
                 1. Human (Homo sapiens) [TaxId: 9606] [101300] (1)
              2. NALP1 [101301]
                 1. Human (Homo sapiens) [TaxId: 9606] [101302] (1)
   152. GntR ligand-binding domain-like [48007] (1)
        core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
        1. GntR ligand-binding domain-like [48008] (1)
           uperfamily
           1. GntR ligand-binding domain-like [48009] (2)
              1. Fatty acid responsive transcription factor FadR, C-terminal domain [48010]
                 1. Escherichia coli [TaxId: 562] [48011] (5)
              2. Putative transcriptional regulator RHA1_ro03477 [158665]
                 1. Rhodococcus sp. RHA1 [TaxId: 101510] [158666] (1)
                    SQ Q0SB06 94-231
   153. AF0941-like [140725] (1)
        6 helices, arranged into two interconnected 3-helical bundles; can also be described as a 'kinked' four-helical bundle; right-handed superhelix
        1. AF0941-like [140726] (1)
           uperfamily
           1. AF0941-like [140727] (1)
              1. Hypothetical protein AF0941 [140728]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [140729] (2)
                    SQ O29321 1-114
   154. NusB-like [48012] (1)
        6 helices: bundle; one central helix is surrounded by 5 others
        1. NusB-like [48013] (3)
           uperfamily
           1. Antitermination factor NusB [48014] (3)
              1. Antitermination factor NusB [48015]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [48016] (1)
                 2. Escherichia coli [TaxId: 562] [48017] (1)
                 3. Thermotoga maritima [TaxId: 2336] [109929] (5)
                    SQ Q9X286
           2. Hypothetical protein MG027 [101303] (1)
              1. Hypothetical protein MG027 [101304]
                 1. Mycoplasma genitalium [TaxId: 2097] [101305] (1)
           3. RmsB N-terminal domain-like [109930] (1)
              1. Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain [109931]
                 1. Escherichia coli [TaxId: 562] [109932] (2)
                    SQ P36929
   155. YutG-like [101306] (1)
        core: 6 helices; bundle; one central helix is surrounded by 5 others
        1. YutG-like [101307] (1)
           uperfamily
           1. YutG-like [101308] (3)
              Pfam 01892; DUF64
              1. YutG homologue [101309]
                 1. Bacillus stearothermophilus [TaxId: 1422] [101310] (1)
              2. Hypothetical protein YpjQ [109933]
                 1. Bacillus subtilis [TaxId: 1423] [109934] (1)
                    SQ P54173
              3. Low temperature requirement C protein, LtrC [116955]
                 1. Listeria monocytogenes [TaxId: 1639] [116956] (1)
                    SQ Q9ZIM5
   156. N-terminal domain of DnaB helicase [48023] (1)
        6 helices: array
        1. N-terminal domain of DnaB helicase [48024] (1)
           uperfamily
           1. N-terminal domain of DnaB helicase [48025] (1)
              1. N-terminal domain of DnaB helicase [48026]
                 1. Escherichia coli [TaxId: 562] [48027] (2)
   157. Invasion protein A (SipA) , C-terminal actin binding domain [101311] (1)
        6 helices: orthogonal array
        1. Invasion protein A (SipA) , C-terminal actin binding domain [101312] (1)
           uperfamily
           1. Invasion protein A (SipA) , C-terminal actin binding domain [101313] (1)
              1. Invasion protein A (SipA) , C-terminal actin binding domain [101314]
                 1. Salmonella typhimurium [TaxId: 90371] [101315] (1)
   158. MtlR-like [158667] (1)
        multihelical; 8-helical up-and-down bundle
        1. MtlR-like [158668] (1)
           1. MtlR-like [158669] (2)
              Pfam 05068; mannitol repressor
              1. Putative transcriptional regulator YggD [158670]
                 1. Shigella flexneri [TaxId: 623] [158671] (4)
                    SQ Q83Q96 1-168! SQ Q83Q96 2-168! SQ Q83Q96 3-168
              2. Mannitol operon repressor MtlR [158672]
                 1. Vibrio parahaemolyticus [TaxId: 670] [158673] (4)
                    SQ Q87SQ4 6-172
   159. Guanido kinase N-terminal domain [48033] (1)
        irregular array of 6 short helices
        1. Guanido kinase N-terminal domain [48034] (1)
           uperfamily
           1. Guanido kinase N-terminal domain [48035] (8)
              1. Creatine kinase, N-domain [48036]
                 1. Chicken (Gallus gallus), mitochondria [TaxId: 9031] [48037] (1)
                 2. Chicken (Gallus gallus), brain-type [TaxId: 9031] [48038] (1)
                 3. Human (Homo sapiens), muscle isoform [TaxId: 9606] [89088] (1)
                 4. Human (Homo sapiens), mitochondria [TaxId: 9606] [48039] (1)
                 5. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [48040] (3)
                 6. Cow (Bos taurus), retinal isoform [TaxId: 9913] [48041] (1)
                 7. Pacific electric ray (Torpedo californica) [TaxId: 7787] [81820] (2)
              2. Arginine kinase, N-domain [48042]
                 1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [48043] (7)
                    SQ P51541
   160. Scaffolding protein gpD of bacteriophage procapsid [48044] (1)
        core: 6 helices; one central helix is surrounded by 5 others
        1. Scaffolding protein gpD of bacteriophage procapsid [48045] (1)
           uperfamily
           1. Scaffolding protein gpD of bacteriophage procapsid [48046] (1)
              1. Scaffolding protein gpD of bacteriophage procapsid [48047]
                 1. Bacteriophage phi-X174 [TaxId: 10847] [48048] (3)
   161. Hemocyanin, N-terminal domain [48049] (1)
        6 helices; bundle; one central helix is surrounded by 5 others
        1. Hemocyanin, N-terminal domain [48050] (1)
           uperfamily
           1. Hemocyanin, N-terminal domain [48051] (2)
              1. Hemocyanin, N-terminal domain [48052]
                 Middle domain is all-alpha; C-terminal domain is immunoglobulin-like sandwich
                 1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [48053] (4)
                 2. Spiny lobster (Panulirus interruptus) [TaxId: 6735] [48054] (7)
   162. Sama2622-like [158674] (1)
        core: 6 helices; bundle; one central helix is surrounded by 5 others
        1. Sama2622-like [158675] (1)
           1. Sama2622-like [158676] (1)
              1. Uncharacterized protein Sama2622 [158677]
                 1. Shewanella amazonensis [TaxId: 60478] [158678] (1)
                    SQ A1S8W8 1-144
   163. Di-copper centre-containing domain [48055] (1)
        multihelical
        1. Di-copper centre-containing domain [48056] (2)
           duplication: contains two structural repeats
           uperfamily
           1. Hemocyanin middle domain [48057] (4)
              1. Arthropod hemocyanin [48058]
                 N-terminal domain is all-alpha; C-terminal domain is immunoglobulin-like sandwich
                 1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [48059] (4)
                 2. Spiny lobster (Panulirus interruptus) [TaxId: 6735] [48060] (7)
              2. Mollusc hemocyanin [69079]
                 1. Giant octopus (Octopus dofleini) [TaxId: 267067] [69080] (1)
                 2. Mollusca (Rapana thomasiana) [TaxId: 29165] [89089] (1)
           2. Catechol oxidase [48061] (1)
              1. Catechol oxidase [48062]
                 1. Sweet potato (Ipomoea batatas) [TaxId: 4120] [48063] (4)
   164. DBL homology domain (DH-domain) [48064] (1)
        multihelical; core: 5-helical bundle
        1. DBL homology domain (DH-domain) [48065] (1)
           uperfamily
           1. DBL homology domain (DH-domain) [48066] (10)
              Pfam 00621
              1. Son of sevenless-1 (sos-1) [48067]
                 1. Human (Homo sapiens) [TaxId: 9606] [48068] (3)
                    SQ Q07889 189-1046
              2. beta-pix [48069]
                 1. Human (Homo sapiens) [TaxId: 9606] [48070] (1)
              3. RhoGEF Vav [48071]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48072] (1)
              4. GEF of TIAM1 (T-Lymphoma invasion and metastasis inducing protein 1) [48073]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48074] (1)
              5. Dbl's big sister, Dbs [74743]
                 1. Mouse (Mus musculus) [TaxId: 10090] [74744] (4)
                    SQ Q64096 624-958 # 98% sequence identity; the rat sequence Q63406 region 499-833 is 100% identical to the PDB sequence
              6. GEF of intersectin [74745]
                 1. Human (Homo sapiens) [TaxId: 9606] [74746] (1)
              7. Triple functional domain protein TRIO [109935]
                 1. Human (Homo sapiens) [TaxId: 9606] [109936] (2)
                    SQ O75962 1231-1535
              8. Rho guanine nucleotide exchange factor 12 [109937]
                 1. Human (Homo sapiens), gamma isoform [TaxId: 9606] [109938] (2)
                    SQ Q9NZN5 766-1138
              9. Rho guanine nucleotide exchange factor 11, PDZ-RhoGEF [116957]
                 1. Human (Homo sapiens) [TaxId: 9606] [116958] (1)
                    SQ O15085 714-1081
              10. Rho guanine nucleotide exchange factor 9, Collybistin [158679]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [158680] (1)
                     SQ Q9QX73 97-299
   165. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48075] (1)
        multihelical; contains compact array of 6 short helices
        1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48076] (1)
           uperfamily
           1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48077] (1)
              1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48078]
                 1. Sphingomonas paucimobilis, formerly Pseudomonas paucimobilis [TaxId: 13689] [48079] (2)
   166. RuBisCo LSMT C-terminal, substrate-binding domain [81821] (1)
        multihelical; irregular array of long and short helices
        1. RuBisCo LSMT C-terminal, substrate-binding domain [81822] (1)
           uperfamily
           1. RuBisCo LSMT C-terminal, substrate-binding domain [81823] (1)
              1. RuBisCo LSMT C-terminal, substrate-binding domain [81824]
                 1. Garden pea (Pisum sativum) [TaxId: 3888] [81825] (15)
   167. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48080] (1)
        multihelical bundle; contains buried central helix
        1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48081] (1)
           uperfamily
           1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48082] (6)
              C-terminal domain is all-alpha
              1. Alpha chain [48083]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [48084] (5)
                 2. Archaeon Methanopyrus kandleri [TaxId: 2320] [48085] (1)
                 3. Archaeon Methanosarcina barkeri [TaxId: 2208] [48086] (1)
              2. Beta chain [48087]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [48088] (5)
                 2. Archaeon Methanopyrus kandleri [TaxId: 2320] [48089] (1)
                 3. Archaeon Methanosarcina barkeri [TaxId: 2208] [48090] (1)
   168. YcfC-like [101321] (1)
        multihelical; contains two buried central helices
        1. YcfC-like [101322] (1)
           uperfamily
           1. YcfC-like [101323] (1)
              Pfam 04356; DUF489
              1. Hypothetical protein YcfC [101324]
                 1. Escherichia coli [TaxId: 562] [101325] (2)
                    SQ P25746
   169. PA2201 C-terminal domain-like [140730] (1)
        multihelical; seven-helical bundle with buried central helix
        1. PA2201 C-terminal domain-like [140731] (1)
           uperfamily
           1. PA2201 C-terminal domain-like [140732] (1)
              1. Hypothetical protein PA2201 [140733]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140734] (3)
                    SQ Q9I1R6 135-293
   170. Rv1873-like [140735] (1)
        multihelical; contains unusually short buried central helix
        1. Rv1873-like [140736] (1)
           uperfamily
           1. Rv1873-like [140737] (1)
              contains conserved motif HWuW at the beginning of the central helix
              1. Hypothetical protein Rv1873 (MT1922) [140738]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [140739] (1)
                    SQ O07756 6-145
   171. RUN domain-like [140740] (1)
        multihelical; 3-helical bundle similar to one half of the DEATH domain fold is flanked by two alpha-hairpins forming a four-helical bundle; the axes of the three-helical and four-helical bundles are aproximately orthogonal to each other
        1. RUN domain-like [140741] (1)
           uperfamily
           1. RUN domain [140742] (1)
              Pfam 02759
              1. Rap2 interacting protein X (RUFY3) [140743]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140744] (2)
                    SQ Q9D394 65-231
   172. SipA N-terminal domain-like [140745] (1)
        multihelical; bundle; the last helix is buried inside the bundle
        1. SipA N-terminal domain-like [140746] (1)
           uperfamily
           1. SipA N-terminal domain-like [140747] (1)
              N-terminal part of Pfam 09052
              1. Cell invasion protein SipA, N-terminal domain [140748]
                 1. Salmonella typhimurium [TaxId: 90371] [140749] (2)
                    SQ Q56027 23-262! SQ Q56027 49-263
   173. Transcription factor STAT-4 N-domain [48091] (1)
        multihelical; can be divided into two subdomains
        1. Transcription factor STAT-4 N-domain [48092] (1)
           uperfamily
           1. Transcription factor STAT-4 N-domain [48093] (1)
              1. Transcription factor STAT-4 N-domain [48094]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48095] (1)
   174. TerB-like [158681] (1)
        multihelical; contains two central helices; duplication: there are two three-helical repeats related by pseudo twofold symmetry
        1. TerB-like [158682] (2)
           members of this superfamily probably related to the tellurite resistance protein TerB (Pfam 05099) of yet undetermined structure
           1. COG3793-like [158683] (1)
              Pfam 07049; DUF1332
              1. Tellurite resistance protein of COG3793 [158684]
                 1. Nostoc punctiforme pcc 73102 [TaxId: 63737] [158685] (2)
           2. PG1108-like [158686] (1)
              1. Hypothetical protein PG1108 [158687]
                 1. Porphyromonas gingivalis [TaxId: 837] [158688] (1)
                    SQ Q7MVF6 1-132
   175. Regulator of G-protein signaling, RGS [48096] (1)
        multihelical; consists of two all-alpha subdomains
        contains a 4-helical bundle with left-handed twist and up-and-down topology
        1. Regulator of G-protein signaling, RGS [48097] (1)
           uperfamily
           1. Regulator of G-protein signaling, RGS [48098] (9)
              1. Regulator of G-protein signaling 4, RGS4 [48099]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48100] (3)
              2. RGS9, RGS domain [48101]
                 1. Cow (Bos taurus) [TaxId: 9913] [48102] (3)
              3. Galpha interacting protein, GaIP [48103]
                 1. Human (Homo sapiens) [TaxId: 9606] [48104] (1)
              4. Axin RGS-homologous domain [48105]
                 1. Human (Homo sapiens) [TaxId: 9606] [48106] (2)
              5. p115RhoGEF [63584]
                 1. Human (Homo sapiens) [TaxId: 9606] [63585] (1)
              6. Pdz-RhoGEF RGS-like domain [63586]
                 contains extra helices in the C-terminal extension
                 1. Human (Homo sapiens) [TaxId: 9606] [63587] (1)
              7. G-protein coupled receptor kinase 2, N-terminal domain [89090]
                 1. Cow (Bos taurus) [TaxId: 9913] [89091] (6)
              8. Regulator of G-protein signaling 18, RGS18 [140750]
                 1. Human (Homo sapiens) [TaxId: 9606] [140751] (1)
                    SQ Q9NS28 75-206
              9. Regulator of G-protein signaling 16, RGS16 [158689]
                 1. Human (Homo sapiens) [TaxId: 9606] [158690] (2)
                    SQ O15492 65-184
   176. SopE-like GEF domain [81831] (1)
        multihelical; consists of two all-alpha subdomains each containing a 3-helical bundle with right-handed twist
        1. SopE-like GEF domain [81832] (1)
           uperfamily
           1. SopE-like GEF domain [81833] (3)
              C-terminal part of Pfam 05364
              1. GEF domain of SopE toxin [81834]
                 1. Salmonella typhimurium [TaxId: 90371] [81835] (1)
              2. Effector protein SopE2 [109939]
                 1. Salmonella typhimurium [TaxId: 90371] [109940] (2)
                    SQ Q9KIZ2
              3. Effector protein BopE [158691]
                 1. Burkholderia pseudomallei [TaxId: 28450] [158692] (2)
                    SQ Q63K41 78-261
   177. Variable surface antigen VlsE [74747] (1)
        multihelical; consists of two all-alpha subdomains; contains a 4-helical bundle with left-handed twist and up-and-down topology
        1. Variable surface antigen VlsE [74748] (1)
           uperfamily
           1. Variable surface antigen VlsE [74749] (1)
              1. Variable surface antigen VlsE [74750]
                 1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [74751] (1)
   178. YgfB-like [101326] (1)
        multihelical; consists of two tightly associated 3-helical bundles with different twists
        1. YgfB-like [101327] (1)
           uperfamily
           1. YgfB-like [101328] (1)
              1. Hypothetical protein HI0817 [101329]
                 1. Haemophilus influenzae [TaxId: 727] [101330] (1)
   179. Hypothetical protein MTH393 [101331] (1)
        multihelical; consists of two all-alpha subdomains; dimer
        1. Hypothetical protein MTH393 [101332] (1)
           uperfamily
           1. Hypothetical protein MTH393 [101333] (1)
              1. Hypothetical protein MTH393 [101334]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101335] (1)
   180. PG0816-like [140752] (1)
        multihelical; comprises two helical bundles, both are topologically similar to the RuvA C-terminal domain-like fold (scop_cf 46928)
        1. PG0816-like [140753] (1)
           uperfamily
           1. PG0816-like [140754] (1)
              Pfam 08989; DUF1896
              1. Hypothetical protein PG0816 [140755]
                 1. Porphyromonas gingivalis [TaxId: 837] [140756] (1)
                    SQ Q7MW33 2-150
   181. UraD-like [158693] (1)
        multihelical; irregular array of long and short helices
        1. UraD-Like [158694] (1)
           1. UraD-like [158695] (3)
              Pfam 09349; OHCU decarboxylase (formerly DUF1991)
              1. OHCU decarboxylase, UraD [158696]
                 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [158697] (1)
                    SQ Q9LVM5 6-160
                 2. Zebrafish (Brachydanio rerio) [TaxId: 7955] [158698] (18)
                    SQ A1L259 2-166
              2. Hypothetical protein Atu2327 [158699]
                 1. Agrobacterium tumefaciens [TaxId: 358] [158700] (1)
                    SQ Q8UD01 1-165
   182. Sec63 N-terminal domain-like [158701] (1)
        multihelical; consists of two helical subdomains
        1. Sec63 N-terminal domain-like [158702] (2)
           1. Sec63 N-terminal domain [158703] (1)
              N-terminal part of Pfam 02889
              1. Protein pro2281 [158704]
                 1. Human (Homo sapiens) [TaxId: 9606] [158705] (1)
                    SQ Q9P172 33-208
           2. Achaeal helicase C-terminal domain [158706] (1)
              1. Hel308 helicase [158707]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [158708] (2)
   183. Carbamoyl phosphate synthetase, large subunit connection domain [48107] (1)
        multihelical; consists of two all-alpha subdomains
        possible duplication: subdomains have similar topologies
        1. Carbamoyl phosphate synthetase, large subunit connection domain [48108] (1)
           uperfamily
           1. Carbamoyl phosphate synthetase, large subunit connection domain [48109] (1)
              1. Carbamoyl phosphate synthetase, large subunit connection domain [48110]
                 1. Escherichia coli [TaxId: 562] [48111] (10)
                    SQ P00968
   184. Heme-dependent peroxidases [48112] (1)
        multihelical; consists of two all-alpha domains
        1. Heme-dependent peroxidases [48113] (3)
           uperfamily
           1. CCP-like [48114] (14)
              1. Fungal peroxidase (ligninase) [88935]
                 1. White rot basidiomycete (Phanerochaete chrysosporium) [TaxId: 5306] [48116] (6)
                 2. Arthromyces ramosus [TaxId: 5451] [48118] (14)
                 3. Inky cap (Coprinus cinereus) [TaxId: 5346] [74752] (5)
                 4. Basidomycetos fungus (Phanerochaete chrysosporium) [TaxId: 5306] [48122] (7)
              2. Cytochrome c peroxidase, CCP [48119]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48120] (126)
                    SQ P00431
              3. Ascorbate peroxidase [48123]
                 1. Pea (Pisum sativum) [TaxId: 3888] [48124] (1)
                 2. Soybean (Glycine max) [TaxId: 3847] [89092] (6)
                    SQ Q43758
                 3. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [101336] (1)
                    chloroplastic isoform
              4. Plant peroxidase [48125]
                 1. Horseradish (Armoracia rusticana) [TaxId: 3704] [48126] (30)
                 2. Peanut (Arachis hypogaea) [TaxId: 3818] [48127] (1)
                 3. Soybean (Glycine max) [TaxId: 3847] [48128] (1)
                 4. Barley (Hordeum vulgare), peroxidase 1 [TaxId: 4513] [48129] (1)
                 5. Mouse-ear cress (Arabidopsis thaliana), peroxidase N [TaxId: 3702] [48130] (1)
                 6. Mouse-ear cress (Arabidopsis thaliana), peroxidase A2 [TaxId: 3702] [48131] (2)
           2. Catalase-peroxidase KatG [74753] (4)
              duplication: tandem repeat of two CCP-like domains
              1. Catalase-peroxidase KatG [74754]
                 only the N-terminal CCP-like domain binds heme
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [74755] (1)
                 2. Burkholderia pseudomallei [TaxId: 28450] [89093] (41)
                    SQ P13029 Q939D2 35-748
                 3. Synechococcus sp. pcc 7942 [TaxId: 1140] [101337] (1)
                 4. Mycobacterium tuberculosis [TaxId: 1773] [109941] (9)
                    SQ Q08129
           3. Myeloperoxidase-like [48132] (4)
              1. Myeloperoxidase [48133]
                 1. Human (Homo sapiens) [TaxId: 9606] [48134] (7)
                 2. Dog (Canis familiaris) [TaxId: 9615] [48135] (1)
              2. Prostaglandin H2 synthase [48136]
                 contains EGF-like module
                 1. Sheep (Ovis aries) [TaxId: 9940] [48137] (22)
                    SQ P05979 32-584
                 2. Mouse (Mus musculus) [TaxId: 10090] [48138] (8)
   185. Ribosomal protein L19 (L19e) [48139] (1)
        multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
        1. Ribosomal protein L19 (L19e) [48140] (1)
           uperfamily
           1. Ribosomal protein L19 (L19e) [48141] (1)
              1. Ribosomal protein L19 (L19e) [48142]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [48143] (58)
                    SQ P14119
   186. PSPTO4464-like [158709] (1)
        multihelical; consists of two subdomains at the ends of a long connecting helix
        1. PSPTO4464-like [158710] (1)
           1. PSPTO4464-like [158711] (1)
              Pfam 04751; DUF615
              1. Uncharacterized protein PSPTO4464 [158712]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [158713] (1)
                    SQ Q87WS9 22-169
   187. GatB/YqeY motif [89094] (1)
        multihelical; consists of two different alpha-helical bundles (4-helical and 3-helical)
        1. GatB/YqeY motif [89095] (2)
           uperfamily
           1. GatB/YqeY domain [89096] (1)
              1. Hypothetical protein YqeY [89097]
                 1. Bacillus subtilis [TaxId: 1423] [89098] (1)
           2. GatB/GatE C-terminal domain-like [140757] (3)
              assigned to the same Pfam 02637 family as YeqY by the presence of a common sequence motif with an alpha-hairpin structure
              1. Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, GatB, C-terminal domain [140758]
                 1. Staphylococcus aureus [TaxId: 1280] [140759] (5)
                    SQ P64201 294-400
              2. Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE, C-terminal domain [140760]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [140761] (2)
                    SQ O26803 445-503
                 2. Pyrococcus abyssi [TaxId: 29292] [140762] (2)
                    SQ Q9V0U0 457-512
   188. YfbU-like [116959] (1)
        multihelical; consist of two subdomains; forms 24-mer with the N-terminal sudbomains packing around the 4-fold axis and the C-terminal domains interacting at the 2-fold and 3-fold axes
        1. YfbU-like [116960] (1)
           uperfamily
           1. YfbU-like [116961] (1)
              Pfam 03887
              1. Hypothetical protein YfbU [116962]
                 1. Escherichia coli [TaxId: 562] [116963] (1)
                    SQ P0A8W8
   189. MG296-like [158714] (1)
        multihelical; in crystal forms helical polymers by swapping the two N-terminal helices to the next subunit in polymer; three subunits per turn of polymer helix
        1. MG296-like [158715] (1)
           1. MG296-like [158716] (1)
              Pfam 09644
              1. Hypothetical protein MPN423 [158717]
                 MG296 homologue
                 1. Mycoplasma pneumoniae [TaxId: 2104] [158718] (3)
                    SQ P75364 1-129
   190. Hypothetical protein MPN330 [116964] (1)
        multihelical; consists of three different 4-helical bundles
        1. Hypothetical protein MPN330 [116965] (1)
           uperfamily
           1. Hypothetical protein MPN330 [116966] (1)
              1. Hypothetical protein MPN330 [116967]
                 1. Mycoplasma pneumoniae [TaxId: 2104] [116968] (1)
                    SQ P75455
   191. HD-domain/PDEase-like [109603] (1)
        multihelical; consists of two different alpha-helical bundles
        1. HD-domain/PDEase-like [109604] (5)
           uperfamily
           1. HD domain [101340] (13)
              Pfam 01966; metal dependent phosphohydrolases
              1. Stringent response-like protein RelA N-terminal domain [101341]
                 1. Streptococcus equisimilis [TaxId: 119602] [101342] (1)
              2. 5'-nucleotidase YfbR [116969]
                 1. Escherichia coli [TaxId: 562] [116970] (2)
                    SQ P76491
                    Structural genomics target
              3. Oxetanocin-like protein PF0395 [116971]
                 similar fold and oligomeric structure to 5'-nucleotidase YfbR
                 1. Pyrococcus furiosus [TaxId: 2261] [116972] (1)
                    SQ Q8U3R1
              4. Hypothetical protein AF1432 [140763]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [140764] (4)
                    SQ O28840 7-172! SQ O28840 7-173
              5. Hypothetical protein aq_1910 [140765]
                 elaborated with additional structures in C-terminal extension
                 1. Aquifex aeolicus [TaxId: 63363] [140766] (2)
                    SQ O67745 1-369
              6. Hypothetical protein EF1143 [140767]
                 Probable ortholog of aq_1910
                 1. Enterococcus faecalis [TaxId: 1351] [140768] (2)
                    SQ Q836G9 1-453
              7. Predicted hydrolase mes0020 [158719]
                 1. Uncultured thermotogales bacterium [TaxId: 221214] [158720] (1)
                    SQ Q1EM40 1-217
              8. Uncharacterized protein Lin1889 [158721]
                 1. Listeria innocua [TaxId: 1642] [158722] (1)
                    SQ Q92AN1 1-201
              9. Uncharacterized protein SE1688 [158723]
                 1. Staphylococcus epidermidis [TaxId: 1282] [158724] (2)
                    SQ Q8CRP0 1-216
              10. Hypothetical protein Atu1052 [158725]
                  1. Agrobacterium tumefaciens [TaxId: 358] [158726] (4)
                     SQ Q8UGI5 6-205
              11. Uncharacterized protein BH2835 [158727]
                  1. Bacillus halodurans [TaxId: 86665] [158728] (4)
                     SQ Q9K916 2-213
              12. Uncharacterized protein LP2664 [158729]
                  1. Lactobacillus plantarum [TaxId: 1590] [158730] (4)
                     SQ Q88U62 1-215
              13. Uncharacterized protein BT9727_1981 [158731]
                  1. Bacillus thuringiensis [TaxId: 1428] [158732] (2)
                     SQ Q6HJG6 2-214
           2. PDEase [48548] (6)
              Pfam 00233; multihelical; can be divided into three subdomains
              1. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b [48549]
                 1. Human (Homo sapiens) [TaxId: 9606] [48550] (14)
                    SQ Q07343 324-667
              2. Catalytic domain of cyclic nucleotide phosphodiesterase pde4d [89151]
                 1. Human (Homo sapiens) [TaxId: 9606] [89152] (39)
                    SQ Q08499 388-713
              3. cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx [101439]
                 1. Human (Homo sapiens) [TaxId: 9606] [101440] (18)
                    SQ O76074 534-860
              4. cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b [101441]
                 1. Human (Homo sapiens) [TaxId: 9606] [101442] (2)
              5. High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A [109942]
                 1. Human (Homo sapiens) [TaxId: 9606] [109943] (14)
                    SQ O76083 241-566
              6. Catalytic domain of cyclic nucleotide phosphodiesterase 1b, PDE1B [109944]
                 1. Human (Homo sapiens) [TaxId: 9606] [109945] (1)
                    SQ Q01064 126-482
           3. modified HD domain [116973] (1)
              retains the superfamily core fold but lacks the conserved metal-binding site
              1. Hypothetical protein Cj0248 [116974]
                 1. Campylobacter jejuni [TaxId: 197] [116975] (1)
                    SQ Q9PIP7
           4. MioX-like [140769] (2)
              Pfam 05153; DUF706
              1. Myo-inositol oxygenase MioX [140770]
                 1. Human (Homo sapiens) [TaxId: 9606] [140771] (2)
                    SQ Q9UGB7 37-285
                 2. Mouse (Mus musculus) [TaxId: 10090] [140772] (2)
                    SQ Q9QXN5 28-285
           5. Ppx associated domain [140773] (1)
              this domain is C-terminal to Ppx domain in some Exopolyphosphatases
              1. Exopolyphosphatase Ppx C-terminal domain [140774]
                 1. Escherichia coli [TaxId: 562] [140775] (6)
                    SQ P0AFL6 312-508
   192. Superantigen MAM [101343] (1)
        multihelical; consists of two different alpha-helical bundles
        1. Superantigen MAM [101344] (1)
           uperfamily
           1. Superantigen MAM [101345] (1)
              1. Superantigen MAM [101346]
                 1. Mycoplasma arthritidis [TaxId: 2111] [101347] (5)
   193. Influenza virus matrix protein M1 [48144] (1)
        multihelical; consists of two different all-alpha subdomains, 4 helices each
        1. Influenza virus matrix protein M1 [48145] (1)
           superficially similar to membrane translocation domains
           uperfamily
           1. Influenza virus matrix protein M1 [48146] (1)
              1. Influenza virus matrix protein M1 [48147]
                 bifunctional membrane/RNA-binding protein
                 1. Influenza A virus [TaxId: 11320] [48148] (2)
   194. DNA-glycosylase [48149] (1)
        multihelical; consists of two all-alpha domains
        1. DNA-glycosylase [48150] (6)
           uperfamily
           1. Endonuclease III [48151] (1)
              1. Endonuclease III [48152]
                 1. Escherichia coli [TaxId: 562] [48153] (4)
           2. Mismatch glycosylase [48154] (4)
              1. Catalytic domain of MutY [48155]
                 1. Escherichia coli [TaxId: 562] [48156] (13)
                    SQ P17802 1-225
                 2. Bacillus stearothermophilus [TaxId: 1422] [101348] (3)
              2. Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 [89099]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89100] (1)
              3. Thymine-DNA glycosylase [69081]
                 1. Archaeon Methanobacterium thermoformicicum [TaxId: 145262] [69082] (1)
           3. 3-Methyladenine DNA glycosylase I (Tag) [74756] (1)
              1. 3-Methyladenine DNA glycosylase I (Tag) [74757]
                 1. Escherichia coli [TaxId: 562] [74758] (3)
           4. 3-Methyladenine DNA glycosylase III (MagIII) [101349] (1)
              1. 3-Methyladenine DNA glycosylase III (MagIII) [101350]
                 1. Helicobacter pylori [TaxId: 210] [101351] (3)
           5. DNA repair glycosylase, 2 C-terminal domains [48157] (2)
              1. 3-Methyladenine DNA glycosylase II (gene alkA or aidA) [48158]
                 1. Escherichia coli [TaxId: 562] [48159] (35)
                    SQ P04395
              2. 8-oxoguanine glycosylase [48160]
                 1. Human (Homo sapiens) [TaxId: 9606] [48161] (23)
           6. AgoG-like [116976] (2)
              1. 8-oxoguanine DNA glycosylase, AgoG [116977]
                 1. Pyrobaculum aerophilum [TaxId: 13773] [116978] (2)
                    SQ Q8ZVK6 # PAE2237
              2. Hypothetical protein PF0904 [116979]
                 1. Pyrococcus furiosus [TaxId: 2261] [116980] (1)
                    SQ Q8U2D5
   195. An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48162] (1)
        multihelical; consists of two all-alpha domains
        1. An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48163] (2)
           uperfamily
           1. C-terminal domain of glutamyl-tRNA synthetase (GluRS) [48164] (1)
              1. C-terminal domain of glutamyl-tRNA synthetase (GluRS) [48165]
                 1. Thermus thermophilus [TaxId: 274] [48166] (15)
           2. C-terminal domain of class I lysyl-tRNA synthetase [74759] (1)
              1. C-terminal domain of class I lysyl-tRNA synthetase [74760]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [74761] (1)
   196. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101352] (1)
        multihelical; consists of two all-alpha subdomains
        1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101353] (1)
           uperfamily
           1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101354] (1)
              1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101355]
                 1. Aquifex aeolicus [TaxId: 63363] [101356] (7)
   197. R1 subunit of ribonucleotide reductase, N-terminal domain [48167] (1)
        multihelical consists of two all-alpha subdomains
        subdomain 1 (residues 10-100) is a 4-helical bundle
        1. R1 subunit of ribonucleotide reductase, N-terminal domain [48168] (1)
           uperfamily
           1. R1 subunit of ribonucleotide reductase, N-terminal domain [48169] (2)
              1. R1 subunit of ribonucleotide reductase, N-terminal domain [48170]
                 1. Escherichia coli [TaxId: 562] [48171] (8)
                    SQ Q08698
                 2. Salmonella typhimurium [TaxId: 90371] [109946] (6)
   198. BEACH domain [81836] (1)
        multihelical, complex architecture
        1. BEACH domain [81837] (1)
           uperfamily
           1. BEACH domain [81838] (2)
              Pfam 02138
              1. BEACH domain of neurobeachin [81839]
                 1. Human (Homo sapiens) [TaxId: 9606] [81840] (1)
              2. Lipopolysaccharide-responsive and beige-like anchor protein LRBA [116981]
                 1. Human (Homo sapiens) [TaxId: 9606] [116982] (1)
                    SQ P50851 2076-2489
   199. Cryptochrome/photolyase FAD-binding domain [48172] (1)
        multihelical; consists of two all-alpha subdomains
        1. Cryptochrome/photolyase FAD-binding domain [48173] (1)
           uperfamily
           1. Cryptochrome/photolyase FAD-binding domain [48174] (5)
              1. C-terminal domain of DNA photolyase [48175]
                 N-terminal domain is alpha/beta and binds a light-harvesting cofactor
                 1. Escherichia coli [TaxId: 562] [48176] (1)
                 2. Thermus thermophilus [TaxId: 274] [69083] (5)
                 3. Synechococcus elongatus [TaxId: 32046] [48177] (7)
                    SQ P05327 1-474
              2. Cryptochrome C-terminal domain [81841]
                 1. Synechocystis sp., pcc 6803 [TaxId: 1143] [81842] (1)
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [109947] (2)
                    SQ Q43125 13-497
   200. 6-phosphogluconate dehydrogenase C-terminal domain-like [48178] (1)
        multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
        1. 6-phosphogluconate dehydrogenase C-terminal domain-like [48179] (12)
           N-terminal domain is Rossmann-fold with a family-specific C-terminal extension
           uperfamily
           1. Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain [48180] (5)
              Hydroxyisobutyrate dehydrogenase domain is similar to one structural repeat in the 6-phosphogluconate dehydrogenase domain
              1. Hydroxyisobutyrate dehydrogenase [101357]
                 forms similar dimeric and tetrameric structures to the 6-phosphogluconate dehydrogenase domain and its dimer, respectively
                 1. Thermus thermophilus [TaxId: 274] [101358] (8)
                    structural genomics
                 2. Salmonella typhimurium [TaxId: 90371] [109948] (1)
                    SQ Q8ZLV8
                 3. Pseudomonas aeruginosa [TaxId: 287] [158733] (1)
                    SQ Q9I5I6 163-296
              2. 6-phosphogluconate dehydrogenase (6PGD) [48181]
                 duplication; contains two structural repeats
                 1. Sheep (Ovis orientalis aries) [TaxId: 9940] [48182] (5)
                 2. Trypanosoma brucei [TaxId: 5691] [48183] (1)
           2. Mannitol 2-dehydrogenase [81843] (1)
              1. Mannitol 2-dehydrogenase [81844]
                 1. Pseudomonas fluorescens [TaxId: 294] [81845] (2)
           3. Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) [48184] (2)
              1. Class I ketol-acid reductoisomerase [89101]
                 1. Pseudomonas aeruginosa [TaxId: 287] [89102] (1)
              2. Class II ketol-acid reductoisomerase [48185]
                 duplication; contains two structural repeats swapped to fold into a figure eight knot
                 1. Spinach (Spinacia oleracea) [TaxId: 3562] [48186] (2)
           4. HCDH C-domain-like [48187] (3)
              1. Short chain L-3-hydroxyacyl CoA dehydrogenase [48188]
                 Dimer of 5-helical motifs; similar to duplicated motifs of 6PGD and KARI
                 1. Human (Homo sapiens) [TaxId: 9606] [48189] (11)
                 2. Pig (Sus scrofa) [TaxId: 9823] [48190] (1)
              2. Fatty oxidation complex alpha subunit, C-terminal domain [109949]
                 duplication: contains two repeats of this domain
                 1. Pseudomonas fragi [TaxId: 296] [109950] (4)
                    SQ P28793
           5. Conserved hypothetical protein MTH1747 [74762] (1)
              1. Conserved hypothetical protein MTH1747 [74763]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [74764] (1)
           6. UDP-glucose/GDP-mannose dehydrogenase dimerisation domain [48191] (2)
              1. UDP-glucose dehydrogenase (UDPGDH), middle domain [48192]
                 1. Streptococcus pyogenes [TaxId: 1314] [48193] (2)
              2. GDP-mannose 6-dehydrogenase, middle domain [89103]
                 forms segment-swapped dimer, unlike the homologous UDPGDH domain
                 1. Pseudomonas aeruginosa [TaxId: 287] [89104] (3)
           7. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [48194] (1)
              1. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [48195]
                 1. Arthrobacter, strain 1c [TaxId: 1663] [48196] (1)
           8. Glycerol-3-phosphate dehydrogenase [48197] (2)
              1. Glycerol-3-phosphate dehydrogenase [48198]
                 1. Trypanosome (Leishmania mexicana) [TaxId: 5665] [48199] (7)
                    SQ O29390
                 2. Archaeoglobus fulgidus [TaxId: 2234] [116983] (1)
           9. Ketopantoate reductase PanE [69084] (1)
              1. Ketopantoate reductase PanE [69085]
                 1. Escherichia coli [TaxId: 562] [69086] (5)
           10. ProC C-terminal domain-like [116984] (3)
               similar dimer to the class I KARI
               1. Pyrroline-5-carboxylate reductase ProC [116985]
                  1. Neisseria meningitidis, serogroup B [TaxId: 487] [116986] (2)
                     SQ Q9K1N1
                  2. Streptococcus pyogenes [TaxId: 1314] [140776] (10)
                     SQ Q9A1S9 153-256
               2. Hypothetical protein TM1727 [158734]
                  1. Thermotoga maritima [TaxId: 2336] [158735] (2)
                     SQ Q9X250 155-257
           11. HMD dimerization domain-like [140777] (1)
               dimer similar to those of the GDP-mannose 6-dehydrogenase and class I KARI domains
               1. 5,10-methenyltetrahydromethanopterin hydrogenase, HMD [140778]
                  1. Archaeon Methanocaldococcus jannaschii [TaxId: 2190] [140779] (1)
                     SQ Q58194 243-344
           12. TyrA dimerization domain-like [140780] (3)
               new dimerisation mode with swapping of C-terminal helices
               1. Prephenate dehydrogenase TyrA [140781]
                  1. Aquifex aeolicus [TaxId: 63363] [140782] (4)
                     SQ O67636 201-310
                  2. Synechocystis sp. pcc 6803 [TaxId: 1148] [140783] (4)
                     SQ P73906 166-279
                  3. Haemophilus influenzae [TaxId: 727] [158736] (2)
                     SQ P43902 244-371
   201. Uteroglobin-like [48200] (1)
        multihelical
        1. Uteroglobin-like [48201] (1)
           disulfide-linked dimer of two identical chains, 4 helices in each
           uperfamily
           1. Uteroglobin-like [48202] (4)
              1. Uteroglobin [48203]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [48204] (2)
              2. Clara cell 17kDa protein [48205]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48206] (2)
              3. Allergen Fel d I-A chain [101359]
                 forms heterodimer with Fel d I-B chain
                 1. Cat (Felis catus) [TaxId: 9685] [101360] (5)
              4. Allergen Fel d I-B chain [101361]
                 forms heterodimer with Fel d I-A chain
                 1. Cat (Felis catus) [TaxId: 9685] [101362] (5)
   202. alpha/alpha toroid [48207] (6)
        multihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
        1. Six-hairpin glycosidases [48208] (9)
           uperfamily
           1. Glucoamylase [48209] (2)
              1. Glucoamylase [48210]
                 1. Aspergillus awamori, variant x100 [TaxId: 105351] [48211] (6)
                 2. Yeast (Saccharomycopsis fibuligera) [TaxId: 4944] [48212] (3)
           2. Cellulases catalytic domain [48213] (13)
              1. CelA cellulase [48214]
                 1. Clostridium thermocellum [TaxId: 1515] [48215] (3)
              2. Nonprocessive cellulase Cel9M [81846]
                 contains only the catalytic module, which interacts with the substrate
                 1. Clostridium cellulolyticum [TaxId: 1521] [81847] (2)
              3. Endo-1,4-beta-xylanase [89105]
                 cold-adapted family 8 xylanase
                 1. Pseudoalteromonas haloplanktis [TaxId: 228] [89106] (8)
              4. Endo/exocellulase:cellobiose E-4, N-terminal domain [48216]
                 1. Thermomonospora fusca [TaxId: 2021] [48217] (4)
                 2. Clostridium cellulolyticum, atcc 35319 [TaxId: 1521] [89107] (4)
                    endoglucanase 9G
              5. Endo-b-1,4-glucanase [81848]
                 1. Termite (Nasutitermes takasagoensis) [TaxId: 62960] [81849] (3)
              6. CelD cellulase, C-terminal domain [48218]
                 the other, N-terminal, domain is immunoglobulin-like
                 1. Clostridium thermocellum [TaxId: 1515] [48219] (1)
              7. Cellulose 1,4-beta-cellobiosidase CbhA [101363]
                 1. Clostridium thermocellum [TaxId: 1515] [101364] (2)
              8. Processive endocellulase CelF (Cel48F) [48220]
                 1. Clostridium cellulolyticum [TaxId: 1521] [48221] (9)
                 2. Clostridium thermocellum [TaxId: 1515] [74765] (2)
              9. Chitosanase [116987]
                 1. Bacillus sp., strain k17 [TaxId: 1409] [116988] (2)
                    SQ Q9ALZ1 49-434
              10. Xylanase Y [140784]
                  1. Bacillus halodurans [TaxId: 86665] [140785] (3)
                     SQ Q9KB30 6-381
              11. Probable endoglucanase CmcAX [140786]
                  1. Acetobacter xylinus [TaxId: 28448] [140787] (1)
                     SQ P37696 23-341
           3. N-acylglucosamine (NAG) epimerase [48222] (2)
              1. N-acyl-D-glucosamine 2-epimerase [48223]
                 1. Pig (Sus scrofa) [TaxId: 9823] [48224] (1)
              2. Putative NAG isomerase YihS [140788]
                 1. Salmonella typhimurium [TaxId: 90371] [140789] (6)
                    SQ Q8ZKT7 2-413
           4. Glycosyltransferase family 36 C-terminal domain [63588] (2)
              overall domain organization is similar to Bacterial glucoamylase
              1. Lactobacillus maltose phosphorylase, central domain [63589]
                 includes alpha-helical linker to the N-terminal domain and a small C-terminal beta-sandwich subdomain
                 1. Lactobacillus brevis [TaxId: 1580] [63590] (1)
              2. Chitobiose phosphorylase ChbP [109951]
                 1. Vibrio proteolyticus [TaxId: 671] [109952] (3)
                    SQ Q76IQ9
           5. Bacterial glucoamylase C-terminal domain-like [81850] (2)
              overall domain organization is similar to Lactobacillus maltose phosphorylase
              1. Bacterial glucoamylase, C-terminal domain [81851]
                 1. Thermoanaerobacterium thermosaccharolyticum [TaxId: 1517] [81852] (2)
              2. Glucodextranase, domain A [101365]
                 1. Arthrobacter globiformis [TaxId: 1665] [101366] (2)
           6. Hypothetical protein YteR [89108] (1)
              unknown function; weak sequence similarity to the catalytic domain of cellulases
              1. Hypothetical protein YteR [89109]
                 1. Bacillus subtilis [TaxId: 1423] [89110] (2)
           7. Glycosyl Hydrolase Family 88 [109953] (1)
              Pfam 07470
              1. Unsaturated glucuronyl hydrolase [109954]
                 1. Bacillus sp. GL1 [TaxId: 84635] [109955] (4)
                    SQ Q9RC92
           8. CPF0428-like [158737] (2)
              Pfam 06824; DUF1237
              1. Hypothetical protein BT3781 [158738]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [158739] (2)
                    SQ Q8A185 39-481
              2. Hypothetical protein CPF0428 [158740]
                 1. Clostridium perfringens [TaxId: 1502] [158741] (1)
                    SQ Q0TU05 2-427
           9. Trehalase-like [158742] (1)
              Pham 01204
              1. Periplasmic trehalase TreA [158743]
                 1. Escherichia coli [TaxId: 562] [158744] (2)
                    SQ P13482 37-547
        2. Seven-hairpin glycosidases [48225] (1)
           uperfamily
           1. Class I alpha-1;2-mannosidase, catalytic domain [48226] (5)
              1. Class I alpha-1;2-mannosidase, catalytic domain [48227]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48228] (2)
                 2. Trichoderma reesei [TaxId: 51453] [69087] (1)
                 3. Fungus (Penicillium citrinum) [TaxId: 5077] [69088] (7)
                 4. Human (Homo sapiens) [TaxId: 9606] [48229] (4)
                 5. Mouse (Mus musculus) [TaxId: 10090] [101367] (1)
        3. Chondroitin AC/alginate lyase [48230] (2)
           incomplete toroid
           uperfamily
           1. Alginate lyase A1-III [48231] (1)
              1. Alginate lyase A1-III [48232]
                 1. Sphingomonas sp., A1 [TaxId: 28214] [48233] (2)
           2. Hyaluronate lyase-like catalytic, N-terminal domain [48234] (6)
              1. Chondroitinase AC [48235]
                 Chondroitin AC lyase
                 1. Pedobacter heparinus (Flavobacterium heparinum) [TaxId: 984] [48236] (5)
                 2. Arthrobacter aurescens [TaxId: 43663] [101368] (6)
              2. Hyaluronate lyase [48237]
                 1. Streptococcus pneumoniae [TaxId: 1313] [48238] (19)
                    SQ Q54873 287-1007
                 2. Streptococcus agalactiae [TaxId: 1311] [69089] (3)
                    preceded by a small all-beta Ig-like domain
              3. Xanthan lyase [89111]
                 1. Bacillus sp. gl1 [TaxId: 84635] [89112] (7)
              4. Chondroitin ABC lyase I [89113]
                 domain 2; preceded by a beta-domain of the galactose-binding domain-like fold
                 1. Proteus vulgaris [TaxId: 585] [89114] (1)
        4. Family 10 polysaccharide lyase [81853] (1)
           uperfamily
           1. Family 10 polysaccharide lyase [81854] (2)
              incomplete toroid made of four hairpins
              1. Polygalacturonic acid lyase (pectate lyase) [81855]
                 1. Cellvibrio cellulosa [TaxId: 155077] [81856] (3)
                 2. Azospirillum irakense [TaxId: 34011] [109956] (1)
                    SQ Q9X592
        5. Terpenoid cyclases/Protein prenyltransferases [48239] (4)
           uperfamily
           1. Terpenoid cyclase N-terminal domain [48240] (2)
              incomplete toroid made of four hairpins
              1. 5-Epi-aristolochene synthase [48241]
                 1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [48242] (7)
              2. (+)-bornyl diphosphate synthase [81857]
                 1. Garden sage (Salvia officinalis) [TaxId: 38868] [81858] (7)
           2. Terpene synthases [48243] (2)
              consists of two toroid domains: one of six and one of five hairpins
              1. Squalene-hopene cyclase [48244]
                 1. Alicyclobacillus acidocaldarius [TaxId: 405212] [48245] (16)
              2. Lanosterol synthase [116989]
                 1. Human (Homo sapiens) [TaxId: 9606] [116990] (2)
                    SQ P48449
           3. Protein prenyltransferases [48246] (3)
              1. Protein farnesyltransferase, beta-subunit [48247]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48248] (29)
                    SQ Q02293 22-418 P53610
                 2. Human (Homo sapiens) [TaxId: 9606] [69090] (19)
                    SQ P49356
              2. Rab geranylgeranyltransferase, beta subunit [48249]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48250] (9)
           4. Complement components [48251] (3)
              probably related to other families, but has no known enzymatic activity
              1. C3D, a C3 fragment and ligand for complement receptor 2 [48252]
                 1. Human (Homo sapiens) [TaxId: 9606] [48253] (11)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [48254] (2)
              2. C4adg fragment of complement factor C4a [81859]
                 1. Human (Homo sapiens) [TaxId: 9606] [81860] (1)
        6. LanC-like [158745] (1)
           comprises seven hairpins
           1. LanC-like [158746] (1)
              Pfam 05147; there are seven internal sequence repeats
              1. Nisin biosynthesis protein NisC [158747]
                 1. Lactococcus lactis [TaxId: 1358] [158748] (2)
                    SQ Q03202 7-415
   203. Citrate synthase [48255] (1)
        multihelical; consists of two all-alpha domains
        1. Citrate synthase [48256] (1)
           uperfamily
           1. Citrate synthase [48257] (7)
              duplication: large domain consists of two structural repeats
              the second repeat is interrupted by the small domain
              1. Citrate synthase [48258]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [48259] (14)
                 2. Pig (Sus scrofa) [TaxId: 9823] [48260] (3)
                 3. Archaeon Pyrococcus furiosus [TaxId: 2261] [48261] (1)
                 4. Archaeon Sulfolobus solfataricus [TaxId: 2287] [81861] (1)
                 5. Antarctic bacterium DS2-3R [TaxId: 56673] [48262] (1)
                    Cold-active enzyme
                 6. Escherichia coli [TaxId: 562] [81862] (5)
                    SQ P00891
                 7. Thermus thermophilus [TaxId: 274] [89115] (2)
   204. Cytochrome P450 [48263] (1)
        multihelical
        1. Cytochrome P450 [48264] (1)
           uperfamily
           1. Cytochrome P450 [48265] (23)
              1. Cytochrome P450-CAM [48266]
                 1. Pseudomonas putida [TaxId: 303] [48267] (64)
                    SQ P00183
              2. Cytochrome P450 bm-3 [48268]
                 1. Bacillus megaterium [TaxId: 1404] [48269] (25)
                    SQ P14779
              3. Cytochrome P450-NOR, nitric reductase [48270]
                 1. Fungus (Fusarium oxysporum) [TaxId: 5507] [48271] (18)
                    SQ P23295
              4. Cytochrome P450-ERYF [48272]
                 1. Saccharopolyspora erythraea [TaxId: 1836] [48273] (8)
              5. Cytochrome P450epok [101369]
                 1. Sorangium cellulosum [TaxId: 56] [101370] (3)
              6. Cytochrome P450-TERP [48274]
                 1. Pseudomonas sp. [TaxId: 306] [48275] (1)
              7. Cytochrome p450 14 alpha-sterol demethylase (cyp51) [48276]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [48277] (10)
                    SQ P0A512 P77901
              8. Cytochrome p450 152a1 (Bs-beta) [89116]
                 1. Bacillus subtilis [TaxId: 1423] [89117] (1)
              9. p450 monoxygenase OxyB [81863]
                 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis
                 1. Amycolatopsis orientalis [TaxId: 31958] [81864] (3)
              10. p450 monoxygenase OxyC [101371]
                  implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis
                  1. Amycolatopsis orientalis [TaxId: 31958] [101372] (1)
              11. Cyp121 monooxygenase (P450 Mt2) [81865]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [81866] (14)
              12. Cyp154a1 monooxygenase [101373]
                  1. Streptomyces coelicolor [TaxId: 1902] [101374] (1)
              13. Cyp154c1 monooxygenase [81867]
                  functionalizes macrolide ring systems
                  1. Streptomyces coelicolor [TaxId: 1902] [81868] (1)
              14. Cyp175a1 [81869]
                  thermostable P450
                  1. Thermus thermophilus [TaxId: 274] [81870] (2)
                     SQ Q53W59
              15. Cyp119 [48278]
                  thermophilic P450
                  1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [48279] (5)
                  2. Archaeon Sulfolobus tokodaii [TaxId: 111955] [109957] (1)
                     SQ Q972I2
              16. Mammalian cytochrome p450 2c5 [48280]
                  1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [48281] (3)
              17. Mammalian cytochrome p450 2b4 [101375]
                  1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [101376] (10)
                     SQ P00178
              18. Mammalian cytochrome p450 2c8 [101377]
                  1. Human (Homo sapiens) [TaxId: 9606] [101378] (6)
              19. Mammalian cytochrome p450 2c9 [89118]
                  1. Human (Homo sapiens) [TaxId: 9606] [89119] (3)
                     SQ P11712
              20. Mammalian cytochrome P450 3a4 [109958]
                  1. Human (Homo sapiens) [TaxId: 9606] [109959] (6)
                     SQ P08684
              21. Cyp158a2 [116991]
                  1. Streptomyces coelicolor [TaxId: 1902] [116992] (1)
                     SQ Q9FCA6
              22. Vitamin D 25-hydroxylase Cyp2R1 [158749]
                  1. Human (Homo sapiens) [TaxId: 9606] [158750] (6)
                     SQ Q6VVX0 39-501
   205. Flagellar transcriptional activator FlhD [63591] (1)
        multihelical; forms intertwined dimer of identical 5-helical subunits
        1. Flagellar transcriptional activator FlhD [63592] (1)
           uperfamily
           1. Flagellar transcriptional activator FlhD [63593] (1)
              contains an HTH motif
              1. Flagellar transcriptional activator FlhD [63594]
                 1. Escherichia coli [TaxId: 562] [63595] (5)
   206. HP0242-like [158751] (1)
        multihelical; intertwined homodimer of four-helical subunits, forming catenated triangular ring-like structures; pseudo knot
        1. HP0242-like [158752] (1)
           1. HP0242-like [158753] (1)
              Pfam 09442; DUF2018
              1. Hypothetical protein HP0242 [158754]
                 1. Helicobacter pylori [TaxId: 210] [158755] (2)
                    SQ O25025 1-93! SQ O25025 13-92
   207. SMc04008-like [158756] (1)
        multihelcal; intertwined homodimer; there are 4 core helices in each subunits; contains putative metal ion-binding motif MxxxxxCxxC in the conserved surface site
        1. SMc04008-like [158757] (1)
           1. SMc04008-like [158758] (1)
              Pfam 06844; DUF1244
              1. Hypothetical protein SMc04008 [158759]
                 1. Rhizobium meliloti [TaxId: 382] [158760] (2)
                    SQ Q92M60 2-80
   208. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48299] (1)
        multihelical; intertwined tetramer
        1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48300] (1)
           uperfamily
           1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48301] (2)
              1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48302]
                 1. Thermotoga maritima [TaxId: 2336] [48303] (24)
                 2. Escherichia coli [TaxId: 562] [101379] (7)
   209. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48304] (1)
        multihelical; intertwined trimer of identical 3-helical subunits
        1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48305] (1)
           uperfamily
           1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48306] (1)
              1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48307]
                 1. Human (Homo sapiens) [TaxId: 9606] [48308] (1)
   210. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48309] (1)
        multihelical; consists of two all-alpha domains
        1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48310] (1)
           uperfamily
           1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48311] (2)
              1. Aldehyde ferredoxin oxidoreductase [48312]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [48313] (1)
              2. Formaldehyde ferredoxin oxidoreductase [48314]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [48315] (2)
   211. Acid phosphatase/Vanadium-dependent haloperoxidase [48316] (1)
        multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
        1. Acid phosphatase/Vanadium-dependent haloperoxidase [48317] (3)
           uperfamily
           1. Type 2 phosphatidic acid phosphatase, PAP2 [48318] (1)
              1. Bacterial acid phosphatase [48319]
                 1. Escherichia blattae [TaxId: 563] [48320] (3)
           2. Haloperoxidase (bromoperoxidase) [48321] (3)
              contains one core bundle; forms dimer
              1. Haloperoxidase (bromoperoxidase) [48322]
                 1. Ascophyllum nodosum [TaxId: 52969] [48323] (1)
                 2. Red algae (Corallina officinalis) [TaxId: 35170] [48324] (1)
                 3. Red algae (Corallina pilulifera) [TaxId: 78447] [101380] (1)
           3. Chloroperoxidase [48325] (1)
              duplication: contains two core bundles arranged as in the other family dimer
              1. Chloroperoxidase [48326]
                 1. Curvularia inaequalis [TaxId: 38902] [48327] (9)
   212. BRCA2 helical domain [81871] (1)
        multihelical; contains a 3-helical bundle surrounded by several shorter helices
        1. BRCA2 helical domain [81872] (1)
           uperfamily
           1. BRCA2 helical domain [81873] (2)
              1. BRCA2 helical domain [81874]
                 1. Mouse (Mus musculus) [TaxId: 10090] [81875] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [81876] (1)
   213. BRCA2 tower domain [81877] (1)
        multihelical; contains a 3-helical Hin recombinase-like subdomain and two long dimerisation helices
        1. BRCA2 tower domain [81878] (1)
           uperfamily
           1. BRCA2 tower domain [81879] (2)
              1. BRCA2 tower domain [81880]
                 1. Mouse (Mus musculus) [TaxId: 10090] [81881] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [81882] (1)
   214. H-NS histone-like proteins [81274] (1)
        multihelical oligomeric protein; structure of whole subunit is not known yet but are probably composed of three different domains
        1. H-NS histone-like proteins [81273] (1)
           available NMR structures suggest two very different dimerisation modes of the N-terminal domain
           uperfamily
           1. H-NS histone-like proteins [81272] (2)
              1. H1 protein (H-NS) [47733]
                 1. Escherichia coli [TaxId: 562] [47734] (4)
              2. H-NS-like protein VicH [101381]
                 1. Vibrio cholerae [TaxId: 666] [101382] (1)
   215. Sigma2 domain of RNA polymerase sigma factors [88945] (1)
        multihelical; consists of a conserved 4-helical core and a variable insert subdomain
        1. Sigma2 domain of RNA polymerase sigma factors [88946] (1)
           uperfamily
           1. Sigma2 domain of RNA polymerase sigma factors [88947] (6)
              1. Sigma70 [88948]
                 1. Escherichia coli [TaxId: 562] [48332] (1)
                 2. Thermus thermophilus [TaxId: 274] [88949] (16)
                    SQ Q9WX78
              2. Sigma factor SigA [88950]
                 1. Thermus aquaticus [TaxId: 271] [88951] (1)
              3. Sigma factor SigR [81883]
                 1. Streptomyces coelicolor a3(2) [TaxId: 100226] [81884] (1)
              4. SigmaE factor (RpoE) [89120]
                 1. Escherichia coli [TaxId: 562] [89121] (1)
              5. Sigma factor sigma-28 (FliA) [101383]
                 1. Aquifex aeolicus [TaxId: 63363] [101384] (2)
   216. DNA repair protein MutS, domain III [48333] (1)
        multihelical; consists of 2 all-alpha subdomains
        1. DNA repair protein MutS, domain III [48334] (1)
           uperfamily
           1. DNA repair protein MutS, domain III [48335] (2)
              1. DNA repair protein MutS, domain III [48336]
                 1. Thermus aquaticus [TaxId: 271] [48337] (4)
                 2. Escherichia coli [TaxId: 562] [48338] (10)
                    SQ P23909 2-800
   217. Helical scaffold and wing domains of SecA [81885] (1)
        multihelical; consists of 2 all-alpha subdomains
        1. Helical scaffold and wing domains of SecA [81886] (1)
           uperfamily
           1. Helical scaffold and wing domains of SecA [81887] (2)
              1. Helical scaffold and wing domains of SecA [81888]
                 1. Bacillus subtilis [TaxId: 1423] [81889] (4)
                    SQ P28366
                 2. Mycobacterium tuberculosis [TaxId: 1773] [89122] (2)
   218. all-alpha NTP pyrophosphatases [101385] (1)
        multihelical: dimeric 4-helical bundle surrounded by other helices; oligomerizes further in a tetramer
        1. all-alpha NTP pyrophosphatases [101386] (4)
           basic module consist of 5 active site-forming helices; four from one subunit/structural repeat; the fifth from the other subunit/repeat
           uperfamily
           1. MazG-like [116993] (3)
              Pfam 03819
              1. Hypothetical protein SSo12199 (SSo3215) [116994]
                 1. Sulfolobus solfataricus [TaxId: 2287] [116995] (1)
                    SQ Q97U11
              2. Hypothetical protein YpjD [140790]
                 1. Bacillus subtilis [TaxId: 1423] [140791] (1)
                    SQ P42979 1-98
              3. XTP3-transactivated gene A protein homolog RS21-C6 [140792]
                 confirmed prediction of the m5dCTPase activity
                 1. Mouse (Mus musculus) [TaxId: 10090] [140793] (5)
                    SQ Q9QY93 22-134
           2. AF0060-like [140794] (1)
              consists of a single member with an orphan sequence; "circular permutation" of putative active site residues: the catalytic lysine resides in the N-terminal helix instead of the missing in this family C-terminal helix; probable biological unit is a tertramer, distinct from the MazG family tetramer
              1. Hypothetical protein AF0060 [140795]
                 SQ O30176 1-84
                 1. Archaeoglobus fulgidus [TaxId: 2234] [140796] (1)
           3. Type II deoxyuridine triphosphatase [101387] (2)
              one subunit comprises two degenerate structural repeats, organised into the "rigid" and "mobile" subdomains
              1. Type II deoxyuridine triphosphatase [101388]
                 1. Trypanosoma cruzi [TaxId: 5693] [101389] (2)
                 2. Campylobacter jejuni [TaxId: 197] [109960] (2)
                    SQ Q9PMK9
           4. HisE-like (PRA-PH) [140797] (5)
              Pfam 01503
              1. Phosphoribosyl-ATP pyrophosphatase HisE [140798]
                 1. Streptomyces coelicolor [TaxId: 1902] [140799] (8)
                    SQ Q9EWK0 4-91
                 2. Chromobacterium violaceum [TaxId: 536] [140800] (12)
                    SQ Q7P0E6 4-94
                 3. Mycobacterium tuberculosis [TaxId: 1773] [140801] (1)
                    SQ O33257 7-93
                 4. Bacillus cereus [TaxId: 1396] [140802] (4)
                    SQ Q81G00 4-95
                 5. Mycobacterium tuberculosis H37Rv [TaxId: 83332] [158761] (4)
   219. Hsp90 co-chaperone CDC37 [101390] (1)
        multihelical; consists of 2 all-alpha subdomains connected by a long helix
        1. Hsp90 co-chaperone CDC37 [101391] (1)
           uperfamily
           1. Hsp90 co-chaperone CDC37 [101392] (1)
              1. Hsp90 co-chaperone CDC37 [101393]
                 1. Human (Homo sapiens) [TaxId: 9606] [101394] (1)
   220. Nop domain [89123] (1)
        multihelical; array of longer and shorter helices; contains an alpha-hairpin dimerisation subdomain
        1. Nop domain [89124] (1)
           uperfamily
           1. Nop domain [89125] (2)
              putative snoRNA binding domain
              1. Nop5p [89126]
                 also contains an N-terminal, fibrillarin-binding alpha+beta subdomain
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89127] (1)
                    AF2088
              2. U4/U6 small nuclear ribonucleoprotein Prp31 [158762]
                 contains insertion of a small 4-helical bundle at the tip of a long alpha-hairpin arm; this insertion approximately corresponds to the NOSIC (NUC001) domain; Pfam o8060
                 1. Human (Homo sapiens) [TaxId: 9606] [158763] (2)
                    SQ Q8WWY3 85-333
   221. YidB-like [140803] (1)
        multihelical; three strings of short helices are packed across one longer helix
        1. YidB-like [140804] (1)
           uperfamily
           1. YidB-like [140805] (1)
              Pfam 06078; DUF937
              1. Hypothetical protein YidB [140806]
                 1. Shigella flexneri [TaxId: 623] [140807] (1)
                    SQ Q83IZ7 3-131
                    SF3766, S4005
   222. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48339] (1)
        multihelical; bundle of longer and shorter helices
        1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48340] (1)
           uperfamily
           1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48341] (1)
              1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48342]
                 1. Human (Homo sapiens) [TaxId: 9606] [48343] (2)
   223. A virus capsid protein alpha-helical domain [48344] (1)
        multihelical; three-helical bundle in the core is surrounded by non-conserved helices
        1. A virus capsid protein alpha-helical domain [48345] (3)
           this domain is interrupted by a jelly-roll beta-sandwich domain
           uperfamily
           1. Orbivirus capsid [48346] (1)
              1. BTV vp7 [48347]
                 1. Bluetongue virus [TaxId: 40051] [48348] (2)
           2. Phytoreovirus capsid [101395] (1)
              1. RDV p8 [101396]
                 1. Rice dwarf virus [TaxId: 10991] [101397] (1)
           3. vp6, the major capsid protein of group A rotavirus [63596] (1)
              1. vp6, the major capsid protein of group A rotavirus [63597]
                 1. Bovine rotavirus [TaxId: 10927] [63598] (1)
   224. P40 nucleoprotein [101398] (1)
        multihelical; consists of two subdomains
        1. P40 nucleoprotein [101399] (1)
           uperfamily
           1. P40 nucleoprotein [101400] (1)
              1. P40 nucleoprotein [101401]
                 1. Borna disease virus [TaxId: 12455] [101402] (2)
   225. Rhabdovirus nucleoprotein-like [140808] (1)
        multihelical, consist of two helical domains; each domain contains a buried helix
        1. Rhabdovirus nucleoprotein-like [140809] (1)
           uperfamily
           1. Rhabdovirus nucleocapsid protein [140810] (2)
              Pfam 00945; RNA-binding homooligomeric protein
              1. Nucleoprotein [140811]
                 1. Rabies virus [TaxId: 11292] [140812] (22)
                    SQ Q7TBN9 6-448
                 2. Vesicular stomatitis indiana virus [TaxId: 11277] [140813] (5)
                    SQ P03521 2-422
   226. GTPase activation domain, GAP [48349] (1)
        multihelical
        1. GTPase activation domain, GAP [48350] (2)
           uperfamily
           1. BCR-homology GTPase activation domain (BH-domain) [48351] (5)
              Pfam 00620
              1. p50 RhoGAP domain [48352]
                 1. Human (Homo sapiens) [TaxId: 9606] [48353] (4)
              2. p85 alpha subunit RhoGAP domain [48354]
                 1. Human (Homo sapiens) [TaxId: 9606] [48355] (1)
              3. Cdc42GAP [48356]
                 1. Human (Homo sapiens) [TaxId: 9606] [48357] (2)
              4. Graf [48358]
                 GTPase regulator associated with focal adhesion kinase
                 1. Chicken (Gallus gallus) [TaxId: 9031] [48359] (1)
              5. Beta-chimaerin, C-terminal domain [116996]
                 1. Human (Homo sapiens) [TaxId: 9606] [116997] (1)
                    SQ P52757 23-468
           2. p120GAP domain-like [48360] (2)
              1. p120GAP domain [48361]
                 1. Human (Homo sapiens) [TaxId: 9606] [48362] (2)
              2. GAP related domain of neurofibromin [48363]
                 1. Human (Homo sapiens) [TaxId: 9606] [48364] (1)
   227. Ras GEF [48365] (1)
        multihelical
        1. Ras GEF [48366] (1)
           uperfamily
           1. Ras GEF [48367] (1)
              1. Son of sevenless protein homolog 1 (sos-1) [48368]
                 1. Human (Homo sapiens) [TaxId: 9606] [48369] (9)
                    SQ Q07889 189-1046
   228. Telomeric repeat binding factor (TRF) dimerisation domain [63599] (1)
        multihelical; can be divided into an alpha-alpha superhelix domain and a long alpha-hairpin dimerization domain
        1. Telomeric repeat binding factor (TRF) dimerisation domain [63600] (1)
           uperfamily
           1. Telomeric repeat binding factor (TRF) dimerisation domain [63601] (2)
              1. TRF1 [63602]
                 1. Human (Homo sapiens) [TaxId: 9606] [63603] (2)
              2. TRF2 [63604]
                 1. Human (Homo sapiens) [TaxId: 9606] [63605] (7)
   229. Poly A polymerase C-terminal region-like [81890] (1)
        multihelical; can be divided into three subdomains (neck, body and tail)
        1. Poly A polymerase C-terminal region-like [81891] (1)
           the neck subdomain is an alpha-alpha superhelix; the tail subdomain is similar to the RuvA C-terminal domain-like
           uperfamily
           1. Poly A polymerase C-terminal region-like [81892] (3)
              the 'neck' domain corresponds to the C-terminal part of Pfam 01743
              1. tRNA CCA-adding enzyme, C-terminal domains [81893]
                 1. Bacillus stearothermophilus [TaxId: 1422] [81894] (3)
                 2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [89128] (1)
              2. Poly A polymerase PcnB [109961]
                 1. Aquifex aeolicus [TaxId: 63363] [109962] (1)
                    SQ O66728 443-824
   230. alpha-alpha superhelix [48370] (24)
        multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
        1. ARM repeat [48371] (23)
           uperfamily
           1. Armadillo repeat [48372] (9)
              1. beta-Catenin [48373]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48374] (6)
                 2. Human (Homo sapiens) [TaxId: 9606] [48375] (10)
                    SQ P35222 145-664
              2. Importin alpha [48376]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48377] (8)
              3. Importin beta [48378]
                 1. Human (Homo sapiens) [TaxId: 9606] [48379] (11)
                 2. Mouse (Mus musculus) [TaxId: 10090] [48380] (1)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140814] (5)
                    SQ Q06142 1-861
              4. Karyopherin beta2 [48381]
                 1. Human (Homo sapiens) [TaxId: 9606] [48382] (1)
              5. Karyopherin alpha [48383]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48384] (8)
                    SQ Q02821 12-514
              6. Exportin Cse1p [116998]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116999] (3)
                    SQ P33307
           2. Clathrin adaptor core protein [74771] (2)
              1. Adaptin alpha C subunit N-terminal fragment [74772]
                 1. Mouse (Mus musculus) [TaxId: 10090] [74773] (1)
              2. Adaptin beta subunit N-terminal fragment [74774]
                 1. Human (Homo sapiens) [TaxId: 9606] [74775] (1)
           3. HEAT repeat [48385] (2)
              Pfam 02985
              1. Constant regulatory domain of protein phosphatase 2a, pr65alpha [48386]
                 1. Human (Homo sapiens) [TaxId: 9606] [48387] (13)
              2. Cullin-associated NEDD8-dissociated protein 1 (Tip120) [117000]
                 1. Human (Homo sapiens) [TaxId: 9606] [117001] (1)
                    SQ Q86VP6 4-1210
           4. MIF4G domain-like [100908] (5)
              duplication: family members contains 2 or more structurally similar domains of this fold connected by unstructured linkers
              1. Eukaryotic initiation factor eIF4G [48388]
                 1. Human (Homo sapiens) [TaxId: 9606] [48389] (5)
              2. Translation initiation factor eIF-2b epsilon [101403]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101404] (1)
              3. Regulator of nonsense transcripts 2, UPF2 [101405]
                 1. Human (Homo sapiens) [TaxId: 9606] [101406] (1)
              4. CBP80, 80KDa nuclear cap-binding protein [63606]
                 contains three domains of this fold connected with long linkers
                 1. Human (Homo sapiens) [TaxId: 9606] [63607] (6)
              5. Programmed cell death 4, PDCD4 [140815]
                 1. Mouse (Mus musculus) [TaxId: 10090] [140816] (5)
                    SQ Q61823 322-448! SQ Q61823 322-450
           5. PHAT domain [89129] (1)
              pseudo-HEAT repeat
              1. RNA-binding protein Smaug [89130]
                 1. Drosophila melanogaster [TaxId: 7227] [89131] (1)
           6. Mo25 protein [101407] (1)
              1. Mo25 protein [101408]
                 1. Human (Homo sapiens) [TaxId: 9606] [101409] (2)
           7. Leukotriene A4 hydrolase C-terminal domain [63608] (1)
              1. Leukotriene A4 hydrolase C-terminal domain [63609]
                 1. Human (Homo sapiens) [TaxId: 9606] [63610] (15)
                    SQ P09960
           8. Clathrin heavy chain proximal leg segment [48390] (1)
              1. Clathrin heavy chain proximal leg segment [48391]
                 1. Cow (Bos taurus) [TaxId: 9913] [48392] (1)
           9. Clathrin heavy-chain linker domain [48393] (1)
              1. Clathrin heavy-chain linker domain [48394]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48395] (4)
           10. Leucine-rich repeat variant [48396] (1)
               1. Leucine-rich repeat variant [48397]
                  contains a FeS4 centre
                  1. Azotobacter vinelandii [TaxId: 354] [48398] (1)
           11. Phoshoinositide 3-kinase (PI3K) helical domain [48399] (2)
               1. Phoshoinositide 3-kinase (PI3K) helical domain [48400]
                  1. Pig (Sus scrofa) [TaxId: 9823] [48401] (5)
                  2. Human (Homo sapiens) [TaxId: 9606] [48402] (3)
           12. Pumilio repeat [63611] (1)
               1. Pumilio 1 [63612]
                  1. Human (Homo sapiens) [TaxId: 9606] [63613] (9)
           13. Regulatory subunit H of the V-type ATPase [63614] (1)
               1. Regulatory subunit H of the V-type ATPase [63615]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63616] (1)
           14. PBS lyase HEAT-like repeat [101410] (2)
               Pfam 03130
               1. Hypothetical protein YibA [101411]
                  1. Escherichia coli [TaxId: 562] [101412] (1)
               2. MTH187 [109963]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [109964] (1)
                     SQ O26289
           15. BC3264-like [109965] (2)
               Pfam 06352; DUF1061
               1. Hypothetical protein BC3264 [109966]
                  1. Bacillus cereus (strain ATCC 14579 / DSM 31) [TaxId: 226900] [109967] (1)
                     SQ Q81BA8
               2. Hypothetical protein EF3068 [140817]
                  assigned by a closer overall structural similarity to BC3264; predicted DNA alkylation repair enzyme
                  1. Enterococcus faecalis [TaxId: 1351] [140818] (2)
                     SQ Q82ZI8 3-215
           16. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain [109968] (1)
               N-terminal part of Pfam 06272
               1. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain [109969]
                  1. Human (Homo sapiens) [TaxId: 9606] [109970] (1)
                     SQ Q9UBQ5
           17. Exportin HEAT-like repeat [117002] (1)
               1. Exportin-1 (Xpo1, Crm1) [117003]
                  1. Human (Homo sapiens) [TaxId: 9606] [117004] (1)
                     SQ O14980 707-1027
           18. B56-like [140819] (1)
               Pfam 01603; Protein phosphatase 2A regulatory B subunit family
               1. Serine/threonine-protein phosphatase 2A regulatory subunit B56-gamma [140820]
                  1. Human (Homo sapiens) [TaxId: 9606] [140821] (7)
                     SQ Q13362 30-372! SQ Q13362 38-425
           19. HspBP1 domain [140822] (1)
               1. Hsp70-binding protein 1 (HspBP1) [140823]
                  1. Human (Homo sapiens) [TaxId: 9606] [140824] (4)
                     SQ Q9NZL4 87-350
           20. GUN4-associated domain [140825] (2)
               PfamB 089177
               1. Mg-chelatase cofactor Gun4 [140826]
                  Ycf53-like protein sll0558
                  1. Synechocystis sp. pcc 6803 [TaxId: 1148] [140827] (1)
                     SQ P72583 1-82
               2. GUN4-like protein Ycf53, N-terminal domain [140828]
                  1. Thermosynechococcus elongatus [TaxId: 146786] [140829] (2)
                     SQ Q8DIJ1 1-87
           21. Diap1 N-terninal region-like [140830] (1)
               contains two consequitive Pfam domains in one superhelical segment: Pfam 06371 and Pfam 06367
               1. Diaphanous protein homolog 1, Diap1 (Dia1, DRF1) [140831]
                  1. Mouse (Mus musculus) [TaxId: 10090] [140832] (6)
                     SQ O08808 133-475! SQ O08808 135-435! SQ O08808 83-443
           22. Plakophilin 1 helical region [140833] (1)
               1. Plakophilin 1 [140834]
                  1. Human (Homo sapiens) [TaxId: 9606] [140835] (1)
                     SQ Q13835 244-721
           23. RPA1889-like [158764] (1)
               Pfam 09450; DUF2019; similar to the BC3264-like family
               1. Hypothetical protein RPA1889 [158765]
                  1. Rhodopseudomonas palustris [TaxId: 1076] [158766] (1)
                     SQ Q6N8L4 3-123
        2. IP3 receptor type 1 binding core, domain 2 [100909] (1)
           uperfamily
           1. IP3 receptor type 1 binding core, domain 2 [81895] (1)
              1. IP3 receptor type 1 binding core, domain 2 [81896]
                 1. Mouse (Mus musculus) [TaxId: 10090] [81897] (1)
        3. Chemosensory protein Csp2 [100910] (1)
           uperfamily
           1. Chemosensory protein Csp2 [81898] (1)
              1. Chemosensory protein Csp2 [81899]
                 1. Cabbage moth (Mamestra brassicae) [TaxId: 55057] [81900] (5)
        4. Sec7 domain [48425] (1)
           uperfamily
           1. Sec7 domain [48426] (6)
              Pfam 01369
              1. Exchange factor ARNO [48427]
                 1. Human (Homo sapiens) [TaxId: 9606] [48428] (5)
              2. Cytohesin-1/b2-1 [48429]
                 1. Human (Homo sapiens) [TaxId: 9606] [48430] (1)
                 2. Mus musculus [TaxId: 10090] [158767] (4)
              3. ARF guanine-exchange factor 1 [101413]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101414] (1)
              4. ARF guanine-exchange factor 2, Gea2 [74776]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74777] (1)
              5. RalF, N-terminal domain [117005]
                 1. Legionella pneumophila [TaxId: 446] [117006] (2)
                    SQ Q8RT31 2-353
        5. Lipovitellin-phosvitin complex, superhelical domain [48431] (1)
           uperfamily
           1. Lipovitellin-phosvitin complex, superhelical domain [48432] (1)
              1. Lipovitellin-phosvitin complex, superhelical domain [48433]
                 1. Lamprey (Ichthyomyzon unicuspis) [TaxId: 30308] [48434] (1)
        6. Bacterial muramidases [48435] (1)
           uperfamily
           1. Bacterial muramidases [48436] (1)
              1. 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain [48437]
                 1. Escherichia coli [TaxId: 562] [48438] (3)
        7. Aconitase B, N-terminal domain [74778] (1)
           uperfamily
           1. Aconitase B, N-terminal domain [74779] (1)
              1. Aconitase B, N-terminal domain [74780]
                 1. Escherichia coli [TaxId: 562] [74781] (1)
        8. HCP-like [81901] (1)
           uperfamily
           1. HCP-like [81902] (2)
              Helicobacter Cysteine-rich Protein
              1. Cysteine rich protein B (HcpB) [81903]
                 a penicillin-binding protein
                 1. Helicobacter pylori [TaxId: 210] [81904] (1)
              2. Cysteine rich protein C (HcpC) [101415]
                 1. Helicobacter pylori [TaxId: 210] [101416] (1)
        9. Protein prenylyltransferase [48439] (1)
           uperfamily
           1. Protein prenylyltransferase [48440] (3)
              1. Protein farnesyltransferase alpha-subunit [48441]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48442] (29)
                    SQ Q04631 55-369
                 2. Human (Homo sapiens) [TaxId: 9606] [69093] (20)
                    SQ P49354
              2. Rab geranylgeranyltransferase alpha-subunit, N-terminal domain [48443]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48444] (2)
        10. 14-3-3 protein [48445] (1)
            uperfamily
            1. 14-3-3 protein [48446] (5)
               1. zeta isoform [48449]
                  1. Cow (Bos taurus) [TaxId: 9913] [48450] (9)
                  2. Human (Homo sapiens) [TaxId: 9606] [48451] (7)
               2. 14-3-3-like protein C [89132]
                  1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [89133] (6)
               3. 14-3-3 domain containing protein cgd7_2470 [158768]
                  1. Cryptosporidium parvum [TaxId: 5807] [158769] (1)
                     SQ Q5CYG0 8-227
               4. 14-3-3 protein cgd1_2980 [158770]
                  1. Cryptosporidium parvum [TaxId: 5807] [158771] (2)
                     SQ Q5CSF3 25-247
        11. TPR-like [48452] (8)
            uperfamily
            1. Tetratricopeptide repeat (TPR) [48453] (20)
               1. Protein phosphatase 5 [48454]
                  1. Human (Homo sapiens) [TaxId: 9606] [48455] (6)
               2. Hop [48456]
                  1. Human (Homo sapiens) [TaxId: 9606] [48457] (2)
               3. Vesicular transport protein sec17 [48458]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48459] (1)
               4. Neutrophil cytosolic factor 2 (NCF-2, p67-phox) [48460]
                  1. Human (Homo sapiens) [TaxId: 9606] [48461] (3)
               5. Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) [48462]
                  1. Human (Homo sapiens) [TaxId: 9606] [48463] (6)
                  2. Trypanosoma brucei [TaxId: 5691] [63617] (1)
               6. Cyclophilin 40 [63618]
                  1. Cow (Bos taurus) [TaxId: 9913] [63619] (2)
               7. FKBP51, C-terminal domain [81905]
                  1. Human (Homo sapiens) [TaxId: 9606] [81906] (1)
                  2. Monkey (Saimiri boliviensis) [TaxId: 27679] [81907] (1)
               8. Hypothetical protein RSGI Ruh-001 [81908]
                  a Fis1p-like and Cgi-135 homologous domain
                  1. Mouse (Mus musculus) [TaxId: 10090] [81909] (1)
               9. Mitochondria fission protein Fis1 [101417]
                  1. Human (Homo sapiens) [TaxId: 9606] [101418] (2)
                  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140836] (3)
                     SQ P40515 1-138
               10. FKBP52 (FKBP4), C-terminal domain [109971]
                   1. Human (Homo sapiens) [TaxId: 9606] [109972] (2)
                      SQ Q02790 145-427
               11. O-GlcNAc transferase p110 subunit, OGT [109973]
                   1. Human (Homo sapiens) [TaxId: 9606] [109974] (1)
                      SQ O15294 16-400
               12. Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 [117007]
                   1. Human (Homo sapiens) [TaxId: 9606] [117008] (1)
                      SQ P13674 161-254
               13. Lipoprotein NlpI [117009]
                   1. Escherichia coli [TaxId: 562] [117010] (1)
                      SQ P39833 26-294
               14. STIP1 homology and U box-containing protein 1, STUB1 [140837]
                   1. Mouse (Mus musculus) [TaxId: 10090] [140838] (4)
                      SQ Q9WUD1 24-224
               15. Mitochondrial import receptor subunit tom20-3 [140839]
                   1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [140840] (1)
                      SQ P82874 1-145
               16. Putative 70 kda peptidylprolyl isomerase PFL2275c [140841]
                   1. Plasmodium falciparum [TaxId: 5833] [140842] (2)
                      SQ Q8I4V8 128-280
               17. SMG-7 [140843]
                   1. Human (Homo sapiens) [TaxId: 9606] [140844] (2)
                      SQ Q92540 1-497
            2. Transcription factor MalT domain III [69094] (1)
               1. Transcription factor MalT domain III [69095]
                  1. Escherichia coli [TaxId: 562] [69096] (1)
            3. BTAD-like [140845] (1)
               Pfam 03704; Bacterial transcriptional activator domain
               1. Probable regulatory protein EmbR, middle domain [140846]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [140847] (3)
                     SQ P66799 105-283
            4. PrgX C-terminal domain-like [140848] (1)
               1. PrgX [140849]
                  1. Enterococcus faecalis [TaxId: 1351] [140850] (40)
                     SQ Q04114 70-287! SQ Q04114 71-301
            5. Atu0120-like [158772] (1)
               Pfam 06041; DUF924
               1. Hypothetical protein Atu0120 [158773]
                  1. Agrobacterium tumefaciens [TaxId: 358] [158774] (2)
                     SQ Q8UJ18 1-179
            6. SusD-like [158775] (3)
               TPR-like structure resides in the N-terminal part; the C-terminal part is structurally unique and is covered by Pfam 07980
               1. Uncharacterized protein BT3984 [158776]
                  1. Bacteroides thetaiotaomicron [TaxId: 818] [158777] (1)
                     SQ Q8A0N7 31-537
               2. Uncharacterized protein BF3025 [158778]
                  1. Bacteroides fragilis [TaxId: 817] [158779] (1)
                     SQ Q5LB02 32-490
               3. Starch utilization system protein SusD [158780]
                  1. Bacteroides thetaiotaomicron [TaxId: 818] [158781] (12)
                     SQ Q8A1G2 42-551
            7. HAT/Suf repeat [158782] (1)
               includes Pfam 05843
               1. Cleavage stimulation factor 77 kDa subunit CSTF3 [158783]
                  1. Mouse (Mus musculus) [TaxId: 10090] [158784] (3)
                     SQ Q99LI7 21-549! SQ Q99LI7 242-549
            8. CT2138-like [158785] (1)
               probable biological unit is a homohexamer
               1. Hypothetical protein CT2138 [158786]
                  1. Chlorobium tepidum [TaxId: 1097] [158787] (6)
                     SQ Q8KAL8 2-157
        12. ENTH/VHS domain [48464] (4)
            uperfamily
            1. ENTH domain [48465] (2)
               1. Epsin 1 [48466]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [48467] (3)
                  2. Human (Homo sapiens) [TaxId: 9606] [63620] (1)
            2. VHS domain [48468] (5)
               1. Hrs [48469]
                  protein involved in membrane trafficking and signal transduction
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [48470] (1)
               2. Tom1 protein [48471]
                  1. Human (Homo sapiens) [TaxId: 9606] [48472] (1)
               3. ADP-ribosylation factor binding protein Gga1 [74782]
                  1. Human (Homo sapiens) [TaxId: 9606] [74783] (5)
               4. ADP-ribosylation factor binding protein Gga2 [89134]
                  1. Human (Homo sapiens) [TaxId: 9606] [89135] (1)
               5. ADP-ribosylation factor binding protein Gga3 [69097]
                  1. Human (Homo sapiens) [TaxId: 9606] [69098] (3)
            3. Phosphoinositide-binding clathrin adaptor, N-terminal domain [100911] (2)
               1. Clathrin assembly lymphoid myeloid leukaemia protein, Calm [100912]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [100913] (4)
               2. AP180 (Lap) [100914]
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [100915] (1)
            4. RPR domain (SMART 00582 ) [109975] (1)
               found in proteins involved in regulation of nuclear pre-mRNA; some sequence similarity to VHS domain
               1. PCF11 protein [109976]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109977] (3)
                     SQ P39081 1-140
        13. Translin [74784] (1)
            uperfamily
            1. Translin [74785] (2)
               1. Translin [74786]
                  synonym: testis/brain RNA-binding protein, TB-RBP
                  1. Mouse (Mus musculus) [TaxId: 10090] [74787] (1)
                  2. Human (Homo sapiens) [TaxId: 9606] [101419] (1)
        14. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69099] (1)
            uperfamily
            1. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69100] (2)
               1. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69101]
                  1. Mouse (Mus musculus) [TaxId: 10090] [69102] (1)
                  2. Human (Homo sapiens) [TaxId: 9606] [158788] (9)
                     SQ P46060 431-587! SQ P46060 432-587
        15. Arp2/3 complex 16 kDa subunit ARPC5 [69103] (1)
            uperfamily
            1. Arp2/3 complex 16 kDa subunit ARPC5 [69104] (1)
               1. Arp2/3 complex 16 kDa subunit ARPC5 [69105]
                  1. Cow (Bos taurus) [TaxId: 9913] [69106] (10)
                     SQ Q9CPW4 # 99% sequence identity
        16. FliG [48029] (1)
            fragmented superhelix; consist of 3/4-helical motifs and connecting helices
            uperfamily
            1. FliG [48030] (1)
               1. FliG [48031]
                  1. Thermotoga maritima [TaxId: 2336] [48032] (2)
        17. Cullin repeat-like [74788] (2)
            uperfamily
            1. Cullin repeat [74789] (2)
               1. Cullin homolog 1, Cul-1 [74790]
                  1. Human (Homo sapiens) [TaxId: 9606] [74791] (3)
                     SQ Q13616 17-776
               2. Cullin-4A [158789]
                  1. Human (Homo sapiens) [TaxId: 9606] [158790] (1)
                     SQ Q13619 55-401
            2. Exocyst complex component [140851] (2)
               includes Pfam 03081
               1. Exocyst complex component EXO84 [140852]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140853] (1)
                     SQ P38261 525-753
               2. Exocyst complex component EXO70 [140854]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140855] (1)
                     SQ P19658 73-623
        18. C-terminal domain of Ku80 [101420] (1)
            uperfamily
            1. C-terminal domain of Ku80 [101421] (1)
               1. C-terminal domain of Ku80 [101422]
                  1. Human (Homo sapiens) [TaxId: 9606] [101423] (2)
        19. Hypothetical protein ST1625 [101424] (1)
            uperfamily
            1. Hypothetical protein ST1625 [101425] (1)
               1. Hypothetical protein ST1625 [101426]
                  1. Archaeon Sulfolobus tokodaii [TaxId: 111955] [101427] (1)
                     structural genomics
        20. Cytochrome c oxidase subunit E [48479] (1)
            uperfamily
            1. Cytochrome c oxidase subunit E [48480] (1)
               1. Cytochrome c oxidase subunit E [48481]
                  1. Cow (Bos taurus) [TaxId: 9913] [48482] (21)
        21. USP8 N-terminal domain-like [140856] (1)
            uperfamily
            1. USP8 N-terminal domain-like [140857] (1)
               PfamB 029795
               1. Ubiquitin carboxyl-terminal hydrolase 8, USH8 [140858]
                  1. Human (Homo sapiens) [TaxId: 9606] [140859] (2)
                     SQ P40818 6-139
        22. Pseudo ankyrin repeat-like [140860] (1)
            contains three helices per turn of the superhelix
            uperfamily
            1. Pseudo ankyrin repeat [140861] (1)
               one repeat consist of 3 helices; there are similarities in the repeat sequence and assembly with the ankyrin repeat (scop_fa 48404)
               1. Hypothetical protein LPG2416 [140862]
                  there are regular repeats in the middle part and iess regular superhelical turns at both ends
                  1. Legionella pneumophila [TaxId: 446] [140863] (2)
                     SQ Q5ZSV0 3-348
        23. TROVE domain-like [140864] (1)
            consist of two superhelical sections arranged like a horse-shoe
            uperfamily
            1. TROVE domain-like [140865] (1)
               Pfam 05731
               1. 60-kda SS-aARo ribonucleoprotein [140866]
                  1. African clawed frog (Xenopus laevis) [TaxId: 8355] [140867] (5)
                     SQ P42700 5-363
        24. MgtE N-terminal domain-like [158791] (1)
            made of short helices; approximately 2.5 helices per turn of superhelix
            1. MgtE N-terminal domain-like [158792] (2)
               Pfam 03448
               1. Magnesium transporter MgtE [158793]
                  1. Enterococcus faecalis [TaxId: 1351] [158794] (1)
                     SQ Q830V1 6-135
                  2. Thermus thermophilus [TaxId: 274] [158795] (4)
                     SQ Q5SMG8 7-131
   231. GUN4-like [140868] (1)
        multihelical; open array, trapping inside an extended region before the C-terminal helix
        1. GUN4-like [140869] (1)
           uperfamily
           1. GUN4-like [140870] (2)
              Pfam 05419
              1. Mg-chelatase cofactor Gun4 [140871]
                 Ycf53-like protein sll0558
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [140872] (1)
                    SQ P72583 83-233
              2. GUN4-like protein Ycf53 [140873]
                 1. Thermosynechococcus elongatus [TaxId: 146786] [140874] (2)
                    SQ Q8DIJ1 88-235
   232. Lipoxigenase [48483] (1)
        multihelical
        large nearly all-alpha domain
        1. Lipoxigenase [48484] (2)
           uperfamily
           1. Plant lipoxigenases [48485] (2)
              1. Lipoxigenase, C-terminal domain [48486]
                 N-terminal domain is beta-sandwich similar to colipase-binding domain of pancreatic lipase
                 contains alpha plus beta subdomain: res. 341-495; alpha-beta(5)-alpha
                 1. Soybean (Glycine max), isozyme L1 [TaxId: 3847] [48487] (14)
                 2. Soybean (Glycine max), isozyme L3 [TaxId: 3847] [48488] (9)
                    SQ P09186
           2. Animal lipoxigenases [48489] (1)
              1. 15-Lipoxygenase [48490]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [48491] (3)
   233. gene 59 helicase assembly protein [48492] (1)
        multihelical; consists of two all-alpha subdomains
        1. gene 59 helicase assembly protein [48493] (1)
           uperfamily
           1. gene 59 helicase assembly protein [48494] (1)
              1. gene 59 helicase assembly protein [48495]
                 1. Bacteriophage T4 [TaxId: 10665] [48496] (1)
   234. Tetracyclin repressor-like, C-terminal domain [48497] (1)
        multihelical; interlocked (homo)dimer
        1. Tetracyclin repressor-like, C-terminal domain [48498] (1)
           uperfamily
           1. Tetracyclin repressor-like, C-terminal domain [48499] (34)
              1. Tetracyclin repressor (Tet-repressor, TetR) [48500]
                 1. Escherichia coli [TaxId: 562] [48501] (13)
              2. Multidrug binding protein QacR [69107]
                 1. Staphylococcus aureus [TaxId: 1280] [69108] (47)
                    SQ P23217
              3. Hypothetical transcriptional regulator YcdC [89136]
                 1. Escherichia coli [TaxId: 562] [89137] (1)
              4. Hypothetical transcriptional regulator YsiA [101428]
                 1. Bacillus subtilis [TaxId: 1423] [101429] (1)
              5. Hypothetical transcriptional regulator YfiR [101430]
                 1. Bacillus subtilis [TaxId: 1423] [101431] (1)
              6. Ethr repressor [109978]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [109979] (3)
                    SQ P96222 22-215
              7. A-factor receptor homolog CprB [109980]
                 gamma-butyrolactone receptor
                 1. Streptomyces coelicolor [TaxId: 1902] [109981] (2)
                    SQ O66122
              8. Putative transcriptional repressor YbiH [109982]
                 1. Salmonella typhimurium [TaxId: 90371] [109983] (1)
                    SQ Q8ZQN9
              9. Putative transcriptional regulator YxaF [109984]
                 1. Bacillus subtilis [TaxId: 1423] [109985] (1)
                    SQ P42105
              10. Putative transcriptional regulator SCO5951 [140875]
                  1. Streptomyces coelicolor [TaxId: 1902] [140876] (2)
                     SQ O54180 81-203
              11. Transcriptional regulator TM1030 [140877]
                  1. Thermotoga maritima [TaxId: 2336] [140878] (5)
                     SQ Q9X0C0 76-200
              12. Putative transcriptional regulator RHA1_ro09068 [140879]
                  1. Rhodococcus sp. [TaxId: 1831] [140880] (2)
                     SQ Q0RX74 79-194
              13. Probable transcriptional regulator PA1836 [140881]
                  1. Pseudomonas aeruginosa [TaxId: 287] [140882] (1)
                     SQ Q9I2Q9 76-193
              14. Putative regulator SCO4008 [140883]
                  1. Streptomyces coelicolor [TaxId: 1902] [140884] (2)
                     SQ Q9ADP7 75-192
              15. Putative transcriptional regulator SCO7704 [140885]
                  1. Streptomyces coelicolor [TaxId: 1902] [140886] (1)
                     SQ Q93JG8 87-230
              16. Putative transcriptional regulator SCO0857 [140887]
                  1. Streptomyces coelicolor [TaxId: 1902] [140888] (2)
                     SQ Q9RCV4 100-211
              17. Hemolysin II regulatory protein, HlyIIR [140889]
                  1. Bacillus cereus [TaxId: 1396] [140890] (1)
                     SQ Q7X506 77-198
              18. Transcriptional regulator BC5000 [140891]
                  1. Bacillus cereus [TaxId: 1396] [140892] (2)
                     SQ Q815X4 78-182
              19. Probable transcriptional regulator PA3133 [140893]
                  1. Pseudomonas aeruginosa [TaxId: 287] [140894] (1)
                     SQ Q9HZ91 77-180
              20. Transcriptional regulator Cgl2612 [140895]
                  1. Corynebacterium glutamicum [TaxId: 1718] [140896] (4)
                     SQ Q8NMG3 75-175
              21. Transcriptional regulator EF0787 [140897]
                  1. Enterococcus faecalis [TaxId: 1351] [140898] (2)
                     SQ Q837P6 72-220
              22. Probable transcriptional regulator RHA1_ro04631 [140899]
                  1. Rhodococcus sp. rha1 [TaxId: 101510] [140900] (2)
                     SQ Q0S7R9 81-199
              23. Transcriptional regulator PsrA [140901]
                  1. Pseudomonas aeruginosa [TaxId: 287] [140902] (1)
                     SQ Q9HZJ9 81-214
              24. Putative transcriptional regulator Rha04620 [140903]
                  1. Rhodococcus sp. rha1 [TaxId: 101510] [140904] (1)
              25. Transcriptional regulator RHA1_ro04179 [140905]
                  1. Rhodococcus sp. [TaxId: 1831] [140906] (4)
                     SQ Q0S914 9-195
              26. Transcriptional regulator BC3163 [140907]
                  1. Bacillus cereus [TaxId: 1396] [140908] (1)
                     SQ Q81BJ4 78-192
              27. Putative transcriptional regulator [140909]
                  1. Rhodococcus sp. rha1 [TaxId: 101510] [140910] (2)
              28. Putative transcriptional regulator Atu0279 [140911]
                  1. Agrobacterium tumefaciens [TaxId: 358] [140912] (1)
                     SQ Q8UIL4 77-192
              29. Putative transcriptional regulator SCO4850 [158796]
                  1. Streptomyces coelicolor [TaxId: 1902] [158797] (1)
                     SQ Q9KZ96 90-235
              30. Putative transcriptional regulator SCO4940 [158798]
                  1. Streptomyces coelicolor [TaxId: 1902] [158799] (1)
                     SQ Q8CJS4 83-200
              31. Putative regulatory protein Sco4313 [158800]
                  1. Streptomyces coelicolor [TaxId: 1902] [158801] (1)
                     SQ Q9KXS8 87-216
              32. Transcriptional regulator Cgl1640/Cg1846 [158802]
                  1. Corynebacterium glutamicum [TaxId: 1718] [158803] (1)
                     SQ Q8NQ14 79-188
              33. Transcriptional activator DhaS [158804]
                  1. Lactococcus lactis [TaxId: 1358] [158805] (2)
                     SQ Q9CIV9 79-187
              34. Putative transcriptional regulator RHA1_ro03468 [158806]
                  1. Rhodococcus sp. RHA1 [TaxId: 101510] [158807] (2)
                     SQ Q0SB15 88-208
   235. Skp1 dimerisation domain-like [81384] (1)
        multihelical; interlocked heterodimer with F-box proteins
        1. Skp1 dimerisation domain-like [81382] (1)
           uperfamily
           1. Skp1 dimerisation domain-like [81380] (2)
              1. Cyclin A/CDK2-associated p45, Skp1 [81378]
                 1. Human (Homo sapiens) [TaxId: 9606] [81376] (8)
              2. Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D [81910]
                 Suppressor of kinetochore protein 1,Scskp1
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81911] (1)
   236. F-box domain [81385] (1)
        multihelical; interlocked heterodimer with the Skp1 dimerisation domain
        1. F-box domain [81383] (1)
           uperfamily
           1. F-box domain [81381] (4)
              1. Skp2 [81379]
                 1. Human (Homo sapiens) [TaxId: 9606] [81377] (6)
              2. Cdc4 F-box and linker domains [81912]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81913] (1)
              3. F-box/WD-repeat protein 1 (beta-TRCP1) [89138]
                 1. Human (Homo sapiens) [TaxId: 9606] [89139] (1)
              4. F-box/WD repeat-containing protein 7, FBXW7 [158808]
                 1. Human (Homo sapiens) [TaxId: 9606] [158809] (3)
                    SQ Q969H0 263-364
   237. Nuclear receptor ligand-binding domain [48507] (1)
        multihelical; 3 layers or orthogonally packed helices
        1. Nuclear receptor ligand-binding domain [48508] (1)
           uperfamily
           1. Nuclear receptor ligand-binding domain [48509] (44)
              1. Retinoid-X receptor alpha (RXR-alpha) [48510]
                 1. Human (Homo sapiens) [TaxId: 9606] [48511] (21)
                    SQ P19793 227-458
                 2. Mouse (Mus musculus) [TaxId: 10090] [48512] (2)
                    SQ P28700 232-463
              2. Retinoid-X receptor beta (RXR-beta) [74792]
                 1. Human (Homo sapiens) [TaxId: 9606] [74793] (2)
                    SQ P28702 298-528
              3. Retinoic acid receptor alpha (RAR-alpha) [48513]
                 1. Human (Homo sapiens) [TaxId: 9606] [48514] (1)
              4. Retinoic acid receptor gamma (RAR-gamma) [48515]
                 1. Human (Homo sapiens) [TaxId: 9606] [48516] (9)
              5. Glucocorticoid receptor [89140]
                 1. Human (Homo sapiens) [TaxId: 9606] [89141] (4)
              6. Orphan nuclear receptor NURR1 [89142]
                 1. Human (Homo sapiens) [TaxId: 9606] [89143] (1)
              7. Nuclear hormone receptor HR38 [89144]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89145] (1)
              8. Progesterone receptor [48517]
                 1. Human (Homo sapiens) [TaxId: 9606] [48518] (8)
                    SQ P06401 679-932
              9. Estrogen receptor alpha [48519]
                 1. Human (Homo sapiens) [TaxId: 9606] [48520] (36)
                    SQ P03372 307-551
              10. Estrogen receptor beta [48521]
                  1. Human (Homo sapiens) [TaxId: 9606] [48522] (36)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [48523] (4)
              11. Androgen receptor [63621]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [63622] (7)
                  2. Human (Homo sapiens) [TaxId: 9606] [63623] (36)
                     SQ P10275 671-919
                  3. Chimpanzee (Pan troglodytes) [TaxId: 9598] [109986] (8)
                     SQ O97775 661-910 # 100% sequence identity to human sequence (SQ P10275 669-918)
              12. Peroxisome proliferator activated receptor alpha, PPAR-alpha [69109]
                  1. Human (Homo sapiens) [TaxId: 9606] [69110] (5)
              13. Peroxisome proliferator activated receptor gamma, PPAR-gamma [48524]
                  1. Human (Homo sapiens) [TaxId: 9606] [48525] (72)
                     SQ P37231 232-505
              14. Peroxisome proliferator-activated receptor delta, PPAR-DELTA [48526]
                  1. Human (Homo sapiens) [TaxId: 9606] [48527] (18)
              15. Pregnane x receptor, PXR [63624]
                  1. Human (Homo sapiens) [TaxId: 9606] [63625] (6)
              16. Vitamin D nuclear receptor [48528]
                  1. Human (Homo sapiens) [TaxId: 9606] [48529] (13)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [101432] (12)
              17. Thyroid hormone receptor beta (TR-beta) [48530]
                  1. Human (Homo sapiens) [TaxId: 9606] [48531] (11)
                     SQ P10828 202-460
              18. Thyroid hormone receptor alpha1 (TR-alpha1) [48532]
                  1. Human (Homo sapiens) [TaxId: 9606] [88962] (1)
              19. Ultraspiracle protein, usp [48534]
                  the ortholog of RXRs in insects
                  1. Drosophila melanogaster [TaxId: 7227] [48535] (1)
                  2. Heliothis virescens [TaxId: 7102] [63626] (4)
              20. Orphan nuclear receptor ROR-alpha [81914]
                  1. Human (Homo sapiens) [TaxId: 9606] [81915] (2)
              21. Orphan nuclear receptor ROR-beta [74794]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [74795] (3)
              22. Orphan nuclear receptor ERR3 [81916]
                  1. Human (Homo sapiens) [TaxId: 9606] [81917] (26)
                     SQ O75454 233-458
              23. Hepatocyte nuclear factor 4-gamma [81918]
                  1. Human (Homo sapiens) [TaxId: 9606] [81919] (1)
              24. Hepatocyte nuclear factor 4-alpha [109605]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [89146] (1)
                  2. Human (Homo sapiens) [TaxId: 9606] [109987] (1)
                     SQ P41235 139-369
              25. Orphan nuclear receptor NR5a2 (LRH-1) [89147]
                  1. Mouse (Mus musculus) [TaxId: 10090] [89148] (1)
              26. Oxysterols receptor LXR-beta [89149]
                  1. Human (Homo sapiens) [TaxId: 9606] [89150] (6)
                     SQ P55055 219-461
              27. Bile acid receptor FXR [101433]
                  1. Human (Homo sapiens) [TaxId: 9606] [101434] (5)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [101435] (2)
              28. Ecdysone receptor [101436]
                  1. Noctuid moth (Heliothis virescens) [TaxId: 7102] [101437] (3)
              29. Oxysterols receptor LXR-alpha [109988]
                  1. Human (Homo sapiens) [TaxId: 9606] [109989] (1)
                     SQ Q13133 207-445
                  2. Mouse (Mus musculus) [TaxId: 10090] [158810] (4)
                     SQ Q9Z0Y9 203-443
              30. Steroid hormone receptor ERR1 [109990]
                  1. Human (Homo sapiens) [TaxId: 9606] [109991] (3)
                     SQ P11474 289-516
              31. Retinoic acid receptor beta (RAR-beta) [117011]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117012] (1)
                     SQ P22605 209-453
                  2. Human (Homo sapiens) [TaxId: 9606] [117013] (1)
                     SQ P10826 182-416
              32. Orphan nuclear receptor NR1I3 (CAR) [117014]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117015] (2)
                     SQ O35627 109-358
                  2. Human (Homo sapiens) [TaxId: 9606] [117016] (2)
                     SQ Q14994 103-352
              33. Orphan nuclear receptor NR4A1 [158811]
                  1. Human (Homo sapiens) [TaxId: 9606] [158812] (4)
                     SQ P22736 363-595
   238. Phospholipase C/P1 nuclease [48536] (1)
        multihelical
        1. Phospholipase C/P1 nuclease [48537] (2)
           duplication: all chain but the N-terminal helix forms two structural repeats
           uperfamily
           1. Phospholipase C [48538] (3)
              1. Bacterial phosholipase C [48539]
                 1. Bacillus cereus [TaxId: 1396] [48540] (4)
              2. Alpha-toxin, N-terminal domain [48541]
                 1. Clostridium perfringens, different strains [TaxId: 1502] [48542] (5)
                 2. Clostridium absonum [TaxId: 29369] [101438] (1)
           2. P1 nuclease [48543] (1)
              1. P1 nuclease [48544]
                 1. Penicillium citrinum [TaxId: 5077] [48545] (1)
   239. ATP-dependent DNA ligase DNA-binding domain [117017] (1)
        multihelical; duplication: contains two intertwined structural repeats related by pseudo twofold symmetry
        1. ATP-dependent DNA ligase DNA-binding domain [117018] (1)
           uperfamily
           1. ATP-dependent DNA ligase DNA-binding domain [117019] (1)
              Pfam 04675
              1. DNA ligase I (LIG1) [117020]
                 1. Human (Homo sapiens) [TaxId: 9606] [117021] (1)
                    SQ P18858 262-901
   240. DNA primase DnaG, C-terminal domain [117022] (1)
        multihelical; segment-swapped dimer
        1. DNA primase DnaG, C-terminal domain [117023] (1)
           uperfamily
           1. DNA primase DnaG, C-terminal domain [117024] (1)
              1. DNA primase DnaG, C-terminal domain [117025]
                 1. Escherichia coli [TaxId: 562] [117026] (2)
                    SQ P02923 447-580 # structure of the core domain (115-427) is also known, scop_sp 56734
   241. PriB N-terminal domain-like [140913] (1)
        multihelical bundle; contains buried central helix; also includes the PriA interface-forming insert subdomain (alpha+beta)
        1. PriB N-terminal domain-like [140914] (1)
           uperfamily
           1. PriB N-terminal domain-like [140915] (1)
              1. DNA primase large subunit PriB, N-terminal domain [140916]
                 1. Sulfolobus solfataricus [TaxId: 2287] [140917] (2)
                    SQ Q9UWW1 3-206
   242. VPS9 domain [109992] (1)
        multihelical; consist of two subdomains
        1. VPS9 domain [109993] (1)
           uperfamily
           1. VPS9 domain [109994] (1)
              Pfam 02204
              1. Rab5 GDP/GTP exchange factor (Rabex-5) [109995]
                 1. Human (Homo sapiens), gamma isoform [TaxId: 9606] [109996] (2)
                    SQ Q9UJ41
   243. Triger factor/SurA peptide-binding domain-like [109997] (1)
        multihelical; irregular array of long and short helices
        1. Triger factor/SurA peptide-binding domain-like [109998] (2)
           there are sequence and functional similarities between the families, but their structural similarity is obscured by conformational flexibility (in the TF family)
           uperfamily
           1. TF C-terminus [109999] (2)
              Pfam 05698; includes the upstream linker region not covered by the Pfam model
              1. Trigger factor, C-terminal domain [110000]
                 1. Escherichia coli [TaxId: 562] [110001] (2)
                    SQ P22257
                 2. Vibrio cholerae [TaxId: 666] [110002] (1)
                    SQ Q9KQS5
           2. Porin chaperone SurA, peptide-binding domain [81828] (1)
              1. Porin chaperone SurA, peptide-binding domain [81829]
                 1. Escherichia coli [TaxId: 562] [81830] (3)
   244. DNA terminal protein [140918] (1)
        multihelical, open array; contains the C-terminal four-helical bundle, left-handed superhelix
        1. DNA terminal protein [140919] (1)
           uperfamily
           1. DNA terminal protein [140920] (1)
              Pfam 05435
              1. DNA terminal protein [140921]
                 1. Bacteriophage phi-29 [TaxId: 10756] [140922] (6)
                    SQ P03681 71-259
   245. Glycolipid transfer protein, GLTP [110003] (1)
        multihelical; 2 layers or orthogonally packed helices
        1. Glycolipid transfer protein, GLTP [110004] (1)
           uperfamily
           1. Glycolipid transfer protein, GLTP [110005] (1)
              1. Glycolipid transfer protein, GLTP [110006]
                 1. Human (Homo sapiens) [TaxId: 9606] [110007] (7)
                    SQ Q9NZD2
   246. Hypothetical protein MG354 [110008] (1)
        multihelical bundle; contains buried central helix
        1. Hypothetical protein MG354 [110009] (1)
           uperfamily
           1. Hypothetical protein MG354 [110010] (1)
              1. Hypothetical protein MG354 [110011]
                 1. Mycoplasma genitalium [TaxId: 2097] [110012] (1)
                    SQ P47596
   247. Duffy binding domain-like [140923] (1)
        consist of two subdomains, each containing a three-helical bundle
        1. Duffy binding domain-like [140924] (1)
           uperfamily
           1. Duffy binding domain [140925] (2)
              Pfam 05424
              1. Duffy receptor, alpha form [140926]
                 1. Plasmodium knowlesi [TaxId: 5850] [140927] (1)
                    SQ P22545 213-506
              2. Erythrocyte binding antigen region II [140928]
                 duplication; tandem repeat of two Duffy-binding domain
                 1. Plasmodium falciparum [TaxId: 5833] [140929] (6)
                    SQ Q25735 283-596! SQ Q25735 8-282
   248. Fic-like [140930] (1)
        multihelical; one central helix is surrounded by seven helices
        1. Fic-like [140931] (1)
           uperfamily
           1. Fic-like [140932] (2)
              Pfam 02661; the conserved motif HPFXXGNG is at the N-terminus of the central helix
              1. Cell filamentation protein Fic [140933]
                 1. Helicobacter pylori [TaxId: 210] [140934] (2)
                    SQ O25774 1-177
              2. Hypothetical protein NMA0004 [140935]
                 1. Neisseria meningitidis [TaxId: 487] [140936] (1)
                    SQ Q9JQR9 11-187
   249. Her-1 [110013] (1)
        multihelical; consists of two topologically similar alpha-helical bundles
        1. Her-1 [110014] (1)
           uperfamily
           1. Her-1 [110015] (1)
              1. Her-1 [110016]
                 1. Caenorhabditis elegans [TaxId: 6239] [110017] (1)
                    SQ P34704
   250. ERO1-like [110018] (1)
        multihelical; consists of 2 four-helical bundles
        1. ERO1-like [110019] (1)
           similar active site architecture to scop_sf 69000
           uperfamily
           1. ERO1-like [110020] (1)
              Pfam 04137
              1. Endoplasmic oxidoreductin 1, Ero1p [110021]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110022] (2)
                    SQ Q03103 56-424
   251. Serum albumin-like [48551] (1)
        multihelical; one domain consists of two similar disulfide-linked subdomains
        1. Serum albumin-like [48552] (1)
           uperfamily
           1. Serum albumin-like [48553] (2)
              1. Serum albumin [48554]
                 duplication: consists of three domains of this fold
                 1. Human (Homo sapiens) [TaxId: 9606] [48555] (91)
                    SQ P02768 29-596
              2. Vitamin D binding protein [69111]
                 domain 3 lacks the last subdomain
                 1. Human (Homo sapiens) [TaxId: 9606] [69112] (6)
   252. L-aspartase-like [48556] (1)
        multihelical, consists of three all-alpha domains
        1. L-aspartase-like [48557] (2)
           uperfamily
           1. L-aspartase/fumarase [48558] (14)
              1. L-aspartate ammonia lyase [48559]
                 1. Escherichia coli [TaxId: 562] [48560] (1)
                 2. Bacillus sp., ym55-1 [TaxId: 1409] [89153] (1)
              2. Fumarase [48561]
                 1. Escherichia coli [TaxId: 562] [48562] (7)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48563] (1)
                 3. Thermus thermophilus [TaxId: 274] [101443] (1)
              3. Argininosuccinate lyase/delta-crystallin [48564]
                 1. Human (Homo sapiens) [TaxId: 9606] [48565] (2)
                 2. Domestic duck (Anas platyrhynchos), delta-crystallin [TaxId: 8839] [48566] (10)
                    SQ P24058 P24057
                 3. Turkey (Meleagris gallopavo), delta-crystallin [TaxId: 9103] [48567] (1)
                 4. Escherichia coli [TaxId: 562] [117027] (1)
                    SQ P11447
              4. Adenylosuccinate lyase [48568]
                 1. Thermotoga maritima [TaxId: 2336] [48569] (2)
                 2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [48570] (1)
                 3. Bacillus subtilis [TaxId: 1423] [48571] (1)
              5. 3-carboxy-cis,cis-muconate cycloisomerase (CMLE) [101444]
                 1. Acinetobacter calcoaceticus [TaxId: 471] [101445] (1)
                 2. Pseudomonas putida, strain KT2440 [TaxId: 303] [110023] (1)
                    SQ Q88N37
           2. HAL/PAL-like [48572] (3)
              Pfam 00221
              1. Histidine ammonia-lyase (HAL) [48573]
                 1. Pseudomonas putida [TaxId: 303] [48574] (6)
              2. Phenylalanine ammonia-lyase, PAL [117028]
                 1. Fungi (Rhodosporidium toruloides) [TaxId: 5286] [117029] (2)
                    SQ P11544
                 2. Parsley (Petroselinum crispum), PAL1 [TaxId: 4043] [117030] (1)
                    SQ P24481 25-716
   253. Formin homology 2 domain (FH2 domain) [101446] (1)
        multihelical, consists of three all-alpha domains
        1. Formin homology 2 domain (FH2 domain) [101447] (1)
           uperfamily
           1. Formin homology 2 domain (FH2 domain) [101448] (2)
              1. Diaphanous protein homolog 1, dia1 [101449]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101450] (1)
              2. Bni1 [101451]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101452] (3)
   254. Terpenoid synthases [48575] (1)
        multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
        1. Terpenoid synthases [48576] (5)
           duplication: two metal-binding sites are related by a pseudo dyad that also relates helices C-F to helices G-J
           uperfamily
           1. Isoprenyl diphosphate synthases [48577] (5)
              1. Farnesyl diphosphate synthase (geranyltranstransferase) [48578]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [48579] (5)
                 2. Escherichia coli [TaxId: 562] [101453] (2)
                 3. Staphylococcus aureus [TaxId: 1280] [101454] (1)
              2. Octoprenyl-diphosphate synthase [101455]
                 1. Thermotoga maritima [TaxId: 2336] [101456] (10)
                    SQ Q9X1M1
              3. Geranylgeranyl pyrophosphate synthetase [158813]
                 1. Human (Homo sapiens) [TaxId: 9606] [158814] (6)
                    SQ O95749 6-296
           2. Squalene synthase [48580] (1)
              1. Squalene synthase [48581]
                 synonym: Farnesyl diphosphate farnesyltransferase
                 1. Human (Homo sapiens) [TaxId: 9606] [48582] (1)
           3. Terpenoid cyclase C-terminal domain [48583] (2)
              1. 5-Epi-aristolochene synthase [48584]
                 1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [48585] (7)
              2. (+)-bornyl diphosphate synthase [81920]
                 1. Garden sage (Salvia officinalis) [TaxId: 38868] [81921] (7)
           4. Aristolochene/pentalenene synthase [48586] (2)
              1. Aristolochene synthase [48587]
                 1. Fungus (Penicillium roqueforti) [TaxId: 5082] [48588] (2)
              2. Pentalenene synthase [48589]
                 1. Streptomyces sp., UC5319 [TaxId: 1931] [48590] (3)
           5. Trichodiene synthase [69113] (1)
              1. Trichodiene synthase [69114]
                 1. Fusarium sporotrichioides [TaxId: 5514] [69115] (12)
   255. GroEL equatorial domain-like [48591] (1)
        multihelical; 8 helices arranged in 2 parallel layers
        1. GroEL equatorial domain-like [48592] (2)
           duplication: two 4-helical subdomains are related by a pseudo dyad passing through the ATP-binding site
           uperfamily
           1. GroEL chaperone, ATPase domain [48593] (4)
              1. GroEL, E domain [48594]
                 1. Escherichia coli [TaxId: 562] [48595] (15)
                 2. Paracoccus denitrificans [TaxId: 266] [69116] (1)
                 3. Thermus thermophilus [TaxId: 274] [110024] (2)
                    SQ P61491
                 4. Mycobacterium tuberculosis, GroEL2 [TaxId: 1773] [117031] (1)
                    SQ P0A520 60-514
           2. Group II chaperonin (CCT, TRIC), ATPase domain [48596] (3)
              1. Thermosome, E domain [48597]
                 1. Archaeon Thermoplasma acidophilum, alpha chain [TaxId: 2303] [100916] (2)
                 2. Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679] [101457] (4)
                 3. Archaeon Thermoplasma acidophilum, beta chain [TaxId: 2303] [100917] (2)
   256. TorD-like [89154] (1)
        multihelical; bundle
        1. TorD-like [89155] (1)
           uperfamily
           1. TorD-like [89156] (4)
              Pfam 06192
              1. TorA specific chaperone TorD [89157]
                 segment-swapped dimer
                 1. Shewanella massilia [TaxId: 76854] [89158] (1)
              2. Putative component of anaerobic dehydrogenases YnfI [110025]
                 1. Salmonella typhimurium [TaxId: 90371] [110026] (1)
                    SQ Q8ZPK0
              3. Reductase assembly protein AF0173 [158815]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [158816] (1)
                    SQ O30064 1-153
              4. Hypothetical protein AF0160 [158817]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [158818] (3)
                    SQ O30077 1-160
   257. Chorismate mutase II [48599] (1)
        multihelical; core: 6 helices, bundle
        1. Chorismate mutase II [48600] (4)
           uperfamily
           1. Dimeric chorismate mutase [48601] (4)
              intertwined homodimer of 3-helical subunits
              1. Chorismate mutase domain of P-protein [48602]
                 1. Escherichia coli [TaxId: 562] [48603] (1)
                 2. Thermus thermophilus [TaxId: 274] [140937] (3)
                    SQ Q5SLA5 3-82
              2. Salicylate biosynthesis protein PchB [140938]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140939] (6)
                    SQ Q51507 1-94
              3. mono-domain chorismate mutase [140940]
                 1. Pyrococcus furiosus [TaxId: 2261] [140941] (1)
                    SQ Q8U098 2-75
           2. Allosteric chorismate mutase [48604] (1)
              duplication: 2 weak structural repeats resembling subunits of E. coli protein
              1. Allosteric chorismate mutase [48605]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48606] (5)
           3. monomeric chorismate mutase [140942] (1)
              "un-swapped" four-helical relative of the homodimeric chorismate mutase domain
              1. Chorismate mutase-like protein MJ0246 [140943]
                 1. Methanococcus jannaschii [TaxId: 2190] [140944] (1)
                    SQ Q57696 1-93
           4. Secreted chorismate mutase-like [140945] (1)
              duplication; two structural repeats, like in the yeast enzyme, but with a different location of the remaining active site
              1. Secreted chorismate mutase [140946]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [140947] (9)
                    SQ O07746 34-199
   258. Peridinin-chlorophyll protein [48607] (1)
        multihelical: forms a boat-shaped protein shell around cofactors
        1. Peridinin-chlorophyll protein [48608] (1)
           duplication: consists of two 8-helical repeats
           uperfamily
           1. Peridinin-chlorophyll protein [48609] (1)
              1. Peridinin-chlorophyll protein [48610]
                 soluble light harvesting protein
                 1. Dinoflagellate (Amphidinium carterae) [TaxId: 2961] [48611] (1)
   259. Heme oxygenase-like [48612] (1)
        multihelical; bundle
        1. Heme oxygenase-like [48613] (4)
           duplication: contains two structural repeats of 3-helical motif
           uperfamily
           1. Eukaryotic type heme oxygenase [48614] (5)
              1. Heme oxygenase-1 (HO-1) [48615]
                 1. Human (Homo sapiens) [TaxId: 9606] [48616] (26)
                    SQ P09601
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [48617] (13)
                    SQ P06762 11-222
                 3. Synechocystis sp. [TaxId: 1143] [117032] (1)
                    SQ P72849 2-223
              2. Heme oxygenase HmuO [89159]
                 1. Corynebacterium diphtheriae [TaxId: 1717] [89160] (14)
                    SQ P71119
              3. Heme oxygenase 2 [140948]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [140949] (6)
                    SQ P74133 2-250
           2. Heme oxygenase HemO (PigA) [63627] (2)
              1. Heme oxygenase HemO (PigA) [63628]
                 gram-negative bacterial heme oxygenase/iron-starvation protein
                 1. Neisseria meningitidis [TaxId: 487] [63629] (4)
                 2. Pseudomonas aeruginosa [TaxId: 287] [110027] (1)
                    SQ O69002
           3. TENA/THI-4 [101458] (8)
              Pfam 03070; HO-related family lacking the heme-binding site
              1. Putative transcriptional activator PF1337 [101459]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [101460] (1)
              2. Seed maturation protein-related At3g16990 [101461]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101462] (4)
                    structural genomics
              3. Hypothetical transcriptional regulator PH1161 [110028]
                 1. Pyrococcus horikoshii [TaxId: 53953] [110029] (1)
                    SQ O58873
              4. Transcriptional activator TenA [110030]
                 1. Bacillus subtilis [TaxId: 1423] [110031] (10)
                    SQ P25052
              5. Hypothetical protein TTHA0169 (TT2028) [140950]
                 1. Thermus thermophilus [TaxId: 274] [140951] (2)
                    SQ Q5SLX4 9-188
              6. TenA homolog PAE0170 [140952]
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [140953] (8)
                    SQ Q8ZZM9 2-212
              7. Putative transcriptional regulator SP0716 (SPr0628) [140954]
                 1. Streptococcus pneumoniae [TaxId: 1313] [140955] (3)
                    SQ Q97RS7 3-221
              8. Hypothetical protein BT3146 [140956]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [140957] (9)
                    SQ Q8A309 10-240
           4. PqqC-like [101463] (2)
              Pfam 05312
              1. Coenzyme PQQ synthesis protein C, PqqC [101464]
                 1. Klebsiella pneumoniae [TaxId: 573] [101465] (2)
              2. Hypothetical protein CT610 [101466]
                 contains a di-iron centre similar to that of the ferritin-like superfamily
                 1. Chlamydia trachomatis [TaxId: 813] [101467] (1)
   260. Indolic compounds 2,3-dioxygenase-like [140958] (1)
        multihelical; bundle, contains interrupted helices
        1. Indolic compounds 2,3-dioxygenase-like [140959] (2)
           contains heme-dependent enzymes
           uperfamily
           1. Bacterial tryptophan 2,3-dioxygenase [140960] (1)
              Pfam 03301
              1. Tryptophan 2,3-dioxygenase [140961]
                 1. Xanthomonas campestris pv. campestris [TaxId: 340] [140962] (12)
                    SQ Q8PDA8 23-284
           2. Indoleamine 2,3-dioxygenase-like [140963] (2)
              Pfam 01231; contains extra N-terminal all-alpha subdomain of similar fold to the GST C-terminal domain (scop_cf 47615)
              1. Hypothetical protein SO4414 [140964]
                 1. Shewanella oneidensis [TaxId: 70863] [140965] (2)
                    SQ Q8E972 6-392
              2. Indoleamine 2,3-dioxygenase [140966]
                 1. Human (Homo sapiens) [TaxId: 9606] [140967] (4)
                    SQ P14902 12-403
   261. AhpD-like [69117] (1)
        multihelical; contains 4-helical bundle and 2-helical arm
        1. AhpD-like [69118] (4)
           probable biological unit contains six domains of this fold arranged with 32 symmetry
           uperfamily
           1. CMD-like [101468] (2)
              Pfam 02627; hexamer of single-domain subunits
              1. Hypothetical protein TM1620 [101469]
                 1. Thermotoga maritima [TaxId: 2336] [101470] (2)
                    SQ Q9X1V5
              2. Gamma-carboxymuconolactone decarboxylase, CMD [140968]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [140969] (9)
                    SQ O26336 1-119
           2. AhpD [69119] (2)
              duplication: two-domain subunits form a helix-swapped trimer
              1. Antioxidant defense protein AhpD [69120]
                 a novel enzyme with thioredoxin-like activity
                 1. Mycobacterium tuberculosis [TaxId: 1773] [69121] (4)
              2. Hypothetical protein Bxeno_B2006 [158819]
                 1. Burkholderia xenovorans [TaxId: 36873] [158820] (3)
                    SQ Q13LR5 1-257
           3. Atu0492-like [140970] (5)
              duplication: similar subunit structure to the AhpD family, but the putative active site is conserved in different relative location; new hexameric architecture; similar dimeric interface to the CMD-like family
              1. Hypothetical protein Atu0492 [140971]
                 1. Agrobacterium tumefaciens [TaxId: 358] [140972] (6)
                    SQ Q8UI08 2-148
              2. Hypothetical protein PA0269 [140973]
                 1. Pseudomonas aeruginosa [TaxId: 287] [140974] (10)
                    SQ Q9I6M1 2-144! SQ Q9I6M1 2-145
              3. Uncharacterized protein Dgeo_1446 [158821]
                 1. Deinococcus geothermalis [TaxId: 68909] [158822] (2)
                    SQ Q1IYE3 10-195
              4. Uncharacterized protein TM1040_2465 [158823]
                 1. Silicibacter sp. tm1040 [TaxId: 292414] [158824] (2)
                    SQ Q1GDR9 1-190
              5. Uncharacterized protein Reut_A2532 [158825]
                 1. Ralstonia eutropha [TaxId: 106590] [158826] (12)
                    SQ Q46Y90 5-194
           4. TTHA0727-like [140975] (2)
              similar to the CMD-like family by the subunit sequence and hexameric architecture; the segment-swapped subunit fold is similar to the AhpD domains
              1. Hypothetical protein TTHA0727 [140976]
                 1. Thermus thermophilus [TaxId: 274] [140977] (3)
                    SQ Q5SMF5 1-117
              2. Hypothetical protein Rru_A0301 [158827]
                 1. Rhodospirillum rubrum [TaxId: 1085] [158828] (2)
                    SQ Q2RXN9 1-134
   262. Double Clp-N motif [81922] (1)
        multihelical; array
        1. Double Clp-N motif [81923] (1)
           duplication: contains two structural repeats of 4-helical motif
           uperfamily
           1. Double Clp-N motif [81924] (3)
              1. N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone [81925]
                 1. Escherichia coli [TaxId: 562] [81926] (13)
                    SQ Q83LR6
              2. N-terminal domain of ClpB (heat shock protein F84.1) [81927]
                 1. Escherichia coli [TaxId: 562] [81928] (1)
                 2. Thermus thermophilus [TaxId: 274] [101471] (1)
   263. Orange carotenoid protein, N-terminal domain [81929] (1)
        multihelical; array
        1. Orange carotenoid protein, N-terminal domain [81930] (1)
           duplication: contains four structural repeats arranged into two intertwined 4-helical subdomains
           uperfamily
           1. Orange carotenoid protein, N-terminal domain [81931] (1)
              1. Orange carotenoid protein, N-terminal domain [81932]
                 1. Cyanobacteria (Arthrospira maxima) [TaxId: 129910] [81933] (1)
   264. DhaL-like [101472] (1)
        multihelical; bundle
        1. DhaL-like [101473] (1)
           uperfamily
           1. DhaL-like [101474] (2)
              1. Citrobacter dihydroxyacetone kinase extra ATP-binding domain [101475]
                 eight-helical up-and-down barrel with a central ligand-binding cavity
                 1. Citrobacter freundii [TaxId: 546] [101476] (2)
              2. PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL [158829]
                 1. Lactococcus lactis [TaxId: 1358] [158830] (2)
                    SQ Q9CIV7 1-192
   265. ADP-ribosylglycohydrolase [101477] (1)
        multihelical; bundle
        1. ADP-ribosylglycohydrolase [101478] (1)
           uperfamily
           1. ADP-ribosylglycohydrolase [101479] (1)
              Pfam 03747
              1. Hypothetical protein MJ1187 [101480]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [101481] (1)
   266. Topoisomerase V catalytic domain-like [140978] (1)
        multihelical; irregular array; contains small amount of beta-structure and a 3-helical bundle with a variant homeofomain-like fold and HTH motif (scop_cf 46688)
        1. Topoisomerase V catalytic domain-like [140979] (1)
           uperfamily
           1. Topoisomerase V catalytic domain-like [140980] (1)
              1. Topoisomerase V, catalytic domain [140981]
                 1. Methanopyrus kandleri [TaxId: 2320] [140982] (1)
                    SQ Q977W1 3-293
                    the HTH-like subdomain is formed by residues 180-232
   267. PTPA-like [140983] (1)
        multihelical
        1. PTPA-like [140984] (1)
           uperfamily
           1. PTPA-like [140985] (2)
              Pfam 03095
              1. Serine/threonine-protein phosphatase 2A regulatory subunit B', PTPA [140986]
                 1. Human (Homo sapiens) [TaxId: 9606] [140987] (12)
                    SQ Q15257 22-322! SQ Q15257 23-322
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140988] (8)
                    SQ Q12461 2-317! SQ Q12461 3-299
   268. Tex N-terminal region-like [158831] (1)
        multihelical; irregular array of long and short helices; can be divided into several subdomains
        1. Tex N-terminal region-like [158832] (1)
           1. Tex N-terminal region-like [158833] (1)
              Pfam 09371
              1. Transcriptional accessory factor Tex [158834]
                 1. Pseudomonas aeruginosa [TaxId: 287] [158835] (3)
                    SQ Q9HTY8 1-324! SQ Q9HTY8 2-324
   269. AGR_C_984p-like [158836] (1)
        multihelical, consists of two subdomains; duplication: there are two 5-helical structural repeats, one in each subdomain
        1. AGR_C_984p-like [158837] (1)
           1. AGR_C_984p-like [158838] (1)
              Pfam 06748; DUF1217
              1. Uncharacterized protein AGR_C_984p [158839]
                 1. Agrobacterium tumefaciens [TaxId: 358] [158840] (2)
                    SQ Q7D182 54-278
   270. PMT central region-like [158841] (1)
        multihelical; comprises two four-helical bundles of different topologies and an irregular helical array packed against a small beta-sheet
        1. PMT central region-like [158842] (1)
           1. PMT central region-like [158843] (1)
              1. Dermonecrotic toxin, ToxA [158844]
                 Synonym: Mitogenic toxin PMT
                 1. Pasteurella multocida [TaxId: 747] [158845] (4)
                    SQ P17452 575-874
   271. FtsH protease domain-like [140989] (1)
        array of 6 helices and a 2-stranded beta-ribbon
        1. FtsH protease domain-like [140990] (1)
           contains zincin-like (scop_sf 55486) metal-binding motif HExxH, embedded into a topologically different fold
           uperfamily
           1. FtsH protease domain-like [140991] (2)
              Pfam 01434; Peptidase family M41
              1. Cell division protein FtsH, C-terminal domain [140992]
                 1. Aquifex aeolicus [TaxId: 63363] [140993] (2)
                    SQ O67077 406-607
                 2. Thermotoga maritima [TaxId: 2336] [140994] (12)
                    SQ Q9WZ49 411-603
   272. Gametocyte protein Pfg27 [89161] (1)
        multihelical; bundle
        1. Gametocyte protein Pfg27 [89162] (1)
           duplication: contains two structural repeats of four helices each
           uperfamily
           1. Gametocyte protein Pfg27 [89163] (1)
              1. Gametocyte protein Pfg27 [89164]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [89165] (1)
   273. N-terminal domain of bifunctional PutA protein [81934] (1)
        multihelical; array
        1. N-terminal domain of bifunctional PutA protein [81935] (1)
           uperfamily
           1. N-terminal domain of bifunctional PutA protein [81936] (1)
              1. N-terminal domain of bifunctional PutA protein [81937]
                 includes the N-terminal swapping arm made of three helices; possible DNA-binding function
                 1. Escherichia coli [TaxId: 562] [81938] (7)
                    SQ P09546 87-610
   274. Cysteine alpha-hairpin motif [47071] (1)
        core: alpha-hairpin crosslinked with two disulfides
        1. Cysteine alpha-hairpin motif [47072] (2)
           uperfamily
           1. p8-MTCP1 [47073] (1)
              1. p8-MTCP1 [47074]
                 1. Human (Homo sapiens) [TaxId: 9606] [47075] (2)
           2. COX17-like [117033] (1)
              Pfam 05051
              1. Cytochrome C oxidase copper chaperone, COX17 [117034]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117035] (2)
                    SQ Q12287
   275. Phospholipase A2, PLA2 [48618] (1)
        common core: 2 helices, disulfide-linked, and a calcium-binding loop
        1. Phospholipase A2, PLA2 [48619] (3)
           uperfamily
           1. Vertebrate phospholipase A2 [48623] (39)
              1. Snake phospholipase A2 [48624]
                 1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [48625] (2)
                 2. Indian cobra (Naja naja) [TaxId: 35670] [48626] (5)
                 3. Indian cobra (Naja naja), a C49 isoform 2 [TaxId: 35670] [89166] (1)
                 4. Indian cobra (Naja naja), isoform 3 [TaxId: 35670] [89167] (1)
                 5. Andaman cobra (Naja sagittifera), acidic isoform 1 [TaxId: 195058] [89168] (1)
                 6. Andaman cobra (Naja sagittifera), isoform 2 [TaxId: 195058] [89169] (2)
                    heterodimer of two different isoforms
                 7. Andaman cobra (Naja sagittifera), isoform 3 [TaxId: 195058] [89170] (2)
                    heterodimer of two different isoforms
                 8. Andaman cobra (Naja sagittifera), isoform 4 [TaxId: 195058] [89171] (7)
                    SQ P60045 8-126 # ! yet another isoform, 98% identity
                 9. Andaman cobra (Naja sagittifera), calcium-free isoform 5 [TaxId: 195058] [89172] (2)
                 10. King cobra (Ophiophagus hannah) [TaxId: 8665] [81939] (1)
                 11. King cobra (Ophiophagus hannah), an acidic isoform [TaxId: 8665] [101482] (1)
                 12. Western diamondback rattlesnake (Crotalus atrox) [TaxId: 8730] [48627] (1)
                 13. Snake (Agkistrodon halys) [TaxId: 8714] [48628] (9)
                 14. Eastern cottonmouth snake (Agkistrodon piscivorus piscivorus) [TaxId: 8716] [48629] (2)
                 15. Broad-banded copperhead (Agkistrodon contortrix laticinctus) [TaxId: 37195] [101483] (3)
                 16. Viper (Deinagkistrodon acutus) [TaxId: 36307] [69122] (1)
                 17. Snake (Daboia russellii pulchella), different isoforms [TaxId: 97228] [48630] (57)
                     SQ P59071
                 18. Mainland tiger snake (Notechis scutatus scutatus), notexin [TaxId: 8663] [48631] (1)
                     presynaptic neurotoxic phospholipase A2
                 19. Mainland tiger snake (Notechis scutatus scutatus), notechis II-5 [TaxId: 8663] [48632] (1)
                     neurotoxic phospholipase a2
                 20. Bothrops pirajai, Piratoxin-II (PRTX-II) [TaxId: 113192] [48633] (1)
                 21. Russell's viper (Vipera russelli) [TaxId: 8707] [48634] (1)
                     anticoagulant class II phospholipase A2
                 22. Sand viper (Vipera ammodytes meridionalis), vipoxin inhibitor [TaxId: 8704] [88517] (8)
                 23. Sand viper (Vipera ammodytes meridionalis), vipoxin catalytic subunit [TaxId: 8704] [88518] (2)
                 24. Siamese russell's viper (Daboia russelli siamensis), RV7 inhibitory subunit [TaxId: 343250] [101484] (1)
                 25. Siamese russell's viper (Daboia russelli siamensis), RV4 catalytic subunit [TaxId: 343250] [101485] (1)
                 26. Saw-scaled viper (Echis carinatus) [TaxId: 40353] [101486] (1)
                 27. Indian krait (Bungarus caeruleus), different isoforms [TaxId: 132961] [48636] (8)
                     SQ Q6SLM1 # fragment; SQ Q9DF52 28-145 # ! 74% sequence identity
                 28. Hundred-pace snake (Agkistrodon acutus) [TaxId: 36307] [74796] (2)
                     monomeric Lys-49 phospholipase A2 homologue
                 29. Many-banded krait (Bungarus multicinctus), beta2-bungarotoxin [TaxId: 8616] [48642] (1)
                 30. Jararacussu (Bothrops jararacussu) [TaxId: 8726] [101487] (4)
                     SQ Q8AXY1 17-138
                 31. Terciopelo (Bothrops asper), myotoxin I [TaxId: 8722] [48644] (3)
                 32. Cerrophidion godmani, formerly Bothrops godmani [TaxId: 44722] [48645] (1)
                     Monomeric Lys-49 phospholipase A2 homologue
                 33. Snake (Bothrops pirajai), piratoxin III [TaxId: 113192] [69123] (1)
                     SQ Q9IAT9; Asp-49 phospholipase A2 homologue
                 34. Neuwied's lancehead (Bothrops neuwiedi pauloensis), different isoforms [TaxId: 95649] [110032] (2)
                 35. Small-eye snake (Micropechis ikaheka), different isoforms [TaxId: 66188] [110033] (2)
                     SQ Q8JFB2 # 65% sequence identity
              2. Phospholipase A2 [48637]
                 1. Human (Homo sapiens), synovial fluid [TaxId: 9606] [48638] (12)
                 2. Cow (Bos taurus), pancreas [TaxId: 9913] [48639] (26)
                    SQ P00593
                 3. Pig (Sus scrofa), pancreas [TaxId: 9823] [48640] (19)
                 4. Human (Homo sapiens), SPLA2 [TaxId: 9606] [74797] (2)
                    group X secretory phospholipase A2
           2. Insect phospholipase A2 [48620] (1)
              1. Phospholipase A2 [48621]
                 1. European honeybee (Apis mellifera) [TaxId: 7460] [48622] (1)
           3. Prokaryotic phospholipase A2 [63630] (1)
              1. Prokaryotic phospholipase A2 [63631]
                 1. Streptomyces violaceoruber [TaxId: 1935] [63632] (5)
   276. Fungal elicitin [48646] (1)
        5 helices: irregular disulfide-linked array; also contains a small beta-hairpin
        1. Fungal elicitin [48647] (1)
           uperfamily
           1. Fungal elicitin [48648] (2)
              1. beta-cryptogein [48649]
                 1. Phytophthora cryptogea [TaxId: 4786] [48650] (4)
              2. beta-cinnamomin [74798]
                 1. Fungus (Phytophthora cinnamomi) [TaxId: 4785] [74799] (5)
   277. Tetraspanin [48651] (1)
        5 helices: irregular disulfide-linked array; form homodimer
        1. Tetraspanin [48652] (1)
           uperfamily
           1. Tetraspanin [48653] (1)
              1. CD81 extracellular domain [48654]
                 1. Human (Homo sapiens) [TaxId: 9606] [48655] (2)
   278. GDNF receptor-like [110034] (1)
        5 helices: irregular disulfide-linked array; topological similarity to the Fungal elicitin fold (scop_cf 48646)
        1. GDNF receptor-like [110035] (1)
           uperfamily
           1. GDNF receptor-like [110036] (1)
              Pfam 02351
              1. GDNF receptor alpha [110037]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [110038] (1)
                    SQ Q62997 239-346
   279. FinO-like [48656] (1)
        6 helices: irregular non-globular array; also contains two small beta-hairpins
        1. FinO-like [48657] (1)
           uperfamily
           1. FinO-like [48658] (2)
              1. Repressor of bacterial conjugation FinO [48659]
                 1. Escherichia coli [TaxId: 562] [48660] (1)
              2. Hypothetical protein NMB1681 [158846]
                 1. Neisseria meningitidis [TaxId: 487] [158847] (5)
                    SQ Q9JY98 3-118
   280. Nuclear receptor coactivator interlocking domain [69124] (1)
        3 helices, non-globular array; forms interlocked heterodimers with its targets
        1. Nuclear receptor coactivator interlocking domain [69125] (1)
           not a true superfamily
           uperfamily
           1. Nuclear receptor coactivator interlocking domain [69126] (3)
              1. Nuclear receptor coactivator CBP/p300 ibid domain [69127]
                 1. Mouse (Mus musculus) [TaxId: 10090] [69128] (5)
              2. Nuclear receptor coactivator ACTR [69129]
                 1. Human (Homo sapiens) [TaxId: 9606] [69130] (1)
              3. Nuclear receptor coactivator 1, NCOA1 [158848]
                 1. Human (Homo sapiens) [TaxId: 9606] [158849] (1)
                    SQ Q4PJW2 920-970
   281. Hermes dimerisation domain [140995] (1)
        multihelical, intertwinned dimer of two 4-helical strings
        1. Hermes dimerisation domain [140996] (1)
           uperfamily
           1. Hermes dimerisation domain [140997] (1)
              1. Transposase Hermes, dimerisation domain [140998]
                 1. House fly (Musca domestica) [TaxId: 7370] [140999] (2)
                    SQ Q25442 79-158! SQ Q25442 79-162
   282. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101488] (1)
        5 helices, non-globular array; wraps around the N-terminal tail of its target
        1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101489] (1)
           not a true superfamily
           uperfamily
           1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101490] (1)
              1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101491]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101492] (1)
   283. Non-globular all-alpha subunits of globular proteins [48661] (14)
        not a true fold
        1. Ribosomal protein L39e [48662] (1)
           interrupted alpha-helix
           uperfamily
           1. Ribosomal protein L39e [48663] (1)
              1. Ribosomal protein L39e [48664]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [48665] (58)
                    SQ P22452
        2. Methanol dehydrogenase subunit [48666] (1)
           consists of single alpha-helix and irregular N-terminal tail
           uperfamily
           1. Methanol dehydrogenase subunit [48667] (3)
              1. Methanol dehydrogenase, light chain [48668]
                 1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [48669] (8)
                 2. Methylobacterium extorquens [TaxId: 408] [63633] (3)
                    SQ P14775
                 3. Paracoccus denitrificans [TaxId: 266] [101493] (1)
        3. Transducin (heterotrimeric G protein), gamma chain [48670] (1)
           long alpha-helix interrupted in the middle
           uperfamily
           1. Transducin (heterotrimeric G protein), gamma chain [48671] (2)
              1. Transducin (heterotrimeric G protein), gamma chain [48672]
                 1. Cow (Bos taurus) [TaxId: 9913] [48673] (11)
                 2. Homo sapiens [TaxId: 9606] [158850] (1)
        4. Fe-only hydrogenase smaller subunit [48674] (1)
           uperfamily
           1. Fe-only hydrogenase smaller subunit [48675] (1)
              1. Fe-only hydrogenase smaller subunit [48676]
                 string of short helices wrapped around the larger subunit
                 1. Desulfovibrio desulfuricans [TaxId: 876] [48677] (1)
        5. Moesin tail domain [48678] (1)
           uperfamily
           1. Moesin tail domain [48679] (1)
              1. Moesin tail domain [48680]
                 string of short helices masking the FERM domain surface
                 1. Human (Homo sapiens) [TaxId: 9606] [48681] (1)
        6. Proteinase A inhibitor IA3 [48686] (1)
           uperfamily
           1. Proteinase A inhibitor IA3 [48687] (1)
              1. Proteinase A inhibitor IA3 [48688]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48689] (3)
        7. Epsilon subunit of mitochondrial F1F0-ATP synthase [48690] (1)
           uperfamily
           1. Epsilon subunit of mitochondrial F1F0-ATP synthase [48691] (1)
              1. Epsilon subunit of mitochondrial F1F0-ATP synthase [48692]
                 1. Cow (Bos taurus) [TaxId: 9913] [48693] (3)
        8. Quinohemoprotein amine dehydrogenase C chain [69131] (1)
           uperfamily
           1. Quinohemoprotein amine dehydrogenase C chain [69132] (2)
              1. Quinohemoprotein amine dehydrogenase C chain [69133]
                 1. Paracoccus denitrificans [TaxId: 266] [69134] (2)
                 2. Pseudomonas putida [TaxId: 303] [69135] (2)
        9. Stathmin [101494] (1)
           single long helix crosslinking four tubulin subunits
           uperfamily
           1. Stathmin [101495] (1)
              1. Stathmin 4 [101496]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101497] (5)
        10. Anti-sigma factor FlgM [101498] (1)
            uperfamily
            1. Anti-sigma factor FlgM [101499] (1)
               1. Anti-sigma factor FlgM [101500]
                  1. Aquifex aeolicus [TaxId: 63363] [101501] (2)
        11. Glu-tRNAGln amidotransferase C subunit [141000] (1)
            uperfamily
            1. Glu-tRNAGln amidotransferase C subunit [141001] (1)
               Pfam 02686
               1. Glu-tRNAGln amidotransferase C subunit, GatC [141002]
                  1. Staphylococcus aureus [TaxId: 1280] [141003] (5)
                     SQ P68807 2-100
        12. RelB-like [141004] (1)
            wraps around RelE subunit
            uperfamily
            1. RelB-like [141005] (1)
               1. Hypothetical protein PHS014 [141006]
                  1. Pyrococcus horikoshii [TaxId: 53953] [141007] (2)
                     SQ O73967 7-67
        13. Lag-3 N-terminal region [158851] (1)
            long kinked helix, part of the CSL-Notch-Mastermind ternary complex
            1. Lag-3 N-terminal region [158852] (1)
               1. Abnormal cell lineage protein 3, Lag-3 [158853]
                  1. Caenorhabditis elegans [TaxId: 6239] [158854] (1)
                     SQ Q09260 52-114
        14. Lipase chaperone-like [158855] (1)
            open single layer scaffold of 11 helices, which engulfs the substrate protein
            1. Lipase chaperone LifO-like [158856] (1)
               Pfam 03280
               1. Lipase chaperone LifO (LipB) [158857]
                  1. Burkholderia glumae [TaxId: 337] [158858] (2)
                     SQ Q05490 73-352
   284. Multiheme cytochromes [48694] (1)
        variable number of helices and little beta structure; not a true fold
        1. Multiheme cytochromes [48695] (3)
           duplication: contains multiple CxxCH motifs
           uperfamily
           1. Cytochrome c3-like [48696] (13)
              1. Cytochrome c3 [48697]
                 contains four heme groups
                 1. Desulfovibrio desulfuricans, different strains [TaxId: 876] [48698] (8)
                    SQ Q9L915
                 2. Desulfovibrio vulgaris [TaxId: 881] [48699] (11)
                    SQ P00132
                 3. Desulfovibrio gigas [TaxId: 879] [48700] (3)
                 4. Desulfovibrio gigas, di-tetraheme cytochrome c3 [TaxId: 879] [74804] (1)
                    disulfide-crosslinked dimer
                 5. Desulfovibrio africanus [TaxId: 873] [48701] (2)
                 6. Desulfomicrobium norvegicum [TaxId: 52561] [48702] (1)
                    synonym: Desulfovibrio desulfuricans Norway
                 7. Desulfovibrio baculatus (Desulfomicrobium baculatus) [TaxId: 899] [117036] (1)
                    SQ Q6XCI5 # fragment
              2. Cytochrome c7 (cytochrome c551.5, PpcA) [48703]
                 contains three heme groups; deletion of one of Cyt c3 heme-binding sites
                 1. Desulfuromonas acetoxidans [TaxId: 891] [48704] (8)
                 2. Geobacter sulfurreducens, PpcA [TaxId: 35554] [101502] (1)
                 3. Geobacter sulfurreducens, GSU1996 [TaxId: 35554] [110039] (1)
                    SQ Q74BP5
              3. Nine-heme cytochrome c [48705]
                 tandem repeat of two cytochrome c3-like domains with additional heme-binding site in the domain interface
                 1. Desulfovibrio desulfuricans, ATCC 27774 [TaxId: 876] [48706] (3)
                 2. Desulfovibrio desulfuricans, ATCC 29577 [TaxId: 876] [63634] (1)
              4. 16-heme cytochrome c HmcA [81940]
                 tandem repeat of four cytochrome c3-like domains
                 1. Desulfovibrio vulgaris [TaxId: 881] [81941] (3)
           2. Photosynthetic reaction centre (cytochrome subunit) [48707] (2)
              consists of four heme-binding repeats
              1. Photosynthetic reaction centre (cytochrome subunit) [48708]
                 1. Rhodopseudomonas viridis [TaxId: 1079] [48709] (11)
                 2. Thermochromatium tepidum [TaxId: 1050] [48710] (1)
           3. Di-heme elbow motif [48711] (13)
              the main characteristic feature of this motif is the packing of its two hemes
              many members contains one or more complete motifs flanked by incomplete motifs and/or other domains
              1. Periplasmic nitrate reductase subunit NapB [74805]
                 1. Haemophilus influenzae [TaxId: 727] [74806] (1)
                 2. Rhodobacter sphaeroides [TaxId: 1063] [101503] (1)
              2. Hydroxylamine oxidoreductase, HAO [48712]
                 contains 3 complete motifs
                 1. Nitrosomonas europaea [TaxId: 915] [48713] (1)
              3. Cytochrome c554 [48714]
                 contains 1 complete motif
                 1. Nitrosomonas europaea [TaxId: 915] [48715] (3)
              4. Dimeric di-heme split-soret cytochrome c [48716]
                 1. Desulfovibrio desulfuricans, ATCC 27774 [TaxId: 876] [48717] (1)
              5. Cytochrome c nitrite reductase [48718]
                 1. Sulfurospirillum deleyianum [TaxId: 65553] [48719] (1)
                 2. Wolinella succinogenes [TaxId: 844] [48720] (6)
                 3. Escherichia coli [TaxId: 562] [74807] (5)
                 4. Desulfovibrio desulfuricans [TaxId: 876] [89173] (1)
              6. Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain [48721]
                 1. Shewanella frigidimarina [TaxId: 56812] [48722] (16)
                 2. Shewanella putrefaciens [TaxId: 24] [48723] (3)
                 3. Shewanella oneidensis [TaxId: 70863] [74808] (3)
              7. Putative Cytochrome c [110040]
                 1. Shewanella oneidensis [TaxId: 70863] [110041] (1)
                    SQ Q8E9W8 # SO4144
2. All beta proteins [48724] (174)
   1. Immunoglobulin-like beta-sandwich [48725] (28)
      sandwich; 7 strands in 2 sheets; greek-key
      some members of the fold have additional strands
      1. Immunoglobulin [48726] (4)
         uperfamily
         1. V set domains (antibody variable domain-like) [48727] (90)
            1. Immunoglobulin light chain kappa variable domain, VL-kappa [88519]
               VL-kappa domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VL-kappa domains with artificial or grafted exogenous CDRs are listed as engineered species
               1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88520] (18)
               2. Human (Homo sapiens), cluster 2 [TaxId: 9606] [88521] (10)
               3. Human (Homo sapiens), cluster 3.1 [TaxId: 9606] [88522] (10)
               4. Human (Homo sapiens), cluster 3.2 [TaxId: 9606] [88523] (68)
               5. Mouse (Mus musculus), cluster 1.1 [TaxId: 10090] [88524] (128)
                  SQ P01631 #KV2G_MOUSE Ig kappa chain V-II region 26-10; 79% sequence identity ! SQ P06310 # KV2F_HUMAN IG KAPPA CHAIN V-II REGION RPMI 6410 PRECURSOR ! SQ P03976 # KV2E_MOUSE (P03976) Ig kappa chain V-II region 17S29.1 ! SQ P01642 21-115 # ! KV2G_MOUSE IG KAPPA CHAIN V-II REGION 26-10
               6. Mouse (Mus musculus), cluster 1.2 [TaxId: 10090] [88525] (36)
               7. Mouse (Mus musculus), cluster 2 [TaxId: 10090] [88526] (34)
               8. Mouse (Mus musculus), cluster 3.1 [TaxId: 10090] [88527] (14)
               9. Mouse (Mus musculus), cluster 3.2 [TaxId: 10090] [88528] (65)
                  SQ P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1
               10. Mouse (Mus musculus), cluster 3.3 [TaxId: 10090] [88529] (2)
               11. Mouse (Mus musculus), cluster 3.4 [TaxId: 10090] [88530] (6)
               12. Mouse (Mus musculus), cluster 4 [TaxId: 10090] [88531] (189)
                   SQ P01645 1-106 # 95% sequense identity; KV5L_MOUSE Ig kappa chain V-V region HP 93G7 ! SQ NA # natural chimera; best hits are: SQ P01637 (Ig kappa chain V-V region T1) and SQ P01837 (Ig kappa chain C region) ! SQ NA # humanized antibody ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01642 21-115 # ! KV5I_MOUSE Ig kappa chain V-V region L7 precursor
               13. Rat (Rattus norvegicus) [TaxId: 10116] [88532] (11)
               14. Engineered (including hybrid species) [88533] (53)
                   SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
               15. synthetic construct [158859] (1)
               16. Escherichia coli [TaxId: 562] [158860] (8)
            2. Immunoglobulin light chain lambda variable domain, VL-lambda [88534]
               VL-lambda domains of human antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the human genome; mouse VL-lambda domains belong to a single germline family
               1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88535] (4)
                  SQ NA # Bence-Jones protein JTO ! SQ P06317 # Ig lambda chain V-VI region SUT
               2. Human (Homo sapiens), cluster 2 [TaxId: 9606] [88536] (11)
               3. Human (Homo sapiens), cluster 3.1 [TaxId: 9606] [88537] (3)
               4. Human (Homo sapiens), cluster 3.2 [TaxId: 9606] [88538] (1)
               5. Human (Homo sapiens), cluster 4 [TaxId: 9606] [88539] (23)
               6. Human (Homo sapiens), cluster 5 [TaxId: 9606] [88540] (9)
                  SQ Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
               7. Mouse (Mus musculus) [TaxId: 10090] [88541] (35)
               8. Rat (Rattus norvegicus) [TaxId: 10116] [101504] (8)
               9. Hamster (Cricetulus griseus) [TaxId: 10029] [88542] (1)
            3. Immunoglobulin heavy chain variable domain, VH [88543]
               VH domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VH domains with artificial or grafted exogenous CDRs are listed as engineered species
               1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88544] (47)
               2. Human (Homo sapiens), cluster 2.1 [TaxId: 9606] [88545] (3)
               3. Human (Homo sapiens), cluster 2.2 [TaxId: 9606] [88546] (3)
               4. Human (Homo sapiens), cluster 3 [TaxId: 9606] [88547] (66)
                  SQ Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
               5. Human (Homo sapiens), cluster 4 [TaxId: 9606] [101505] (4)
               6. Mouse (Mus musculus), cluster 1 [TaxId: 10090] [88548] (51)
                  SQ P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
               7. Mouse (Mus musculus), cluster 2.1 [TaxId: 10090] [88549] (14)
                  SQ P18527 # HV56_MOUSE Ig heavy chain V region 914; 90% sequence identity
               8. Mouse (Mus musculus), cluster 2.2 [TaxId: 10090] [88550] (55)
                  SQ P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
               9. Mouse (Mus musculus), cluster 3.1 [TaxId: 10090] [88551] (34)
                  SQ NA # natural chimera; best hits are: SQ P01751 (Ig heavy chain V region B1-8/186-2) and SQ P01864 (Ig gamma-2A chain C region secreted form)
               10. Mouse (Mus musculus), cluster 3.2 [TaxId: 10090] [88552] (156)
                   SQ P01756 1-117 # 78% sequense identity; HV12_MOUSE Ig heavy chain V region MOPC 104E ! SQ NA # humanized antibody ! SQ P01750 # HV06_MOUSE Ig heavy chain V region 102 precursor ! SQ P01750 20-116 # ! HV06_MOUSE Ig heavy chain V region 102 precursor
               11. Mouse (Mus musculus), cluster 3.3 [TaxId: 10090] [88553] (1)
               12. Mouse (Mus musculus), cluster 4 [TaxId: 10090] [88554] (35)
                   SQ P06327 20-117 # HV52_MOUSE (P06327) Ig heavy chain V region VH558 A1/A4 precursor; 57% sequence identity ! SQ P01631 # KV2G_MOUSE (P01631) Ig kappa chain V-II region 26-10
               13. Mouse (Mus musculus), cluster 5 [TaxId: 10090] [88555] (36)
               14. Mouse (Mus musculus), cluster 6 [TaxId: 10090] [88556] (12)
                   SQ NA # part of Fab 28 against HIV-1 RT
               15. Mouse (Mus musculus), cluster 7.1 [TaxId: 10090] [88557] (41)
                   SQ P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
               16. Mouse (Mus musculus), cluster 7.2 [TaxId: 10090] [88558] (29)
               17. Mouse (Mus musculus), cluster 7.3 [TaxId: 10090] [88559] (2)
               18. Rat (Rattus norvegicus) [TaxId: 10116] [88560] (17)
               19. Hamster (Cricetulus griseus) [TaxId: 10029] [88561] (1)
               20. Engineered (including hybrid species) [88562] (82)
                   SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
               21. Escherichia coli [TaxId: 562] [158861] (3)
               22. synthetic construct [158862] (2)
            4. Camelid IG heavy chain variable domain, VHh [88563]
               1. Camel (Camelus dromedarius) [TaxId: 9838] [88564] (23)
                  SQ NA # camelid antibody
               2. Llama (Lama glama) [TaxId: 9844] [88565] (9)
               3. Homo sapiens [TaxId: 9606] [158863] (2)
            5. T-cell antigen receptor [48933]
               sequences may differ within each classified species
               1. Mouse (Mus musculus), alpha-chain [TaxId: 10090] [48934] (25)
               2. Human (Homo sapiens), alpha-chain [TaxId: 9606] [48935] (21)
               3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [48936] (36)
               4. Human (Homo sapiens), beta-chain [TaxId: 9606] [48937] (52)
               5. Human (Homo sapiens), gamma-chain [TaxId: 9606] [63651] (11)
               6. Human (Homo sapiens), delta-chain [TaxId: 9606] [48938] (4)
            6. Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939]
               1. Human (Homo sapiens) [TaxId: 9606] [48940] (3)
               2. Mouse (Mus musculus) [TaxId: 10090] [48941] (1)
            7. Myelin membrane adhesion molecule P0 [48728]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [48729] (1)
            8. Myelin oligodendrocyte glycoprotein (MOG) [89174]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [89175] (3)
            9. Coxsackie virus and adenovirus receptor (Car), domain 1 [48730]
               1. Human (Homo sapiens) [TaxId: 9606] [48731] (19)
            10. N-terminal domain of sialoadhesin [48732]
                1. Mouse (Mus musculus) [TaxId: 10090] [48733] (8)
                   SQ Q62230 20-130
            11. N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176]
                1. Human (Homo sapiens) [TaxId: 9606] [89177] (6)
            12. NK cell activating receptor NKP44 [89178]
                a triggering partner in natural cytotoxicity
                1. Human (Homo sapiens) [TaxId: 9606] [89179] (1)
            13. TREM-1 (triggering receptor expressed on myeloid cells 1) [101506]
                1. Human (Homo sapiens) [TaxId: 9606] [101507] (2)
                   SQ Q9NP99 21-133
                2. Mouse (Mus musculus) [TaxId: 10090] [117037] (1)
                   SQ Q9JKE2 25-134
            14. CD8 [48734]
                1. Human (Homo sapiens) [TaxId: 9606] [48735] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [48736] (6)
                3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [158864] (2)
                   SQ P10300 22-136
            15. CD4 V-set domains [48737]
                1. Human (Homo sapiens) [TaxId: 9606] [48738] (27)
                2. Rat (Rattus rattus) [TaxId: 10117] [48739] (1)
            16. CD2, first domain [48740]
                1. Human (Homo sapiens) [TaxId: 9606] [48741] (4)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [48742] (5)
            17. CD2-binding domain of CD58, N-terminal domain [48743]
                1. Human (Homo sapiens) [TaxId: 9606] [48744] (3)
            18. CD80, N-terminal domain [48745]
                a soluble form of b7-1
                1. Human (Homo sapiens) [TaxId: 9606] [48746] (2)
            19. CD86 (b7-2), N-terminal domain [63635]
                1. Human (Homo sapiens) [TaxId: 9606] [63636] (2)
            20. Junction adhesion molecule, JAM, N-terminal domain [48747]
                1. Mouse (Mus musculus) [TaxId: 10090] [48748] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [89180] (1)
            21. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942]
                1. Mouse (Mus musculus) [TaxId: 10090] [81943] (1)
            22. Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508]
                1. Human (Homo sapiens) [TaxId: 9606] [101509] (1)
            23. Programmed cell death protein 1, PD1, extracellular domain [101510]
                1. Mouse (Mus musculus) [TaxId: 10090] [101511] (4)
            24. HSV glycoprotein D [63637]
                1. Herpes simplex virus type 1 [TaxId: 10298] [63638] (2)
                   elaborated with insertions and N- and C-terminal extensions
            25. Novel antigen receptor (against lysozyme) [110042]
                1. Nurse shark (Ginglymostoma cirratum) [TaxId: 7801] [110043] (7)
                   SQ Q8AXI4 # fragment
            26. Novel antigen receptor 12Y-1 [110044]
                1. Spotted wobbegong (Orectolobus maculatus) [TaxId: 168098] [110045] (1)
                   SQ Q6X1E7 # fragment
            27. Novel antigen receptor 12Y-2 [110046]
                1. Spotted wobbegong (Orectolobus maculatus) [TaxId: 168098] [110047] (1)
                   SQ Q6X1E6 # fragment
            28. Polymeric-immunoglobulin receptor, PIGR [117038]
                1. Human (Homo sapiens) [TaxId: 9606] [117039] (1)
                   SQ P01833 20-127 # N-terminal, ligand-binding domain
            29. Alphaherpesvirus glycoprotein E [141008]
                elaborated with insertions and C-terminal extensions
                1. Human herpesvirus 1 [TaxId: 10298] [141009] (4)
                   SQ P04488 218-394! SQ P04488 220-390
            30. CD28 [158865]
                T-cell-specific surface glycoprotein
                1. Human (Homo sapiens) [TaxId: 9606] [158866] (1)
                   SQ P10747 19-136
            31. Kin of IRRE-like protein 3, KIRREL3 [158867]
                1. Human (Homo sapiens) [TaxId: 9606] [158868] (1)
                   SQ Q8IZU9 413-521
            32. B- and T-lymphocyte attenuator CD272 [158869]
                1. Human (Homo sapiens) [TaxId: 9606] [158870] (2)
                   SQ Q7Z6A9 34-137
         2. C1 set domains (antibody constant domain-like) [48942] (70)
            1. Immunoglobulin light chain kappa constant domain, CL-kappa [88566]
               1. Mouse (Mus musculus) [TaxId: 10090] [88567] (347)
                  SQ P01837# KAC_MOUSE Ig kappa chain C region; 99% sequence identity ! SQ NA # natural chimera; best hits are: SQ P01637 (Ig kappa chain V-V region T1) and SQ P01837 (Ig kappa chain C region) ! SQ P01837 # KAC_MOUSE Ig kappa chain C region ! SQ P01837 # KAC_MOUSE (P01837) Ig kappa chain C region ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01837 # ! KAC_MOUSE Ig kappa chain C region
               2. Rat (Rattus norvegicus) [TaxId: 10116] [88568] (8)
               3. Human (Homo sapiens) [TaxId: 9606] [88569] (168)
                  SQ NA # humanized antibody ! SQ P01834 # KAC_HUMAN Ig kappa chain C region ! SQ P01834 # KAC_HUMAN Ig kappa chain C region. ! SQ NA # engineered antibody
                  including humanized antibodies (chimeric proteins with human constant domains)
               4. synthetic construct [158871] (1)
               5. Escherichia coli [TaxId: 562] [158872] (8)
            2. Immunoglobulin light chain lambda constant domain, CL-lambda [88570]
               1. Mouse (Mus musculus) [TaxId: 10090] [88571] (21)
                  SQ Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
               2. Human (Homo sapiens) [TaxId: 9606] [88572] (49)
               3. Hamster (Cricetulus griseus) [TaxId: 10029] [88573] (1)
            3. Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma [88574]
               1. Human (Homo sapiens) [TaxId: 9606] [88575] (256)
                  SQ Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3) ! SQ NA # humanized antibody ! SQ P01857 # IGHG1_HUMAN Ig gamma-1 chain C region ! SQ NA # engineered antibody
                  including humanized antibodies (chimeric proteins with human constant domains)
               2. Mouse (Mus musculus) [TaxId: 10090] [88576] (412)
                  SQ P01864 # GCAB_MOUSE Ig gamma-2A chain C region secreted form (B allele) ! SQ P01863 #GCAA_MOUSE Ig gamma-2A chain C region, A allele; 86% sequence identity ! SQ NA # natural chimera; best hits are: SQ P01751 (Ig heavy chain V region B1-8/186-2) and SQ P01864 (Ig gamma-2A chain C region secreted form) ! SQ P01868 # GC1_MOUSE Ig gamma-1 chain C region secreted form ! SQ P01864 # GCAB_MOUSE (P01864) Ig gamma-2A chain C region ! SQ P01837 # KAC_MOUSE (P01837) Ig kappa chain C region ! SQ P01863 # GCAA_MOUSE Ig gamma-2A chain C region, A allele ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01868 # ! GC1_MOUSE Ig gamma-1 chain C region secreted form
               3. Mouse (Mus musculus), gamma3 [TaxId: 10090] [88577] (8)
                  SQ P22436 # GC3_MOUSE (P22436) Ig gamma-3 chain C region
               4. Rat (Rattus norvegicus) [TaxId: 10116] [88578] (6)
               5. Hamster (Cricetulus griseus) [TaxId: 10029] [88579] (1)
               6. Escherichia coli [TaxId: 562] [158873] (3)
               7. synthetic construct [158874] (2)
            4. Immunoglobulin heavy chain alpha constant domain 1, CH1-alpha [88580]
               1. Mouse (Mus musculus) [TaxId: 10090] [88581] (3)
            5. Immunoglobulin heavy chain mu constant domain 1, CH1-mu [88582]
               1. Human (Homo sapiens) [TaxId: 9606] [88583] (8)
            6. Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma [88584]
               1. Human (Homo sapiens) [TaxId: 9606] [88585] (34)
                  SQ P01857 #118-327 ! SQ P01857 118-327 # GC1_HUMAN Ig gamma-1 chain C region
               2. Mouse (Mus musculus) [TaxId: 10090] [88586] (1)
               3. Mouse (Mus musculus), gamma2 [TaxId: 10090] [88587] (1)
               4. Rat (Rattus norvegicus) [TaxId: 10116] [88588] (2)
            7. Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma [88589]
               1. Human (Homo sapiens) [TaxId: 9606] [88590] (37)
                  SQ P01857 #118-327 ! SQ P01857 118-327 # GC1_HUMAN Ig gamma-1 chain C region
               2. Mouse (Mus musculus) [TaxId: 10090] [88591] (2)
               3. Mouse (Mus musculus), gamma2 [TaxId: 10090] [88592] (1)
               4. Rat (Rattus norvegicus) [TaxId: 10116] [88593] (2)
               5. Guinea pig (Cavia porcellus) [TaxId: 10141] [49123] (1)
            8. Immunoglobulin heavy chain alpha constant domain 2, CH2-alpha [89181]
               1. Human (Homo sapiens) [TaxId: 9606] [89182] (3)
            9. Immunoglobulin heavy chain alpha constant domain 3, CH3-alpha [89183]
               1. Human (Homo sapiens) [TaxId: 9606] [89184] (3)
            10. Immunoglobulin heavy chain epsilon constant domain 2, CH2-epsilon [88594]
                1. Human (Homo sapiens) [TaxId: 9606] [88595] (2)
            11. Immunoglobulin heavy chain epsilon constant domain 3, CH3-epsilon [88596]
                1. Human (Homo sapiens) [TaxId: 9606] [88597] (3)
            12. Immunoglobulin heavy chain epsilon constant domain 4, CH4-epsilon [88598]
                1. Human (Homo sapiens) [TaxId: 9606] [88599] (3)
            13. T-cell antigen receptor [49125]
                1. Mouse (Mus musculus), alpha-chain [TaxId: 10090] [49126] (15)
                2. Human (Homo sapiens), alpha-chain [TaxId: 9606] [49127] (24)
                3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [49128] (19)
                4. Human (Homo sapiens), beta-chain [TaxId: 9606] [49129] (39)
                5. Human (Homo sapiens), gamma-chain [TaxId: 9606] [63661] (3)
                6. Human (Homo sapiens), delta-chain [TaxId: 9606] [63662] (3)
            14. beta2-microglobulin [88600]
                1. Cow (Bos taurus) [TaxId: 9913] [48946] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [88601] (6)
                3. Human (Homo sapiens) [TaxId: 9606] [88602] (228)
                   SQ P61769 21-119 ! SQ P01884
                4. Mouse (Mus musculus) [TaxId: 10090] [88603] (106)
                   SQ P01887
            15. Class I MHC, alpha-3 domain [88604]
                1. Human (Homo sapiens) [TaxId: 9606] [88605] (189)
                   SQ P30685 25-300 ! SQ P30443 25-298 # 1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain precursor ! SQ P30481 25-300 ! SQ P01892 25-298 ! SQ P13746 25-299 # 1A11_HUMAN HLA class I histocompatibility antigen, A-11 alpha chain precursor
                2. Mouse (Mus musculus) [TaxId: 10090] [88606] (109)
                   SQ P01901 22-299
                3. Rat (Rattus norvegicus), RT1-AA [TaxId: 10116] [88607] (3)
                4. Rhesus monkey (Macaca mulatta) [TaxId: 9544] [158875] (2)
            16. Hemochromatosis protein Hfe, alpha-3 domain [88608]
                1. Human (Homo sapiens) [TaxId: 9606] [88609] (2)
            17. Zinc-alpha-2-glycoprotein, ZAG, alpha-3 domain [48965]
                fat depleting factor related to class I MHC
                1. Human (Homo sapiens) [TaxId: 9606] [48966] (7)
                   SQ P25311 22-294
            18. Class I MHC homolog, alpha-3 domain [88610]
                gamma, delta T-cell ligand
                1. Human (Homo sapiens), Mic-a [TaxId: 9606] [48968] (2)
                2. Human (Homo sapiens), Mic-b [TaxId: 9606] [74826] (1)
                3. Mouse (Mus musculus), t22 [TaxId: 10090] [88611] (3)
                4. Mouse (Mus musculus), t10 [TaxId: 10090] [101512] (1)
            19. Fc (IgG) receptor, alpha-3 domain [88612]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88613] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [88614] (1)
            20. CD1, alpha-3 domain [88615]
                1. Mouse (Mus musculus) [TaxId: 10090] [88616] (10)
                2. Human (Homo sapiens), CD1b [TaxId: 9606] [88617] (3)
                3. Human (Homo sapiens), CD1a [TaxId: 9606] [101513] (4)
                4. Human (Homo sapiens), CD1d [TaxId: 9606] [158876] (4)
                   SQ P15813 202-295
            21. Class II MHC alpha chain, C-terminal domain [88618]
                1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88619] (1)
                   probably orthologous to the mouse H2-DM
                2. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88620] (1)
                   probably orthologous to the human HLA-DM
                3. Human (Homo sapiens), HLA-DR group [TaxId: 9606] [88621] (29)
                   SQ P01903 28-207
                   probably orthologous to the mouse I-E group
                4. Mouse (Mus musculus), I-E group [TaxId: 10090] [88622] (9)
                   probably orthologous to the human HLA-DR group
                5. Human (Homo sapiens), HLA-DQ group [TaxId: 9606] [88623] (3)
                   probably orthologous to the mouse I-A group
                6. Mouse (Mus musculus), I-A group [TaxId: 10090] [88624] (39)
                   probably orthologous to the human HLA-DQ group
            22. Class II MHC beta chain, C-terminal domain [88625]
                1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88626] (1)
                   probably orthologous to the mouse H2-DM
                2. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88627] (1)
                   probably orthologous to the human HLA-DM
                3. Human (Homo sapiens), HLA-DR group [TaxId: 9606] [88628] (48)
                   SQ P04229 30-219
                   probably orthologous to the mouse I-E group
                4. Mouse (Mus musculus), I-E group [TaxId: 10090] [88629] (9)
                   probably orthologous to the human HLA-DR group
                5. Human (Homo sapiens), HLA-DQ group [TaxId: 9606] [88630] (3)
                   probably orthologous to the mouse I-A group
                6. Mouse (Mus musculus), I-A group [TaxId: 10090] [88631] (20)
                   probably orthologous to the human HLA-DQ group
            23. Immunomodulatory protein m144, alpha-3 domain [110048]
                1. Murine cytomegalovirus [TaxId: 10366] [110049] (2)
                   SQ Q69G19 27-263 # 95% sequence identity
         3. C2 set domains [49142] (10)
            1. Vascular cell adhesion molecule-1 (VCAM-1) [49143]
               1. Human (Homo sapiens) [TaxId: 9606] [49144] (3)
            2. Intercellular cell adhesion molecule-1 (ICAM-1) [49145]
               1. Human (Homo sapiens) [TaxId: 9606] [49146] (8)
            3. Intercellular cell adhesion molecule-2 (ICAM-2) [49147]
               1. Human (Homo sapiens) [TaxId: 9606] [49148] (1)
            4. CD4 C2-set domains [49149]
               1. Human (Homo sapiens) [TaxId: 9606] [49150] (27)
               2. Rat (Rattus rattus) [TaxId: 10117] [49151] (1)
            5. CD2, second domain [49152]
               1. Human (Homo sapiens) [TaxId: 9606] [49153] (1)
               2. Rat (Rattus norvegicus) [TaxId: 10116] [49154] (1)
            6. CD2-binding domain of CD58, second domain [49155]
               1. Human (Homo sapiens) [TaxId: 9606] [49156] (1)
            7. CD80, second domain [49157]
               a soluble form of b7-1
               1. Human (Homo sapiens) [TaxId: 9606] [49158] (2)
            8. Granulocyte colony-stimulating factor (GC-SF) receptor, N-terminal domain [141010]
               1. Human (Homo sapiens) [TaxId: 9606] [141011] (1)
                  SQ Q99062 26-119
         4. I set domains [49159] (53)
            1. Vascular cell adhesion molecule-1 (VCAM-1) [49160]
               1. Human (Homo sapiens) [TaxId: 9606] [49161] (3)
            2. Intercellular adhesion molecule-1, ICAM-1 [49162]
               1. Human (Homo sapiens) [TaxId: 9606] [49163] (10)
            3. Intercellular adhesion molecule-2, ICAM-2 [49164]
               1. Human (Homo sapiens) [TaxId: 9606] [49165] (1)
            4. Neural cell adhesion molecule (NCAM) [49166]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [49167] (4)
                  Rat and mouse sequences are identical for the two N-terminal modules
               2. Chicken (Gallus gallus) [TaxId: 9031] [63664] (1)
            5. Mucosal addressin cell adhesion molecule-1 (MADCAM-1) [49168]
               1. Human (Homo sapiens) [TaxId: 9606] [49169] (2)
            6. Telokin [49170]
               1. Turkey (Meleagris gallopavo) [TaxId: 9103] [49171] (2)
               2. Human (Homo sapiens) [TaxId: 9606] [141012] (1)
                  SQ Q9UIT9 1238-1338
            7. Cardiac myosin binding protein C, different domains [89185]
               1. Human (Homo sapiens) [TaxId: 9606] [89186] (3)
                  SQ Q14896 358-451, 641-770
            8. Titin [49172]
               1. Human (Homo sapiens), different modules [TaxId: 9606] [49173] (5)
            9. Twitchin [49174]
               1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [49175] (3)
                  different modules
               2. Human (Homo sapiens), Ig repeat 27 [TaxId: 9606] [49176] (2)
            10. Type-1 interleukin-1 receptor [49177]
                duplication: tandem repeat of 3 domains
                1. Human (Homo sapiens) [TaxId: 9606] [49178] (3)
            11. Fibroblast growth factor receptor, FGFR [49179]
                1. Human (Homo sapiens), FGFR1 [TaxId: 9606] [49180] (7)
                2. Human (Homo sapiens), FGFR2a [TaxId: 9606] [49181] (8)
                3. Human (Homo sapiens), FGFR2b [TaxId: 9606] [81955] (1)
                4. Human (Homo sapiens), FGFR3c [TaxId: 9606] [101514] (1)
            12. Hemolin [49182]
                Duplication: tandem repeat of 4 domains, known as L1 domains
                1. Moth (Hyalophora cecropia) [TaxId: 7123] [49183] (1)
            13. Semaphorin 4d Ig-like domain [101515]
                1. Human (Homo sapiens) [TaxId: 9606] [101516] (1)
            14. Axonin-1 [49184]
                tandem repeat of 4 L1 domains
                1. Chicken (Gallus gallus) [TaxId: 9031] [49185] (1)
            15. Perlecan Ig3 domain [69158]
                1. Mouse (Mus musculus) [TaxId: 10090] [69159] (1)
            16. Junction adhesion molecule, JAM, C-terminal domain [49186]
                1. Mouse (Mus musculus) [TaxId: 10090] [49187] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [89187] (1)
            17. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), C-terminal domain [81956]
                1. Mouse (Mus musculus) [TaxId: 10090] [81957] (1)
            18. Second domain of the Flt-1 receptor [49188]
                1. Human (Homo sapiens) [TaxId: 9606] [49189] (5)
            19. Tyrosine-protein kinase receptor tyro3, second domain [101517]
                1. Human (Homo sapiens) [TaxId: 9606] [101518] (1)
            20. High affinity nerve growth factor receptor TrkA, different domains [49190]
                1. Human (Homo sapiens) [TaxId: 9606] [49191] (7)
            21. Ligand binding domain of trkB receptor [49192]
                1. Human (Homo sapiens) [TaxId: 9606] [49193] (2)
            22. NT3 binding domain of trkC receptor [49194]
                1. Human (Homo sapiens) [TaxId: 9606] [49195] (1)
            23. Fc gamma receptor ectodomain (CD32) [49196]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens), IIa [TaxId: 9606] [49197] (2)
                2. Human (Homo sapiens), IIb [TaxId: 9606] [49198] (1)
                3. Human (Homo sapiens), III [TaxId: 9606] [49199] (5)
                   SQ O75015 23-189
            24. IgE high affinity receptor alpha subunit [49200]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens) [TaxId: 9606] [49201] (7)
                   SQ P12319 29-196
            25. Ig alpha Fc receptor, FCARI (CD89) [89188]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens) [TaxId: 9606] [89189] (3)
            26. Killer cell inhibitory receptor [49202]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens), kir2dl3 [TaxId: 9606] [49203] (2)
                2. Human (Homo sapiens), kir2ds3, CD158j [TaxId: 9606] [89190] (1)
                3. Human (Homo sapiens), p58-cl42 kir [TaxId: 9606] [49204] (2)
                4. Human (Homo sapiens), 2dl2 [TaxId: 9606] [49205] (2)
            27. Ligand binding domain of lir-1 (ilt2) [49206]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens) [TaxId: 9606] [49207] (8)
                   SQ Q8NHL6 25-218
            28. Ligand binding domain of NK receptor NKp46 [101519]
                possibly an intermediate structure between the I set and FnIII domains
                1. Human (Homo sapiens) [TaxId: 9606] [101520] (2)
            29. The p40 domain of interleukin-12 (IL-12 beta chain), N-terminal domain [63665]
                1. Human (Homo sapiens) [TaxId: 9606] [63666] (7)
            30. Interleukin-6 receptor alpha chain, N-terminal domain [81958]
                1. Human (Homo sapiens) [TaxId: 9606] [81959] (1)
            31. CD3 gamma chain ectodomain fragment [69160]
                possibly an intermediate structure between the I set and FnIII domains
                1. Mouse (Mus musculus) [TaxId: 10090] [69161] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [110050] (1)
                   SQ P09693 # CD3G_HUMAN T-cell surface glycoprotein CD3 gamma chain precursor
            32. CD3 epsilon chain ectodomain fragment [69162]
                possibly an intermediate structure between the I set and FnIII domains
                1. Mouse (Mus musculus) [TaxId: 10090] [69163] (2)
                   SQ P22646 22-100
                2. Human (Homo sapiens) [TaxId: 9606] [110051] (2)
                   SQ P07766 33-123 ! SQ P07766 # CD3E_HUMAN T-cell surface glycoprotein CD3 epsilon chain precursor
                3. Sheep (Ovis aries) [TaxId: 9940] [117040] (1)
                   SQ P18438 22-88
            33. B and T lymphocyte attenuator, Btla [117041]
                1. Mouse (Mus musculus) [TaxId: 10090] [117042] (1)
                   SQ Q7TSA3 40-143
            34. CD3 delta chain ectodomain fragment [117043]
                1. Human (Homo sapiens) [TaxId: 9606] [117044] (1)
                   SQ P04234 23-95
            35. Myosin-binding protein C, slow-type [141013]
                1. Human (Homo sapiens) [TaxId: 9606] [141014] (2)
                   SQ Q00872 342-431! SQ Q00872 58-170
            36. Receptor-type tyrosine-protein phosphatase mu [141015]
                1. Human (Homo sapiens) [TaxId: 9606] [141016] (1)
                   SQ P28827 184-279
            37. Cervical EMMPRIN [158877]
                contains two Ig-domains in the N-terminal part
                1. Human (Homo sapiens) [TaxId: 9606] [158878] (8)
                   SQ Q54A51 103-203! SQ Q54A51 23-102
            38. Ligand binding domain of lir-2 (ilt4) [158879]
                1. Human (Homo sapiens) [TaxId: 9606] [158880] (2)
                   SQ Q8N423 120-218! SQ Q8N423 26-109
      2. E set domains [81296] (23)
         "Early" Ig-like fold families possibly related to the immunoglobulin and/or fibronectin type III superfamilies
         uperfamily
         1. NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain [81279] (10)
            subgroup of the larger IPT/TIG domain family
            1. T-cell transcription factor NFAT1 (NFATC2) [49246]
               1. Human (Homo sapiens) [TaxId: 9606] [49247] (10)
            2. T-cell transcription factor NFAT5 (TONEBP) [69170]
               1. Human (Homo sapiens) [TaxId: 9606] [69171] (1)
            3. p50 subunit of NF-kappa B transcription factor [49248]
               1. Human (Homo sapiens) [TaxId: 9606] [49249] (9)
                  SQ P25799 245-350
               2. Mouse (Mus musculus) [TaxId: 10090] [49250] (10)
            4. p52 subunit of NF-kappa B (NFKB) [49251]
               1. Human (Homo sapiens) [TaxId: 9606] [49252] (1)
            5. p65 subunit of NF-kappa B (NFKB), dimerization domain [49253]
               1. Mouse (Mus musculus) [TaxId: 10090] [49254] (10)
               2. Human (Homo sapiens) [TaxId: 9606] [49255] (4)
               3. Chicken (Gallus gallus), C-rel [TaxId: 9031] [74848] (1)
            6. DNA-binding protein LAG-1 (CSL) [110052]
               1. Caenorhabditis elegans [TaxId: 6239] [110053] (4)
                  SQ Q9TYY1 195-660
            7. Calmodulin binding transcription activator 1 [141017]
               this domain is in the middle of long protein chain
               1. Human (Homo sapiens) [TaxId: 9606] [141018] (5)
                  SQ Q9Y6Y1 872-953
         2. E-set domains of sugar-utilizing enzymes [81282] (30)
            domains of unknown function associated with different type of catalytic domains in a different sequential location
            subgroup of the larger IPT/TIG domain family
            1. Galactose oxidase, C-terminal domain [49209]
               follows the catalytic seven-bladed beta-propeller domain
               1. Dactylium dendroides [TaxId: 5132] [49210] (8)
                  SQ Q01745 42-680
               2. Fungi (Fusarium sp.) [TaxId: 29916] [69164] (1)
                  sequence identical to that of Dactylium dendroides
               3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [158881] (3)
            2. Sialidase, "linker" domain [49237]
               follows the catalytic six-bladed beta-propeller domain
               1. Micromonospora viridifaciens [TaxId: 1881] [49238] (8)
                  SQ Q02834 47-647
            3. CelD cellulase, N-terminal domain [49231]
               precedes the catalytic alpha6/alpha6 domain
               1. Clostridium thermocellum [TaxId: 1515] [49232] (1)
            4. Cellulose 1,4-beta-cellobiosidase CbhA, precatalytic domain [101521]
               1. Clostridium thermocellum [TaxId: 1515] [101522] (2)
            5. Hyaluronate lyase precatalytic domain [69167]
               precedes the catalytic incomplete alpha5/alpha5 barrel
               a rudiment form of Ig-like domain
               1. Streptococcus agalactiae [TaxId: 1311] [69168] (3)
            6. Bacterial chitobiase (N-acetyl-beta-glucoseaminidase), C-terminal domain [49211]
               rudiment form of Ig-like domain; follows the catalytic (beta/alpha)8-barrel domain; family 20 glycosyl hydrolases
               1. Serratia marcescens [TaxId: 615] [49212] (4)
            7. Cyclomaltodextrin glycanotransferase, domain D [49215]
               follows the starch-binding domain C; the catalytic domain A has (beta/alpha)8-barrel fold; family 13 glycosyl hydrolases
               1. Bacillus circulans, different strains [TaxId: 1397] [49216] (36)
               2. Bacillus stearothermophilus [TaxId: 1422] [49217] (1)
               3. Bacillus sp., strain 1011 [TaxId: 1409] [49219] (8)
                  SQ P05618
               4. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [49220] (2)
               5. Thermoanaerobacterium [TaxId: 28895] [158882] (2)
            8. Five domain "maltogenic" alpha-amylase (glucan 1,4-alpha-maltohydrolase), domain D [81280]
               domain architecture similar to cyclomaltodextrin glycosylhydrolases
               1. Bacillus stearothermophilus [TaxId: 1422] [81281] (2)
            9. Maltogenic amylase, N-terminal domain N [49221]
               precedes the catalytic (beta/alpha)8-barrel domain
               1. Thermus sp. [TaxId: 275] [49222] (2)
               2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [74842] (1)
               3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [74843] (9)
               4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [49223] (25)
            10. Neopullulanase, N-terminal domain [81960]
                homologous to maltogenic amylase
                1. Bacillus stearothermophilus [TaxId: 1422] [81961] (4)
            11. Cyclomaltodextrinase, N-terminal domain [101523]
                protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
                1. Flavobacterium sp. 92 [TaxId: 197856] [101524] (1)
            12. Isoamylase, N-terminal domain N [49226]
                elaborated with a few large insertions in the common fold
                precedes the catalytic (beta/alpha)8-barrel domain, the domain architecture similar to maltogenic amylases
                1. Pseudomonas amyloderamosa [TaxId: 32043] [49227] (1)
            13. Glycosyltrehalose trehalohydrolase, N-terminal domain N [49224]
                domain architecture similar to isoamylase
                1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [49225] (2)
                2. Deinococcus radiodurans [TaxId: 1299] [141019] (9)
                   SQ Q9RX51 14-110
            14. 1,4-alpha-glucan branching enzyme, N-terminal domain N [81962]
                domain architecture similar to isoamylase
                1. Escherichia coli [TaxId: 562] [81963] (1)
            15. Chitinase A, N-terminal domain N [49233]
                precedes the catalytic (beta/alpha)8-barrel domain
                1. Serratia marcescens [TaxId: 615] [49234] (11)
                   SQ P07254 24-563
            16. Glucodextranase, domain B [101525]
                1. Arthrobacter globiformis [TaxId: 1665] [101526] (2)
            17. Glucans biosynthesis protein G (MdoG, OpgG), C-terminal domain [110054]
                1. Escherichia coli [TaxId: 562] [110055] (1)
                   SQ P33136 23-511
            18. Chitin-binding protein CBP21 [117045]
                member of Pfam 03067; elaborated fold with a large insertion between strands A and A'
                1. Serratia marcescens [TaxId: 615] [117046] (2)
                   SQ O83009 28-197
            19. Beta-1,4-mannanase domain 2 (postcatalytic) [141020]
                1. Cellulomonas fimi [TaxId: 1708] [141021] (3)
                   SQ Q9XCV5 421-514
            20. Pullulanase PulA [158883]
                contains two E-set domains in tandem
                1. Klebsiella pneumoniae [TaxId: 573] [158884] (6)
                   SQ P07206 170-294! SQ P07206 295-409
         3. Other IPT/TIG domains [89191] (1)
            apart from the domains of transcription factors and sugar-utilizing enzymes
            1. Exocyst complex component Sec5, Ral-binding domain [89192]
               1. Mouse (Mus musculus) [TaxId: 10090] [89193] (2)
         4. Arthropod hemocyanin, C-terminal domain [81283] (2)
            1. Arthropod hemocyanin, C-terminal domain [49228]
               elaborated with many loop insertions in the common fold
               1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [49229] (4)
               2. Spiny lobster (Panulirus interruptus) [TaxId: 6735] [49230] (7)
         5. Class II viral fusion proteins C-terminal domain [81284] (6)
            1. Envelope glycoprotein [49213]
               1. Tick-borne encephalitis virus [TaxId: 11084] [49214] (2)
               2. Dengue virus type 2 [TaxId: 11060] [89194] (12)
                  SQ P12823 281-675 # 99% sequence identity
               3. Japanese encephalitis virus [TaxId: 11072] [101527] (1)
               4. West Nile virus [TaxId: 11082] [110056] (5)
                  SQ Q8JU42 586-696
               5. Langat virus [TaxId: 11085] [141022] (2)
                  SQ P29838 583-765
            2. Fusion glycoprotein E1 [74840]
               1. Semliki forest virus [TaxId: 11033] [74841] (5)
         6. Cytomegalovirus protein US2 [81285] (1)
            1. Cytomegalovirus protein US2 [63668]
               similar to both C1 and C2 set
               1. Human cytomegalovirus [TaxId: 10359] [63669] (1)
         7. Molybdenum-containing oxidoreductases-like dimerisation domain [81286] (2)
            1. Sulfite oxidase, C-terminal domain [49259]
               1. Chicken (Gallus gallus) [TaxId: 9031] [49260] (5)
               2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [101528] (1)
         8. ML domain [81287] (3)
            implicated in lipid recognition, particularly in the recognition of pathogen related products
            1. Epididymal secretory protein E1 (Niemann-Pick C2 protein) [81964]
               a cholesterol binding protein
               1. Cow (Bos taurus) [TaxId: 9913] [81965] (4)
            2. Major mite allergen [49256]
               contains additional N-terminal strand
               1. House-dust mite (Dermatophagoides farinae), Der f 2 [TaxId: 6954] [49257] (8)
                  SQ Q00855 18-146
               2. House-dust mite (Dermatophagoides pteronyssinus), Der p 2 [TaxId: 6956] [49258] (2)
         9. RhoGDI-like [81288] (3)
            1. Rho GDP-dissociation inhibitor 1, RhoGDI [49241]
               1. Human (Homo sapiens) [TaxId: 9606] [49242] (17)
               2. Cow (Bos taurus) [TaxId: 9913] [49243] (4)
            2. GMP-PDE delta [74846]
               1. Human (Homo sapiens) [TaxId: 9606] [74847] (3)
         10. Cytoplasmic domain of inward rectifier potassium channel [81966] (3)
             1. G protein-gated inward rectifier Girk1 [81967]
                forms tetrameric cytoplasmic pore; contains a C-terminal extension
                1. Mouse (Mus musculus) [TaxId: 10090] [81968] (1)
             2. Inward rectifier potassium channel Kirbac1.1 [89195]
                1. Burkholderia pseudomallei [TaxId: 28450] [89196] (1)
             3. Inward rectifier potassium channel kirbac3.1 [117047]
                1. Magnetospirillum magnetotacticum [TaxId: 188] [117048] (2)
                   SQ Q8YY97 # 46% sequence identity; Anabaena sp. PCC 7120 TaxID: 103690
         11. Transglutaminase N-terminal domain [81289] (4)
             1. Transglutaminase N-terminal domain [49235]
                elaborated with many loop insertions in the common fold
                1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [49236] (8)
                   Coagulation factor XIII
                2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [74844] (2)
                   GDP-binding protein
                3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [74845] (8)
                4. Red sea bream (Chrysophrys major) [TaxId: 143350] [63667] (1)
         12. Filamin repeat (rod domain) [81290] (4)
             Pfam 00630
             1. F-actin cross-linking gelation factor (ABP-120) repeats [49239]
                1. Dictyostelium discoideum [TaxId: 44689] [49240] (3)
                   SQ P13466 547-857
             2. Filamin C [117049]
                1. Human (Homo sapiens) [TaxId: 9606] [117050] (7)
                   SQ Q14315 2633-2725
             3. Filamin a [141023]
                1. Human (Homo sapiens) [TaxId: 9606] [141024] (8)
                   SQ P21333 1863-1953! SQ P21333 1863-1955! SQ P21333 2236-2328
             4. Filamin b [141025]
                1. Human (Homo sapiens) [TaxId: 9606] [141026] (14)
                   SQ O75369 1017-1134! SQ O75369 1130-1229! SQ O75369 1215-1329! SQ O75369 1325-1442! SQ O75369 1418-1518! SQ O75369 1611-1721! SQ O75369 1899-2001! SQ O75369 1999-2096! SQ O75369 2104-2192
         13. Arrestin/Vps26-like [81291] (2)
             1. Arrestin [49244]
                duplication: contains tandem repeat of two elaborated Ig-like domains contacting each other head-to-head
                1. Cow (Bos taurus), visual arrestin [TaxId: 9913] [49245] (2)
                2. Cow (Bos taurus), beta-arrestin 1 [TaxId: 9913] [69169] (5)
         14. Gingipain R (RgpB), C-terminal domain [81292] (1)
             1. Gingipain R (RgpB), C-terminal domain [49261]
                Arginine-specific cysteine proteinase
                follows the catalytic alpha/beta domains
                1. Porphyromonas gingivalis [TaxId: 837] [49262] (1)
         15. Copper resistance protein C (CopC, PcoC) [81969] (2)
             1. Copper resistance protein C (CopC, PcoC) [81970]
                1. Pseudomonas syringae [TaxId: 317] [81971] (7)
                2. Escherichia coli [TaxId: 562] [81972] (2)
         16. Cellulosomal scaffoldin protein CipC, module x2.1 [81293] (1)
             1. Cellulosomal scaffoldin protein CipC, module x2.1 [49263]
                1. Clostridium cellulolyticum [TaxId: 1521] [49264] (1)
         17. Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 [81294] (2)
             1. Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 [69176]
                duplication: tandem repeat of two Ig-like domains
                1. Paracoccus denitrificans [TaxId: 266] [69177] (2)
                2. Pseudomonas putida [TaxId: 303] [69178] (2)
         18. Internalin Ig-like domain [81295] (3)
             truncated fold fused to an LRR domain
             1. Internalin A [81973]
                1. Listeria monocytogenes [TaxId: 1639] [81974] (7)
             2. Internalin B [69172]
                1. Listeria monocytogenes [TaxId: 1639] [69173] (5)
             3. Internalin H [69174]
                1. Listeria monocytogenes [TaxId: 1639] [69175] (1)
         19. SoxZ-like [141027] (1)
             1. Sulfur oxidation protein SoxZ [141028]
                1. Thermus thermophilus [TaxId: 274] [141029] (2)
                   SQ Q5SME6 2-107
                   TTHA1420
         20. Enterochelin esterase N-terminal domain-like [141030] (2)
             PfamB 013071
             1. Enterochelin esterase [141031]
                1. Shigella flexneri [TaxId: 623] [141032] (1)
                   SQ Q83SB9 3-150
                2. Shigella flexneri 2a str. 2457T [TaxId: 198215] [158885] (10)
         21. AMPK-beta glycogen binding domain-like [158886] (3)
             lacks the N-terminal strand (A) and contains a beta-hairpin insertion in the C-terminal strand (G)
             1. 5'-AMP-activated protein kinase subunit beta-2 [158887]
                1. Human (Homo sapiens) [TaxId: 9606] [158888] (1)
                   SQ O43741 75-163
             2. SIP2 [158889]
                1. Saccharomyces cerevisiae [TaxId: 4932] [158890] (2)
                   SQ P34164 161-247
             3. 5'-AMP-activated protein kinase subunit beta-1 [158891]
                1. Rattus norvegicus [TaxId: 10116] [158892] (6)
                   SQ P80386 76-162
         22. Sec63 C-terminal domain-like [158893] (1)
             C-terminal part of Pfam 02889
             1. Protein pro2281 [158894]
                1. Human (Homo sapiens) [TaxId: 9606] [158895] (1)
                   SQ Q9P172 209-322
         23. SVA-like [158896] (1)
             Pfam 05326
             1. Prolactin-inducible protein, PIP [158897]
                1. Human (Homo sapiens) [TaxId: 9606] [158898] (1)
                   SQ P12273 29-146
      3. Fibronectin type III [49265] (1)
         uperfamily
         1. Fibronectin type III [49266] (53)
            Pfam 00041
            1. Extracellular region of human tissue factor [49267]
               tandem of fibronectin type III domains
               1. Human (Homo sapiens) [TaxId: 9606] [49268] (13)
                  SQ P13726 33-242
               2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [49269] (35)
            2. Fibronectin, different Fn3 modules [49270]
               1. Human (Homo sapiens) [TaxId: 9606] [49271] (9)
               2. Mouse (Mus musculus) [TaxId: 10090] [49272] (2)
               3. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [158899] (1)
            3. Tenascin [49273]
               1. Chicken (Gallus gallus) [TaxId: 9031] [49274] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [49275] (1)
               3. Rat (Rattus norvegicus) [TaxId: 10116] [110057] (1)
                  SQ Q05546 502-770
            4. Neuroglian, two amino proximal Fn3 repeats [49276]
               tandem of fibronectin type III domains
               1. Drosophila melanogaster [TaxId: 7227] [49277] (1)
            5. Neural cell adhesion molecule 1, NCAM [89197]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [89198] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [141033] (17)
                  SQ P13592 498-598
            6. Fibronectin type III domain from chitinase A1. [81975]
               1. Bacillus circulans [TaxId: 1397] [81976] (1)
            7. Integrin beta-4 subunit [49278]
               1. Human (Homo sapiens) [TaxId: 9606] [49279] (1)
            8. Growth hormone receptor [49280]
               1. Human (Homo sapiens) [TaxId: 9606] [49281] (10)
                  tandem of fibronectin type III domains
            9. Erythropoietin (EPO) receptor [49282]
               1. Human (Homo sapiens) [TaxId: 9606] [49283] (5)
               2. Escherichia coli [TaxId: 562] [158900] (6)
            10. Prolactin receptor [49284]
                1. Human (Homo sapiens) [TaxId: 9606] [49285] (3)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [49286] (1)
            11. Interleukin-4 receptor alpha chain [49287]
                1. Human (Homo sapiens) [TaxId: 9606] [49288] (1)
            12. Common beta-chain in the GM-CSF, IL-3 and IL-5 receptors [49289]
                duplication: consists of four similar domains; dimerizes by swapping the C-terminal strands of domains 1 and 3
                1. Human (Homo sapiens) [TaxId: 9606] [49290] (11)
            13. Granulocyte colony-stimulating factor (GC-SF) receptor [49291]
                1. Mouse (Mus musculus) [TaxId: 10090] [49292] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [141034] (2)
                   SQ Q99062 120-226! SQ Q99062 227-331
            14. Interferon-gamma receptor alpha chain [49293]
                1. Human (Homo sapiens) [TaxId: 9606] [49294] (3)
            15. Cytokine receptor gp130 cytokine-binding domains [49295]
                1. Human (Homo sapiens) [TaxId: 9606] [49296] (5)
            16. Interleukin-10 receptor 1, IL-10R1 [63670]
                1. Human (Homo sapiens) [TaxId: 9606] [63671] (8)
            17. Type I titin module [49297]
                1. Human (Homo sapiens) [TaxId: 9606] [49298] (1)
            18. The p40 domain of interleukin-12 (IL-12 beta chain), domains 2 and 3 [63672]
                1. Human (Homo sapiens) [TaxId: 9606] [63673] (12)
            19. Interleukin-6 receptor alpha chain, domains 2 and 3 [81977]
                1. Human (Homo sapiens) [TaxId: 9606] [81978] (3)
            20. Interferon-alpha/beta receptor beta chain [89199]
                1. Human (Homo sapiens) [TaxId: 9606] [89200] (4)
            21. KIAA1568 protein [101529]
                1. Human (Homo sapiens) [TaxId: 9606] [101530] (2)
            22. KIAA0343 protein [101531]
                1. Human (Homo sapiens) [TaxId: 9606] [101532] (2)
            23. KIAA1355 [110058]
                1. Human (Homo sapiens) [TaxId: 9606] [110059] (1)
                   SQ Q9P2J2 [Fragment] 634-728
            24. Ciliary neurotrophic factor receptor alpha [110060]
                1. Human (Homo sapiens) [TaxId: 9606] [110061] (1)
                   SQ P26992 202-305
            25. Host cell factor 2, HCF-2 [117051]
                1. Mouse (Mus musculus) [TaxId: 10090] [117052] (1)
                   SQ Q9D968 127-236
            26. Fibronectin type 3 and ankyrin repeat domains 1 protein, FANK1 [117053]
                1. Mouse (Mus musculus) [TaxId: 10090] [117054] (1)
                   SQ Q9DAM9 1-107
            27. Contactin 3 (KIAA1496) [117055]
                1. Human (Homo sapiens) [TaxId: 9606] [117056] (1)
                   SQ Q9P232 893-996
            28. Fibronectin type-III domain containing protein 3a, FNDC3A (KIAA0970) [117057]
                1. Human (Homo sapiens) [TaxId: 9606] [117058] (6)
                   SQ Q9Y2H6 192-315
            29. Ephrin type-B receptor 1 [141035]
                1. Human (Homo sapiens) [TaxId: 9606] [141036] (1)
                   SQ P54762 434-528
            30. Brother of CDO precursor (BOC) [141037]
                1. Mouse (Mus musculus) [TaxId: 10090] [141038] (2)
                   SQ Q6AZB0 591-689! SQ Q6AZB0 707-807
            31. Ephrin type-A receptor 8 [141039]
                1. Human (Homo sapiens) [TaxId: 9606] [141040] (1)
                   SQ P29322 473-534
                   structure of the C-terminal SAM domain is known (scop_sp 101243)
            32. Cytokine receptor common gamma chain [141041]
                1. Human (Homo sapiens) [TaxId: 9606] [141042] (8)
                   SQ P31785 142-246! SQ P31785 142-248! SQ P31785 54-141! SQ P31785 56-141
            33. Rim binding protein 2 [141043]
                1. Human (Homo sapiens) [TaxId: 9606] [141044] (1)
                   SQ O15034 477-593
            34. Tenascin-X [141045]
                1. Human (Homo sapiens) [TaxId: 9606] [141046] (3)
                   SQ P22105 3699-3798! SQ P22105 3890-3991! SQ P22105 3977-4069
            35. Interleukin-2 receptor beta chain [141047]
                1. Human (Homo sapiens) [TaxId: 9606] [141048] (6)
                   SQ P14784 130-232! SQ P14784 130-233! SQ P14784 32-129
            36. Receptor-type tyrosine-protein phosphatase delta, PTPRD [141049]
                1. Human (Homo sapiens) [TaxId: 9606] [141050] (1)
                   SQ P23468 504-607
            37. Sidekick 2 [141051]
                1. Human (Homo sapiens) [TaxId: 9606] [141052] (4)
                   SQ Q58EX2 1279-1395! SQ Q58EX2 578-685! SQ Q58EX2 881-988! SQ Q58EX2 981-1081
            38. Neogenin [141053]
                1. Human (Homo sapiens) [TaxId: 9606] [141054] (6)
                   SQ Q92859 429-535! SQ Q92859 529-631! SQ Q92859 623-741! SQ Q92859 718-830! SQ Q92859 853-952! SQ Q92859 942-1054
            39. Down syndrome cell adhesion molecule-like protein 1, DSCAML1 [141055]
                1. Human (Homo sapiens) [TaxId: 9606] [141056] (1)
                   SQ Q8TD84 979-1087
            40. Myosin binding protein C, fast-type [141057]
                1. Mouse (Mus musculus) [TaxId: 10090] [141058] (1)
                   SQ Q5XKE0 731-828
            41. Receptor-type tyrosine-protein phosphatase F, PTPRF [141059]
                1. Human (Homo sapiens) [TaxId: 9606] [141060] (1)
                   SQ P10586 811-904
            42. Hedgehog receptor iHog [141061]
                Cg9211-PA
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141062] (12)
                   SQ Q9VM64 466-572! SQ Q9VM64 573-667
            43. Ephrin type-A receptor 1 [141063]
                1. Mouse (Mus musculus) [TaxId: 10090] [141064] (1)
                   SQ Q60750 446-539
            44. Insulin receptor [158901]
                1. Human (Homo sapiens) [TaxId: 9606] [158902] (3)
                   SQ P06213 495-618
      4. PKD domain [49299] (1)
         uperfamily
         1. PKD domain [49300] (3)
            Pfam 00801
            1. Polycystein-1, PKD-1 [49301]
               1. Human (Homo sapiens) [TaxId: 9606] [49302] (1)
            2. Surface layer protein [81979]
               1. Archaeon Methanosarcina mazei [TaxId: 2209] [81980] (1)
            3. VPS10 domain-containing receptor SorCS2 [117059]
               1. Human (Homo sapiens) [TaxId: 9606] [117060] (1)
                  SQ Q96PQ0 760-869
      5. beta-Galactosidase/glucuronidase domain [49303] (1)
         uperfamily
         1. beta-Galactosidase/glucuronidase domain [49304] (5)
            1. beta-Galactosidase, domains 2 and 4 [49305]
               1. Escherichia coli [TaxId: 562] [49306] (25)
                  SQ P00722
               2. Arthrobacter sp. c2-2 [TaxId: 192168] [141065] (12)
                  SQ Q8KRF6 220-312! SQ Q8KRF6 610-721
            2. beta-Glucuronidase [49307]
               1. Human (Homo sapiens) [TaxId: 9606] [49308] (1)
            3. Exochitosanase CsxA, domains 2, 4 and 5 [158903]
               1. Amycolatopsis orientalis [TaxId: 31958] [158904] (6)
                  SQ Q56F26 226-335! SQ Q56F26 675-777! SQ Q56F26 778-899
            4. Beta-mannosidase, domains 2, 4 and 5 [158905]
               truncated domain 5 lacks the last strand
               1. Bacteroides thetaiotaomicron [TaxId: 818] [158906] (54)
                  SQ Q8AAK6 220-330! SQ Q8AAK6 679-783! SQ Q8AAK6 784-864
      6. Transglutaminase, two C-terminal domains [49309] (1)
         uperfamily
         1. Transglutaminase, two C-terminal domains [49310] (4)
            1. Transglutaminase, two C-terminal domains [49311]
               duplication
               1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [49312] (8)
                  Coagulation factor XIII,
               2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [74849] (3)
                  GDP-binding protein
               3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [74850] (8)
               4. Red sea bream (Chrysophrys major) [TaxId: 143350] [63674] (1)
      7. Cadherin-like [49313] (2)
         uperfamily
         1. Cadherin [49314] (4)
            1. N-cadherin (neural) [49315]
               1. Mouse (Mus musculus) [TaxId: 10090] [49316] (7)
            2. E-cadherin (epithelial) [49317]
               synonym: uvomorulin
               1. Mouse (Mus musculus) [TaxId: 10090] [49318] (5)
               2. Human (Homo sapiens) [TaxId: 9606] [81981] (7)
            3. C-cadherin ectodomain [74851]
               five-domain fragment
               1. African clawed frog (Xenopus laevis) [TaxId: 8355] [74852] (1)
         2. Dystroglycan, N-terminal domain [110062] (1)
            1. Dystroglycan, N-terminal domain [110063]
               1. Mouse (Mus musculus) [TaxId: 10090] [110064] (1)
                  SQ Q62165 58-303
      8. Actinoxanthin-like [49319] (1)
         uperfamily
         1. Actinoxanthin-like [49320] (5)
            1. Macromycin [49321]
               1. Streptomyces macromomyceticus [TaxId: 1917] [49322] (1)
            2. Neocarzinostatin [49323]
               1. Streptomyces carzinostaticus [TaxId: 1897] [49324] (7)
            3. Actinoxanthin [49325]
               1. Actinomyces globisporus, number 1131 [TaxId: 1908] [49326] (1)
            4. Antitumor antibiotic C-1027 [63675]
               1. Streptomyces globisporus [TaxId: 1908] [63676] (3)
            5. Kedarcidin [49327]
               1. Actinomycete ATCC 53650, strain L585-6 [TaxId: 38989] [49328] (1)
      9. Cu,Zn superoxide dismutase-like [49329] (1)
         has additional strand at N-terminus
         uperfamily
         1. Cu,Zn superoxide dismutase-like [49330] (13)
            1. Cu,Zn superoxide dismutase, SOD [49331]
               1. Cow (Bos taurus) [TaxId: 9913] [49332] (27)
               2. Human (Homo sapiens) [TaxId: 9606] [49333] (32)
               3. African clawed frog (Xenopus laevis) [TaxId: 8355] [49334] (1)
               4. Spinach (Spinacia oleracea) [TaxId: 3562] [49335] (1)
               5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49336] (12)
               6. Photobacterium leiognathi [TaxId: 553611] [49337] (9)
               7. Escherichia coli [TaxId: 562] [49338] (1)
                  Monomeric enzyme
               8. Salmonella typhimurium [TaxId: 90371] [49339] (1)
               9. Actinobacillus pleuropneumoniae [TaxId: 715] [49340] (1)
               10. Mycobacterium tuberculosis [TaxId: 1773] [110065] (1)
                   SQ P96278
               11. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [110066] (2)
                   SQ Q01137
            2. Copper chaperone for superoxide dismutase, C-terminal domain [49341]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49342] (3)
               2. Human (Homo sapiens) [TaxId: 9606] [49343] (1)
      10. CBD9-like [49344] (3)
          has additional strand at N-terminus; the active site in a similar topological location as the Cu,Zn SOD site
          uperfamily
          1. Cytochrome domain of cellobiose dehydrogenase [49345] (1)
             1. Cytochrome domain of cellobiose dehydrogenase [49346]
                1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [49347] (4)
          2. Family 9 carbohydrate-binding module, CBD9 [63677] (1)
             1. Xylanase 10A [63678]
                1. Thermotoga maritima [TaxId: 2336] [63679] (3)
          3. Glucodextranase, domain C [101533] (1)
             1. Glucodextranase, domain C [101534]
                1. Arthrobacter globiformis [TaxId: 1665] [101535] (2)
      11. Lamin A/C globular tail domain [74853] (1)
          uperfamily
          1. Lamin A/C globular tail domain [74854] (2)
             1. Lamin A/C globular tail domain [74855]
                1. Human (Homo sapiens) [TaxId: 9606] [74856] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [110067] (1)
                   SQ P48678 408-546
      12. Clathrin adaptor appendage domain [49348] (3)
          contains an additional N-terminal strand
          uperfamily
          1. Alpha-adaptin ear subdomain-like [49349] (2)
             ear domain consists of two different subdomains
             1. Alpha-adaptin AP2 ear domain, N-terminal subdomain [49350]
                1. Mouse (Mus musculus) [TaxId: 10090] [49351] (10)
                   SQ P17427 694-938 # 98% sequence identity
             2. Beta2-adaptin AP2 ear domain, N-terminal subdomain [49352]
                1. Human (Homo sapiens) [TaxId: 9606] [49353] (5)
          2. gamma-adaptin C-terminal appendage domain-like [74857] (3)
             consist of a single subdomain
             1. Gamma1-adaptin domain [74858]
                1. Human (Homo sapiens) [TaxId: 9606] [74859] (5)
             2. ADP-ribosylation factor binding protein Gga1 domain [89201]
                1. Human (Homo sapiens) [TaxId: 9606] [89202] (10)
             3. ADP-ribosylation factor binding protein Gga3 domain [89203]
                1. Human (Homo sapiens) [TaxId: 9606] [89204] (1)
          3. Coatomer appendage domain [101536] (2)
             1. Coatomer gamma subunit C-terminal domain, first subdomain [101537]
                1. Human (Homo sapiens) [TaxId: 9606] [101538] (1)
                2. Cow (Bos taurus) [TaxId: 9913] [101539] (1)
      13. Integrin domains [69179] (1)
          uperfamily
          1. Integrin domains [69180] (2)
             1. Thigh, calf-1 and calf-2 domains of integrin alpha [69181]
                1. Human (Homo sapiens) [TaxId: 9606] [69182] (4)
                   SQ P06756 31-986
             2. Hybrid domain of integrin beta [69183]
                1. Human (Homo sapiens) [TaxId: 9606] [69184] (5)
                   SQ P05106 27-466
      14. PapD-like [49354] (2)
          contains PP switch between strands D and C'
          uperfamily
          1. Pilus chaperone [49355] (5)
             1. Pilus chaperone PapD, N-domain [49356]
                consists of two domains of this fold; domain 2 has an additional strand at the C-terminus
                1. Escherichia coli [TaxId: 562] [49357] (12)
             2. Periplasmic chaperone FimC [49358]
                1. Escherichia coli [TaxId: 562] [49359] (6)
             3. Periplasmic chaperone SfaE [74860]
                1. Escherichia coli [TaxId: 562] [74861] (1)
             4. Chaperone protein Caf1m [89205]
                1. Yersinia pestis [TaxId: 632] [89206] (9)
             5. Periplasmic chaperone SafB [158907]
                1. Salmonella typhimurium [TaxId: 90371] [158908] (2)
                   SQ Q8ZRK3 21-151
          2. MSP-like [49360] (5)
             Pfam 00635
             1. Major sperm protein, MSP [49361]
                1. Pig roundworm (Ascaris suum), alpha isoform [TaxId: 6253] [49362] (3)
                2. Nematode (Caenorhabditis elegans) [TaxId: 6239] [74862] (1)
             2. WR4 [89207]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89208] (1)
                   4L504 (ZC168.6) gene product
             3. SSP-19 [101540]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [101541] (1)
                   C55C2.2 gene product
             4. MSP domain containing protein 2, Mospd2 [117061]
                1. Mouse (Mus musculus) [TaxId: 10090] [117062] (1)
                   SQ Q9CWP6 317-455
      15. Purple acid phosphatase, N-terminal domain [49363] (1)
          uperfamily
          1. Purple acid phosphatase, N-terminal domain [49364] (2)
             1. Purple acid phosphatase, N-terminal domain [49365]
                1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49366] (9)
                2. Sweet potato (Ipomoea batatas) [TaxId: 4120] [117063] (1)
                   SQ Q9SE00 39-462
      16. Fungal immunomodulatory protein, FIP [101542] (1)
          uperfamily
          1. Fungal immunomodulatory protein, FIP [101543] (1)
             1. Fungal immunomodulatory protein, FIP [101544]
                contains extra N-terminal sudbomain involved in dimerisation
                1. Golden needle mushroom (Flammulina velutipes) [TaxId: 38945] [101545] (1)
      17. Superoxide reductase-like [49367] (1)
          uperfamily
          1. Superoxide reductase-like [49368] (3)
             binds iron in the site that is topologically equivalent to the copper-binding site of cupredoxins
             1. Superoxide reductase (SOR) [49369]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [49370] (3)
             2. Desulfoferrodoxin C-terminal domain [49371]
                1. Desulfovibrio desulfuricans [TaxId: 876] [49372] (13)
                2. Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887] [110068] (3)
                   SQ Q46495
      18. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74863] (1)
          uperfamily
          1. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74864] (1)
             1. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74865]
                1. Escherichia coli [TaxId: 562] [74866] (6)
      19. Invasin/intimin cell-adhesion fragments [49373] (1)
          uperfamily
          1. Invasin/intimin cell-adhesion fragments [49374] (2)
             1. Intimin [49375]
                1. Escherichia coli [TaxId: 562] [49376] (3)
                   an enteropathogenic serotype
             2. Invasin [49377]
                1. Yersinia pseudotuberculosis [TaxId: 633] [49378] (1)
      20. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81982] (1)
          uperfamily
          1. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81983] (1)
             1. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81984]
                1. Mycobacterium tuberculosis [TaxId: 1773] [81985] (1)
      21. Tp47 lipoprotein, middle and C-terminal domains [81986] (1)
          uperfamily
          1. Tp47 lipoprotein, middle and C-terminal domains [81987] (1)
             contains two different domains of immunoglobulin-like fold
             1. Tp47 lipoprotein, middle and C-terminal domains [81988]
                a penicillin-binding protein with carboxypeptidase activity
                1. Treponema pallidum [TaxId: 160] [81989] (1)
      22. ASF1-like [101546] (1)
          contains extra C-terminal strand
          uperfamily
          1. ASF1-like [101547] (3)
             1. Anti-silencing protein 1, ASF1 [101548]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101549] (3)
                2. Schizosaccharomyces pombe [TaxId: 4896] [158909] (13)
                   SQ O74515 1-161
                3. Human (Homo sapiens) [TaxId: 9606] [158910] (5)
                   SQ Q6IA08 1-154! SQ Q9Y294 1-154! SQ Q9Y294 1-156
      23. ApaG-like [110069] (1)
          uperfamily
          1. ApaG-like [110070] (3)
             Pfam 04379; dimeric in crystals; this dimer is a probable biological unit
             1. ApaG [110071]
                1. Shewanella oneidensis [TaxId: 70863] [110072] (1)
                   SQ Q8EB92
                2. Bordetella pertussis [TaxId: 520] [117064] (1)
                   SQ Q7VU61
                3. Vibrio cholerae [TaxId: 666] [117065] (1)
                   SQ Q9KUS3
      24. Accessory protein X4 (ORF8, ORF7a) [117066] (1)
          uperfamily
          1. Accessory protein X4 (ORF8, ORF7a) [117067] (1)
             1. Accessory protein X4 (ORF8, ORF7a) [117068]
                1. SARS coronavirus [TaxId: 227859] [117069] (1)
                   SQ P59635 15-82
      25. LEA14-like [117070] (1)
          uperfamily
          1. LEA14-like [117071] (1)
             Pfam 03168
             1. Putative dessication related protein LEA14 [117072]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117073] (1)
                   SQ O03983
      26. ICP-like [141066] (1)
          topological variant with similarity to the Cupredoxin-like fold (scop_cf 49502) in the N-terminal region
          uperfamily
          1. ICP-like [141067] (2)
             PfamB 014070
             1. Chagasin [141068]
                1. Trypanosoma cruzi [TaxId: 5693] [141069] (9)
                   SQ Q966X9 3-110
             2. Inhibitor of cysteine peptidases, ICP [141070]
                1. Leishmania mexicana [TaxId: 5665] [141071] (1)
                   SQ Q868H1 1-113
      27. CalX-like [141072] (1)
          uperfamily
          1. CalX-beta domain [141073] (1)
             Pfam 03160
             1. Sodium/calcium exchanger 1 [141074]
                1. Dog (Canis familiaris) [TaxId: 9615] [141075] (3)
                   SQ P23685 402-534! SQ P23685 403-541! SQ P23685 533-724
      28. NEAT domain-like [158911] (1)
          1. NEAT domain [158912] (3)
             Pfam 05031; iron transport-associated domain
             1. Iron-regulated surface determinant protein C, IsdC [158913]
                1. Staphylococcus aureus [TaxId: 1280] [158914] (2)
                   SQ Q7A654 29-150
             2. Iron-regulated surface determinant protein A, IsdA [158915]
                1. Staphylococcus aureus [TaxId: 1280] [158916] (7)
                   SQ Q7A152 64-184! SQ Q99UX4 63-184
             3. Iron-regulated surface determinant protein H, IsdH [158917]
                1. Staphylococcus aureus [TaxId: 1280] [158918] (1)
                   SQ Q6G8J7 86-229
   2. Common fold of diphtheria toxin/transcription factors/cytochrome f [49379] (10)
      sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
      1. Diphtheria toxin, C-terminal domain [49380] (1)
         uperfamily
         1. Diphtheria toxin, C-terminal domain [49381] (1)
            1. Diphtheria toxin, C-terminal domain [49382]
               1. Corynebacterium diphtheriae [TaxId: 1717] [49383] (6)
      2. Carbohydrate-binding domain [49384] (3)
         uperfamily
         1. Cellulose-binding domain family II [49385] (2)
            1. Exo-1,4-beta-D-glycanase (cellulase, xylanase), cellulose-binding domain, CBD [49386]
               belongs to subfamily IIa
               1. Cellulomonas fimi [TaxId: 1708] [49387] (2)
            2. Endo-1,4-beta xylanase D, xylan binding domain, XBD [49388]
               belongs to subfamily IIb
               1. Cellulomonas fimi [TaxId: 1708] [49389] (6)
         2. Cellulose-binding domain family III [49390] (11)
            Pfam 00963
            1. Cellusomal scaffolding protein A, scaffoldin [49391]
               1. Clostridium thermocellum [TaxId: 1515] [49392] (1)
               2. Clostridium cellulolyticum [TaxId: 1521] [49393] (1)
            2. Endo/exocellulase:cellobiose E-4, C-terminal domain [49394]
               1. Thermomonospora fusca [TaxId: 2021] [49395] (4)
               2. Clostridium cellulolyticum, atcc 35319 [TaxId: 1521] [89209] (4)
                  endoglucanase 9G
            3. Cohesin domain [49396]
               1. Clostridium thermocellum, cellulosome, various modules [TaxId: 1515] [49397] (6)
               2. Clostridium cellulolyticum [TaxId: 1521] [158919] (3)
            4. Cellulosomal scaffoldin adaptor protein B, ScaB [110073]
               1. Acetivibrio cellulolyticus [TaxId: 35830] [110074] (2)
                  SQ Q7WYN3 29-199
            5. Cellulosomal scaffoldin ScaA [141076]
               1. Bacteroides cellulosolvens [TaxId: 35825] [141077] (1)
                  SQ Q9FDJ9 2073-2242
            6. Scaffolding dockerin binding protein A, SdbA [141078]
               1. Clostridium thermocellum [TaxId: 1515] [141079] (2)
                  SQ P71143 30-191! SQ P71143 30-195
            7. Exo-alpha-sialidase [158920]
               pre C-terminal domain
               1. Clostridium perfringens [TaxId: 1502] [158921] (1)
                  SQ Q0TTQ4 945-1080
            8. O-GlcNAcase NagJ [158922]
               pre C-terminal domain
               1. Clostridium perfringens [TaxId: 1502] [158923] (5)
                  SQ Q0TR53 768-909! SQ Q0TR53 774-906
         3. Bacterial chitobiase, n-terminal domain [49398] (1)
            1. Bacterial chitobiase, n-terminal domain [49399]
               1. Serratia marcescens [TaxId: 615] [49400] (4)
      3. Bacterial adhesins [49401] (6)
         uperfamily
         1. Collagen-binding domain of adhesin [49402] (1)
            1. Collagen-binding domain of adhesin [49403]
               1. Staphylococcus aureus [TaxId: 1280] [49404] (1)
         2. Fibrinogen-binding domain [89210] (2)
            duplication: contains two differently decorated domains of this fold
            1. Clumping factor A [89211]
               1. Staphylococcus aureus [TaxId: 1280] [89212] (1)
            2. Fibrinogen-binding adhesin SdrG [101550]
               1. Staphylococcus epidermidis [TaxId: 1282] [101551] (6)
         3. Pilus subunits [49405] (8)
            1. Mannose-specific adhesin FimH [49406]
               duplication: consists of two domains of this fold; C-terminal domain lacks the last strand
               1. Escherichia coli [TaxId: 562] [49407] (9)
            2. PapK pilus subunit [49408]
               similar to C-terminal domain of FimH
               1. Escherichia coli [TaxId: 562] [49409] (1)
            3. PapE pilus subunit [81990]
               1. Escherichia coli [TaxId: 562] [81991] (2)
            4. F1 capsule antigen Caf1 [89213]
               1. Yersinia pestis [TaxId: 632] [89214] (3)
            5. SafA pilus subunit [141080]
               1. Salmonella typhimurium [TaxId: 90371] [141081] (13)
                  SQ Q8ZRK4 36-168! SQ Q8ZRK4 46-170
            6. PAP fimbrial minor pilin protein PapH [158924]
               1. Escherichia coli [TaxId: 562] [158925] (1)
                  SQ P07111 46-195
            7. Pap fimbrial major pilin protein PapA [158926]
               1. Escherichia coli [TaxId: 562] [158927] (5)
                  SQ P04127 30-185! SQ P04127 32-185
            8. Invasin AfaD [158928]
               1. Escherichia coli [TaxId: 562] [158929] (4)
                  SQ Q47038 27-147
         4. PapG adhesin receptor-binding domain [63680] (1)
            1. PapG adhesin receptor-binding domain [63681]
               1. Escherichia coli [TaxId: 562] [63682] (2)
         5. F17c-type adhesin [89215] (2)
            1. Fimbrial adhesin F17-AG lectin domain [89216]
               1. Escherichia coli [TaxId: 562] [89217] (6)
            2. Fimbrial lectin GafD [101552]
               1. Escherichia coli [TaxId: 562] [101553] (1)
         6. Dr-family adhesin [110075] (1)
            Pfam 04619
            1. DraA/Afimbrial adhesin Afa-III [110076]
               1. Escherichia coli [TaxId: 562] [110077] (7)
                  SQ Q57254 P24093 23-159
      4. Alpha-macroglobulin receptor domain [49410] (1)
         uperfamily
         1. Alpha-macroglobulin receptor domain [49411] (3)
            1. alpha-1-macroglobulin [49412]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [49413] (1)
            2. alpha-2-macroglobulin [49414]
               1. Human (Homo sapiens) [TaxId: 9606] [49415] (1)
               2. Cow (Bos taurus) [TaxId: 9913] [49416] (1)
      5. p53-like transcription factors [49417] (7)
         uperfamily
         1. p53 DNA-binding domain-like [81314] (3)
            1. p53 tumor suppressor, DNA-binding domain [49419]
               1. Human (Homo sapiens) [TaxId: 9606] [49420] (37)
               2. Mouse (Mus musculus) [TaxId: 10090] [63683] (1)
            2. Transcription factor CEP-1 [110078]
               1. Caenorhabditis elegans [TaxId: 6239] [110079] (1)
                  SQ Q20646 223-418
         2. Rel/Dorsal transcription factors, DNA-binding domain [81315] (9)
            1. T-cell transcription factor NFAT1 (NFATC), DNA-binding domain [49421]
               1. Human (Homo sapiens) [TaxId: 9606] [49422] (12)
            2. T-cell transcription factor NFAT5 (TONEBP), DNA-binding domain [69185]
               1. Human (Homo sapiens) [TaxId: 9606] [69186] (1)
            3. p50 subunit of NF-kappa B (NFKB), N-terminal domain [49423]
               1. Human (Homo sapiens) [TaxId: 9606] [49424] (2)
               2. Mouse (Mus musculus) [TaxId: 10090] [49425] (8)
            4. p52 subunit of NF-kappa B (NFKB), N-terminal domain [49426]
               1. Human (Homo sapiens) [TaxId: 9606] [49427] (1)
            5. p65 subunit of NF-kappa B (NFKB), N-terminal domain [49428]
               1. Mouse (Mus musculus) [TaxId: 10090] [49429] (8)
               2. Human (Homo sapiens) [TaxId: 9606] [49430] (1)
               3. Chicken (Gallus gallus), C-rel [TaxId: 9031] [74867] (1)
            6. Dorsal homologue Gambif1 [49431]
               1. African malaria mosquito (Anopheles gambiae) [TaxId: 7165] [49432] (1)
         3. T-box [81316] (2)
            1. T domain from Brachyury transcription factor [49433]
               1. African clawed frog (Xenopus laevis) [TaxId: 8355] [49434] (1)
            2. T-box protein 3, tbx3 [74868]
               1. Human (Homo sapiens) [TaxId: 9606] [74869] (1)
         4. STAT DNA-binding domain [81317] (3)
            1. STAT-1, DNA-binding domain [49435]
               1. Human (Homo sapiens) [TaxId: 9606] [49436] (1)
            2. STAT3b [49437]
               1. Mouse (Mus musculus) [TaxId: 10090] [49438] (1)
            3. STAT homologue [101554]
               1. Dictyostelium discoideum [TaxId: 44689] [101555] (2)
         5. RUNT domain [81318] (2)
            1. Acute myeloid leukemia 1 protein (AML1), RUNT domain [49439]
               synonym: core binding factor alpha, cbfa
               1. Human (Homo sapiens) [TaxId: 9606] [49440] (5)
               2. Mouse (Mus musculus) [TaxId: 10090] [63684] (6)
                  almost identical sequence to the human protein
         6. DNA-binding domain from NDT80 [81992] (1)
            1. DNA-binding domain from NDT80 [81993]
               common fold is decorated with many additional structures
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81994] (14)
         7. DNA-binding protein LAG-1 (CSL) [110080] (1)
            1. DNA-binding protein LAG-1 (CSL) [110081]
               1. Caenorhabditis elegans [TaxId: 6239] [110082] (4)
                  SQ Q9TYY1 195-660
      6. Cytochrome f, large domain [49441] (1)
         uperfamily
         1. Cytochrome f, large domain [49442] (5)
            1. Cytochrome f, large domain [49443]
               this domain is interrupted by a small domain which is barrel-sandwich hybrid fold
               1. Turnip (Brassica rapa) [TaxId: 3711] [49444] (2)
               2. Chlamydomonas reinhardtii [TaxId: 3055] [49445] (6)
               3. Phormidium laminosum [TaxId: 32059] [49446] (1)
               4. Mastigocladus laminosus [TaxId: 83541] [101556] (1)
               5. Anabaena sp., PCC 7120 [TaxId: 1167] [158930] (1)
                  SQ Q93SW9 45-213,280-298
      7. beta-sandwich domain of Sec23/24 [81995] (1)
         uperfamily
         1. beta-sandwich domain of Sec23/24 [81996] (2)
            1. Sec23 [81997]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81998] (3)
            2. Sec24 [81999]
               includes the N-terminal tail
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82000] (4)
      8. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49447] (1)
         duplication: one domain of this fold is inserted into another domain of the same fold
         uperfamily
         1. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49448] (2)
            1. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49449]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [49450] (6)
               2. Human (Homo sapiens) [TaxId: 9606] [69187] (1)
      9. Peptidylarginine deiminase Pad4, middle domain [110083] (1)
         uperfamily
         1. Peptidylarginine deiminase Pad4, middle domain [110084] (1)
            1. Peptidylarginine deiminase Pad4, middle domain [110085]
               1. Human (Homo sapiens) [TaxId: 9606] [110086] (7)
                  SQ Q9UM07
      10. DR1885-like metal-binding protein [110087] (1)
          uperfamily
          1. DR1885-like metal-binding protein [110088] (1)
             Pfam 04314
             1. Hypothetical protein DR1885 [110089]
                1. Deinococcus radiodurans [TaxId: 1299] [110090] (2)
                   SQ Q9RT80 35-178
   3. Prealbumin-like [49451] (7)
      sandwich; 7 strands in 2 sheets, greek-key
      variations: some members have additional 1-2 strands to common fold
      1. Starch-binding domain-like [49452] (3)
         uperfamily
         1. Rhamnogalacturonase B, RhgB, middle domain [110091] (1)
            1. Rhamnogalacturonase B, RhgB, middle domain [110092]
               1. Aspergillus aculeatus [TaxId: 5053] [110093] (1)
                  SQ Q00019
         2. Starch-binding domain [49453] (8)
            1. Cyclodextrin glycosyltransferase, C-terminal domain [49454]
               this domain is the last one in the protein chain
               1. Bacillus circulans, different strains [TaxId: 1397] [49455] (36)
               2. Bacillus stearothermophilus [TaxId: 1422] [49456] (1)
               3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [49457] (2)
               4. Bacillus sp., strain 1011 [TaxId: 1409] [49458] (8)
                  SQ P05618
               5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [49459] (2)
               6. Thermoanaerobacterium [TaxId: 28895] [158931] (2)
            2. Glucoamylase, granular starch-binding domain [49460]
               1. Aspergillus niger [TaxId: 5061] [49461] (4)
            3. beta-amylase [49462]
               1. Bacillus cereus [TaxId: 1396] [49463] (15)
         3. PUD-like [158932] (4)
            Pfam 03714; bacterial pullanase-associated domain
            1. Pullulanase PulA [158933]
               1. Klebsiella pneumoniae [TaxId: 573] [158934] (3)
                  SQ P07206 39-169
               2. Streptococcus pneumoniae [TaxId: 1313] [158935] (2)
                  SQ Q97SQ7 135-237! SQ Q97SQ7 238-353
               3. Streptococcus pyogenes [TaxId: 1314] [158936] (4)
                  SQ Q1JEU6 105-211! SQ Q1JEU6 212-323
               4. Thermotoga maritima [TaxId: 2336] [158937] (5)
                  SQ O33840 19-102
      2. Carboxypeptidase regulatory domain-like [49464] (2)
         uperfamily
         1. Carboxypeptidase regulatory domain [49465] (2)
            1. Carboxypeptidase D C-terminal domain [49466]
               1. Crested duck (Lophonetta specularioides) [TaxId: 8836] [49467] (2)
            2. Carboxypeptidase M C-terminal domain [101557]
               1. Human (Homo sapiens) [TaxId: 9606] [101558] (1)
         2. Pre-dockerin domain [141082] (1)
            PfamB 085396
            1. Cellulosomal scaffolding protein A [141083]
               1. Clostridium thermocellum [TaxId: 1515] [141084] (1)
                  SQ Q06851 1697-1792
      3. VHL [49468] (1)
         uperfamily
         1. VHL [49469] (1)
            1. VHL [49470]
               1. Human (Homo sapiens) [TaxId: 9606] [49471] (3)
      4. Transthyretin (synonym: prealbumin) [49472] (1)
         uperfamily
         1. Transthyretin (synonym: prealbumin) [49473] (4)
            1. Transthyretin (synonym: prealbumin) [49474]
               sandwich; 8 strands in 2 sheets
               1. Human (Homo sapiens) [TaxId: 9606] [49475] (117)
                  SQ P02766 31-143
               2. Rat (Rattus norvegicus) [TaxId: 10116] [49476] (4)
               3. Chicken (Gallus gallus) [TaxId: 9031] [49477] (1)
               4. Gilthead seabream (Sparus aurata) [TaxId: 8175] [101559] (4)
                  SQ Q9PTT3
      5. Cna protein B-type domain [49478] (1)
         uperfamily
         1. Cna protein B-type domain [49479] (2)
            Pfam 05738
            1. B repeat unit of collagen binding surface protein (cna) [49480]
               duplication: consists of two similar prealbumin-like domains
               1. Staphylococcus aureus [TaxId: 1280] [49481] (2)
            2. Transhydroxylase beta subunit, BthL, C-terminal domain [110094]
               the penultimate strand is in the other beta-sheet than in the Cna repeats
               1. Pelobacter acidigallici [TaxId: 35816] [110095] (6)
                  SQ P80564
      6. Aromatic compound dioxygenase [49482] (1)
         uperfamily
         1. Aromatic compound dioxygenase [49483] (6)
            sandwich; 9 strands in 2 sheets
            1. Catechol 1,2-dioxygenase [49484]
               contains alpha-helical dimerization subdomain at the N-terminus
               1. Acinetobacter calcoaceticus [TaxId: 471] [49485] (4)
            2. Protocatechuate-3,4-dioxygenase, alpha chain [49486]
               alpha and beta chains are derived from a single-chain protomer and share this fold
               1. Pseudomonas putida [TaxId: 303] [49487] (51)
               2. Acinetobacter calcoaceticus, adp1 [TaxId: 471] [49488] (16)
            3. Protocatechuate-3,4-dioxygenase, beta chain [49489]
               1. Pseudomonas putida [TaxId: 303] [49490] (51)
               2. Acinetobacter calcoaceticus, adp1 [TaxId: 471] [49491] (16)
            4. Chlorocatechol 1,2-dioxygenase [110096]
               similar overall structure to Catechol 1,2-dioxygenase
               1. Rhodococcus opacus [TaxId: 37919] [110097] (1)
                  SQ O67987
      7. Hypothetical protein PA1324 [117074] (1)
         uperfamily
         1. Hypothetical protein PA1324 [117075] (1)
            1. Hypothetical protein PA1324 [117076]
               1. Pseudomonas aeruginosa [TaxId: 287] [117077] (1)
                  SQ Q9I420 21-170
   4. HSP40/DnaJ peptide-binding domain [49492] (1)
      sandwich; 6 strands in 2 sheets
      1. HSP40/DnaJ peptide-binding domain [49493] (1)
         uperfamily
         1. HSP40/DnaJ peptide-binding domain [49494] (2)
            1. Heat shock protein 40 Sis1 [49495]
               duplication: contains two domains of this fold
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49496] (5)
            2. Mitochondrial protein import protein mas5 (Hsp40, Ydj1), C-terminal domain [101560]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101561] (1)
   5. Penicillin-binding protein associated domain [69188] (1)
      sandwich; 6 strands in 2 sheets
      1. Penicillin-binding protein associated domain [69189] (2)
         uperfamily
         1. PBP5 C-terminal domain-like [69190] (2)
            1. Penicillin-binding protein 5, C-terminal domain [69191]
               1. Escherichia coli [TaxId: 562] [69192] (8)
            2. D,D-carboxypeptidase DacA, C-terminal domain [117078]
               1. Streptococcus pneumoniae [TaxId: 1313] [117079] (1)
                  SQ P72518 25-393
         2. Pencillin binding protein 4 (PbpD), C-terminal domain [110098] (1)
            rudiment form of the PBP-5-like domain
            1. Pencillin binding protein 4 (PbpD), C-terminal domain [110099]
               1. Staphylococcus aureus [TaxId: 1280] [110100] (1)
                  SQ Q53613 21-383
   6. alpha-Amylase inhibitor tendamistat [49497] (1)
      sandwich; 6 strands in 2 sheets
      1. alpha-Amylase inhibitor tendamistat [49498] (1)
         uperfamily
         1. alpha-Amylase inhibitor tendamistat [49499] (1)
            1. alpha-Amylase inhibitor tendamistat [49500]
               1. Streptomyces tendae [TaxId: 1932] [49501] (6)
   7. C-terminal domain of mollusc hemocyanin [81278] (1)
      six-stranded beta-sandwich, jelly-roll/greek-key topology
      1. C-terminal domain of mollusc hemocyanin [81277] (1)
         analogous to the Ig-like domain of arthropod hemocyanin; similar sequential but different spatial position relative the shared domain
         uperfamily
         1. C-terminal domain of mollusc hemocyanin [81276] (2)
            1. C-terminal domain of mollusc hemocyanin [69165]
               1. Giant octopus (Octopus dofleini) [TaxId: 267067] [69166] (1)
               2. Mollusca (Rapana thomasiana) [TaxId: 29165] [89218] (1)
   8. HPA-like [141085] (1)
      sandwich, 6 strands in 2 sheets; jelly-roll (truncated); also includes the pending PCSK9 V domain-like superfamily (the C-terminal domains of 2p4e and 2pmw)
      1. Agglutinin HPA-like [141086] (1)
         forms similar trimers to the PCSK9 V domain; strand directions of the subunit beta-sheets are parallel to the three-fold symmetry axis;
         uperfamily
         1. Agglutinin HPA-like [141087] (1)
            1. Agglutinin HPA [141088]
               1. Roman snail (Helix pomatia) [TaxId: 6536] [141089] (2)
                  SQ Q2F1K8 21-119! SQ Q2F1K8 21-120
   9. L21p-like [141090] (1)
      core: sandwich, 6 strands in 2 sheets
      1. L21p-like [141091] (1)
         uperfamily
         1. Ribosomal protein L21p [141092] (3)
            Pfam 00829
            1. Ribosomal protein L21p [141093]
               1. Escherichia coli [TaxId: 562] [141094] (27)
                  SQ P0AG48 1-103
               2. Deinococcus radiodurans [TaxId: 1299] [158938] (10)
                  SQ Q9RY64 5-98
               3. Thermus thermophilus [TaxId: 274] [158939] (11)
                  SQ P60492 1-101
   10. Cupredoxin-like [49502] (2)
       sandwich; 7 strands in 2 sheets, greek-key
       variations: some members have additional 1-2 strands
       1. Cupredoxins [49503] (7)
          contains copper-binding site
          uperfamily
          1. Plastocyanin/azurin-like [49504] (32)
             mono-domain proteins
             1. Amicyanin [49505]
                1. Paracoccus denitrificans [TaxId: 266] [49506] (31)
                   SQ P22364
                2. Paracoccus versutus (Thiobacillus versutus) [TaxId: 34007] [63685] (1)
             2. Plastocyanin [49507]
                1. Poplar (Populus nigra), variant italica [TaxId: 3691] [49508] (10)
                2. French bean (Phaseolus vulgaris) [TaxId: 3885] [49509] (1)
                3. Parsley (Petroselinum crispum) [TaxId: 4043] [49510] (2)
                4. Spinach (Spinacia oleracea) [TaxId: 3562] [49511] (2)
                5. White campion (Silene pratensis) [TaxId: 52853] [49512] (2)
                6. Ulva pertusa, a sea lettuce [TaxId: 3120] [49513] (1)
                7. Green alga (Chlamydomonas reinhardtii) [TaxId: 3055] [49514] (1)
                8. Green alga (Enteromorpha prolifera) [TaxId: 3117] [49515] (1)
                9. Fern (Adiantum capillus-veneris) [TaxId: 13818] [49516] (2)
                10. Anabaena variabilis [TaxId: 1172] [49517] (7)
                11. Cyanobacterium (Phormidium laminosum) [TaxId: 32059] [49518] (4)
                12. Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId: 1143] [49519] (6)
                13. Cyanobacterium (Synechocystis sp.), pcc 7942 [TaxId: 1143] [49520] (2)
                14. Photosynthetic prokaryote (Prochlorothrix hollandica) [TaxId: 1223] [49521] (3)
             3. Pseudoazurin [49522]
                1. Alcaligenes faecalis, strain s-6 [TaxId: 511] [49523] (12)
                   SQ P04377
                2. Methylobacterium extorquens, strain am1 [TaxId: 408] [49524] (1)
                3. Achromobacter cycloclastes [TaxId: 223] [49525] (4)
                4. Thiosphaera pantotropha [TaxId: 82367] [49526] (1)
             4. Plantacyanin [49527]
                basic blue protein
                1. Cucumber (Cucumis sativus) [TaxId: 3659] [49528] (1)
                2. Spinach (Spinacia oleracea) [TaxId: 3562] [49529] (1)
             5. Azurin [49530]
                1. Alcaligenes denitrificans [TaxId: 32002] [49531] (8)
                2. Alcaligenes xylosoxidans, NCIMB (11015), different isoforms [TaxId: 85698] [49532] (4)
                3. Pseudomonas aeruginosa [TaxId: 287] [49533] (36)
                   SQ P00282
                4. Pseudomonas fluorescens [TaxId: 294] [49534] (1)
                5. Pseudomonas putida [TaxId: 303] [49535] (2)
                6. Methylomonas sp. j [TaxId: 32038] [49536] (2)
             6. Auracyanin [63686]
                azurin-related protein
                1. Chloroflexus aurantiacus [TaxId: 1108] [63687] (2)
             7. Rusticyanin [49537]
                1. Thiobacillus ferrooxidans [TaxId: 920] [49538] (7)
             8. Stellacyanin [49539]
                1. Cucumber (Cucumis sativus) [TaxId: 3659] [49540] (1)
             9. Mavicyanin [117080]
                Plantacyanin and stellacyanin homologue
                1. Zucchini (Cucurbita pepo) [TaxId: 3663] [117081] (2)
                   SQ P80728
          2. Nitrosocyanin [63392] (3)
             1. Red copper protein nitrosocyanin [63688]
                1. Nitrosomonas europaea [TaxId: 915] [63689] (3)
             2. Nitrous oxide reductase, C-terminal domain [49548]
                1. Pseudomonas nautica [TaxId: 2743] [49549] (1)
                2. Paracoccus denitrificans [TaxId: 266] [63690] (1)
          3. Periplasmic domain of cytochrome c oxidase subunit II [49541] (5)
             1. Quinol oxidase (CyoA) [49542]
                1. Escherichia coli [TaxId: 562] [49543] (3)
             2. Cytochrome c oxidase [49544]
                1. Cow (Bos taurus) [TaxId: 9913] [49545] (21)
                2. Paracoccus denitrificans [TaxId: 266] [49546] (3)
                3. Rhodobacter sphaeroides [TaxId: 1063] [74870] (6)
                4. Thermus thermophilus, ba3 type [TaxId: 274] [49547] (7)
          4. Multidomain cupredoxins [49550] (15)
             1. Nitrite reductase, NIR [49551]
                consists of two domains of this fold
                1. Achromobacter cycloclastes [TaxId: 223] [49552] (10)
                2. Alcaligenes faecalis, strain s-6 [TaxId: 511] [49553] (83)
                   SQ P38501
                3. Alcaligenes xylosoxidans [TaxId: 85698] [49554] (78)
                   SQ O68601 25-360 ! SQ O68601 26-359 ! SQ O68601
                4. Neisseria gonorrhoeae, AniA [TaxId: 485] [69193] (2)
                5. Rhodobacter sphaeroides [TaxId: 1063] [110101] (13)
                   SQ Q53239
             2. multi-copper oxidase CueO [69194]
                1. Escherichia coli [TaxId: 562] [69195] (15)
             3. Spore coat protein A, CotA [89219]
                1. Bacillus subtilis [TaxId: 1423] [89220] (22)
                   SQ P07788
             4. Ascorbate oxidase [49555]
                consists of three domains of this fold
                1. Zucchini (Cucurbita pepo var. medullosa) [TaxId: 3663] [49556] (4)
             5. Laccase [49557]
                consists of three domains of this fold
                1. Inky cap fungus (Coprinus cinereus) [TaxId: 5346] [49558] (2)
                2. Trametes versicolor, laccase 1 [TaxId: 5325] [74871] (1)
                3. Trametes versicolor, laccase 2 [TaxId: 5325] [74872] (1)
                4. Melanocarpus albomyces [TaxId: 204285] [74873] (19)
                5. Rigidoporus lignosus [TaxId: 219653] [110102] (1)
                   SQ Q6H9H7 22-515
             6. Ceruloplasmin [49559]
                consists of 6 domains of this fold
                1. Human (Homo sapiens) [TaxId: 9606] [49560] (6)
             7. Coagulation factor V [110103]
                1. Cow (Bos taurus) [TaxId: 9913] [110104] (1)
                   SQ Q28107 29-324, 1566-2210
          5. Ephrin ectodomain [74874] (2)
             eukaryotic signaling domain probably related to cupredoxins but lacking the metal-binding site
             1. Ephrin-b2 ectodomain [74875]
                1. Mouse (Mus musculus) [TaxId: 10090] [74876] (3)
             2. Ephrin-a5 [110105]
                1. Mouse (Mus musculus) [TaxId: 10090] [110106] (3)
                   SQ O08543
          6. Peptidylarginine deiminase Pad4, N-terminal domain [110107] (1)
             probably related to cupredoxins but lacking the metal-binding site
             1. Peptidylarginine deiminase Pad4, N-terminal domain [110108]
                1. Human (Homo sapiens) [TaxId: 9606] [110109] (7)
                   SQ Q9UM07
          7. SO1698-like [141095] (1)
             probably related to cupredoxins but lacking the metal-binding site
             1. Hypothetical protein SO1698 [141096]
                1. Shewanella oneidensis [TaxId: 70863] [141097] (1)
                   SQ Q8EGA7 6-116,117-124
       2. Major surface antigen p30, SAG1 [74877] (1)
          SS-crosslinked beta-sandwich of distinct geometry but topologically similar to cupredoxins
          uperfamily
          1. Major surface antigen p30, SAG1 [74878] (1)
             1. Major surface antigen p30, SAG1 [74879]
                duplication: tandem repeat of two homologous domains
                1. Toxoplasma gondii [TaxId: 5811] [74880] (5)
   11. Ctag/Cox11 [110110] (1)
       sandwich; 7 strands in 2 sheets, greek-key; permutation of the immunoglobulin-like fold
       1. Ctag/Cox11 [110111] (1)
          uperfamily
          1. Ctag/Cox11 [110112] (1)
             Pfam 04442
             1. Cytochrome C oxidase assembly protein CtaG [110113]
                1. Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382] [110114] (2)
                   SQ Q92RG6
   12. Atu1913-like [141098] (1)
       sandwich; 7 strands in two sheets, greek-key/jelly-roll; forms segment swapped dimers, swapping is probably facilitated by the helix insertion after strand 3
       1. Atu1913-like [141099] (1)
          uperfamily
          1. Atu1913-like [141100] (1)
             1. Hypothetical protein Atu1913 [141101]
                1. Agrobacterium tumefaciens [TaxId: 358] [141102] (1)
                   SQ Q8UE48 4-104
   13. C2 domain-like [49561] (5)
       sandwich; 8 strands in 2 sheets; greek-key
       1. C2 domain (Calcium/lipid-binding domain, CaLB) [49562] (2)
          two constituent families are related by circular permutation
          uperfamily
          1. PLC-like (P variant) [49563] (12)
             1. PI-specific phospholipase C isozyme D1 (PLC-D1), C-terminal domain [49564]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49565] (10)
             2. Domain from cytosolic phospholipase A2 [49566]
                1. Human (Homo sapiens) [TaxId: 9606] [49567] (3)
             3. Pten tumor suppressor (Phoshphoinositide phosphatase), C-terminal domain [49568]
                1. Human (Homo sapiens) [TaxId: 9606] [49569] (1)
             4. Phoshoinositide 3-kinase (PI3K) [49570]
                1. Pig (Sus scrofa) [TaxId: 9823] [49571] (5)
                2. Human (Homo sapiens) [TaxId: 9606] [49572] (3)
             5. Domain from protein kinase C delta [49573]
                rudiment form lacking calcium-binding site
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49574] (1)
             6. Domain from protein kinase C epsilon [69196]
                Calcium-independent
                1. Rat (Rattus rattus) [TaxId: 10117] [69197] (1)
             7. E3 ubiquitin-protein ligase Itchy [141103]
                1. Human (Homo sapiens) [TaxId: 9606] [141104] (1)
                   SQ Q96J02 13-145
             8. Unc-13 homolog A [141105]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [141106] (6)
                   SQ Q62768 1-128! SQ Q62768 2-150
             9. Multiple C2 and transmembrane domain-containing protein 2, MCTP2 [158940]
                1. Human (Homo sapiens) [TaxId: 9606] [158941] (1)
                   SQ Q6DN12 504-629
             10. Fantom [158942]
                 RPGR-interacting protein 1-like protein
                 1. Human (Homo sapiens) [TaxId: 9606] [158943] (1)
                    SQ Q68CZ1 596-737
             11. Phospholipase C-beta-2 [158944]
                 1. Human (Homo sapiens) [TaxId: 9606] [158945] (2)
                    SQ Q00722 678-799
          2. Synaptotagmin-like (S variant) [49575] (12)
             topologically similar to the C-terminal domain of PapD
             1. Synaptogamin I [49576]
                duplication: contains tandem repeat of two similar domains
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49577] (7)
                   SQ P21707 271-419 ! SQ P21707 271-419
                2. Homo sapiens [TaxId: 9606] [158946] (2)
             2. Synaptotagmin III [109606]
                duplication: contains 2 C2 domains
                1. Rat (Rattus norvegicus) [TaxId: 10116] [109607] (1)
                   SQ P40748 293-588
             3. Synaptotagmin IV [101562]
                duplication: contains 2 C2 domains
                1. Human (Homo sapiens) [TaxId: 9606] [101563] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [110115] (2)
                   SQ P50232 288-425
             4. Regulating synaptic membrane exocytosis protein, rim2 [101564]
                1. Human (Homo sapiens) [TaxId: 9606] [101565] (2)
             5. Piccolo [101566]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [101567] (1)
             6. C2 domain from protein kinase c (alpha) [49578]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49579] (1)
             7. C2 domain from protein kinase c (beta) [49580]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49581] (1)
             8. C2b-domain of rabphilin [49582]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49583] (4)
             9. C2 domain protein At1g63220 [117082]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117083] (1)
                   SQ Q9C8S6 2-125
             10. Synaptotagmin XIII [117084]
                 1. Human (Homo sapiens) [TaxId: 9606] [117085] (1)
                    SQ Q7L8C5 155-280
       2. Periplasmic chaperone C-domain [49584] (1)
          uperfamily
          1. Periplasmic chaperone C-domain [49585] (5)
             1. PapD [49586]
                1. Escherichia coli [TaxId: 562] [49587] (12)
             2. FimC [49588]
                1. Escherichia coli [TaxId: 562] [49589] (6)
             3. SfaE [74881]
                1. Escherichia coli [TaxId: 562] [74882] (1)
             4. Caf1m [89221]
                chaperone of F1 capsule antigen Caf1
                1. Yersinia pestis [TaxId: 632] [89222] (9)
             5. Periplasmic chaperone SafB [158947]
                1. Salmonella typhimurium [TaxId: 90371] [158948] (2)
                   SQ Q8ZRK3 152-236
       3. PHL pollen allergen [49590] (1)
          uperfamily
          1. PHL pollen allergen [49591] (2)
             1. PHL P 2 [49592]
                1. Timothy grass (Phleum pratense) [TaxId: 15957] [49593] (3)
             2. PHL P 1 C-terminal domain [82001]
                1. Timothy grass (Phleum pratense) [TaxId: 15957] [82002] (1)
       4. Rab geranylgeranyltransferase alpha-subunit, insert domain [49594] (1)
          uperfamily
          1. Rab geranylgeranyltransferase alpha-subunit, insert domain [49595] (1)
             1. Rab geranylgeranyltransferase alpha-subunit, insert domain [49596]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49597] (2)
       5. Smr-associated domain-like [158949] (1)
          1. Smr-associated domain [158950] (1)
             Pfam 09640; DUF2027
             1. Putative DNA mismatch repair protein BT2179 [158951]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [158952] (1)
                   SQ Q8A5Q9 81-227
   14. TRAF domain-like [49598] (1)
       sandwich; 8 strands in 2 sheets; greek-key
       1. TRAF domain-like [49599] (2)
          has a circularly permuted immunoglobulin-fold topology with extra strand
          uperfamily
          1. MATH domain [49600] (4)
             1. TNF receptor associated factor 2 (TRAF2) [49601]
                1. Human (Homo sapiens) [TaxId: 9606] [49602] (10)
             2. TNF receptor associated factor 3 (TRAF3) [49603]
                1. Human (Homo sapiens) [TaxId: 9606] [49604] (5)
                   SQ Q13114 377-568
             3. TNF receptor associated factor 6 (TRAF6) [74883]
                1. Human (Homo sapiens) [TaxId: 9606] [74884] (3)
             4. Speckle-type poz protein SPOP [141107]
                1. Human (Homo sapiens) [TaxId: 9606] [141108] (1)
                   SQ O43791 28-173
          2. SIAH, seven in absentia homolog [69198] (1)
             1. SIAH, seven in absentia homolog [69199]
                1. Mouse (Mus musculus) [TaxId: 10090] [69200] (5)
   15. Neurophysin II [49605] (1)
       sandwich; 8 strands in 2 sheets; meander
       1. Neurophysin II [49606] (1)
          duplication: composed of two structural repeats
          uperfamily
          1. Neurophysin II [49607] (1)
             1. Neurophysin II [49608]
                can be classified as disulfide-rich
                1. Cow (Bos taurus) [TaxId: 9913] [49609] (6)
   16. N-utilization substance G protein NusG, insert domain [82003] (1)
       sandwich; 8 strands in 2 sheets; meander
       1. N-utilization substance G protein NusG, insert domain [82004] (1)
          uperfamily
          1. N-utilization substance G protein NusG, insert domain [82005] (1)
             1. N-utilization substance G protein NusG, insert domain [82006]
                found only in some NusG species
                1. Aquifex aeolicus [TaxId: 63363] [82007] (4)
                   interrupted by an insert beta-sandwich domain
   17. Nucleoplasmin-like/VP (viral coat and capsid proteins) [88632] (7)
       sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands
       characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
       1. Nucleoplasmin-like core domain [69203] (1)
          oligomerizes into a pentameric ring structure
          uperfamily
          1. Nucleoplasmin-like core domain [69204] (3)
             1. Nucleoplasmin core [69205]
                1. Xenopus laevis [TaxId: 8355] [69206] (1)
             2. Chromatin decondensation protein 1 (Crp1, Nlp) [89223]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89224] (1)
             3. Nucleophosmin (NO38) [117086]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [117087] (2)
                   SQ P07222 16-122
       2. Positive stranded ssRNA viruses [88633] (9)
          uperfamily
          1. Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [88634] (18)
             the order of the chains N-VP0-VP3-VP1-C is as in the polyprotein; VP0 is cleaved later upon capsid assembly to VP4 and VP2
             there is a different order in the shuffled genome of insect picorna-like proteins (Cricket paralysis virus)
             1. Human enterovirus B coat proteins [88635]
                1. Human coxsackievirus B3 [TaxId: 12072] [49681] (1)
                2. Human coxsackievirus A9 [TaxId: 12067] [49683] (1)
                3. Human echovirus 1 [TaxId: 46633] [49685] (1)
                4. Human echovirus 11 [TaxId: 12078] [74890] (4)
             2. Bovine enterovirus coat proteins [49676]
                1. Bovine enterovirus, VG-5-27 [TaxId: 12064] [49677] (1)
             3. Poliovirus coat proteins [49666]
                1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [49667] (12)
                2. Poliovirus type 2, strain Lansing [TaxId: 12083] [49668] (1)
                3. Poliovirus type 3, strain Sabin [TaxId: 12086] [49669] (7)
             4. Rhinovirus coat proteins [49670]
                1. Human rhinovirus B 14 (HRV-14) [TaxId: 12131] [49671] (30)
                2. Human rhinovirus 16, (HRV-16) [TaxId: 31708] [49672] (9)
                3. Human rhinovirus A 1A (HRV-1A) [TaxId: 12134] [49673] (4)
                4. Human rhinovirus A 2 (HRV-2) [TaxId: 12130] [49674] (2)
                5. Human rhinovirus 3, (HRV-3) [TaxId: 44130] [49675] (1)
             5. Aphthovirus (Foot-and-mouth disease virus) coat proteins [49659]
                1. FMDV (Foot-and-mouth disease virus), strain bfs, 1860 [TaxId: 12110] [49660] (4)
             6. Theilovirus capsid proteins [49686]
                1. Theiler's murine encephalomyelitis virus, strain da [TaxId: 12124] [49687] (2)
             7. Mengo encephalomyocarditis virus coat proteins [49678]
                1. Mengovirus [TaxId: 12107] [49679] (2)
             8. Swine vesicular disease virus coat proteins [89225]
                1. Swine vesicular disease virus [TaxId: 12075] [89226] (2)
             9. Insect picorna-like virus coat proteins [49654]
                different genetic order of VP segments due to extensive genome shuffling
                1. Cricket paralysis virus [TaxId: 12136] [49655] (1)
          2. Comoviridae-like VP [88636] (3)
             duplication: mature coat protein consists of three similar domains that can be in a single chain or in two separate chains
             1. Nepovirus capsid protein [49629]
                duplication: cnosists of three very similar domains
                1. TRSV (Tobacco ringspot virus) [TaxId: 12282] [49630] (1)
             2. Comovirus coat proteins (VP37 and VP23) [49627]
                chain 1 is one-domain VP23; chain 2 is two-domain VP37
                1. CPMV (Cowpea mosaic virus) [TaxId: 12264] [89227] (4)
                2. BPMV (Bean pod mottle virus) [TaxId: 12260] [49628] (3)
          3. Caliciviridae-like VP [88637] (1)
             1. Calicivirus capsid protein [63691]
                includes the P (protruding) domain of complex beta-structure containing a beta-barrel similar to the second domain of EF-TU
                1. Norwalk virus [TaxId: 11983] [63692] (1)
          4. Nodaviridae-like VP [88638] (3)
             1. Alphanodavirus capsid protein [49648]
                1. Black beetle virus [TaxId: 12285] [49649] (1)
                2. Nodamura virus [TaxId: 12288] [49650] (1)
                3. Pariacoto virus [TaxId: 103782] [49651] (1)
          5. Tetraviridae-like VP [101568] (1)
             1. Tetraomegavirus capsid protein [101569]
                contains an insert beta-sandwich domain
                1. Nudaurelia capensis omega virus [TaxId: 12541] [101570] (1)
          6. Bromoviridae-like VP [88639] (4)
             1. Cucumovirus coat protein [88640]
                1. CMV (Cucumber mosaic virus), strain fny [TaxId: 12305] [49646] (1)
                2. TAV (Tomato aspermy virus) [TaxId: 12315] [82012] (1)
                3. BMV (Brome mosaic virus) [TaxId: 12302] [74886] (31)
                4. Cowpea chlorotic mottle virus [TaxId: 12303] [49636] (1)
          7. Tymoviridae-like VP [88641] (3)
             1. Tymovirus coat protein [88642]
                1. PHMV (Physalis mottle virus) [TaxId: 72539] [49642] (2)
                2. DYMV (Desmodium yellow mottle tymovirus) [TaxId: 70821] [49644] (1)
                3. TYMV (Turnip yellow mosaic virus) [TaxId: 12154] [49640] (2)
                   SQ P03608
          8. Tombusviridae-like VP [88643] (7)
             1. Necrovirus coat protein [49637]
                1. TNV (Tobacco necrosis virus) [TaxId: 12054] [49638] (1)
             2. Tombusvirus coat protein [49633]
                1. TBSV (Tomato bushy stunt virus) [TaxId: 12145] [49634] (1)
             3. Carmovirus coat protein [89228]
                1. CarMV (Carnation mottle virus) [TaxId: 11986] [89229] (1)
             4. Sobemovirus coat protein [88644]
                1. SMV (Sesbania mosaic virus) [TaxId: 12558] [49624] (7)
                   SQ Q9EB06
                2. SBMV (Southern bean mosaic virus), cow pea strain [TaxId: 12139] [49632] (1)
                3. RYMV (Rice yellow mottle virus) [TaxId: 31744] [49626] (1)
                4. Cocksfoot mottle virus [TaxId: 40979] [82010] (1)
          9. Birnaviridae-like VP [141109] (1)
             dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses; includes Pfam 01766; Birnavirus VP2 protein
             1. Birnavirus VP2 [141110]
                Link between +sRNA and dsRNA viruses two domains - the first similar to scop_sf 88633 and the second, insert domain is similar to scop_sf 49818. dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses
                1. Infectious bursal disease virus [TaxId: 10995] [141111] (41)
                   SQ P15480 11-431! SQ P61825 8-440! SQ Q6S9I7 11-429
       3. ssDNA viruses [88645] (3)
          uperfamily
          1. Microviridae-like VP [49612] (3)
             1. Microvirus capsid proteins [49613]
                include capsid protein F and spike protein G
                1. Bacteriophage phi-X174 [TaxId: 10847] [49614] (4)
                2. Bacteriophage G4 [TaxId: 10843] [49615] (1)
                3. Bacteriophage alpha3 [TaxId: 10849] [82008] (2)
          2. Parvoviridae-like VP [88646] (7)
             1. Parvovirus (panleukopenia virus) capsid protein [49661]
                1. Feline panleukopenia virus, strain b [TaxId: 10786] [49689] (1)
                2. Canine parvovirus [TaxId: 10788] [49662] (7)
                3. Feline parvovirus [TaxId: 10785] [49663] (3)
                4. Porcine parvovirus [TaxId: 10796] [69201] (1)
                5. Murine minute virus, strain i [TaxId: 10794] [49665] (2)
                6. Human parvovirus B19 [TaxId: 10798] [110116] (1)
                   SQ Q9JGS0 246-781
             2. Dependovirus capsid protein [74887]
                1. Adeno-associated virus, aav-2 [TaxId: 272636] [74888] (1)
                   a vector for human genome therapy
          3. Densovirinae-like VP [88647] (1)
             1. Densovirus capsid protein [49652]
                1. Galleria mellonella densovirus [TaxId: 37138] [49653] (1)
       4. Group I dsDNA viruses [88648] (1)
          uperfamily
          1. Papovaviridae-like VP [88649] (3)
             1. Polyomavirus coat proteins [49657]
                1. Murine polyomavirus, strain small-plaque 16 [TaxId: 10634] [49658] (5)
                2. Simian virus 40, Sv40 [TaxId: 10633] [49691] (1)
             2. Papillomavirus L1 protein [49692]
                1. Human papillomavirus type 16 [TaxId: 333760] [49693] (1)
       5. Group II dsDNA viruses VP [49749] (3)
          duplication: consists of two domains of this fold packed together like the nucleoplasmin subunits
          trimeric; in the trimers, the domains are arranged around pseudo six-fold axis
          uperfamily
          1. Coat protein p3 [49750] (1)
             1. Coat protein p3 [63403]
                1. Bacteriophage prd1 [TaxId: 10658] [49752] (3)
          2. Major capsid protein vp54 [82013] (1)
             1. Major capsid protein vp54 [82014]
                1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82015] (2)
                   a large, lipid-containing, DNA virus
          3. Adenovirus hexon [49753] (2)
             each domain is heavily decorated with many insertions
             1. Adenovirus hexon [63404]
                1. Human adenovirus type 2 [TaxId: 10515] [49755] (1)
                2. Human adenovirus type 5 [TaxId: 28285] [49756] (25)
       6. Satellite viruses [88650] (1)
          uperfamily
          1. Satellite viruses [88651] (3)
             1. SPMV coat protein [49617]
                1. Satellite panicum mosaic virus [TaxId: 154834] [49618] (1)
             2. STMV coat protein [49619]
                1. Satellite tobacco mosaic virus [TaxId: 12881] [49620] (1)
             3. STNV coat protein [49621]
                1. Satellite tobacco necrosis virus [TaxId: 12881] [49622] (1)
       7. PHM/PNGase F [49742] (2)
          members of this superfamily bind peptide substrates
          duplication: consists of two domains of this fold packed together like the adjacent nucleoplasmin subunits
          uperfamily
          1. Glycosyl-asparaginase [49743] (1)
             1. Peptide:N-glycosidase F, PNGase F [49744]
                1. Flavobacterium meningosepticum [TaxId: 238] [49745] (3)
          2. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [49746] (1)
             1. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [63402]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49748] (12)
   18. gamma-Crystallin-like [49694] (1)
       sandwich; 8 strands in 2 sheets; greek-key
       duplication: has internal pseudo twofold symmetry
       1. gamma-Crystallin-like [49695] (6)
          uperfamily
          1. Crystallins/Ca-binding development proteins [49696] (13)
             1. gamma-Crystallin [49697]
                duplication consists of two domains of this fold
                1. Cow (Bos taurus), isoform II (B) [TaxId: 9913] [49698] (6)
                2. Cow (Bos taurus), isoform IIIb (D) [TaxId: 9913] [49699] (1)
                3. Human (Homo sapiens), isoform D [TaxId: 9606] [89230] (6)
                4. Cow (Bos taurus), isoform S [TaxId: 9913] [49700] (1)
                5. Human (Homo sapiens) [TaxId: 9606] [69202] (1)
                6. Cow (Bos taurus), isoform F [TaxId: 9913] [49701] (1)
                7. Cow (Bos taurus), isoform E [TaxId: 9913] [101571] (1)
             2. beta-Crystallin [49702]
                duplication consists of two domains of this fold
                1. Cow (Bos taurus) [TaxId: 9913] [49703] (4)
                2. Rat (Rattus norvegicus), isoform E [TaxId: 10116] [49704] (10)
                3. Mouse (Mus musculus) [TaxId: 10090] [49705] (1)
                4. Human (Homo sapiens) [TaxId: 9606] [101572] (1)
             3. Protein S [49706]
                duplication consists of two domains of this fold
                1. Myxococcus xanthus [TaxId: 34] [49707] (3)
             4. Spherulin 3a (S3a) [49708]
                1. Physarum polycephalum [TaxId: 5791] [49709] (2)
          2. Yeast killer toxin [49710] (1)
             1. Yeast killer toxin [49711]
                1. Williopsis mrakii [TaxId: 4963] [49712] (1)
          3. Streptomyces metalloproteinase inhibitor, SMPI [49713] (1)
             1. Streptomyces metalloproteinase inhibitor, SMPI [49714]
                1. Streptomyces nigrescens [TaxId: 1920] [49715] (1)
          4. Killer toxin-like protein SKLP [49716] (1)
             1. Killer toxin-like protein SKLP [49717]
                1. Streptomyces sp. [TaxId: 1931] [49718] (1)
          5. Antifungal protein AFP1 [63693] (1)
             shares putative chitin-binding site with SKLP
             1. Antifungal protein AFP1 [63694]
                1. Streptomyces tendae, tu901 [TaxId: 1932] [63695] (2)
          6. Plant antimicrobial protein MIAMP1 [49719] (1)
             1. Plant antimicrobial protein MIAMP1 [49720]
                1. Macadamia nut (Macadamia integrifolia) [TaxId: 60698] [49721] (1)
   19. Lipase/lipooxygenase domain (PLAT/LH2 domain) [49722] (1)
       sandwich; 8 strands in 2 sheets; complex topology
       duplication: has weak internal pseudo twofold symmetry
       1. Lipase/lipooxygenase domain (PLAT/LH2 domain) [49723] (3)
          uperfamily
          1. Lipoxigenase N-terminal domain [49724] (3)
             1. Plant lipoxigenase [49725]
                1. Soybean (Glycine max), isozyme L1 [TaxId: 3847] [49726] (14)
                2. Soybean (Glycine max), isozyme L3 [TaxId: 3847] [49727] (9)
                   SQ P09186
             2. 15-Lipoxygenase [49728]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [49729] (3)
          2. Colipase-binding domain [49730] (6)
             1. Pancreatic lipase, C-terminal domain [49731]
                1. Horse (Equus caballus) [TaxId: 9796] [49732] (1)
                2. Pig (Sus scrofa) [TaxId: 9823] [49733] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [49734] (3)
                4. Guinea pig (Cavia porcellus) [TaxId: 10141] [49735] (1)
                5. Dog (Canis familiaris) [TaxId: 9615] [49736] (1)
                   pancreatic lipase related protein 1
                6. Rat (Rattus norvegicus) [TaxId: 10116] [49737] (1)
                   pancreatic lipase related protein 2
          3. Alpha-toxin, C-terminal domain [49738] (2)
             1. Alpha-toxin, C-terminal domain [49739]
                1. Clostridium perfringens, different strains [TaxId: 1502] [49740] (5)
                2. Clostridium absonum [TaxId: 29369] [101573] (1)
   20. Calpain large subunit, middle domain (domain III) [49757] (1)
       sandwich; 8 strands in 2 sheets; jelly-roll
       1. Calpain large subunit, middle domain (domain III) [49758] (1)
          uperfamily
          1. Calpain large subunit, middle domain (domain III) [49759] (3)
             1. Calpain large subunit, middle domain (domain III) [49760]
                1. Human (Homo sapiens), M-type [TaxId: 9606] [49761] (2)
                2. Rat (Rattus norvegicus), M-type [TaxId: 10116] [49762] (2)
                3. Rat (Rattus norvegicus), mu-type [TaxId: 10116] [101574] (1)
   21. Supernatant protein factor (SPF), C-terminal domain [101575] (1)
       sandwich; 8 strands in 2 sheets; jelly-roll; similarity to the Nucleoplasmin-like/VP fold
       1. Supernatant protein factor (SPF), C-terminal domain [101576] (1)
          uperfamily
          1. Supernatant protein factor (SPF), C-terminal domain [101577] (1)
             1. Supernatant protein factor (SPF), C-terminal domain [101578]
                1. Human (Homo sapiens) [TaxId: 9606] [101579] (2)
                   SQ O76054
   22. Hypothetical protein TM1070 [89231] (1)
       sandwich; 8 strands in 2 sheets; jelly-roll
       1. Hypothetical protein TM1070 [89232] (1)
          uperfamily
          1. Hypothetical protein TM1070 [89233] (1)
             1. Hypothetical protein TM1070 [89234]
                1. Thermotoga maritima [TaxId: 2336] [89235] (1)
   23. Olfactory marker protein [63696] (1)
       sandwich; 8 strands in 2 sheets; jelly-roll
       1. Olfactory marker protein [63697] (1)
          uperfamily
          1. Olfactory marker protein [63698] (2)
             1. Olfactory marker protein [63699]
                1. Mouse (Mus musculus) [TaxId: 10090] [63700] (3)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [69207] (2)
   24. HSP20-like chaperones [49763] (1)
       sandwich; 8 strands in 2 sheets; greek-key
       1. HSP20-like chaperones [49764] (4)
          uperfamily
          1. HSP20 [49765] (2)
             1. Small heat shock protein [49766]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [49767] (1)
                2. Wheat (Triticum aestivum) [TaxId: 4565] [69208] (49)
          2. Co-chaperone p23-like [49768] (2)
             1. Co-chaperone p23 [49769]
                1. Human (Homo sapiens) [TaxId: 9606] [49770] (1)
             2. Hypothetical protein At3g03773 [117088]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117089] (1)
                   SQ Q6ID70
          3. GS domain [101580] (2)
             Pfam 04969
             1. Suppressor of G2 allele of skp1 homolog, gst1 [101581]
                1. Human (Homo sapiens) [TaxId: 9606] [101582] (1)
             2. Ubiquitin carboxyl-terminal hydrolase 19, USP19 [117090]
                1. Human (Homo sapiens) [TaxId: 9606] [117091] (1)
                   SQ O94966 326-446
          4. Nuclear movement domain [117092] (2)
             Pfam 03593
             1. Nuclear migration protein nudC [117093]
                1. Mouse (Mus musculus) [TaxId: 10090] [117094] (1)
                   SQ O35685 171-288
             2. NudC domain containing protein 3, NUDCD3 (KIAA1068) [117095]
                1. Human (Homo sapiens) [TaxId: 9606] [117096] (1)
                   SQ Q8IVD9 176-286
   25. Heat shock protein 70kD (HSP70), peptide-binding domain [100919] (1)
       beta-sandwich: 8 strands in 2 sheets
       1. Heat shock protein 70kD (HSP70), peptide-binding domain [100920] (1)
          uperfamily
          1. Heat shock protein 70kD (HSP70), peptide-binding domain [100921] (4)
             1. DnaK [100922]
                1. Escherichia coli [TaxId: 562] [100923] (7)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [56782] (3)
                3. Cow (Bos taurus) [TaxId: 9913] [158953] (1)
             2. Chaperone protein hscA (Hsc66) [117097]
                1. Escherichia coli [TaxId: 562] [117098] (1)
                   SQ P0A6Z1 390-615
   26. Ecotin, trypsin inhibitor [49771] (1)
       sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
       1. Ecotin, trypsin inhibitor [49772] (1)
          uperfamily
          1. Ecotin, trypsin inhibitor [49773] (1)
             1. Ecotin, trypsin inhibitor [49774]
                1. Escherichia coli [TaxId: 562] [49775] (17)
                   SQ P23827 23-162
   27. PEBP-like [49776] (1)
       sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
       1. PEBP-like [49777] (2)
          uperfamily
          1. Phosphatidylethanolamine binding protein [49778] (5)
             1. Phosphatidylethanolamine binding protein, PEBP [49779]
                1. Human (Homo sapiens) [TaxId: 9606] [49780] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [49781] (2)
                3. Mouse (Mus musculus), PEBP-2 [TaxId: 10090] [74891] (1)
             2. Centroradialis protein Cen [49782]
                1. Garden snapdragon (Antirrhinum majus) [TaxId: 4151] [49783] (1)
             3. Carboxypeptidase Y inhibitor [158954]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [158955] (1)
                   SQ P14306 1-219
          2. Prokaryotic PEBP-like proteins [63701] (2)
             1. Hypothetical protein YbhB [63702]
                1. Escherichia coli [TaxId: 562] [63703] (2)
             2. Hypothetical protein YbcL [63704]
                1. Escherichia coli [TaxId: 562] [63705] (1)
   28. Ganglioside M2 (gm2) activator [63706] (1)
       sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
       1. Ganglioside M2 (gm2) activator [63707] (1)
          uperfamily
          1. Ganglioside M2 (gm2) activator [63708] (1)
             1. Ganglioside M2 (gm2) activator [63709]
                1. Human (Homo sapiens) [TaxId: 9606] [63710] (10)
                   SQ P17900 31-193
   29. Nicotinic receptor ligand binding domain-like [63711] (1)
       sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
       1. Nicotinic receptor ligand binding domain-like [63712] (1)
          uperfamily
          1. Nicotinic receptor ligand binding domain-like [63713] (1)
             1. Acetylcholine binding protein (ACHBP) [63714]
                1. Great pond snail (Lymnaea stagnalis) [TaxId: 6523] [63715] (9)
   30. Beta-galactosidase LacA, domain 3 [117099] (1)
       sandwich; 8 strands in 2 sheets
       1. Beta-galactosidase LacA, domain 3 [117100] (1)
          uperfamily
          1. Beta-galactosidase LacA, domain 3 [117101] (1)
             1. Beta-galactosidase LacA, domain 3 [117102]
                1. Penicillium sp. [TaxId: 5081] [117103] (2)
                   SQ Q700S9 41-1011
   31. Galactose-binding domain-like [49784] (1)
       sandwich; 9 strands in 2 sheets; jelly-roll
       1. Galactose-binding domain-like [49785] (32)
          uperfamily
          1. Galactose-binding domain [49786] (4)
             1. Galactose oxidase, N-terminal domain [49787]
                1. Dactylium dendroides [TaxId: 5132] [49788] (4)
                   SQ Q01745 42-680
                2. Fungi (Fusarium sp.) [TaxId: 29916] [69209] (5)
                   sequence identical to that of Dactylium dendroides
                3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [158956] (3)
             2. Sialidase, C-terminal domain [49789]
                1. Micromonospora viridifaciens [TaxId: 1881] [49790] (8)
                   SQ Q02834 47-647
          2. Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) [49791] (4)
             1. C2 domain of factor V [49792]
                1. Human (Homo sapiens) [TaxId: 9606] [49793] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [110117] (1)
                   SQ Q28107 29-324,1566-2210
             2. C2 domain of factor VIII [49794]
                1. Human (Homo sapiens) [TaxId: 9606] [49795] (4)
             3. B1 domain of neuropilin-1 [82016]
                1. Human (Homo sapiens) [TaxId: 9606] [82017] (4)
          3. APC10-like [69210] (3)
             Pfam 03256
             1. APC10/DOC1 subunit of the anaphase-promoting complex [69211]
                1. Human (Homo sapiens) [TaxId: 9606] [69212] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74892] (1)
             2. Placental protein 25, pp25 [117104]
                1. Human (Homo sapiens) [TaxId: 9606] [117105] (2)
                   SQ Q9Y547
          4. delta-Endotoxin, C-terminal domain [49796] (4)
             1. delta-Endotoxin, C-terminal domain [49797]
                1. Bacillus thuringiensis tenebrionis, CRYIIIA (BT13) [TaxId: 1444] [49798] (1)
                2. Bacillus thuringiensis, CRY3bb1 [TaxId: 1428] [63716] (1)
                3. Bacillus thuringiensis, CRYIA (A) [TaxId: 1428] [49799] (1)
                4. Bacillus thuringiensis subsp. kurstaki, CRY2AA [TaxId: 29339] [63717] (1)
          5. Ephrin receptor ligand binding domain [49800] (2)
             1. Ligand-binding domain of the ephb2 receptor tyrosine kinase [49801]
                1. Mouse (Mus musculus) [TaxId: 10090] [49802] (3)
                   SQ P54763 27-207
             2. Ephrin type-B receptor 4 [158957]
                1. Human (Homo sapiens) [TaxId: 9606] [158958] (2)
                   SQ P54760 17-196
          6. beta-Galactosidase/glucuronidase, N-terminal domain [49803] (5)
             1. beta-Galactosidase [49804]
                1. Escherichia coli [TaxId: 562] [49805] (25)
                   SQ P00722
                2. Arthrobacter sp. c2-2 [TaxId: 192168] [141112] (6)
                   SQ Q8KRF6 4-219
             2. beta-Glucuronidase [49806]
                1. Human (Homo sapiens) [TaxId: 9606] [49807] (1)
             3. Beta-mannosidase [158959]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [158960] (18)
                   SQ Q8AAK6 28-219
             4. Exochitosanase CsxA [158961]
                1. Amycolatopsis orientalis [TaxId: 31958] [158962] (2)
                   SQ Q56F26 42-225
          7. Chondroitin ABC lyase I, N-terminal domain [89236] (1)
             1. Chondroitin ABC lyase I, N-terminal domain [89237]
                1. Proteus vulgaris [TaxId: 585] [89238] (1)
          8. CBM4/9 [74893] (3)
             1. Cellulose-binding domain of cellulase C [49809]
                1. Cellulomonas fimi [TaxId: 1708] [49810] (4)
             2. Carbohydrate binding module from a thermostable xylanase [74894]
                1. Rhodothermus marinus [TaxId: 29549] [74895] (2)
             3. Carbohydrate binding module from laminarinase 16A [82018]
                1. Thermotoga maritima [TaxId: 2336] [82019] (1)
          9. Family 6 carbohydrate binding module, CBM6 [69213] (4)
             1. Carbohydrate binding module from xylanase U [69214]
                1. Clostridium thermocellum [TaxId: 1515] [69215] (2)
             2. Cellulase B (lichenase 5a) [101583]
                1. Cellvibrio mixtus [TaxId: 39650] [101584] (6)
             3. Putative xylanase [89239]
                1. Clostridium stercorarium [TaxId: 1510] [89240] (8)
                   SQ P33558 243-374, 384-512
             4. Hypothetical protein BH0236 [117106]
                1. Bacillus halodurans [TaxId: 86665] [117107] (3)
                   SQ Q9KG76 790-923
          10. CBM15 [69216] (1)
              1. Xylan-binding module from xylanase 10c [69217]
                 1. Cellvibrio japonicus [TaxId: 155077] [69218] (3)
                    synonym: Pseudomonas cellulosa
          11. Family 17 carbohydrate binding module, CBM17 [69219] (1)
              1. Endo-1,4-beta glucanase EngF [69220]
                 1. Clostridium cellulovorans [TaxId: 1493] [69221] (2)
          12. CBM22 [49811] (1)
              CBM family 22, formerly x6b domain
              1. Xylan-binding domain [49812]
                 1. Clostridium thermocellum [TaxId: 1515] [49813] (3)
          13. Family 27 carbohydrate binding module, CBM27 [89241] (2)
              1. Beta-mannosidase, C-terminal domain [89242]
                 1. Thermotoga maritima [TaxId: 2336] [89243] (3)
              2. Beta-1,4-mannanase ManA [110118]
                 1. Caldicellulosiruptor saccharolyticus [TaxId: 44001] [110119] (2)
                    SQ P77847 36-220
          14. Family 29 carbohydrate binding module, CBM29 [89244] (1)
              1. Non-catalytic protein 1, Ncp1 [89245]
                 1. Piromyces equi [TaxId: 99929] [89246] (4)
                    SQ Q9C171 337-477
          15. Fucose binding lectin [74896] (1)
              1. Fucose binding lectin [74897]
                 1. European eel (Anguilla anguilla) [TaxId: 7936] [74898] (1)
          16. N-terminal domain of xrcc1 [49814] (1)
              1. N-terminal domain of xrcc1 [49815]
                 the single-strand break repair protein
                 1. Human (Homo sapiens) [TaxId: 9606] [49816] (2)
          17. F-box associated region, FBA [101585] (1)
              1. F-box only protein 2 [101586]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101587] (3)
          18. Allantoicase repeat [101588] (1)
              1. Allantoicase [101589]
                 duplication: tandem repeat of two similar domains
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101590] (2)
                    Yir029w
          19. PepX C-terminal domain-like [69222] (4)
              1. Bacterial cocaine esterase, C-terminal domain [69223]
                 1. Rhodococcus sp. mb1 [TaxId: 51612] [69224] (4)
              2. Alpha-amino acid ester hydrolase [89247]
                 1. Xanthomonas citri [TaxId: 346] [89248] (1)
                 2. Acetobacter pasteurianus [TaxId: 438] [101591] (29)
              3. X-Prolyl dipeptidyl aminopeptidase PepX [82020]
                 1. Lactococcus lactis [TaxId: 1358] [82021] (1)
          20. PA-IL, galactose-binding lectin 1 [82022] (1)
              a truncated form of this fold lacking one of the N-terminal strands
              1. PA-IL, galactose-binding lectin 1 [82023]
                 1. Pseudomonas aeruginosa [TaxId: 287] [82024] (27)
          21. Proprotein convertase P-domain [89249] (3)
              a truncated form of this fold lacking one of the N-terminal strands
              1. Kexin, C-terminal domain [89250]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89251] (4)
              2. Furin, C-terminal domain [89252]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89253] (1)
              3. Alkaline serine protease kp-43, C-terminal domain [110120]
                 1. Bacillus sp. KSM-KP43 [TaxId: 109322] [110121] (3)
                    SQ Q93UV9 207-640
          22. Family 28 carbohydrate binding module, CBM28 [110122] (1)
              1. Endoglucanase (alkaline cellulase) [110123]
                 1. Bacillus sp. 1139 [TaxId: 1411] [110124] (1)
                    SQ P06564 578-761
          23. Family 30 carbohydrate binding module, CBM30 (PKD repeat) [110125] (1)
              1. Endoglucanase CelJ [110126]
                 1. Clostridium thermocellum [TaxId: 1515] [110127] (7)
                    SQ P71140 34-228 # chain B coverage
          24. Rhamnogalacturonase B, RhgB, C-terminal domain [110128] (1)
              1. Rhamnogalacturonase B, RhgB, C-terminal domain [110129]
                 1. Aspergillus aculeatus [TaxId: 5053] [110130] (1)
                    SQ Q00019
          25. Hypothetical protein AT3g04780/F7O18_27 [117108] (1)
              Pfam 06201; DUF1000
              1. Hypothetical protein AT3g04780/F7O18_27 [117109]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117110] (1)
                    SQ Q93Z56
          26. Beta-galactosidase LacA, domains 4 and 5 [117111] (1)
              duplication: tandem repeat of two similar domains; some sequence similarity to the beta-Galactosidase/glucuronidase N-terminal domain (scop_fa 49803)
              1. Beta-galactosidase LacA, domains 4 and 5 [117112]
                 1. Penicillium sp. [TaxId: 5081] [117113] (2)
                    SQ Q700S9 41-1011
          27. Family 36 carbohydrate binding module, CBM36 [117114] (1)
              1. Endo-1,4-beta-xylanase D [117115]
                 1. Paenibacillus polymyxa [TaxId: 1406] [117116] (2)
                    SQ P45796 516-635
          28. Extended PAW domain [141113] (1)
              single domain; the N-terminal half is covered by Pfam 04721; DUF750 (Smart 00613; PAW), the C-terminal half by PfamB 028386
              1. Peptide:N-glycanase, PNGase, C-terminal domain [141114]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141115] (4)
                    SQ Q9JI78 454-561! SQ Q9JI78 472-651
          29. CBM11 [141116] (1)
              Pfam 03425; Carbohydrate binding domain (family 11)
              1. Endoglucanase H [141117]
                 1. Clostridium thermocellum [TaxId: 1515] [141118] (1)
                    SQ P16218 655-821
          30. beta-mannanase CBM [141119] (1)
              1. Endo-beta-1,4-mannanase C-terminal domain [141120]
                 1. Bacillus sp. JAMB-602 [TaxId: 244966] [141121] (1)
                    SQ Q4W8M3 340-490
          31. YxiM N-terminal domain-like [158963] (1)
              PfamB 038265
              1. Hypothetical protein YxiM [158964]
                 1. Bacillus subtilis [TaxId: 1423] [158965] (1)
                    SQ P42304 29-174
          32. NPCBM-like [158966] (2)
              Pfam 08305
              1. Uncharacterized Protein CPF2129 [158967]
                 1. Clostridium perfringens [TaxId: 1502] [158968] (3)
                    SQ Q0TP83 906-1050
              2. Uncharacterized protein CPE0329 [158969]
                 1. Clostridium perfringens [TaxId: 1502] [158970] (5)
                    SQ Q8XNK4 34-204
   32. Viral protein domain [49817] (1)
       sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
       1. Viral protein domain [49818] (3)
          forms homotrimers
          uperfamily
          1. Top domain of virus capsid protein [49819] (4)
             this domain is inserted into a multihelical domain
             1. BTV vp7, central (top) domain [49820]
                1. Bluetongue virus [TaxId: 40051] [49821] (2)
             2. RDV p8, central (top) domain [100924]
                1. Rice dwarf virus [TaxId: 10991] [101592] (1)
                2. African horse sickness virus [TaxId: 40050] [49822] (1)
             3. vp6, the major capsid protein of group A rotavirus [63718]
                1. Bovine rotavirus [TaxId: 10927] [63719] (1)
          2. Influenza hemagglutinin headpiece [49823] (1)
             1. Hemagglutinin [49824]
                includes rudiment esterase domain
                1. Influenza A virus, different strains [TaxId: 11320] [49825] (49)
          3. Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [49826] (1)
             1. Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [49827]
                includes irregular N- and C-terminal extensions
                1. Influenza C virus [TaxId: 11552] [49828] (1)
   33. Calcium-mediated lectin [82025] (1)
       sandwich; 9 strands in 2 sheets; greek-key
       1. Calcium-mediated lectin [82026] (1)
          uperfamily
          1. Calcium-mediated lectin [82027] (2)
             1. Fucose-binding lectin II (PA-LII) [82028]
                1. Pseudomonas aeruginosa [TaxId: 287] [82029] (32)
                   SQ Q9HYN5 # PA3361
             2. Mannose-specific lectin RS-IIL [101593]
                1. Ralstonia solanacearum [TaxId: 305] [101594] (2)
   34. Dextranase, N-terminal domain [101595] (1)
       sandwich; 9 strands in 2 sheets; greek-key
       1. Dextranase, N-terminal domain [101596] (1)
          uperfamily
          1. Dextranase, N-terminal domain [101597] (1)
             1. Dextranase, N-terminal domain [101598]
                1. Penicillium minioluteum [TaxId: 28574] [101599] (2)
   35. Smp-1-like [101600] (1)
       sandwich; 9 strands in 2 sheets; greek-key/jelly-roll
       1. Smp-1-like [101601] (1)
          uperfamily
          1. Smp-1-like [101602] (2)
             1. Unnamed hypothetical protein [101603]
                similar to calpain-like protein fragment from Trypanosoma brucei and the L2230.07 gene product from Leishmania major
                1. Leishmania major [TaxId: 5664] [101604] (1)
             2. Small myristoylated protein 1, Smp-1 [158971]
                1. Leishmania major [TaxId: 5664] [158972] (1)
                   SQ Q5SDH5 1-131
   36. Superantigen (mitogen) Ypm [101605] (1)
       sandwich; 9 strands in 2 sheets; jelly-roll
       1. Superantigen (mitogen) Ypm [101606] (1)
          uperfamily
          1. Superantigen (mitogen) Ypm [101607] (1)
             1. Superantigen (mitogen) Ypm [101608]
                1. Yersinia pseudotuberculosis [TaxId: 633] [101609] (2)
   37. ENV polyprotein, receptor-binding domain [49829] (1)
       sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
       1. ENV polyprotein, receptor-binding domain [49830] (1)
          uperfamily
          1. ENV polyprotein, receptor-binding domain [49831] (2)
             1. F-MuLV receptor-binding domain [49832]
                1. Friend murine leukemia virus [TaxId: 11795] [49833] (1)
             2. FLV receptor-binding domain [89254]
                1. Feline leukemia virus, strain b/lambda-b1 [TaxId: 11768] [89255] (1)
   38. BTV NS2-like ssRNA-binding domain [110131] (1)
       sandwich; 9 strands in 2 sheets; unusual topology with 2 crossover loops
       1. BTV NS2-like ssRNA-binding domain [110132] (1)
          uperfamily
          1. BTV NS2-like ssRNA-binding domain [110133] (1)
             N-terminal half of Pfam 04514
             1. Nonstructural protein NS2 [110134]
                1. Bluetongue virus [TaxId: 40051] [110135] (1)
                   SQ P23065 8-160
   39. WSSV envelope protein-like [158973] (1)
       beta-sandwich; 9 strands in 2 sheets; greek-key
       1. WSSV envelope protein-like [158974] (1)
          1. WSSV envelope protein-like [158975] (2)
             1. Envelope protein VP28 [158976]
                1. White spot syndrome virus, WSSV [TaxId: 92652] [158977] (12)
                   SQ Q9ICB7 32-201
             2. Envelope protein VP26 [158978]
                1. White spot syndrome virus, WSSV [TaxId: 92652] [158979] (1)
                   SQ Q9ICG6 41-201
   40. Virus attachment protein globular domain [49834] (1)
       sandwich, 10 strands in 2 sheets; greek-key
       1. Virus attachment protein globular domain [49835] (3)
          uperfamily
          1. Adenovirus fiber protein "knob" domain [49836] (7)
             1. Adenovirus fiber protein "knob" domain [49837]
                1. Human adenovirus type 5 [TaxId: 28285] [49838] (1)
                2. Human adenovirus type 2 [TaxId: 10515] [49839] (2)
                3. Human adenovirus type 3 [TaxId: 45659] [63720] (1)
                4. Human adenovirus type 12 [TaxId: 28282] [49840] (4)
                5. Human adenovirus type 37 [TaxId: 52275] [110136] (4)
                   SQ Q64823 182-365 ! SQ Q64823 181-365
                6. Human adenovirus type 11P [TaxId: 343462] [158980] (2)
                   SQ P35774 129-325
                7. Canine adenovirus 2 [TaxId: 10514] [158981] (18)
                   SQ Q65914 361-542
          2. Reovirus attachment protein sigma 1 head domain [69225] (1)
             1. Reovirus attachment protein sigma 1 head domain [69226]
                1. Reovirus [TaxId: 10891] [69227] (1)
          3. Lactophage receptor-binding protein head domain [141122] (2)
             1. Baseplate protein (bpp), C-terminal domain [141123]
                1. Lactococcus phage tp901-1 [TaxId: 35345] [141124] (3)
                   SQ Q9G096 63-163
             2. receptor binding protein, rbp, C-terminal domain [141125]
                1. Lactococcus lactis phage p2 [TaxId: 100641] [141126] (6)
                   SQ Q71AW2 162-264
   41. TNF-like [49841] (1)
       sandwich, 10 strands in 2 sheets; jelly-roll
       1. TNF-like [49842] (1)
          uperfamily
          1. TNF-like [49843] (18)
             1. Extracellular domain of CD40 ligand [49844]
                1. Human (Homo sapiens) [TaxId: 9606] [49845] (2)
             2. 30 kDa adipocyte complement-related protein [49846]
                1. Mouse (Mus musculus) [TaxId: 10090] [49847] (2)
             3. Tumor necrosis factor (TNF) [49848]
                1. Human (Homo sapiens) [TaxId: 9606] [49849] (10)
                2. Mouse (Mus musculus) [TaxId: 10090] [49850] (1)
             4. Apoptosis-2 ligand, apo2l/TRAIL [49851]
                1. Human (Homo sapiens) [TaxId: 9606] [49852] (5)
             5. TRANCE/RANKL cytokine [63721]
                1. Mouse (Mus musculus) [TaxId: 10090] [63722] (5)
             6. Soluble part of TALL-1, sTALL-1 (BAFF) [69228]
                1. Human (Homo sapiens) [TaxId: 9606] [69229] (6)
                   also includes the PDB entry (1otz) that together with the entry (1p0t) provides the multimeric structure of the complex of this protein with its receptor, BAFF-R. In these entries protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
             7. Ectodysplasin A, Eda-a1 [101610]
                1. Human (Homo sapiens) [TaxId: 9606] [101611] (2)
             8. Collagen NC1 trimerisation domain [69230]
                1. Human (Homo sapiens), isoform X [TaxId: 9606] [69231] (1)
                2. Mouse (Mus musculus), isoform VIII [TaxId: 10090] [101612] (1)
             9. Complement c1q globular head, A chain [101613]
                hetrotrimer of A, B and C chains
                1. Human (Homo sapiens) [TaxId: 9606] [101614] (5)
             10. Complement c1q globular head, B chain [101615]
                 hetrotrimer of A, B and C chains
                 1. Human (Homo sapiens) [TaxId: 9606] [101616] (5)
             11. Complement c1q globular head, C chain [101617]
                 hetrotrimer of A, B and C chains
                 1. Human (Homo sapiens) [TaxId: 9606] [101618] (5)
             12. A proliferation-inducing ligand, APRIL [117117]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117118] (5)
                    SQ Q9D777 105-251 ! SQ Q9D777 105-241
             13. Tumor necrosis factor ligand superfamily member 4, OX40L [141127]
                 1. Human (Homo sapiens) [TaxId: 9606] [141128] (1)
                    SQ P23510 58-183
                 2. Mouse (Mus musculus) [TaxId: 10090] [141129] (3)
                    SQ P43488 58-185
             14. Glucocorticoid-induced TNF-related ligand, TNFSF18 [158982]
                 1. Mouse (Mus musculus) [TaxId: 10090] [158983] (6)
                    SQ Q7TS55 51-173! SQ Q80YG2 49-173
                 2. Human (Homo sapiens) [TaxId: 9606] [158984] (10)
                    SQ Q9UNG2 55-177! SQ Q9UNG2 57-172! SQ Q9UNG2 57-176
   42. CUB-like [49853] (3)
       sandwich, 10 strands in 2 sheets; jelly-roll
       1. Spermadhesin, CUB domain [49854] (1)
          uperfamily
          1. Spermadhesin, CUB domain [49855] (6)
             1. Acidic seminal fluid protein (ASFP) [49856]
                1. Cow (Bos taurus) [TaxId: 9913] [49857] (1)
             2. Major seminal plasma glycoprotein PSP-I [49858]
                1. Pig (Sus scrofa) [TaxId: 9823] [49859] (1)
             3. Major seminal plasma glycoprotein PSP-II [49860]
                1. Pig (Sus scrofa) [TaxId: 9823] [49861] (1)
             4. Mannose-binding protein associated serine protease 2, MASP2 [89256]
                duplication: contains two CUB domains separated by an EGF-like domain
                1. Rat (Rattus norvegicus) [TaxId: 10116] [89257] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [110137] (2)
                   SQ O00187 17-181
             5. Complement C1S component [89258]
                1. Human (Homo sapiens) [TaxId: 9606] [89259] (1)
       2. Collagen-binding domain [89260] (1)
          N-terminal strand appears only in calcium-free form
          uperfamily
          1. Collagen-binding domain [89261] (1)
             1. Class 1 collagenase [89262]
                1. Bacteria (Clostridium histolyticum) [TaxId: 1498] [89263] (4)
       3. Acetamidase/Formamidase-like [141130] (1)
          decorated fold with additional structures; contains extra C-terminal alpha+beta subdomain: beta(2)-alpha(2)-beta(2): antiparallel beta-sheet, order 1243
          uperfamily
          1. Acetamidase/Formamidase-like [141131] (1)
             Pfam 03069
             1. Putative acetamidase TM0119 [141132]
                1. Thermotoga maritima [TaxId: 2336] [141133] (4)
                   SQ Q9WXX3 1-283
   43. Hyaluronate lyase-like, C-terminal domain [49862] (1)
       sandwich, 10 strands in 2 sheets; "folded meander"
       1. Hyaluronate lyase-like, C-terminal domain [49863] (1)
          uperfamily
          1. Hyaluronate lyase-like, C-terminal domain [49864] (6)
             1. Chondroitinase AC [49865]
                1. Pedobacter heparinus (Flavobacterium heparinum) [TaxId: 984] [49866] (5)
                2. Arthrobacter aurescens [TaxId: 43663] [101619] (6)
             2. Hyaluronate lyase [49867]
                1. Streptococcus pneumoniae [TaxId: 1313] [49868] (19)
                   SQ Q54873 287-1007
                2. Streptococcus agalactiae [TaxId: 1311] [69232] (3)
             3. Xanthan lyase [89264]
                1. Bacillus sp. gl1 [TaxId: 84635] [89265] (7)
             4. Chondroitin ABC lyase I [89266]
                domain 4
                1. Proteus vulgaris [TaxId: 585] [89267] (1)
   44. Cytolysin/lectin [63723] (1)
       sandwich, 10 strands in 2 sheets;
       1. Cytolysin/lectin [63724] (2)
          some topological similarity to osmotin
          uperfamily
          1. Anemone pore-forming cytolysin [63725] (2)
             Pfam 06369
             1. Equinatoxin II (eqtII, tenebrosin C) [63726]
                1. European sea anemone (Actinia equina) [TaxId: 6106] [63727] (3)
                   SQ P61914 40-214
             2. Sticholysin II [89268]
                1. Carribean sea anemone (Stoichactis helianthus) [TaxId: 6123] [89269] (3)
          2. Fungal fruit body lectin [117119] (2)
             Pfam 07367
             1. Lectin xcl [117120]
                1. Xerocomus chrysenteron [TaxId: 5386] [117121] (1)
                   SQ Q8WZC9
             2. TF antigen-binding lectin [117122]
                1. Common mushroom (Agaricus bisporus) [TaxId: 5341] [117123] (5)
                   SQ Q00022
   45. Putative glucosidase YicI, C-terminal domain [117124] (1)
       sandwich; 10 strands in two sheets
       1. Putative glucosidase YicI, C-terminal domain [117125] (1)
          uperfamily
          1. Putative glucosidase YicI, C-terminal domain [117126] (1)
             1. Putative glucosidase YicI, C-terminal domain [117127]
                1. Escherichia coli [TaxId: 562] [117128] (15)
                   SQ P31434
   46. CsrA-like [117129] (1)
       sandwich; 10 strands in 2 sheets; intertwined dimer (segment-swapped, 5-stranded greek-key sandwich?)
       1. CsrA-like [117130] (1)
          uperfamily
          1. CsrA-like [117131] (1)
             Pfam 02599
             1. Carbon storage regulator homolog, CsrA [117132]
                1. Pseudomonas aeruginosa [TaxId: 287] [117133] (1)
                   SQ O69078
   47. Osmotin, thaumatin-like protein [49869] (1)
       sandwich; 11 strands in 2 sheets
       1. Osmotin, thaumatin-like protein [49870] (1)
          has two smaller insertion domains
          uperfamily
          1. Osmotin, thaumatin-like protein [49871] (4)
             1. Osmotin [101620]
                antifungal protein
                1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [101621] (1)
             2. Pathogenesis-related protein 5d [49872]
                1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [49873] (1)
             3. Zeamatin [49874]
                antifungal protein
                1. Maize (Zea mays) [TaxId: 4577] [49875] (1)
             4. Thaumatin [49876]
                1. Ketemfe (Thaumatococcus daniellii) [TaxId: 4621] [49877] (19)
                   SQ P02883
   48. SMAD/FHA domain [49878] (1)
       sandwich; 11 strands in 2 sheets; greek-key
       1. SMAD/FHA domain [49879] (4)
          has a few short helices inserted in loops
          uperfamily
          1. SMAD domain [49880] (4)
             1. Smad4 tumor suppressor C-terminal domain [49881]
                1. Human (Homo sapiens) [TaxId: 9606] [49882] (6)
                   SQ Q13485 314-546
             2. Smad3 MH2 domain [82030]
                1. Human (Homo sapiens) [TaxId: 9606] [82031] (4)
                   SQ P84022 228-425
             3. Smad2 MH2 domain [49883]
                1. Human (Homo sapiens) [TaxId: 9606] [49884] (2)
             4. Smad1 [69233]
                1. Human (Homo sapiens) [TaxId: 9606] [69234] (1)
          2. FHA domain [49885] (12)
             1. Phosphotyrosine binding domain of Rad53 [49886]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49887] (18)
             2. Cell cycle checkpoint protein Chfr [74899]
                1. Human (Homo sapiens) [TaxId: 9606] [74900] (2)
             3. Chk2 kinase [74901]
                1. Human (Homo sapiens) [TaxId: 9606] [74902] (1)
             4. Kinase associated protein phosphatase [101622]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101623] (1)
             5. FHA domain containing protein At4G14490 [101624]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101625] (1)
             6. Antigen ki-67 [101626]
                1. Human (Homo sapiens) [TaxId: 9606] [101627] (2)
             7. Polynucleotide kinase 3'-phosphatase [101628]
                1. Mouse (Mus musculus) [TaxId: 10090] [101629] (5)
                2. Human (Homo sapiens) [TaxId: 9606] [141134] (1)
                   SQ Q96T60 8-108
             8. Afadin [141135]
                1. Mouse (Mus musculus) [TaxId: 10090] [141136] (1)
                   SQ Q9QZQ1 382-487
             9. Kinesin-like protein kif1c [141137]
                1. Human (Homo sapiens) [TaxId: 9606] [141138] (1)
                   SQ O43896 498-599
             10. Probable regulatory protein EmbR, C-terminal domain [141139]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141140] (3)
                    SQ P66799 284-382
             11. Ubiquitin ligase protein RNF8 [141141]
                 1. Human (Homo sapiens) [TaxId: 9606] [141142] (2)
                    SQ O76064 8-139
          3. Interferon regulatory factor 3 (IRF3), transactivation domain [101630] (1)
             weak sequence similarity to SMAD domain
             1. Interferon regulatory factor 3 (IRF3), transactivation domain [101631]
                1. Human (Homo sapiens) [TaxId: 9606] [101632] (2)
          4. EssC N-terminal domain-like [141143] (1)
             PfamB 051221 covers two consecutive domains; the first one is of canonical topology, whereas the second domain has a cirular permutation, beginnig at strand 2 and ending at strand 1 of the canonical fold
             1. Protein EssC [141144]
                SAV0287; similar to DNA segregation ATPase and related proteins
                1. Staphylococcus aureus [TaxId: 1280] [141145] (2)
                   SQ Q8NYF3 1-78! SQ Q8NYF3 79-186
   49. Soluble secreted chemokine inhibitor, VCCI [49888] (1)
       sandwich; 11 strands in 2 sheets; greek-key
       1. Soluble secreted chemokine inhibitor, VCCI [49889] (1)
          uperfamily
          1. Soluble secreted chemokine inhibitor, VCCI [49890] (1)
             1. Soluble secreted chemokine inhibitor, VCCI [49891]
                1. Cowpox virus [TaxId: 10243] [49892] (1)
   50. Baculovirus p35 protein [49893] (1)
       sandwich; 14 strands in 2 sheets; greek-key
       1. Baculovirus p35 protein [49894] (1)
          has a few helices inserted in loops
          uperfamily
          1. Baculovirus p35 protein [49895] (1)
             1. Baculovirus p35 protein [49896]
                Apoptotic caspase inhibitor
                1. AcMNPV (Autographa californica nuclear polyhedrosis virus) [TaxId: 46015] [49897] (6)
   51. Concanavalin A-like lectins/glucanases [49898] (1)
       sandwich; 12-14 strands in 2 sheets; complex topology
       1. Concanavalin A-like lectins/glucanases [49899] (25)
          uperfamily
          1. Legume lectins [49900] (28)
             1. Concanavalin A [49901]
                natural circle permutation: the "old" N- and C-termini are linked with a peptide bond, whereas the "new" ones correspond to a cleaved loop
                1. Jack bean (Canavalia ensiformis) [TaxId: 3823] [49902] (52)
                   SQ P81461
                2. Brazilian jackbean (Canavalia brasiliensis) [TaxId: 61861] [49903] (1)
             2. Legume lectin [49904]
                1. Garden pea (Pisum sativum) [TaxId: 3888] [49905] (6)
                   two-chain protein resulted from a single-chain precursor
                2. Common lentil (Lens culinaris) [TaxId: 3864] [49906] (4)
                   two-chain protein resulted from a single-chain precursor
                3. West-central african legume (Griffonia simplicifolia) [TaxId: 3850] [49907] (3)
                4. Griffonia simplicifolia, lectin I-b4 [TaxId: 3850] [69235] (2)
                5. Coral tree (Erythrina corallodendron) [TaxId: 3843] [49908] (8)
                   SQ P16404
                6. Cockspur coral tree (Erythrina crista-galli) [TaxId: 49817] [74903] (5)
                   SQ Q6YD91
                7. Winged bean (Psophocarpus tetragonolobus), basic agglutinin [TaxId: 3891] [49909] (50)
                8. Winged bean (Psophocarpus tetragonolobus), acidic lectin [TaxId: 3891] [63728] (2)
                9. Lathyrus ochrus, isolectin I [TaxId: 3858] [49910] (7)
                10. Lathyrus ochrus, isolectin II [TaxId: 3858] [49911] (2)
                11. Peanut (Arachis hypogaea) [TaxId: 3818] [49912] (44)
                    SQ P02872 24-255
                12. Soybean (Glycine max) [TaxId: 3847] [49913] (5)
                13. Field bean (Dolichos lablab), Fril [TaxId: 35936] [49914] (1)
                    a legume lectin that delays hematopoietic progenitor maturation
                14. Horse gram (Dolichos biflorus), different isoforms [TaxId: 3840] [49915] (5)
                15. Mucana (Dioclea grandiflora) [TaxId: 3837] [49916] (1)
                    natural circle permutation resulting from a post-translational modification of precursor
                16. Duke (Dioclea guianensis) [TaxId: 99571] [63729] (2)
                    natural circle permutation resulting from a post-translational modification of precursor
                17. Cratylia mollis, isoform 1 [TaxId: 252530] [101633] (1)
                    natural circle permutation resulting from a post-translational modification of precursor
                18. Furze (Ulex europaeus), UEA-I [TaxId: 3902] [49917] (2)
                19. Furze (Ulex europaeus), UEA-II [TaxId: 3902] [49918] (5)
                20. Bloodwood tree (Pterocarpus angolensis) [TaxId: 182271] [82032] (51)
                21. Maackia amurensis, leukoagglutinin [TaxId: 37501] [49919] (1)
                22. Black locust (Robinia pseudoacacia) [TaxId: 35938] [63730] (2)
                23. Hairy vetch (Vicia villosa), isolectin b4 [TaxId: 3911] [82033] (1)
             3. Phytohemagglutinin-L, PHA-L, also arcelin [49920]
                single-chain subunit has "generic" topology
                1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49921] (4)
                2. Kidney bean (Phaseolus vulgaris), G02771, arcelin-5a [TaxId: 3885] [49922] (1)
             4. alpha-Amylase inhibitor [49923]
                1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49924] (1)
          2. Lectin leg-like [74904] (3)
             mammalian protein related to legume lectins
             1. Carbohydrate-recognition domain of P58/ERGIC-53 [74905]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [74906] (2)
             2. Emp47p N-terminal domain [141146]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141147] (8)
                   SQ P43555 35-255! SQ P43555 36-259
             3. Emp46p N-terminal domain [141148]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141149] (6)
                   SQ Q12396 54-271! SQ Q12396 55-272
          3. Glycosyl hydrolases family 16 [49925] (8)
             Pfam 00722
             beta-Glucanase-like
             1. Bacillus 1-3,1-4-beta-glucanase [49926]
                1. Bacillus licheniformis [TaxId: 1402] [49927] (1)
                2. synthetic, hybrid between Bacillus amyloliquefaciens and Bacillus macerans proteins [49928] (3)
                3. Bacillus macerans [TaxId: 44252] [49929] (6)
                4. Fibrobacter succinogenes [TaxId: 833] [89270] (3)
                   a natural circularly permuted protein
             2. kappa-Carrageenase, catalytic [49930]
                1,3-alpha-1,4-beta-D-galactose-4-sulfate-3,6-anhydro-D-galactose 4 galactohydrolase
                1. Pseudoalteromonas carrageenovora [TaxId: 227] [49931] (1)
             3. Xyloglucan endotransglycosylase [101634]
                1. European aspen (Populus tremula) [TaxId: 113636] [101635] (2)
             4. beta-Agarase A [101636]
                1. Zobellia galactanivorans [TaxId: 63186] [101637] (3)
             5. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, catalytic domain [117134]
                1. Clostridium perfringens [TaxId: 1502] [117135] (1)
                   SQ Q934G8 17-420
          4. Galectin (animal S-lectin) [49932] (11)
             1. Galectin-1 [100925]
                1. Cow (Bos taurus) [TaxId: 9913] [49934] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [101638] (6)
                   SQ P09382
                3. Chicken (Gallus gallus) [TaxId: 9031] [49936] (1)
                   galectin-1 homologue CG-16
                4. Toad (Bufo arenarum) [TaxId: 38577] [49937] (2)
             2. Galectin-7 [100926]
                1. Human (Homo sapiens) [TaxId: 9606] [49935] (5)
             3. S-lac lectin, L-14-II [100927]
                1. Human (Homo sapiens) [TaxId: 9606] [100928] (1)
             4. Charcot-Leyden crystal (CLC) protein [49938]
                1. Human (Homo sapiens) [TaxId: 9606] [49939] (4)
             5. Galectin-2 [101639]
                1. Inky cap fungus (Coprinopsis cinerea) [TaxId: 5346] [101640] (6)
             6. Galectin-3 CRD [49940]
                1. Human (Homo sapiens) [TaxId: 9606] [49941] (6)
             7. Congerin I [49942]
                1. Conger eel (Conger myriaster) [TaxId: 7943] [49943] (2)
             8. Congerin II [82034]
                1. Conger eel (Conger myriaster) [TaxId: 7943] [82035] (4)
          5. Laminin G-like module [49944] (7)
             1. Sex hormone-binding globulin [49945]
                1. Human (Homo sapiens) [TaxId: 9606] [49946] (9)
             2. Laminin alpha2 chain [49947]
                1. Mouse (Mus musculus) [TaxId: 10090] [49948] (3)
             3. Ligand-binding domain of neurexin 1beta [49949]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [49950] (16)
                2. Homo sapiens [TaxId: 9606] [158985] (2)
             4. Growth-arrest-specific protein Gas6 [82036]
                1. Human (Homo sapiens) [TaxId: 9606] [82037] (1)
             5. Agrin [101641]
                alternative splicing
                1. Chicken (Gallus gallus) [TaxId: 9031] [101642] (4)
             6. Thrombospondin 1 N-terminal domain [141150]
                1. Human (Homo sapiens) [TaxId: 9606] [141151] (8)
                   SQ P07996 28-233! SQ P07996 29-233
          6. Thrombospondin C-terminal domain [101643] (1)
             Pfam 05735
             1. Thrombospondin C-terminal domain [101644]
                1. Human (Homo sapiens) [TaxId: 9606] [101645] (1)
          7. Pentraxin (pentaxin) [49951] (2)
             1. Serum amyloid P component (SAP) [49952]
                1. Human (Homo sapiens) [TaxId: 9606] [49953] (38)
             2. C-reactive protein (CRP) [49954]
                1. Human (Homo sapiens) [TaxId: 9606] [49955] (3)
          8. Calnexin/calreticulin [69236] (1)
             1. Calnexin [69237]
                1. Dog (Canis familiaris) [TaxId: 9615] [69238] (1)
          9. vp4 sialic acid binding domain [74907] (1)
             1. vp4 sialic acid binding domain [74908]
                1. Rhesus rotavirus [TaxId: 10969] [74909] (4)
          10. Hypothetical protein YesU [101646] (1)
              1. Hypothetical protein YesU [101647]
                 1. Bacillus subtilis [TaxId: 1423] [101648] (1)
          11. Alginate lyase [101649] (3)
              members have same function and similar structures but low sequence similarity
              1. Alginate lyase [101650]
                 1. Alteromonas sp. [TaxId: 232] [101651] (1)
              2. Alginate lyase PA1167 [110138]
                 1. Pseudomonas aeruginosa [TaxId: 287] [110139] (1)
                    SQ Q9I4H0
              3. Polyguluronate lyase [110140]
                 1. Corynebacterium sp. ALY-1 [TaxId: 101519] [110141] (1)
                    SQ Q9RB42
          12. Clostridium neurotoxins, the second last domain [49956] (3)
              1. Tetanus neurotoxin [49957]
                 1. Clostridium tetani [TaxId: 1513] [49958] (10)
              2. Botulinum neurotoxin [49959]
                 1. Clostridium botulinum, serotype A [TaxId: 1491] [49960] (1)
                 2. Clostridium botulinum, serotype B [TaxId: 1491] [49961] (17)
          13. Exotoxin A, N-terminal domain [49962] (1)
              1. Exotoxin A, N-terminal domain [49963]
                 1. Pseudomonas aeruginosa [TaxId: 287] [49964] (2)
          14. Vibrio cholerae sialidase, N-terminal and insertion domains [49965] (1)
              1. Vibrio cholerae sialidase, N-terminal and insertion domains [49966]
                 both domains have this fold
                 rest of protein is beta-propeller of six sheets
                 1. Vibrio cholerae [TaxId: 666] [49967] (3)
                    SQ P37060
          15. Leech intramolecular trans-sialidase, N-terminal domain [49968] (1)
              1. Leech intramolecular trans-sialidase, N-terminal domain [49969]
                 1. North american leech (Macrobdella decora) [TaxId: 6405] [49970] (5)
          16. Trypanosoma sialidase, C-terminal domain [82038] (2)
              1. Trypanosoma sialidase, C-terminal domain [82039]
                 1. Trypanosoma rangeli [TaxId: 5698] [82040] (10)
                    SQ O44049 20-653
                 2. Parasitic flagellate protozoan (Trypanosoma cruzi) [TaxId: 5693] [89271] (12)
                    SQ Q26966
          17. Glycosyl hydrolase family 7 catalytic core [49971] (6)
              contains many insertions in the common fold
              1. Cellobiohydrolase I (cellulase, Endoglucanase I, CBH1) [68900]
                 1. Trichoderma reesei, Cel7A [TaxId: 51453] [68898] (13)
                 2. Trichoderma reesei, Endoglucanase I [TaxId: 51453] [68899] (1)
                 3. Fusarium oxysporum [TaxId: 5507] [49976] (4)
                 4. Humicola insolens, Cel7b [TaxId: 34413] [49977] (6)
                 5. Phanerochaete chrysosporium, Cel7d [TaxId: 5306] [69239] (5)
                 6. Talaromyces emersonii [TaxId: 68825] [117136] (1)
                    SQ Q8TFL9
          18. Glycosyl hydrolases family 32 C-terminal domain [101652] (2)
              Pfam 08244
              flat sheet beta-sandwich lacking the characteristic beta-bulge in the C-terminal strand
              1. Beta-fructosidase (invertase), C-terminal domain [101653]
                 1. Thermotoga maritima [TaxId: 2336] [101654] (7)
              2. Exo-inulinase [117137]
                 1. Aspergillus awamori [TaxId: 105351] [117138] (3)
                    SQ Q96TU3 20-536
          19. Xylanase/endoglucanase 11/12 [49978] (24)
              1. Xylanase II [49979]
                 Partial overlap with common fold and the active sites of the other endoglucanases
                 1. Bacillus circulans [TaxId: 1397] [49980] (10)
                 2. Bacillus subtilis [TaxId: 1423] [49981] (7)
                 3. Bacillus agaradhaerens [TaxId: 76935] [49982] (4)
                 4. Bacillus subtilis, B230 [TaxId: 1423] [74910] (1)
                 5. Streptomyces sp. s38, xyl1 [TaxId: 181109] [69240] (1)
                 6. Trichoderma harzianum [TaxId: 5544] [49983] (1)
                 7. Trichoderma reesei, xynI [TaxId: 51453] [49984] (1)
                 8. Trichoderma reesei, xynII [TaxId: 51453] [49985] (10)
                 9. Thermomyces lanuginosus [TaxId: 5541] [49986] (1)
                 10. Aspergillus niger [TaxId: 5061] [49987] (1)
                 11. Aspergillus kawachii [TaxId: 40384] [49988] (2)
                     SQ P55328 29-210 # 100% sequence identity; Aspergillus awamori TaxID: 105351
                 12. Paecilomyces variotii, Bainier 1907 [TaxId: 45996] [49989] (1)
                 13. Dictyoglomus thermophilum [TaxId: 14] [49990] (1)
                 14. Chaetomium thermophilum [TaxId: 209285] [89272] (3)
                     endoxylanase 11a
                 15. Nonomuraea flexuosa [TaxId: 103836] [89273] (1)
                 16. Penicillium funiculosum [TaxId: 28572] [110142] (1)
                     SQ Q9HFH0
                 17. Trichoderma longibrachiatum [TaxId: 5548] [158986] (1)
              2. Family 12 endo-1,4-beta-glucanase (cellulase) catalytic domain [49991]
                 1. Streptomyces lividans, CelB2 [TaxId: 1916] [49992] (2)
                 2. Streptomyces sp. 11ag8 [TaxId: 133452] [89274] (1)
                 3. Rhodothermus marinus [TaxId: 29549] [89275] (7)
                 4. Trichoderma reesei, Cel12A [TaxId: 51453] [63731] (3)
                 5. Humicola grisea [TaxId: 5527] [101655] (5)
                    SQ Q8NJY3 31-254
                 6. Hypocrea schweinitzii [TaxId: 36924] [89276] (1)
                 7. Aspergillus niger [TaxId: 5061] [82041] (2)
          20. Peptidase A4 [101656] (2)
              circular permutation of the canonical fold
              1. Scytalidopepsin B [101657]
                 1. Fungus (Scytalidium lignicola) [TaxId: 5539] [101658] (5)
              2. Aspergillopepsin II [141152]
                 1. Aspergillus niger [TaxId: 5061] [141153] (1)
                    SQ P24665 60-91,112-282
          21. Alpha-L-arabinofuranosidase B, N-terminal domain [110143] (1)
              1. Alpha-L-arabinofuranosidase B, N-terminal domain [110144]
                 1. Aspergillus kawachii [TaxId: 40384] [110145] (4)
                    SQ Q8NK89 19-499
          22. SPRY domain [141154] (5)
              Pfam 00622
              1. LD34464p [141155]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141156] (1)
                    SQ Q7JUY1 103-319
                    Cg2944-pf, isoform f
              2. Similar to Ret finger protein-like 1 [141157]
                 1. Human (Homo sapiens) [TaxId: 9606] [141158] (4)
              3. SPRY domain-containing SOCS box protein 2 [141159]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141160] (1)
                    SQ O88838 12-224
              4. 52 kDa Ro protein [158987]
                 1. Human (Homo sapiens) [TaxId: 9606] [158988] (2)
                    SQ P19474 287-465
              5. Cg2944-PF (gus) [158989]
                 isoform F
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [158990] (2)
                    SQ A1Z6E2 31-234
          23. Beta-D-xylosidase C-terminal domain-like [141161] (4)
              1. Beta-D-xylosidase C-terminal domain [141162]
                 1. Bacillus subtilis [TaxId: 1423] [141163] (4)
                    SQ P94489 325-533
                 2. Clostridium acetobutylicum [TaxId: 1488] [141164] (8)
                    SQ Q97DM1 323-532
                 3. Geobacillus stearothermophilus [TaxId: 1422] [141165] (16)
                    SQ Q68HB3 325-535
                 4. Bacillus halodurans [TaxId: 86665] [141166] (2)
                    SQ Q9K6P5 321-525
          24. SO2946-like [141167] (1)
              1. Hypothetical protein SO2946 [141168]
                 1. Shewanella oneidensis [TaxId: 70863] [141169] (3)
                    SQ Q8ED25 24-262
          25. MAM domain [141170] (1)
              Pfam 00629
              1. Receptor-type tyrosine-protein phosphatase mu [141171]
                 1. Human (Homo sapiens) [TaxId: 9606] [141172] (1)
                    SQ P28827 21-183
   52. Supersandwich [49993] (3)
       sandwich; 18 strands in 2 sheets
       1. Galactose mutarotase-like [74650] (11)
          probable carbohydrate-binding domain in enzymes acting on sugars
          uperfamily
          1. Aldose 1-epimerase (mutarotase) [74911] (4)
             1. Galactose mutarotase [74912]
                1. Lactococcus lactis [TaxId: 1358] [74913] (19)
                2. Human (Homo sapiens) [TaxId: 9606] [101659] (2)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141173] (1)
                   SQ P04397 358-699
                   C-terminal domain of Gal10 bifunctional protein
             2. Aldose 1-epimerase homologue [89277]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89278] (1)
                   5C981 (C01B4.6 or YK2391) gene product
          2. Hypothetical protein HI1317 [89279] (1)
             1. Hypothetical protein HI1317 [89280]
                1. Haemophilus influenzae [TaxId: 727] [89281] (1)
          3. beta-Galactosidase, domain 5 [49995] (2)
             1. beta-Galactosidase, domain 5 [49996]
                1. Escherichia coli [TaxId: 562] [49997] (25)
                   SQ P00722
                2. Arthrobacter sp. c2-2 [TaxId: 192168] [141174] (6)
                   SQ Q8KRF6 722-1023
          4. Hyaluronate lyase-like, central domain [50006] (6)
             1. Chondroitinase AC [50007]
                1. Pedobacter heparinus (Flavobacterium heparinum) [TaxId: 984] [50008] (5)
                2. Arthrobacter aurescens [TaxId: 43663] [101660] (6)
             2. Hyaluronate lyase [50009]
                1. Streptococcus pneumoniae [TaxId: 1313] [50010] (19)
                   SQ Q54873 287-1007
                2. Streptococcus agalactiae [TaxId: 1311] [69241] (3)
             3. Xanthan lyase [89282]
                1. Bacillus sp. gl1 [TaxId: 84635] [89283] (7)
             4. Chondroitin ABC lyase I [89284]
                domain 3
                1. Proteus vulgaris [TaxId: 585] [89285] (1)
          5. Glycosyltransferase family 36 N-terminal domain [63733] (2)
             overall domain organization is similar to Bacterial glucoamylase
             1. Lactobacillus maltose phosphorylase, N-terminal domain [63734]
                1. Lactobacillus brevis [TaxId: 1580] [63735] (1)
             2. Chitobiose phosphorylase ChbP [110146]
                1. Vibrio proteolyticus [TaxId: 671] [110147] (3)
                   SQ Q76IQ9
          6. Bacterial glucoamylase N-terminal domain-like [82042] (2)
             overall domain organization is similar to Lactobacillus maltose phosphorylase
             1. Bacterial glucoamylase, N-terminal domain [82043]
                1. Thermoanaerobacterium thermosaccharolyticum [TaxId: 1517] [82044] (2)
             2. Glucodextranase, domain N [101661]
                1. Arthrobacter globiformis [TaxId: 1665] [101662] (2)
          7. 4-alpha-glucanotransferase, C-terminal domain [89286] (1)
             family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
             1. 4-alpha-glucanotransferase, C-terminal domain [89287]
                1. Archaeon Thermococcus litoralis [TaxId: 2265] [89288] (3)
          8. alpha-mannosidase, C-terminal domain [88656] (2)
             family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
             the supersandwich domain is elaborated with additional beta-strands and beta-sandwich subdomains
             1. Golgi alpha-mannosidase II [88657]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [88658] (46)
                   SQ Q24451 94-1107
             2. Lysosomal alpha-mannosidase [89289]
                the single-chain precursor is processed into 5 peptides; heavily glycosylated
                1. Cow (Bos taurus) [TaxId: 9913] [89290] (1)
          9. MdoG-like [110148] (1)
             Pfam 04349; Pfam coverage extends to the C-terminal immunoglobulin-like domain
             1. Glucans biosynthesis protein G (MdoG, OpgG), N-terminal domain [110149]
                1. Escherichia coli [TaxId: 562] [110150] (1)
                   SQ P33136 23-511
          10. Rhamnogalacturonase B, RhgB, N-terminal domain [110151] (1)
              1. Rhamnogalacturonase B, RhgB, N-terminal domain [110152]
                 1. Aspergillus aculeatus [TaxId: 5053] [110153] (1)
                    SQ Q00019
          11. YicI N-terminal domain-like [117139] (2)
              1. Putative glucosidase YicI, N-terminal domain [117140]
                 1. Escherichia coli [TaxId: 562] [117141] (15)
                    SQ P31434
              2. Alpha-galactosidase GalA N-terminal domain [141175]
                 rudiment, partly refolded form of supersandwich fold
                 1. Thermotoga maritima [TaxId: 2336] [141176] (1)
                    SQ O33835 1-177
       2. V-region of surface antigen I/II (SA I/II, PAC) [74914] (1)
          uperfamily
          1. V-region of surface antigen I/II (SA I/II, PAC) [74915] (1)
             1. V-region of surface antigen I/II (SA I/II, PAC) [74916]
                1. Streptococcus mutans [TaxId: 1309] [74917] (1)
       3. Amine oxidase catalytic domain [49998] (1)
          uperfamily
          1. Amine oxidase catalytic domain [49999] (5)
             1. Copper amine oxidase, domain 3 [50000]
                1. Escherichia coli [TaxId: 562] [50001] (11)
                2. Pea seedling (Pisum sativum) [TaxId: 3888] [50002] (2)
                   SQ Q43077
                3. Arthrobacter globiformis [TaxId: 1665] [50003] (53)
                   SQ P46881 9-628
                4. Yeast (Hansenula polymorpha) [TaxId: 4905] [50004] (14)
             2. Lysyl oxidase PplO, domain 3 [101663]
                1. Yeast (Pichia pastoris) [TaxId: 4922] [101664] (3)
                   SQ Q96X16 43-777
   53. Leukotriene A4 hydrolase N-terminal domain [63736] (1)
       duplication: two beta-sandwiches of similar topologies are fused together in a single three beta-sheet domain
       1. Leukotriene A4 hydrolase N-terminal domain [63737] (1)
          uperfamily
          1. Leukotriene A4 hydrolase N-terminal domain [63738] (1)
             1. Leukotriene A4 hydrolase N-terminal domain [63739]
                1. Human (Homo sapiens) [TaxId: 9606] [63740] (15)
                   SQ P09960
   54. EV matrix protein [50011] (1)
       consists of two beta-sandwich domains of similar topologies
       1. EV matrix protein [50012] (1)
          uperfamily
          1. EV matrix protein [50013] (1)
             1. EV matrix protein [50014]
                1. Ebola virus [TaxId: 205488] [50015] (3)
   55. Viral chemokine binding protein m3 [82045] (1)
       consists of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds
       1. Viral chemokine binding protein m3 [82046] (1)
          uperfamily
          1. Viral chemokine binding protein m3 [82047] (1)
             1. Viral chemokine binding protein m3 [82048]
                1. Murid herpesvirus 4, MuHV-4 [TaxId: 33708] [82049] (7)
   56. gp9 [50016] (1)
       consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
       1. gp9 [50017] (1)
          uperfamily
          1. gp9 [50018] (1)
             1. gp9 [50019]
                the trigger of tail contraction and the long tail fibers connector
                1. Bacteriophage T4 [TaxId: 10665] [50020] (20)
   57. Flagellar hook protein flgE [117142] (1)
       consists of two different domains; d1: [complex fold made of bifurcated beta-sheets]; d2 (inserted into d1): [beta-sandwich; 8 strands in 2 sheets]
       1. Flagellar hook protein flgE [117143] (1)
          uperfamily
          1. Flagellar hook protein flgE [117144] (1)
             1. Flagellar hook protein flgE [117145]
                1. Salmonella typhimurium [TaxId: 90371] [117146] (1)
                   SQ P16322 71-363
   58. ISP domain [50021] (1)
       consists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich of two 3-stranded sheets or closed barrel (n=6; S=8)
       1. ISP domain [50022] (3)
          uperfamily
          1. Rieske iron-sulfur protein (ISP) [50023] (11)
             1. ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain [50024]
                1. Cow (Bos taurus) [TaxId: 9913] [50025] (10)
                2. Chicken (Gallus gallus) [TaxId: 9031] [50026] (6)
                   SQ P13272 79-274 ! SQ P13272 # precursor of chains I,E and V,R
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63741] (9)
             2. ISP subunit from the cytochrome b6f complex, soluble domain [101665]
                1. Mastigocladus laminosus [TaxId: 83541] [101666] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [101667] (1)
             3. ISP subunit from chloroplast cytochrome bf complex [50027]
                1. Spinach (Spinacia oleracea) [TaxId: 3562] [50028] (1)
             4. Arsenite oxidase Rieske subunit [50029]
                1. Alcaligenes faecalis [TaxId: 511] [50030] (2)
             5. Rieske protein II (SoxF) [74918]
                1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [74919] (1)
             6. Soluble Rieske protein [89291]
                1. Thermus thermophilus [TaxId: 274] [89292] (1)
             7. Rieske-type ferredoxin associated with biphenyl dioxygenase [50031]
                1. Burkholderia cepacia [TaxId: 292] [50032] (1)
             8. Toluene-4-monooxygenase system protein C, TmoC [110154]
                1. Pseudomonas mendocina [TaxId: 300] [110155] (3)
                   SQ Q00458
          2. Ring hydroxylating alpha subunit ISP domain [50033] (7)
             1. Naphthalene 1,2-dioxygenase alpha subunit, N-domain [50034]
                1. Pseudomonas putida [TaxId: 303] [50035] (16)
                2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [141177] (6)
                   SQ Q9X3R9 1-162
             2. Biphenyl dioxygenase large subunit BphA1, N-terminal domain [110156]
                1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [110157] (2)
                   SQ Q53122 17-451
             3. 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO [141178]
                1. Pseudomonas putida [TaxId: 303] [141179] (1)
                   SQ O05935 16-163
             4. Nitrobenzene dioxygenase alpha subunit, NBDO-alpha [141180]
                1. Comamonas sp. JS765 [TaxId: 58226] [141181] (3)
                   SQ Q8RTL4 3-152
             5. Large subunit of cumene dioxygenase cumA1 [141182]
                1. Pseudomonas fluorescens [TaxId: 294] [141183] (1)
                   SQ Q51743 19-180
             6. Terminal oxygenase component of carbazole CarAa [141184]
                1. Janthinobacterium sp. j3 [TaxId: 213804] [141185] (10)
                   SQ Q84II6 1-142
          3. NirD-like [158991] (3)
             retains the common fold but lacks the Fe-S cluster
             1. NADH-nitrite reductase small subunit NirD [158992]
                1. Escherichia coli [TaxId: 562] [158993] (1)
                   SQ P0A9I8 1-108
                2. Erwinia carotovora [TaxId: 554] [158994] (1)
                   SQ Q6CZS1 1-122
                3. Vibrio parahaemolyticus [TaxId: 670] [158995] (8)
                   SQ Q87HB1 4-111
   59. Trm112p-like [158996] (1)
       similar to the small domain of the ISP (scop_cf 50021)
       1. Trm112p-like [158997] (1)
          possibly have evolved from a metal ion (or cofactor)-binding protein of a rubredoxin-like fold; in the known members, from one to three of the four metal-binding positions are occupied by cysteine residues
          1. Trm112p-like [158998] (3)
             Pfam 03966; previously DUF343
             1. Uncharacterized protein Cgl1405/cg1592 [158999]
                1. Corynebacterium glutamicum [TaxId: 1718] [159000] (1)
                   SQ Q8NQM9 1-59
             2. Hypothetical protein CV3345 [159001]
                annotated in PDB 2HF1 as Tetraacyldisaccharide-1-P 4-kinase LpxK
                1. Chromobacterium violaceum [TaxId: 536] [159002] (2)
                   SQ Q7NSS5 2-60
             3. Uncharacterized protein PFL1779 [159003]
                1. Pseudomonas fluorescens [TaxId: 294] [159004] (2)
                   SQ Q4KFT4 3-61
   60. YopX-like [159005] (1)
       consists of two domains: the N-terminal dimerisation domain of variable structure and the C-terminal domain with similarity to the SH3-like fold
       1. YopX-like [159006] (1)
          conmrises proteins of plasmid and phage origins
          1. YopX-like [159007] (3)
             Pfam 09643
             1. Hypothetical protein EF1440 [159008]
                1. Enterococcus faecalis [TaxId: 1351] [159009] (4)
                   SQ Q835D7 1-143
             2. Hypothetical protein YopX [159010]
                1. Bacillus subtilis [TaxId: 1423] [159011] (3)
                   SQ O34401 1-134
             3. Orf041 product [159012]
                1. Staphylococcus phage 37 [TaxId: 320840] [159013] (1)
                   SQ Q4ZC86 1-133
   61. Obg-fold [82050] (1)
       this fold is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich
       these regions form six left-handed collagen-like helices packed and H-bonded together
       1. Obg GTP-binding protein N-terminal domain [82051] (1)
          uperfamily
          1. Obg GTP-binding protein N-terminal domain [82052] (2)
             1. Obg GTP-binding protein N-terminal domain [82053]
                1. Bacillus subtilis [TaxId: 1423] [82054] (1)
                2. Thermus thermophilus [TaxId: 274] [101668] (1)
                   TT1381
   62. SH3-like barrel [50036] (21)
       barrel, partly opened; n*=4, S*=8; meander
       the last strand is interrupted by a turn of 3-10 helix
       1. C-terminal domain of transcriptional repressors [50037] (3)
          the N-terminal domains of these repressors bind DNA
          uperfamily
          1. Biotin repressor (BirA) [50038] (2)
             1. Biotin repressor/biotin holoenzyme synthetase, C-terminal domain [50039]
                1. Escherichia coli [TaxId: 562] [50040] (5)
             2. Biotin--[acetyl-CoA-carboxylase] ligase C-terminal domain [141186]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141187] (28)
                   SQ O57883 189-235
          2. FeoA-like [50041] (4)
             1. Diphtheria toxin repressor (DtxR) [50042]
                1. Corynebacterium diphtheriae [TaxId: 1717] [50043] (15)
                   SQ P33120
             2. Iron-dependent regulator IdeR [63742]
                1. Mycobacterium tuberculosis [TaxId: 1773] [63743] (2)
                   SQ Q50495
             3. Ferrous iron transport protein A, FeoA [159014]
                1. Klebsiella pneumoniae [TaxId: 573] [159015] (1)
                   SQ A6TF31 1-75
             4. Hypothetical protein PA4359 [159016]
                1. Pseudomonas aeruginosa [TaxId: 287] [159017] (1)
                   SQ Q9HW42 1-75
          3. Transcriptional repressor protein KorB [69242] (1)
             1. Transcriptional repressor protein KorB [69243]
                1. Escherichia coli [TaxId: 562] [69244] (2)
       2. SH3-domain [50044] (1)
          uperfamily
          1. SH3-domain [50045] (48)
             1. C-Crk, N-terminal SH3 domain [50046]
                1. Mouse (Mus musculus) [TaxId: 10090] [50047] (9)
             2. Fyn proto-oncogene tyrosine kinase, SH3 domain [50048]
                1. Human (Homo sapiens) [TaxId: 9606] [50049] (11)
             3. SH3 domain from nebulin [50050]
                1. Human (Homo sapiens) [TaxId: 9606] [50051] (2)
             4. Abl tyrosine kinase, SH3 domain [50052]
                1. Mouse (Mus musculus) [TaxId: 10090] [50053] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [50054] (5)
             5. Phosphatidylinositol 3-kinase (p85-alpha subunit, pi3k), SH3 domain [50055]
                1. Human (Homo sapiens) [TaxId: 9606] [50056] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [50057] (2)
             6. alpha-Spectrin, SH3 domain [50058]
                1. Chicken (Gallus gallus) [TaxId: 9031] [50059] (21)
             7. IL-2 inducible T-cell (Itc) kinase [50060]
                1. Mouse (Mus musculus) [TaxId: 10090] [50061] (1)
             8. Hemapoetic cell kinase Hck [50062]
                1. Human (Homo sapiens) [TaxId: 9606] [50063] (6)
             9. Carboxyl-terminal src kinase (csk) [74654]
                1. Human (Homo sapiens) [TaxId: 9606] [74658] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [74655] (1)
             10. c-src protein tyrosine kinase [50064]
                 1. Human (Homo sapiens) [TaxId: 9606] [50065] (5)
                 2. Chicken (Gallus gallus) [TaxId: 9031] [50066] (9)
                 3. Avian sarcoma virus [TaxId: 11876] [50067] (2)
                    v-src
             11. Bruton's tyrosine kinase [50068]
                 1. Human (Homo sapiens) [TaxId: 9606] [50069] (3)
                 2. Mus musculus [TaxId: 10090] [159018] (2)
             12. tyrosine kinase tec [69246]
                 1. Mouse (Mus musculus) [TaxId: 10090] [69247] (1)
             13. Growth factor receptor-bound protein 2 (GRB2), N- and C-terminal domains [50070]
                 1. Human (Homo sapiens) [TaxId: 9606] [50071] (6)
                 2. Mouse (Mus musculus) [TaxId: 10090] [50072] (5)
                 3. Caenorhabditis elegans, SEM-5 [TaxId: 6239] [50073] (5)
                    Sex muscle abnormal protein 5
             14. Grb2-related adaptor protein 2 (Mona/Gads) [89293]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89294] (5)
             15. Phospholipase C, SH3 domain [50074]
                 1. Human (Homo sapiens) [TaxId: 9606] [50075] (2)
             16. p56-lck tyrosine kinase, SH3 domain [50076]
                 1. Human (Homo sapiens) [TaxId: 9606] [50077] (10)
             17. 53BP2 [50078]
                 1. Human (Homo sapiens) [TaxId: 9606] [50079] (1)
             18. Amphiphysin 2 [50080]
                 synonyms: Myc box dependent interacting protein 1, bin1
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50081] (4)
             19. EPS8 SH3 domain [50082]
                 1. Mouse (Mus musculus) [TaxId: 10090] [50083] (3)
             20. Vav N-terminal SH3 domain [63744]
                 1. Mouse (Mus musculus) [TaxId: 10090] [63745] (3)
             21. Melanoma inhibitory activity protein [63746]
                 1. Human (Homo sapiens) [TaxId: 9606] [63747] (3)
             22. Psd-95 [69248]
                 associates with a guanylate kinase domain
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [69249] (3)
             23. Actin binding protein ABP1 [74920]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74921] (2)
             24. p47pox (neutrophil cytosolic factor 1) [89295]
                 1. Human (Homo sapiens) [TaxId: 9606] [89296] (5)
             25. p67phox [74922]
                 1. Human (Homo sapiens) [TaxId: 9606] [74923] (1)
             26. Peroxisomal membrane protein Pex13p [82055]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82056] (5)
             27. Intersectin 2 (KIAA1256) [101669]
                 1. Human (Homo sapiens) [TaxId: 9606] [101670] (5)
                    SQ Q9NZM3 761-841, 897-957, 982-1037, 1055-1121, 1102-1186
             28. Hypothetical protein Baa76854.1 (KIAA1010) [101671]
                 1. Human (Homo sapiens) [TaxId: 9606] [101672] (2)
             29. Olygophrenin-1 like protein (KIAA0621) [101673]
                 1. Human (Homo sapiens) [TaxId: 9606] [101674] (1)
             30. Signal transducing adaptor molecule Stam2 [101675]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101676] (1)
             31. Rac/CDC42 GEF 6 [101677]
                 1. Human (Homo sapiens) [TaxId: 9606] [101678] (1)
             32. Hypothetical protein YFR024c [101679]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101680] (2)
             33. Fyn-binding protein (T-cell adapter protein adap) [101681]
                 1. Human (Homo sapiens) [TaxId: 9606] [101682] (1)
             34. SH3-like domain of the L-type calcium channel [110158]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110159] (4)
                    SQ P54288
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [110160] (3)
                    SQ P54287 38-362
             35. BAI1-associated protein 2-like 1 (RIKEN cDNA 1300006m19) [110161]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110162] (1)
                    SQ Q9DBJ3 343-401
             36. Kalirin-9a [117147]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117148] (1)
                    SQ Q8BTT9 594-651
             37. RIM binding protein 2, RIMBP2 [117149]
                 1. Human (Homo sapiens) [TaxId: 9606] [117150] (1)
                    SQ O15034 160-242
             38. BZZ1 [141188]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141189] (1)
                    SQ P38822 497-552
             39. Nck-2 [159019]
                 1. Human (Homo sapiens) [TaxId: 9606] [159020] (1)
                    SQ O43639 192-262
                    unclassified SH3 domains of this protein species are: 1WX6, 2B86, 2FRW, 2FRY
       3. Prokaryotic SH3-related domain [82057] (4)
          uperfamily
          1. GW domain [82058] (1)
             1. Internalin B, C-terminal domains [82059]
                duplication: tandem repeat of three SH3-like GW domains
                1. Listeria monocytogenes [TaxId: 1639] [82060] (1)
          2. PhnA-like [141190] (2)
             Pfam 03831
             1. Hypothetical protein PA0128, C-terminal domain [141191]
                1. Pseudomonas aeruginosa [TaxId: 287] [141192] (1)
                   SQ Q9I704 40-113
             2. Hypothetical protein RPA4501 [141193]
                1. Rhodopseudomonas palustris [TaxId: 1076] [141194] (1)
                   SQ Q6N1A7 1-72
          3. Spr N-terminal domain-like [141195] (1)
             1. Cell wall-associated hydrolase Spr N-terminal domain [141196]
                1. Nostoc punctiforme [TaxId: 272131] [141197] (3)
                   SQ Q8YRR4 13-86
          4. Ply C-terminal domain-like [141198] (1)
             duplication: tandem repeat of two SH3-like domains swapped with the N-terminal strands; non-overlapping parts of sequence are covered by PfamB 062324 and PfamB 020199
             1. Endolysin Ply, C-terminal domain [141199]
                1. Bacteriophage Psa [TaxId: 171618] [141200] (1)
                   SQ Q8W5Y8 181-314
       4. Myosin S1 fragment, N-terminal domain [50084] (1)
          uperfamily
          1. Myosin S1 fragment, N-terminal domain [50085] (4)
             1. Myosin S1 fragment, N-terminal domain [50086]
                1. Chicken (Gallus gallus), pectoral muscle [TaxId: 9031] [50087] (4)
                2. Chicken (Gallus gallus), Va isoform [TaxId: 9031] [101683] (3)
                3. Bay scallop (Aequipecten irradians) [TaxId: 31199] [50088] (11)
                   SQ P24733 3-836 ! SQ P24733 6-837
                4. Dictyostelium discoideum [TaxId: 44689] [50089] (21)
       5. Tudor/PWWP/MBT [63748] (4)
          uperfamily
          1. Tudor domain [63749] (7)
             Pfam 00567
             1. Survival motor neuron protein 1, smn [63750]
                1. Human (Homo sapiens) [TaxId: 9606] [63751] (2)
             2. p53-binding protein 1, 53BP1 [110163]
                duplication; contains two Tudor domains in tandem
                1. Human (Homo sapiens) [TaxId: 9606] [110164] (6)
                   SQ Q12888 1485-1602 ! SQ Q12888 1484-1606
             3. Tudor domain-containing protein 3, TDRD3 [141201]
                1. Mouse (Mus musculus) [TaxId: 10090] [141202] (1)
                   SQ Q91W18 553-612
             4. Jumonji domain-containing protein 2A [141203]
                contains tandem repeat of two segment-swapped Tudor domains
                1. Human (Homo sapiens) [TaxId: 9606] [141204] (20)
                   SQ O75164 897-955! SQ O75164 956-1011
             5. Tudor and KH domain-containing protein TDRKH [141205]
                1. Human (Homo sapiens) [TaxId: 9606] [141206] (1)
                   SQ Q9Y2W6 329-425
             6. P100 co-activator, SND1 [141207]
                1. Human (Homo sapiens) [TaxId: 9606] [141208] (2)
                   SQ Q7KZF4 705-794
             7. Lamin-b receptor [141209]
                1. Human (Homo sapiens) [TaxId: 9606] [141210] (1)
                   SQ Q14739 1-55
          2. PWWP domain [69250] (6)
             includes the C-terminal all-alpha subdomain
             1. DNA methyltransferase DNMT3B [69251]
                1. Mouse (Mus musculus) [TaxId: 10090] [69252] (1)
             2. Hypothetical protein SPBC215.07c [89297]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [89298] (1)
             3. Hepatoma-derived growth factor, related protein 3 [101684]
                1. Mouse (Mus musculus) [TaxId: 10090] [101685] (1)
             4. Hepatoma-derived growth factor, HDGF [117151]
                1. Human (Homo sapiens) [TaxId: 9606] [117152] (3)
                   SQ P51858 1-100
                2. Rat (Rattus norvegicus) [TaxId: 10116] [141211] (1)
                   SQ Q8VHK7 1-110
             5. Histone-lysine N-methyltransferase NSD3 [141212]
                WHSC1L1
                1. Human (Homo sapiens) [TaxId: 9606] [141213] (1)
                   SQ Q9BZ95 957-1053
          3. MBT repeat [89299] (4)
             Pfam 02820
             contains extended 'arm', N-terminal to the common fold core
             1. Scml2 protein [89300]
                duplication: contains tandem repeat of two MBT repeats
                1. Human (Homo sapiens) [TaxId: 9606] [89301] (7)
             2. Lethal(3)malignant brain tumor-like protein [101686]
                1. Human (Homo sapiens) [TaxId: 9606] [101687] (3)
             3. Lethal(3)malignant brain tumor-like 3 protein, L3MBTL3 (KIAA1798) [117153]
                1. Human (Homo sapiens) [TaxId: 9606] [117154] (2)
                   SQ Q96JM7 259-372, 469-562
             4. Scm-like with four MBT domains protein 2, SFMBT2 (KIAA1617) [117155]
                1. Human (Homo sapiens) [TaxId: 9606] [117156] (1)
                   SQ Q5VUG0 181-285
          4. CPH domain [159021] (1)
             1. Cullin-7 [159022]
                1. Human (Homo sapiens) [TaxId: 9606] [159023] (1)
                   SQ Q14999 360-435
       6. Chromo domain-like [54160] (3)
          SH3-like barrel is capped by a C-terminal helix
          uperfamily
          1. "Histone-like" proteins from archaea [54161] (2)
             1. DNA-binding protein [54162]
                1. Archaeon Sulfolobus solfataricus, Sso7d [TaxId: 2287] [54163] (8)
                   SQ P61991
                2. Archaeon Sulfolobus acidocaldarius, Sac7d [TaxId: 2285] [54164] (10)
                   SQ P13123
          2. Chromo domain [54165] (10)
             lacks the SH3-like barrel first strand that can be complemented by bound peptide ligand; in shadow chromo domain the corresponding site is altered by insertion; similarity to the IL8-like fold
             1. Heterochromatin protein 1, HP1 [54166]
                duplication: consists of two homologous domains, N-terminal chromo domain and C-terminal chromo shadow domain
                1. Mouse (Mus musculus), HP1 beta (MOD1, M31) [TaxId: 10090] [54167] (8)
                2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75343] (3)
                   SQ P05205 23-74
                3. Fission yeast (Schizosaccharomyces pombe), SWI6 [TaxId: 4896] [54169] (1)
             2. Polycomb protein, Pc [101688]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101689] (2)
             3. Histone methyltransferase clr4, chromo domain [64217]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64218] (1)
             4. Chromobox protein homolog 8 [141214]
                Polycomb 3 homolog, Pc3
                1. Mouse (Mus musculus) [TaxId: 10090] [141215] (1)
                   SQ Q9QXV1 7-58
             5. CpSRP43 [141216]
                Signal recognition particle 43 kDa protein, chloroplast precursor (CAO)
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141217] (6)
                   SQ O22265 265-319! SQ O22265 320-373! SQ O22265 84-128
             6. Chromodomain protein, Y-like isoform [141218]
                1. Human (Homo sapiens) [TaxId: 9606] [141219] (1)
                   SQ Q32NC5 1-66
             7. ATP-dependent helicase CHD1 (Chromo domain protein 1) [141220]
                1. Human (Homo sapiens) [TaxId: 9606] [141221] (25)
                   SQ O14646 269-366! SQ O14646 270-355! SQ O14646 366-445! SQ O14646 367-443! SQ O14646 367-445
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141222] (2)
                   SQ P32657 172-252! SQ P32657 249-347
          3. Chromo barrel domain [117157] (3)
             typical SH3-like barrel fold; similar sequence motif to the canonical chromo domain
             1. Probable histone acetyltransferase MYST1 [117158]
                1. Mouse (Mus musculus) [TaxId: 10090] [117159] (1)
                   SQ Q9D1P2 49-169
             2. Putative histone acetyltransferase MOF [141223]
                Males-absent on the first protein
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141224] (1)
                   SQ O02193 367-454
             3. Mortality factor 4-like protein 1, MRG15 [141225]
                MORF-related gene 15 isoform 1
                1. Human (Homo sapiens) [TaxId: 9606] [141226] (7)
                   SQ Q9UBU8 6-88
       7. BAH domain [82061] (1)
          uperfamily
          1. BAH domain [82062] (1)
             1. Origin-recognition complex protein 120kDa subunit, Orc1p [82063]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82064] (3)
       8. PAZ domain [101690] (1)
          uperfamily
          1. PAZ domain [101691] (5)
             1. Argonaute 2 [101692]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101693] (4)
                   SQ Q9VUQ5 602-717 ! SQ Q9VUQ5 602-720
             2. Argonaute 1 [101694]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101695] (1)
             3. Eukaryotic translation initiation factor 2C 1, EIF2C1 [110165]
                1. Human (Homo sapiens) [TaxId: 9606] [110166] (2)
                   SQ Q9UL18 225-349
             4. Argonaute homologue PF0537 [110167]
                includes the N-terminal domain
                1. Pyrococcus furiosus [TaxId: 2261] [110168] (3)
                   SQ Q8U3D2
             5. Argonaute homologue Aq_1447 [141227]
                includes the N-terminal domain
                1. Aquifex aeolicus [TaxId: 63363] [141228] (6)
                   SQ O67434 4-314
       9. Cap-Gly domain [74924] (1)
          uperfamily
          1. Cap-Gly domain [74925] (12)
             Pfam 01302
             1. Cytoskeleton-associated protein F53F4.3 [74926]
                1. Caenorhabditis elegans [TaxId: 6239] [74927] (2)
                   SQ Q20728 132-229
             2. Cylindromatosis tumour-suppressor Cyld [82065]
                1. Human (Homo sapiens) [TaxId: 9606] [82066] (3)
                   SQ Q9NQC7 125-206, 228-304, 460-550
             3. Tubulin-specific chaperone B (SKAP1) [117160]
                1. Mouse (Mus musculus) [TaxId: 10090] [117161] (1)
                   SQ Q9D1E6 134-233
             4. CLIP170-related 59kda protein CLIPR-59 (1500005P14Rik) [117162]
                1. Mouse (Mus musculus) [TaxId: 10090] [117163] (1)
                   SQ Q9DB67 19-107
                2. Human (Homo sapiens) [TaxId: 9606] [141229] (1)
                   SQ Q96DZ5 285-366
             5. Restin-like protein 2, Rsnl2 [117164]
                1. Mouse (Mus musculus) [TaxId: 10090] [117165] (2)
                   SQ Q8CI96 266-354; 617-696
             6. CLIP-115 [141230]
                1. Human (Homo sapiens) [TaxId: 9606] [141231] (4)
                   SQ Q9UDT6 219-289! SQ Q9UDT6 68-149
             7. Centrosome-associated protein 350 [141232]
                1. Human (Homo sapiens) [TaxId: 9606] [141233] (1)
                   SQ Q5VT06 2473-2581
             8. Dynactin 1 [141234]
                1. Human (Homo sapiens) [TaxId: 9606] [141235] (6)
                   SQ Q14203 1-99! SQ Q14203 25-98
             9. Restin [141236]
                1. Human (Homo sapiens) [TaxId: 9606] [141237] (3)
                   SQ P30622 1-128! SQ P30622 181-340
                2. Mouse (Mus musculus) [TaxId: 10090] [141238] (1)
                   SQ Q922J3 58-128
             10. Kinesin-like protein kif13b [141239]
                 1. Human (Homo sapiens) [TaxId: 9606] [141240] (1)
                    SQ Q9NQT8 1684-1771
       10. Electron transport accessory proteins [50090] (4)
           uperfamily
           1. R67 dihydrofolate reductase [50091] (1)
              1. R67 dihydrofolate reductase [50092]
                 1. Escherichia coli, plasmid PLZ1 [TaxId: 562] [50093] (6)
           2. Photosystem I accessory protein E (PsaE) [50094] (4)
              1. Photosystem I accessory protein E (PsaE) [50095]
                 1. Cyanobacterium (Synechococcus sp.), pcc 7002 [TaxId: 1131] [50096] (2)
                 2. Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId: 1143] [89302] (1)
                 3. Cyanobacterium (Nostoc sp.), strain pcc8009 [TaxId: 1180] [50097] (2)
                 4. Synechococcus elongatus [TaxId: 32046] [63752] (1)
           3. Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain [50098] (1)
              1. Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain [50099]
                 1. Synechocystis sp. [TaxId: 1143] [50100] (6)
           4. Nitrile hydratase beta chain [50101] (3)
              contains irregular array of helices in the N-terminal extension
              1. Iron-containing nitrile hydratase [50102]
                 1. Rhodococcus erythropolis [TaxId: 1833] [50103] (16)
                    also Rhodococcus sp. R312
              2. Cobalt-containing nitrile hydratase [82067]
                 1. Pseudonocardia thermophila [TaxId: 1848] [82068] (5)
                    SQ Q7SID3
                 2. Bacillus smithii [TaxId: 1479] [117166] (1)
                    SQ Q84FS6 # 85% sequence identity; Bacillus sp. RAPc8 TaxID: 218609
       11. Translation proteins SH3-like domain [50104] (7)
           many known members contain KOW motif
           uperfamily
           1. Ribosomal proteins L24p and L21e [50105] (5)
              1. Ribosomal proteins L24 (L24p) [50106]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [50107] (44)
                    SQ P10972
                 2. Escherichia coli [TaxId: 562] [141241] (30)
                    SQ P60624 1-102
                 3. Deinococcus radiodurans [TaxId: 1299] [159024] (7)
                    SQ Q9RXJ1 4-113
                 4. Thermus thermophilus [TaxId: 274] [159025] (11)
                    SQ Q72I15 2-102
              2. Ribosomal proteins L21e [50108]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [50109] (40)
                    SQ P12734
           2. eIF5a N-terminal domain-like [50110] (7)
              1. Eukaryotic initiation translation factor 5a (eIF5a) [50111]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50112] (2)
                 2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50113] (1)
                 3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82069] (1)
                 4. Leishmania infantum [TaxId: 5671] [110169] (1)
                    SQ Q9N9V6
                 5. Leishmania mexicana [TaxId: 5665] [117167] (1)
                    SQ Q9N9V6 97% sequence identity
              2. Woronin body major protein (Hex1) [82070]
                 1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82071] (1)
              3. Elongation factor P N-terminal domain [110170]
                 1. Thermus thermophilus HB8 [TaxId: 300852] [110171] (1)
                    SQ Q76G20
           3. C-terminal domain of ribosomal protein L2 [50114] (5)
              1. C-terminal domain of ribosomal protein L2 [50115]
                 1. Bacillus stearothermophilus [TaxId: 1422] [50116] (2)
                 2. Archaeon Haloarcula marismortui [TaxId: 2238] [50117] (40)
                    SQ P20276
                 3. Thermus thermophilus [TaxId: 274] [159026] (5)
                    SQ Q72I07 126-272
                 4. Escherichia coli [TaxId: 562] [159027] (27)
                    SQ P60422 125-269
                 5. Deinococcus radiodurans [TaxId: 1299] [159028] (5)
                    SQ Q9RXJ9 128-272
           4. N-utilization substance G protein NusG, C-terminal domain [82072] (2)
              1. N-utilization substance G protein NusG, C-terminal domain [82073]
                 1. Aquifex aeolicus [TaxId: 63363] [82074] (3)
                 2. Thermus thermophilus [TaxId: 274] [101696] (1)
           5. SPT5 KOW domain-like [141242] (1)
              part of Pfam 00467
              1. Transcription elongation factor SPT5 [141243]
                 1. Human (Homo sapiens) [TaxId: 9606] [141244] (1)
                    SQ O00267 462-523
           6. Ribosomal protein L19 [141245] (3)
              Pfam 01245
              1. Ribosomal protein L19 [141246]
                 1. Escherichia coli [TaxId: 562] [141247] (9)
                    SQ P0A7K6 1-114
                 2. Deinococcus radiodurans [TaxId: 1299] [159029] (6)
                    SQ Q9RWB4 2-109
                 3. Thermus thermophilus [TaxId: 274] [159030] (4)
                    SQ P60490 1-138
           7. Ribosomal protein L14e [159031] (1)
              PfamB 032577
              1. Ribosomal protein L14e [159032]
                 1. Sulfolobus solfataricus [TaxId: 2287] [159033] (1)
                    SQ Q980C1 1-96
       12. Cell growth inhibitor/plasmid maintenance toxic component [50118] (3)
           contains insert beta-sheet subdomain and C-terminal helix
           uperfamily
           1. CcdB [50119] (1)
              1. CcdB [50120]
                 topoisomerase poison
                 1. Escherichia coli [TaxId: 562] [50121] (6)
           2. Kid/PemK [82075] (3)
              1. Kid toxin protein (ParD) [82076]
                 1. Plasmid R1, from Escherichia coli [TaxId: 2482] [82077] (3)
              2. MazF protein [89303]
                 1. Escherichia coli [TaxId: 562] [89304] (1)
              3. PemK-like protein YdcE [82078]
                 1. Bacillus subtilis [TaxId: 1423] [82079] (1)
           3. Rv2302-like [141248] (1)
              different orientation for the extra C-terminal helix relative the SH3-like barrel
              1. Hypothetical protein Rv2302/MT2359 [141249]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141250] (1)
                    SQ P64983 1-80
       13. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63433] (1)
           uperfamily
           1. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63434] (1)
              contains 5 short helices in the loop between the third and fourth strands
              1. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63435]
                 1. Mouse (Mus musculus) [TaxId: 10090] [63436] (6)
       14. DNA-binding domain of retroviral integrase [50122] (1)
           uperfamily
           1. DNA-binding domain of retroviral integrase [50123] (3)
              1. DNA-binding domain of retroviral integrase [50124]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [50125] (4)
                 2. Rous sarcoma virus RSV [TaxId: 11886] [50126] (2)
                 3. Simian immunodeficiency virus [TaxId: 11723] [50127] (1)
       15. Hypothetical protein YfhH [101697] (1)
           contains extra N-terminal all-alpha subdomain
           uperfamily
           1. Hypothetical protein YfhH [101698] (1)
              1. Hypothetical protein YfhH [101699]
                 1. Bacillus subtilis [TaxId: 1423] [101700] (1)
       16. Kinase-associated protein B-like [141251] (1)
           contains extra C-terminal alpha-hairpin
           uperfamily
           1. Kinase-associated protein B-like [141252] (1)
              1. Kinase-associated protein B [141253]
                 1. Bacillus cereus [TaxId: 1396] [141254] (2)
                    SQ Q816F1 4-127
                    BC4909
       17. YccV-like [141255] (1)
           contains extra C-terminal helix packed against barrel
           uperfamily
           1. YccV-like [141256] (1)
              1. Hypothetical protein YccV [141257]
                 1. Escherichia coli [TaxId: 562] [141258] (1)
                    SQ P0AB20 21-114
       18. CarD-like [141259] (1)
           uperfamily
           1. CarD-like [141260] (1)
              Pfam 02559
              1. Transcription-repair coupling factor, RRCF, middle domain [141261]
                 1. Escherichia coli [TaxId: 562] [141262] (2)
                    SQ P30958 466-545
       19. Mib/herc2 domain-like [159034] (1)
           1. Mib/herc2 domain [159035] (1)
              Pfam 06701
              1. E3 ubiquitin-protein ligase hectd1 [159036]
                 1. Human (Homo sapiens) [TaxId: 9606] [159037] (1)
                    SQ Q9ULT8 1268-1340
       20. YorP-like [159038] (1)
           1. YorP-like [159039] (1)
              Pfam 09629
              1. Uncharacterized protein YorP [159040]
                 1. Bacillus subtilis [TaxId: 1423] [159041] (1)
                    SQ O31898 1-71
       21. Plus3-like [159042] (1)
           1. Plus3 [159043] (1)
              Pfam 03126
              1. RNA polymerase-associated protein RTF1 homolog [159044]
                 1. Human (Homo sapiens) [TaxId: 9606] [159045] (2)
                    SQ Q92541 307-442! SQ Q92541 313-444
   63. GroES-like [50128] (2)
       contains barrel, partly opened; n*=4, S*=8; meander
       1. GroES-like [50129] (2)
          uperfamily
          1. GroES [50130] (5)
             1. Chaperonin-10 (GroES) [50131]
                1. Escherichia coli [TaxId: 562] [50132] (31)
                2. Mycobacterium tuberculosis [TaxId: 1773] [63753] (2)
                3. Mycobacterium leprae [TaxId: 1769] [50133] (1)
                4. Thermus thermophilus [TaxId: 274] [110172] (3)
                   SQ P61493 ! SQ P61492
             2. GP31 co-chaperonin [50134]
                1. Bacteriophage T4 [TaxId: 10665] [50135] (8)
          2. Alcohol dehydrogenase-like, N-terminal domain [50136] (27)
             C-terminal domain is alpha/beta (classical Rossmann-fold)
             1. Alcohol dehydrogenase [50137]
                contains a Zn-finger subdomain, residues 94-117
                1. Horse (Equus caballus) [TaxId: 9796] [50138] (38)
                   SQ P00327
                2. Human (Homo sapiens), different isozymes [TaxId: 9606] [50139] (26)
                   SQ P00326 ! SQ P00325 ! SQ P07327
                3. Mouse (Mus musculus), class II [TaxId: 10090] [50140] (3)
                4. Frog (Rana perezi) [TaxId: 8403] [89305] (2)
                5. Cod (Gadus callarias) [TaxId: 8053] [50141] (1)
                6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82080] (4)
                7. Archaeon Aeropyrum pernix [TaxId: 56636] [101701] (1)
                8. Pseudomonas aeruginosa [TaxId: 287] [101702] (1)
                9. Bacillus stearothermophilus [TaxId: 1422] [101703] (1)
             2. Hypothetical protein TM0436 [101704]
                1. Thermotoga maritima [TaxId: 2336] [101705] (1)
             3. Hypothetical protein YhdH [101706]
                1. Escherichia coli [TaxId: 562] [101707] (2)
                   SQ P26646
             4. Hypothetical protein YahK [101708]
                1. Escherichia coli [TaxId: 562] [101709] (1)
             5. Benzyl alcohol dehydrogenase [89306]
                1. Acinetobacter calcoaceticus [TaxId: 471] [89307] (1)
             6. Bacterial secondary alcohol dehydrogenase [50142]
                1. Clostridium beijerinckii [TaxId: 1520] [50143] (3)
                2. Thermoanaerobacter brockii [TaxId: 29323] [50144] (10)
             7. Ketose reductase (sorbitol dehydrogenase) [50145]
                1. Silverleaf whitefly (Bemisia argentifolii) [TaxId: 77855] [50146] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [101710] (3)
             8. Formaldehyde dehydrogenase [82081]
                1. Pseudomonas putida [TaxId: 303] [82082] (1)
             9. Quinone oxidoreductase [50147]
                1. Escherichia coli [TaxId: 562] [50148] (1)
                2. Thermus thermophilus [TaxId: 274] [89308] (2)
                3. Human (Homo sapiens) [TaxId: 9606] [117168] (1)
                   SQ Q08257
             10. 2,4-dienoyl-CoA reductase [89309]
                 1. Yeast (Candida tropicalis) [TaxId: 5482] [89310] (5)
             11. Putative zinc-binding alcohol dehydrogenase [101711]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101712] (1)
             12. Cinnamyl alcohol dehydrogenase, ADH6 [110173]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110174] (3)
                    SQ Q04894
             13. Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase [110175]
                 1. Guinea pig (Cavia porcellus) [TaxId: 10141] [110176] (5)
                    SQ Q9EQZ5
             14. B. subtilis YhfP homologue [117169]
                 1. Bacillus stearothermophilus [TaxId: 1422] [117170] (1)
                    SQ Q5L022; 96% sequence identity; Geobacillus kaustophilus TaxID:1462
             15. Hypothetical protein YhfP [117171]
                 1. Bacillus subtilis [TaxId: 1423] [117172] (2)
                    SQ O07615
       2. SacY-like RNA-binding domain [50151] (1)
          uperfamily
          1. BglG-like antiterminator proteins [50152] (2)
             1. SacY [50153]
                1. Bacillus subtilis [TaxId: 1423] [50154] (1)
             2. LicT [74928]
                1. Bacillus subtilis [TaxId: 1423] [74929] (1)
   64. PDZ domain-like [50155] (1)
       contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
       1. PDZ domain-like [50156] (6)
          peptide-binding domain
          uperfamily
          1. PDZ domain [50157] (55)
             Pfam 00595
             1. Discs large protein homolog [50158]
                1. Human (Homo sapiens) [TaxId: 9606] [50159] (4)
             2. Cask/Lin-2 [50160]
                1. Human (Homo sapiens) [TaxId: 9606] [50161] (1)
             3. Synapse-associated protein 102 [101713]
                1. Human (Homo sapiens) [TaxId: 9606] [101714] (2)
             4. Synaptic protein PSD-95 [50162]
                Synonym: synapse associated protein 90, sap90
                duplication: contains three PDZ domains
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50163] (9)
                   SQ P31016 62-154
                2. Human (Homo sapiens) [TaxId: 9606] [74932] (1)
             5. Syntrophin [50164]
                1. Mouse (Mus musculus) [TaxId: 10090] [50165] (3)
             6. Syntenin 1 [89311]
                1. Human (Homo sapiens) [TaxId: 9606] [89312] (26)
             7. Segment polarity protein dishevelled homolog Dvl-2 [89313]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [89314] (5)
                2. Mouse (Mus musculus) [TaxId: 10090] [101715] (1)
             8. Neuronal nitric oxide synthase, NNOS [50166]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50167] (3)
             9. Phosphatase hPTP1e [50168]
                1. Human (Homo sapiens) [TaxId: 9606] [50169] (3)
                2. Mouse (Mus musculus) [TaxId: 10090] [74930] (3)
             10. Na+/H+ exchanger regulatory factor, NHERF [63754]
                 1. Human (Homo sapiens) [TaxId: 9606] [63755] (4)
             11. Inad [63756]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63757] (1)
             12. Glutamate receptor interacting protein [82083]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [82084] (3)
                 2. Mouse (Mus musculus) [TaxId: 10090] [110177] (1)
                    SQ Q925T6 461-570
             13. Erbin [82085]
                 1. Human (Homo sapiens) [TaxId: 9606] [82086] (5)
             14. GTPase-binding domain of the cell polarity protein par6 (Par-6B) [89315]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89316] (1)
                 2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101716] (3)
                    SQ O97111 156-253; Cg5884-pa
             15. Glutamate receptor-interacting protein 1, GRIP1 [101717]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101718] (2)
             16. Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) [101719]
                 1. Human (Homo sapiens) [TaxId: 9606] [101720] (5)
                    SQ Q86UL8 412-522, 600-682, 774-865, 913-1015, 1141-1230
             17. KIAA1526 protein [101721]
                 1. Human (Homo sapiens) [TaxId: 9606] [101722] (3)
             18. Hypothetical protein KIAA1095 [101723]
                 1. Human (Homo sapiens) [TaxId: 9606] [101724] (2)
                    SQ Q9UPQ7 246-339, 404-512
             19. Discs large 5 protein KIAA0583 [101725]
                 1. Human (Homo sapiens) [TaxId: 9606] [101726] (1)
             20. Hypothetical protein KIAA0559 [101727]
                 1. Human (Homo sapiens) [TaxId: 9606] [101728] (1)
             21. Hypothetical protein KIAA1849 [101729]
                 1. Human (Homo sapiens) [TaxId: 9606] [101730] (1)
             22. Scribble (KIAA0147) [101731]
                 1. Human (Homo sapiens) [TaxId: 9606] [101732] (3)
                    SQ Q14160 680-951, 1096-1193 # structure of 1st PDZ domain is also known, 1XQ5
             23. Shank1, PDZ domain [101733]
                 SH3 and multiple ankyrin repeat domains protein 1
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [101734] (2)
             24. Zasp (Cypher, Oracle 1) [101735]
                 1. Human (Homo sapiens) [TaxId: 9606] [101736] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [117173] (1)
                    SQ Q9D130 1-83
             25. Alpha-actinin-2 associated LIM protein [110178]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110179] (1)
                    SQ O70209 4-93
             26. Glutamate receptor interacting protein 2, GRIP2 (KIAA1719) [110180]
                 1. Human (Homo sapiens) [TaxId: 9606] [110181] (2)
                    SQ Q9C0E4 238-341
             27. Harmonin [110182]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110183] (1)
                    SQ Q9ES64 741-850
                 2. Human (Homo sapiens) [TaxId: 9606] [141263] (1)
                    SQ Q9Y6N9 201-301
             28. Rhophilin-2 [110184]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110185] (1)
                    SQ Q8BWR8 506-603
             29. PDZ-LIM protein mystique [110186]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110187] (1)
                    SQ Q8R1G6 3-83
             30. Enigma homolog ENH [117174]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117175] (1)
                    SQ Q8CI51 5-94
             31. DNA Regulating synaptic membrane exocytosis protein 2, RIMS2 [117176]
                 1. Human (Homo sapiens) [TaxId: 9606] [117177] (1)
                    SQ Q9UQ26 637-754; the structure of the 1st C2 domain (807-934) is also known (scop_sp 101565)
             32. Partitioning-defective 3-like protein, PAR3-L (RIKEN cDNA 2810455b10) [117178]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117179] (1)
                    SQ Q5SV53 478-591
             33. Regulator of G-protein signaling 3, RGS3 [117180]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117181] (1)
                    SQ Q9DC04 18-94
                 2. Human (Homo sapiens) [TaxId: 9606] [141264] (2)
                    SQ P49796 300-376
             34. PDZ domain containing protein 11, Pdzk11 [117182]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117183] (1)
                    SQ Q9CZG9 37-127
             35. hypothetical PDZ domain containing protein Uqcrc2 (4930408O21Rik) [117184]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117185] (1)
                    SQ Q9CR71 8-120
             36. Tight junction protein ZO-2, Tjp2 [141265]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141266] (1)
                    SQ Q9Z0U1 1-104
             37. Multiple PDZ domain protein [141267]
                 1. Human (Homo sapiens) [TaxId: 9606] [141268] (4)
                    SQ Q5VZ62 1138-1243! SQ Q5VZ62 1955-2042
             38. Afadin [141269]
                 1. Human (Homo sapiens) [TaxId: 9606] [141270] (3)
                    SQ P55196 985-1079! SQ P55196 987-1077
             39. Syntaxin binding protein 4 [141271]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141272] (1)
                    SQ Q9WV89 12-107
             40. Channel associated protein of synapse-110 [141273]
                 Discs large homolog 2, PSD-93
                 1. Human (Homo sapiens) [TaxId: 9606] [141274] (1)
                    SQ Q15700 190-283
             41. Maguk p55 subfamily member 5 [141275]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141276] (1)
                    SQ Q9JLB2 236-335
                    Structure of the second L27 domain is known (scop_sp 101293)
             42. Neurabin-i [141277]
                 1. Human (Homo sapiens) [TaxId: 9606] [141278] (1)
                    SQ Q9ULJ8 500-593
             43. Regulating synaptic membrane exocytosis protein 1, RIMS1 [141279]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [141280] (1)
                    SQ Q9JIR4 597-705
                 2. Human (Homo sapiens) [TaxId: 9606] [141281] (1)
                    SQ Q86UR5 585-694
             44. Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) [141282]
                 1. Human (Homo sapiens) [TaxId: 9606] [141283] (7)
                    SQ Q02410 656-740! SQ Q02410 657-743! SQ Q02410 657-745! SQ Q02410 743-822! SQ Q02410 745-823! SQ Q02410 746-839
                    structure of the PTB domain is also known (scop_sp 50757)
             45. Presynaptic protein sap97 [141284]
                 PSD-95 homologue
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [141285] (1)
                    SQ Q62696 221-313
             46. Tyrosine-protein phosphatase non-receptor type 4, PTPN4 [141286]
                 1. Human (Homo sapiens) [TaxId: 9606] [141287] (1)
                    SQ P29074 507-612
          2. Tail specific protease PDZ domain [68933] (2)
             1. Photosystem II D1 C-terminal processing protease [68934]
                1. Algae (Scenedesmus obliquus) [TaxId: 3088] [50171] (4)
             2. Tricorn protease [69253]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69254] (4)
          3. HtrA-like serine proteases [74933] (4)
             1. Protease Do (DegP, HtrA), C-terminal domains [74934]
                duplication: tandem repeat of two PDZ domains
                1. Escherichia coli [TaxId: 562] [74935] (27)
             2. Mitochondrial serine protease HtrA2 [74936]
                1. Human (Homo sapiens) [TaxId: 9606] [74937] (3)
             3. Stress sensor protease DegS, C-terminal domain [110188]
                1. Escherichia coli [TaxId: 562] [110189] (7)
                   SQ P31137 37-354 ! SQ P31137
             4. Protease PepD [141288]
                1. Mycobacterium tuberculosis [TaxId: 1773] [141289] (6)
                   SQ O53896 375-462
                   Rv0983
          4. Interleukin 16 [50172] (1)
             1. Interleukin 16 [50173]
                1. Human (Homo sapiens) [TaxId: 9606] [50174] (2)
          5. EpsC C-terminal domain-like [159046] (1)
             PfamB 005596
             1. General secretion pathway protein C, EpsC [159047]
                1. Vibrio cholerae [TaxId: 666] [159048] (3)
                   SQ P45777 204-305! SQ P45777 219-305
          6. MTH1368 C-terminal domain-like [159049] (1)
             middle part of Pfam 02163
             1. Uncharacterized protein MTH1368 [159050]
                1. Methanobacterium thermoautotrophicum [TaxId: 145262] [159051] (1)
                   SQ O27421 208-310
   65. N-terminal domains of the minor coat protein g3p [50175] (1)
       core: barrel, in some members open; n*=4, S*=8; meander
       1. N-terminal domains of the minor coat protein g3p [50176] (1)
          uperfamily
          1. N-terminal domains of the minor coat protein g3p [50177] (2)
             1. N-terminal domains of the minor coat protein g3p [50178]
                duplication: the two domains share a common fold
                1. Bacteriophage M13 [TaxId: 10870] [50179] (2)
                2. Bacteriophage fd [TaxId: 10864] [50180] (2)
   66. Sm-like fold [50181] (5)
       core: barrel, open; n*=4, S*=8; meander; SH3-like topology
       1. Sm-like ribonucleoproteins [50182] (6)
          uperfamily
          1. Sm motif of small nuclear ribonucleoproteins, SNRNP [50183] (13)
             forms homo and heteroheptameric ring structures
             1. D1 core SNRNP protein [50184]
                1. Human (Homo sapiens) [TaxId: 9606] [50185] (1)
             2. D2 core SNRNP protein [50186]
                1. Human (Homo sapiens) [TaxId: 9606] [50187] (1)
             3. D3 core SNRNP protein [50188]
                1. Human (Homo sapiens) [TaxId: 9606] [50189] (1)
             4. B core SNRNP protein [50190]
                1. Human (Homo sapiens) [TaxId: 9606] [50191] (1)
             5. Small nuclear ribonucleoprotein F, Smf [82087]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82088] (2)
             6. Archaeal homoheptameric Sm protein [63758]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63759] (5)
                   MTH649, smap1
                2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [63760] (2)
                   smap1
                3. Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234] [63761] (2)
                4. Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234] [74938] (1)
                5. Archaeon Pyrococcus abyssi [TaxId: 29292] [82089] (2)
                6. Sulfolobus solfataricus [TaxId: 2287] [141290] (14)
                   SQ Q97ZQ0 1-76
                   SnRNP-2
             7. Sm-Like archaeal protein Smap3 [89317]
                contains additional C-terminal alpha+beta domain
                1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [89318] (1)
             8. U6 snRNA-associated sm-like protein LSM5 [141291]
                1. Cryptosporidium parvum [TaxId: 5807] [141292] (2)
                   SQ Q5CXX3 24-115
          2. Pleiotropic translational regulator Hfq [74939] (3)
             forms homohexameric ring structures
             1. Pleiotropic translational regulator Hfq [74940]
                1. Staphylococcus aureus [TaxId: 1280] [74941] (2)
                2. Escherichia coli [TaxId: 562] [89319] (1)
                3. Pseudomonas aeruginosa [TaxId: 287] [141293] (12)
                   SQ Q9HUM0 6-71
          3. Mechanosensitive channel protein MscS (YggB), middle domain [82090] (1)
             1. Mechanosensitive channel protein MscS (YggB), middle domain [82091]
                forms homoheptameric ring structure very similar to those of the archaeal and eukaryotic Sm proteins
                1. Escherichia coli [TaxId: 562] [82092] (14)
          4. PF1955-like [141294] (1)
             homohexadecameric assembly: two stacked octameric rings
             1. Hypothetical protein PF1955 [141295]
                1. Pyrococcus furiosus [TaxId: 2261] [141296] (4)
                   SQ Q8TZN2 5-70
          5. LSM14 N-terminal domain-like [141297] (1)
             1. LSM14 homolog A (Lsm14a) [141298]
                1. Zebrafish (Danio rerio) [TaxId: 7955] [141299] (2)
                   SQ Q6P111 6-85
          6. YgdI/YgdR-like [159052] (6)
             Pfam 06004; DUF903, putative lipoprotein; both homohexameric and homoheptameric ring assemblies are observed in the crystals
             1. Uncharacterized protein SO0963 [159053]
                1. Shewanella oneidensis [TaxId: 70863] [159054] (2)
                   SQ Q8EI81 25-76
             2. Uncharacterized protein YgdI [159055]
                1. Salmonella typhimurium [TaxId: 90371] [159056] (6)
                   SQ Q7CPV8 23-75
             3. Uncharacterized protein ECA1013 [159057]
                1. Erwinia carotovora [TaxId: 554] [159058] (7)
                   SQ Q6D8G1 21-73
             4. Putative outer membrane lipoprotein STM1585 [159059]
                1. Salmonella typhimurium [TaxId: 90371] [159060] (3)
                   SQ Q7CQI7 22-73
             5. Uncharacterized protein PSPPH2109 [159061]
                1. Pseudomonas syringae [TaxId: 317] [159062] (1)
                   SQ Q48JU9 23-74
             6. Hypothetical lipoprotein YgdR [159063]
                1. Escherichia coli [TaxId: 562] [159064] (1)
                   SQ P65294 23-72
       2. YhbC-like, C-terminal domain [74942] (1)
          uperfamily
          1. YhbC-like, C-terminal domain [74943] (1)
             1. Hypothetical protein SP14.3 (SP0552) [74944]
                1. Streptococcus pneumoniae [TaxId: 1313] [74945] (1)
       3. GatD N-terminal domain-like [141300] (1)
          uperfamily
          1. GatD N-terminal domain-like [141301] (2)
             PfamB 010580
             1. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [141302]
                1. Pyrococcus abyssi [TaxId: 29292] [141303] (2)
                   SQ Q9V0T9 2-75
                2. Methanobacterium thermoautotrophicum [TaxId: 145262] [141304] (2)
                   SQ O26802 2-73
       4. Dom34/Pelota N-terminal domain-like [159065] (1)
          1. Dom34/Pelota N-terminal domain-like [159066] (2)
             Warning: Pfam incorrectly assigns this domain to the same family as the structurally unrelated N-terminal domain of eRF1 (Pfam 03463)
             1. Cell division protein pelota [159067]
                1. Thermoplasma acidophilum [TaxId: 2303] [159068] (1)
                   SQ Q9HJ74 1-126
             2. Dom34 [159069]
                1. Saccharomyces cerevisiae [TaxId: 4932] [159070] (3)
                   SQ P33309 1-135
       5. TrmB C-terminal domain-like [159071] (1)
          sugar-binding domain; permuted OB-fold?
          1. TrmB C-terminal domain-like [159072] (1)
             C-terminal part of PfamB 004822
             1. Transcriptional regulator TrmB [159073]
                1. Thermococcus litoralis [TaxId: 2265] [159074] (1)
                   SQ Q7LYW4 247-338
   67. SspB-like [101737] (1)
       core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
       1. SspB-like [101738] (2)
          uperfamily
          1. Stringent starvation protein B, SspB [101739] (2)
             1. Stringent starvation protein B, SspB [101740]
                a specificity-enhancing factor for the ClpXP proteolytic machine
                1. Escherichia coli [TaxId: 562] [101741] (6)
                2. Haemophilus influenzae [TaxId: 727] [101742] (7)
                   SQ P45206 5-110
          2. AGR_C_3712p-like [159075] (1)
             Pfam 07031; DUF1321
             1. Uncharacterized protein AGR_C_3712p [159076]
                1. Agrobacterium tumefaciens [TaxId: 358] [159077] (2)
                   SQ Q8U561 3-119
   68. Rof/RNase P subunit-like [101743] (1)
       core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
       1. Rof/RNase P subunit-like [101744] (2)
          uperfamily
          1. RNase P subunit p29-like [101745] (3)
             two available NMR structures display similar topologies but different barrel shapes
             the barrel shape of the full-length X-ray structures of AF1917 differs from both earlier NMR structures
             1. Hypothetical protein AF1917 [101746]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [101747] (3)
                   SQ O28362
             2. Hypothetical protein MTH11 [101748]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101749] (1)
             3. Hypothetical protein PH1771 [117186]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [117187] (1)
                   SQ O59425
          2. Rof-like [141305] (1)
             Pfam 07073; ROF
             1. Inhibitor of Rho Rof [141306]
                formerly hypothetical protein YaeO
                1. Escherichia coli [TaxId: 562] [141307] (1)
                   SQ P0AFW8 1-86
   69. Hydrophobin II, HfbII [101750] (1)
       core: barrel, closed; n=4, S=8; complex topology; helix-containing crossover connection
       1. Hydrophobin II, HfbII [101751] (1)
          uperfamily
          1. Hydrophobin II, HfbII [101752] (1)
             a self-assembling amphiphile
             1. Hydrophobin II, HfbII [101753]
                1. Trichoderma reesei [TaxId: 51453] [101754] (13)
   70. Ribosomal protein L14 [50192] (1)
       barrel, closed; n=5, S=8, meander
       1. Ribosomal protein L14 [50193] (1)
          uperfamily
          1. Ribosomal protein L14 [50194] (5)
             1. Ribosomal protein L14 [50195]
                1. Bacillus stearothermophilus [TaxId: 1422] [50196] (5)
                2. Archaeon Haloarcula marismortui [TaxId: 2238] [50197] (42)
                   SQ P22450
                3. Thermus thermophilus [TaxId: 274] [141308] (9)
                   SQ Q5SHP8 1-122
                4. Escherichia coli [TaxId: 562] [159078] (29)
                   SQ P02411 2-122
                5. Deinococcus radiodurans [TaxId: 1299] [159079] (6)
                   SQ Q9RXJ2 1-134
   71. OB-fold [50198] (16)
       barrel, closed or partly opened n=5, S=10 or S=8; greek-key
       1. Staphylococcal nuclease [50199] (1)
          uperfamily
          1. Staphylococcal nuclease [50200] (1)
             barrel, closed; n=5, S=10
             1. Staphylococcal nuclease [50201]
                1. Staphylococcus aureus [TaxId: 1280] [50202] (68)
                   SQ P00644 89-223
       2. Bacterial enterotoxins [50203] (2)
          uperfamily
          1. Bacterial AB5 toxins, B-subunits [50204] (9)
             1. Heat-labile toxin [50205]
                1. Escherichia coli, type IB [TaxId: 562] [50206] (29)
                2. Escherichia coli, type IIB [TaxId: 562] [50207] (3)
             2. Cholera toxin [50208]
                barrel, partly opened; n*=5, S*=10
                1. Vibrio cholerae [TaxId: 666] [50209] (33)
                   SQ P01556 22-124
             3. Verotoxin-1/shiga-toxin, B-pentamer [50210]
                phage-borne toxin; bacteriophages H30 and H19B
                1. Escherichia coli [TaxId: 562] [50211] (22)
                2. Shigella dysenteriae, toxin I [TaxId: 622] [50212] (3)
                   identical sequence with verotoxin-1 B
                3. Shigella dysenteriae, toxin II [TaxId: 622] [101755] (6)
             4. Pertussis toxin S2/S3 subunits, C-terminal domain [50213]
                N-terminal domain in S2/S3 has C-lectin-like fold
                1. Bordetella pertussis [TaxId: 520] [50214] (3)
             5. Pertussis toxin S4 subunit [50215]
                1. Bordetella pertussis [TaxId: 520] [50216] (3)
             6. Pertussis toxin S5 subunit [50217]
                1. Bordetella pertussis [TaxId: 520] [50218] (3)
          2. Superantigen toxins, N-terminal domain [50219] (15)
             1. Staphylococcal enterotoxin A, SEA [50220]
                1. Staphylococcus aureus [TaxId: 1280] [50221] (6)
             2. Staphylococcal enterotoxin C2, SEC2 [50222]
                1. Staphylococcus aureus [TaxId: 1280] [50223] (8)
             3. Toxic shock syndrome toxin-1 (TSST-1) [50224]
                1. Staphylococcus aureus [TaxId: 1280] [50225] (13)
             4. Staphylococcal enterotoxin B, SEB [50226]
                1. Staphylococcus aureus [TaxId: 1280] [50227] (12)
             5. Staphylococcal enterotoxin C3, SEC3 [50228]
                1. Staphylococcus aureus [TaxId: 1280] [50229] (11)
                   SQ P23313
             6. Staphylococcal enterotoxin H, SEH [50230]
                1. Staphylococcus aureus [TaxId: 1280] [50231] (4)
             7. Superantigen-like protein SET3 [74946]
                1. Staphylococcus aureus [TaxId: 1280] [74947] (3)
             8. Streptococcal superantigen Spe-C [50232]
                1. Streptococcus pyogenes [TaxId: 1314] [50233] (3)
             9. Streptococcal superantigen Spe-H [50234]
                1. Streptococcus pyogenes [TaxId: 1314] [50235] (2)
             10. Streptococcal superantigen Smez-2 [50236]
                 1. Streptococcus pyogenes [TaxId: 1314] [50237] (2)
             11. Streptococcal superantigen SSA [50238]
                 1. Streptococcus pyogenes [TaxId: 1314] [50239] (10)
             12. Streptococcal pyrogenic exotoxin A1 [50240]
                 1. Streptococcus pyogenes [TaxId: 1314] [50241] (8)
                    SQ P08095
             13. Exotoxin 1 (SET1, Superantigen-like protein 7) [110190]
                 1. Staphylococcus aureus [TaxId: 1280] [110191] (2)
                    SQ Q9ZFS5 36-231
             14. Streptococcal pyrogenic exotoxin Spe-J [110192]
                 1. Streptococcus pyogenes [TaxId: 1314] [110193] (2)
                    SQ Q7BAE3
             15. Enterotoxin type I, SEI [159080]
                 1. Staphylococcus aureus [TaxId: 1280] [159081] (1)
                    SQ Q52T95 4-86
       3. TIMP-like [50242] (3)
          uperfamily
          1. Tissue inhibitor of metalloproteinases, TIMP [50243] (3)
             contains an irregular alpha+beta subdomain in the C-terminal extension
             1. TIMP-1 [50244]
                1. Human (Homo sapiens) [TaxId: 9606] [50245] (6)
             2. TIMP-2 [50246]
                1. Human (Homo sapiens) [TaxId: 9606] [50247] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [50248] (3)
          2. Netrin-like domain (NTR/C345C module) [89320] (2)
             Pfam 01759
             1. Procollagen c-proteinase enhancer protein PCOLCE [89321]
                1. Human (Homo sapiens) [TaxId: 9606] [89322] (1)
             2. Complement C5 domain [117188]
                1. Human (Homo sapiens) [TaxId: 9606] [117189] (1)
                   SQ P01031 1530-1676 # structure of the C5a anaphylotoxin domain (679-751) is also known (scop_sp 47689)
          3. The laminin-binding domain of agrin [63767] (1)
             1. The laminin-binding domain of agrin [63768]
                1. Chicken (Gallus gallus) [TaxId: 9031] [63769] (3)
                   SQ Q90685 # ! Fragment
       4. Heme chaperone CcmE [82093] (1)
          uperfamily
          1. Heme chaperone CcmE [82094] (2)
             1. Heme chaperone CcmE [82095]
                1. Escherichia coli [TaxId: 562] [82096] (1)
                2. Shewanella putrefaciens [TaxId: 24] [82097] (2)
       5. gp5 N-terminal domain-like [69255] (1)
          uperfamily
          1. gp4 N-terminal domain-like [69256] (2)
             1. Tail-associated lysozyme gp5, N-terminal domain [69257]
                1. Bacteriophage T4 [TaxId: 10665] [69258] (1)
             2. Hypothetical protein c3393 [159082]
                1. Escherichia coli o6 [TaxId: 217992] [159083] (1)
                   SQ Q8FED2 378-468
       6. Hypothetical protein YgiW [101756] (1)
          uperfamily
          1. Hypothetical protein YgiW [101757] (1)
             Pfam 04076, Domain of unknown function DUF388
             1. Hypothetical protein YgiW [101758]
                1. Escherichia coli [TaxId: 562] [101759] (1)
       7. Nucleic acid-binding proteins [50249] (16)
          uperfamily
          1. Anticodon-binding domain [50250] (7)
             barrel, closed; n=5, S=10
             1. Aspartyl-tRNA synthetase (AspRS) [50251]
                this is N-terminal domain in prokaryotic enzymes and the first "visible" domain in eukaryotic enzymes
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50252] (3)
                2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [50253] (1)
                3. Thermus thermophilus, AspRS-2 [TaxId: 274] [89323] (1)
                   non-discriminating and archaeal-type enzyme
                4. Escherichia coli [TaxId: 562] [50254] (3)
                5. Thermus thermophilus, AspRS-1 [TaxId: 274] [50255] (3)
             2. Lysyl-tRNA synthetase (LysRS) [50256]
                1. Escherichia coli, gene lysS [TaxId: 562] [50257] (4)
                2. Escherichia coli, gene lysU [TaxId: 562] [50258] (5)
          2. RecG "wedge" domain [69259] (1)
             1. RecG "wedge" domain [69260]
                1. Thermotoga maritima [TaxId: 2336] [69261] (1)
          3. DNA helicase RuvA subunit, N-terminal domain [50259] (3)
             barrel, closed; n=5, S=10
             1. DNA helicase RuvA subunit, N-terminal domain [50260]
                tetramer; binds Holliday junction
                1. Escherichia coli [TaxId: 562] [50261] (5)
                2. Mycobacterium leprae [TaxId: 1769] [50262] (1)
                3. Thermus thermophilus [TaxId: 274] [82098] (1)
          4. Single strand DNA-binding domain, SSB [50263] (17)
             barrel, closed; n=5, S=10
             1. ssDNA-binding protein [50264]
                1. Human (Homo sapiens), mitochondria [TaxId: 9606] [50265] (4)
                   SQ Q04837
                2. Escherichia coli [TaxId: 562] [50266] (5)
                   SQ P02339
                3. Mycobacterium tuberculosis [TaxId: 1773] [101760] (4)
                4. Deinococcus radiodurans [TaxId: 1299] [110194] (1)
                   SQ Q9RY51
             2. Archaeal ssDNA-binding protein [89324]
                similar to the domains of the Replication protein A
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89325] (1)
             3. Replication protein A 70 KDa subunit (RPA70) [50267]
                duplication: consists of three domains of this fold; contains zinc-finger insert in the C-terminal domain, residues 479-511
                1. Human (Homo sapiens) [TaxId: 9606] [50268] (6)
             4. Replication protein A 32 KDa subunit (RPA32) fragment [50269]
                1. Human (Homo sapiens) [TaxId: 9606] [50270] (10)
             5. Replication protein A 14 KDa (RPA14) subunit [50271]
                1. Human (Homo sapiens) [TaxId: 9606] [50272] (10)
             6. CDC13 ssDNA-binding domain [74948]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74949] (2)
             7. Telomere end binding protein alpha subunit [50273]
                duplication: consists of three domains of this fold
                1. Oxytricha nova [TaxId: 200597] [50274] (18)
             8. Core domain of telomere end binding protein beta subunit [50275]
                1. Oxytricha nova [TaxId: 200597] [50276] (14)
             9. Protection of telomeres protein 1, Pot1 [101761]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [101762] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [117190] (1)
                   SQ Q9NUX5 6-299
             10. OB-fold domains of BRCA2 [82099]
                 duplication: tandem repeat of three OB-fold domains
                 1. Mouse (Mus musculus) [TaxId: 10090] [82100] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [82101] (1)
             11. Primosomal replication protein N, PriB [117191]
                 1. Escherichia coli [TaxId: 562] [117192] (4)
                    SQ P07013
             12. Hypothetical protein At4g28440 (F20O9.120) [117193]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117194] (1)
                    SQ O49453 14-145
          5. Myf domain [50277] (7)
             1. Domain B2 of PheRS-beta, PheT [50278]
                1. Thermus thermophilus [TaxId: 274] [50279] (9)
                   identical sequence to Thermus aquaticus, TaxId: 271
             2. C-terminal domain of methionyl-tRNA synthetase, MetRS-CD [82102]
                1. Archaeon Pyrococcus abyssi [TaxId: 29292] [82103] (1)
             3. EMAP II [50280]
                domain of the p43 protein
                1. Human (Homo sapiens) [TaxId: 9606] [50281] (3)
             4. C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS [89326]
                EMAP II-like domain found in vertebrata and insect enzymes; free domain possesses a cytokine activity
                1. Human (Homo sapiens) [TaxId: 9606] [89327] (1)
             5. Structure-specific tRNA-binding protein TRBP111 [89328]
                1. Escherichia coli [TaxId: 562] [89329] (1)
                   YgjH
                2. Aquifex aeolicus [TaxId: 63363] [101763] (1)
                   aq_422; putative methionyl-tRNA synthetase beta subunit
             6. TRBP111 homolog CsaA [63770]
                possesses export-related chaperone and tRNA-binding activities
                1. Thermus thermophilus [TaxId: 274] [63771] (1)
          6. Cold shock DNA-binding domain-like [50282] (56)
             barrel, closed; n=5, S=8
             1. Major cold shock protein [50283]
                1. Escherichia coli [TaxId: 562] [50284] (2)
                2. Bacillus subtilis [TaxId: 1423] [50285] (6)
                3. Bacillus caldolyticus [TaxId: 1394] [50286] (8)
                4. Thermotoga maritima [TaxId: 2336] [69262] (1)
             2. Y-box protein 1 cold shock domain (YB1-CSD) [69263]
                1. Human (Homo sapiens) [TaxId: 9606] [69264] (1)
             3. S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287]
                1. Escherichia coli [TaxId: 562] [50288] (1)
                2. Streptomyces antibioticus [TaxId: 1890] [50289] (1)
             4. S1 domain of NusA [69265]
                1. Thermotoga maritima [TaxId: 2336] [69266] (2)
                2. Mycobacterium tuberculosis [TaxId: 1773] [69267] (4)
             5. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88671] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117195] (7)
                   SQ P34087
                3. Human (Homo sapiens) [TaxId: 9606] [141309] (4)
                   SQ P62487 78-171
             6. Translational initiation factor 1, IF1 [50290]
                1. Escherichia coli [TaxId: 562] [50291] (3)
             7. Archaeal initiation factor-1a, aIF1a [63772]
                evolutionary link between IF1 and eIF1a
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63773] (1)
             8. Translation initiation factor-1a, eIF1a [50292]
                1. Human (Homo sapiens) [TaxId: 9606] [50293] (1)
             9. Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950]
                1. Human (Homo sapiens) [TaxId: 9606] [74951] (2)
                   SQ P05198
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101764] (1)
                3. Sulfolobus solfataricus [TaxId: 2287] [141310] (1)
                   SQ Q97Z79 1-84
             10. Viral structural mimic of eIF2alpha [74952]
                 1. Vaccinia virus [TaxId: 10245] [74953] (1)
                 2. Myxoma virus, m156r [TaxId: 10273] [74954] (1)
             11. Rho termination factor, RNA-binding domain [68910]
                 1. Escherichia coli [TaxId: 562] [68911] (14)
                    SQ P03002
             12. C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50297] (2)
                 2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50298] (1)
                 3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82104] (1)
                 4. Leishmania infantum [TaxId: 5671] [110195] (1)
                    SQ Q9N9V6
                 5. Leishmania mexicana [TaxId: 5665] [117196] (1)
                    SQ Q9N9V6 97% sequence identity
             13. C-terminal domain of eIF5a homologue (Hex1) [82105]
                 1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82106] (1)
             14. N-terminal domain of ribosomal protein L2 [50299]
                 incomplete OB-fold lacking the last strand
                 1. Bacillus stearothermophilus [TaxId: 1422] [50300] (2)
                 2. Archaeon Haloarcula marismortui [TaxId: 2238] [50301] (40)
                    SQ P20276
                    includes the N-terminal tail
                 3. Thermus thermophilus [TaxId: 274] [159084] (5)
                    SQ Q72I07 1-125
                 4. Deinococcus radiodurans [TaxId: 1299] [159085] (5)
                    SQ Q9RXJ9 33-127
                 5. Escherichia coli [TaxId: 562] [159086] (27)
                    SQ P60422 3-124
             15. Ribosomal protein S12 [50302]
                 1. Thermus thermophilus [TaxId: 274] [50303] (36)
                    SQ P17293
                 2. Escherichia coli [TaxId: 562] [159087] (25)
                    SQ P0A7S3 1-123
             16. Ribosomal protein S17 [50304]
                 1. Thermus thermophilus [TaxId: 274] [50305] (45)
                    SQ P24321
                 2. Bacillus stearothermophilus [TaxId: 1422] [50306] (1)
                 3. Escherichia coli [TaxId: 562] [159088] (26)
                    SQ P02373 3-82
             17. Ribosomal protein S28e [101765]
                 incomplete OB-fold lacking the last strand
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101766] (1)
                 2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101767] (1)
             18. Elongation factor P middle and C-terminal domains [110196]
                 duplication: contains two domains of this fold
                 1. Thermus thermophilus HB8 [TaxId: 300852] [110197] (1)
                    SQ Q76G20
             19. S1-domain of Ribonuclease E [110198]
                 1. Escherichia coli [TaxId: 562] [110199] (3)
                    SQ P21513 35-125
             20. Probable GTPase EngC (YjeQ), N-terminal domain [110200]
                 1. Thermotoga maritima [TaxId: 2336] [110201] (1)
                    SQ Q9X242 # TM1717
                 2. Bacillus subtilis [TaxId: 1423] [117197] (1)
                    SQ O34530
             21. Cold shock domain protein E1 (UNR) [117198]
                 1. Human (Homo sapiens) [TaxId: 9606] [117199] (1)
                    SQ O75534 15-90
             22. S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200]
                 1. Human (Homo sapiens) [TaxId: 9606] [117201] (1)
                    SQ Q14690 173-278
             23. Exoribonuclease 2, RNB [159089]
                 RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
                 1. Escherichia coli [TaxId: 562] [159090] (18)
                    SQ P30850 1-82! SQ P30850 4-82! SQ P30850 5-82! SQ P30850 558-643! SQ P30850 558-644! SQ P30850 83-172
             24. S1-domain of exosome component 3 (RRP40) [159091]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [159092] (1)
                    SQ Q08285 62-151
                 2. Human (Homo sapiens) [TaxId: 9606] [159093] (1)
                    SQ Q9NQT5 108-195
             25. Ribonuclease II family protein DR0020 [159094]
                 1. Deinococcus radiodurans [TaxId: 1299] [159095] (4)
                    SQ Q9RYD0 404-461
             26. S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096]
                 1. Human (Homo sapiens) [TaxId: 9606] [159097] (1)
                    SQ Q13868 73-167
             27. Exosome component 1, EXOSC1 [159098]
                 3'-5' exoribonuclease CSL4 homolog
                 1. Human (Homo sapiens) [TaxId: 9606] [159099] (1)
                    SQ Q9Y3B2 61-185
             28. S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100]
                 1. Aeropyrum pernix [TaxId: 56636] [159101] (1)
                    SQ Q9YC02 60-147
                 2. Sulfolobus solfataricus [TaxId: 2287] [159102] (2)
                    SQ Q9UXC4 66-152
                 3. Archaeoglobus fulgidus [TaxId: 2234] [159103] (3)
                    SQ O29758 53-135
             29. Exosome complex exonuclease RRP44 [159104]
                 member or the RNase II family; contains 3 S1-like domains; two of them are in tandem N-terminally to the catalytic domain and one is C-terminally to the catalytic domain that also contains an OB-fold
                 1. Saccharomyces cerevisiae [TaxId: 4932] [159105] (3)
                    SQ Q08162 252-399! SQ Q08162 400-494! SQ Q08162 911-998
             30. Tex S1-domain [159106]
                 1. Pseudomonas aeruginosa [TaxId: 287] [159107] (3)
                    SQ Q9HTY8 637-730
          7. TRAM domain [101768] (3)
             Pfam 01938
             1. rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain [101769]
                1. Escherichia coli [TaxId: 562] [101770] (3)
             2. Hypothetical protein MM1357 [141311]
                1. Methanosarcina mazei [TaxId: 2209] [141312] (1)
                   SQ Q8PX65 1-68
             3. Hypothetical protein MMP0076 [141313]
                1. Methanococcus maripaludis [TaxId: 39152] [141314] (1)
                   SQ Q6M142 1-69
          8. Hypothetical protein MTH1 (MT0001), insert domain [74955] (1)
             1. Hypothetical protein MTH1 (MT0001), insert domain [74956]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [74957] (1)
          9. DNA ligase/mRNA capping enzyme postcatalytic domain [50307] (6)
             1. RNA guanylyltransferase (mRNA capping enzyme) [50308]
                1. Chlorella virus PBCV-1 [TaxId: 10506] [50309] (3)
             2. mRNA capping enzyme alpha subunit [89330]
                1. Yeast (Candida albicans) [TaxId: 5476] [89331] (1)
             3. ATP-dependent DNA ligase [50310]
                1. Bacteriophage T7 [TaxId: 10760] [50311] (1)
                2. Chlorella virus PBCV-1 [TaxId: 10506] [50312] (7)
             4. NAD+-dependent DNA ligase [50313]
                1. Thermus filiformis [TaxId: 276] [50314] (2)
             5. DNA ligase I (LIG1) [117202]
                1. Human (Homo sapiens) [TaxId: 9606] [117203] (1)
                   SQ P18858 262-901
          10. Phage ssDNA-binding proteins [50315] (5)
              barrel, open; n*=5, S*=8; the members' structures vary greater that those from cellular organisms
              1. Gene V protein [50316]
                 1. Enterobacteria phage M13, including coliphage f1 [TaxId: 10870] [50317] (19)
                 2. Pseudomonas phage Pf3 [TaxId: 10872] [50318] (1)
              2. Gene 32 protein (gp32) core [50319]
                 contains a Zn-finger subdomain, res. 63-111
                 1. Bacteriophage T4 [TaxId: 10665] [50320] (1)
                 2. Enterobacteria phage RB69 [TaxId: 12353] [159108] (3)
                    SQ Q7Y265 32-241
              3. gp2.5 [63774]
                 1. Bacteriophage T7 [TaxId: 10760] [63775] (1)
          11. DNA replication initiator (cdc21/cdc54) N-terminal domain [89332] (1)
              1. DNA replication initiator (cdc21/cdc54) N-terminal domain [89333]
                 MCM complex protein; dodecamer assembly; includes the N-terminal all-alpha subdomain and inserted Zn-finger
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89334] (1)
          12. RNA polymerase subunit RBP8 [50321] (1)
              duplication; contains tandem repeat of two incomplete OB-folds; forms a single barrel; n=8, S=10
              1. RNA polymerase subunit RBP8 [50322]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50323] (31)
                    SQ P20436
          13. RecO N-terminal domain-like [117204] (1)
              N-terminal part of Pfam 02565
              1. Recombinational repair protein RecO, N-terminal domain [117205]
                 1. Deinococcus radiodurans [TaxId: 1299] [117206] (1)
                    SQ Q9RW50 # DR0819
          14. TIP49 domain [141315] (1)
              N-terminal part of Pfam 06068; the RuvA-like OB-fold domain in RuvB-like eukaryotic proteins
              1. RuvB-like 2 protein, RUVBL2 (TIP49b) [141316]
                 1. Human (Homo sapiens) [TaxId: 9606] [141317] (1)
                    SQ Q9Y230 131-212
          15. SSO2064-like [159109] (1)
              Pfam 01796; DUF35; contains extra N-terminal zinc finger subdomain of the rubredoxin-like fold
              1. Hypothetical protein SSO2064 [159110]
                 1. Sulfolobus solfataricus [TaxId: 2287] [159111] (2)
                    SQ Q97WQ4 8-144
          16. RNB domain-like [159112] (3)
              Pfam 00773; RNase II catalytic domain; decorated OB-fold domain with extra C-terminal structures forming the active site
              1. Exosome complex exonuclease RRP44 [159113]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [159114] (1)
                    SQ Q08162 495-910
              2. Ribonuclease II family protein DR0020 [159115]
                 Includes extra N-terminal all-alpha subdomain
                 1. Deinococcus radiodurans [TaxId: 1299] [159116] (4)
                    SQ Q9RYD0 3-403
              3. Exoribonuclease 2, RNB [159117]
                 RNase II
                 1. Escherichia coli [TaxId: 562] [159118] (6)
                    SQ P30850 173-557
       8. Inorganic pyrophosphatase [50324] (1)
          uperfamily
          1. Inorganic pyrophosphatase [50325] (6)
             barrel, closed; n=5, S=8
             1. Inorganic pyrophosphatase [50326]
                eukaryotic enzyme has additional secondary structures at both N- and C-termini
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50327] (16)
                2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [50328] (1)
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101771] (1)
                4. Escherichia coli [TaxId: 562] [50329] (17)
                5. Thermus thermophilus [TaxId: 274] [50330] (1)
                6. Pyrococcus furiosus [TaxId: 2261] [117207] (1)
                   SQ Q8U438
       9. MOP-like [50331] (3)
          uperfamily
          1. Molybdate/tungstate binding protein MOP [50332] (2)
             1. Molybdate/tungstate binding protein MOP [50333]
                homohexamer: trimer of the C-terminal strand swapped dimers
                1. Sporomusa ovata [TaxId: 2378] [50334] (1)
                2. Clostridium pasteurianum, MOP II [TaxId: 1501] [69270] (5)
          2. BiMOP, duplicated molybdate-binding domain [50335] (2)
             duplication: tandem repeat of two OB-fold domains with swapped C-terminal strands
             1. Cytoplasmic molybdate-binding protein ModG [63776]
                1. Azotobacter vinelandii [TaxId: 354] [63777] (3)
             2. C-terminal domain of molybdate-dependent transcriptional regulator ModE [63405]
                1. Escherichia coli [TaxId: 562] [50337] (5)
          3. ABC-transporter additional domain [50338] (5)
             probably stems out from the biMOP domain
             1. Maltose transport protein MalK, C-terminal domain [63406]
                1. Archaeon Thermococcus litoralis [TaxId: 2265] [50340] (1)
                2. Escherichia coli [TaxId: 562] [101772] (13)
             2. Glucose transport protein GlcV, N-terminal domain [89335]
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89336] (5)
             3. Hypothetical protein PH0022, C-terminal domain [117208]
                1. Pyrococcus horikoshii [TaxId: 53953] [117209] (2)
                   SQ O57758
             4. Sulfate/molybdate ABC transporter, ATP-binding protein [159119]
                1. Methanosarcina acetivorans [TaxId: 2214] [159120] (2)
                   SQ Q8TTZ3 230-348
       10. CheW-like [50341] (1)
           uperfamily
           1. CheW-like [50342] (2)
              duplication: tandem repeat of two swapped domains, one with a canonical OB-fold topology and one with a circular permutation
              1. Histidine kinase CheA, C-terminal domain [50343]
                 1. Thermotoga maritima [TaxId: 2336] [50344] (3)
              2. Chemotaxis protein CheW [69271]
                 1. Thermotoga maritima [TaxId: 2336] [69272] (3)
       11. TM0957-like [141318] (1)
           extra N-terminal region and large insertion after strand 3 together form an alpha-helical subdomain
           uperfamily
           1. TM0957-like [141319] (1)
              1. Hypothetical protein TM0957 [141320]
                 1. Thermotoga maritima [TaxId: 2336] [141321] (4)
                    SQ Q9X052 39-214
       12. NfeD domain-like [141322] (1)
           close structural similarity to some members of the Nucleic acid-binding OB-fold proteins, possibly related to this superfamily
           uperfamily
           1. NfeD domain-like [141323] (1)
              C-terminal part of Pfam 01957
              1. Hypothetical protein PH0471 [141324]
                 NfeD short homolog
                 1. Pyrococcus horikoshii [TaxId: 53953] [141325] (1)
                    SQ O58204 72-143
       13. BC4932-like [159121] (1)
           1. BC4932-like [159122] (2)
              Pfam 06486; DUF1093
              1. Uncharacterized protein BC2438 [159123]
                 1. Bacillus cereus [TaxId: 1396] [159124] (1)
                    SQ Q813L1 22-129
              2. Uncharacterized protein BC4932 [159125]
                 1. Bacillus cereus [TaxId: 1396] [159126] (1)
                    SQ Q812L6 22-117
       14. HupF/HypC-like [159127] (1)
           contains extra C-terminal helix packed against the beta-barrel side
           1. HupF/HypC-like [159128] (3)
              Pfam 01455
              1. Hydrogenase expression/formation protein HypC [159129]
                 1. Escherichia coli [TaxId: 562] [159130] (1)
                    SQ P0AAM3 1-90
                 2. Shewanella oneidensis [TaxId: 70863] [159131] (2)
                    SQ Q8EF93 1-76
                 3. Thermococcus kodakaraensis [TaxId: 311400] [159132] (3)
                    SQ Q5JII0 2-72
       15. EutN/CcmL-like [159133] (1)
           homohexameric unit
           1. EutN/CcmL-like [159134] (3)
              Pfam 03319
              1. Ethanolamine utilization protein EutN [159135]
                 1. Escherichia coli [TaxId: 562] [159136] (18)
                    SQ P0AEJ9 1-95
              2. Carboxysome shell protein [159137]
                 Unidentified carboxysome polypeptide
                 1. Thiobacillus neapolitanus [TaxId: 927] [159138] (5)
                    SQ O85043 1-82
              3. Carbon dioxide concentrating mechanism protein CcmL [159139]
                 1. Synechocystis sp. (strain PCC 6803) [TaxId: 1148] [159140] (10)
                    SQ P72759 1-96
       16. HIN-2000 domain-like [159141] (1)
           duplication: tandem repeat of two OB-fold domains
           1. HIN-200/IF120x domain [159142] (1)
              Pfam 02760
              1. Gamma-interferon-inducible protein Ifi-16 [159143]
                 1. Human (Homo sapiens) [TaxId: 9606] [159144] (8)
                    SQ Q16666 199-301! SQ Q16666 302-389
   72. PRC-barrel domain [50345] (1)
       core: barrel, partly opened; n*=5, S*=8; meander
       1. PRC-barrel domain [50346] (4)
          uperfamily
          1. MTH1895 [101773] (1)
             homodimeric protein; subunits are composed of a stand-alone copy of this domain
             1. MTH1895 [101774]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101775] (1)
          2. Photosynthetic reaction centre, H-chain, cytoplasmic domain [50347] (3)
             1. Photosynthetic reaction centre [50348]
                1. Rhodopseudomonas viridis [TaxId: 1079] [50349] (11)
                2. Rhodobacter sphaeroides [TaxId: 1063] [50350] (39)
                   SQ P11846
                3. Thermochromatium tepidum [TaxId: 1050] [50351] (1)
          3. RIKEN cDNA 2310057j16 protein (KIAA1543) [110202] (1)
             contains an N-terminal alpha-haipin and other fold decorations
             1. RIKEN cDNA 2310057j16 protein (KIAA1543) [110203]
                1. Mouse (Mus musculus) [TaxId: 10090] [110204] (1)
                   SQ Q80VC9 1112-1240
          4. RimM C-terminal domain-like [141326] (1)
             1. 16S rRNA processing protein RimM, C-terminal domain [141327]
                1. Pseudomonas aeruginosa [TaxId: 287] [141328] (1)
                   SQ Q9HXQ0 101-175
   73. beta-Trefoil [50352] (8)
       barrel, closed; n=6, S=12; and a hairpin triplet; meander
       duplication: has internal pseudo threefold symmetry
       1. Cytokine [50353] (2)
          uperfamily
          1. Fibroblast growth factors (FGF) [50354] (11)
             1. Basic FGF (FGF2) [50355]
                1. Human (Homo sapiens) [TaxId: 9606] [50356] (16)
             2. Acidic FGF (FGF1) [50357]
                1. Cow (Bos taurus) [TaxId: 9913] [50358] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [50359] (28)
                   SQ P05230 16-152 ! SQ P05230
                3. Eastern newt (Notophthalmus viridescens) [TaxId: 8316] [63778] (1)
             3. Fibroblast growth factor 4 (FGF4) [63779]
                1. Human (Homo sapiens) [TaxId: 9606] [63780] (1)
             4. Keratinocyte growth factor, FGF7 [50360]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50361] (2)
             5. Fibroblast growth factor 9, FGF9 [63781]
                1. Human (Homo sapiens) [TaxId: 9606] [63782] (2)
             6. Fibroblast growth factor-10, FGF10 [82107]
                1. Human (Homo sapiens) [TaxId: 9606] [82108] (1)
             7. Fibrobast growth factor homologous factor 1 (FHF1b, FGF12b) [101776]
                1. Human (Homo sapiens) [TaxId: 9606] [101777] (1)
             8. Fibroblast growth factor-19 (FGF19) [101778]
                1. Human (Homo sapiens) [TaxId: 9606] [101779] (3)
             9. Fibroblast growth factor 8, FGF8 [159145]
                1. Human (Homo sapiens) [TaxId: 9606] [159146] (2)
                   SQ P55075 52-198
          2. Interleukin-1 (IL-1) [50362] (6)
             1. Interleukin-1beta [50363]
                1. Human (Homo sapiens) [TaxId: 9606] [50364] (20)
                   SQ P01584 117-269
                2. Mouse (Mus musculus) [TaxId: 10090] [50365] (2)
             2. Interleukin-1 receptor antagonist protein [50366]
                1. Human (Homo sapiens) [TaxId: 9606] [50367] (5)
             3. Interleukin-1alpha [50368]
                1. Human (Homo sapiens) [TaxId: 9606] [50369] (1)
             4. Interleukin-1F5 [101780]
                1. Mouse (Mus musculus) [TaxId: 10090] [101781] (1)
             5. Interleukin-18 [101782]
                1. Human (Homo sapiens) [TaxId: 9606] [101783] (1)
       2. MIR domain [82109] (1)
          uperfamily
          1. MIR domain [82110] (2)
             Pfam 02815
             1. IP3 receptor type 1 binding core, domain 1 [82111]
                1. Mouse (Mus musculus) [TaxId: 10090] [82112] (1)
             2. Hypothetical protein R12E2.13 (1D10) [110205]
                1. Caenorhabditis elegans [TaxId: 6239] [110206] (1)
                   SQ O61793
       3. Ricin B-like lectins [50370] (3)
          uperfamily
          1. Ricin B-like [50371] (18)
             1. Plant cytotoxin B-chain (lectin) [50372]
                duplication: consists of two domains of this fold
                1. Castor bean (Ricinus communis), Ricin [TaxId: 3988] [50373] (2)
                   SQ P06750 303-564
                2. Abrus precatorius [TaxId: 3816] [50374] (1)
                3. Mongolian snake-gourd (Trichosanthes kirilowii), Lectin 1 [TaxId: 3677] [89337] (1)
                4. European mistletoe (Viscum album) [TaxId: 3972] [50375] (18)
                   different sequence variants
                   SQ Q6ITZ3 266-520; SQ P81446 269-531 # 91% sequence identity
                5. Sambucus ebulus, ebulin [TaxId: 28503] [50376] (4)
             2. Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain) [50377]
                1. Streptomyces olivaceoviridis [TaxId: 1921] [50378] (11)
                2. Streptomyces lividans [TaxId: 1916] [74958] (3)
             3. Hemagglutinin component Ha1 [101784]
                1. Clostridium botulinum D phage [TaxId: 29342] [101785] (1)
                2. Clostridium botulinum [TaxId: 1491] [159147] (12)
             4. Cytolethal distending toxin subunit A [110207]
                1. Haemophilus ducreyi [TaxId: 730] [110208] (1)
                   SQ O06522 57-223
                2. Actinobacillus actinomycetemcomitans [TaxId: 714] [141329] (2)
                   SQ O87120 70-222
             5. Cytolethal distending toxin subunit C [110209]
                1. Haemophilus ducreyi [TaxId: 730] [110210] (1)
                   SQ O06524 25-178
                2. Actinobacillus actinomycetemcomitans [TaxId: 714] [141330] (2)
                   SQ Q7DK11 25-178
             6. Hemolytic lectin CEL-III, domains 1 and 2 [110211]
                1. Cucumaria echinata [TaxId: 40245] [110212] (9)
                   SQ Q868M7 11-442
             7. Polypeptide N-acetylgalactosaminyltransferase 1, C-terminal domain [117210]
                1. Mouse (Mus musculus) [TaxId: 10090] [117211] (1)
                   SQ O08912
             8. 29-kDa galactose-binding lectin [159148]
                duplication: tadem repeat of two Ricin B-like domains
                1. Lumbricus terrestris [TaxId: 6398] [159149] (4)
                   SQ O96048 131-260
             9. Agglutinin-1 chain B [159150]
                1. Abrus precatorius [TaxId: 3816] [159151] (2)
                   SQ Q9M6E9 287-420! SQ Q9M6E9 421-547
             10. Agglutinin MOA, N-terminal domain [159152]
                 1. Fairy-ring mushroom (Marasmius oreades) [TaxId: 181124] [159153] (1)
                    SQ Q8X123 2-155
          2. Cysteine rich domain [50379] (1)
             1. Mannose receptor [50380]
                1. Mouse (Mus musculus) [TaxId: 10090] [50381] (4)
          3. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [117212] (1)
             1. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [117213]
                1. Clostridium perfringens [TaxId: 1502] [117214] (1)
                   SQ Q934G8 17-420
       4. Agglutinin [50382] (1)
          this superfamily is distinct from the ricin B-like lectin superfamily
          uperfamily
          1. Agglutinin [50383] (1)
             1. Agglutinin [50384]
                duplication: the tandem repeat of beta-trefoil domains
                1. Love-lies-bleeding (Amaranthus caudatus) [TaxId: 3567] [50385] (2)
       5. STI-like [50386] (2)
          uperfamily
          1. Kunitz (STI) inhibitors [50387] (7)
             1. Winged bean albumin 1 [50388]
                1. Goa bean (Psophocarpus tetragonolobus) [TaxId: 3891] [50389] (1)
             2. Erythrina cafra trypsin inhibitor [50390]
                1. Erythrina caffra [TaxId: 3842] [50391] (1)
             3. chymotrypsin inhibitor WCI [50392]
                1. Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891] [50393] (6)
             4. Soybean trypsin inhibitor [50394]
                1. Soybean (Glycine max) [TaxId: 3847] [50395] (4)
             5. Amylase/subtilisin inhibitor [50396]
                1. Barley (Hordeum vulgare), seed [TaxId: 4513] [50397] (3)
             6. Serine protease inhibitor DrTI [110213]
                1. Royal poinciana (Delonix regia) [TaxId: 72433] [110214] (1)
                   SQ P83667
             7. Two-chain trypsin inhibitor [110215]
                1. Balsam copaiba (Copaifera langsdorffii) [TaxId: 280048] [110216] (1)
                   SQ P84144,P84145 # two chains probably resulted from a single chain precursor
          2. Clostridium neurotoxins, C-terminal domain [50399] (3)
             overall fold is very similar to that of the STI family
             1. Tetanus neurotoxin [50400]
                1. Clostridium tetani [TaxId: 1513] [50401] (10)
             2. Botulinum neurotoxin [50402]
                1. Clostridium botulinum, serotype A [TaxId: 1491] [50403] (1)
                2. Clostridium botulinum, serotype B [TaxId: 1491] [50404] (17)
       6. Actin-crosslinking proteins [50405] (2)
          uperfamily
          1. Fascin [50406] (1)
             1. Fascin [50407]
                duplication: tandem repeat of four domains
                1. Human (Homo sapiens) [TaxId: 9606] [50408] (1)
          2. Histidine-rich actin-binding protein (hisactophilin) [50409] (1)
             1. Histidine-rich actin-binding protein (hisactophilin) [50410]
                1. Dictyostelium discoideum [TaxId: 44689] [50411] (2)
       7. DNA-binding protein LAG-1 (CSL) [110217] (1)
          contains rudiment hairpin triplet lacking one hairpin
          uperfamily
          1. DNA-binding protein LAG-1 (CSL) [110218] (1)
             1. DNA-binding protein LAG-1 (CSL) [110219]
                1. Caenorhabditis elegans [TaxId: 6239] [110220] (4)
                   SQ Q9TYY1 195-660
       8. AbfB domain [110221] (1)
          uperfamily
          1. AbfB domain [110222] (1)
             Pfam 05270
             1. Alpha-L-arabinofuranosidase B (AbfB), C-terminal domain [110223]
                1. Aspergillus kawachii [TaxId: 40384] [110224] (4)
                   SQ Q8NK89 19-499
   74. Reductase/isomerase/elongation factor common domain [50412] (4)
       barrel, closed; n=6, S=10; greek-key
       1. Riboflavin synthase domain-like [63380] (3)
          uperfamily
          1. Riboflavin synthase [63783] (2)
             duplication: consists of two homologous domains
             1. Riboflavin synthase [63784]
                trimerizes via the additional C-terminal helix
                1. Escherichia coli [TaxId: 562] [63785] (4)
                   SQ P29015 1-87
                2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82113] (1)
          2. Ferredoxin reductase FAD-binding domain-like [63381] (19)
             coupled with a NADP-binding domain of alpha/beta class
             1. Ferredoxin reductase (flavodoxin reductase) N-terminal domain [50415]
                1. Spinach (Spinacia oleracea) [TaxId: 3562] [50416] (7)
                2. Garden pea (Pisum sativum) [TaxId: 3888] [50417] (4)
                3. Paprika (Capsicum annuum) [TaxId: 4072] [50418] (1)
                4. Maize (Zea mays), leaf isoform [TaxId: 4577] [50419] (2)
                5. Maize (Zea mays), root isoform [TaxId: 4577] [63786] (1)
                6. Cyanobacterium (Anabaena sp.), pcc 7119 [TaxId: 1167] [50420] (25)
                7. Escherichia coli [TaxId: 562] [50421] (1)
                8. Azotobacter vinelandii [TaxId: 354] [50422] (1)
             2. NAD(P)H:flavin oxidoreductase [50423]
                1. Escherichia coli [TaxId: 562] [50424] (1)
             3. Nitrate reductase core domain [50425]
                1. Corn (Zea mays) [TaxId: 4577] [50426] (3)
             4. cytochrome b5 reductase [50427]
                1. Pig (Sus scrofa), liver [TaxId: 9823] [50428] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [69273] (3)
                   SQ P20070 33-300
                3. Human (Homo sapiens) [TaxId: 9606] [117215] (1)
                   SQ P00387 30-300
             5. Phthalate dioxygenase reductase [50430]
                contains additional 2Fe-2S ferredoxin domain
                1. Pseudomonas cepacia, db01 [TaxId: 292] [50431] (1)
             6. Benzoate dioxygenase reductase [74959]
                1. Acinetobacter sp. [TaxId: 472] [74960] (1)
             7. Dihydroorotate dehydrogenase B, PyrK subunit [50433]
                1. Lactococcus lactis, isozyme B [TaxId: 1358] [50434] (3)
             8. Flavohemoglobin, central domain [50436]
                contains additional globin domain
                1. Alcaligenes eutrophus [TaxId: 106590] [50437] (1)
                2. Escherichia coli [TaxId: 562] [74961] (1)
             9. Methane monooxygenase component C, MmoC [117216]
                1. Methylococcus capsulatus [TaxId: 414] [117217] (1)
                   SQ P22868 99-348 # structure of the N-terminal, 2Fe-2S ferredoxin domain is also known (1JQ4; scop_sp 69669)
          3. NADPH-cytochrome p450 reductase FAD-binding domain-like [50438] (3)
             there is an alpha-helical subdomain inserted in this domain
             1. NADPH-cytochrome p450 reductase [50439]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50440] (4)
             2. Sulfite reductase flavoprotein [50441]
                1. Escherichia coli [TaxId: 562] [50442] (2)
             3. Neuronal nitric-oxide synthase FAD/NADP+ domain [69274]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [69275] (2)
                   SQ P29476 750-1413
       2. Riboflavin kinase-like [82114] (2)
          uperfamily
          1. ATP-dependent riboflavin kinase-like [82115] (3)
             1. Riboflavin kinase [82116]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82117] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [89338] (4)
                   encoded by FLJ11149
             2. Riboflavin kinase domain of bifunctional FAD synthetase [101786]
                1. Thermotoga maritima [TaxId: 2336] [101787] (7)
                   SQ Q9WZW1
                   TM0379
          2. CTP-dependent riboflavin kinase-like [159154] (2)
             Pfam 01982; newly characterized archaeal family (formerly DUF120)
             1. CTP-dependent riboflavin kinase, Rfk [159155]
                1. Thermoplasma acidophilum [TaxId: 2303] [159156] (1)
                   SQ Q9HJA6 90-220
                2. Methanococcus jannaschii [TaxId: 2190] [159157] (7)
                   SQ Q60365 1-136
       3. FucI/AraA C-terminal domain-like [50443] (2)
          uperfamily
          1. L-fucose isomerase, C-terminal domain [50444] (1)
             1. L-fucose isomerase, C-terminal domain [50445]
                1. Escherichia coli [TaxId: 562] [50446] (1)
          2. AraA C-terminal domain-like [141331] (1)
             C-terminal part of Pfam 02610
             1. L-arabinose isomerase AraA [141332]
                1. Escherichia coli [TaxId: 562] [141333] (6)
                   SQ P08202 329-498
       4. Translation proteins [50447] (6)
          uperfamily
          1. Elongation factors [50448] (18)
             1. Elongation factor Tu (EF-Tu), domain 2 [50449]
                N-terminal domain is related to G proteins; C-terminal domain is (6,10) barrel of circularly permuted topology
                1. Escherichia coli [TaxId: 562] [50450] (8)
                   SQ P02990
                2. Thermus aquaticus [TaxId: 271] [50451] (4)
                3. Thermus thermophilus [TaxId: 274] [50452] (9)
                4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [50453] (2)
                   SQ P49410 56-452
             2. Elongation factor eEF-1alpha, domain 2 [50454]
                eukaryotic and archaeal homologue of EF-Tu
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50455] (6)
                2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69276] (2)
                   SQ P35021
             3. Elongation factor G (EF-G), domain II [50456]
                1. Thermus thermophilus [TaxId: 274] [50457] (9)
                2. Thermus thermophilus, EF-G-2 [TaxId: 274] [141334] (2)
                   SQ Q5SI76 268-370
                   TTHA1498
             4. Elongation factor 2 (eEF-2), domain II [82118]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82119] (22)
                   SQ P32324
             5. Initiation factor eIF2 gamma subunit, domain II [74962]
                1. Archaeon Pyrococcus abyssi [TaxId: 29292] [74963] (5)
                2. Archaeon Methanococcus jannaschii [TaxId: 2190] [101788] (1)
                3. Sulfolobus solfataricus [TaxId: 2287] [141335] (6)
                   SQ Q980A5 207-320
             6. Initiation factor IF2/eIF5b, domains 2 and 4 [50458]
                the C-terminal domain 4 has the same fold as domain 2; it probably binds fMet-tRNAfmet
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [50459] (3)
                2. Bacillus stearothermophilus [TaxId: 1422] [50460] (1)
             7. Eukaryotic peptide chain release factor ERF2, post-G domain [110225]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110226] (3)
                   SQ O74718
             8. Hypothetical protein PF0907 [110227]
                stand-alone protein related to this domain
                1. Pyrococcus furiosus [TaxId: 2261] [110228] (1)
                   SQ Q8U2D2 18-108
             9. Elongation factor SelB, domains 2 and 4 [117218]
                EF-Tu homologue, contains extra C-terminal domain (domain 4) of the same fold as the postG domain 2
                1. Methanococcus maripaludis [TaxId: 39152] [117219] (3)
                   SQ Q8J307
             10. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain [141336]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [141337] (1)
                    SQ Q87WW1 238-329
          2. Ribosomal protein L3 [50461] (4)
             1. Ribosomal protein L3 [50462]
                superfamily fold is elaborated with additional structures
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [50463] (58)
                   SQ P20279
                2. Thermus thermophilus [TaxId: 274] [159158] (11)
                   SQ Q72I04 1-205
                3. Escherichia coli [TaxId: 562] [159159] (29)
                   SQ P60438 1-209
                4. Deinococcus radiodurans [TaxId: 1299] [159160] (9)
                   SQ Q9RXK2 1-205
          3. Ribosomal protein L35ae [117220] (1)
             Pfam 01247
             1. Ribosomal protein L35ae [117221]
                1. Pyrococcus furiosus [TaxId: 2261] [117222] (1)
                   SQ Q8TZV6
          4. RimM N-terminal domain-like [141338] (1)
             Pfam 01782
             1. 16S rRNA processing protein RimM, N-terminal domain [141339]
                1. Pseudomonas aeruginosa [TaxId: 287] [141340] (1)
                   SQ Q9HXQ0 7-95
          5. Gar1-like SnoRNP [141341] (1)
             stand alone proteins, which are similar structurally but not sequentially to the elongation factor domains, unlike PF0907
             1. Gar1 homolog PF1791 [141342]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [141343] (4)
                   SQ Q8U029 1-73
          6. AlaX-M N-terminal domain-like [159161] (1)
             Does NOT belong to Pfam 01411
             1. AlaX-M trans-editing enzyme, N-terminal domain [159162]
                1. Pyrococcus horikoshii [TaxId: 53953] [159163] (1)
                   SQ O57848 1-87
   75. Elongation factor/aminomethyltransferase common domain [50464] (2)
       barrel, closed; n=6, S=10; greek-key
       1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50465] (1)
          probably related to the second domain and its superfamiy by a circular permutation
          uperfamily
          1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50466] (12)
             1. Elongation factor Tu (EF-Tu) [50467]
                1. Escherichia coli [TaxId: 562] [50468] (8)
                   SQ P02990
                2. Thermus aquaticus [TaxId: 271] [50469] (4)
                3. Thermus thermophilus [TaxId: 274] [50470] (9)
                4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [50471] (2)
                   SQ P49410 56-452
             2. Elongation factor eEF-1alpha, C-terminal domain [50472]
                eukaryotic and archaeal homologue of EF-Tu
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50473] (6)
                2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69277] (2)
                   SQ P35021
             3. Initiation factor eIF2 gamma subunit [74964]
                1. Archaeon Pyrococcus abyssi [TaxId: 29292] [74965] (5)
                2. Archaeon Methanococcus jannaschii [TaxId: 2190] [101789] (1)
                3. Sulfolobus solfataricus [TaxId: 2287] [141344] (6)
                   SQ Q980A5 321-415
             4. Eukaryotic peptide chain release factor ERF2, C-terminal domain [110229]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110230] (3)
                   SQ O74718
             5. Elongation factor SelB, domain 3 [117223]
                1. Methanococcus maripaludis [TaxId: 39152] [117224] (3)
                   SQ Q8J307
             6. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 3-like domain [141345]
                1. Pseudomonas syringae pv. tomato [TaxId: 323] [141346] (1)
                   SQ Q87WW1 330-434
       2. Aminomethyltransferase beta-barrel domain [101790] (1)
          uperfamily
          1. Aminomethyltransferase beta-barrel domain [101791] (5)
             1. N,N-dimethylglycine oxidase, C-terminal domain [101792]
                1. Arthrobacter globiformis [TaxId: 1665] [101793] (3)
             2. Hypothetical protein YgfZ, C-terminal domain [101794]
                1. Escherichia coli [TaxId: 562] [101795] (2)
                   SQ P39179
             3. Glycine cleavage system T protein, GcvT [110231]
                1. Thermotoga maritima [TaxId: 2336] [110232] (4)
                   SQ Q9WY54
                2. Escherichia coli [TaxId: 562] [110233] (1)
                   SQ P27248
                3. Pyrococcus horikoshii [TaxId: 53953] [117225] (1)
                   SQ O58888
   76. Split barrel-like [50474] (3)
       barrel; n=6, S=10; greek-key
       1. FMN-binding split barrel [50475] (4)
          related to the ferredoxin reductase-like FAD-binding domain
          uperfamily
          1. PNP-oxidase like [50476] (21)
             1. FMN-binding protein [50477]
                1. Desulfovibrio vulgaris, strain Miyazaki F [TaxId: 881] [50478] (10)
             2. Pyridoxine 5'-phoshate oxidase (PNP oxidase) [50479]
                elaborated with additional secondary structures; active as dimer
                1. Human (Homo sapiens) [TaxId: 9606] [82120] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50480] (1)
                3. Escherichia coli [TaxId: 562] [50481] (7)
                   SQ P28225
                4. Pseudomonas aeruginosa [TaxId: 287] [117226] (1)
                   SQ Q820A5
                5. Pseudomonas fluorescens [TaxId: 294] [117227] (1)
                   SQ Q51793
                6. Mycobacterium tuberculosis [TaxId: 1773] [141347] (2)
                   SQ P65682 24-112
             3. Hypothetical protein Alr5027 [110234]
                1. Cyanobacterium (Nostoc sp. PCC 7120) [TaxId: 103690] [110235] (1)
                   SQ Q8YMA7
             4. NimA-related protein DR0842 [117228]
                1. Deinococcus radiodurans [TaxId: 1299] [117229] (5)
                   SQ Q9RW27
             5. Hypothetical protein Rv1155 [117230]
                1. Mycobacterium tuberculosis [TaxId: 1773] [117231] (6)
                   SQ O06553
             6. Hypothetical protein Rv2991 [117232]
                1. Mycobacterium tuberculosis [TaxId: 1773] [117233] (1)
                   SQ O53240
             7. Hypothetical protein BH0577 [141348]
                1. Bacillus halodurans [TaxId: 86665] [141349] (1)
                   SQ Q9KFA8 10-165
             8. Hypothetical protein PA4388 [141350]
                1. Pseudomonas aeruginosa [TaxId: 287] [141351] (2)
                   SQ Q9HW16 2-239
             9. General stress protein 26 [141352]
                1. Nostoc punctiforme pcc 73102 [TaxId: 63737] [141353] (2)
             10. Hypothetical protein Mll6688 [141354]
                 binds FAD cofactor
                 1. Mesorhizobium loti [TaxId: 381] [141355] (2)
                    SQ Q988L5 1-148
             11. Cellular repressor of E1A-stimulated genes CREG1 [141356]
                 1. Human (Homo sapiens) [TaxId: 9606] [141357] (4)
                    SQ O75629 49-218
             12. Putative general stress protein BT1439 [141358]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [141359] (2)
                    SQ Q8A7U5 3-137
             13. Hypotheical protein CAC3491 [141360]
                 related to general stress protein 26(GS26) of B.subtilis
                 1. Clostridium acetobutylicum [TaxId: 1488] [141361] (2)
                    SQ Q97DI6 2-142
             14. Hypothetical protein Rv2074 [141362]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141363] (1)
                    SQ Q10682 11-135
             15. 5-nitroimidazole resistance protein BT3078 [141364]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [141365] (1)
                    SQ Q8A377 1-157
             16. Hypothetical protein Ta1372 [141366]
                 1. Thermoplasma acidophilum [TaxId: 2303] [141367] (2)
                    SQ Q9HIG7 16-208
          2. NADH:FMN oxidoreductase-like [50482] (5)
             different dimerization mode than in the PNP-oxidase like family
             1. FMN-binding protein MTH152 [50483]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [50484] (1)
             2. Ferric reductase [63787]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [63788] (2)
             3. Putative styrene monooxygenase small component [101796]
                1. Thermus thermophilus [TaxId: 274] [101797] (2)
             4. Phenol 2-hydroxylase component B (PheA2) [101798]
                utilizes FAD rather than FMN
                1. Geobacillus thermoglucosidasius [TaxId: 1426] [101799] (2)
             5. Putative flavoprotein TTHA0420 [117234]
                1. Thermus thermophilus [TaxId: 274] [117235] (2)
                   SQ Q5SL73
          3. UbiD middle domain-like [141368] (1)
             N terminal part of Pfam 01977; overall structural similarity to one subunit of the NADH:FMN oxidoreductase-like family (scop_fa 50482); not known to bind a flavin cofactor; also includes the N-terminal alpha+beta subdomain (~110 residues)
             1. 3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD [141369]
                1. Escherichia coli [TaxId: 562] [141370] (3)
                   SQ P0AAB4 6-325
          4. MTH863-like [159164] (3)
             Pfam 04289; DUF447; a new dimerisation mode involving (included) all-alpha subdomain of the spectrin-like fold (scop_cf 46965)
             1. Hypothetical protein AF1834 [159165]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159166] (4)
                   SQ O28442 1-189
             2. Hypothetical protein MM1853 [159167]
                1. Methanosarcina mazei [TaxId: 2209] [159168] (2)
                   SQ Q8PVV4 19-210
             3. Uncharacterized protein MTH863 [159169]
                1. Methanobacterium thermoautotrophicum [TaxId: 145262] [159170] (2)
                   SQ O26951 15-220
       2. PilZ domain-like [141371] (2)
          uperfamily
          1. PilZ domain [141372] (3)
             Pfam 07238
             1. Hypothetical protein VCA0042, C-terminal domain [141373]
                1. Vibrio cholerae [TaxId: 666] [141374] (1)
                   SQ Q9KNC3 138-248
                2. Vibrio cholerae O395 [TaxId: 345073] [159171] (2)
             2. Hypothetical protein PA4608 [141375]
                1. Pseudomonas aeruginosa [TaxId: 287] [141376] (1)
                   SQ Q9HVI1 1-125
          2. PilZ domain-associated domain [141377] (2)
             this domain preceeds PilZ domain in some proteins
             1. Hypothetical protein VCA0042, N-terminal domain [141378]
                1. Vibrio cholerae [TaxId: 666] [141379] (1)
                   SQ Q9KNC3 23-137
                2. Vibrio cholerae O395 [TaxId: 345073] [159172] (2)
       3. YkvR-like [159173] (1)
          provisional classification, pending better resolution structures
          1. YkvR-like [159174] (1)
             PfamB 102647
             1. Uncharacterized protein YkvR [159175]
                1. Bacillus subtilis [TaxId: 1423] [159176] (1)
                   SQ O31683 1-96
   77. Phage tail proteins [69278] (1)
       core: barrel; n=6, S=10; greek-key; topologically similar to the FMN-binding split barrel
       1. Phage tail proteins [69279] (3)
          uperfamily
          1. Baseplate protein-like [69280] (5)
             duplication: consists of two similar barrel domains that differ by the first strand directions; the barrels are differently decorated by alpha+beta insertions
             1. Baseplate structural protein gp27 [69281]
                1. Bacteriophage T4 [TaxId: 10665] [69282] (3)
             2. Hypothetical protein c3393 [159177]
                probable phage-related protein; similar to fusion of the T4 phage gp27 and (a part of) gp5
                1. Escherichia coli o6 [TaxId: 217992] [159178] (2)
                   SQ Q8FED2 15-201! SQ Q8FED2 202-377
             3. Baseplate protein gpP [159179]
                43 kda tail protein; Pfam 06893
                1. Neisseria meningitidis [TaxId: 487] [159180] (4)
                   SQ Q9JZC8 179-347! SQ Q9JZC8 6-178
                   unidentified prophage?
                2. Bacteriophage mu [TaxId: 10677] [159181] (2)
                   SQ P08558 177-346! SQ P08558 3-176
                3. Shewanella oneidensis [TaxId: 70863] [159182] (12)
                   SQ Q8EDP4 181-348! SQ Q8EDP4 2-180
                   Prophage MuSo2
          2. gpFII-like [74966] (2)
             similar to the N-terminal barrel of T4 gp27
             1. Tail attachment protein gpF3 [74967]
                1. Bacteriophage lambda [TaxId: 10710] [74968] (1)
             2. Gifsy-2 prophage protein STM1035 [159183]
                ATP-binding sugar transporter-like protein
                1. Salmonella typhimurium [TaxId: 90371] [159184] (1)
                   SQ Q8ZQ92 1-93
          3. XkdM-like [159185] (1)
             Pfam 09393; DUF2001
             1. Phage-like element PBSX protein XkdM [159186]
                1. Bacillus subtilis [TaxId: 1423] [159187] (2)
                   SQ P54332 5-143
   78. Surface presentation of antigens (SPOA) [101800] (1)
       segment-swapped dimer forming two identical conjoint barrels (n=6, S=10) topologically similar to the FMN-binding split barrel
       1. Surface presentation of antigens (SPOA) [101801] (1)
          uperfamily
          1. Surface presentation of antigens (SPOA) [101802] (2)
             1. Putative flagelar motor switch protein FliN [101803]
                1. Thermotoga maritima [TaxId: 2336] [101804] (3)
                   TM0680a
             2. Structural protein HrcQ2, C-terminal domain [101805]
                1. Pseudomonas syringae [TaxId: 317] [101806] (1)
   79. FMT C-terminal domain-like [50485] (1)
       barrel, open; n*=6, S*=10; greek-key
       1. FMT C-terminal domain-like [50486] (2)
          uperfamily
          1. Post formyltransferase domain [50487] (5)
             1. Methionyl-tRNAfmet formyltransferase, C-terminal domain [50488]
                1. Escherichia coli [TaxId: 562] [50489] (2)
                2. Clostridium thermocellum [TaxId: 1515] [117236] (1)
                   SQ Q4HJX2; 47% sequence identity; truncated C-terminal domain
                   Structural genomics target; GI:67850689
             2. 10-formyltetrahydrofolate dehydrogenase domain 2 [101807]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [101808] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [141380] (2)
                   SQ O75891 204-307
             3. Polymyxin resistance protein ArnA, domain 2 [141381]
                1. Escherichia coli [TaxId: 562] [141382] (9)
                   SQ P77398 201-304! SQ P77398 204-304
          2. 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) [50490] (1)
             1. 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) [50491]
                1. Human (Homo sapiens) [TaxId: 9606] [50492] (4)
   80. Trypsin-like serine proteases [50493] (1)
       barrel, closed; n=6, S=8; greek-key
       duplication: consists of two domains of the same fold
       1. Trypsin-like serine proteases [50494] (4)
          uperfamily
          1. Prokaryotic proteases [50495] (16)
             1. Achromobacter protease [50496]
                1. Achromobacter lyticus, strain m497-1 [TaxId: 224] [50497] (2)
             2. alpha-Lytic protease [50498]
                1. Lysobacter enzymogenes, 495 [TaxId: 69] [50499] (41)
             3. Protease A [50500]
                1. Streptomyces griseus, strain k1 [TaxId: 1911] [50501] (5)
             4. Glutamic acid-specific protease [50502]
                1. Streptomyces griseus [TaxId: 1911] [50503] (1)
             5. Trypsin [50504]
                1. Streptomyces griseus, strain k1 [TaxId: 1911] [50505] (3)
             6. Serine proteinase [50506]
                1. Streptomyces fradiae [TaxId: 1906] [50507] (1)
             7. Protease B [50508]
                1. Streptomyces griseus, strain k1 [TaxId: 1911] [50509] (29)
                   Streptogrisin B
             8. Epidermolytic (exfoliative) toxin A [50510]
                probable glutamic acid-specific protease
                1. Staphylococcus aureus [TaxId: 1280] [50511] (4)
             9. Exfoliative toxin B [50512]
                1. Staphylococcus aureus [TaxId: 1280] [50513] (2)
             10. V8 protease [101809]
                 glutamic acid-specific protease
                 1. Staphylococcus aureus [TaxId: 1280] [101810] (3)
                    SQ P04188 69-284
             11. Glutamyl endopeptidase [101811]
                 1. Bacillus intermedius [TaxId: 1400] [101812] (2)
             12. Protease Do (DegP, HtrA), catalytic domain [74969]
                 1. Escherichia coli [TaxId: 562] [74970] (14)
                 2. Thermotoga maritima [TaxId: 2336] [89339] (1)
             13. Mitochondrial serine protease HtrA2, catalytic domain [74971]
                 1. Human (Homo sapiens) [TaxId: 9606] [74972] (1)
             14. Stress sensor protease DegS, catalytic domain [110236]
                 1. Escherichia coli [TaxId: 562] [110237] (31)
                    SQ P31137 37-354 ! SQ P31137
             15. Protease PepD [141383]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141384] (6)
                    SQ O53896 154-374
                    Rv0983
          2. Eukaryotic proteases [50514] (68)
             1. Trypsin(ogen) [50515]
                1. Cow (Bos taurus) [TaxId: 9913] [50516] (282)
                   SQ P00760
                2. Pig (Sus scrofa) [TaxId: 9823] [50517] (26)
                   SQ P00761 9-231 ! SQ P00761
                3. Rat (Rattus norvegicus) [TaxId: 10116] [50518] (33)
                4. Human (Homo sapiens) [TaxId: 9606] [50519] (1)
                5. Human (Homo sapiens), trypsin IV (brain isoform) [TaxId: 9606] [69283] (1)
                6. North atlantic salmon (Salmo salar) [TaxId: 8030] [50520] (11)
                7. Pacific chum salmon (Oncorhynchus keta) [TaxId: 8018] [82121] (1)
                8. Mold (Fusarium oxysporum) [TaxId: 5507] [50521] (16)
                9. Narrow-clawed crayfish (Pontastacus leptodactylus) [TaxId: 6717] [141385] (1)
                   SQ Q52V24 1-237
             2. (alpha,gamma)-chymotrypsin(ogen) [50522]
                1. Cow (Bos taurus) [TaxId: 9913] [50523] (62)
                   SQ P00766
                2. Rat (Rattus norvegicus) [TaxId: 10116] [89340] (1)
                3. Red fire ant (Solenopsis invicta) [TaxId: 13686] [50524] (1)
             3. Neuropsin [50525]
                1. Mouse (Mus musculus) [TaxId: 10090] [50526] (1)
             4. Crab collagenase [50527]
                1. Atlantic sand fiddler crab (Uca pugilator) [TaxId: 6772] [50528] (1)
             5. HL collagenase [50529]
                1. Common cattle grub (Hypoderma lineatum) [TaxId: 7389] [50530] (2)
             6. Thrombin [50531]
                1. Human (Homo sapiens) [TaxId: 9606] [50532] (164)
                   SQ P00734 331-361,364-421 ! SQ P00734 334-360 364-510 518-619 ! SQ P00734 328-620 ! SQ P00734 355-621 ! SQ P00734 328-620
                2. Cow (Bos taurus) [TaxId: 9913] [50533] (26)
                   SQ P00734 333-622
             7. Procarboxypeptidase A-S6 subunit III (zymogen E) [50534]
                1. Cow (Bos taurus) [TaxId: 9913] [50535] (2)
             8. Elastase [50536]
                1. Human (Homo sapiens) [TaxId: 9606] [50537] (7)
                2. Pig (Sus scrofa) [TaxId: 9823] [50538] (94)
                3. Salmon (Salmo salar) [TaxId: 8030] [50539] (1)
                4. Worm (Eisenia fetida) [TaxId: 6396] [74973] (1)
                   fibrinolytic enzyme component A
             9. Enteropeptidase (enterokinase light chain) [50540]
                1. Cow (Bos taurus) [TaxId: 9913] [50541] (1)
             10. Urokinase [50542]
                 1. Human (Homo sapiens) [TaxId: 9606] [50543] (1)
             11. Heparin binding protein, HBP [50544]
                 multifunctional protein (synonym: CAP37, azurocidin)
                 1. Human (Homo sapiens) [TaxId: 9606] [50545] (4)
             12. Alpha tryptase I [89341]
                 1. Human (Homo sapiens) [TaxId: 9606] [89342] (1)
             13. beta-Tryptase [50546]
                 ring-like tetramer with active sites facing a central pore
                 1. Human (Homo sapiens) [TaxId: 9606] [50547] (33)
             14. Cathepsin G [50548]
                 1. Human (Homo sapiens) [TaxId: 9606] [50549] (4)
             15. Coagulation factor VIIa [50550]
                 1. Human (Homo sapiens) [TaxId: 9606] [50551] (35)
                    SQ P08709 213-466 ! SQ P08709 213-446
             16. Chymase (mast cell protease I) [89343]
                 1. Human (Homo sapiens) [TaxId: 9606] [89344] (1)
             17. Chymase II (mast cell proteinase II) [50552]
                 1. Rat (Rattus rattus) [TaxId: 10117] [50553] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [50554] (4)
             18. Kallikrein A [50555]
                 1. Pig (Sus scrofa) [TaxId: 9823] [50556] (3)
             19. Kallikrein-13 [50572]
                 1. Mouse (Mus musculus) [TaxId: 10090] [50573] (1)
             20. Kallikrein 6 [74974]
                 1. Human (Homo sapiens) [TaxId: 9606] [74975] (3)
             21. Tonin [50557]
                 1. Rat (Rattus rattus) [TaxId: 10117] [50558] (1)
             22. 7S NGF protease subunits [50559]
                 two pairs of homologous but non-identical chains
                 1. Mouse (Mus musculus) [TaxId: 10090] [50560] (1)
             23. Prostate specific antigen (PSA kallikrein) [82122]
                 1. Horse (Equus caballus) [TaxId: 9796] [82123] (1)
             24. Factor B [50561]
                 1. Human (Homo sapiens) [TaxId: 9606] [50562] (4)
                    SQ P00751 268-764
             25. Factor D [50563]
                 1. Human (Homo sapiens) [TaxId: 9606] [50564] (7)
             26. Two-chain tissue plasminogen activator (TC)-T-PA [50565]
                 1. Human (Homo sapiens) [TaxId: 9606] [50566] (2)
             27. Single chain tissue plasminogen activator [50567]
                 1. Human (Homo sapiens) [TaxId: 9606] [50568] (1)
                 2. Vampire bat (Desmodus rotundus) [TaxId: 9430] [50569] (1)
             28. Venom serine protease [50570]
                 1. Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] [50571] (1)
                 2. Hundred-pace snake (Agkistrodon acutus) [TaxId: 36307] [110238] (2)
                    SQ Q9I8X1
             29. Coagulation factor IXa, protease domain [50583]
                 1. Pig (Sus scrofa) [TaxId: 9823] [50584] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [50585] (1)
             30. Coagulation factor Xa, protease domain [50574]
                 1. Human (Homo sapiens) [TaxId: 9606] [50575] (76)
                    SQ P00742 235-467
                 2. Cow (Bos taurus) [TaxId: 9913] [50576] (1)
             31. Coagulation factor Xa-trypsin chimera [50577]
                 1. Synthetic, based on Homo sapiens sequence [50578] (1)
                    Xa: residues 16-121; trypsin: residues 122-246
             32. Complement C1S protease, catalytic domain [63789]
                 1. Human (Homo sapiens) [TaxId: 9606] [63790] (1)
             33. Complement C1R protease, catalytic domain [74976]
                 1. Human (Homo sapiens) [TaxId: 9606] [74977] (5)
             34. Activated protein c (autoprothrombin IIa) [50579]
                 1. Human (Homo sapiens) [TaxId: 9606] [50580] (1)
             35. Myeloblastin, PR3 [50581]
                 1. Human (Homo sapiens) [TaxId: 9606] [50582] (1)
             36. Urokinase-type plasminogen activator (LMW U-PA), catalytic domain [50586]
                 1. Human (Homo sapiens) [TaxId: 9606] [50587] (49)
                    SQ P00749 156-178,179-424
             37. Plasmin(ogen), catalytic domain [50588]
                 1. Human (Homo sapiens) [TaxId: 9606] [50589] (7)
             38. Granzyme A [89345]
                 1. Human (Homo sapiens) [TaxId: 9606] [89346] (2)
             39. Granzyme B [50590]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50591] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [50592] (2)
             40. Granzyme K [82124]
                 1. Human (Homo sapiens) [TaxId: 9606] [82125] (2)
             41. Duodenase [63791]
                 new serine protease
                 1. Cow (Bos taurus) [TaxId: 9913] [63792] (1)
             42. Beta-acrosin [50593]
                 1. Sheep (Ovis aries) [TaxId: 9940] [50594] (1)
                 2. Pig (Sus scrofa) [TaxId: 9823] [50595] (1)
             43. Matriptase MTSP1 [69284]
                 1. Human (Homo sapiens) [TaxId: 9606] [69285] (4)
             44. Hepsin, catalytic domain [101813]
                 1. Human (Homo sapiens) [TaxId: 9606] [101814] (4)
                    SQ P05981 163-417
             45. Hepatocyte growth factor, HGF [110239]
                 1. Human (Homo sapiens) [TaxId: 9606] [110240] (2)
                    SQ P14210 495-728 ! SQ P14210 495-722
             46. Mannan-binding lectin serine protease 2 (MASP-2), catalytic domain [110241]
                 1. Human (Homo sapiens) [TaxId: 9606] [110242] (2)
                    SQ O00187 366-686
             47. Coagulation factor XI [117237]
                 1. Human (Homo sapiens) [TaxId: 9606] [117238] (4)
                    SQ P03951 388-624
          3. Viral proteases [50596] (9)
             beta sheet in the first domain is opened rather than forms a barrel
             1. Viral capsid protein [50597]
                1. Sindbis virus [TaxId: 11034] [50598] (14)
                2. Semliki forest virus [TaxId: 11033] [50599] (2)
                3. Venezuelan equine encephalitis virus [TaxId: 11036] [89347] (2)
             2. TEV protease (nucleat inclusion protein A, NIA) [82126]
                1. Tobacco etch virus, TEV [TaxId: 12227] [82127] (3)
                   SQ P04517 2041-2279
             3. NS3 protease [50600]
                1. Human hepatitis C virus (HCV), different isolates [TaxId: 11103] [50601] (14)
                   SQ P27958 1027-1206,1678-1669
                   SQ P26662 1029-1202,1677-1689
                   SQ O36579 1054-1207
                2. Dengue virus type 2 [TaxId: 11060] [50602] (3)
                3. West nile virus [TaxId: 11082] [141386] (2)
                   SQ P06935 1520-1671
                4. Dengue virus [TaxId: 12637] [159188] (2)
             4. NSP4 proteinase [82128]
                minimal fold; contains C-terminal extension
                1. Equine arteritis virus, EAV [TaxId: 11047] [82129] (1)
          4. Viral cysteine protease of trypsin fold [50603] (8)
             1. 3C cysteine protease (picornain 3C) [50604]
                1. Human rhinovirus 2 [TaxId: 12130] [50605] (1)
                2. Human hepatitis A virus [TaxId: 208726] [50606] (7)
                3. Human poliovirus 1 Mahoney [TaxId: 12081] [74978] (3)
                4. Foot-and-mouth disease virus FMDV [TaxId: 12110] [159189] (4)
                   SQ P49303 1657-1755! SQ P49303 1657-1857
             2. 2A cysteine proteinase [50607]
                1. Human rhinovirus 2 [TaxId: 12130] [50608] (1)
             3. Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) [74979]
                contains an extra alpha-helical domain
                1. Transmissible gastroenteritis virus [TaxId: 11149] [74980] (4)
                2. Human coronavirus 229E [TaxId: 11137] [89348] (1)
                3. SARS coronavirus [TaxId: 227859] [89349] (26)
   81. Replicase NSP9 [101815] (1)
       barrel; n=6, S=8, greek-key; similar to one trypsin-like protease barrel
       1. Replicase NSP9 [101816] (1)
          uperfamily
          1. Replicase NSP9 [101817] (1)
             1. Replicase NSP9 [101818]
                part of polyprotein 1AB; binds ssRNA
                1. SARS coronavirus [TaxId: 227859] [101819] (2)
   82. mu transposase, C-terminal domain [50609] (1)
       barrel; n=6, S=8, greek-key
       1. mu transposase, C-terminal domain [50610] (1)
          uperfamily
          1. mu transposase, C-terminal domain [50611] (1)
             1. mu transposase, C-terminal domain [50612]
                1. Bacteriophage mu [TaxId: 10677] [50613] (2)
   83. Domain of alpha and beta subunits of F1 ATP synthase-like [50614] (3)
       barrel, closed; n=6, S=8; greek-key
       1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50615] (1)
          uperfamily
          1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50616] (8)
             6 domains form a ring structure which contains a barrel, closed; n=24, S=24(?)
             1. F1 ATP synthase alpha subunit, domain 1 [88672]
                1. Cow (Bos taurus) [TaxId: 9913] [88673] (18)
                   SQ P19483
                2. Rat (Rattus norvegicus) [TaxId: 10116] [88674] (2)
                3. Bacillus sp., strain ps3 [TaxId: 1409] [88675] (1)
                4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88676] (2)
             2. F1 ATP synthase beta subunit, domain 1 [88677]
                1. Cow (Bos taurus) [TaxId: 9913] [88678] (12)
                   SQ P00829
                2. Rat (Rattus norvegicus) [TaxId: 10116] [88679] (8)
                3. Bacillus sp., strain ps3 [TaxId: 1409] [88680] (1)
                4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88681] (2)
       2. Alanine racemase C-terminal domain-like [50621] (2)
          the barrel is decorated with additional structures
          uperfamily
          1. Alanine racemase [88682] (3)
             1. Alanine racemase [50623]
                1. Bacillus stearothermophilus [TaxId: 1422] [50624] (8)
                2. Pseudomonas aeruginosa [TaxId: 287] [110243] (1)
                   SQ Q9HTQ2
                3. Streptomyces lavendulae [TaxId: 1914] [110244] (3)
                   SQ Q65YW7
          2. Eukaryotic ODC-like [88683] (6)
             barrel is open with strands 4 and 5 having swapped their positions, compared to the alanine racemase barrel
             1. Eukaryotic ornithine decarboxylase (ODC) [50625]
                1. Human (Homo sapiens) [TaxId: 9606] [50626] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [50627] (1)
                3. Trypanosoma brucei [TaxId: 5691] [50628] (5)
                   SQ P07805
             2. Diaminopimelate decarboxylase LysA [89350]
                1. Mycobacterium tuberculosis [TaxId: 1773] [89351] (2)
                2. Escherichia coli [TaxId: 562] [101820] (2)
                3. Archaeon Methanococcus jannaschii [TaxId: 2190] [110245] (2)
                   SQ Q58497
       3. Aminopeptidase/glucanase lid domain [101821] (1)
          uperfamily
          1. Aminopeptidase/glucanase lid domain [101822] (7)
             1. Hypothetical protein YsdC [101823]
                1. Bacillus subtilis [TaxId: 1423] [101824] (1)
             2. Putative endoglucanase TM1048 [101825]
                1. Thermotoga maritima [TaxId: 2336] [101826] (1)
             3. Frv operon protein FrvX [117239]
                1. Pyrococcus horikoshii [TaxId: 53953] [117240] (3)
                   SQ O59196 # PH1527
             4. Probable aminopeptidase ApeA [117241]
                1. Borrelia burgdorferi [TaxId: 139] [117242] (1)
                   SQ Q45055; BB0366
             5. Deblocking aminopeptidase YhfE [141387]
                1. Bacillus cereus [TaxId: 1396] [141388] (16)
                   SQ Q81HB5 74-186
                   BC0901
             6. Aminopeptidase YpdE [141389]
                1. Shigella flexneri [TaxId: 623] [141390] (6)
                   SQ Q83K87 67-147
                   hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)
             7. Endoglucanase TM1049 [141391]
                1. Thermotoga maritima [TaxId: 2336] [141392] (1)
                   SQ Q9X0D9 65-148
   84. Small protein B (SmpB) [74981] (1)
       barrel, closed; n=6, S=8, greek-key, partial similarity to the OB-fold
       1. Small protein B (SmpB) [74982] (1)
          uperfamily
          1. Small protein B (SmpB) [74983] (2)
             1. Small protein B (SmpB) [74984]
                tmRNA-binding protein; SsrA-binding protein
                1. Aquifex aeolicus [TaxId: 63363] [74985] (5)
                2. Thermus thermophilus [TaxId: 274] [82130] (6)
                   SQ Q8RR57 4-123
   85. Acid proteases [50629] (1)
       barrel, closed; n=6, S=10, complex topology
       1. Acid proteases [50630] (3)
          uperfamily
          1. Retroviral protease (retropepsin) [50631] (8)
             dimer of identical mono-domain chains, each containing (6,10) barrel
             1. Human immunodeficiency virus type 1 protease [50632]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [50633] (317)
                   SQ P35963 57-155 ! SQ P04587 69-167 ! SQ P03366 69-167 ! SQ P03367 69-167 ! SQ P03368 69-167
             2. Human immunodeficiency virus type 2 (HIV-2) protease [50634]
                1. Human immunodeficiency virus type 2 [TaxId: 11709] [50635] (21)
             3. Simian immunodeficiency virus (SIV) protease [50636]
                1. Simian immunodeficiency virus, different strains [TaxId: 11723] [50637] (18)
             4. Feline immunodeficiency virus (FIV) protease [50638]
                1. Feline immunodeficiency virus [TaxId: 11673] [50639] (7)
             5. Rous sarcoma virus protease [50640]
                1. Rous sarcoma virus, strain pr-C [TaxId: 11886] [50641] (2)
             6. Myeloblastosis-associated viral protease [50642]
                1. Avian myeloblastosis associated virus [TaxId: 11960] [50643] (1)
             7. EIAV protease [50644]
                1. Equine infectious anemia virus [TaxId: 11665] [50645] (2)
             8. Mason-Pfizer monkey virus protease [82131]
                1. Simian retrovirus 1, SRV-1 [TaxId: 11942] [82132] (1)
          2. Pepsin-like [50646] (26)
             duplication: consists of two similar barrel domains
             N-terminal: barrel, partly opened; n*=6, S*=10
             1. Endothiapepsin [50647]
                1. Chestnut blight fungus (Endothia parasitica) [TaxId: 5116] [50648] (36)
             2. Acid protease [50649]
                1. Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079] [50650] (14)
                2. Fungus (Aspergillus phoenicis), aspergillopepsin [TaxId: 5063] [63794] (1)
                3. Fungus (Aspergillus oryzae) [TaxId: 5062] [89352] (2)
                4. Bread mold (Rhizopus chinensis) [TaxId: 4843] [50651] (8)
                   SQ P06026 69-393
                5. Rhizomucor miehei [TaxId: 4839] [50652] (2)
                6. Yeast (Candida albicans) [TaxId: 5476] [50653] (2)
                7. Yeast (Candida tropicalis) [TaxId: 5482] [63795] (1)
                8. Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932] [50654] (11)
                   synonym: saccharopepsin
                9. Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319] [110246] (1)
                   SQ P17576 1-329
             3. Plant acid proteinase, phytepsin [50655]
                1. Cynara cardunculus [TaxId: 4265] [50656] (1)
                2. Barley (Hordeum vulgare) [TaxId: 4513] [50657] (1)
             4. Pepsin(ogen) [50658]
                1. Pig (Sus scrofa) [TaxId: 9823] [50659] (8)
                2. Human (Homo sapiens), isoform 3A [TaxId: 9606] [50660] (4)
                3. Human (Homo sapiens), progastricsin (pepsinogen C) [TaxId: 9606] [50661] (2)
                4. Atlantic cod (Gadus morhua) [TaxId: 8049] [50662] (1)
             5. Pepsin [50663]
                1. Mucor pusillus [TaxId: 4840] [50664] (1)
             6. Cathepsin D [50665]
                1. Human (Homo sapiens) [TaxId: 9606] [50666] (3)
             7. Chymosin (synonym: renin) [50667]
                1. Cow (Bos taurus) [TaxId: 9913] [50668] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [50669] (7)
                3. Mouse (Mus musculus) [TaxId: 10090] [50670] (4)
             8. beta-secretase (memapsin) [50671]
                1. Human (Homo sapiens) [TaxId: 9606] [50672] (90)
                   SQ P56817 58-446 ! SQ P56817 60-447
             9. Plasmepsin (a hemoglobin-degrading enzyme) [50673]
                1. Plasmodium falciparum, plasmepsin II [TaxId: 5833] [50674] (24)
                2. Plasmodium falciparum, plasmepsin IV [TaxId: 5833] [74986] (1)
                3. Plasmodium vivax [TaxId: 5855] [50675] (2)
             10. Xylanase inhibitor TAXI-I [110247]
                 pepsin-like protein that probably lost the protease activity
                 1. Wheat (Triticum aestivum) [TaxId: 4565] [110248] (3)
                    SQ Q8H0K8 22-402
          3. LPG0085-like [159190] (1)
             Pfam 05618; DUF785; single-domain protein similar to one pepsin domain with the conserved catalytic Asp motif (not in a few archaeal members of this Pfam family)
             1. Uncharacterized protein LPG0085 [159191]
                1. Legionella pneumophila [TaxId: 446] [159192] (2)
                   SQ Q5ZZC6 26-166
   86. ValRS/IleRS/LeuRS editing domain [50676] (1)
       core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
       1. ValRS/IleRS/LeuRS editing domain [50677] (1)
          uperfamily
          1. ValRS/IleRS/LeuRS editing domain [50678] (4)
             inserted into the catalytic domain
             1. Isoleucyl-tRNA synthetase (IleRS) [50679]
                1. Thermus thermophilus [TaxId: 274] [50680] (5)
                2. Staphylococcus aureus [TaxId: 1280] [50681] (3)
             2. Valyl-tRNA synthetase (ValRS) [50682]
                1. Thermus thermophilus [TaxId: 274] [50683] (5)
             3. Leucyl-tRNA synthetase (LeuRS) [82133]
                in the prokaryotic and mitochondrial LeuRS this domain is inserted into a different sequential position
                1. Thermus thermophilus [TaxId: 274] [82134] (3)
   87. Urease metallochaperone UreE, N-terminal domain [69286] (1)
       barrel, closed; n=6, S=8; a crossover loop topology
       1. Urease metallochaperone UreE, N-terminal domain [69287] (1)
          uperfamily
          1. Urease metallochaperone UreE, N-terminal domain [69288] (2)
             1. Urease metallochaperone UreE, N-terminal domain [69289]
                1. Klebsiella aerogenes [TaxId: 28451] [69290] (3)
                2. Bacillus pasteurii [TaxId: 1474] [69291] (2)
   88. Double psi beta-barrel [50684] (2)
       barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
       1. Barwin-like endoglucanases [50685] (4)
          uperfamily
          1. Eng V-like [50686] (3)
             1. Endoglucanase V (Eng V) [50687]
                1. Humicola insolens [TaxId: 34413] [50688] (4)
                2. Fungus (Melanocarpus albomyces) [TaxId: 204285] [89353] (3)
             2. Endoglucanase (CMCase) [159193]
                1. Blue mussel (Mytilus edulis) [TaxId: 6550] [159194] (1)
                   SQ P82186 1-180
          2. Pollen allergen PHL P 1 N-terminal domain [82135] (1)
             conserved Eng V active site residues and disulfides; better structural similarity to the ADC-like superfamily
             1. Pollen allergen PHL P 1 N-terminal domain [82136]
                1. Timothy grass (Phleum pratense) [TaxId: 15957] [82137] (1)
          3. Barwin [50689] (1)
             1. Barwin [50690]
                1. Barley (Hordeum vulgare) [TaxId: 4513] [50691] (2)
          4. MLTA-like [159195] (3)
             Pfam 03562 and Pfam 06725 cover the middle and C-terminal parts, respectively; contains large insert domain of the L25-like fold (scop_cf 50714)
             1. Membrane-bound lytic murein transglycosylase A, MLTA [159196]
                1. Agrobacterium tumefaciens [TaxId: 358] [159197] (1)
                   SQ Q8UJB9 5-369
                2. Escherichia coli [TaxId: 562] [159198] (8)
                   SQ P0A935 22-357! SQ P0A935 23-357! SQ P0A935 24-356
                3. Neisseria gonorrhoeae [TaxId: 485] [159199] (2)
                   SQ Q9L6H1 40-441
       2. ADC-like [50692] (3)
          uperfamily
          1. Pyruvoyl dependent aspartate decarboxylase, ADC [50693] (2)
             1. Pyruvoyl dependent aspartate decarboxylase, ADC [50694]
                autocatalytic enzyme
                1. Escherichia coli [TaxId: 562] [50695] (9)
                2. Helicobacter pylori [TaxId: 210] [110249] (2)
                   SQ P56065
          2. Formate dehydrogenase/DMSO reductase, C-terminal domain [50696] (12)
             molybdopterine enzyme
             1. Dimethylsulfoxide reductase (DMSO reductase) [50697]
                1. Rhodobacter sphaeroides [TaxId: 1063] [50698] (1)
                2. Rhodobacter capsulatus [TaxId: 1061] [50699] (10)
             2. Formate dehydrogenase H [50700]
                1. Escherichia coli [TaxId: 562] [50701] (4)
             3. Formate dehydrogenase N, alpha subunit [74987]
                1. Escherichia coli [TaxId: 562] [74988] (2)
             4. Tungsten containing formate dehydrogenase, large subunit [82138]
                1. Desulfovibrio gigas [TaxId: 879] [82139] (1)
             5. Trimethylamine N-oxide reductase [50702]
                1. Shewanella massilia [TaxId: 76854] [50703] (1)
             6. Arsenite oxidase large subunit [50704]
                1. Alcaligenes faecalis [TaxId: 511] [50705] (2)
             7. Periplasmic nitrate reductase alpha chain, NapA [50706]
                1. Desulfovibrio desulfuricans [TaxId: 876] [50707] (8)
                   dissimilatory nitrate reductase (NAP)
                2. Rhodobacter sphaeroides [TaxId: 1063] [101827] (1)
             8. Respiratory nitrate reductase 1 alpha chain [101828]
                1. Escherichia coli [TaxId: 562] [101829] (7)
                   SQ P09152
             9. Transhydroxylase alpha subunit, AthL [110250]
                1. Pelobacter acidigallici [TaxId: 35816] [110251] (6)
                   SQ P80563
             10. NADH-quinone oxidoreductase chain 3, Nqo3, C-terminal domain [141393]
                 topoisomer of the common fold, lacking the second psi loop
                 1. Thermus thermophilus [TaxId: 274] [141394] (4)
                    SQ Q56223 686-767
          3. Cdc48 N-terminal domain-like [50708] (5)
             1. N-terminal domain of NSF-N, NSF-Nn [50709]
                NSF-N, the N-terminal 'functional' domain of the N-ethylmaleimide sensitive fusion protein, consists of two structural domains
                1. Hamster (Cricetulus griseus) [TaxId: 10029] [50710] (2)
                2. Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932] [50711] (1)
             2. N-terminal domain of VAT-N, VAT-Nn [50712]
                VAT-N is the N-terminal 'functional' domain of the VCP-like ATPase
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [50713] (2)
             3. Membrane fusion ATPase p97 N-terminal domain , P97-Nn [63796]
                1. Mouse (Mus musculus) [TaxId: 10090] [63797] (5)
             4. Peroxisome biogenesis factor 1 (PEX-1), N-terminal domain [110252]
                1. Mouse (Mus musculus) [TaxId: 10090] [110253] (1)
                   SQ Q5BL07 13-179
   89. Ribosomal protein L25-like [50714] (1)
       barrel, closed; n=6, S=10; complex topology
       1. Ribosomal protein L25-like [50715] (2)
          uperfamily
          1. Ribosomal protein L25-like [50716] (3)
             1. Ribosomal protein L25 [50717]
                1. Escherichia coli [TaxId: 562] [50718] (32)
             2. Ribosomal protein TL5 (general stress protein CTC) [63798]
                contains additional all-beta (sub)domain in the C-terminal extension
                1. Thermus thermophilus [TaxId: 274] [63799] (12)
                2. Deinococcus radiodurans [TaxId: 1299] [159200] (10)
                   SQ Q9RX88 1-175
          2. Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [50719] (2)
             1. Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [50720]
                duplication, consists of two barrel domains with the swapping of N-terminal strands
                1. Escherichia coli [TaxId: 562] [50721] (14)
                2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159201] (2)
   90. Core binding factor beta, CBF [50722] (1)
       barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
       1. Core binding factor beta, CBF [50723] (1)
          uperfamily
          1. Core binding factor beta, CBF [50724] (2)
             1. Core binding factor beta, CBF [50725]
                1. Human (Homo sapiens) [TaxId: 9606] [50726] (3)
                2. Mouse (Mus musculus) [TaxId: 10090] [50727] (3)
   91. NifT/FixU barrel-like [159202] (1)
       barrel, closed, n=6, S=10; meander
       1. NifT/FixU-like [159203] (1)
          1. NifT/FixU [159204] (1)
             Pfam 06988
             1. Uncharacterized protein FixU (NifT) [159205]
                1. Rhodopseudomonas palustris [TaxId: 1076] [159206] (1)
                   SQ Q6N0Y6 1-66
   92. PH domain-like barrel [50728] (2)
       barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
       1. PH domain-like [50729] (13)
          uperfamily
          1. Pleckstrin-homology domain (PH domain) [50730] (51)
             Pfam 00169
             1. Phospholipase C delta-1 [50731]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50732] (1)
             2. beta-spectrin [50733]
                1. Mouse (Mus musculus), brain [TaxId: 10090] [50734] (2)
                2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [50735] (1)
                3. Human (Homo sapiens), brain 2 isoform [TaxId: 9606] [117243] (1)
                   SQ O15020 2219-2324
             3. Dynamin [50736]
                1. Human (Homo sapiens) [TaxId: 9606] [50737] (2)
             4. Bruton's tyrosine kinase [50738]
                contains Btk zinc-binding motif
                1. Human (Homo sapiens) [TaxId: 9606] [50739] (7)
             5. Pleckstrin [50740]
                1. Human (Homo sapiens) [TaxId: 9606] [50741] (9)
             6. Son of sevenless-1 (sos-1) [50742]
                1. Mouse (Mus musculus) [TaxId: 10090] [50743] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [50744] (4)
                   SQ Q07889 189-1046
             7. GEF of TIAM1 (T-Lymphoma invasion and metastasis inducing protein 1) [50745]
                1. Mouse (Mus musculus) [TaxId: 10090] [50746] (1)
             8. Dbl's big sister, Dbs [74989]
                1. Mouse (Mus musculus) [TaxId: 10090] [74990] (4)
                   SQ Q64096 624-958 # 98% sequence identity; the rat sequence Q63406 region 499-833 is 100% identical to the PDB sequence
             9. GEF of intersectin [74991]
                1. Human (Homo sapiens) [TaxId: 9606] [74992] (1)
             10. G-protein coupled receptor kinase 2 (beta-adrenergic receptor kinase 1) [50747]
                 1. Human (Homo sapiens) [TaxId: 9606] [50748] (1)
                 2. Cow (Bos taurus) [TaxId: 9913] [89354] (6)
             11. Dual adaptor of phosphotyrosine and 3-phosphoinositides DAPP1/PHISH [50749]
                 1. Human (Homo sapiens) [TaxId: 9606] [50750] (2)
             12. Grp1 [50751]
                 ARF1 Guanine nucleotide exchange factor and integrin binding protein homolog
                 1. Mouse (Mus musculus) [TaxId: 10090] [50752] (8)
             13. UNC-89 [50753]
                 1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [50754] (1)
             14. Tapp1 [74993]
                 1. Human (Homo sapiens) [TaxId: 9606] [74994] (1)
             15. Rac-alpha serine/threonine kinase [89355]
                 1. Human (Homo sapiens) [TaxId: 9606] [89356] (5)
                    SQ P31749 1-117
             16. Rac-beta serine/threonine protein kinase (PKB/AKT) [110254]
                 1. Human (Homo sapiens) [TaxId: 9606] [110255] (1)
                    SQ P31751 1-111
             17. SH2 and PH domain-containing adapter protein APS [110256]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110257] (1)
                    SQ Q9JID9 178-299
             18. Tapp2 [110258]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110259] (1)
                    SQ Q9ERS5 1-113
             19. SET binding factor 1, Sbf1 [110260]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110261] (1)
                    SQ Q8K2Z0 256-367
             20. Rac/CDC42 GEF 6, alpha-pix [110262]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110263] (1)
                    SQ Q8K4I3 429-551
             21. Triple functional domain protein TRIO [110264]
                 1. Human (Homo sapiens) [TaxId: 9606] [110265] (2)
                    SQ O75962 1231-1535
             22. Oxysterol binding protein-related protein 8 (ORP-8, KIAA1451) [110266]
                 1. Human (Homo sapiens) [TaxId: 9606] [110267] (1)
                    SQ Q9BZF1 149-265
             23. Rho-GTPase-activating protein 25 (KIAA0053) [110268]
                 1. Human (Homo sapiens) [TaxId: 9606] [110269] (1)
                    SQ P42331 40-144
             24. Rho guanine nucleotide exchange factor 12 [110270]
                 1. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110271] (2)
                    SQ Q9NZN5 766-1138
             25. Phosphoinositol 3-phosphate binding protein-1, PEPP1 [117244]
                 1. Human (Homo sapiens) [TaxId: 9606] [117245] (2)
                    SQ Q9H4M7 47-153
             26. 3-phosphoinositide dependent protein kinase-1 [117246]
                 1. Human (Homo sapiens) [TaxId: 9606] [117247] (3)
                    SQ O15530 409-550
             27. Dedicator of cytokinesis protein 9, DOCK9 [117248]
                 1. Human (Homo sapiens) [TaxId: 9606] [117249] (1)
                    SQ Q9BZ29 165-301
             28. FYVE, RhoGEF and PH domain containing protein 6, Fgd6 (KIAA1362) [117250]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117251] (1)
                    SQ Q69ZL1 1303-1389
             29. Calcium-dependent activator protein for secretion, CAPS [117252]
                 1. Human (Homo sapiens) [TaxId: 9606] [117253] (1)
                    SQ Q8NFR0 522-634
             30. Rho guanine nucleotide exchange factor 11, PDZ-RhoGEF [117254]
                 1. Human (Homo sapiens) [TaxId: 9606] [117255] (1)
                    SQ O15085 714-1081
             31. Centaurin-delta 1 [141395]
                 1. Human (Homo sapiens) [TaxId: 9606] [141396] (1)
                    SQ Q8WZ64 483-584
             32. Cytohesin 3 [141397]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141398] (1)
                    SQ O08967 261-387
             33. Exocyst complex protein EXO84 [141399]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [141400] (4)
                    SQ O54924 171-283
             34. Cytohesin 2 [141401]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141402] (2)
                    SQ P63034 260-378
             35. Src kinase-associated phosphoprotein SKAP55 (SCAP1) [141403]
                 1. Human (Homo sapiens) [TaxId: 9606] [141404] (4)
                    SQ O15268 108-213
             36. Signal-transducing adaptor protein 1, STAP-1 [141405]
                 1. Human (Homo sapiens) [TaxId: 9606] [141406] (1)
                    SQ Q9ULZ2 16-151
             37. KIAA1914 [141407]
                 1. Human (Homo sapiens) [TaxId: 9606] [141408] (1)
                    SQ Q8N4X5 354-448
             38. Pleckstrin-2 [141409]
                 1. Human (Homo sapiens) [TaxId: 9606] [141410] (1)
                    SQ Q9NYT0 238-353
             39. Alpha-1-syntrophin [141411]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141412] (1)
                    SQ Q61234 2-44,203-264
             40. Phosphoinositide phospholipase C, PLC-gamma-1 [141413]
                 contains split PH domain
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [141414] (1)
                    SQ P10686 489-525,870-933
             41. FYVE, RhoGEF and PH domain containing protein 3, FGD3 [141415]
                 1. Human (Homo sapiens) [TaxId: 9606] [141416] (1)
                    SQ Q5JSP0 605-703
             42. Src-associated adaptor protein Skap2 [141417]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141418] (9)
                    SQ Q9Z2K4 105-212! SQ Q9Z2K4 109-219! SQ Q9Z2K4 14-222
             43. Protein kinase c, d2 type [141419]
                 1. Human (Homo sapiens) [TaxId: 9606] [141420] (1)
                    SQ Q9BZL6 398-509
             44. Phospholipase C-beta-2 [159207]
                 1. Human (Homo sapiens) [TaxId: 9606] [159208] (2)
                    SQ Q00722 11-141
             45. Rho guanine nucleotide exchange factor 9, Collybistin [159209]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [159210] (1)
                    SQ Q9QX73 300-461
             46. DCC-interacting protein 13-alpha, APPL1 [159211]
                 1. Human (Homo sapiens) [TaxId: 9606] [159212] (1)
                    SQ Q9UKG1 274-374
             47. Rho GTPase-activating protein 21 [159213]
                 1. Human (Homo sapiens) [TaxId: 9606] [159214] (6)
                    SQ Q5T5U3 931-1063
          2. Phosphotyrosine-binding domain (PTB) [50755] (14)
             Pfam 00640
             1. X11 [50756]
                1. Human (Homo sapiens) [TaxId: 9606] [50757] (2)
             2. Insulin receptor substrate 1, IRS-1 [50758]
                duplication: contains two domains of this fold
                1. Human (Homo sapiens) [TaxId: 9606] [50759] (2)
             3. Shc adaptor protein [50760]
                1. Human (Homo sapiens) [TaxId: 9606] [50761] (3)
             4. Numb [50762]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [50763] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [117256] (1)
                   SQ Q9QZS3 19-172
             5. Disabled homolog 1 (Dab1) [89357]
                1. Mouse (Mus musculus) [TaxId: 10090] [89358] (3)
             6. Disabled homolog 2 (Dab2) [101830]
                1. Mouse (Mus musculus) [TaxId: 10090] [101831] (2)
             7. Downstream of tyrosine kinase 5, Dok-5 [101832]
                1. Human (Homo sapiens) [TaxId: 9606] [101833] (1)
             8. Docking protein 1, Dok1 [101834]
                1. Mouse (Mus musculus) [TaxId: 10090] [101835] (2)
                   SQ P97465 152-254
             9. FGFR substrate 2 (SNT-1) [117257]
                1. Human (Homo sapiens) [TaxId: 9606] [117258] (1)
                   SQ Q7LDQ6 11-129
             10. Amyloid beta A4 precursor protein-binding family B member 2, Apbb2 [117259]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117260] (2)
                    SQ Q9DBR4 582-704
             11. Tensin [141421]
                 1. Human (Homo sapiens) [TaxId: 9606] [141422] (1)
                    SQ Q9UPS7 1139-1285
                    Tensin2
                 2. Chicken (Gallus gallus) [TaxId: 9031] [141423] (1)
                    SQ Q04205 1606-1738
             12. EPS8-like protein 1, EPS8L1 [141424]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141425] (2)
                    SQ Q8R5F8 31-159
          3. Ran-binding domain [50764] (4)
             1. Nuclear pore complex protein Nup358 [50765]
                1. Human (Homo sapiens) [TaxId: 9606] [50766] (1)
             2. Ran-binding protein 1, Ranbp1 [69292]
                1. Human (Homo sapiens) [TaxId: 9606] [69293] (2)
             3. Ran binding protein 3 [141426]
                1. Human (Homo sapiens) [TaxId: 9606] [141427] (1)
                   SQ Q9H6Z4 380-516
             4. Ran-binding protein 2 [141428]
                1. Human (Homo sapiens) [TaxId: 9606] [141429] (1)
                   SQ P49792 2027-2154
          4. Enabled/VASP homology 1 domain (EVH1 domain) [50767] (8)
             1. Enabled [50768]
                1. Mouse (Mus musculus) [TaxId: 10090] [50769] (1)
                2. Homo sapiens [TaxId: 9606] [159215] (4)
             2. Ena/vasp-like protein [50770]
                1. Mouse (Mus musculus) [TaxId: 10090] [50771] (1)
             3. Vasodilator-stimulated phosphoprotein (VASP) [50772]
                1. Human (Homo sapiens) [TaxId: 9606] [50773] (1)
             4. Homer [50774]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [50775] (3)
                2. Mouse (Mus musculus), 2b/vesl 2 [TaxId: 10090] [63800] (1)
             5. Actin regulatory protein WASP [82140]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [82141] (1)
             6. Sprouty-related, EVH1 domain-containing protein 1, Spred-1 [141430]
                1. Western clawed frog (Xenopus tropicalis) [TaxId: 8364] [141431] (4)
                   SQ Q66JG9 10-123! SQ Q66JG9 9-123
          5. Dcp1 [101836] (1)
             close structural similarity to EVH1 domain
             1. Dcp1 [101837]
                decapping protein involved in mRNA degradation
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101838] (1)
          6. Third domain of FERM [50776] (9)
             1. Moesin [50777]
                1. Human (Homo sapiens) [TaxId: 9606] [50778] (3)
                   SQ P26038 4-297
             2. Radixin [50779]
                1. Mouse (Mus musculus) [TaxId: 10090] [50780] (20)
             3. Ezrin [82142]
                complexed with the icam-2 cytoplasmic peptide, chain B
                1. Human (Homo sapiens) [TaxId: 9606] [82143] (1)
             4. Erythroid membrane protein 4.1R [50781]
                1. Human (Homo sapiens) [TaxId: 9606] [50782] (1)
             5. Merlin [69294]
                the neurofibromatosis 2 tumor suppressor protein
                1. Human (Homo sapiens) [TaxId: 9606] [69295] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [74995] (1)
             6. Talin [82144]
                1. Chicken (Gallus gallus) [TaxId: 9031] [82145] (6)
             7. Talin-1 [117261]
                1. Mouse (Mus musculus) [TaxId: 10090] [117262] (1)
                   SQ P26039 209-410
             8. Focal adhesion kinase 1 [141432]
                1. Chicken (Gallus gallus) [TaxId: 9031] [141433] (5)
                   SQ Q00944 254-363
          7. PreBEACH PH-like domain [82146] (2)
             1. PH-like domain of neurobeachin [82147]
                1. Human (Homo sapiens) [TaxId: 9606] [82148] (1)
             2. Lipopolysaccharide-responsive and beige-like anchor protein LRBA [117263]
                1. Human (Homo sapiens) [TaxId: 9606] [117264] (1)
                   SQ P50851 2076-2489
          8. GRAM domain [101839] (1)
             1. Myotubularin-related protein 2, N-terminal domain [101840]
                1. Human (Homo sapiens) [TaxId: 9606] [101841] (4)
          9. TFIIH domain [110272] (2)
             1. TFIIH basal transcription factor complex p62 subunit (BTF2-p62), N-terminal domain [110273]
                1. Human (Homo sapiens) [TaxId: 9606] [110274] (2)
                   SQ P32780 1-108
             2. RNA polymerase II transcription factor B 73 kDa, TFB1 [141434]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141435] (3)
                   SQ P32776 2-115
          10. SSRP1-like [141436] (1)
              Pfam 03531; Structure-specific recognition protein family; duplication: comprises tandem repeat of two domains of this fold
              1. FACT complex subunit POB3, middle domain [141437]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141438] (6)
                    SQ Q04636 237-474! SQ Q04636 238-474
          11. Necap1 N-terminal domain-like [141439] (1)
              Pfam 07933; DUF1681
              1. Necap1 [141440]
                 1. Mouse (Mus musculus) [TaxId: 10090] [141441] (1)
                    SQ Q9CR95 1-133
          12. VPS36 N-terminal domain-like [141442] (3)
              PfamB 030385
              1. Vacuolar protein sorting protein 36, VPS36 [141443]
                 1. Human (Homo sapiens) [TaxId: 9606] [141444] (1)
                    SQ Q86VN1 3-131
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141445] (2)
                    SQ Q06696 1-99,252-282
                 3. Mouse (Mus musculus) [TaxId: 10090] [141446] (1)
                    SQ Q91XD6 10-130
          13. BPHL domain [159216] (2)
              Pfam 08000; DUF1696, bacterial proteins with PH-like domain
              1. Uncharacterized protein Exig2160 [159217]
                 homododecameric ring assembly; olizomerization is mediated by the C-terminal alpha-hairpin extension
                 1. Exiguobacterium sibiricum 255-15 [TaxId: 262543] [159218] (6)
                    SQ B1YJX4 14-203
              2. Uncharacterized protein Shew0819 [159219]
                 homopentameric ring assembly through the pairing of the beta-barrel edge strands
                 1. Shewanella loihica [TaxId: 359303] [159220] (5)
                    SQ A3QB43 9-124
       2. PA2021-like [141447] (1)
          prokaryotiic proteins of PH domain-like fold lacking the N-terminal strand
          uperfamily
          1. PA2021-like [141448] (1)
             small family specific to Pseudomonas
             1. Hypothetical protein PA2021 [141449]
                1. Pseudomonas aeruginosa [TaxId: 287] [141450] (1)
                   SQ Q9I293 1-74
   93. Transcription factor IIA (TFIIA), beta-barrel domain [50783] (1)
       barrel, closed; n=6, S=12; mixed beta-sheet
       1. Transcription factor IIA (TFIIA), beta-barrel domain [50784] (1)
          dimer of non-identical beta-sheet domains
          uperfamily
          1. Transcription factor IIA (TFIIA), beta-barrel domain [50785] (4)
             heterodimer of two homologous chains
             1. Large chain TOA1, C-terminal domain [88684]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88685] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [101842] (1)
             2. Small chain TOA2, C-terminal domain [88686]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88687] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [101843] (1)
   94. Hcp1-like [141451] (1)
       barrel, closed; n=6, S=12; contains extra, non-barrel strand 7 at the C-terminus
       1. Hcp1-like [141452] (1)
          probable biological unit is a ring-like hexamer containing a 24-stranded beta-barrel made of the subunit beta-sheets
          uperfamily
          1. Hcp1-like [141453] (1)
             Pfam 05638; DUF796
             1. Hemolysin-corregulated protein 1, Hcp1 [141454]
                1. Pseudomonas aeruginosa [TaxId: 287] [141455] (3)
                   SQ Q9I747 2-162
                   PA0085
   95. YopT-like [159221] (1)
       beta-sheet barrel, closed, n=6, S=12, capped at both ends by helices; intertwined dimer of beta-alpha-beta(2) subinits;
       1. YopT-like [159222] (1)
          1. YopT-like [159223] (1)
             Pfam 09467
             1. Uncharacterized protein YopT [159224]
                probably of phage origin
                1. Bacillus subtilis [TaxId: 1423] [159225] (2)
                   SQ O34498 2-71
   96. Herpes virus serine proteinase, assemblin [50788] (1)
       core: barrel, closed; n=7, S=8; complex topology
       1. Herpes virus serine proteinase, assemblin [50789] (1)
          uperfamily
          1. Herpes virus serine proteinase, assemblin [50790] (5)
             1. Human cytomegalovirus protease [50791]
                1. Human cytomegalovirus [TaxId: 10359] [50792] (15)
             2. HSV-2 protease [50793]
                1. Herpes simplex virus type 2 [TaxId: 10310] [50794] (1)
             3. KSHV protease [50795]
                1. Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] [50796] (3)
             4. Epstein-Barr virus protease [82149]
                1. Human herpesvirus 4 [TaxId: 10376] [82150] (1)
             5. VZV protease [50797]
                1. Varicella-Zoster virus [TaxId: 10335] [50798] (1)
   97. PK beta-barrel domain-like [50799] (1)
       barrel, closed; n=7, S=10; complex topology
       1. PK beta-barrel domain-like [50800] (2)
          uperfamily
          1. Pyruvate kinase beta-barrel domain [50801] (6)
             this domain interrupts beta/alpha-barrel domain
             C-terminal domain is alpha/beta
             1. Pyruvate kinase (PK) [50802]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [50803] (14)
                2. Cat (Felis catus) [TaxId: 9685] [50804] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [82151] (4)
                4. Leishmania mexicana [TaxId: 5665] [50805] (8)
                5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50806] (2)
                6. Escherichia coli [TaxId: 562] [50807] (3)
          2. MOSC (MOCO sulphurase C-terminal) domain [101844] (2)
             Pfam 03473
             1. Hypothetical protein YuaD [101845]
                1. Bacillus subtilis [TaxId: 1423] [101846] (1)
             2. Hypothetical protein YiiM [101847]
                1. Escherichia coli [TaxId: 562] [101848] (2)
   98. XRCC4, N-terminal domain [50808] (1)
       barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
       1. XRCC4, N-terminal domain [50809] (1)
          an HTH motif connects strands 4 and 5
          uperfamily
          1. XRCC4, N-terminal domain [50810] (1)
             1. XRCC4, N-terminal domain [50811]
                1. Human (Homo sapiens) [TaxId: 9606] [50812] (2)
   99. HesB-like domain [89359] (1)
       barrel, closed; n=7, S=10; complex topology
       1. HesB-like domain [89360] (1)
          uperfamily
          1. HesB-like domain [89361] (3)
             Pfam 01521; Iron-sulfur cluster scaffold domain
             1. Fe-S scaffold protein IscA (YfhF) [101849]
                1. Escherichia coli [TaxId: 562] [101850] (3)
                   SQ P36539
             2. Hypothetical protein Aq_1857 [89362]
                1. Aquifex aeolicus [TaxId: 63363] [89363] (1)
             3. Putative Fe-S biosynthesis protein LSL1730 [159226]
                1. Lactobacillus salivarius [TaxId: 1624] [159227] (1)
                   SQ Q1WRG6 1-118
   100. Bacterial fluorinating enzyme, C-terminal domain [101851] (1)
        barrel, closed; n=7, S=10; greek-key topology; one overside connection
        1. Bacterial fluorinating enzyme, C-terminal domain [101852] (1)
           uperfamily
           1. Bacterial fluorinating enzyme, C-terminal domain [101853] (1)
              1. 5'-fluoro-5'-deoxyadenosine synthase [101854]
                 1. Streptomyces cattleya [TaxId: 29303] [101855] (41)
   101. SPOC domain-like [100938] (1)
        barrel, closed; n=7, S=10; complex topology
        1. SPOC domain-like [100939] (3)
           uperfamily
           1. SPOC domain [101856] (1)
              1. SMART/HDAC1 associated repressor protein, SHARP [101857]
                 1. Human (Homo sapiens) [TaxId: 9606] [101858] (1)
           2. Ku70 subunit middle domain [100940] (1)
              includes C-terminal alpha-helical arm and DNA encircling insertion
              1. Ku70 subunit middle domain [100941]
                 1. Human (Homo sapiens) [TaxId: 9606] [100942] (2)
           3. Ku80 subunit middle domain [100943] (1)
              includes C-terminal alpha-helical arm and DNA encircling insertion
              1. Ku80 subunit middle domain [100944]
                 1. Human (Homo sapiens) [TaxId: 9606] [100945] (2)
   102. BH3618-like [141456] (1)
        barrel, closed; n=7, S=10; meander
        1. BH3618-like [141457] (1)
           uperfamily
           1. BH3618-like [141458] (1)
              Pfam 02623; DUF180
              1. Hypothetical protein BH3618 [141459]
                 B. subtilis YviF homolog
                 1. Bacillus halodurans [TaxId: 86665] [141460] (2)
                    SQ Q9K6V7 1-148
   103. FAS1 domain [82152] (1)
        core: barrel, closed; n=7, S=12; meander
        1. FAS1 domain [82153] (1)
           uperfamily
           1. FAS1 domain [82154] (2)
              1. Immunogenic protein MPT70 [101859]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [101860] (1)
              2. Fasciclin I [82155]
                 duplication: tandem repeat of four FAS1 domain
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [82156] (1)
   104. Lipocalins [50813] (1)
        barrel, closed or opened; n=8, S=12; meander
        1. Lipocalins [50814] (9)
           bind hydrophobic ligands in their interior
           uperfamily
           1. Retinol binding protein-like [50815] (30)
              barrel, closed; n=8, S=12, meander
              1. Retinol binding protein [50816]
                 1. Cow (Bos taurus) [TaxId: 9913] [50817] (13)
                 2. Pig (Sus scrofa domestica) [TaxId: 9823] [50818] (1)
                 3. Human (Homo sapiens) [TaxId: 9606] [50819] (4)
                 4. Chicken (Gallus gallus) [TaxId: 9031] [50820] (1)
                 5. Chicken (Gallus gallus), plasma isoform [TaxId: 9031] [69297] (1)
              2. Odorant-binding protein [50821]
                 C-termini swapping dimer
                 1. Cow (Bos taurus) [TaxId: 9913] [50822] (8)
                 2. Pig (Sus scrofa) [TaxId: 9823] [50823] (9)
              3. Lipocalin allergen [50824]
                 1. Cow (Bos taurus), bos d 2 [TaxId: 9913] [50825] (1)
                 2. Horse (Equus caballus), equ c 1 [TaxId: 9796] [50826] (1)
              4. Salivary lipocalin [74996]
                 1. Pig (Sus scrofa) [TaxId: 9823] [74997] (1)
              5. Aphrodisin, a sex pheromone [63805]
                 1. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [63806] (1)
              6. beta-Lactoglobulin [50827]
                 1. Cow (Bos taurus) [TaxId: 9913] [50828] (26)
                    SQ P02754
                 2. Pig (Sus scrofa) [TaxId: 9823] [50829] (1)
                 3. Reindeer (Rangifer tarandus) [TaxId: 9870] [141461] (6)
                    SQ P02755 19-180
              7. Retinoic acid-binding protein [50830]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50831] (2)
              8. Major urinary protein/alpha-2u-globulin [50832]
                 1. Mouse (Mus musculus) [TaxId: 10090] [50833] (19)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [50834] (2)
              9. Neutrophil gelatinase-associated lipocalin (NGAL) [50835]
                 1. Human (Homo sapiens) [TaxId: 9606] [50836] (13)
              10. Lipocalin q83 [89364]
                  activated expression by the myc oncogene
                  1. Common quail (Coturnix coturnix) [TaxId: 9091] [89365] (1)
              11. Complement protein C8gamma [74998]
                  1. Human (Homo sapiens) [TaxId: 9606] [74999] (2)
              12. Bilin-binding protein [50837]
                  1. Cabbage butterfly (Pieris brassicae) [TaxId: 7116] [50838] (6)
              13. Alpha-crustacyanin [63807]
                  1. European lobster (Homarus gammarus) [TaxId: 6707] [63808] (7)
              14. Outer membrane lipoprotein Blc [101861]
                  bacterial lipocalin
                  1. Escherichia coli [TaxId: 562] [101862] (1)
              15. Histamine binding protein [50839]
                  1. Brown ear tick (Rhipicephalus appendiculatus) [TaxId: 34631] [50840] (2)
              16. Nitrophorin 1 [50841]
                  1. Rhodnius prolixus [TaxId: 13249] [50842] (8)
              17. Nitrophorin 2 (prolixin-s) [50843]
                  1. Rhodnius prolixus [TaxId: 13249] [50844] (14)
                     SQ Q26241
              18. Nitrophorin 4 [50845]
                  1. Rhodnius prolixus [TaxId: 13249] [50846] (34)
                     SQ Q94734 22-205
              19. Von Ebner's gland protein (VEGP, tear lipocalin) [117265]
                  1. Human (Homo sapiens) [TaxId: 9606] [117266] (1)
                     SQ P31025 30-168
              20. Insecticyanin [141462]
                  1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [141463] (1)
                     SQ P00305 1-189
              21. Hypothetical protein YxeF [159228]
                  1. Bacillus subtilis [TaxId: 1423] [159229] (1)
                     SQ P54945 19-144
           2. Fatty acid binding protein-like [50847] (28)
              ten-stranded meander beta-sheet folded upon itself
              relates to the common fold by opening the barrel and insertion of beta-hairpin
              1. Muscle fatty acid binding protein (m-fabp) [50848]
                 1. Human (Homo sapiens) [TaxId: 9606] [50849] (5)
                 2. Cow (Bos taurus) [TaxId: 9913] [50850] (1)
              2. Intestinal fatty acid binding protein [50851]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50852] (11)
                    SQ P02693
                 2. Human (Homo sapiens) [TaxId: 9606] [50853] (3)
              3. Brain fatty acid binding protein [63809]
                 1. Human (Homo sapiens) [TaxId: 9606] [63810] (3)
              4. Epidermal fatty acid binding protein [50854]
                 1. Human (Homo sapiens) [TaxId: 9606] [50855] (2)
              5. Adipocyte lipid-binding protein, ALBP [50856]
                 1. Mouse (Mus musculus) [TaxId: 10090] [50857] (17)
                 2. Human (Homo sapiens) [TaxId: 9606] [110275] (4)
                    SQ P15090
              6. Fatty acid-binding protein homolog 1 [89366]
                 1. Flat worm (Echinococcus granulosus) [TaxId: 6210] [89367] (1)
              7. Fatty acid-binding protein [50858]
                 1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [50859] (1)
                 2. Desert locust (Schistocerca gregaria) [TaxId: 7010] [50860] (1)
              8. Cellular retinoic-acid-binding protein (CRABP) [50861]
                 1. Human (Homo sapiens), CRABP-II [TaxId: 9606] [50862] (12)
                 2. Cow and mouse (Bos taurus) and (Mus musculus), CRABP-I, identical sequences [TaxId: 9913] [50863] (3)
              9. Cellular retinol-binding protein II (CRBP) [50864]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50865] (9)
                 2. Zebrafish (Danio rerio) [TaxId: 7955] [75000] (2)
              10. Cellular retinol-binding protein III [63811]
                  1. Human (Homo sapiens) [TaxId: 9606] [63812] (1)
              11. Liver fatty acid binding protein [50866]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [50867] (4)
                  2. Human (Homo sapiens) [TaxId: 9606] [141464] (8)
                     SQ P07148 1-127
              12. Liver basic fatty acid binding protein, LB_FABP [89368]
                  1. Chicken (Gallus gallus) [TaxId: 9031] [89369] (5)
                     SQ P80226
                  2. Argentine common toad (Bufo arenarum) [TaxId: 38577] [89370] (1)
                  3. Axolotl (Ambystoma mexicanum) [TaxId: 8296] [141465] (2)
                     SQ P81400 1-125
              13. Cellular retinol-binding protein IV [82157]
                  1. Human (Homo sapiens) [TaxId: 9606] [82158] (1)
              14. P2 myelin protein [50868]
                  1. Cow (Bos taurus), caudal spinal root myelin [TaxId: 9913] [50869] (1)
                  2. Horse (Equus caballus) [TaxId: 9796] [141466] (1)
                     SQ P02690 1-131
              15. Ileal lipid-binding protein [50870]
                  1. Human (Homo sapiens) [TaxId: 9606] [82159] (2)
                  2. Pig (Sus scrofa) [TaxId: 9823] [50871] (2)
              16. Fatty acid-binding protein Sm14 [110276]
                  1. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [110277] (2)
                     SQ P29498
              17. Der f 13 allergen [141467]
                  1. House dust mite (Dermatophagoides farinae) [TaxId: 6954] [141468] (1)
                     SQ Q1M2P5 1-131
           3. Thrombin inhibitor [50872] (1)
              topology permutation: strands 2 and 3 swapped their positions in the barrel
              1. Thrombin inhibitor [50873]
                 1. Triatomine bug (Triatoma pallidipennis) [TaxId: 30077] [50874] (1)
           4. Hypothetical protein YodA [101863] (1)
              bacterial metal-binding, lipocalin-like protein
              1. Hypothetical protein YodA [101864]
                 1. Escherichia coli [TaxId: 562] [101865] (5)
                    SQ P76344
           5. Hypothetical protein YwiB [101866] (1)
              bacterial proteins with a fatty acid binding protein-like fold
              1. Hypothetical protein YwiB [101867]
                 1. Bacillus subtilis [TaxId: 1423] [101868] (1)
           6. Phenolic acid decarboxylase (PAD) [141469] (1)
              Pfam 05870; dimeric enzyme made of lipocalin-like subunits
              1. P-coumaric acid decarboxylase, pdc [141470]
                 1. Lactobacillus plantarum [TaxId: 1590] [141471] (1)
                    SQ Q88RY7 1-178
           7. Dinoflagellate luciferase repeat [141472] (1)
              PfamB 017809; comprises a fatty acid binding protein-like fold, wrapped into the extra N- and C-terminal 'tails'
              1. Dinoflagellate luciferase [141473]
                 1. Lingulodinium polyedrum [TaxId: 160621] [141474] (1)
                    SQ O77206 868-1218
           8. Rv2717c-like [141475] (2)
              bacterial and plant proteins with a fatty acid binding protein-like fold
              1. Hypothetical protein Rv2717c [141476]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141477] (1)
                    SQ O07216 4-164
              2. Hypothetical protein At1g79260 [141478]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141479] (3)
                    SQ O64527 14-166
           9. All1756-like [159230] (1)
              cyanobacterial proteins with duplicated fatty acid binding protein-like domains; N-terminal and C-terminal domains correspond to PfamB 40396 and PfamB 60468, respectively
              1. Uncharacterized protein All1756 ortholog [159231]
                 1. Nostoc punctiforme [TaxId: 272131] [159232] (4)
   105. Streptavidin-like [50875] (8)
        barrel, closed; n=8, S=10; meander
        1. Avidin/streptavidin [50876] (1)
           uperfamily
           1. Avidin/streptavidin [50877] (2)
              1. Streptavidin [50878]
                 1. Streptomyces avidinii [TaxId: 1895] [50879] (122)
              2. Avidin [50880]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [50881] (16)
        2. beta-Barrel protease inhibitors [50882] (2)
           uperfamily
           1. Metalloprotease inhibitor [50883] (2)
              1. Metalloprotease inhibitor [50884]
                 1. Erwinia chrysanthemi [TaxId: 556] [50885] (1)
                 2. Pseudomonas aeruginosa, aprin [TaxId: 287] [63813] (1)
           2. Staphostatin [101869] (2)
              cysteine protease inhibitor; topology permutation: strand 3 is replaced with the N-terminal extra strand
              1. Staphostatin A (SAV1910, SA1726) [101870]
                 1. Staphylococcus aureus [TaxId: 1280] [101871] (1)
              2. Staphostatin B (SspC) [101872]
                 1. Staphylococcus aureus [TaxId: 1280] [101873] (5)
        3. D-aminopeptidase, middle and C-terminal domains [50886] (1)
           uperfamily
           1. D-aminopeptidase, middle and C-terminal domains [50887] (1)
              1. D-aminopeptidase, middle and C-terminal domains [50888]
                 duplication: both domains have this barrel fold
                 1. Ochrobactrum anthropi [TaxId: 529] [50889] (1)
        4. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69298] (1)
           uperfamily
           1. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69299] (2)
              1. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69300]
                 1. Paracoccus denitrificans [TaxId: 266] [69301] (2)
                 2. Pseudomonas putida [TaxId: 303] [69302] (2)
        5. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75001] (1)
           uperfamily
           1. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75002] (2)
              1. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75003]
                 1. Human (Homo sapiens) [TaxId: 9606] [75004] (3)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [82160] (1)
        6. YceI-like [101874] (1)
           uperfamily
           1. YceI-like [101875] (2)
              Pfam 04264
              1. Polyisoprenoid-binding protein TTHA0802 (TT1927B) [101876]
                 1. Thermus thermophilus [TaxId: 274] [101877] (1)
                    SQ P83815
                    structural genomics
              2. Lipid binding protein YceI [117267]
                 1. Escherichia coli [TaxId: 562] [117268] (1)
                    SQ P0A8X2
        7. Extracellular hemoglobin linker subunit, receptor domain [141480] (1)
           uperfamily
           1. Extracellular hemoglobin linker subunit, receptor domain [141481] (3)
              1. Hemoglobin linker chain l1 [141482]
                 1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141483] (1)
                    SQ Q9GV76 127-240
              2. Extracellular hemoglobin linker l3 subunit [141484]
                 1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141485] (1)
                    SQ Q2I742 119-240
              3. Extracellular hemoglobin linker l2 subunit [141486]
                 1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141487] (1)
                    SQ Q2I743 139-299
        8. YdhA-like [141488] (1)
           uperfamily
           1. YdhA-like [141489] (1)
              1. Hypothetical protein YdhA [141490]
                 1. Escherichia coli [TaxId: 562] [141491] (1)
                    SQ P28224 28-109
   106. FomD barrel-like [159233] (1)
        barrel, closed; n=8, S=12; meander; similar topology to the AOC barrel-like fold (reversed to the lipocalin barrel topology)
        1. FomD-like [159234] (1)
           1. FomD-like [159235] (1)
              Pfam 04167; DUF402
              1. Hypothetical protein RHA1_ro00977 [159236]
                 1. Rhodococcus sp. RHA1 [TaxId: 101510] [159237] (2)
                    SQ Q0SI31 8-172
   107. AOC barrel-like [141492] (2)
        barrel, closed; n=8, S=10; meander; mirrored (reversed) topology to the Spreptavidin-like and Lipocalin-like folds
        1. Allene oxide cyclase-like [141493] (1)
           uperfamily
           1. Allene oxide cyclase-like [141494] (2)
              Pfam 06351
              1. Allene oxide cyclase, AOC [141495]
                 1. Thale cress (Arabidopsis thaliana), chloroplast AOC2 [TaxId: 3702] [141496] (18)
                    SQ Q9LS02 80-253
                 2. Thale cress (Arabidopsis thaliana), chloroplast AOC1 [TaxId: 3702] [141497] (1)
                    SQ Q9LS03 81-254
        2. SO1590-like [159238] (1)
           1. SO1590-like [159239] (2)
              1. Hypothetical protein SO1590 [159240]
                 1. Shewanella oneidensis [TaxId: 70863] [159241] (2)
                    SQ Q8EGL1 2-134
              2. Uncharacterized protein Sden_2034 [159242]
                 1. Shewanella denitrificans [TaxId: 192073] [159243] (2)
                    SQ Q12ML0 5-137
   108. AttH-like [159244] (1)
        duplication: two flattened beta-barrels of lipocalin-like topology are orthogonally packed with a pseudo twofold symmetry
        1. AttH-like [159245] (1)
           1. AttH-like [159246] (1)
              Pfam 09410; DUF2006
              1. AttH-related protein NE1406 [159247]
                 1. Nitrosomonas europaea [TaxId: 915] [159248] (2)
                    SQ Q82US3 24-351
   109. Cyclophilin-like [50890] (1)
        barrel, closed; n=8, S=10; complex topology
        1. Cyclophilin-like [50891] (4)
           uperfamily
           1. Cyclophilin (peptidylprolyl isomerase) [50892] (25)
              1. Cyclophilin (eukaryotic) [50893]
                 1. Human (Homo sapiens), variant A [TaxId: 9606] [50894] (50)
                    SQ P05092
                 2. Human (Homo sapiens), variant B [TaxId: 9606] [50895] (1)
                 3. Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606] [50896] (2)
                 4. Mouse (Mus musculus), variant C [TaxId: 10090] [50897] (1)
                 5. Nematode (Brugia malayi) [TaxId: 6279] [50898] (3)
                 6. Caenorhabditis elegans, isoform 3 [TaxId: 6239] [50899] (5)
                 7. Caenorhabditis elegans, isoform 5 [TaxId: 6239] [82161] (1)
                 8. Plasmodium falciparum [TaxId: 5833] [50900] (2)
                 9. Baker's yeast (Saccharomyces cerevisiae), variant A [TaxId: 4932] [101878] (2)
                 10. Trypanosoma cruzi [TaxId: 5693] [117269] (2)
                     SQ Q4DPB9 30-194
                 11. Human (Homo sapiens), variant C [TaxId: 9606] [141498] (6)
                     SQ P45877 32-212
                 12. Aspergillus fumigatus [TaxId: 5085] [141499] (2)
                     SQ Q9Y7F6 8-178
                 13. Plasmodium yoelii [TaxId: 5861] [141500] (1)
                     SQ Q7RSH5 25-210
              2. Cyclophilin 40 isomerase domain [63814]
                 the other domain is formed by TPR repeats
                 1. Cow (Bos taurus) [TaxId: 9913] [63815] (2)
              3. Peptidyl-prolyl cis-trans isomerase A, PpiA [50901]
                 1. Escherichia coli [TaxId: 562] [50902] (6)
                    SQ P20752
                 2. Mycobacterium tuberculosis [TaxId: 1773] [117270] (1)
                    SQ P65762
              4. Cyclophilin-like allergen Mal s 6 [141501]
                 1. Malassezia sympodialis [TaxId: 76777] [141502] (1)
                    SQ O93970 1-162
              5. Peptidyl-prolyl cis-trans isomerase E, PPIE, C-terminal domain [141503]
                 N-terminal domain belongs to the RBD family (scop_fa 54929)
                 1. Human (Homo sapiens) [TaxId: 9606] [141504] (1)
                    SQ Q9UNP9 138-301
                    structure of the N-terminal RBD is known, PDB 2cqb
              6. Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain [141505]
                 1. Human (Homo sapiens) [TaxId: 9606] [141506] (2)
                    SQ Q13356 280-457
              7. Cyclophilin-like protein PY00693 [141507]
                 1. Plasmodium yoelii [TaxId: 5861] [141508] (1)
                    SQ Q7RRM6 29-197
              8. Cyclophilin-like protein PPIL3B [141509]
                 1. Human (Homo sapiens) [TaxId: 9606] [141510] (4)
                    SQ Q9H2H8 1-160
              9. Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F [141511]
                 1. Human (Homo sapiens) [TaxId: 9606] [141512] (5)
                    SQ P30405 44-207
              10. Putative cyclophilin PFE0505w [141513]
                  PPWD1 homologue
                  1. Plasmodium falciparum [TaxId: 5833] [141514] (1)
                     SQ Q8I402 592-746
              11. Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain [141515]
                  1. Human (Homo sapiens) [TaxId: 9606] [141516] (3)
                     SQ Q96BP3 483-646
              12. Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 [141517]
                  1. Human (Homo sapiens) [TaxId: 9606] [141518] (1)
                     SQ Q9Y3C6 1-166
           2. Outer surface protein, C-terminal domain [110278] (1)
              lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 05913
              1. Outer surface protein, C-terminal domain [110279]
                 1. Bacillus cereus [TaxId: 1396] [110280] (1)
                    SQ Q81HJ5
           3. TM1367-like [141519] (1)
              Pfam 04126; DUF369
              1. Hypothetical protein TM1367 [141520]
                 1. Thermotoga maritima [TaxId: 2336] [141521] (3)
                    SQ Q9X187 1-124
           4. PH0987 C-terminal domain-like [159249] (1)
              lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
              1. Uncharacterized protein PH0987 [159250]
                 1. Pyrococcus horikoshii [TaxId: 53953] [159251] (1)
                    SQ O58715 86-217
   110. Oncogene products [50903] (1)
        barrel, closed; n=8, S=10; one overside connection
        1. Oncogene products [50904] (1)
           duplication: N- and C-terminal halves are related by pseudo dyad
           uperfamily
           1. Oncogene products [50905] (3)
              1. p14-TCL1 [50906]
                 an oncogene product involved in T-cell prolymphocytic leukemia
                 1. Human (Homo sapiens) [TaxId: 9606] [50907] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [69303] (1)
              2. p13-MTCP1 [50908]
                 involved in T cell malignancies
                 1. Human (Homo sapiens) [TaxId: 9606] [50909] (3)
   111. L,D-transpeptidase catalytic domain-like [141522] (1)
        barrel, closed; n=8, S=10; one overside connection
        1. L,D-transpeptidase catalytic domain-like [141523] (1)
           uperfamily
           1. L,D-transpeptidase catalytic domain-like [141524] (2)
              Pfam 03734; ErfK/YbiS/YcfS/YnhG
              1. L,D-transpeptidase, C-terminal, catalytic domain [141525]
                 1. Enterococcus faecium [TaxId: 1352] [141526] (1)
                    SQ Q3Y185 339-466
              2. Hypothetical protein YkuD, C-terminal domain [141527]
                 1. Bacillus subtilis [TaxId: 1423] [141528] (2)
                    SQ O34816 49-164
   112. Sortase [63816] (1)
        barrel, closed; n=8, S=10; mixed sheet; two overside connections
        1. Sortase [63817] (1)
           uperfamily
           1. Sortase [63818] (3)
              1. Sortase A [63819]
                 1. Staphylococcus aureus [TaxId: 1280] [63820] (4)
                    SQ Q9S446 61-206
              2. Sortase B [101879]
                 1. Staphylococcus aureus [TaxId: 1280] [101880] (4)
              3. Hypothetical protein BA4783 [110281]
                 1. Bacillus anthracis [TaxId: 1392] [110282] (3)
                    SQ Q81L49
   113. PTSIIA/GutA-like [141529] (1)
        barrel, closed; n=8, S=12; mixed sheet; two overside connections; duplication: consists of two intertwinned structural repeats
        1. PTSIIA/GutA-like [141530] (1)
           uperfamily
           1. PTSIIA/GutA-like [141531] (1)
              Pfam 03829
              1. PTS system, IIa component (PTSIIA) [141532]
                 1. Enterococcus faecalis [TaxId: 1351] [141533] (2)
                    SQ Q831B0 3-123
                    EF2603
   114. Mannose 6-phosphate receptor domain [50910] (1)
        barrel, partly open; n*=8, S*=10; one psi loop
        1. Mannose 6-phosphate receptor domain [50911] (1)
           uperfamily
           1. Mannose 6-phosphate receptor domain [50912] (3)
              1. Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain [50913]
                 1. Cow (Bos taurus) [TaxId: 9913] [50914] (15)
              2. Cation-independent mannose-6-phosphate receptor (MIR-receptor) [63821]
                 1. Human (Homo sapiens) [TaxId: 9606] [63822] (5)
                 2. Cow (Bos taurus) [TaxId: 9913] [110283] (3)
                    SQ P08169 49-476
   115. triple barrel [50915] (1)
        dimer of two non-identical subunits; forms two similar barrels, n=8, S=10 each, that are fused together with the formation of third barrel, n=6, S=8
        1. Rap30/74 interaction domains [50916] (1)
           uperfamily
           1. Rap30/74 interaction domains [50917] (2)
              1. TFIIF beta subunit, Rap30 [50918]
                 1. Human (Homo sapiens) [TaxId: 9606] [50919] (1)
              2. TFIIF alpha subunit, Rap74 [50920]
                 1. Human (Homo sapiens) [TaxId: 9606] [50921] (1)
   116. 4-bladed beta-propeller [50922] (1)
        consists of four 4-stranded beta-sheet motifs; meander
        1. Hemopexin-like domain [50923] (1)
           uperfamily
           1. Hemopexin-like domain [50924] (6)
              1. Hemopexin [50925]
                 duplication: consists of two domains of this fold
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [50926] (3)
              2. Gelatinase A (MMP-2), C-terminal domain [50927]
                 1. Human (Homo sapiens) [TaxId: 9606] [50928] (4)
              3. Gelatinase B (MMP-9) [82162]
                 1. Human (Homo sapiens) [TaxId: 9606] [82163] (1)
              4. Collagenase (MMP1), C-terminal domain [50929]
                 1. Pig (Sus scrofa) [TaxId: 9823] [50930] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [117271] (1)
                    SQ P03956 32-466
              5. Collagenase-3 (MMP-13), C-terminal domain [50931]
                 1. Human (Homo sapiens) [TaxId: 9606] [50932] (1)
   117. 5-bladed beta-propeller [50933] (3)
        consists of five 4-stranded beta-sheet motifs; meander
        1. Tachylectin-2 [50934] (1)
           uperfamily
           1. Tachylectin-2 [50935] (1)
              1. Tachylectin-2 [50936]
                 1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [50937] (1)
        2. Arabinanase/levansucrase/invertase [75005] (5)
           uperfamily
           1. alpha-L-arabinanase-like [75006] (7)
              1. alpha-L-arabinanase [75007]
                 1. Cellvibrio cellulosa [TaxId: 155077] [75008] (3)
              2. Arabinanase-TS [141534]
                 1. Bacillus thermodenitrificans [TaxId: 33940] [141535] (1)
                    SQ Q93HT9 1-312
              3. Endo-1,5-arabinanase [141536]
                 1. Bacillus subtilis [TaxId: 1423] [141537] (1)
                    SQ Q5MPF4 33-323
              4. Beta-D-xylosidase N-terminal domain [141538]
                 1. Geobacillus stearothermophilus [TaxId: 1422] [141539] (16)
                    SQ Q68HB3 3-324
                 2. Bacillus subtilis [TaxId: 1423] [141540] (4)
                    SQ P94489 2-324
                 3. Bacillus halodurans [TaxId: 86665] [141541] (2)
                    SQ Q9K6P5 4-320
                 4. Clostridium acetobutylicum [TaxId: 1488] [141542] (8)
                    SQ Q97DM1 2-322
           2. Levansucrase [101881] (1)
              1. Levansucrase [101882]
                 1. Bacillus subtilis [TaxId: 1423] [101883] (4)
           3. Glycosyl hydrolases family 32 N-terminal domain [101884] (2)
              Pfam 00251; Glycosyl hydrolase family 32
              1. Beta-fructosidase (invertase), N-terminal domain [101885]
                 1. Thermotoga maritima [TaxId: 2336] [101886] (7)
              2. Exo-inulinase [117272]
                 1. Aspergillus awamori [TaxId: 105351] [117273] (3)
                    SQ Q96TU3 20-536
           4. TM1225-like predicted glycosylases [110284] (1)
              Pfam 04041 DUF377
              1. Hypothetical protein TM1225 [110285]
                 1. Thermotoga maritima [TaxId: 2336] [110286] (1)
                    SQ Q9X0V2
           5. LmjF10.1260-like [141543] (1)
              1. Hypothetical protein LmjF10.1260 [141544]
                 1. Leishmania major [TaxId: 5664] [141545] (1)
                    SQ Q4QH86 2-311
        3. Apyrase [101887] (1)
           distorted propeller with an alpha helix inserted between the second and third blades
           uperfamily
           1. Apyrase [101888] (1)
              Pfam 06079
              1. Soluble calcium-activated nucleotidase SCAN-1 [101889]
                 1. Human (Homo sapiens) [TaxId: 9606] [101890] (4)
   118. 6-bladed beta-propeller [50938] (11)
        consists of six 4-stranded beta-sheet motifs; meander
        1. Sialidases [50939] (2)
           uperfamily
           1. Sialidases (neuraminidases) [50940] (11)
              1. Salmonella sialidase [50941]
                 1. Salmonella typhimurium, strain lt2 [TaxId: 90371] [50942] (5)
              2. Influenza neuraminidase [50943]
                 1. Influenza A virus, different strains [TaxId: 11320] [50944] (59)
                    SQ P03472 84-470
                 2. Influenza B virus, different strains [TaxId: 11520] [50945] (12)
              3. Paramyxovirus hemagglutinin-neuraminidase head domain [63823]
                 1. Newcastle disease virus [TaxId: 11176] [63824] (5)
              4. Hemagglutinin-neuraminidase glycoprotein [101891]
                 1. Human parainfluenza virus type 3 [TaxId: 11216] [101892] (5)
              5. Micromonospora sialidase, N-terminal domain [50946]
                 1. Micromonospora viridifaciens [TaxId: 1881] [50947] (10)
                    SQ Q02834 47-647
              6. Leech intramolecular trans-sialidase, C-terminal domain [50948]
                 contains incomplete beta-barrel subdomain inserted in the second blade
                 1. North american leech (Macrobdella decora) [TaxId: 6405] [50949] (5)
              7. Vibrio cholerae sialidase [50950]
                 contains 2 additional domains of ConA-like fold
                 1. Vibrio cholerae [TaxId: 666] [50951] (3)
                    SQ P37060
              8. Trypanosoma sialidase [82164]
                 1. Parasitic flagellate protozoan (Trypanosoma cruzi) [TaxId: 5693] [89371] (12)
                    SQ Q26966
                 2. Trypanosoma rangeli [TaxId: 5698] [82165] (10)
                    SQ O44049 20-653
              9. Sialidase 2 (Neu2) [117274]
                 1. Human (Homo sapiens) [TaxId: 9606] [117275] (8)
                    SQ Q9Y3R4
           2. Endo-alpha-sialidase [117276] (1)
              possibly related by the other family by circular permutation; includes extra N-terminal domain [dN: alpha/beta ] and insert domain [dI: beta-barrel, similar to the Reductase/isomerase/elongation factor common domain (scop_cf 50412)]
              1. Endo-alpha-sialidase [117277]
                 1. Bacteriophage K1F [TaxId: 344021] [117278] (2)
                    SQ Q04830 245-909
        2. Soluble quinoprotein glucose dehydrogenase [50952] (1)
           uperfamily
           1. Soluble quinoprotein glucose dehydrogenase [50953] (1)
              1. Soluble quinoprotein glucose dehydrogenase [50954]
                 1. Acinetobacter calcoaceticus [TaxId: 471] [50955] (4)
        3. Thermostable phytase (3-phytase) [50956] (1)
           uperfamily
           1. Thermostable phytase (3-phytase) [50957] (1)
              1. Thermostable phytase (3-phytase) [50958]
                 1. Bacillus amyloliquefaciens [TaxId: 1390] [50959] (5)
        4. TolB, C-terminal domain [50960] (1)
           uperfamily
           1. TolB, C-terminal domain [50961] (1)
              1. TolB, C-terminal domain [50962]
                 1. Escherichia coli [TaxId: 562] [50963] (10)
        5. YWTD domain [63825] (1)
           uperfamily
           1. YWTD domain [63826] (2)
              1. Low density lipoprotein (LDL) receptor [63827]
                 1. Human (Homo sapiens) [TaxId: 9606] [63828] (2)
              2. Nidogen [101893]
                 1. Mouse (Mus musculus) [TaxId: 10090] [101894] (1)
        6. Calcium-dependent phosphotriesterase [63829] (3)
           uperfamily
           1. SGL-like [63830] (3)
              1. Diisopropylfluorophosphatase (phosphotriesterase, DFP) [63831]
                 1. Squid (Loligo vulgaris) [TaxId: 6622] [63832] (4)
                    SQ Q7SIG4
              2. Lactonase Drp35 [141546]
                 1. Staphylococcus aureus [TaxId: 1280] [141547] (24)
                    SQ Q7A338 5-324! SQ Q99QV3 5-324
              3. Regucalcin [141548]
                 Agr_c_1268p/Atu0702
                 1. Agrobacterium tumefaciens [TaxId: 358] [141549] (1)
                    SQ Q7D0W3 20-314
           2. Serum paraoxonase/arylesterase 1, PON1 [101895] (1)
              1. Serum paraoxonase/arylesterase 1, PON1 [101896]
                 1. Rabit (Oryctolagus cuniculus) [TaxId: 9986] [101897] (1)
           3. All0351-like [159252] (1)
              N-terminal half is PfamB 89298 and C-terminal half is PfamB 80276; includes recent entry 2qe8 (Ava4197)
              1. Hypothetical protein All0351 homologue [159253]
                 1. Nostoc punctiforme [TaxId: 272131] [159254] (1)
        7. Tricorn protease N-terminal domain [69304] (1)
           possibly related to the second domain of tricorn protease (a distorted 7-bladed beta-propeller)
           uperfamily
           1. Tricorn protease N-terminal domain [69305] (1)
              1. Tricorn protease N-terminal domain [69306]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69307] (4)
        8. Fucose-specific lectin [89372] (1)
           uperfamily
           1. Fucose-specific lectin [89373] (1)
              1. Fucose-specific lectin [89374]
                 1. Orange peel mushroom (Aleuria aurantia) [TaxId: 5188] [89375] (3)
        9. NHL repeat [101898] (1)
           uperfamily
           1. NHL repeat [101899] (2)
              Pfam 01436
              1. Brain tumor cg10719-pa [101900]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101901] (1)
              2. Serine/threonine-protein kinase PknD [101902]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [101903] (2)
        10. GyrA/ParC C-terminal domain-like [101904] (1)
            beta-pinwheel, a variant of beta-propeller fold; unlike an canonical beta-propeller, strands 1 and 4 of each four-strand repeat unit are in one blade whereas strands 2 and 3 are in the next blade
            uperfamily
            1. GyrA/ParC C-terminal domain-like [101905] (2)
               Pfam 03989; functional conformational changes result in breaking the interface between the N- and C-terminal blades
               1. DNA gyrase A C-terminal domain [101906]
                  1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [101907] (1)
               2. Topoisomerase IV subunit A, ParC, C-terminal domain [117279]
                  1. Bacillus stearothermophilus [TaxId: 1422] [117280] (1)
                     SQ Q45066 499-805 # 63% sequence identity; Bacillus subtilis TaxID: 1423
        11. Kelch motif [117281] (1)
            uperfamily
            1. Kelch motif [117282] (2)
               Pfam 01344; sequence motif corresponding to one beta-sheet blade; similar sequences are found in the Galactose oxidase 7-bladed beta-propeller domain (scop_pr 50967)
               1. Kelch-like ECH-associated protein 1, KEAP1 [117283]
                  1. Human (Homo sapiens) [TaxId: 9606] [117284] (3)
                     SQ Q14145 322-609
                  2. Mouse (Mus musculus) [TaxId: 10090] [141550] (4)
                     SQ Q9Z2X8 324-613
   119. 7-bladed beta-propeller [50964] (14)
        consists of seven 4-stranded beta-sheet motifs; meander
        1. Galactose oxidase, central domain [50965] (1)
           uperfamily
           1. Galactose oxidase, central domain [50966] (3)
              1. Galactose oxidase, central domain [50967]
                 N-terminal domain is a jelly-roll sandwich
                 C-terminal domain is Immunoglobulin-like
                 1. Dactylium dendroides [TaxId: 5132] [50968] (8)
                    SQ Q01745 42-680
                 2. Fungi (Fusarium sp.) [TaxId: 29916] [69308] (1)
                    sequence identical to that of Dactylium dendroides
                 3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [159255] (3)
        2. YVTN repeat-like/Quinoprotein amine dehydrogenase [50969] (3)
           uperfamily
           1. YVTN repeat [82166] (1)
              more regular propeller with clear sequence repeats
              1. Surface layer protein [82167]
                 1. Archaeon Methanosarcina mazei [TaxId: 2209] [82168] (1)
           2. Quinohemoprotein amine dehydrogenase B chain [69309] (2)
              less regular propeller with imperfect sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
              1. Quinohemoprotein amine dehydrogenase B chain [69310]
                 1. Paracoccus denitrificans [TaxId: 266] [69311] (2)
                 2. Pseudomonas putida [TaxId: 303] [69312] (2)
           3. Methylamine dehydrogenase, H-chain [50970] (2)
              less regular propeller without notable sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
              1. Methylamine dehydrogenase, H-chain [50971]
                 1. Paracoccus denitrificans [TaxId: 266] [50972] (21)
                 2. Gram negative methylotrophic bacteria (Thiobacillus versutus) [TaxId: 34007] [50973] (3)
        3. Nitrous oxide reductase, N-terminal domain [50974] (1)
           uperfamily
           1. Nitrous oxide reductase, N-terminal domain [50975] (2)
              1. Nitrous oxide reductase, N-terminal domain [50976]
                 1. Pseudomonas nautica [TaxId: 2743] [50977] (1)
                 2. Paracoccus denitrificans [TaxId: 266] [63833] (1)
        4. WD40 repeat-like [50978] (2)
           also contains 8-bladed propellers
           uperfamily
           1. WD40-repeat [50979] (12)
              1. beta1-subunit of the signal-transducing G protein heterotrimer [50980]
                 1. Cow (Bos taurus) [TaxId: 9913] [50981] (11)
                 2. Homo sapiens [TaxId: 9606] [159256] (1)
              2. Tup1, C-terminal domain [50983]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50984] (1)
              3. Groucho/tle1, C-terminal domain [75009]
                 1. Human (Homo sapiens) [TaxId: 9606] [75010] (9)
              4. Arp2/3 complex 41 kDa subunit ARPC1 [69313]
                 1. Cow (Bos taurus) [TaxId: 9913] [69314] (10)
                    SQ Q58CQ2
              5. Cdc4 propeller domain [82169]
                 8-bladed beta-propeller without perfect 8-fold symmetry
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82170] (1)
              6. F-box/WD-repeat protein 1 (beta-TRCP1) [89376]
                 1. Human (Homo sapiens) [TaxId: 9606] [89377] (1)
              7. Actin interacting protein 1 [89378]
                 14 repeats are arranged into two seven-bladed beta-propeller domains swapped with the N-terminal strands
                 1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89379] (2)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89380] (2)
              8. Antiviral protein Ski8 (Ski8p) [110287]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110288] (2)
                    SQ Q02793
              9. Platelet-activating factor acetylhydrolase IB subunit alpha [159257]
                 1. Mouse (Mus musculus) [TaxId: 10090] [159258] (10)
                    SQ P43034 91-407
              10. F-box/WD repeat-containing protein 7, FBXW7 [159259]
                  1. Human (Homo sapiens) [TaxId: 9606] [159260] (3)
                     SQ Q969H0 365-706
           2. Cell cycle arrest protein BUB3 [110289] (1)
              possibly related to the WD-repeat family; both sequence similarity between the blades and the WD40 repeat signature are very weak
              1. Cell cycle arrest protein BUB3 [110290]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110291] (9)
                    SQ P26449
        5. RCC1/BLIP-II [50985] (2)
           two families are clearly related but differ by the number of strands per blade
           uperfamily
           1. Regulator of chromosome condensation RCC1 [50986] (1)
              1. Regulator of chromosome condensation RCC1 [50987]
                 1. Human (Homo sapiens) [TaxId: 9606] [50988] (2)
           2. beta-lactamase inhibitor protein-II, BLIP-II [69315] (1)
              lacks the outer strands
              1. beta-lactamase inhibitor protein-II, BLIP-II [69316]
                 1. Streptomyces exfoliatus [TaxId: 1905] [69317] (1)
        6. Clathrin heavy-chain terminal domain [50989] (1)
           uperfamily
           1. Clathrin heavy-chain terminal domain [50990] (1)
              1. Clathrin heavy-chain terminal domain [50991]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [50992] (4)
        7. Integrin alpha N-terminal domain [69318] (1)
           uperfamily
           1. Integrin alpha N-terminal domain [69319] (2)
              1. Integrin alpha N-terminal domain [69320]
                 1. Human (Homo sapiens), isoform V [TaxId: 9606] [69321] (4)
                    SQ P06756 31-986
                 2. Human (Homo sapiens), isoform IIb [TaxId: 9606] [117285] (1)
                    SQ P08514 32-483
        8. Peptidase/esterase 'gauge' domain [50993] (2)
           uperfamily
           1. Prolyl oligopeptidase, N-terminal domain [50994] (1)
              1. Prolyl oligopeptidase, N-terminal domain [50995]
                 1. Pig (Sus scrofa) [TaxId: 9823] [50996] (16)
                    SQ P23687
           2. Acylamino-acid-releasing enzyme, N-terminal donain [117286] (1)
              1. Acylamino-acid-releasing enzyme, N-terminal donain [117287]
                 1. Aeropyrum pernix [TaxId: 56636] [117288] (12)
                    SQ Q9YBQ2
        9. Tricorn protease domain 2 [69322] (1)
           distorted 7-bladed beta-propeller fold; possibly related to the N-terminal domain of tricorn protease (a 6-bladed beta-propeller)
           uperfamily
           1. Tricorn protease domain 2 [69323] (1)
              1. Tricorn protease domain 2 [69324]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69325] (4)
        10. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75011] (1)
            uperfamily
            1. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75012] (1)
               1. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75013]
                  1. Neurospora crassa [TaxId: 5141] [75014] (1)
        11. Putative isomerase YbhE [101908] (1)
            uperfamily
            1. Putative isomerase YbhE [101909] (1)
               1. Putative isomerase YbhE [101910]
                  1. Escherichia coli [TaxId: 562] [101911] (1)
        12. Sema domain [101912] (1)
            irregular 7-bladed beta-propeller with a large insertion in the fifth blade
            uperfamily
            1. Sema domain [101913] (3)
               Pfam 01403
               1. Semaphorin 4d [101914]
                  1. Human (Homo sapiens) [TaxId: 9606] [101915] (1)
               2. Hepatocyte growth factor receptor [110292]
                  1. Human (Homo sapiens) [TaxId: 9606] [110293] (1)
                     SQ P08581 40-564
               3. Semaphorin 3a [110294]
                  1. Mouse (Mus musculus) [TaxId: 10090] [110295] (1)
                     SQ O08665 26-520
        13. Oligoxyloglucan reducing end-specific cellobiohydrolase [110296] (1)
            duplication: # two beta-propeller domains are swapped with the N-terminal strands; similar domain arrangment to the Actin interacting protein 1 (scop_pr 89378)
            uperfamily
            1. Oligoxyloglucan reducing end-specific cellobiohydrolase [110297] (1)
               contains at least 9 BNR/Asp-box repeats (Pfam 02012) usually associated with the 6-bladed propeller Neuraminidases (scop_sf 50939)
               1. Oligoxyloglucan reducing end-specific cellobiohydrolase [110298]
                  1. Yeast (Geotrichum sp. M128) [TaxId: 203496] [110299] (5)
                     SQ Q8J0D2
        14. Nucleoporin domain [117289] (1)
            uperfamily
            1. Nucleoporin domain [117290] (2)
               1. Nuclear pore complex protein Nup133 [117291]
                  1. Human (Homo sapiens) [TaxId: 9606] [117292] (1)
                     SQ Q8WUM0 75-477
               2. Nucleoporin NUP159 [117293]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117294] (1)
                     SQ P40477 2-381
   120. 8-bladed beta-propeller [50997] (3)
        consists of eight 4-stranded beta-sheet motifs; meander
        also found in some members of the WD40-repeat superfamily
        1. Quinoprotein alcohol dehydrogenase-like [50998] (1)
           uperfamily
           1. Quinoprotein alcohol dehydrogenase-like [50999] (6)
              1. Methanol dehydrogenase, heavy chain [51000]
                 1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51001] (8)
                 2. Methylobacterium extorquens [TaxId: 408] [63834] (3)
                    SQ P16027
                 3. Paracoccus denitrificans [TaxId: 266] [101916] (1)
              2. Ethanol dehydrogenase [51002]
                 1. Pseudomonas aeruginosa [TaxId: 287] [51003] (1)
              3. Quinoprotein alcohol dehydrogenase, N-terminal domain [69326]
                 fused with the C-terminal cytochrome c domain
                 1. Comamonas testosteroni [TaxId: 285] [69327] (1)
                 2. Pseudomonas putida, hk5 [TaxId: 303] [75015] (1)
        2. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51004] (1)
           uperfamily
           1. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51005] (3)
              1. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51006]
                 the N-terminal domain is cytochrome c-like
                 1. Paracoccus pantotrophus [TaxId: 82367] [51007] (12)
                    formerly Thiosphaera pantotropha
                 2. Pseudomonas aeruginosa [TaxId: 287] [51008] (9)
                 3. Paracoccus denitrificans [TaxId: 266] [51009] (2)
        3. DPP6 N-terminal domain-like [82171] (1)
           uperfamily
           1. DPP6 N-terminal domain-like [82172] (3)
              Pfam 00930
              1. Dipeptidyl peptidase IV/CD26, N-terminal domain [82173]
                 1. Human (Homo sapiens) [TaxId: 9606] [82174] (58)
                    SQ P27487 39-776 ! SQ P27487 ! SQ P27487
                 2. Pig (Sus scrofa) [TaxId: 9823] [89381] (76)
              2. Dipeptidyl aminopeptidase-like protein 6, DPP6, N-terminal domain [117295]
                 1. Human (Homo sapiens) [TaxId: 9606] [117296] (1)
                    SQ P42658 127-849
   121. Glycosyl hydrolase domain [51010] (1)
        folded sheet; greek-key
        1. Glycosyl hydrolase domain [51011] (5)
           this domain is C-terminal to the catalytic beta/alpha barrel domain
           uperfamily
           1. alpha-Amylases, C-terminal beta-sheet domain [51012] (46)
              this domain follows the catalytic beta/alpha barrel domain
              1. Bacterial alpha-Amylase [51013]
                 1. Bacillus licheniformis [TaxId: 1402] [51014] (8)
                 2. Pseudoalteromonas haloplanktis (Alteromonas haloplanktis) [TaxId: 228] [51015] (9)
                 3. Bacillus subtilis [TaxId: 1423] [51016] (2)
                    SQ P00691
                 4. Bacillus stearothermophilus [TaxId: 1422] [51017] (1)
                 5. Bacillus sp., ksm-k38 [TaxId: 1409] [89382] (6)
                 6. Archaeon Pyrococcus woesei [TaxId: 2262] [89383] (3)
                 7. Bacillus sp. 707 [TaxId: 1416] [117297] (4)
                    SQ P19571 38-518
                 8. Bacillus halmapalus [TaxId: 79882] [141551] (3)
                    SQ P19571 432-518
                 9. Halothermothrix orenii [TaxId: 31909] [141552] (1)
                    SQ Q8GPL8 437-515
              2. Maltosyltransferase [63835]
                 1. Thermotoga maritima [TaxId: 2336] [63836] (2)
              3. Cyclodextrin glycosyltransferase [51018]
                 contains two more all-beta domains in C-terminal region, Immunoglobulin-like and trasthyretin-like
                 1. Bacillus circulans, different strains [TaxId: 1397] [51019] (36)
                 2. Bacillus stearothermophilus [TaxId: 1422] [51020] (1)
                 3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [51021] (2)
                 4. Bacillus sp., strain 1011 [TaxId: 1409] [51022] (8)
                    SQ P05618
                 5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [51023] (2)
                 6. Thermoanaerobacterium [TaxId: 28895] [159261] (2)
              4. Animal alpha-amylase [51024]
                 1. Pig (Sus scrofa) [TaxId: 9823] [51025] (14)
                 2. Human (Homo sapiens) [TaxId: 9606] [51026] (43)
                    SQ P04746 16-511 ! SQ 04746
                 3. Yellow mealworm (Tenebrio molitor), larva [TaxId: 7067] [51027] (4)
              5. Fungal alpha-amylase [51028]
                 1. Aspergillus niger, acid amylase [TaxId: 5061] [51029] (1)
                 2. Aspergillus oryzae, Taka-amylase [TaxId: 5062] [51030] (8)
              6. Maltogenic amylase [51031]
                 1. Thermus sp. [TaxId: 275] [51032] (2)
                 2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [75016] (1)
                 3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [75017] (9)
                 4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [51033] (25)
              7. Neopullulanase [82175]
                 homologous to Maltogenic amylase
                 1. Bacillus stearothermophilus [TaxId: 1422] [82176] (4)
              8. Cyclomaltodextrinase [101917]
                 protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
                 1. Flavobacterium sp. 92 [TaxId: 197856] [101918] (1)
              9. Maltooligosyl trehalose synthase [82177]
                 1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82178] (1)
              10. Glycosyltrehalose trehalohydrolase [51034]
                  1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [51035] (2)
                  2. Deinococcus radiodurans [TaxId: 1299] [141553] (9)
                     SQ Q9RX51 529-600
              11. 1,4-alpha-glucan branching enzyme [82179]
                  1. Escherichia coli [TaxId: 562] [82180] (1)
              12. Isoamylase [51036]
                  1. Pseudomonas amyloderamosa [TaxId: 32043] [51037] (1)
              13. G4-amylase (1,4-alpha-D-glucan maltotetrahydrolase) [51038]
                  single beta-sheet; probable result of a decay of the common-fold
                  1. Pseudomonas stutzeri [TaxId: 316] [51039] (9)
              14. Plant alpha-amylase [51040]
                  single beta-sheet; probable result of a decay of the common-fold
                  1. Barley (Hordeum vulgare), seeds, AMY2 isozyme [TaxId: 4513] [51041] (3)
                  2. Barley (Hordeum vulgare), AMY1 isozyme [TaxId: 4513] [89384] (10)
              15. 4-alpha-glucanotransferase [75018]
                  1. Thermotoga maritima [TaxId: 2336] [75019] (2)
              16. Oligo-1,6-glucosidase [51042]
                  1. Bacillus cereus [TaxId: 1396] [51043] (1)
              17. Isomaltulose synthase PalI [89385]
                  1. Klebsiella sp., lx3 [TaxId: 576] [89386] (1)
              18. Amylosucrase [69328]
                  1. Neisseria polysaccharea [TaxId: 489] [69329] (10)
              19. Melibiase [75020]
                  1. Chicken (Gallus gallus) [TaxId: 9031] [75021] (2)
                     alpha-N-acetylgalactosaminidase
                  2. Rice (Oryza sativa) [TaxId: 4530] [89387] (1)
                     alpha-galactosidase
                  3. Human (Homo sapiens) [TaxId: 9606] [101919] (2)
                     alpha-galactosidase A
                  4. Trichoderma reesei [TaxId: 51453] [110300] (2)
                     SQ Q92456; Alpha-galactosidase agl1;
              20. A4 beta-galactosidase [82181]
                  the catalytic domain of this protein is similar to that of the bacterial beta-amylase
                  1. Thermus thermophilus [TaxId: 274] [82182] (2)
              21. Sucrose phosphorylase [101920]
                  single beta-sheet; probable result of a decay of the common-fold
                  1. Bifidobacterium adolescentis [TaxId: 1680] [101921] (5)
              22. Pullulanase PulA [159262]
                  1. Klebsiella pneumoniae [TaxId: 573] [159263] (3)
                     SQ P07206 973-1090
           2. Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 [89388] (6)
              interrupted by the catalytic domain; the C-terminal core is similar to the alpha-amylase domain
              1. Glucosylceramidase [89389]
                 glycosyl hydrolase family 30; the N-terminal extension wraps around the C-terminal core
                 1. Human (Homo sapiens) [TaxId: 9606] [89390] (27)
              2. Glycosyl hydrolase family 5 xylanase [101922]
                 1. Erwinia chrysanthemi [TaxId: 556] [101923] (1)
              3. Alpha-l-arabinofuranosidase [101924]
                 glycosyl hydrolase family 51
                 1. Bacillus stearothermophilus [TaxId: 1422] [101925] (4)
                 2. Clostridium thermocellum [TaxId: 1515] [141554] (12)
                    SQ Q4CJG5 2-16,387-502
              4. Beta-D-xylosidase [101926]
                 glycosyl hydrolase family 39
                 1. Thermoanaerobacterium saccharolyticum [TaxId: 28896] [101927] (2)
                 2. Bacillus stearothermophilus [TaxId: 1422] [141555] (24)
                    SQ Q9ZFM2 5-14,362-503
           3. Putative alpha-L-fucosidase C-terminal domain [101928] (1)
              glycosyl hydrolase family 29; beta-sheet forms a closed beta-barrel (n=8, S=10)
              1. Putative alpha-L-fucosidase C-terminal domain [101929]
                 1. Thermotoga maritima [TaxId: 2336] [101930] (3)
                    TM0306
           4. Putative glucosidase YicI, domain 3 [117298] (1)
              1. Putative glucosidase YicI, domain 3 [117299]
                 1. Escherichia coli [TaxId: 562] [117300] (15)
                    SQ P31434
           5. Beta-galactosidase LacA, domain 2 [117301] (1)
              contains extra C-terminal beta-sandwich subdomain [greek-key; partial topological similarity to the immunoglobulin-like fold]
              1. Beta-galactosidase LacA, domain 2 [117302]
                 1. Penicillium sp. [TaxId: 5081] [117303] (2)
                    SQ Q700S9 41-1011
   122. WW domain-like [51044] (3)
        core: 3-stranded meander beta-sheet
        1. WW domain [51045] (1)
           uperfamily
           1. WW domain [51046] (13)
              1. Mitotic rotamase PIN1 [51047]
                 1. Human (Homo sapiens) [TaxId: 9606] [51048] (8)
              2. Formin binding protein FBP28 domain [51049]
                 1. Domestic mouse (Mus musculus) [TaxId: 10090] [51050] (4)
              3. Dystrophin [51051]
                 1. Human (Homo sapiens) [TaxId: 9606] [51052] (2)
              4. Ubiquitin ligase NEDD4 WWIII domain [63837]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [63838] (2)
                 2. fruit fly (Drosophila melanogaster) [TaxId: 7227] [159264] (1)
              5. Hypothetical protein Yjq8 (Set2p) [51053]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51054] (1)
              6. Yap65 ww domain [69330]
                 1. Human (Homo sapiens) [TaxId: 9606] [69331] (4)
              7. Splicing factor prp40 [82183]
                 duplication: contains two WW domains connected by a helical linker
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82184] (1)
              8. Suppressor of deltex (Cg4244-pb) [110301]
                 duplication: contains two WW domains connected by a helical linker
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110302] (1)
                    SQ Q9Y0H4 474-554
              9. WW domain-binding protein 4, WBP4 [141556]
                 1. Human (Homo sapiens) [TaxId: 9606] [141557] (1)
                    SQ O75554 126-163
              10. Huntingtin-interacting protein HYPA/FBP11 [141558]
                  1. Human (Homo sapiens) [TaxId: 9606] [141559] (4)
                     SQ O75400 144-171! SQ O75400 146-173
              11. Amyloid beta A4 precursor protein-binding family B member 3, APBB3 [159265]
                  1. Human (Homo sapiens) [TaxId: 9606] [159266] (1)
                     SQ O95704 30-61
              12. Amyloid beta A4 precursor protein-binding family B member 1, APBB1 [159267]
                  1. Human (Homo sapiens) [TaxId: 9606] [159268] (11)
                     SQ O00213 241-290! SQ O00213 253-285
        2. Carbohydrate binding domain [51055] (1)
           uperfamily
           1. Carbohydrate binding domain [51056] (3)
              1. Cellulose-binding domain of endoglucanase Z [51057]
                 1. Erwinia chrysanthemi [TaxId: 556] [51058] (1)
              2. Chitin-binding domain of chitinase A1 [51059]
                 1. Bacillus circulans [TaxId: 1397] [51060] (1)
              3. Chitinase B, C-terminal domain [51061]
                 1. Serratia marcescens [TaxId: 615] [51062] (14)
        3. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101931] (1)
           uperfamily
           1. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101932] (1)
              1. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101933]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101934] (1)
   123. Head domain of nucleotide exchange factor GrpE [51063] (1)
        small mixed beta-sheet, 4 "generalized" strands
        1. Head domain of nucleotide exchange factor GrpE [51064] (1)
           uperfamily
           1. Head domain of nucleotide exchange factor GrpE [51065] (1)
              1. Head domain of nucleotide exchange factor GrpE [51066]
                 1. Escherichia coli [TaxId: 562] [51067] (1)
   124. Coronavirus RNA-binding domain [110303] (1)
        coiled antiparallel beta-sheet of 5 strands, order 51324; complex topology, crossing loops
        1. Coronavirus RNA-binding domain [110304] (1)
           uperfamily
           1. Coronavirus RNA-binding domain [110305] (2)
              N-terminal part of Pfam 00937
              1. Nucleocapsid protein [110306]
                 1. SARS coronavirus, (SARS-CoV) [TaxId: 227859] [110307] (1)
                    SQ P59595 45-181
                 2. Avian infectious bronchitis virus [TaxId: 11120] [141560] (8)
                    SQ P32923 23-160! SQ P69596 29-160! SQ P69597 29-160
                    different strains
   125. Ribonuclease domain of colicin E3 [63839] (1)
        twisted meander beta-sheet of 6 strands
        1. Ribonuclease domain of colicin E3 [63840] (1)
           uperfamily
           1. Ribonuclease domain of colicin E3 [63841] (1)
              1. Ribonuclease domain of colicin E3 [63842]
                 1. Escherichia coli [TaxId: 562] [63843] (4)
   126. NAC domain [101940] (1)
        core: twisted 7-stranded beta-sheet (half-barrel)
        1. NAC domain [101941] (1)
           uperfamily
           1. NAC domain [101942] (1)
              Pfam 02365, NAM; transcription factor domain
              1. No apical meristem (NAM, ANAC) [101943]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [101944] (2)
   127. At5g01610-like [141561] (1)
        contains large meander beta-sheet bent into a scoop-like shape
        1. At5g01610-like [141562] (1)
           uperfamily
           1. At5g01610-like [141563] (1)
              Pfam 04398; DUF538
              1. Hypothetical protein At5g01610 [141564]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141565] (1)
                    SQ Q9M015 2-170
   128. Carbonic anhydrase [51068] (1)
        single sheet; 10 strands
        1. Carbonic anhydrase [51069] (1)
           uperfamily
           1. Carbonic anhydrase [51070] (10)
              1. Carbonic anhydrase [51071]
                 1. Human (Homo sapiens), erythrocytes, isozyme I [TaxId: 9606] [51072] (21)
                 2. Human (Homo sapiens), erythrocytes, isozyme II [TaxId: 9606] [51073] (221)
                    SQ P00918
                 3. Cow (Bos taurus), isozyme II [TaxId: 9913] [51074] (3)
                 4. Rat (Rattus norvegicus), isozyme III [TaxId: 10116] [51075] (1)
                 5. Human (Homo sapiens), isozyme IV [TaxId: 9606] [51076] (1)
                 6. Mouse (Mus musculus), isozyme IV [TaxId: 10090] [51077] (2)
                 7. Mouse (Mus musculus), liver, isozyme V [TaxId: 10090] [51078] (4)
                 8. Human (Homo sapiens), isozyme XII [TaxId: 9606] [63844] (2)
                 9. Mouse (Mus musculus), isozyme XIV [TaxId: 10090] [101945] (2)
                 10. Neisseria gonorrhoeae [TaxId: 485] [51079] (2)
   129. LolA-like prokaryotic lipoproteins and lipoprotein localization factors [89391] (1)
        11 stranded sheet partly folded in a corner-like structure filled with a few short helices
        1. Prokaryotic lipoproteins and lipoprotein localization factors [89392] (3)
           uperfamily
           1. Outer-membrane lipoproteins carrier protein LolA [89393] (1)
              1. Outer-membrane lipoproteins carrier protein LolA [89394]
                 1. Escherichia coli [TaxId: 562] [89395] (2)
           2. Outer membrane lipoprotein receptor LolB [89396] (1)
              1. Outer membrane lipoprotein receptor LolB [89397]
                 1. Escherichia coli [TaxId: 562] [89398] (2)
           3. LppX-like [141566] (1)
              Pfam 07161; DUF1396; contains a large cavity between the 'flattened' beta-sheet and helix-containing loops
              1. Putative lipoprotein LppX [141567]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141568] (1)
                    SQ P65306 46-233
   130. YmcC-like [159269] (1)
        12-stranded meander beta-sheet, folded into a deformed beta-barrel; topological similarity to the LolA-like fold (scop_cf 89391)
        1. YmcC-like [159270] (1)
           1. YmcC-like [159271] (1)
              PfamB 007600
              1. Hypothetical lipoprotein YmcC [159272]
                 1. Escherichia coli [TaxId: 562] [159273] (2)
                    SQ P75884 17-214
   131. Spiral beta-roll [159274] (1)
        a large 15-stranded beta-sheet rolled about a single helix core; overlapping edges form a sandwich-like structure; topological similarity to the LolA-like fold (scop_cf 89391)
        1. PA1994-like [159275] (1)
           1. PA1994-like [159276] (1)
              Pfam 06475; DUF1089
              1. Hypothetical protein PA1994 [159277]
                 1. Pseudomonas aeruginosa [TaxId: 287] [159278] (2)
                    SQ Q9I2B5 2-187
   132. Bacteriochlorophyll A protein [51080] (1)
        single sheet; 16 strands; meander
        1. Bacteriochlorophyll A protein [51081] (1)
           uperfamily
           1. Bacteriochlorophyll A protein [51082] (2)
              1. Bacteriochlorophyll A protein [51083]
                 1. Prosthecochloris aestuarii, strain 2k [TaxId: 1102] [51084] (1)
                 2. Green sulfur bacterium (Chlorobium tepidum) [TaxId: 1097] [51085] (3)
   133. open-sided beta-meander [51086] (2)
        single sheet formed by beta-hairpin repeats; exposed on both sides in the middle
        1. Outer surface protein [51087] (1)
           21 stranded sheet partly folded upon itself at the ends
           uperfamily
           1. Outer surface protein [51088] (2)
              1. Outer surface protein A [51089]
                 1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [51090] (2)
              2. Outer surface protein B [101946]
                 1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [101947] (2)
                    SQ P17739 202-296
        2. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82185] (1)
           11+ stranded sheet partly folded upon itself at the C-end
           uperfamily
           1. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82186] (1)
              1. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82187]
                 1. Human (Homo sapiens) [TaxId: 9606] [82188] (11)
                    SQ Q8WTS6 52-366
   134. beta-Prism I [51091] (3)
        consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
        duplication: has internal pseudo threefold symmetry
        1. Vitelline membrane outer protein-I (VMO-I) [51092] (1)
           uperfamily
           1. Vitelline membrane outer protein-I (VMO-I) [51093] (1)
              1. Vitelline membrane outer protein-I (VMO-I) [51094]
                 1. Hen (Gallus gallus) [TaxId: 9031] [51095] (1)
        2. delta-Endotoxin (insectocide), middle domain [51096] (1)
           uperfamily
           1. delta-Endotoxin (insectocide), middle domain [51097] (4)
              1. delta-Endotoxin (insectocide), middle domain [51098]
                 1. Bacillus thuringiensis tenebrionis, CRYIIIA (BT13) [TaxId: 1444] [51099] (1)
                 2. Bacillus thuringiensis, CRY3bb1 [TaxId: 1428] [63845] (1)
                 3. Bacillus thuringiensis, CRYIA (A) [TaxId: 1428] [51100] (1)
                 4. Bacillus thuringiensis subsp. kurstaki, CRY2AA [TaxId: 29339] [63846] (1)
        3. Mannose-binding lectins [51101] (1)
           uperfamily
           1. Mannose-binding lectins [51102] (8)
              1. Jacalin [51103]
                 1. Jackfruit (Artocarpus heterophyllus) [TaxId: 3489] [51104] (10)
                 2. Artocarpus hirsuta [TaxId: 291940] [110308] (2)
                    SQ Q38723 64-217 95% sequence identity
              2. Artocarpin [75022]
                 1. Jackfruit (Artocarpus heterophyllus) [TaxId: 3489] [75023] (5)
                    SQ Q7M1T4
              3. Lectin MPA [51105]
                 1. Osage orange (Maclura pomifera) [TaxId: 3496] [51106] (1)
              4. Heltuba lectin [51107]
                 1. Jerusalem artishoke (Helianthus tuberosus) [TaxId: 4233] [51108] (3)
              5. Calystegia sepium agglutinin [101948]
                 1. Hedge bindweed (Calystegia sepium) [TaxId: 47519] [101949] (1)
              6. Griffithsin [141569]
                 single-chain subunits form a segment-swapped dimer
                 1. Red alga (Griffithsia) [TaxId: 35158] [141570] (13)
                    SQ P84801 1-121
                 2. Griffithsia sp. Q66D336 [TaxId: 373036] [159279] (4)
   135. beta-Prism II [51109] (1)
        consists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axis
        duplication: consists of two domains of this fold
        1. alpha-D-mannose-specific plant lectins [51110] (1)
           uperfamily
           1. alpha-D-mannose-specific plant lectins [51111] (6)
              1. Lectin (agglutinin) [51112]
                 1. Snowdrop (Galanthus nivalis) [TaxId: 4670] [51113] (3)
                 2. Garlic (Allium sativum) [TaxId: 4682] [51114] (2)
                 3. Daffodil (Narcissus pseudonarcissus) [TaxId: 39639] [51115] (1)
                 4. Bluebell (Scilla campanulata) [TaxId: 81759] [51116] (1)
              2. Fetuin-binding protein Scafet precursor [51117]
                 duplication: consists of two beta-prism II domains
                 1. Bluebell (Scilla campanulata) [TaxId: 81759] [51118] (1)
              3. Gastrodianin (antifungal protein) [117304]
                 1. Gastrodia elata [TaxId: 91201] [117305] (2)
                    SQ Q9AXZ2 29-140 # different isoforms
   136. Single-stranded right-handed beta-helix [51125] (8)
        superhelix turns are made of parallel beta-strands and (short) turns
        1. beta-Roll [51120] (1)
           superhelix turns are made of two short strands each
           uperfamily
           1. Serralysin-like metalloprotease, C-terminal domain [51121] (4)
              duplication: halfturs of beta-helix are sequence and structural repeats; binds calcium ions between the turns
              1. Metalloprotease [51122]
                 The catalytic N-terminal domain belong to the "zincin" superfamily
                 1. Pseudomonas aeruginosa [TaxId: 287] [51123] (3)
                    alkaline protease
                 2. Serratia marcescens [TaxId: 615] [51124] (4)
                    serralysin
                 3. Erwinia chrysanthemi [TaxId: 556] [82189] (5)
                    protease C
                 4. Pseudomonas sp., tac ii 18 [TaxId: 306] [82190] (8)
                    psychrophilic alkaline protease
        2. Pectin lyase-like [51126] (11)
           superhelix turns are made of 3 strands each
           uperfamily
           1. Pectate lyase-like [51127] (6)
              1. Pectate lyase [51128]
                 1. Erwinia chrysanthemi, type C [TaxId: 556] [51129] (14)
                 2. Erwinia chrysanthemi, type A [TaxId: 556] [75024] (4)
                 3. Erwinia chrysanthemi, type E [TaxId: 556] [51130] (1)
                 4. Bacillus subtilis [TaxId: 1423] [51131] (2)
                 5. Bacillus sp., strain ksmp15 [TaxId: 1409] [51132] (1)
                    Low-molecular weight high-alkaline enzyme
              2. Major pollen allergen Jun a 1 [117306]
                 1. Ozark white cedar (Juniperus ashei) [TaxId: 13101] [117307] (1)
                    SQ P81294 22-367
           2. Pectin lyase [51133] (2)
              1. Pectin lyase [51134]
                 1. Aspergillus niger, type A [TaxId: 5061] [51135] (2)
                 2. Aspergillus niger, type B [TaxId: 5061] [51136] (1)
           3. Galacturonase [51137] (7)
              1. Rhamnogalacturonase A [51138]
                 1. Aspergillus aculeatus [TaxId: 5053] [51139] (1)
              2. Polygalacturonase [51140]
                 1. Erwinia carotovora, subsp. carotovora [TaxId: 554] [51141] (1)
                 2. Fungus (Aspergillus aculeatus) [TaxId: 5053] [63847] (2)
                 3. Fungus (Stereum purpureum), endo-polygalacturonase I [TaxId: 58369] [75025] (3)
                 4. Fungus (Aspergillus niger), endo-polygalacturonase I [TaxId: 5061] [101950] (1)
                 5. Fungus (Aspergillus niger), endo-polygalacturonase II [TaxId: 5061] [63382] (1)
                 6. Fusarium moniliforme [TaxId: 117187] [69332] (1)
           4. Chondroitinase B [51144] (1)
              1. Chondroitinase B [51145]
                 1. Pedobacter heparinus [TaxId: 984] [51146] (4)
                    SQ Q46079 27-506
                    synonym: Flavobacterium heparinum
           5. iota-carrageenase [69333] (1)
              1. iota-carrageenase [69334]
                 1. Alteromonas sp., atcc 43554 [TaxId: 232] [69335] (2)
           6. Pectate transeliminase [101951] (1)
              1. Pectate transeliminase [101952]
                 type L pectate lyase, pel9a
                 1. Erwinia chrysanthemi [TaxId: 556] [101953] (1)
           7. Dextranase, catalytic domain [101954] (1)
              1. Dextranase, catalytic domain [101955]
                 1. Penicillium minioluteum [TaxId: 28574] [101956] (2)
           8. Pectin methylesterase [51147] (2)
              1. Pectin methylesterase PemA [51148]
                 1. Erwinia chrysanthemi [TaxId: 556] [51149] (1)
                 2. Carrot (Daucus carota) [TaxId: 4039] [75026] (1)
           9. P22 tailspike protein [51150] (1)
              1. P22 tailspike protein [51151]
                 1. Salmonella phage P22 [TaxId: 10754] [51152] (12)
           10. Virulence factor P.69 pertactin [51153] (1)
               1. Virulence factor P.69 pertactin [51154]
                  1. Bordetella pertussis [TaxId: 520] [51155] (1)
           11. Filamentous hemagglutinin FhaB, secretion domain [101957] (1)
               1. Filamentous hemagglutinin FhaB, secretion domain [101958]
                  1. Bordetella pertussis [TaxId: 520] [101959] (1)
        3. Insect cysteine-rich antifreeze protein [51156] (1)
           superhelix turns are made of two short strands each
           uperfamily
           1. Insect cysteine-rich antifreeze protein [51157] (1)
              1. Insect cysteine-rich antifreeze protein [51158]
                 1. Yellow mealworm (Tenebrio molitor) [TaxId: 7067] [51159] (2)
        4. Cell-division inhibitor MinC, C-terminal domain [63848] (1)
           superhelix turns are made of three short strands each
           uperfamily
           1. Cell-division inhibitor MinC, C-terminal domain [63849] (1)
              1. Cell-division inhibitor MinC, C-terminal domain [63850]
                 1. Thermotoga maritima [TaxId: 2336] [63851] (1)
        5. Alpha subunit of glutamate synthase, C-terminal domain [69336] (1)
           uperfamily
           1. Alpha subunit of glutamate synthase, C-terminal domain [69337] (2)
              1. Alpha subunit of glutamate synthase, C-terminal domain [69338]
                 Central domain (residues 423-780) may be a rudiment form of the FMN domain
                 1. Azospirillum brasilense [TaxId: 192] [69339] (7)
                 2. Synechocystis sp. [TaxId: 1143] [75027] (5)
        6. C-terminal domain of adenylylcyclase associated protein [69340] (1)
           superhelix turns are made of two strands each
           uperfamily
           1. C-terminal domain of adenylylcyclase associated protein [69341] (2)
              1. C-terminal domain of adenylylcyclase associated protein [69342]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69343] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [89399] (1)
        7. Stabilizer of iron transporter SufD [101960] (1)
           superhelix turns are made of two very long strands each
           uperfamily
           1. Stabilizer of iron transporter SufD [101961] (1)
              1. Stabilizer of iron transporter SufD [101962]
                 1. Escherichia coli [TaxId: 562] [101963] (1)
        8. Pentapeptide repeat-like [141571] (1)
           superhelix turns are made of four short strands each; duplication: the sequence pentapeptide repeats correspond to individual strands
           uperfamily
           1. Pentapeptide repeats [141572] (3)
              Pfam 00805 (covers eight repeats or two full superhelical turns)
              1. Hypothetical protein Rv3361c (MT3469) [141573]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [141574] (8)
                    SQ O50390 2-182
              2. NP275-NP276 [141575]
                 Two consecuitive ORFs in the same frame that maintain the sequence periodicity; probable single ORF disrupted by the nonsense mutation
                 1. Nostoc punctiforme [TaxId: 272131] [141576] (3)
              3. Lumenal RFR-domain protein [141577]
                 1. Cyanothece sp. atcc 51142 [TaxId: 43989] [141578] (2)
   137. Single-stranded left-handed beta-helix [51160] (4)
        superhelix turns are made of parallel beta-strands and (short) turns
        1. Trimeric LpxA-like enzymes [51161] (8)
           superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands
           uperfamily
           1. UDP N-acetylglucosamine acyltransferase [51162] (2)
              1. UDP N-acetylglucosamine acyltransferase [51163]
                 1. Escherichia coli, gene lpxA [TaxId: 562] [51164] (6)
                 2. Helicobacter pylori [TaxId: 210] [101964] (1)
           2. Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [51165] (1)
              contains extra N-terminal 3-helical domain
              1. Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [51166]
                 1. Mycobacterium bovis [TaxId: 1765] [51167] (5)
           3. Galactoside acetyltransferase-like [51168] (4)
              1. Galactoside acetyltransferase [75028]
                 1. Escherichia coli [TaxId: 562] [75029] (4)
              2. Maltose O-acetyltransferase [89400]
                 1. Escherichia coli [TaxId: 562] [89401] (1)
              3. Xenobiotic acetyltransferase [51169]
                 1. Pseudomonas aeruginosa [TaxId: 287] [51170] (2)
                 2. Enterococcus faecium, VAT(D) [TaxId: 1352] [69344] (7)
                    streptogramin A acetyltransferase
           4. GlmU C-terminal domain-like [51171] (4)
              1. N-acetylglucosamine 1-phosphate uridyltransferase GlmU, C-terminal domain [51172]
                 1. Escherichia coli [TaxId: 562] [51173] (9)
                 2. Streptococcus pneumoniae [TaxId: 1313] [63852] (5)
              2. Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain [141579]
                 1. Potato (Solanum tuberosum) [TaxId: 4113] [141580] (12)
                    SQ P23509 387-521
              3. UDP-glucose pyrophosphorylase 2 (UDPGP 2) [141581]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141582] (8)
                    SQ Q9M9P3 384-469
           5. gamma-carbonic anhydrase-like [51174] (3)
              archaeal hexapeptide repeat proteins
              1. gamma-carbonic anhydrase [51175]
                 1. Archaeon Methanosarcina thermophila [TaxId: 2210] [51176] (7)
              2. Ferripyochelin binding protein [101965]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101966] (3)
              3. Putative acetyltransferase/acyltransferase BC4754 [117308]
                 1. Bacillus cereus [TaxId: 1396] [117309] (1)
                    SQ Q816R4
           6. Serine acetyltransferase [110309] (2)
              1. Serine acetyltransferase [110310]
                 extra N-terminal all-alpha subdomain belongs to Pfam 06426
                 1. Haemophilus influenzae [TaxId: 727] [110311] (4)
                    SQ P43886 1-241
                 2. Escherichia coli [TaxId: 562] [110312] (1)
                    SQ P05796
           7. YdcK-like [141583] (1)
              part of Pfam 00132
              1. Hypothetical protein YdcK [141584]
                 1. Salmonella enterica [TaxId: 28901] [141585] (1)
                    SQ Q5PHU6 3-322
           8. PglD-like [159280] (1)
              contains extra N-terminal alpha/beta subdomain
              1. Acetyltransferase PglD [159281]
                 1. Campylobacter jejuni [TaxId: 197] [159282] (9)
                    SQ Q0P9D1 3-197
        2. An insect antifreeze protein [51177] (1)
           superhelical turns are made of three short strands
           uperfamily
           1. An insect antifreeze protein [51178] (2)
              1. Thermal hysteresis protein [51179]
                 there are different numbers of superhelical turns (and sequence repeats) in different isoforms
                 1. Spruce budworm (Choristoneura fumiferana), 5-turn isoforms [TaxId: 7141] [88689] (3)
                 2. Spruce budworm (Choristoneura fumiferana), 7-turn isoforms [TaxId: 7141] [88690] (2)
        3. Adhesin YadA, collagen-binding domain [101967] (1)
           superhelical turns are made of two short strands
           uperfamily
           1. Adhesin YadA, collagen-binding domain [101968] (1)
              1. Adhesin YadA, collagen-binding domain [101969]
                 1. Yersinia enterocolitica [TaxId: 630] [101970] (1)
        4. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159283] (1)
           probable rudiment form of the LpxA-like hexapeptide domain
           1. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159284] (1)
              corresponds to the N-terminal part of Pfam 01050, but does not extend to the conserved functional motif; the predicted cupin fold may reside in the rest of the Pfam domain
              1. Putative mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase TTHA1750 [159285]
                 there is no the functional mannose-6-phosphate isomerase domain in this protein; this would-be the linker domain is the C-terminal one
                 1. Thermus thermophilus [TaxId: 274] [159286] (1)
                    SQ Q5SHI0 269-335
   138. Double-stranded beta-helix [51181] (7)
        one turn of helix is made by two pairs of antiparallel strands linked with short turns
        has appearance of a sandwich of distinct architecture and jelly-roll topology
        1. RmlC-like cupins [51182] (24)
           uperfamily
           1. dTDP-sugar isomerase [51183] (9)
              1. dTDP-4-dehydrorhamnose 3,5-epimerase RmlC [51184]
                 synonym: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
                 1. Salmonella typhimurium [TaxId: 90371] [51185] (2)
                 2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51186] (2)
                 3. Streptococcus suis [TaxId: 1307] [89402] (7)
                 4. Mycobacterium tuberculosis [TaxId: 1773] [101971] (6)
                 5. Pseudomonas aeruginosa [TaxId: 287] [101972] (4)
                 6. Archaeon Sulfolobus tokodaii [TaxId: 111955] [141586] (2)
                    SQ Q96Z62 1-176
              2. dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD [101973]
                 1. Amycolatopsis orientalis [TaxId: 31958] [101974] (2)
                    SQ O52806
              3. Novobiocin biosynthesis protein NovW [141587]
                 1. Streptomyces caeruleus [TaxId: 195949] [141588] (1)
                    SQ Q9L9E5 1-190
              4. dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA [159287]
                 1. Aneurinibacillus thermoaerophilus [TaxId: 143495] [159288] (8)
                    SQ Q6T1W8 1-136! SQ Q6T1W8 2-136
           2. Glucose-6-phosphate isomerase, GPI [89403] (2)
              1. Glucose-6-phosphate isomerase, GPI [89404]
                 Type II phosphoglucose isomerase
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89405] (6)
                    SQ P83194
                 2. Archaeon Thermococcus litoralis [TaxId: 2265] [101975] (11)
           3. Hypothetical protein TM1112 [89406] (1)
              1. Hypothetical protein TM1112 [89407]
                 1. Thermotoga maritima [TaxId: 2336] [89408] (2)
           4. TM1287-like [89409] (4)
              1. Hypothetical protein TM1287 [89410]
                 1. Thermotoga maritima [TaxId: 2336] [89411] (1)
              2. Hypothetical protein TTHA0104 [117310]
                 1. Thermus thermophilus [TaxId: 274] [117311] (3)
                    SQ Q5SM39
              3. Hypothetical protein TM1010 [141589]
                 1. Thermotoga maritima [TaxId: 2336] [141590] (4)
                    SQ Q9X0A3 2-135
              4. Hypothetical protein SPy1581 [141591]
                 1. Streptococcus pyogenes [TaxId: 1314] [141592] (1)
                    SQ Q99YR1 1-112
           5. TM1459-like [101976] (2)
              1. Hypothetical protein TM1459 [101977]
                 1. Thermotoga maritima [TaxId: 2336] [101978] (1)
              2. Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain [141593]
                 1. Streptomyces wedmorensis [TaxId: 43759] [141594] (20)
                    SQ Q56185 77-198
           6. Germin/Seed storage 7S protein [51187] (9)
              1. Germin [63853]
                 Metal (manganese)-binding protein with oxalate oxidase and superoxide dismutase activities; homohexamer
                 1. Barley (Hordeum vulgare) [TaxId: 4513] [63854] (5)
              2. Auxin binding protein [75030]
                 1. Maize (Zea mays) [TaxId: 4577] [75031] (2)
              3. Seed storage 7S protein [51188]
                 duplication: consists of two germin-like domains spatially arranged as subunits in the RmlC dimer; trimer is similar to the germin hexamer
                 1. French bean (Phaseolus vulgaris), phaseolin [TaxId: 3885] [51189] (2)
                 2. Jack bean (Canavalia ensiformis), canavalin/vinculin [TaxId: 3823] [51190] (8)
                 3. Soybean (Glycine max), proglycinin [TaxId: 3847] [69345] (3)
                 4. Soybean (Glycine max), beta-conglycinin beta subunit [TaxId: 3847] [109608] (3)
                    SQ P25974
                 5. Soybean (Glycine max), glycinin A3B4 [TaxId: 3847] [89412] (1)
                 6. Soybean (Glycine max), beta-conglycinin alpha prime subunit [TaxId: 3847] [110313] (1)
                    SQ Q7XXT2 204-621
              4. Oxalate decarboxylase OxdC (YvrK) [75033]
                 duplication: consists of two germin-like metal-ion binding domains
                 1. Bacillus subtilis [TaxId: 1423] [75034] (3)
           7. YlbA-like [101979] (4)
              Pfam 05899; formerly pfam06038; duplication: consists of two germin-like domains
              1. Hypothetical protein YlbA [101980]
                 1. Escherichia coli [TaxId: 562] [101981] (1)
              2. Glyoxylate-induced protein PA1140 [101982]
                 1. Pseudomonas aeruginosa [TaxId: 287] [101983] (1)
              3. Hypothetical protein EF2996 [110314]
                 1. Enterococcus faecalis [TaxId: 1351] [110315] (1)
                    SQ Q82ZQ3
              4. Hypothetical protein DR1152 [110316]
                 1. Deinococcus radiodurans [TaxId: 1299] [110317] (1)
                    SQ Q9RV77
           8. Pirin-like [101984] (2)
              Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
              1. Pirin [101985]
                 Bcl-3 and nuclear factor I-interacting protein
                 1. Human (Homo sapiens) [TaxId: 9606] [101986] (1)
              2. Hypothetical protein YhhW [141595]
                 1. Escherichia coli [TaxId: 562] [141596] (1)
                    SQ P46852 1-231
           9. Quercetin 2,3-dioxygenase-like [75035] (2)
              Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
              1. Quercetin 2,3-dioxygenase [75036]
                 1. Aspergillus japonicus [TaxId: 34381] [75037] (5)
              2. Hypothetical protein YxaG [141597]
                 1. Bacillus subtilis [TaxId: 1423] [141598] (2)
                    SQ P42106 5-334
           10. Type I phosphomannose isomerase [51191] (3)
               Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
               1. Phosphomannose isomerase [51192]
                  1. Yeast (Candida albicans) [TaxId: 5476] [51193] (1)
                     contains insert all-alpha subdomain; residues 152-266
               2. Mannose-6-phosphate isomerase ManA [101987]
                  1. Bacillus subtilis [TaxId: 1423] [101988] (1)
               3. Putative mannosephosphate isomerase AF0035 [141599]
                  1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141600] (1)
                     SQ O30200 1-299
           11. Homogentisate dioxygenase [51194] (1)
               Share a common two-domain fold with the 7S protein; there is a metal-binding site in the C-terminal domain similar to the metal-binding site of germin
               1. Homogentisate dioxygenase [51195]
                  1. Human (Homo sapiens) [TaxId: 9606] [51196] (2)
           12. Acireductone dioxygenase [82191] (2)
               1. Acireductone dioxygenase [82192]
                  1. Klebsiella pneumoniae [TaxId: 573] [82193] (1)
                     NMR-derived model
                  2. Mouse (Mus musculus) [TaxId: 10090] [141601] (1)
                     SQ Q99JT9 1-179
           13. KduI-like [110318] (2)
               Pfam 04962: duplication: consists of two germin-like domains
               1. 5-keto-4-deoxyuronate isomerase KduI [110319]
                  1. Escherichia coli [TaxId: 562] [110320] (3)
                     SQ Q46938 1-266
                  2. Enterococcus faecalis [TaxId: 1351] [141602] (6)
                     SQ Q838L9 1-260
           14. Ureidoglycolate hydrolase AllA [117312] (3)
               Pfam 04115; beta-hairpin-swapped dimeric protein of the germin-like fold
               1. Ureidoglycolate hydrolase AllA [117313]
                  1. Shigella flexneri [TaxId: 623] [117314] (2)
                     SQ P77731 ! SQ P63487
                  2. Pseudomonas putida [TaxId: 303] [141603] (2)
                     SQ P59285 1-166
                  3. Escherichia coli [TaxId: 562] [141604] (2)
                     SQ P63486 1-160
           15. Probable transcriptional regulator VC1968, C-terminal domain [117315] (1)
               1. Probable transcriptional regulator VC1968, C-terminal domain [117316]
                  1. Vibrio cholerae [TaxId: 666] [117317] (1)
                     SQ Q9KQN0
           16. YML079-like [117318] (3)
               Pfam 06172; DUF985
               1. Hypothetical protein YML079W [117319]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117320] (2)
                     SQ Q03629
               2. Hypothetical protein Atu3615 [141605]
                  1. Agrobacterium tumefaciens [TaxId: 358] [141606] (7)
                     SQ Q8U9W0 4-143
               3. Hypothetical protein SO0799 [141607]
                  1. Shewanella oneidensis [TaxId: 70863] [141608] (10)
                     SQ Q8EIN8 1-158
           17. PA5104-like [141609] (1)
               Pfam 05962; DUF886; duplication: consists of two germin-like domains; overall structural similarity to the YlbA-like family (scop_fa 101979) except a deletion in the interdomain linker region
               1. Hypothetical protein PA5104 [141610]
                  1. Pseudomonas aeruginosa [TaxId: 287] [141611] (4)
                     SQ Q9HU79 2-196
           18. MJ0764-like [141612] (1)
               1. Hypothetical protein MJ0764 [141613]
                  1. Archaeon Methanococcus jannaschii [TaxId: 2190] [141614] (1)
                     SQ Q58174 1-108
           19. Cysteine dioxygenase type I [141615] (4)
               Pfam 05995, CDO_I
               1. Cysteine dioxygenase type I [141616]
                  1. Mouse (Mus musculus) [TaxId: 10090] [141617] (4)
                     SQ P60334 5-190
                  2. Ralstonia eutropha [TaxId: 106590] [159289] (1)
                     SQ Q46R41 11-202
                  3. Human (Homo sapiens) [TaxId: 9606] [159290] (1)
                     SQ Q16878 6-190
                  4. Rattus norvegicus [TaxId: 10116] [159291] (1)
           20. 3-hydroxyanthranilic acid dioxygenase-like [141618] (2)
               Pfam 06052; 3-HAO
               1. 3-hydroxyanthranilate-3,4-dioxygenase [141619]
                  1. Ralstonia metallidurans [TaxId: 119219] [141620] (4)
                     SQ Q1LCS4 1-174
                  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159292] (2)
                     SQ P47096 1-175
           21. Acetylacetone-cleaving enzyme-like [159293] (1)
               PfamB 026844
               1. Putative acetyl/propionyl-CoA carboxylase subunit alpha Mpe_A3659 [159294]
                  1. Rubrivivax gelatinosus [TaxId: 28068] [159295] (2)
                     SQ A2SM23 1-144
           22. VPA0057-like [159296] (1)
               Pfam 06865; DUF1255; non-canonical dimerisation mode
               1. Uncharacterized protein VPA0057 [159297]
                  1. Vibrio parahaemolyticus [TaxId: 670] [159298] (1)
                     SQ Q87K41 2-94
           23. Gentisate 1,2-dioxygenase-like [159299] (3)
               Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin; homotetramer
               1. Gentisate 1,2-dioxygenase [159300]
                  Salicylate 1,2-dioxygenase
                  1. Escherichia coli [TaxId: 562] [159301] (4)
                     SQ Q8X655 35-342
                  2. Silicibacter pomeroyi [TaxId: 89184] [159302] (2)
                     SQ Q5LLB1 19-373
                  3. Pseudaminobacter salicylatoxidans [TaxId: 93369] [159303] (4)
                     SQ Q67FT0 17-367
           24. EutQ-like [159304] (1)
               Pfam 06249
               1. Ethanolamine utilization protein EutQ [159305]
                  1. Salmonella typhimurium [TaxId: 90371] [159306] (2)
                     SQ Q9ZFV5 100-227
        2. Clavaminate synthase-like [51197] (13)
           Iron and ketoglutarate-dependent enzymes; elaborated version of this common fold
           uperfamily
           1. Penicillin synthase-like [51198] (4)
              common fold is rather distorted
              1. Isopenicillin N synthase [51199]
                 1. Emericella nidulans [TaxId: 162425] [51200] (29)
                    SQ P05326
              2. Deacetoxycephalosporin C synthase [51201]
                 1. Streptomyces clavuligerus [TaxId: 1901] [51202] (17)
                    SQ P18548
              3. Anthocyanidin synthase [69346]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [69347] (4)
              4. 1-aminocyclopropane-1-carboxylate oxidase 1 [141621]
                 1. Petunia hybrida [TaxId: 4102] [141622] (2)
                    SQ Q08506 2-308
           2. Clavaminate synthase [51203] (1)
              1. Clavaminate synthase [51204]
                 1. Streptomyces clavuligerus [TaxId: 1901] [51205] (5)
           3. Gab protein (hypothetical protein YgaT) [63855] (1)
              1. Gab protein (hypothetical protein YgaT) [63856]
                 unknown function
                 1. Escherichia coli [TaxId: 562] [63857] (1)
           4. YhcH-like [89413] (1)
              1. Hypothetical protein HI0227 [89414]
                 1. Haemophilus influenzae [TaxId: 727] [89415] (5)
           5. Type II Proline 3-hydroxylase (proline oxidase) [63858] (1)
              1. Type II Proline 3-hydroxylase (proline oxidase) [63859]
                 1. Streptomyces sp. [TaxId: 1931] [63860] (2)
           6. TauD/TfdA-like [75038] (2)
              1. Taurine/alpha-ketoglutarate dioxygenase TauD [75039]
                 1. Escherichia coli [TaxId: 562] [75040] (4)
              2. Putative alkylsulfatase AtsK [101989]
                 1. Pseudomonas putida [TaxId: 303] [101990] (6)
                    SQ Q9WWU5
           7. gamma-Butyrobetaine hydroxylase [89416] (2)
              Pfam 03322
              1. Carbapenem synthase, CarC [89417]
                 1. Erwinia carotovora [TaxId: 554] [89418] (2)
              2. Clavaminate synthase-like protein At3g21360 [117321]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117322] (3)
                    SQ Q9LIG0
           8. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82194] (1)
              1. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82195]
                 1. Human (Homo sapiens) [TaxId: 9606] [82196] (10)
           9. PhyH-like [141623] (2)
              Pfam 05721
              1. Syringomycin biosynthesis enzyme 2, SyrB2 [141624]
                 1. Pseudomonas syringae pv. syringae [TaxId: 321] [141625] (6)
                    SQ Q9RBY6 3-310
              2. Phytanoyl-CoA dioxygenase, PhyH [141626]
                 1. Human (Homo sapiens) [TaxId: 9606] [141627] (1)
                    SQ O14832 43-338
           10. AlkB-like [141628] (2)
               1. Alkylated DNA repair protein AlkB [141629]
                  1. Escherichia coli [TaxId: 562] [141630] (7)
                     SQ P05050 15-214
               2. AlkB homolog 3 [141631]
                  Prostate cancer antigen 1, DEPC-1
                  1. Human (Homo sapiens) [TaxId: 9606] [141632] (1)
                     SQ Q96Q83 70-279
           11. Asparaginyl hydroxylase-like [141633] (1)
               Pfam 08007
               1. Putative asparaginyl hydroxylase YxbC [141634]
                  1. Bacillus subtilis [TaxId: 1423] [141635] (4)
                     SQ P46327 8-326
           12. YbiU-like [141636] (1)
               Pfam 07350; DUF1479
               1. Hypothetical protein YbiU [141637]
                  1. Salmonella typhimurium [TaxId: 90371] [141638] (1)
                     SQ Q8ZQM7 3-419
           13. TehB-like [159307] (2)
               Pfam 09313; DUF1971
               1. Uncharacterized protein YeaR [159308]
                  1. Escherichia coli [TaxId: 562] [159309] (4)
                     SQ P64488 1-109
               2. Tellurite resistance protein B, TehB [159310]
                  1. Vibrio fischeri [TaxId: 668] [159311] (8)
                     SQ Q5E3X2 5-100
        3. cAMP-binding domain-like [51206] (3)
           uperfamily
           1. CO-sensing protein CooA, N-terminal domain [51207] (1)
              heme-binding domain
              1. CO-sensing protein CooA, N-terminal domain [51208]
                 1. Rhodospirillum rubrum [TaxId: 1085] [51209] (1)
           2. Listeriolysin regulatory protein PrfA, N-terminal domain [89419] (1)
              1. Listeriolysin regulatory protein PrfA, N-terminal domain [89420]
                 1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [89421] (11)
           3. cAMP-binding domain [51210] (14)
              Pfam 00027
              1. Catabolite gene activator protein, N-terminal domain [51211]
                 1. Escherichia coli [TaxId: 562] [51212] (26)
              2. CRP-like transcriptional regulator TM1171, N-terminal domain [101991]
                 1. Thermotoga maritima [TaxId: 2336] [101992] (1)
              3. Regulatory subunit of Protein kinase A [51213]
                 duplication: consists of two similar domains
                 1. Cow (Bos taurus) [TaxId: 9913] [51214] (4)
                    SQ P00514 109-376
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [63861] (1)
              4. Regulatory domain of Epac2, domains 1 and 3 [82197]
                 duplication: two homologous domains of this fold are separated in the sequence by a DEP domain
                 1. Mouse (Mus musculus) [TaxId: 10090] [82198] (1)
              5. HCN pacemaker channel [101993]
                 potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel
                 1. Mouse (Mus musculus) [TaxId: 10090] [101994] (5)
              6. Putative ion channel CnbD [110321]
                 1. Mesorhizobium loti [TaxId: 381] [110322] (4)
                    SQ Q98GN8 218-350 # mll3241
              7. Probable cyclic nucleotide-gated ion channel 6 [117323]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117324] (1)
                    SQ O82226 509-632
              8. Probable transcription regulator BT4300, N-terminal domain [141639]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [141640] (1)
                    SQ Q89ZS6 1-147
              9. Transcriptional regulator TTHA1359, N-terminal domain [141641]
                 1. Thermus thermophilus [TaxId: 274] [141642] (1)
                    SQ Q5SIL0 6-117
              10. Transcriptional regulator PG0396, N-terminal domain [141643]
                  1. Porphyromonas gingivalis [TaxId: 837] [141644] (1)
                     SQ Q7MAW7 10-151
              11. Cyclic AMP receptor-like protein Vfr [159312]
                  1. Pseudomonas aeruginosa [TaxId: 287] [159313] (1)
                     SQ P55222 9-142
              12. Chlorophenol reduction protein CprK [159314]
                  1. Desulfitobacterium hafniense [TaxId: 49338] [159315] (7)
                     SQ Q18R04 3-147! SQ Q18R04 9-147
                  2. Desulfitobacterium dehalogenans [TaxId: 36854] [159316] (2)
                     SQ Q9LAS2 19-147
        4. Regulatory protein AraC [51215] (1)
           uperfamily
           1. Regulatory protein AraC [51216] (1)
              1. Regulatory protein AraC [51217]
                 contains an alpha-hairpin in the C-terminal extension
                 1. Escherichia coli [TaxId: 562] [51218] (4)
                    SQ P03021
        5. Thiamin pyrophosphokinase, substrate-binding domain [63862] (1)
           uperfamily
           1. Thiamin pyrophosphokinase, substrate-binding domain [63863] (2)
              1. Thiamin pyrophosphokinase, substrate-binding domain [63864]
                 1. Mouse (Mus musculus) [TaxId: 10090] [63865] (2)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63866] (1)
        6. Calcium ATPase, transduction domain A [81653] (1)
           a distorted variant of double-helix
           uperfamily
           1. Calcium ATPase, transduction domain A [81652] (1)
              1. Calcium ATPase, transduction domain A [81651]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81650] (17)
                    SQ P04191
        7. TRAP-like [51219] (2)
           shorter variant of double-helix; assembles in large ring-like structures containing from 9 to 11 domains
           uperfamily
           1. Trp RNA-binding attenuation protein (TRAP) [51220] (2)
              oligomeric ring consists of 11 single-domain subunits
              1. Trp RNA-binding attenuation protein (TRAP) [51221]
                 1. Bacillus subtilis [TaxId: 1423] [51222] (1)
                 2. Bacillus stearothermophilus [TaxId: 1422] [51223] (19)
           2. PA3696/SPS0176-like [101995] (2)
              duplication: there are three structural repeats per subunit; nine domains per ring-like trimer
              1. Hypothetical protein SPyM3_0169 (SPyM18_0222, SPS0176) [101996]
                 1. Streptococcus pyogenes [TaxId: 1314] [101997] (1)
              2. Hypothetical protein PA3696 [141645]
                 1. Pseudomonas aeruginosa [TaxId: 287] [141646] (6)
                    SQ Q9HXU4 5-244
   139. Triple-stranded beta-helix [69348] (1)
        (homo)trimer; each chain donates 3 beta-strands per turn of the helix
        1. Phage fibre proteins [69349] (5)
           uperfamily
           1. Middle part of short tail fibre protein gp12 [69350] (1)
              1. Middle part of short tail fibre protein gp12 [88691]
                 includes the N-terminal cap (sub)domain
                 1. Bacteriophage T4 [TaxId: 10665] [88692] (1)
           2. Tail-associated lysozyme gp5, C-terminal domain [69353] (1)
              1. Tail-associated lysozyme gp5, C-terminal domain [69354]
                 1. Bacteriophage T4 [TaxId: 10665] [69355] (1)
           3. Endo-alpha-sialidase [117325] (1)
              1. Endo-alpha-sialidase [117326]
                 1. Bacteriophage K1F [TaxId: 344021] [117327] (2)
                    SQ Q04830 245-909
           4. Lactophage receptor-binding protein domain [141647] (2)
              1. Baseplate protein (bpp), N-terminal domain [141648]
                 includes extra N-terminal trimerization helix
                 1. Lactococcus phage tp901-1 [TaxId: 35345] [141649] (3)
                    SQ Q9G096 17-62
              2. Receptor binding protein, rbp, middle domain [141650]
                 1. Lactococcus lactis phage p2 [TaxId: 100641] [141651] (6)
                    SQ Q71AW2 141-161
           5. HylP-like [159317] (1)
              Pfam 07212
              1. Phage-associated hyaluronidase, HylP1 [159318]
                 1. Streptococcus pyogenes [TaxId: 1314] [159319] (6)
                    SQ Q9A0M7 7-336! SQ Q9A0M7 7-337
   140. Triple beta-spiral [51224] (1)
        trimer formed by the interlocking beta-hairpin repeat units
        1. Fibre shaft of virus attachment proteins [51225] (2)
           uperfamily
           1. Adenovirus [51226] (1)
              1. Adenovirus [51227]
                 1. Human adenovirus type 2 [TaxId: 10515] [51228] (3)
                    SQ P10104
           2. Reovirus attachment protein sigma 1 [69356] (1)
              1. Reovirus attachment protein sigma 1 [69357]
                 1. Reovirus [TaxId: 10891] [69358] (1)
   141. Trimeric adhesin [101998] (1)
        trimer; contains two different beta-prism-like domains connected by an linker subdomain of less regular structure
        1. Trimeric adhesin [101999] (1)
           uperfamily
           1. Trimeric adhesin [102000] (1)
              1. Autotransporter Hia [102001]
                 1. Haemophilus influenzae [TaxId: 727] [102002] (1)
   142. beta-hairpin stack [69359] (1)
        Trp-rich beta-hairpin repeat units form helical structures of 3 units per turn
        1. Cell wall binding repeat [69360] (1)
           uperfamily
           1. Cell wall binding repeat [69361] (3)
              1. Choline binding domain of autolysin C-LytA [69362]
                 1. Streptococcus pneumoniae [TaxId: 1313] [69363] (5)
              2. C-terminal domain of endolysin [89422]
                 1. Bacteriophage cp-1 [TaxId: 10747] [89423] (6)
              3. Teichoic acid phosphorylcholine esterase Pce (LytD), C-terminal domain [141652]
                 1. Streptococcus pneumoniae [TaxId: 1313] [141653] (1)
                    SQ Q8DQ62 335-566
   143. Barrel-sandwich hybrid [51229] (4)
        sandwich of half-barrel shaped beta-sheets
        1. Single hybrid motif [51230] (1)
           7 to 8 strands in 2 beta-sheets
           uperfamily
           1. Biotinyl/lipoyl-carrier proteins and domains [51231] (13)
              1. Biotinyl domain of acetyl-CoA carboxylase [51232]
                 1. Escherichia coli [TaxId: 562] [51233] (4)
              2. Biotin carboxyl carrier domain of transcarboxylase (TC 1.3S) [51234]
                 1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [51235] (3)
              3. Protein H of glycine cleavage system [51236]
                 1. Pea (Pisum sativum) [TaxId: 3888] [51237] (3)
                 2. Thermus thermophilus [TaxId: 274] [102003] (1)
              4. Lipoyl domain of dihydrolipoamide acetyltransferase [51238]
                 component of the pyruvate dehydrogenase complex
                 1. Bacillus stearothermophilus [TaxId: 1422] [51239] (2)
                 2. Azotobacter vinelandii [TaxId: 354] [51240] (2)
                 3. Escherichia coli [TaxId: 562] [51241] (1)
                 4. Neisseria meningitidis [TaxId: 487] [69364] (1)
                 5. Human (Homo sapiens) [TaxId: 9606] [51242] (4)
              5. Lipoyl domain of the 2-oxoglutarate dehydrogenase complex [51243]
                 1. Azotobacter vinelandii [TaxId: 354] [51244] (2)
                 2. Escherichia coli [TaxId: 562] [51245] (1)
                 3. Homo sapiens [TaxId: 9606] [159320] (3)
              6. Lipoyl domain of the mitochondrial branched-chain alpha-ketoacid dehydrogenase [69365]
                 1. Human (Homo sapiens) [TaxId: 9606] [69366] (2)
        2. Rudiment single hybrid motif [51246] (2)
           uperfamily
           1. BC C-terminal domain-like [51247] (7)
              probable rudiment form of the biotinyl-carrier domain
              1. Biotin carboxylase (BC), C-domain [51248]
                 subunit of acetyl-CoA and pyruvate carboxylases
                 1. Escherichia coli [TaxId: 562] [51249] (13)
                 2. Aquifex aeolicus [TaxId: 63363] [102004] (1)
              2. Glycinamide ribonucleotide synthetase (GAR-syn), C-domain [51250]
                 1. Escherichia coli [TaxId: 562] [51251] (1)
                 2. Thermotoga maritima [TaxId: 2336] [110323] (1)
                    SQ Q9X0X7
              3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), C-domain [51252]
                 1. Escherichia coli [TaxId: 562] [51253] (6)
              4. Glycinamide ribonucleotide transformylase PurT, C-domain [51254]
                 1. Escherichia coli [TaxId: 562] [51255] (7)
              5. Acetyl-CoA carboxylase, BC-C subdomain [117328]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117329] (2)
                    SQ Q00955 13-566
           2. Cytochrome f, small domain [51256] (5)
              1. Cytochrome f, small domain [51257]
                 1. Turnip (Brassica rapa) [TaxId: 3711] [51258] (2)
                 2. Chlamydomonas reinhardtii [TaxId: 3055] [51259] (6)
                 3. Phormidium laminosum [TaxId: 32059] [51260] (1)
                 4. Mastigocladus laminosus [TaxId: 83541] [102005] (1)
                 5. Anabaena sp., strain PCC 7120 [TaxId: 1167] [159321] (1)
                    SQ Q93SW9 214-279
        3. Duplicated hybrid motif [51261] (2)
           half-barrel sheet of 8 strands sandwiched with two 3-stranded sheets
           uperfamily
           1. Glucose permease-like [51262] (3)
              1. Glucose permease IIa domain, IIa-glc [51263]
                 1. Bacillus subtilis [TaxId: 1423] [51264] (2)
                 2. Mycoplasma capricolum [TaxId: 2095] [51265] (1)
              2. Glucose-specific factor III (glsIII) [51266]
                 synonym: enzyme IIa-glc
                 1. Escherichia coli [TaxId: 562] [51267] (10)
           2. Peptidoglycan hydrolase LytM [102006] (1)
              Peptidase family M23; contains extra N-terminal, non-conserved beta-sheet subdomain
              1. Peptidoglycan hydrolase LytM [102007]
                 1. Staphylococcus aureus [TaxId: 1280] [102008] (1)
        4. Ribosomal L27 protein-like [110324] (2)
           rudiment single hybrid fold with a permuted topology
           uperfamily
           1. Ribosomal L27 protein [110325] (3)
              Pfam 01016
              1. Ribosomal protein L27 [110326]
                 1. Thermus thermophilus [TaxId: 274] [110327] (2)
                    SQ P84123
                 2. Escherichia coli [TaxId: 562] [159322] (29)
                    SQ P0A7L8 1-84
                 3. Deinococcus radiodurans [TaxId: 1299] [159323] (11)
                    SQ Q9RY65 2-85
           2. ECR1 N-terminal domain-like [159324] (5)
              ECR1 - Exosome complex RNA-binding protein 1
              1. Ribosomal RNA-processing protein 40, RRP40 [159325]
                 1. Human (Homo sapiens) [TaxId: 9606] [159326] (1)
                    SQ Q9NQT5 17-107
              2. Exosome component 1, EXOSC1 [159327]
                 3'-5' exoribonuclease CSL4 homolog
                 1. Human (Homo sapiens) [TaxId: 9606] [159328] (1)
                    SQ Q9Y3B2 6-60
              3. Exosome complex RNA-binding protein 1, ECR1 [159329]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [159330] (3)
                    SQ O29758 2-52
                 2. Sulfolobus solfataricus [TaxId: 2287] [159331] (2)
                    SQ Q9UXC4 7-65
              4. Ribosomal RNA-processing protein 4, RRP4 [159332]
                 1. Human (Homo sapiens) [TaxId: 9606] [159333] (1)
                    SQ Q13868 25-72
   144. beta-clip [51268] (7)
        double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
        1. AFP III-like domain [51269] (1)
           duplication: consists of two structural repeats related by pseudo dyad
           uperfamily
           1. AFP III-like domain [51270] (5)
              Pfam 01354
              1. Type III antifreeze protein, AFP III [51271]
                 1. Ocean pout (Macrozoarces americanus), different isoforms [TaxId: 8199] [51272] (31)
                 2. Antarctic eel pout (Lycodichthys dearborni), RD1 isoform [TaxId: 8201] [89424] (1)
                 3. Antarctic eel pout (Austrolycichthys brachycephalus) and (Lycodichthys dearborni), RD3 isoform [TaxId: 36221] [51273] (4)
                    duplication: intramolecular dimer
              2. Spore coat polysaccharide biosynthesis protein SpsE, C-terminal domain [110328]
                 1. Bacillus subtilis [TaxId: 1423] [110329] (1)
                    SQ P39625
              3. Capsule biosynthesis protein SiaC, C-terminal domain [117330]
                 1. Neisseria meningitidis [TaxId: 487] [117331] (4)
                    SQ Q57265
        2. SET domain [82199] (3)
           duplication: the core is composed of two structural repeats similar to (circularly permuted) repeats of AFPIII
           also contains a substrate-binding alpha+beta subdomain inserted in the core
           uperfamily
           1. Histone lysine methyltransferases [82200] (3)
              contains metal-binding preSET and postSET domains
              1. Dim-5 [82201]
                 1. Fungus (Neurospora crassa) [TaxId: 5141] [82202] (2)
              2. SET domain of Clr4 [82203]
                 ortholog of Dim-5
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82204] (2)
              3. Histone H3 K4-specific methyltransferase SET7/9 catalytic domain [82205]
                 1. Human (Homo sapiens) [TaxId: 9606] [82206] (11)
                    SQ Q8WTS6 52-336
           2. Viral histone H3 Lysine 27 Methyltransferase [82207] (1)
              consists of SET domain only; dimeric
              1. Viral histone H3 Lysine 27 Methyltransferase [82208]
                 1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82209] (3)
           3. RuBisCo LSMT catalytic domain [82210] (1)
              1. RuBisCo LSMT catalytic domain [82211]
                 1. Garden pea (Pisum sativum) [TaxId: 3888] [82212] (15)
        3. Head decoration protein D (gpD, major capsid protein D) [51274] (1)
           uperfamily
           1. Head decoration protein D (gpD, major capsid protein D) [51275] (2)
              1. Head decoration protein D (gpD, major capsid protein D) [51276]
                 1. Bacteriophage lambda [TaxId: 10710] [51277] (3)
                    SQ P03712
                 2. Bacteriophage P21 [TaxId: 10711] [117332] (3)
                    SQ P36275
        4. Urease, beta-subunit [51278] (1)
           uperfamily
           1. Urease, beta-subunit [51279] (3)
              1. Urease, beta-subunit [51280]
                 1. Klebsiella aerogenes [TaxId: 28451] [51281] (27)
                 2. Bacillus pasteurii [TaxId: 1474] [51282] (6)
                 3. Helicobacter pylori [TaxId: 210] [69367] (2)
                    fused with gamma subunit
        5. MoeA C-terminal domain-like [63867] (1)
           uperfamily
           1. MoeA C-terminal domain-like [63868] (5)
              1. Molybdenum cofactor biosynthesis protein MoeA, C-terminal domain [63869]
                 1. Escherichia coli [TaxId: 562] [63870] (27)
                 2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102009] (1)
                 3. Pyrococcus furiosus [TaxId: 2261] [117333] (1)
                    SQ Q8U034
                 4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117334] (1)
                    SQ O59354; PH1647
              2. Gephyrin, C-terminal domain [110330]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [110331] (4)
                    SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
        6. dUTPase-like [51283] (1)
           forms tight trimer through an additional beta-sheet in each subunit
           subunit beta-sheets are orthogonally packed around the three-fold axis
           uperfamily
           1. dUTPase-like [51284] (9)
              1. Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) [51285]
                 1. Escherichia coli [TaxId: 562] [51286] (10)
                    SQ P06968
                 2. Mycobacterium tuberculosis, rv2697c [TaxId: 1773] [82213] (8)
                 3. Human (Homo sapiens) [TaxId: 9606] [102010] (11)
                 4. Feline immunodeficiency virus [TaxId: 11673] [51287] (8)
                 5. Equine infectious anemia virus [TaxId: 11665] [51288] (2)
                 6. Plasmodium falciparum [TaxId: 5833] [141654] (3)
                    SQ Q8II92 1-159
              2. Bifunctional dCTP deaminase/dUTPase [89425]
                 elaborated fold with additional structures
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [89426] (5)
                    synonym: Methanocaldococcus jannaschii
              3. Deoxycytidine triphosphate deaminase (dCTP deaminase) [117335]
                 1. Escherichia coli [TaxId: 562] [117336] (3)
                    SQ P28248
              4. Monomeric viral dUTPase [141655]
                 related to the trimeric dUTPase domain by domain duplication, fusion and partial deletion; retains only one of the three ancestral active sites
                 1. Epstein-barr virus [TaxId: 10376] [141656] (4)
                    SQ P03195 121-256! SQ P03195 4-116
                    Human herpesvirus 4
        7. Tlp20, baculovirus telokin-like protein [51289] (1)
           similar to dUTPase in fold and trimeric assembly
           uperfamily
           1. Tlp20, baculovirus telokin-like protein [51290] (1)
              1. Tlp20, baculovirus telokin-like protein [51291]
                 1. AcMNPV (Autographa californica nuclear polyhedrosis virus) [TaxId: 46015] [51292] (1)
   145. PheT/TilS domain [56036] (1)
        core: 3 layers; contains beta-sandwich of unusual topology
        1. PheT/TilS domain [56037] (2)
           contains putative tRNA-binding structural motif
           uperfamily
           1. tRNA-Ile-lysidine synthetase, TilS, C-terminal domain [116720] (1)
              PfamB 001050
              1. tRNA-Ile-lysidine synthetase, TilS, C-terminal domain [116721]
                 formerly putative cell cycle protein MesJ
                 1. Escherichia coli [TaxId: 562] [116722] (1)
           2. B3/B4 domain of PheRS, PheT [56038] (1)
              Pfam 03483; decorated with additional structures
              1. B3/B4 domain of PheRS, PheT [56039]
                 1. Thermus thermophilus [TaxId: 274] [56040] (9)
                    identical sequence to Thermus aquaticus, TaxId: 271
   146. C-terminal autoproteolytic domain of nucleoporin nup98 [82214] (1)
        multisheet protein with a mixture of beta-sandwich and beta-prism features
        1. C-terminal autoproteolytic domain of nucleoporin nup98 [82215] (1)
           uperfamily
           1. C-terminal autoproteolytic domain of nucleoporin nup98 [82216] (1)
              1. C-terminal autoproteolytic domain of nucleoporin nup98 [82217]
                 pore-targeting domain
                 1. Human (Homo sapiens) [TaxId: 9606] [82218] (1)
   147. Pseudo beta-prism [141657] (1)
        beta-sandwich with one regular beta-sheet and the other beta-sheet bent in the middle with a set of aligned beta-bulges
        1. Bacteriophage trimeric proteins domain [141658] (2)
           found in phage proteins that form trimers, but is not involved in the trimerisation
           uperfamily
           1. Mtd domain-like [141659] (1)
              1. Major tropism determinant (Mtd), N-terminal domain [141660]
                 includes extra N-terminal trimerization domain; beta-alpha-beta(3)
                 1. Bordetella phage bpp-1 [TaxId: 194699] [141661] (13)
                    SQ Q775D6 5-170
                    includes other related Bordetella phages
           2. Lactophage receptor-binding protein N-terminal domain [141662] (1)
              1. Receptor binding protein, rbp, N-terminal domain [141663]
                 includes extra N-terminal trimerization helix
                 1. Lactococcus lactis phage p2 [TaxId: 100641] [141664] (6)
                    SQ Q71AW2 2-140
   148. SARS ORF9b-like [141665] (1)
        complex dimeric fold with three intersubunit beta-sheets packed around a single core
        1. 'SARS ORF9b-like [141666] (1)
           uperfamily
           1. SARS ORF9b-like [141667] (1)
              PfamB 005852
              1. Hypothetical protein 5 (ORF-9b) [141668]
                 1. SARS coronavirus [TaxId: 227859] [141669] (8)
                    SQ P59636 9-98
   149. Adsorption protein p2 [89427] (1)
        multisheet protein containing partial beta-propeller and beta-sandwich regions
        1. Adsorption protein p2 [89428] (1)
           uperfamily
           1. Adsorption protein p2 [89429] (1)
              1. Adsorption protein p2 [89430]
                 synonym: receptor-binding protein p2
                 1. Bacteriophage prd1 [TaxId: 10658] [89431] (2)
   150. Baseplate structural protein gp8 [89432] (1)
        multisheet protein with a mixture of beta-sandwich and beta-barrel features
        1. Baseplate structural protein gp8 [89433] (1)
           uperfamily
           1. Baseplate structural protein gp8 [89434] (1)
              1. Baseplate structural protein gp8 [89435]
                 1. Bacteriophage T4 [TaxId: 10665] [89436] (3)
   151. Hedgehog/intein (Hint) domain [51293] (1)
        complex fold made of five beta-hairpin units and a b-ribbon arc
        1. Hedgehog/intein (Hint) domain [51294] (2)
           duplication: contains two intertwined structural repeats
           uperfamily
           1. Hedgehog C-terminal (Hog) autoprocessing domain [51295] (1)
              1. Hedgehog [51296]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [51297] (1)
           2. Intein (protein splicing domain) [51298] (4)
              1. VMA1-derived endonuclease (VDE) PI-Scei intein [51299]
                 also contains a homing endonuclease and DNA-binding domains
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51300] (8)
                    SQ P17255 284-737
              2. PI-Pfui intein [51301]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [51302] (1)
              3. GyrA intein [51303]
                 miniintein lacking the homing endonuclease domain
                 1. Mycobacterium xenopi [TaxId: 1789] [51304] (1)
              4. DnaB intein [102011]
                 miniintein lacking the homing endonuclease domain
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [102012] (1)
   152. LexA/Signal peptidase [51305] (1)
        complex fold made of several coiled beta-sheets; contains an SH3-like barrel
        1. LexA/Signal peptidase [51306] (2)
           uperfamily
           1. LexA-related [51307] (3)
              1. UmuD' [51308]
                 self-processed fragment of UmuD SOS response protein
                 1. Escherichia coli [TaxId: 562] [51309] (3)
              2. LexA C-terminal domain [63871]
                 1. Escherichia coli [TaxId: 562] [63872] (6)
              3. lambda repressor C-terminal domain [51310]
                 1. Bacteriophage lambda [TaxId: 10710] [51311] (2)
           2. Type 1 signal peptidase [51312] (1)
              contains additional all-beta subdomain inserted in the superfamily fold
              1. Type 1 signal peptidase [51313]
                 1. Escherichia coli [TaxId: 562] [51314] (3)
                    SQ P00803 81-324
   153. Cloacin translocation domain [69368] (1)
        complex fold made of several coiled beta-sheets
        1. Cloacin translocation domain [69369] (1)
           uperfamily
           1. Cloacin translocation domain [69370] (2)
              Pfam 03515
              1. Colicin E3 N-terminal domain [69371]
                 1. Escherichia coli [TaxId: 562] [69372] (3)
              2. Colicin B N-terminal domain [102013]
                 1. Escherichia coli [TaxId: 562] [102014] (1)
   154. Mss4-like [51315] (1)
        complex fold made of several coiled beta-sheets
        1. Mss4-like [51316] (4)
           duplication: tandem repeat of two similar structural motifs
           uperfamily
           1. RabGEF Mss4 [51317] (2)
              contains zinc-binding site
              1. RabGEF Mss4 [51318]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [51319] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [51320] (3)
           2. Translationally controlled tumor protein TCTP (histamine-releasing factor) [63873] (3)
              contains an insertion of alpha helical hairpin; lacks zinc-binding site
              1. Translationally controlled tumor protein TCTP (histamine-releasing factor) [63874]
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [63875] (2)
                 2. Plasmodium knowlesi [TaxId: 5850] [110332] (1)
                    SQ P84152
                 3. Human (Homo sapiens) [TaxId: 9606] [117337] (5)
                    SQ P13693
           3. SelR domain [75041] (2)
              1. C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB [75042]
                 1. Neisseria gonorrhoeae [TaxId: 485] [75043] (1)
              2. Peptide methionine sulfoxide reductase MsrB [141670]
                 1. Bacillus subtilis [TaxId: 1423] [141671] (1)
                    SQ P54155 1-143
           4. Glutathione-dependent formaldehyde-activating enzyme, Gfa [117338] (1)
              Pfam 04828; DUF636
              1. Glutathione-dependent formaldehyde-activating enzyme, Gfa [117339]
                 1. Paracoccus denitrificans [TaxId: 266] [117340] (2)
                    SQ Q51669
   155. Cyanovirin-N [51321] (1)
        complex fold
        1. Cyanovirin-N [51322] (1)
           duplication: tandem repeat of two homologous motifs made three stranded beta-sheet and beta-hairpins
           uperfamily
           1. Cyanovirin-N [51323] (1)
              1. Cyanovirin-N [51324]
                 1. Cyanobacterium (Nostoc ellipsosporum) [TaxId: 45916] [51325] (11)
   156. Tp47 lipoprotein, N-terminal domain [82219] (1)
        complex fold; consists of two intertwined subdomains
        1. Tp47 lipoprotein, N-terminal domain [82220] (1)
           uperfamily
           1. Tp47 lipoprotein, N-terminal domain [82221] (1)
              1. Tp47 lipoprotein, N-terminal domain [82222]
                 a penicillin-binding protein with carboxypeptidase activity
                 1. Treponema pallidum [TaxId: 160] [82223] (1)
   157. Methuselah ectodomain [63876] (1)
        complex fold
        1. Methuselah ectodomain [63877] (1)
           duplication: contains two similar sub domains connected by a structured linker
           uperfamily
           1. Methuselah ectodomain [63878] (1)
              1. Methuselah ectodomain [63879]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63880] (5)
   158. Head-binding domain of phage P22 tailspike protein [51326] (1)
        complex fold made of bifurcated and partly folded beta-sheet
        1. Head-binding domain of phage P22 tailspike protein [51327] (1)
           uperfamily
           1. Head-binding domain of phage P22 tailspike protein [51328] (1)
              1. Head-binding domain of phage P22 tailspike protein [51329]
                 1. Salmonella bacteriophage P22 [TaxId: 10754] [51330] (1)
   159. E2 regulatory, transactivation domain [51331] (1)
        complex fold made of bifurcated and coiled beta-sheets
        1. E2 regulatory, transactivation domain [51332] (1)
           uperfamily
           1. E2 regulatory, transactivation domain [51333] (3)
              1. E2 regulatory, transactivation domain [51334]
                 1. Human papillomavirus type 18 [TaxId: 333761] [51335] (2)
                    SQ Q80B71 1-193
                 2. Human papillomavirus type 16 [TaxId: 333760] [51336] (2)
                 3. Human papillomavirus type 11 [TaxId: 10580] [102015] (2)
   160. MoeA N-terminal region -like [63881] (1)
        complex fold made of bifurcated and coiled b-sheets
        1. MoeA N-terminal region -like [63882] (1)
           uperfamily
           1. MoeA N-terminal region -like [63883] (5)
              1. Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains [63884]
                 1. Escherichia coli [TaxId: 562] [63885] (27)
                 2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102016] (1)
                 3. Pyrococcus furiosus [TaxId: 2261] [117341] (1)
                    SQ Q8U034
                 4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117342] (1)
                    SQ O59354
              2. Gephyrin, domains 3 and 4 [110333]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [110334] (4)
                    SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
   161. MOSC N-terminal domain-like [141672] (1)
        complex fold; comprises a beta-hairpin and a meander 3-stranded sheet packed against beta-barrel: closed, n=5, S=8; contains three short helices
        1. MOSC N-terminal domain-like [141673] (1)
           uperfamily
           1. MOSC N-terminal domain-like [141674] (1)
              Pfam 03476
              1. Hypothetical protein BB0938 [141675]
                 1. Bordetella bronchiseptica [TaxId: 518] [141676] (1)
                    SQ Q7WNU7 1-128
   162. MAL13P1.257-like [141677] (1)
        complex fold; duplication: consists of two intertwinned structural repeats related by pseudo dyad
        1. MAL13P1.257-like [141678] (1)
           uperfamily
           1. MAL13P1.257-like [141679] (1)
              PANTHER 12857; DUF866_euk
              1. Hypothetical protein MAL13P1.257 [141680]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141681] (2)
                    SQ Q8IDI8 1-156
   163. Composite domain of metallo-dependent hydrolases [51337] (1)
        pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
        1. Composite domain of metallo-dependent hydrolases [51338] (11)
           this domain is interrupted by the catalytic beta/alpha barrel domain
           uperfamily
           1. Cytosine deaminase [69373] (1)
              1. Cytosine deaminase [69374]
                 1. Escherichia coli [TaxId: 562] [69375] (8)
                    SQ P25524
           2. alpha-Subunit of urease [51339] (3)
              1. alpha-Subunit of urease [51340]
                 1. Klebsiella aerogenes [TaxId: 28451] [51341] (27)
                 2. Bacillus pasteurii [TaxId: 1474] [51342] (6)
                 3. Helicobacter pylori [TaxId: 210] [69376] (2)
           3. Hydantoinase (dihydropyrimidinase) [75044] (9)
              1. D-hydantoinase [75045]
                 1. Thermus sp. [TaxId: 275] [75046] (2)
                 2. Bacillus stearothermophilus [TaxId: 1422] [75047] (1)
                 3. Burkholderia pickettii [TaxId: 329] [89437] (1)
                 4. Bacillus sp. AR9 [TaxId: 301298] [141682] (2)
                    SQ Q5DLU2 2-52,385-460
              2. L-hydantoinase [75048]
                 1. Arthrobacter aurescens [TaxId: 43663] [75049] (1)
              3. Dihydropyrimidinase related protein-1 [102017]
                 1. Mouse (Mus musculus) [TaxId: 10090] [102018] (1)
              4. Dihydropyrimidine amidohydrolase Pyd2 [141683]
                 1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [141684] (12)
                    SQ Q9P903 2-56,441-541
                 2. Dictyostelium discoideum [TaxId: 44689] [141685] (1)
                    SQ Q86LT2 7-59,394-490
              5. Two-domain dihydroorotase [141686]
                 1. Aquifex aeolicus [TaxId: 63363] [141687] (3)
                    SQ O66990 1-55,366-422
           4. SAH/MTA deaminase-like [82224] (5)
              1. Hypothetical protein TM0936 [82225]
                 1. Thermotoga maritima [TaxId: 2336] [82226] (3)
              2. Hypothetical protein GOS_1943094 [159334]
                 1. Environmental samples [159335] (1)
              3. Guanine deaminase [159336]
                 1. Bradyrhizobium japonicum [TaxId: 375] [159337] (1)
                    SQ Q89NG0 1-70,396-465
                    Blr3880
                 2. Human (Homo sapiens) [TaxId: 9606] [159338] (1)
                    SQ Q9Y2T3 8-75,389-451
                 3. Clostridium acetobutylicum [TaxId: 1488] [159339] (2)
                    SQ Q97MB6 6-63,374-424
           5. Isoaspartyl dipeptidase [89438] (1)
              1. Isoaspartyl dipeptidase [89439]
                 1. Escherichia coli [TaxId: 562] [89440] (5)
                    SQ P39377
           6. N-acetylglucosamine-6-phosphate deacetylase, NagA [82227] (3)
              1. N-acetylglucosamine-6-phosphate deacetylase, NagA [82228]
                 1. Bacillus subtilis [TaxId: 1423] [102019] (1)
                 2. Thermotoga maritima [TaxId: 2336] [82229] (1)
                    TM0814
                 3. Escherichia coli [TaxId: 562] [141688] (10)
                    SQ P0AF18 1-53,351-382
           7. D-aminoacylase [82230] (1)
              1. N-acyl-D-aminoacid amidohydrolase [82231]
                 1. Alcaligenes faecalis [TaxId: 511] [82232] (8)
           8. Adenine deaminase [141689] (1)
              1. Putative adenine deaminase EF0837 [141690]
                 1. Enterococcus faecalis [TaxId: 1351] [141691] (1)
                    SQ Q837K0 2-52,320-369
           9. Zn-dependent arginine carboxypeptidase-like [159340] (3)
              1. Uncharacterized protein EAJ56179 [159341]
                 1. Unidentified organism [TaxId: 32644] [159342] (8)
                    94% identity to the Burkholderia phytofirmans ortholog Bphyt_2089 (SQ B2T4I1)
              2. Zn-dependent arginine carboxypeptidase [159343]
                 1. Unidentified organism [TaxId: 32644] [159344] (16)
              3. Xaa-Pro dipeptidase [159345]
                 1. Alteromonas macleodii [TaxId: 28108] [159346] (2)
           10. Imidazolonepropionase-like [159347] (4)
               1. Imidazolonepropionase [159348]
                  1. Bacillus subtilis [TaxId: 1423] [159349] (4)
                     SQ P42084 3-73,374-415
                  2. Agrobacterium tumefaciens [TaxId: 358] [159350] (4)
                     SQ Q8U8Z6 15-77,379-418
               2. Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421 [159351]
                  1. Environmental samples [159352] (2)
                     marine metagenome
               3. Uncharacterized protein BL1453 [159353]
                  1. Bifidobacterium longum [TaxId: 216816] [159354] (1)
                     SQ Q8G4D5 7-68,393-448
           11. DR0824-like [159355] (1)
               1. Hypothetical protein DR0824 [159356]
                  1. Deinococcus radiodurans [TaxId: 1299] [159357] (1)
                     SQ Q9RW45 34-90,399-418
   164. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51343] (1)
        pseudobarrel: sandwich of two sheets packed at a positive interstrand angle and interconnected with many short turns
        1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51344] (1)
           uperfamily
           1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51345] (2)
              1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51346]
                 delta subunit in mitochondria
                 1. Escherichia coli [TaxId: 562] [51347] (4)
                 2. Cow (Bos taurus) [TaxId: 9913] [51348] (5)
   165. N-terminal domain of MutM-like DNA repair proteins [81625] (1)
        pseudobarrel; capped on both ends by alpha-helices
        1. N-terminal domain of MutM-like DNA repair proteins [81624] (1)
           uperfamily
           1. N-terminal domain of MutM-like DNA repair proteins [81623] (6)
              1. DNA repair protein MutM (Fpg) [81621]
                 1. Thermus thermophilus [TaxId: 274] [81609] (1)
                 2. Bacillus stearothermophilus [TaxId: 1422] [81612] (9)
                 3. Escherichia coli [TaxId: 562] [81616] (1)
                 4. Lactococcus lactis [TaxId: 1358] [81617] (7)
                    SQ P42371
              2. Endonuclease VIII [82233]
                 1. Escherichia coli [TaxId: 562] [82234] (9)
                    SQ P50465
              3. Endonuclease VIII-like 1 (NEIL1) [110335]
                 1. Human (Homo sapiens) [TaxId: 9606] [110336] (1)
                    SQ Q96FI4 1-333
   166. Hypothetical protein YojF [89441] (1)
        pseudobarrel; capped at one end by an alpha-helix
        1. Hypothetical protein YojF [89442] (1)
           uperfamily
           1. Hypothetical protein YojF [89443] (1)
              1. Hypothetical protein YojF [89444]
                 1. Bacillus subtilis [TaxId: 1423] [89445] (1)
   167. DNA-binding pseudobarrel domain [101935] (1)
        core: barrel, open; n=7, S*=10; capped with helices at both ends; partial similarity to the AbrB/MazE/MraZ-like fold (scop_cf 89446)
        1. DNA-binding pseudobarrel domain [101936] (2)
           uperfamily
           1. Type II restriction endonuclease effector domain [101937] (1)
              1. Restriction endonuclease EcoRII, N-terminal domain [101938]
                 1. Escherichia coli [TaxId: 562] [101939] (1)
           2. B3 DNA binding domain [117343] (2)
              Pfam 02362
              1. DNA-binding protein RAV1 [117344]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117345] (1)
                    SQ Q9ZWM9 182-298
              2. At1g16640 [141692]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141693] (1)
                    SQ Q9FX77 1-102
   168. Double-split beta-barrel [89446] (2)
        pseudobarrel; capped on both ends by alpha-helices
        1. AbrB/MazE/MraZ-like [89447] (3)
           members of this superfamily are known or predicted to have DNA-binding function
           uperfamily
           1. Kis/PemI addiction antidote [89448] (1)
              forms intertwined homodimer
              1. MazE [89449]
                 1. Escherichia coli [TaxId: 562] [89450] (2)
           2. AbrB N-terminal domain-like [54743] (2)
              dimeric fold similar to MazE; the DNA-binding site is similar to the conserved surface site of MraZ
              1. Transcription-state regulator AbrB, the N-terminal DNA recognition domain [54744]
                 1. Bacillus subtilis [TaxId: 1423] [54745] (6)
              2. Putative transition state regulator ABH [159358]
                 1. Bacillus subtilis [TaxId: 1423] [159359] (2)
                    SQ P39758 1-54
           3. Hypothetical protein MraZ [102020] (1)
              duplication: contains two interlocking repeats of similar sequence arranged as subunits in the MazE homodimer
              1. Hypothetical protein MraZ [102021]
                 1. Mycoplasma pneumoniae [TaxId: 2104] [102022] (3)
        2. AF2212/PG0164-like [141694] (2)
           six-stranded barrel, topologically similar to the Reductase/isomerase/elongation factor domain fold (scop_cf 50412)
           uperfamily
           1. PG0164-like [141695] (1)
              duplication: comprises two intertwinned beta(2)-alpha-beta structural repeats
              1. Hypothetical protein PG0164 [141696]
                 1. Porphyromonas gingivalis [TaxId: 837] [141697] (1)
                    SQ Q7MXL1 20-104
           2. AF2212-like [159360] (1)
              Pfam 01954; DUF104; intertwinned homodimer of beta(2)-loop-beta subunits; the capping helices are replaced with extended loops
              1. Uncharacterized protein AF2212 [159361]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [159362] (2)
                    SQ O28071 1-61
   169. PUA domain-like [88696] (1)
        pseudobarrel; mixed folded sheet of 5 strands; order 13452; strand 1 and 3 are parallel to each other
        1. PUA domain-like [88697] (13)
           uperfamily
           1. PUA domain [88698] (10)
              RNA-binding domain
              1. Pseudouridine synthase II TruB, C-terminal domain [88699]
                 1. Escherichia coli [TaxId: 562] [88700] (3)
                 2. Thermotoga maritima [TaxId: 2336] [102023] (8)
                 3. Mycobacterium tuberculosis [TaxId: 1773] [102024] (1)
                 4. Archaeon Methanococcus jannaschii [TaxId: 2190] [141698] (1)
                    SQ Q57612 247-331
                 5. Archaeon Pyrococcus furiosus [TaxId: 2261] [141699] (4)
                    SQ Q7LWY0 250-333
              2. Archaeosine tRNA-guanine transglycosylase, C3 domain [88701]
                 the last of the 3 additional C-terminal domains to the TGT-like domain
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [88702] (4)
              3. Hypothetical protein Ta1423, C-terminal domain [102025]
                 this protein is related to the C-terminal part (domains C2 and C3) of Archaeosine tRNA-guanine transglycosylase
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102026] (1)
              4. Nip7p homolog, C-terminal domain [110337]
                 1. Human (Homo sapiens) [TaxId: 9606] [110338] (2)
                    SQ Q9Y221
              5. Hypothetical protein APE0525, C-terminal domain [141700]
                 1. Archaeon Aeropyrum pernix [TaxId: 56636] [141701] (3)
                    SQ Q9YEQ6 91-186
              6. Uncharacterized protein AF0587 [159363]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [159364] (1)
                    SQ O29668 460-527
           2. ATP sulfurylase N-terminal domain [63801] (5)
              contains extra structures; some similarity to the PK beta-barrel domain
              1. ATP sulfurylase N-terminal domain [63802]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63803] (8)
                 2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [63804] (2)
                 3. Sulfur-oxidizing endosymbiont of Riftia pachyptila [TaxId: 35843] [69296] (1)
                 4. Thermus thermophilus [TaxId: 274] [102027] (1)
                 5. Human (Homo sapiens) [TaxId: 9606] [141702] (6)
                    SQ O43252 229-389
           3. YggJ N-terminal domain-like [89451] (3)
              1. Hypothetical protein HI0303 [89452]
                 1. Haemophilus influenzae [TaxId: 727] [89453] (2)
              2. Hypothetical protein YqeU [102028]
                 1. Bacillus subtilis [TaxId: 1423] [102029] (1)
              3. Hypothetical protein TTHA0657 (TT1575) [117346]
                 1. Thermus thermophilus [TaxId: 274] [117347] (3)
                    SQ Q5SKI6
           4. Hypothetical protein EF3133 [110339] (1)
              Pfam 06171; DUF984
              1. Hypothetical protein EF3133 [110340]
                 1. Enterococcus faecalis [TaxId: 1351] [110341] (1)
                    SQ Q82ZD1
           5. Hypothetical protein TTHA0113 [117348] (1)
              Pfam 04266; DUF437
              1. Hypothetical protein TTHA0113 [117349]
                 1. Thermus thermophilus [TaxId: 274] [117350] (2)
                    SQ Q5SM30
           6. ProFAR isomerase associated domain [117351] (2)
              Pfam 07060; DUF1530
              1. Hypothetical protein PF0470 [117352]
                 1. Pyrococcus furiosus [TaxId: 2261] [117353] (1)
                    SQ Q8U3J6
              2. Hypothetical protein PF0455 [117354]
                 1. Pyrococcus furiosus [TaxId: 2261] [117355] (1)
                    SQ Q8U3L1
           7. yqfB-like [117356] (1)
              Pfam 06164; DUF978
              1. Hypothetical protein YqfB [117357]
                 1. Escherichia coli [TaxId: 562] [117358] (1)
                    SQ P67603
           8. Atu2648/PH1033-like [141703] (6)
              Pfam 01878; DUF55
              1. Hypothetical protein PP5205 [141704]
                 1. Pseudomonas putida kt2440 [TaxId: 160488] [141705] (3)
                    SQ Q88CH6 2-149
              2. Hypothetical protein PH1033 [141706]
                 1. Pyrococcus horikoshii [TaxId: 53953] [141707] (3)
                    SQ O58764 1-145
              3. Hypothetical protein PSPTO5229 [141708]
                 PP5205 ortholog
                 1. Pseudomonas syringae [TaxId: 317] [141709] (1)
                    SQ Q87UR7 2-149
              4. Hypothetical protein RPA0253 [141710]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [141711] (1)
                    SQ Q6ND56 2-137
              5. Hypothetical protein Atu2648 [141712]
                 1. Agrobacterium tumefaciens [TaxId: 358] [141713] (1)
                    SQ Q8UC50 2-147
              6. Hypothetical protein LmjF36.6870 [141714]
                 1. Leishmania major [TaxId: 5664] [141715] (1)
                    SQ Q4Q067 7-163
           9. Hypothetical RNA methyltransferase domain (HRMD) [141716] (3)
              N-terminal part of Pfam 03602, structurally similar to PUA domain family
              1. Hypothetical protein TTHA1280, N-terminal domain [141717]
                 1. Thermus thermophilus [TaxId: 274] [141718] (10)
                    SQ Q5SIT4 1-164
              2. Hypothetical protein SMu776, N-terminal domain [141719]
                 1. Streptococcus mutans [TaxId: 1309] [141720] (1)
                    SQ Q8DUW5 1-68
              3. Hypothetical protein PH1915, N-terminal domain [141721]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141722] (2)
                    SQ O59578 1-72
           10. LON domain-like [141723] (2)
               Pfam 02190
               1. ATP-dependent protease La (Lon), N-terminal domain [141724]
                  1. Escherichia coli [TaxId: 562] [141725] (8)
                     SQ P0A9M0 8-117
               2. Hypothetical protein BPP1347 [141726]
                  identical sequence to BP2131 and BB2413 from other Bordetella species
                  1. Bordetella parapertussis [TaxId: 519] [141727] (2)
                     SQ Q7WAM7 2-198
           11. PrgU-like [159365] (1)
               Pfam 09627
               1. Uncharacterized protein PrgU [159366]
                  1. Enterococcus faecalis [TaxId: 1351] [159367] (2)
                     SQ Q8KUD5 12-113
                     EF0006
           12. SRA domain-like [159368] (2)
               Pfam 02182; recognizes the modified cytosine base (m5C) by flipping it out of DNA
               1. E3 ubiquitin-protein ligase UHRF1 [159369]
                  1. Human (Homo sapiens) [TaxId: 9606] [159370] (7)
                     SQ Q96T88 409-615! SQ Q96T88 414-617
                  2. Mouse (Mus musculus) [TaxId: 10090] [159371] (7)
                     SQ Q8VDF2 405-613! SQ Q8VDF2 418-625
           13. YtmB-like [159372] (1)
               PfamB 020780
               1. Hypothetical protein YtmB [159373]
                  1. Bacillus subtilis [TaxId: 1423] [159374] (8)
                     SQ O34365 1-80
   170. AXH domain [102030] (1)
        pseudobarrel; some similarity to OB-fold
        1. AXH domain [102031] (1)
           uperfamily
           1. AXH domain [102032] (1)
              1. Ataxin-1 [102033]
                 1. Human (Homo sapiens) [TaxId: 9606] [102034] (1)
   171. FimD N-terminal domain-like [141728] (1)
        pseudo barrel, capped by an alpha-helix; some topological similarity to the PRC-barrel domain (scop_sf 50346) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
        1. FimD N-terminal domain-like [141729] (1)
           uperfamily
           1. Usher N-domain [141730] (1)
              N-terminal part of Pfam 00577
              1. Outer membrane usher protein FimD [141731]
                 1. Escherichia coli [TaxId: 562] [141732] (4)
                    SQ P30130 46-170! SQ P30130 70-170! SQ P30130 70-184
   172. HisI-like [141733] (1)
        pseudo barrel, capped by an alpha-helix; contains a beta-triangle structure on one side; some topological similarity to the Ribosomal protein L25-like fold (scop_cf 50714) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
        1. HisI-like [141734] (1)
           uperfamily
           1. HisI-like [141735] (1)
              Pfam 01502; PRA-CH; metalloenzyme, probable biological unit is dimeric
              1. Phosphoribosyl-AMP cyclohydrolase HisI [141736]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [141737] (2)
                    SQ O26347 8-131
   173. MFPT repeat-like [141738] (1)
        consists of two similar pseudo barrel subdomains with structural similarity to a circularly permuted SAND domain (scop_fa 63764)
        1. MFPT repeat-like [141739] (1)
           uperfamily
           1. MFPT repeat [141740] (2)
              PfamB 008194
              1. Sperm motility protein MFP2 [141741]
                 1. Pig roundworm (Ascaris suum), isoform B [TaxId: 6253] [141742] (4)
                    SQ Q7YXJ9 185-368! SQ Q7YXJ9 6-184
                    MFPTb
                 2. Pig roundworm (Ascaris suum), isoform A [TaxId: 6253] [141743] (2)
                    SQ Q7YXK2 175-344! SQ Q7YXK2 5-174
                    MFPTa
   174. P-domain of calnexin/calreticulin [63886] (1)
        non-globular proline-rich hairpin
        1. P-domain of calnexin/calreticulin [63887] (1)
           uperfamily
           1. P-domain of calnexin/calreticulin [63888] (2)
              1. Calreticulin [63889]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [63890] (3)
              2. Calnexin [69377]
                 1. Dog (Canis familiaris) [TaxId: 9615] [69378] (1)
3. Alpha and beta proteins (a/b) [51349] (147)
   Mainly parallel beta sheets (beta-alpha-beta units)
   1. TIM beta/alpha-barrel [51350] (33)
      contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
      the first seven superfamilies have similar phosphate-binding sites
      1. Triosephosphate isomerase (TIM) [51351] (1)
         uperfamily
         1. Triosephosphate isomerase (TIM) [51352] (18)
            1. Triosephosphate isomerase [51353]
               1. Chicken (Gallus gallus) [TaxId: 9031] [51354] (16)
                  SQ P00940
               2. Human (Homo sapiens) [TaxId: 9606] [51355] (5)
               3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [102035] (3)
               4. Nematode (Caenorhabditis elegans) [TaxId: 6239] [82235] (1)
               5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51356] (7)
               6. Trypanosoma brucei [TaxId: 5691] [51357] (19)
               7. Trypanosoma cruzi [TaxId: 5693] [51358] (5)
                  SQ P52270
               8. Plasmodium falciparum [TaxId: 5833] [51359] (9)
                  SQ Q07412
               9. Leishmania mexicana [TaxId: 5665] [51360] (4)
               10. Entamoeba histolytica [TaxId: 5759] [82236] (1)
               11. Escherichia coli [TaxId: 562] [51361] (1)
               12. Synthetic, hybrid between Escherichia coli and chicken TIM [51362] (1)
               13. Bacillus stearothermophilus [TaxId: 1422] [51363] (2)
               14. Vibrio marinus [TaxId: 90736] [51364] (2)
               15. Thermotoga maritima [TaxId: 2336] [51365] (1)
               16. Archaeon Pyrococcus woesei [TaxId: 2262] [63891] (1)
               17. Thermoproteus tenax [TaxId: 2271] [110342] (1)
                   SQ Q8NKN9
               18. Trypanosoma (Trypanozoon) brucei brucei (Trypanosoma brucei brucei) [TaxId: 39700] [159375] (2)
      2. Ribulose-phoshate binding barrel [51366] (6)
         uperfamily
         1. Histidine biosynthesis enzymes [51367] (6)
            structural evidence for the gene duplication within the barrel fold
            1. Phosphoribosylformimino-5-aminoimidazole carboxamide ribotite isomerase HisA [51368]
               1. Thermotoga maritima [TaxId: 2336] [51369] (1)
               2. Streptomyces coelicolor [TaxId: 1902] [141744] (2)
                  SQ P16250 2-240
            2. Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF [51370]
               1. Thermotoga maritima [TaxId: 2336] [51371] (4)
               2. Thermus thermophilus [TaxId: 274] [82237] (1)
               3. Baker's yeast (Saccharomyces cerevisiae), His7 [TaxId: 4932] [69379] (4)
               4. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69380] (1)
         2. D-ribulose-5-phosphate 3-epimerase [51372] (5)
            1. D-ribulose-5-phosphate 3-epimerase [51373]
               1. Potato (Solanum tuberosum) [TaxId: 4113] [51374] (1)
               2. Rice (Oryza sativa) [TaxId: 4530] [82238] (2)
               3. Synechocystis sp. PCC 6803 [TaxId: 1148] [110343] (1)
                  SQ P74061
               4. Plasmodium falciparum [TaxId: 5833] [117359] (1)
                  SQ Q8I5L3
               5. Streptococcus pyogenes [TaxId: 1314] [141745] (12)
                  SQ Q9A1H8 3-219
         3. Decarboxylase [51375] (13)
            1. Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase) [51376]
               1. Bacillus subtilis [TaxId: 1423] [51377] (1)
               2. Escherichia coli [TaxId: 562] [51378] (3)
               3. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51379] (20)
               4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51380] (2)
               5. Thermotoga maritima [TaxId: 2336] [141746] (1)
                  SQ Q9WYG7 1-198
               6. Plasmodium vivax [TaxId: 5855] [141747] (1)
               7. Pyrococcus horikoshii [TaxId: 53953] [141748] (8)
                  SQ O58462 1-208
            2. 3-keto-L-gulonate 6-phosphate decarboxylase [75050]
               1. Escherichia coli [TaxId: 562] [75051] (18)
                  SQ P39304
            3. Protozoan orotidine monophosphate decarboxylase [141749]
               1. Plasmodium vivax [TaxId: 5855] [141750] (1)
               2. Plasmodium falciparum [TaxId: 5833] [141751] (2)
                  SQ Q8T6J6 1-323
               3. Plasmodium berghei [TaxId: 5821] [141752] (2)
                  SQ Q4Z4C3 2-325
               4. Plasmodium yoelii [TaxId: 5861] [141753] (1)
                  SQ Q7RPE4 2-322
               5. Plasmodium falciparum (isolate 3D7) (Plasmodium falciparum 3D7) [TaxId: 36329] [159376] (14)
         4. Tryptophan biosynthesis enzymes [51381] (12)
            1. N-(5'phosphoribosyl)antranilate isomerase, PRAI [51382]
               1. Escherichia coli [TaxId: 562] [51383] (1)
                  merged in bifunctional enzyme with IPG synthase
               2. Thermotoga maritima [TaxId: 2336] [51384] (3)
               3. Thermus thermophilus [TaxId: 274] [102036] (1)
            2. Indole-3-glycerophosphate synthase, IPGS [51385]
               1. Escherichia coli [TaxId: 562] [51386] (2)
                  merged in bifunctional enzyme with PRA isomerase
               2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51387] (6)
               3. Thermotoga maritima [TaxId: 2336] [75052] (2)
                  TM0140
               4. Thermus thermophilus [TaxId: 274] [102037] (1)
            3. Trp synthase alpha-subunit [51388]
               1. Salmonella typhimurium [TaxId: 90371] [51389] (49)
               2. Thermus thermophilus [TaxId: 274] [102038] (2)
               3. Archaeon Pyrococcus furiosus [TaxId: 2261] [51390] (7)
               4. Escherichia coli [TaxId: 562] [117360] (6)
                  SQ P00928
               5. Maize (Zea mays) [TaxId: 4577] [117361] (3)
                  SQ P42390
         5. NanE-like [117362] (2)
            Pfam 04131
            1. Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE [117363]
               1. Staphylococcus aureus [TaxId: 1280] [117364] (1)
                  SQ P65517
               2. Streptococcus pyogenes [TaxId: 1314] [141754] (2)
                  SQ P65522 4-233
         6. PdxS-like [141755] (1)
            Pfam 01680; SOR/SNZ
            1. Pyridoxal biosynthesis lyase PdxS [141756]
               PLP synthase
               1. Bacillus stearothermophilus [TaxId: 1422] [141757] (6)
                  SQ Q5L3Y2 18-271
      3. Thiamin phosphate synthase [51391] (1)
         uperfamily
         1. Thiamin phosphate synthase [51392] (2)
            1. Thiamin phosphate synthase [51393]
               1. Bacillus subtilis [TaxId: 1423] [51394] (8)
               2. Archaeon (Pyrococcus furiosus) [TaxId: 2261] [110344] (1)
                  SQ Q8U192
      4. Pyridoxine 5'-phosphate synthase [63892] (1)
         uperfamily
         1. Pyridoxine 5'-phosphate synthase [63893] (1)
            1. Pyridoxine 5'-phosphate synthase [63894]
               1. Escherichia coli [TaxId: 562] [63895] (7)
      5. FMN-linked oxidoreductases [51395] (1)
         uperfamily
         1. FMN-linked oxidoreductases [51396] (30)
            1. Dihydroorotate dehydrogenase [51397]
               1. Lactococcus lactis, isozyme A [TaxId: 1358] [51398] (13)
               2. Lactococcus lactis, isozyme B [TaxId: 1358] [51399] (3)
                  PyrD subunit
               3. Escherichia coli [TaxId: 562] [82239] (1)
               4. Human (Homo sapiens) [TaxId: 9606] [51400] (11)
               5. Rat (Rattus norvegicus) [TaxId: 10116] [102039] (2)
               6. Trypanosoma brucei [TaxId: 5691] [141758] (4)
                  SQ Q57U83 2-313
               7. Plasmodium falciparum [TaxId: 5833] [141759] (1)
                  SQ Q08210 158-566
                  homolog, mitochonrial
            2. Old yellow enzyme (OYE) [51401]
               1. Lager yeast (Saccharomyces pastorianus) [TaxId: 27292] [51402] (5)
               2. Yeast (Candida albicans) [TaxId: 5476] [51403] (2)
            3. 12-oxophytodienoate reductase (OPR, OYE homolog) [63896]
               1. Tomato (Lycopersicon esculentum), OPR1 [TaxId: 4081] [63897] (3)
               2. Thale cress (Arabidopsis thaliana), OPR1 [TaxId: 3702] [102040] (2)
                  At1G76680
               3. Thale cress (Arabidopsis thaliana), OPR3 [TaxId: 3702] [102041] (5)
            4. Glycolate oxidase [51404]
               1. Spinach (Spinacia oleracea) [TaxId: 3562] [51405] (4)
            5. Membrane-associated (S)-mandelate dehydrogenase [63898]
               1. Pseudomonas putida [TaxId: 303] [63899] (3)
            6. Pentaerythritol tetranirate reductase [63900]
               1. Enterobacter cloacae [TaxId: 550] [63901] (15)
                  SQ P71278
            7. Morphinone reductase [75053]
               1. Pseudomonas putida [TaxId: 303] [75054] (1)
            8. Trimethylamine dehydrogenase, N-terminal domain [51406]
               two other domains are alpha/beta Rossmann-like fold and beta/beta/alpha fold
               1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51407] (5)
            9. 2,4-dienoyl-CoA reductase, N-terminal domain [102042]
               1. Escherichia coli [TaxId: 562] [102043] (1)
            10. Flavocytochrome b2, C-terminal domain [51408]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51409] (16)
                   SQ P00175
                   N-terminal domain homologous to cytochrome b5
            11. Dihydropyrimidine dehydrogenase, domain 4 [51410]
                1. Pig (Sus scrofa) [TaxId: 9823] [51411] (5)
            12. Alpha subunit of glutamate synthase, central and FMN domains [69381]
                Central domain (residues 423-780) may be a rudiment form of the FMN domain
                1. Azospirillum brasilense [TaxId: 192] [69382] (7)
                2. Synechocystis sp. [TaxId: 1143] [75055] (5)
            13. Isopentenyl-diphosphate delta-isomerase [89454]
                1. Bacillus subtilis [TaxId: 1423] [89455] (2)
                2. Thermus thermophilus [TaxId: 274] [141760] (6)
                   SQ Q53W52 23-332
                3. Thermus thermophilus HB8 [TaxId: 300852] [159377] (4)
            14. Putative flavin oxidoreducatase TM0096 [102044]
                Dihydrouridine synthase (Dus) homologue; contains extra C-terminal alpha-helical domain
                1. Thermotoga maritima [TaxId: 2336] [102045] (1)
            15. PcrB protein homolog YerE [102046]
                provisional classification; it is not known whether this protein binds FMN or not
                1. Bacillus subtilis [TaxId: 1423] [102047] (1)
            16. Hydroxyacid oxidase [141761]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [141762] (8)
                   SQ Q07523 1-349
            17. NADPH dehydrogenase NamA [141763]
                OYE homolog
                1. Bacillus subtilis [TaxId: 1423] [141764] (8)
                   SQ P54550 1-337
                   probable NADH-dependent flavin oxidoreductase YqjM
            18. (S)-3-O-geranylgeranylglyceryl phosphate synthase [141765]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141766] (4)
                   SQ O29844 1-231
                   PcrB homolog AF0403
      6. Inosine monophosphate dehydrogenase (IMPDH) [51412] (1)
         The phosphate moiety of substrate binds in the 'common' phosphate-binding site
         uperfamily
         1. Inosine monophosphate dehydrogenase (IMPDH) [51413] (8)
            1. Inosine monophosphate dehydrogenase (IMPDH) [51414]
               1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [51415] (1)
               2. Streptococcus pyogenes [TaxId: 1314] [51416] (1)
               3. Tritrichomonas foetus [TaxId: 5724] [51417] (9)
               4. Human (Homo sapiens), type I [TaxId: 9606] [89456] (1)
               5. Human (Homo sapiens), type II [TaxId: 9606] [51418] (3)
               6. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [63902] (1)
               7. Thermotoga maritima [TaxId: 2336] [159378] (1)
                  SQ Q9X168 1-85,213-457
               8. Pyrococcus horikoshii [TaxId: 53953] [159379] (1)
                  SQ O58045 3-96,207-480
      7. PLP-binding barrel [51419] (2)
         circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
         uperfamily
         1. Alanine racemase-like, N-terminal domain [51420] (9)
            1. Alanine racemase [51421]
               1. Bacillus stearothermophilus [TaxId: 1422] [51422] (8)
               2. Pseudomonas aeruginosa [TaxId: 287] [110345] (1)
                  SQ Q9HTQ2
               3. Streptomyces lavendulae [TaxId: 1914] [110346] (3)
                  SQ Q65YW7
            2. Eukaryotic ornithine decarboxylase [51423]
               1. Human (Homo sapiens) [TaxId: 9606] [51424] (1)
               2. Mouse (Mus musculus) [TaxId: 10090] [51425] (1)
               3. Trypanosoma brucei [TaxId: 5691] [51426] (5)
                  SQ P07805
            3. Diaminopimelate decarboxylase LysA [89457]
               most similar to eukaryotic ODC
               1. Mycobacterium tuberculosis [TaxId: 1773] [89458] (2)
               2. Escherichia coli [TaxId: 562] [102048] (2)
               3. Archaeon Methanococcus jannaschii [TaxId: 2190] [110347] (2)
                  SQ Q58497
         2. "Hypothetical" protein ybl036c [51427] (1)
            1. "Hypothetical" protein ybl036c [51428]
               structure from BNL's human proteome project
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51429] (2)
      8. NAD(P)-linked oxidoreductase [51430] (1)
         uperfamily
         1. Aldo-keto reductases (NADP) [51431] (20)
            Common fold covers whole protein structure
            1. FR-1 (fibroblast growth factor-induced) protein [51432]
               1. Mouse (Mus musculus) [TaxId: 10090] [51433] (1)
            2. Voltage-dependent K+ channel beta subunit [51434]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [51435] (6)
            3. Aflatoxin aldehyde reductase (akr7a1) [75056]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [75057] (1)
            4. Aldose reductase (aldehyde reductase) [51436]
               1. Human (Homo sapiens) [TaxId: 9606] [51437] (57)
                  SQ P15121
               2. Pig (Sus scrofa) [TaxId: 9823] [51438] (8)
            5. 3-alpha-hydroxysteroid dehydrogenase [51439]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [51440] (3)
               2. Human (Homo sapiens), type III [TaxId: 9606] [69383] (6)
                  bile acid binding protein
            6. CHO reductase [51441]
               1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [51442] (1)
            7. Hypothetical protein C07D8.6 [102049]
               Aldo-keto reductase family 1 member c1
               1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102050] (1)
            8. Prostaglandin d2 11-ketoreductase (akr1c3) [102051]
               Aldo-keto reductase family 1 member c3
               1. Human (Homo sapiens) [TaxId: 9606] [102052] (10)
                  SQ P42330
            9. 2,5-diketo-D-gluconic acid reductase A [51443]
               1. Corynebacterium sp. [TaxId: 1720] [51444] (3)
               2. Escherichia coli [TaxId: 562] [102053] (1)
               3. Thermotoga maritima [TaxId: 2336] [117365] (1)
                  SQ Q9X0A2
            10. Hypothetical oxidoreductase YdhF [89459]
                1. Escherichia coli [TaxId: 562] [89460] (2)
            11. Putative oxidoreductase IolS [102054]
                vegetative protein 147, VEG147, AKR11A
                1. Bacillus subtilis [TaxId: 1423] [102055] (2)
            12. Putative oxidoreductase YhdN [102056]
                General stress protein 69, GSP69, AKR11B
                1. Bacillus subtilis [TaxId: 1423] [102057] (1)
            13. Tas protein [89461]
                1. Escherichia coli [TaxId: 562] [89462] (1)
            14. Xylose reductase [75058]
                1. Fungi (Candida tenuis) [TaxId: 45596] [75059] (5)
                   SQ O74237
            15. 20alpha-hydroxysteroid dehydrogenase [109609]
                1. Human (Homo sapiens) [TaxId: 9606] [109610] (2)
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110348] (2)
                   SQ P80508
      9. (Trans)glycosidases [51445] (14)
         uperfamily
         1. Amylase, catalytic domain [51446] (54)
            members of the family may contain various insert subdomains
            in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain
            1. Bacterial alpha-amylase [51447]
               1. Bacillus licheniformis [TaxId: 1402] [51448] (4)
               2. Chimera (Bacillus amyloliquefaciens) and (Bacillus licheniformis) [TaxId: 1390] [63903] (4)
                  the N-terminal 300 residues are from B. amyloliquefaciens
               3. Pseudoalteromonas haloplanktis (Alteromonas haloplanktis) [TaxId: 228] [51449] (9)
               4. Bacillus subtilis [TaxId: 1423] [51450] (2)
                  SQ P00691
               5. Bacillus stearothermophilus [TaxId: 1422] [51451] (1)
               6. Bacillus sp., ksm-k38 [TaxId: 1409] [89463] (6)
               7. Archaeon Pyrococcus woesei [TaxId: 2262] [89464] (3)
               8. Bacillus sp. 707 [TaxId: 1416] [117366] (4)
                  SQ P19571 38-518
               9. Halothermothrix orenii [TaxId: 31909] [141767] (1)
                  SQ Q8GPL8 28-436
               10. Bacillus halmapalus [TaxId: 79882] [141768] (3)
                   SQ P19571 38-431
            2. Maltosyltransferase [63904]
               similar to bacterial alpha-amylase; contains larger insertion domain
               1. Thermotoga maritima [TaxId: 2336] [63905] (2)
            3. Cyclodextrin glycosyltransferase [51452]
               contains two more all-beta domains, one is Immunoglobulin-like and the other is trasthyretin-like
               1. Bacillus circulans, different strains [TaxId: 1397] [51453] (36)
               2. Bacillus stearothermophilus [TaxId: 1422] [51454] (1)
               3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [51455] (2)
               4. Bacillus sp. 1011, alkaliphilic [TaxId: 1410] [51456] (8)
                  SQ P05618
               5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [51457] (2)
               6. Thermoanaerobacterium [TaxId: 28895] [159380] (2)
            4. Animal alpha-amylase [51458]
               contains Ca2+-binding subdomain, residues 100-170
               1. Pig (Sus scrofa) [TaxId: 9823] [51459] (14)
               2. Human (Homo sapiens) [TaxId: 9606] [51460] (43)
                  SQ P04746 16-511 ! SQ 04746
               3. Yellow mealworm (Tenebrio molitor), larva [TaxId: 7067] [51461] (4)
            5. Fungal alpha-amylases [51462]
               1. Aspergillus niger, acid amylase [TaxId: 5061] [51463] (1)
               2. Aspergillus oryzae, Taka-amylase [TaxId: 5062] [51464] (8)
            6. Maltogenic amylase, central domain [51465]
               contains an additional N-terminal domain
               1. Thermus sp. [TaxId: 275] [51466] (2)
               2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [75060] (1)
               3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [75061] (9)
               4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [51467] (25)
            7. Neopullulanase, central domain [82240]
               homologous to Maltogenic amylase
               1. Bacillus stearothermophilus [TaxId: 1422] [82241] (4)
            8. Cyclomaltodextrinase, central domain [102058]
               protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
               1. Flavobacterium sp. 92 [TaxId: 197856] [102059] (1)
            9. Maltooligosyl trehalose synthase [82242]
               elaborated with several large insertions in the common fold
               1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82243] (1)
            10. Glycosyltrehalose trehalohydrolase, central domain [51468]
                contains an additional N-terminal domain
                1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [51469] (2)
                2. Deinococcus radiodurans [TaxId: 1299] [141769] (9)
                   SQ Q9RX51 111-528
            11. 1,4-alpha-glucan branching enzyme, central domain [82244]
                1. Escherichia coli [TaxId: 562] [82245] (1)
            12. Isoamylase, central domain [51470]
                1. Pseudomonas amyloderamosa [TaxId: 32043] [51471] (1)
            13. G4-amylase (1,4-alpha-D-glucan maltotetrahydrolase) [51472]
                1. Pseudomonas stutzeri [TaxId: 316] [51473] (9)
            14. Plant alpha-amylase [51474]
                1. Barley (Hordeum vulgare), seeds, AMY2 isozyme [TaxId: 4513] [51475] (3)
                2. Barley (Hordeum vulgare), AMY1 isozyme [TaxId: 4513] [89465] (10)
            15. 4-alpha-glucanotransferase [75062]
                1. Thermotoga maritima [TaxId: 2336] [75063] (2)
            16. Oligo-1,6, glucosidase [51476]
                1. Bacillus cereus [TaxId: 1396] [51477] (1)
            17. Isomaltulose synthase PalI [89466]
                1. Klebsiella sp., lx3 [TaxId: 576] [89467] (1)
            18. Amylosucrase [69384]
                1. Neisseria polysaccharea [TaxId: 489] [69385] (10)
            19. Sucrose phosphorylase [102060]
                sequence and close structural relationship to amylosucrase; variations in the C-terminal domain fold
                1. Bifidobacterium adolescentis [TaxId: 1680] [102061] (5)
            20. Melibiase [75064]
                1. Chicken (Gallus gallus) [TaxId: 9031] [75065] (2)
                   alpha-N-acetylgalactosaminidase
                2. Rice (Oryza sativa) [TaxId: 4530] [89468] (1)
                   alpha-galactosidase
                3. Human (Homo sapiens) [TaxId: 9606] [102062] (2)
                   alpha-galactosidase A
                4. Trichoderma reesei [TaxId: 51453] [110349] (2)
                   Alpha-galactosidase agl1
                   SQ Q92456
            21. Amylomaltase MalQ [51478]
                4-alpha-glucanotransferase; single-domain amylase with several insertions in the common fold
                1. Thermus aquaticus [TaxId: 271] [51479] (4)
                   synonym: Thermus thermophilus
                2. Aquifex aeolicus [TaxId: 63363] [141770] (2)
                   SQ O66937 1-485
                3. Potato (Solanum tuberosum) [TaxId: 4113] [141771] (1)
                   SQ Q06801 54-576
            22. A4 beta-galactosidase [82246]
                the catalytic domain is very similar to that of the bacterial beta-amylase; but contains a typical alpha-amylase extra domain
                1. Thermus thermophilus [TaxId: 274] [82247] (2)
            23. Bacterial beta-amylase [51485]
                protein contains additional starch-binding domain
                1. Bacillus cereus [TaxId: 1396] [51486] (14)
            24. beta-Amylase [51481]
                Common fold covers whole protein structure
                1. Soybean (Glycine max) [TaxId: 3847] [51482] (19)
                   SQ P10538
                2. Barley (Hordeum vulgare) [TaxId: 4513] [51483] (1)
                3. Sweet potato (Ipomoea batatas) [TaxId: 4120] [51484] (1)
            25. Pullulanase PulA [159381]
                1. Klebsiella pneumoniae [TaxId: 573] [159382] (3)
                   SQ P07206 410-972
         2. beta-glycanases [51487] (54)
            consist of a number of sequence families
            1. Xylanase [51488]
               1. Clostridium thermocellum, XynZ [TaxId: 1515] [51489] (1)
                  belongs to family F
               2. Bacillus stearothermophilus, Xt6 [TaxId: 1422] [69386] (4)
                  SQ P40943
               3. Bacillus stearothermophilus, Ixt6 [TaxId: 1422] [102063] (1)
                  intra-cellular xylanase
               4. Cellvibrio mixtus [TaxId: 39650] [102064] (4)
               5. Penicillium simplicissimum [TaxId: 69488] [51490] (1)
                  belongs to family 10
               6. Thermotoga maritima [TaxId: 2336] [141772] (4)
                  SQ Q9WXS5 23-346
            2. Endoglucanase CelA [51491]
               1. Clostridium cellulolyticum [TaxId: 1521] [51492] (1)
            3. Endoglucanase CelC [51493]
               1. Clostridium thermocellum [TaxId: 1515] [51494] (3)
            4. Exo-beta-(1,3)-glucanase [51495]
               1. Yeast (Candida albicans) [TaxId: 5476] [51496] (4)
               2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102065] (1)
            5. Endoglucanase homologue TM1752 [102066]
               1. Thermotoga maritima [TaxId: 2336] [102067] (1)
            6. Endocellulase E1 [51497]
               1. Acidothermus cellulolyticus [TaxId: 28049] [51498] (3)
            7. Endocellulase EngI [75066]
               1. Thermoascus aurantiacus [TaxId: 5087] [75067] (2)
            8. Endoglucanase Cel5a [51499]
               1. Bacillus agaradhaerens [TaxId: 76935] [51500] (20)
                  SQ O85465 30-329
               2. Erwinia chrysanthemi [TaxId: 556] [51501] (1)
               3. Bacillus subtilis [TaxId: 1423] [75068] (1)
               4. Pseudoalteromonas haloplanktis [TaxId: 228] [141773] (4)
                  SQ O86099 33-325
            9. Alkaline cellulase K catalytic domain [63906]
               1. Bacillus sp. [TaxId: 1409] [63907] (2)
            10. Beta-mannanase [51502]
                1. Thermomonospora fusca [TaxId: 2021] [51503] (3)
                2. Trichoderma reesei [TaxId: 51453] [51504] (5)
                3. Tomato (Lycopersicon esculentum) [TaxId: 4081] [141774] (1)
                   SQ Q93WT4 30-399
                4. Bacillus sp. JAMB-602 [TaxId: 244966] [141775] (1)
                   SQ Q4W8M3 34-490
                   contains additional C-terminal domain (CBM)
            11. Exomannosidase [102068]
                mannosyl-oligosaccharide glucosidase
                1. Cellvibrio mixtus [TaxId: 39650] [102069] (2)
                   SQ Q6QT42 46-455
            12. Beta-1,4-galactanase [89469]
                1. Fungus (Aspergillus aculeatus) [TaxId: 5053] [89470] (2)
                2. Thielavia heterothallica, aka Myceliophthora thermophila [TaxId: 78579] [89471] (2)
                   Myceliophthora thermophila is the anamorph name whilst Thielavia heterothallica is the teleomorph name
                3. Humicola insolens [TaxId: 34413] [89472] (1)
                4. Bacillus licheniformis [TaxId: 1402] [117367] (7)
                   SQ Q65CX5 36-422 ! SQ Q65CX5 28-424
            13. Mannanase A, ManA [63908]
                1. Pseudomonas cellulosa (Cellvibrio japonicus) [TaxId: 155077] [63909] (5)
                2. Cellulomonas fimi [TaxId: 1708] [141776] (3)
                   SQ Q9XCV5 55-420
            14. Plant beta-glucanases [51507]
                1. Barley (Hordeum vulgare), 1,3-beta-glucanase [TaxId: 4513] [51508] (1)
                2. Barley (Hordeum vulgare), 1,3-1,4-beta-glucanase [TaxId: 4513] [51509] (2)
                3. Banana (Musa acuminata), 1,3-beta-glucanase [TaxId: 4641] [141777] (1)
                   SQ O22317 29-340
            15. beta-Galactosidase, domain 3 [51510]
                1. Escherichia coli [TaxId: 562] [51511] (25)
                   SQ P00722
                2. Arthrobacter sp. c2-2 [TaxId: 192168] [141778] (6)
                   SQ Q8KRF6 313-609
            16. beta-Glucuronidase, domain 3 [51512]
                1. Human (Homo sapiens) [TaxId: 9606] [51513] (1)
            17. Xylanase A, catalytic core [51514]
                1. Streptomyces lividans [TaxId: 1916] [51515] (9)
                   SQ P26514 43-344
                2. Penicillium simplicissimum [TaxId: 69488] [51516] (7)
                3. Pseudomonas fluorescens [TaxId: 294] [51517] (8)
                   SQ P14768 265-610
                4. Thermoascus aurantiacus [TaxId: 5087] [51518] (10)
                5. Streptomyces olivaceoviridis [TaxId: 1921] [51519] (12)
                   SQ Q7SI98
                   N-terminal domain; fused with a ricin A-like beta-trefoil domain
                6. Cellulomonas fimi [TaxId: 1708] [51520] (9)
                   synonym: beta-1,4-glycanase Cex
                7. Streptomyces halstedii [TaxId: 1944] [102070] (1)
                8. Emericella nidulans (Aspergillus nidulans) [TaxId: 162425] [110350] (1)
                   SQ Q00177
            18. Xylanase 10c [102071]
                Endo-beta-1,4-xylanase
                1. Cellvibrio japonicus [TaxId: 155077] [102072] (2)
            19. Glucosylceramidase, catalytic domain [89473]
                acid-beta-glucosidase; glycosyl hydrolase family 30; contains additional beta-domain similar to one found in alpha amylases
                1. Human (Homo sapiens) [TaxId: 9606] [89474] (27)
            20. Glycosyl hydrolase family 5 xylanase, catalytic domain [102073]
                overall domain organization is similar to the homologous glucosylceramidase
                1. Erwinia chrysanthemi [TaxId: 556] [102074] (1)
            21. Alpha-L-arabinofuranosidase, catalytic domain [102075]
                glycosyl hydrolase family 51
                1. Bacillus stearothermophilus [TaxId: 1422] [102076] (4)
                2. Clostridium thermocellum [TaxId: 1515] [141779] (12)
                   SQ Q4CJG5 17-386
            22. Beta-D-xylosidase, catalytic domain [102077]
                glycosyl hydrolase family 39
                1. Thermoanaerobacterium saccharolyticum [TaxId: 28896] [102078] (2)
                2. Bacillus stearothermophilus [TaxId: 1422] [141780] (24)
                   SQ Q9ZFM2 15-361
            23. endo-1,4-beta-mannosidase [141781]
                1. Blue mussel (Mytilus edulis) [TaxId: 6550] [141782] (1)
                   SQ Q8WPJ2 18-367
            24. Endoglucanase H N-terminal domain [141783]
                1. Clostridium thermocellum [TaxId: 1515] [141784] (4)
                   SQ P16218 29-304! SQ P16218 31-304
            25. Exochitosanase CsxA [159383]
                1. Amycolatopsis orientalis [TaxId: 31958] [159384] (2)
                   SQ Q56F26 336-674
            26. Five-domain beta-mannosidase, domain 3 [159385]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [159386] (18)
                   SQ Q8AAK6 330-678! SQ Q8AAK6 331-678
         3. Putative alpha-L-fucosidase, catalytic domain [102079] (1)
            glycosyl hydrolase family 29; contains additional beta-barrel with a topological similarity to the C-terminal domain of alpha amylases
            1. Putative alpha-L-fucosidase, catalytic domain [102080]
               1. Thermotoga maritima [TaxId: 2336] [102081] (3)
                  TM0306
         4. Family 1 of glycosyl hydrolase [51521] (15)
            1. Plant beta-glucosidase (myrosinase) [51522]
               1. White mustard (Sinapis alba) [TaxId: 3728] [51523] (17)
               2. Creeping white clover (Trifolium repens) [TaxId: 3899] [51524] (1)
                  Cyanogenic beta-glucosidase
               3. Maize (Zea mays), zmglu1 [TaxId: 4577] [51525] (9)
                  SQ P49235
               4. Sorghum bicolor [TaxId: 4558] [110351] (2)
                  SQ Q41290
            2. 6-phospho-beta-D-galactosidase, PGAL [51526]
               1. Lactococcus lactis [TaxId: 1358] [51527] (4)
            3. Beta-glucosidase A [51528]
               1. Bacillus polymyxa [TaxId: 1406] [51529] (5)
               2. Bacillus circulans, subsp. alkalophilus [TaxId: 1397] [51530] (1)
               3. Streptomyces sp. [TaxId: 1931] [82248] (2)
               4. Thermotoga maritima [TaxId: 2336] [89475] (40)
                  SQ Q08638
               5. Thermus thermophilus [TaxId: 274] [89476] (1)
               6. Thermus nonproteolyticus [TaxId: 116039] [89477] (1)
               7. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141785] (1)
                  SQ O58104 1-423
            4. beta-Glycosidase [51531]
               1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51532] (14)
                  SQ P22498
               2. Archaeon Thermosphaera aggregans [TaxId: 54254] [51533] (1)
            5. Thioglucosidase [141786]
               1. Cabbage aphid (Brevicoryne brassicae) [TaxId: 69196] [141787] (2)
                  SQ Q95X01 3-464
         5. Type II chitinase [51534] (22)
            glycosylase family 18
            1. Hevamine A (chitinase/lysozyme) [51535]
               1. Para rubber tree (Hevea brasiliensis) [TaxId: 3981] [51536] (7)
            2. Xylanase inhibitor protein I, XIP-I [89478]
               1. Wheat (Triticum aestivum) [TaxId: 4565] [89479] (3)
                  SQ Q8L5C6
            3. Seed storage protein [51537]
               close relation of hevamine, may bind chitin
               1. Vicia narbonensis, Narbonin [TaxId: 3912] [51538] (1)
               2. Jack bean (Canavalia ensiformis), Concanavalin B [TaxId: 3823] [51539] (1)
            4. Endo-beta-N-acetylglucosaminidase [51540]
               1. Flavobacterium meningosepticum, endoglycosidase F1 [TaxId: 238] [51541] (1)
               2. Flavobacterium meningosepticum, endoglycosidase F3 [TaxId: 238] [51542] (2)
               3. Streptomyces plicatus, endoglycosidase H [TaxId: 1922] [51543] (8)
            5. Chitinase A, catalytic domain [51544]
               1. Serratia marcescens [TaxId: 615] [51545] (11)
                  SQ P07254 24-563
            6. Chitinase B, catalytic domain [51546]
               1. Serratia marcescens [TaxId: 615] [51547] (14)
            7. Psychrophilic chitinase B [82249]
               1. Arthrobacter sp., tad20 [TaxId: 1667] [82250] (1)
            8. Chitinase A1 [75069]
               1. Bacillus circulans [TaxId: 1397] [75070] (1)
            9. Chitinase 1 [51548]
               1. Fungus (Coccidioides immitis) [TaxId: 5501] [51549] (4)
               2. Aspergillus fumigatus [TaxId: 5085] [117368] (26)
                  SQ Q873X9
            10. Chitotriosidase [82251]
                1. Human (Homo sapiens) [TaxId: 9606] [82252] (10)
            11. Signal processing protein (SPC-40, MGP-40) [89480]
                secreted during involution
                1. Goat (Capra hircus) [TaxId: 9925] [89481] (14)
                2. Cow (Bos taurus) [TaxId: 9913] [110352] (1)
                   SQ P30922
                3. Sheep (Ovis aries) [TaxId: 9940] [109611] (12)
                   SQ Q6TMG6
                4. Buffalo (Bubalus bubalis) [TaxId: 89462] [110353] (3)
                   SQ Q7YS85
                5. Pig (Sus scrofa) [TaxId: 9823] [117369] (4)
                   SQ Q5UC99
            12. Chitinase-3 like protein 1 (GP-39, YKL-40) [89482]
                1. Human (Homo sapiens) [TaxId: 9606] [89483] (7)
            13. Chitinase-like lectin ym1, saccharide binding domain [63910]
                1. Mouse (Mus musculus) [TaxId: 10090] [63911] (2)
            14. Imaginal disc growth factor-2 [75071]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75072] (2)
         6. 1,4-beta-N-acetylmuraminidase [63912] (3)
            Glycosyl hydrolase family 25; probably have evolved from a type II chitinase ancestor
            permutation of the common fold; strand 8 is antiparallel to the rest of the barrel
            1. Streptomyces lysozyme [63913]
               supersedes and corrects the old structure from S. erythraeus; 0LZ6
               1. Streptomyces coelicolor, "mueller" dsm3030 [TaxId: 1902] [63914] (1)
            2. N-terminal domain of endolysin [89484]
               1. Bacteriophage cp-1 [TaxId: 10747] [89485] (6)
            3. Unnamed hypothetical protein [102082]
               homologue of BH2215 from the complete Bacillus halodurans genome
               1. Bacillus stearothermophilus [TaxId: 1422] [102083] (1)
         7. beta-N-acetylhexosaminidase catalytic domain [51550] (5)
            Glycosyl hydrolase family 20, GH20
            1. Bacterial chitobiase (beta-N-acetylhexosaminidase) [51551]
               1. Serratia marcescens [TaxId: 615] [51552] (4)
            2. beta-N-acetylhexosaminidase [63915]
               1. Streptomyces plicatus [TaxId: 1922] [63916] (6)
            3. beta-hexosaminidase B [89486]
               1. Human (Homo sapiens) [TaxId: 9606] [89487] (12)
            4. Dispersin B, DspB [141788]
               N-acetyl-beta-hexosaminidase
               1. Actinobacillus actinomycetemcomitans [TaxId: 714] [141789] (1)
                  SQ Q840G9 16-359
            5. beta-hexosaminidase A [159387]
               1. Human (Homo sapiens) [TaxId: 9606] [159388] (8)
                  SQ P06865 167-528
         8. alpha-D-glucuronidase/Hyaluronidase catalytic domain [82253] (4)
            Glycosyl hydrolase family 67, GH67; structurally related to GH20; contains extra C-terminal alpha-helical subdomain
            1. alpha-D-glucuronidase catalytic domain [82254]
               inverting reaction mechanism
               1. Pseudomonas cellulosa [TaxId: 155077] [82255] (5)
               2. Bacillus stearothermophilus [TaxId: 1422] [82256] (7)
            2. Glucosaminidase GH84, catalytic domain [141790]
               1. Bacteroides thetaiotaomicron [TaxId: 818] [141791] (12)
                  SQ Q89ZI2 148-457
            3. Hyaluronidase catalytic domain [141792]
               1. Clostridium perfringens [TaxId: 1502] [141793] (6)
                  SQ Q8XL08 179-495
         9. NagZ-like [51553] (2)
            Pfam 00933; Glycosyl hydrolase family 3 domain
            1. Beta-D-glucan exohydrolase, N-terminal domain [51554]
               interdomain linker forms an additional, N-terminal strand
               1. Barley (Hordeum vulgare) [TaxId: 4513] [51555] (9)
            2. Beta-hexosaminidase NagZ [117370]
               1. Vibrio cholerae [TaxId: 666] [117371] (2)
                  SQ Q9KU37
         10. Bee venom hyaluronidase [69387] (1)
             distorted barrel lacks the second strand
             1. Bee venom hyaluronidase [69388]
                1. Honeybee (Apis mellifera) [TaxId: 7460] [69389] (4)
         11. Outer surface protein, N-terminal domain [110354] (1)
             corresponds to the N-terminal part of Pfam 05913
             1. Outer surface protein, N-terminal domain [110355]
                1. Bacillus cereus [TaxId: 1396] [110356] (1)
                   SQ Q81HJ5
         12. YicI catalytic domain-like [117372] (2)
             1. Putative glucosidase YicI, domain 2 [117373]
                1. Escherichia coli [TaxId: 562] [117374] (15)
                   SQ P31434
             2. Alpha-galactosidase GalA catalytic domain [141794]
                includes extra C-terminal all-beta subdomain, 4-stranded meander beta-sheet
                1. Thermotoga maritima [TaxId: 2336] [141795] (1)
                   SQ O33835 178-525
         13. Glycosyl hydrolases family 35 catalytic domain [117375] (1)
             Pfam 01301
             1. Beta-galactosidase LacA, N-terminal domain [117376]
                1. Penicillium sp. [TaxId: 5081] [117377] (2)
                   SQ Q700S9 41-1011
         14. TM1410-like [141796] (1)
             Pfam 03537
             1. Hypothetical protein TM1410 [141797]
                1. Thermotoga maritima [TaxId: 2336] [141798] (6)
                   SQ Q9X1D0 28-312
      10. Metallo-dependent hydrolases [51556] (18)
          the beta-sheet barrel is similarly distorted and capped by a C-terminal helix
          has transition metal ions bound inside the barrel
          uperfamily
          1. Adenosine/AMP deaminase [51557] (4)
             1. Adenosine deaminase (ADA) [51558]
                Common fold covers the whole protein structure
                1. Mouse (Mus musculus) [TaxId: 10090] [51559] (8)
                2. Cow (Bos taurus) [TaxId: 9913] [82257] (20)
                   SQ P56658 3-350 ! SQ P56658
                3. Plasmodium yoelii [TaxId: 5861] [141799] (2)
                   SQ Q7RMV2 8-364
             2. AMP deaminase (AMPD), catalytic domain [141800]
                elaborated fold with additional structures
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141801] (1)
                   SQ O80452 212-839
          2. Dihydroorotase [63917] (1)
             1. Dihydroorotase [63918]
                1. Escherichia coli [TaxId: 562] [63919] (9)
          3. Cytosine deaminase catalytic domain [69390] (1)
             1. Cytosine deaminase catalytic domain [69391]
                1. Escherichia coli [TaxId: 562] [69392] (8)
                   SQ P25524
          4. alpha-subunit of urease, catalytic domain [51560] (3)
             1. alpha-subunit of urease, catalytic domain [51561]
                1. Klebsiella aerogenes [TaxId: 28451] [51562] (27)
                2. Bacillus pasteurii [TaxId: 1474] [51563] (6)
                3. Helicobacter pylori [TaxId: 210] [69393] (2)
          5. Hydantoinase (dihydropyrimidinase), catalytic domain [75073] (9)
             1. D-hydantoinase [75074]
                1. Thermus sp. [TaxId: 275] [75075] (2)
                2. Bacillus stearothermophilus [TaxId: 1422] [75076] (1)
                3. Burkholderia pickettii [TaxId: 329] [89488] (1)
                4. Bacillus sp. AR9 [TaxId: 301298] [141802] (2)
                   SQ Q5DLU2 2-460
             2. L-hydantoinase [75077]
                1. Arthrobacter aurescens [TaxId: 43663] [75078] (1)
             3. Dihydropyrimidinase related protein-1 [102084]
                1. Mouse (Mus musculus) [TaxId: 10090] [102085] (1)
             4. Two-domain dihydroorotase [141803]
                1. Aquifex aeolicus [TaxId: 63363] [141804] (3)
                   SQ O66990 56-365
             5. Dihydropyrimidine amidohydrolase Pyd2 [141805]
                1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [141806] (12)
                   SQ Q9P903 57-440
                2. Dictyostelium discoideum [TaxId: 44689] [141807] (1)
                   SQ Q86LT2 60-393
          6. SAH/MTA deaminase-like [82258] (5)
             1. Hypothetical protein TM0936, probable catalytic domain [82259]
                1. Thermotoga maritima [TaxId: 2336] [82260] (3)
             2. Hypothetical protein GOS_1943094 [159389]
                1. Environmental samples [159390] (1)
             3. Guanine deaminase [159391]
                1. Clostridium acetobutylicum [TaxId: 1488] [159392] (2)
                   SQ Q97MB6 64-373
                   CAC0282
                2. Bradyrhizobium japonicum [TaxId: 375] [159393] (1)
                   SQ Q89NG0 71-395
                   Blr3880
                3. Human (Homo sapiens) [TaxId: 9606] [159394] (1)
                   SQ Q9Y2T3 76-388
          7. Isoaspartyl dipeptidase, catalytic domain [89489] (1)
             1. Isoaspartyl dipeptidase, catalytic domain [89490]
                1. Escherichia coli [TaxId: 562] [89491] (5)
                   SQ P39377
          8. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82261] (3)
             1. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82262]
                1. Bacillus subtilis [TaxId: 1423] [102086] (1)
                2. Thermotoga maritima [TaxId: 2336] [82263] (1)
                   TM0814
                3. Escherichia coli [TaxId: 562] [141808] (10)
                   SQ P0AF18 54-350
          9. D-aminoacylase, catalytic domain [82264] (1)
             1. N-acyl-D-aminoacid amidohydrolase, catalytic domain [82265]
                contains small a/b subdomain inserted after strand 7; unusual for the superfamily metal coordination by Cys
                1. Alcaligenes faecalis [TaxId: 511] [82266] (8)
          10. TatD Mg-dependent DNase-like [82267] (4)
              1. Hypothetical protein TM0667 [82268]
                 1. Thermotoga maritima [TaxId: 2336] [82269] (1)
              2. Putative deoxyribonuclease YcfH [141809]
                 1. Escherichia coli [TaxId: 562] [141810] (2)
                    SQ P0AFQ7 1-265
              3. Deoxyribonuclease TatD (MttC) [141811]
                 1. Escherichia coli [TaxId: 562] [141812] (1)
                    SQ P27859 1-260
              4. Putative deoxyribonuclease YjjV [141813]
                 1. Escherichia coli [TaxId: 562] [141814] (1)
                    SQ P39408 1-259
          11. Phosphotriesterase-like [51564] (4)
              1. Phosphotriesterase (parathion hydrolase, PTE) [51565]
                 1. Pseudomonas diminuta [TaxId: 293] [51566] (10)
                    SQ P0A434 30-365
                 2. Flavobacterium sp. atcc 27551 [TaxId: 74567] [102087] (2)
                    identical sequence to the Pseudomonas diminuta PTE
                 3. Agrobacterium tumefaciens [TaxId: 358] [141815] (3)
                    SQ Q93LD7 32-360
              2. Phosphotriesterase homology protein [51567]
                 1. Escherichia coli [TaxId: 562] [51568] (1)
          12. Renal dipeptidase [75079] (1)
              1. Renal dipeptidase [75080]
                 1. Human (Homo sapiens) [TaxId: 9606] [75081] (2)
          13. Uronate isomerase-like [75082] (2)
              contains all-alpha subdomain inserted after the first strand
              1. Uronate isomerase TM0064 [75083]
                 1. Thermotoga maritima [TaxId: 2336] [75084] (1)
              2. Uncharacterized protein BH0493 [159395]
                 1. Bacillus halodurans [TaxId: 86665] [159396] (13)
                    SQ Q9KFI6 1-423
          14. Adenine deaminase-like [141816] (1)
              1. Putative adenine deaminase EF0837 [141817]
                 1. Enterococcus faecalis [TaxId: 1351] [141818] (1)
                    SQ Q837K0 53-319
          15. PP1699/LP2961-like [141819] (5)
              Pfam 04909; Amidohydrolase; stand-alone domain
              1. Putative 2-pyrone-4,6-dicarboxylic acid hydrolase PP1699 [141820]
                 1. Pseudomonas putida [TaxId: 303] [141821] (2)
                    SQ Q88M75 10-280
              2. Thermophilic reversible gamma-resorcylate decarboxylase [141822]
                 1. Rhizobium sp. MTP-10005 [TaxId: 267998] [141823] (12)
                    SQ Q60GU1 1-325
              3. 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase NbaD [141824]
                 1. Pseudomonas fluorescens [TaxId: 294] [141825] (4)
                    SQ Q83V25 3-333
              4. 4-oxalomesaconate hydratase LigJ [141826]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [141827] (2)
                    SQ Q6N0R4 1-342
              5. Putative amidohydrolase LP2961 [141828]
                 1. Lactobacillus plantarum [TaxId: 1590] [141829] (2)
                    SQ Q88TJ2 2-307
          16. DR0824-like [159397] (1)
              1. Hypothetical protein DR0824 [159398]
                 predicted isoguanine deaminase/xanthine hydrolase
                 1. Deinococcus radiodurans [TaxId: 1299] [159399] (1)
                    SQ Q9RW45 91-398
          17. Imidazolonepropionase-like [159400] (4)
              1. Uncharacterized protein BL1453 [159401]
                 Possible prolidase
                 1. Bifidobacterium longum [TaxId: 216816] [159402] (1)
                    SQ Q8G4D5 69-392
              2. Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421 [159403]
                 1. Environmental samples [159404] (2)
                    marine metagenome
              3. Imidazolonepropionase [159405]
                 1. Bacillus subtilis [TaxId: 1423] [159406] (4)
                    SQ P42084 74-373
                 2. Agrobacterium tumefaciens [TaxId: 358] [159407] (4)
                    SQ Q8U8Z6 78-378
          18. Zn-dependent arginine carboxypeptidase-like [159408] (3)
              1. Xaa-Pro dipeptidase [159409]
                 1. Alteromonas macleodii [TaxId: 28108] [159410] (2)
              2. Zn-dependent arginine carboxypeptidase [159411]
                 1. Unidentified organism [TaxId: 32644] [159412] (16)
              3. Uncharacterized protein EAJ56179 [159413]
                 1. Unidentified organism [TaxId: 32644] [159414] (8)
                    94% identity to the Burkholderia phytofirmans ortholog Bphyt_2089 (SQ B2T4I1)
      11. Aldolase [51569] (8)
          Common fold covers whole protein structure
          uperfamily
          1. Class I aldolase [51570] (37)
             the catalytic lysine forms schiff-base intermediate with substrate
             possible link between the aldolase superfamily and the phosphate-binding beta/alpha barrels
             1. Deoxyribose-phosphate aldolase DeoC [69394]
                1. Escherichia coli [TaxId: 562] [69395] (4)
                   SQ P00882
                2. Thermotoga maritima [TaxId: 2336] [82270] (1)
                   TM1559
                3. Aquifex aeolicus [TaxId: 63363] [82271] (1)
                4. Thermus thermophilus [TaxId: 274] [89492] (2)
                5. Archaeon Aeropyrum pernix [TaxId: 56636] [89493] (1)
                6. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [141830] (2)
                   SQ Q8ZXK7 1-226
             2. Archaeal fructose 1,6-bisphosphate aldolase [102088]
                1. Archaeon Thermoproteus tenax [TaxId: 2271] [102089] (23)
             3. N-acetylneuraminate lyase [51571]
                1. Escherichia coli [TaxId: 562] [51572] (4)
                2. Haemophilus influenzae [TaxId: 727] [51573] (6)
             4. Dihydrodipicolinate synthase [51574]
                1. Escherichia coli [TaxId: 562] [51575] (14)
                2. Thermotoga maritima [TaxId: 2336] [102090] (1)
                3. Mycobacterium tuberculosis [TaxId: 1773] [141831] (8)
                   SQ P63945 5-300
                4. Bacillus anthracis [TaxId: 1392] [141832] (8)
                   SQ Q81WN7 1-292
             5. Fructose-1,6-bisphosphate aldolase [51576]
                1. Human (Homo sapiens), muscle isozyme [TaxId: 9606] [51577] (3)
                2. Human (Homo sapiens), liver isozyme [TaxId: 9606] [51578] (17)
                3. Rabbit (Oryctolagus cuniculus), muscle isozyme [TaxId: 9986] [51580] (42)
                4. Rabbit (Oryctolagus cuniculus), liver isozyme [TaxId: 9986] [63920] (1)
                5. Drosophila melanogaster [TaxId: 7227] [51579] (1)
                6. Plasmodium falciparum [TaxId: 5833] [51581] (1)
                7. Trypanosome (Leishmania mexicana) [TaxId: 5665] [51582] (13)
                8. Trypanosome (Trypanosoma brucei) [TaxId: 5691] [51583] (1)
                9. Plasmodium yoelii yoelii [TaxId: 73239] [141833] (2)
                   SQ Q7RMC9 3-258
                10. Human (Homo sapiens), brain isozyme [TaxId: 9606] [141834] (12)
                    SQ P09972 2-343
             6. KDPG aldolase [51584]
                1. Escherichia coli [TaxId: 562] [51585] (11)
                2. Pseudomonas putida [TaxId: 303] [102091] (1)
                3. Thermotoga maritima [TaxId: 2336] [110357] (7)
                   SQ Q9WXS1
             7. Hypothetical protein HI0047 [102092]
                putative KHG/KDPG aldolase
                1. Haemophilus influenzae [TaxId: 727] [102093] (1)
             8. Type I 3-dehydroquinate dehydratase [51586]
                1. Salmonella typhi [TaxId: 90370] [51587] (3)
                2. Staphylococcus aureus [TaxId: 1280] [117378] (2)
                   SQ Q6GII7
             9. Transaldolase [51588]
                probably related to class I aldolases by a circular permutation
                1. Escherichia coli [TaxId: 562] [51589] (7)
                2. Human (Homo sapiens) [TaxId: 9606] [51590] (1)
                3. Mouse (Mus musculus) [TaxId: 10090] [141835] (4)
                   SQ Q93092 13-331
             10. Decameric fructose-6-phosphate aldolase/transaldolase [75085]
                 forms helix-swapped pentamers
                 1. Escherichia coli [TaxId: 562] [75086] (1)
                 2. Thermotoga maritima [TaxId: 2336] [117379] (1)
                    SQ Q9WYD1
                 3. Thermus thermophilus [TaxId: 274] [141836] (10)
                    SQ Q5SJE8 1-211
                    clear orthologue of the E.coli protein; annotated as transaldolase in UniProt
             11. Putative aldolase YihT [110358]
                 1. Salmonella typhimurium [TaxId: 90371] [110359] (1)
                    SQ Q9L7R9
             12. 2-keto-3-deoxy gluconate aldolase Eda [110360]
                 1. Sulfolobus solfataricus [TaxId: 2287] [110361] (4)
                    SQ Q97U28
          2. Class II FBP aldolase [51591] (3)
             metal-dependent
             1. Fructose-bisphosphate aldolase (FBP aldolase) [51592]
                1. Escherichia coli [TaxId: 562] [51593] (4)
                2. Thermus aquaticus [TaxId: 271] [102094] (2)
             2. Tagatose-1,6-bisphosphate aldolase [75087]
                1. Escherichia coli [TaxId: 562] [75088] (1)
          3. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51594] (5)
             hybrid of classes I and II aldolase
             1. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51595]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51596] (12)
                2. Human (Homo sapiens) [TaxId: 9606] [63921] (2)
                3. Pseudomonas aeruginosa [TaxId: 287] [51597] (2)
                4. Escherichia coli [TaxId: 562] [51598] (4)
                5. Prosthecochloris vibrioformis [TaxId: 1098] [110362] (3)
                   SQ Q59334
          4. Class I DAHP synthetase [51599] (6)
             1. 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG) [51600]
                1. Escherichia coli, phenylalanine-regulated isozyme [TaxId: 562] [51601] (4)
                2. Baker's yeast (Saccharomyces cerevisiae), tyrosine-regulated isozyme [TaxId: 4932] [82272] (11)
                3. Thermotoga maritima [TaxId: 2336] [110363] (5)
                   SQ Q9WYH8
             2. 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase) [51602]
                1. Escherichia coli [TaxId: 562] [51603] (10)
                   SQ P17579
                2. Haemophilus influenzae [TaxId: 727] [102095] (1)
                3. Aquifex aeolicus [TaxId: 63363] [63922] (20)
          5. HMGL-like [89494] (3)
             Pfam 00682
             1. 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain [89495]
                1. Pseudomonas sp. [TaxId: 306] [89496] (1)
                   gene product DmpG
             2. 2-isopropylmalate synthase LeuA, catalytic domain [110364]
                1. Mycobacterium tuberculosis [TaxId: 1773] [110365] (1)
                   SQ P96420
             3. Transcarboxylase 5S subunit, N-terminal domain [110366]
                1. Propionibacterium freudenreichii shermanii [TaxId: 1752] [110367] (6)
                   SQ Q70AC7 3-474
          6. NeuB-like [110368] (2)
             Pfam 03102
             1. Spore coat polysaccharide biosynthesis protein SpsE, N-terminal domain [110369]
                1. Bacillus subtilis [TaxId: 1423] [110370] (1)
                   SQ P39625
             2. Capsule biosynthesis protein SiaC, N-terminal domain [117380]
                1. Neisseria meningitidis [TaxId: 487] [117381] (4)
                   SQ Q57265
          7. GatZ-like [141837] (1)
             Pfam 08013
             1. Putative tagatose 6-phosphate kinase 1 GatZ [141838]
                1. Escherichia coli [TaxId: 562] [141839] (4)
                   SQ P37191 1-420
          8. Class-II DAHP synthetase [141840] (1)
             Pfam 01474
             1. Probable DAHP synthetase AroG, phenylalanine-repressible [141841]
                1. Mycobacterium tuberculosis [TaxId: 1773] [141842] (2)
                   SQ O53512 1-462
      12. Enolase C-terminal domain-like [51604] (2)
          binds metal ion (magnesium or manganese) in conserved site inside barrel
          N-terminal alpha+beta domain is common to this superfamily
          uperfamily
          1. Enolase [51605] (8)
             1. Enolase [51606]
                Fold of this protein slightly differs from common fold in topology
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51607] (18)
                2. European lobster (Homarus vulgaris) [TaxId: 6707] [51608] (2)
                3. Trypanosoma brucei brucei [TaxId: 5702] [89497] (1)
                4. Enterococcus hirae [TaxId: 1354] [89498] (1)
                5. Escherichia coli [TaxId: 562] [69396] (5)
                6. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110371] (5)
                   SQ P09104
                7. Streptococcus pneumoniae [TaxId: 1313] [141843] (2)
                   SQ Q8DPS0 138-433
                8. Trypanosoma brucei [TaxId: 5691] [159415] (6)
          2. D-glucarate dehydratase-like [51609] (20)
             1. D-glucarate dehydratase [51610]
                1. Pseudomonas putida [TaxId: 303] [51611] (1)
                2. Escherichia coli [TaxId: 562] [51612] (6)
             2. O-succinylbenzoate synthase [51613]
                1. Escherichia coli [TaxId: 562] [51614] (7)
             3. Muconate-lactonizing enzyme [51615]
                1. Pseudomonas putida [TaxId: 303] [51616] (5)
             4. Mandelate racemase [51617]
                1. Pseudomonas putida [TaxId: 303] [51618] (6)
             5. Chlormuconate cycloisomerase [51619]
                1. Alcaligenes eutrophus [TaxId: 106590] [51620] (2)
                2. Pseudomonas sp. p51 [TaxId: 65067] [102096] (1)
             6. L-Ala-D/L-Glu epimerase [69397]
                1. Escherichia coli [TaxId: 562] [69398] (1)
                2. Bacillus subtilis [TaxId: 1423] [69399] (2)
                   SQ O34508
             7. beta-Methylaspartase [69400]
                1. Clostridium tetanomorphum [TaxId: 1553] [69401] (2)
                2. Citrobacter amalonaticus [TaxId: 35703] [69402] (2)
             8. Hypothetical protein Atu3453 [102097]
                1. Agrobacterium tumefaciens [TaxId: 358] [102098] (1)
             9. N-acylamino acid racemase [110372]
                1. Amycolatopsis sp. [TaxId: 37632] [110373] (4)
                   SQ Q44244 # similar activity to a remotely related O-succinylbenzoate synthase from E. coli
                2. Deinococcus radiodurans [TaxId: 1299] [110374] (4)
                   SQ Q9RYA6
                3. Enterococcus faecalis [TaxId: 1351] [117382] (1)
                   SQ Q838J7; EF0450; protein assignment by sequence similarity
                4. Listeria innocua [TaxId: 1642] [117383] (1)
                   SQ Q927X3; Lin2664; protein assignment by sequence similarity
             10. Hypothetical protein Bll6730 [117384]
                 1. Bradyrhizobium japonicum [TaxId: 375] [117385] (21)
                    SQ Q89FH0
             11. RTS beta protein [117386]
                 1. Xanthomonas campestris pv. campestris [TaxId: 340] [117387] (1)
                    SQ Q8P3K2; extended, mainly helical linker between the domains
             12. Hypothetical protein YitF [141844]
                 1. Bacillus subtilis [TaxId: 1423] [141845] (10)
                    SQ O06741 115-371
             13. Putative dehydratase protein STM2273 [141846]
                 1. Salmonella typhimurium [TaxId: 90371] [141847] (2)
                    SQ Q8ZNH1 123-400
      13. Phosphoenolpyruvate/pyruvate domain [51621] (7)
          uperfamily
          1. Pyruvate kinase [51622] (6)
             1. Pyruvate kinase, N-terminal domain [51623]
                this domain is interrupted by an all-beta domain
                C-terminal domain is alpha/beta
                1. Cat (Felis catus) [TaxId: 9685] [51624] (1)
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [51625] (14)
                3. Human (Homo sapiens) [TaxId: 9606] [82273] (4)
                4. Leishmania mexicana [TaxId: 5665] [51626] (8)
                5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51627] (2)
                6. Escherichia coli [TaxId: 562] [51628] (3)
          2. Pyruvate phosphate dikinase, C-terminal domain [51629] (3)
             1. Pyruvate phosphate dikinase, C-terminal domain [51630]
                1. Clostridium symbiosum [TaxId: 1512] [51631] (7)
                2. Trypanosoma brucei [TaxId: 5691] [75089] (1)
                3. Maize (Zea mays) [TaxId: 4577] [141848] (2)
                   SQ P11155 592-947
          3. Phosphoenolpyruvate carboxylase [51632] (1)
             1. Phosphoenolpyruvate carboxylase [51633]
                the common fold is decorated with many additional helices
                1. Escherichia coli [TaxId: 562] [51634] (4)
          4. Phosphoenolpyruvate mutase/Isocitrate lyase-like [88704] (6)
             forms a swapped dimer
             1. Phosphoenolpyruvate mutase [51636]
                1. Blue mussel (Mytilus edulis) [TaxId: 6550] [51637] (6)
             2. 2-methylisocitrate lyase [89499]
                1. Escherichia coli [TaxId: 562] [89500] (2)
                2. Salmonella typhimurium [TaxId: 90371] [102099] (2)
             3. Isocitrate lyase [51642]
                elaborated with additional subdomains
                1. Aspergillus nidulans [TaxId: 162425] [51643] (1)
                2. Mycobacterium tuberculosis [TaxId: 1773] [51644] (3)
                3. Escherichia coli [TaxId: 562] [63923] (1)
          5. HpcH/HpaI aldolase [51638] (4)
             forms a swapped dimer; contains a PK-type metal-binding site
             1. 2-dehydro-3-deoxy-galactarate aldolase [51639]
                1. Escherichia coli [TaxId: 562] [51640] (2)
             2. Macrophomate synthase [89501]
                Intermolecular Diels-Alderase
                1. Macrophoma commelinae [TaxId: 108330] [89502] (1)
             3. Citrate lyase, beta subunit [110375]
                non-swapped trimer
                1. Deinococcus radiodurans [TaxId: 1299] [110376] (1)
                   SQ Q9RUZ0 4-234
                2. Mycobacterium tuberculosis [TaxId: 1773] [117388] (2)
                   SQ O06162
          6. Ketopantoate hydroxymethyltransferase PanB [89503] (3)
             1. Ketopantoate hydroxymethyltransferase PanB [89504]
                dodecameric enzyme; a C-terminal helix exchange is observed in the M. tuberculosis enzyme but not in the E. coli enzyme
                1. Mycobacterium tuberculosis [TaxId: 1773] [89505] (1)
                2. Escherichia coli [TaxId: 562] [89506] (1)
                3. Neisseria meningitidis [TaxId: 487] [102100] (2)
          7. Mll9387-like [159416] (1)
             Pfam 09370; TIM-barrel signal transduction protein; forms a swapped dimer similar to the Phosphoenolpyruvate mutase/Isocitrate lyase-like and HpcH/HpaI aldolase families
             1. Uncharacterized protein Mll9387 [159417]
                1. Mesorhizobium loti [TaxId: 381] [159418] (6)
                   SQ Q981G2 8-284
      14. Malate synthase G [51645] (1)
          uperfamily
          1. Malate synthase G [51646] (2)
             1. Malate synthase G [51647]
                contains the insert of all-beta (sub)domain and the C-terminal extension of all-alpha (sub)domain
                1. Escherichia coli [TaxId: 562] [51648] (4)
                   SQ P37330 2-722 # NMR-derived model
                2. Mycobacterium tuberculosis [TaxId: 1773] [82274] (4)
      15. RuBisCo, C-terminal domain [51649] (1)
          uperfamily
          1. RuBisCo, large subunit, C-terminal domain [51650] (12)
             N-terminal domain is alpha+beta
             1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [51651]
                1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [51652] (5)
                2. Spinach (Spinacia oleracea) [TaxId: 3562] [51653] (11)
                3. Galdieria partita [TaxId: 83374] [51654] (2)
                4. Chlamydomonas reinhardtii [TaxId: 3055] [69403] (74)
                5. Alcaligenes eutrophus [TaxId: 106590] [51655] (1)
                6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [51656] (16)
                7. Rhodospirillum rubrum [TaxId: 1085] [51657] (5)
                8. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [69404] (1)
                9. Chlorobium tepidum [TaxId: 1097] [117389] (3)
                   SQ Q8KBL4 1-428
                10. Rice (Oryza sativa) [TaxId: 4530] [117390] (1)
                    SQ P12089
                11. Archaeon Halothiobacillus neapolitanus [TaxId: 927] [141849] (1)
                    SQ O85040 143-460
                12. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141850] (10)
                    SQ O58677 134-424
      16. Xylose isomerase-like [51658] (7)
          different families share similar but non-identical metal-binding sites
          uperfamily
          1. Endonuclease IV [51659] (2)
             1. Endonuclease IV [51660]
                DNA repair enzyme
                1. Escherichia coli [TaxId: 562] [51661] (2)
                2. Bacillus anthracis [TaxId: 1392] [141851] (1)
                   SQ Q81LV1 2-298
          2. IolI-like [75090] (3)
             1. Hypothetical protein IolI [75091]
                1. Bacillus subtilis [TaxId: 1423] [75092] (2)
             2. Hypothetical protein Lmo2234 [141852]
                1. Listeria monocytogenes [TaxId: 1639] [141853] (2)
                   SQ Q8Y542 10-284
             3. Putative cytoplasmic protein STM4435 [159419]
                1. Salmonella typhimurium [TaxId: 90371] [159420] (1)
                   SQ Q8ZK48 1-271
          3. Hypothetical protein YgbM (EC1530) [75093] (1)
             1. Hypothetical protein YgbM (EC1530) [75094]
                1. Escherichia coli [TaxId: 562] [75095] (1)
          4. L-rhamnose isomerase [51662] (1)
             1. L-rhamnose isomerase [51663]
                1. Escherichia coli [TaxId: 562] [51664] (3)
          5. Xylose isomerase [51665] (12)
             1. D-xylose isomerase [51666]
                1. Streptomyces albus [TaxId: 1888] [51667] (1)
                2. Streptomyces murinus [TaxId: 33900] [51668] (1)
                3. Streptomyces olivochromogenes [TaxId: 1963] [51669] (9)
                4. Streptomyces rubiginosus [TaxId: 1929] [51670] (24)
                5. Streptomyces diastaticus, M1033 [TaxId: 1956] [51671] (2)
                6. Arthrobacter, strain b3728 [TaxId: 1663] [51672] (17)
                7. Actinoplanes missouriensis [TaxId: 1866] [51673] (14)
                8. Clostridium thermosulfurogenes, also known as Thermoanaerobacter thermosulfurigenes [TaxId: 33950] [51674] (1)
                9. Bacillus stearothermophilus [TaxId: 1422] [51675] (1)
                10. Thermotoga neapolitana [TaxId: 2337] [51676] (1)
                11. Thermus aquaticus, subsp. Caldophilus [TaxId: 271] [51677] (1)
                12. Thermus aquaticus, subsp. Thermophilus [TaxId: 271] [51678] (1)
          6. UxuA-like [110377] (1)
             Pfam 03786
             1. Mannonate dehydratase UxuA [110378]
                1. Enterococcus faecalis (Streptococcus faecalis) [TaxId: 1351] [110379] (1)
                   SQ Q82ZC9
          7. KguE-like [141854] (1)
             part of Pfam 01261
             1. Hypothetical protein PA2260 [141855]
                2-ketogluconate utilization operon protein KguE
                1. Pseudomonas aeruginosa [TaxId: 287] [141856] (3)
                   SQ Q9I1L3 3-252
      17. Bacterial luciferase-like [51679] (4)
          consists of clearly related families of somewhat different folds
          uperfamily
          1. Bacterial luciferase (alkanal monooxygenase) [51680] (2)
             typical (beta/alpha)8-barrel fold
             heterodimer of two similar chains
             1. Bacterial luciferase alpha chain, LuxA [88705]
                1. Vibrio harveyi [TaxId: 669] [88706] (3)
             2. Bacterial luciferase beta chain, LuxB [88707]
                1. Vibrio harveyi [TaxId: 669] [88708] (5)
          2. Non-fluorescent flavoprotein (luxF, FP390) [51683] (2)
             incomplete beta/alpha barrel with mixed beta-sheet of 7 strands
             1. Non-fluorescent flavoprotein (luxF, FP390) [51684]
                1. Photobacterium leiognathi [TaxId: 553611] [51685] (1)
                2. Photobacterium phosphoreum [TaxId: 659] [51686] (1)
          3. F420 dependent oxidoreductases [51687] (3)
             1. Coenzyme F420 dependent tetrahydromethanopterin reductase [51688]
                1. Archaeon Methanopyrus kandleri [TaxId: 2320] [51689] (1)
                2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63924] (1)
             2. Coenzyme F420 dependent secondary alcohol dehydrogenase [102101]
                1. Archaeon Methanoculleus thermophilicus [TaxId: 2200] [102102] (1)
          4. Ssud-like monoxygenases [82275] (2)
             1. Alkanesulfonate monooxygenase SsuD [82276]
                1. Escherichia coli [TaxId: 562] [82277] (2)
             2. Putative monooxygenase YtnJ [110380]
                1. Bacillus subtilis [TaxId: 1423] [110381] (2)
                   SQ O34974
      18. Nicotinate/Quinolinate PRTase C-terminal domain-like [51690] (2)
          incomplete beta/alpha barrel with parallel beta-sheet of 7 strands
          uperfamily
          1. NadC C-terminal domain-like [51691] (6)
             1. Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain [51692]
                1. Salmonella typhimurium [TaxId: 90371] [51693] (1)
                2. Mycobacterium tuberculosis [TaxId: 1773] [51694] (4)
                3. Thermotoga maritima [TaxId: 2336] [89507] (1)
                   TM1645
             2. Nicotinate-nucleotide pyrophosphorylase PF1904 [141857]
                1. Pyrococcus furiosus [TaxId: 2261] [141858] (6)
                   SQ Q8TZS9 111-389
             3. Putative nicotinate phosphoribosyltransferase EF2626 [141859]
                includes extra C-terminal region that wraps around the N-terminal domain and contains an all-beta domain, this domain is distinct from but probably related to the Ta1145 extra domain
                1. Enterococcus faecalis [TaxId: 1351] [141860] (1)
                   SQ Q830Y8 141-485
             4. Nicotinate phosphoribosyltransferase Ta1145 [141861]
                includes extra C-terminal region that wraps around the N-terminal domain and contains a rubredoxin-like subdomain
                1. Thermoplasma acidophilum [TaxId: 2303] [141862] (1)
                   SQ Q9HJ28 120-389
          2. Monomeric nicotinate phosphoribosyltransferase C-terminal domain [110910] (3)
             1. Nicotinate phosphoribosyltransferase, C-terminal domain [110911]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110912] (1)
                   SQ P39683
                2. Agrobacterium tumefaciens [TaxId: 358] [117391] (1)
                   SQ Q8UIS9
                3. Pseudomonas aeruginosa [TaxId: 287] [141863] (4)
                   SQ Q9HW26 143-397
                   NAPRTase 2
      19. PLC-like phosphodiesterases [51695] (3)
          uperfamily
          1. Mammalian PLC [51696] (2)
             1. Phospholipase C isozyme D1 (PLC-D1) [51697]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [51698] (10)
             2. Phospholipase C-beta-2 [159421]
                1. Human (Homo sapiens) [TaxId: 9606] [159422] (2)
                   SQ Q00722 312-660
          2. Bacterial PLC [51699] (2)
             1. Phosphatidylinositol-specific phospholipase C [51700]
                1. Bacillus cereus [TaxId: 1396] [51701] (9)
                2. Listeria monocytogenes [TaxId: 1639] [51702] (2)
          3. Glycerophosphoryl diester phosphodiesterase [89508] (4)
             Pfam 03009
             1. Hypothetical protein TM1621 [89509]
                1. Thermotoga maritima [TaxId: 2336] [89510] (1)
             2. Glycerophosphodiester phosphodiesterase GlpQ [110382]
                1. Escherichia coli [TaxId: 562] [110383] (3)
                   SQ P09394
             3. Putative glycerophosphodiester phosphodiesterase TTHB141 [141864]
                1. Thermus thermophilus [TaxId: 274] [141865] (2)
                   SQ Q53W25 8-224
             4. Glycerophosphodiester phosphodiesterase UgpQ [141866]
                1. Agrobacterium tumefaciens [TaxId: 358] [141867] (4)
                   SQ Q8U887 1-240
      20. Cobalamin (vitamin B12)-dependent enzymes [51703] (4)
          uperfamily
          1. Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [51704] (2)
             the subunits are clearly related but only one (alpha) is active
             1. Methylmalonyl-CoA mutase alpha subunit, domain 1 [88709]
                1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88710] (8)
             2. Methylmalonyl-CoA mutase beta subunit, domain 1 [88711]
                the subunits are clearly related but only one (alpha) is active
                1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88712] (8)
          2. Glutamate mutase, large subunit [51707] (1)
             1. Glutamate mutase, large subunit [51708]
                1. Clostridium cochlearium [TaxId: 1494] [51709] (3)
          3. Diol dehydratase, alpha subunit [51710] (2)
             1. Diol dehydratase, alpha subunit [51711]
                1. Klebsiella oxytoca [TaxId: 571] [51712] (7)
                2. Klebsiella pneumoniae [TaxId: 573] [82278] (2)
          4. D-lysine 5,6-aminomutase alpha subunit, KamD [117392] (1)
             most similar to the glutamate mutase subunit; contains second cofactor, PLP
             1. D-lysine 5,6-aminomutase alpha subunit, KamD [117393]
                1. Clostridium sticklandii [TaxId: 1511] [117394] (1)
                   SQ Q9ZFE6
      21. tRNA-guanine transglycosylase [51713] (1)
          uperfamily
          1. tRNA-guanine transglycosylase [51714] (2)
             1. Queosine tRNA-guanine transglycosylase [51715]
                contains zinc-binding subdomain
                1. Zymomonas mobilis [TaxId: 542] [51716] (34)
                   SQ P28720
             2. Archaeosine tRNA-guanine transglycosylase, N-terminal domain [75096]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75097] (4)
      22. Dihydropteroate synthetase-like [51717] (2)
          uperfamily
          1. Dihydropteroate synthetase [51718] (4)
             1. Dihydropteroate synthetase [51719]
                1. Escherichia coli [TaxId: 562] [51720] (3)
                2. Staphylococcus aureus [TaxId: 1280] [51721] (2)
                3. Mycobacterium tuberculosis [TaxId: 1773] [51722] (1)
                4. Bacillus anthracis [TaxId: 1392] [102103] (5)
                   SQ Q81VW8
          2. Methyltetrahydrofolate-utiluzing methyltransferases [51723] (2)
             1. Methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase MetR [51724]
                1. Moorella thermoacetica [TaxId: 1525] [51725] (1)
             2. Cobalamin-dependent methionine synthase MetH, C-terminal domain [102104]
                5-methyltetrahydrofolate homocysteine S-methyltransferase
                1. Thermotoga maritima [TaxId: 2336] [102105] (10)
      23. UROD/MetE-like [51726] (2)
          uperfamily
          1. Uroporphyrinogen decarboxylase, UROD [51727] (2)
             1. Uroporphyrinogen decarboxylase, UROD [51728]
                1. Human (Homo sapiens) [TaxId: 9606] [51729] (11)
                2. Tobacco (Nicotiana tabacum), UROD-III [TaxId: 4097] [69405] (1)
          2. Cobalamin-independent methionine synthase [110384] (1)
             Pfam 01717; duplication; consists of two related domains
             1. 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE [110385]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110386] (4)
                   SQ O50008
      24. FAD-linked oxidoreductase [51730] (2)
          distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation
          uperfamily
          1. Methylenetetrahydrofolate reductase [51731] (2)
             1. Methylenetetrahydrofolate reductase [51732]
                1. Escherichia coli [TaxId: 562] [51733] (1)
                2. Thermus thermophilus [TaxId: 274] [102106] (1)
          2. Proline dehydrohenase domain of bifunctional PutA protein [82279] (1)
             1. Proline dehydrohenase domain of bifunctional PutA protein [82280]
                1. Escherichia coli [TaxId: 562] [82281] (7)
                   SQ P09546 87-610
      25. Monomethylamine methyltransferase MtmB [75098] (1)
          uperfamily
          1. Monomethylamine methyltransferase MtmB [75099] (1)
             1. Monomethylamine methyltransferase MtmB [75100]
                contains a UAG-encoded L-pyrrolysine residue
                1. Archaeon Methanosarcina barkeri [TaxId: 2208] [75101] (5)
                   SQ O30642
      26. Homocysteine S-methyltransferase [82282] (1)
          uperfamily
          1. Homocysteine S-methyltransferase [82283] (3)
             Pfam 02574
             1. Betaine-homocysteine S-methyltransferase [82284]
                1. Human (Homo sapiens) [TaxId: 9606] [82285] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [102107] (1)
             2. Cobalamin-dependent methionine synthase MetH, N-terminal domain [102108]
                5-methyltetrahydrofolate homocysteine S-methyltransferase
                1. Thermotoga maritima [TaxId: 2336] [102109] (10)
      27. (2r)-phospho-3-sulfolactate synthase ComA [102110] (1)
          uperfamily
          1. (2r)-phospho-3-sulfolactate synthase ComA [102111] (2)
             1. (2r)-phospho-3-sulfolactate synthase ComA [102112]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [102113] (1)
                2. Bacillus subtilis [TaxId: 1423] [110387] (1)
                   SQ O06739
      28. Radical SAM enzymes [102114] (3)
          common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel
          uperfamily
          1. Biotin synthase [102115] (1)
             regular (beta/alpha)8 barrel
             1. Biotin synthase [102116]
                1. Escherichia coli [TaxId: 562] [102117] (1)
          2. Oxygen-independent coproporphyrinogen III oxidase HemN [102118] (1)
             open beta/alpha barrel decorated with additional structures
             1. Oxygen-independent coproporphyrinogen III oxidase HemN [102119]
                1. Escherichia coli [TaxId: 562] [102120] (1)
          3. MoCo biosynthesis proteins [110388] (1)
             open alpha/beta-barrel with a specific second FeS cluster-binding region corresponding to Pfam 06463
             1. Molybdenum cofactor biosynthesis protein A MoaA [110389]
                1. Staphylococcus aureus [TaxId: 1280] [110390] (4)
                   SQ P69848
      29. GlpP-like [110391] (1)
          uperfamily
          1. GlpP-like [110392] (1)
             Pfam 04309
             1. Glycerol uptake operon antiterminator-related protein TM1436 [110393]
                1. Thermotoga maritima [TaxId: 2336] [110394] (1)
                   SQ Q9X1F0
      30. CutC-like [110395] (1)
          uperfamily
          1. CutC-like [110396] (1)
             Pfam 03932
             1. Copper homeostasis protein CutC [110397]
                1. Shigella flexneri [TaxId: 623] [110398] (5)
                   SQ P67825
      31. ThiG-like [110399] (1)
          shares the common phosphate-binding site with other superfamilies
          uperfamily
          1. ThiG-like [110400] (2)
             Pfam 05690
             1. Thiazole biosynthesis protein ThiG [110401]
                1. Bacillus subtilis [TaxId: 1423] [110402] (2)
                   SQ O31618
                2. Pseudomonas aeruginosa [TaxId: 287] [117395] (1)
                   SQ Q9I6B4 9-251
      32. TM1631-like [117396] (1)
          uperfamily
          1. TM1631-like [117397] (2)
             Pfam 01904; DUF72
             1. Hypothetical protein TM1631 [117398]
                1. Thermotoga maritima [TaxId: 2336] [117399] (1)
                   SQ Q9X1W6
             2. Hypothetical protein EF0366 [117400]
                1. Enterococcus faecalis [TaxId: 1351] [117401] (1)
                   SQ Q838R9 1-265
      33. EAL domain-like [141868] (1)
          variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest
          uperfamily
          1. EAL domain [141869] (1)
             Pfam 00563
             1. Hypothetical protein YkuI, N-terminal domain [141870]
                1. Bacillus subtilis [TaxId: 1423] [141871] (2)
                   SQ O35014 2-262
   2. NAD(P)-binding Rossmann-fold domains [51734] (1)
      core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
      The nucleotide-binding modes of this and the next two folds/superfamilies are similar
      1. NAD(P)-binding Rossmann-fold domains [51735] (12)
         uperfamily
         1. Alcohol dehydrogenase-like, C-terminal domain [51736] (28)
            N-terminal all-beta domain defines family
            1. Alcohol dehydrogenase [51737]
               1. Horse (Equus caballus) [TaxId: 9796] [51738] (38)
                  SQ P00327
               2. Human (Homo sapiens), different isozymes [TaxId: 9606] [51739] (26)
                  SQ P00326 ! SQ P00325 ! SQ P07327
               3. Mouse (Mus musculus), class II [TaxId: 10090] [51740] (3)
               4. Frog (Rana perezi) [TaxId: 8403] [89511] (2)
               5. Cod (Gadus callarias) [TaxId: 8053] [51741] (1)
               6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82286] (4)
               7. Archaeon Aeropyrum pernix [TaxId: 56636] [102121] (1)
               8. Pseudomonas aeruginosa [TaxId: 287] [102122] (1)
               9. Bacillus stearothermophilus [TaxId: 1422] [102123] (1)
            2. Hypothetical protein TM0436 [102124]
               1. Thermotoga maritima [TaxId: 2336] [102125] (1)
            3. Hypothetical protein YhdH [102126]
               1. Escherichia coli [TaxId: 562] [102127] (2)
                  SQ P26646
            4. Hypothetical protein YahK [102128]
               1. Escherichia coli [TaxId: 562] [102129] (1)
            5. Benzyl alcohol dehydrogenase [89512]
               1. Acinetobacter calcoaceticus [TaxId: 471] [89513] (1)
            6. Bacterial secondary alcohol dehydrogenase [51742]
               1. Clostridium beijerinckii [TaxId: 1520] [51743] (3)
               2. Thermoanaerobacter brockii [TaxId: 29323] [51744] (10)
            7. Ketose reductase (sorbitol dehydrogenase) [51745]
               1. Silverleaf whitefly (Bemisia argentifolii) [TaxId: 77855] [51746] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [102130] (3)
            8. Formaldehyde dehydrogenase [82287]
               1. Pseudomonas putida [TaxId: 303] [82288] (1)
            9. Quinone oxidoreductase [51747]
               1. Escherichia coli [TaxId: 562] [51748] (1)
               2. Thermus thermophilus [TaxId: 274] [89514] (2)
               3. Human (Homo sapiens) [TaxId: 9606] [117402] (1)
                  SQ Q08257
            10. Putative enoyl reductase domain of polyketide synthase [89515]
                1. Mycobacterium tuberculosis [TaxId: 1773] [89516] (1)
            11. 2,4-dienoyl-CoA reductase [89517]
                1. Yeast (Candida tropicalis) [TaxId: 5482] [89518] (5)
            12. Putative zinc-binding alcohol dehydrogenase [102131]
                1. Mouse (Mus musculus) [TaxId: 10090] [102132] (1)
            13. Cinnamyl alcohol dehydrogenase, ADH6 [110403]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110404] (3)
                   SQ Q04894
            14. Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase [110405]
                1. Guinea pig (Cavia porcellus) [TaxId: 10141] [110406] (5)
                   SQ Q9EQZ5
            15. B. subtilis YhfP homologue [117403]
                1. Bacillus stearothermophilus [TaxId: 1422] [117404] (1)
                   SQ Q5L022; 96% sequence identity; Geobacillus kaustophilus TaxID:1462
            16. Hypothetical protein YhfP [117405]
                1. Bacillus subtilis [TaxId: 1423] [117406] (2)
                   SQ O07615
         2. Tyrosine-dependent oxidoreductases [51751] (108)
            also known as short-chain dehydrogenases and SDR family
            parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7
            1. Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase) [51752]
               1. Escherichia coli [TaxId: 562] [51753] (17)
               2. Human (Homo sapiens) [TaxId: 9606] [51754] (7)
               3. Trypanosoma brucei [TaxId: 5691] [89519] (5)
               4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141872] (1)
                  SQ P04397 11-357
                  N-terminal domain of bifunctional Gal10 protein
            2. dTDP-glucose 4,6-dehydratase (RmlB) [51755]
               1. Escherichia coli [TaxId: 562] [51756] (1)
               2. Salmonella enterica [TaxId: 28901] [63925] (1)
               3. Streptococcus suis, serotype 2 [TaxId: 1307] [69406] (6)
               4. Streptomyces venezuelae [TaxId: 54571] [102133] (2)
            3. dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) [75102]
               1. Salmonella enterica serovar typhimurium [TaxId: 90371] [75103] (4)
            4. GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase) [51757]
               1. Escherichia coli [TaxId: 562] [51758] (8)
            5. GDP-mannose 4,6-dehydratase [51759]
               1. Escherichia coli [TaxId: 562] [51760] (1)
               2. Pseudomonas aeruginosa [TaxId: 287] [102134] (1)
               3. Human (Homo sapiens) [TaxId: 9606] [102135] (1)
               4. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [82289] (2)
            6. ADP-L-glycero-D-mannoheptose 6-epimerase [51761]
               1. Escherichia coli [TaxId: 562] [51762] (1)
            7. CDP-glucose-4,6-dehydratase [102136]
               1. Yersinia pseudotuberculosis [TaxId: 633] [102137] (1)
               2. Salmonella typhimurium [TaxId: 90371] [141873] (2)
                  SQ P26397 2-356
            8. CDP-tyvelose-2-epimerase [102138]
               1. Salmonella typhi [TaxId: 90370] [102139] (1)
            9. Phenylcoumaran benzylic ether reductase [102140]
               1. Loblolly pine (Pinus taeda) [TaxId: 3352] [102141] (1)
            10. Pinoresinol-lariciresinol reductase [102142]
                1. Giant arborvitae (Thuja plicata) [TaxId: 3316] [102143] (1)
            11. Sulfolipid biosynthesis protein SQD1 [51763]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [51764] (4)
            12. Negative transcriptional regulator NmrA [69407]
                has an UDP-galactose 4-epimerase-like structure but evolved a different function
                1. Aspergillus nidulans [TaxId: 162425] [69408] (29)
                   SQ O59919
            13. Carbonyl reductase [51765]
                1. Mouse (Mus musculus) [TaxId: 10090] [51766] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [102144] (5)
                   dicarbonyl/L-xylulose reductase
            14. Sepiapterin reductase [51767]
                1. Mouse (Mus musculus) [TaxId: 10090] [51768] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [141874] (6)
                   SQ P35270 5-261
            15. Dihydropteridin reductase (pteridine reductase) [51769]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [51770] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [51771] (1)
                3. Leishmania major [TaxId: 5664] [63926] (35)
                   SQ Q01782
                4. Leishmania tarentolae [TaxId: 5689] [102145] (1)
                5. Trypanosoma cruzi [TaxId: 5693] [102146] (2)
                6. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89520] (1)
            16. Human estrogenic 17beta-hydroxysteroid dehydrogenase [51772]
                1. Human (Homo sapiens) [TaxId: 9606] [51773] (16)
                   SQ P14061
            17. 7-alpha-hydroxysteroid dehydrogenase [51774]
                1. Escherichia coli [TaxId: 562] [51775] (3)
            18. 3-alpha,20-beta-hydroxysteroid dehydrogenase [51776]
                1. Streptomyces hydrogenans [TaxId: 1905] [51777] (2)
            19. 3-alpha-hydroxysteroid dehydrogenase [51778]
                1. Comamonas testosteroni [TaxId: 285] [51779] (2)
            20. 3beta/17beta hydroxysteroid dehydrogenase [82290]
                1. Comamonas testosteroni [TaxId: 285] [82291] (1)
            21. Putative oxidoreductase Rv2002 [82292]
                1. Mycobacterium tuberculosis [TaxId: 1773] [82293] (3)
            22. R-specific alcohol dehydrogenase [89521]
                1. Lactobacillus brevis [TaxId: 1580] [89522] (15)
            23. Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase [51780]
                1. Pseudomonas sp., lb400 [TaxId: 306] [51781] (1)
            24. Drosophila alcohol dehydrogenase [51782]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102147] (1)
                2. Fly (Drosophila lebanonensis) [TaxId: 7225] [51783] (7)
            25. Glucose dehydrogenase [51784]
                1. Bacillus megaterium [TaxId: 1404] [51785] (4)
            26. Sorbitol dehydrogenase [102148]
                1. Rhodobacter sphaeroides [TaxId: 1063] [102149] (1)
            27. meso-2,3-butanediol dehydrogenase [51786]
                1. Klebsiella pneumoniae [TaxId: 573] [51787] (1)
            28. Levodione reductase [89523]
                1. Corynebacterium aquaticum [TaxId: 144185] [89524] (1)
            29. Mannitol dehydrogenase [63927]
                1. Mushroom (Agaricus bisporus) [TaxId: 5341] [63928] (1)
            30. (3R)-hydroxyacyl-CoA dehydrogenase domain of estradiol 17 beta-Dehydrogenase 4 [82294]
                peroxisomal multifunctional enzyme type 2
                segment swapping involving a C-terminal extension to the family fold
                1. Rat (Rattus norvegicus) [TaxId: 10116] [82295] (1)
            31. beta-keto acyl carrier protein reductase [51788]
                1. Oil seed rape (Brassica napus) [TaxId: 3708] [51789] (7)
                2. Escherichia coli [TaxId: 562] [51790] (3)
                3. Thermotoga maritima [TaxId: 2336] [102150] (1)
                   TM1169
                4. Thermus thermophilus [TaxId: 274] [117407] (1)
                   SQ Q5SK98
                5. Streptomyces coelicolor [TaxId: 1902] [117408] (9)
                   SQ P16544 #SP
                6. Mycobacterium tuberculosis [TaxId: 1773] [141875] (6)
                   SQ P0A5Y4 9-245! SQ P0A5Y4 9-247
                7. Thermus thermophilus, TTHB020 [TaxId: 274] [141876] (2)
                   SQ Q53WH2 2-242
                8. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141877] (1)
                   SQ Q86RB1 54-304
            32. Enoyl-ACP reductase [51791]
                1. Oil seed rape (Brassica napus) [TaxId: 3708] [51792] (4)
                2. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [82296] (27)
                   SQ Q9BJJ9 96-424 # fragment
                3. Mycobacterium tuberculosis, TB, gene InhA [TaxId: 1773] [51793] (44)
                4. Escherichia coli [TaxId: 562] [51794] (14)
                5. Helicobacter pylori [TaxId: 210] [102151] (8)
                6. Thermus thermophilus [TaxId: 274] [117409] (9)
                   SQ Q5SLI9
            33. Tropinone reductase [51795]
                1. Jimsonweed (Datura stramonium), I [TaxId: 4076] [51796] (1)
                2. Jimsonweed (Datura stramonium), II [TaxId: 4076] [51797] (4)
                3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117410] (2)
                   SQ Q9ASX2
            34. 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase) [51798]
                1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51799] (4)
            35. 1,3,6,8-tetrahydroxynaphthalene reductase [63929]
                1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [63930] (1)
            36. Biliverdin IX beta reductase [63931]
                Histidine in the active site instead of the Tyr-Lys dyad
                1. Human (Homo sapiens) [TaxId: 9606] [63932] (5)
            37. Type II 3-hydroxyacyl-CoA dehydrogenase [63933]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [63934] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [102152] (4)
                   SQ Q99714
                3. Thermus thermophilus [TaxId: 274] [89525] (1)
            38. Carbonyl reductase/20beta-hydroxysteroid dehydrogenase [63935]
                1. Pig (Sus scrofa) [TaxId: 9823] [63936] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [141878] (4)
                   SQ P16152 2-276
            39. Halohydrin dehalogenase HheC [102153]
                haloalcohol dehalogenase: evolved a new activity; lost the NAD-binding site
                1. Agrobacterium tumefaciens [TaxId: 358] [102154] (23)
            40. Glucose dehydrogenase (5l265) [102155]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102156] (1)
            41. UDP-N-acetylglucosamine 4-epimerase WbpP [110407]
                1. Pseudomonas aeruginosa [TaxId: 287] [110408] (2)
                   SQ Q8KN66 # list: Q8GGB8 Q9RHD6 99% identity
            42. DTDP-4-dehydrorhamnose reductase RfbD [110409]
                1. Clostridium acetobutylicum [TaxId: 1488] [110410] (1)
                   SQ Q97GQ1
            43. Gluconate 5-dehydrogenase [110411]
                1. Thermotoga maritima [TaxId: 2336] [110412] (1)
                   SQ Q9WYS2
            44. Carbonyl reductase sniffer [110413]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110414] (1)
                   SQ Q9W3H4 # cg10964-pa
            45. Hypothetical protein F25D1.5 [110415]
                1. Caenorhabditis elegans [TaxId: 6239] [110416] (1)
                   SQ Q19774
            46. Putative dehydrogenase ARPG836 (MGC4172) [117411]
                1. Human (Homo sapiens) [TaxId: 9606] [117412] (1)
                   SQ Q6UWP2
            47. Aldehyde reductase II [117413]
                1. Sporobolomyces salmonicolor [TaxId: 5005] [117414] (5)
                   SQ Q9UUN9
            48. Hypothetical protein R05D8.7 [117415]
                1. Caenorhabditis elegans [TaxId: 6239] [117416] (1)
                   SQ Q9N5G4
            49. Hypothetical protein At5g02240 (T7H20_290) [117417]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117418] (7)
                   SQ Q94EG6
            50. Polymyxin resistance protein ArnA (PrmI) [117419]
                evolved new activities: UDP-glucuronic acid decarboxylase, UDP-4-amino-4-deoxy-L-arabinose formyltransferase
                1. Escherichia coli [TaxId: 562] [117420] (12)
                   SQ P77398
            51. 2,4-dienoyl-CoA reductase, mitochondrial (DECR) [117421]
                1. Human (Homo sapiens), [TaxId: 9606] [117422] (3)
                   SQ Q16698 35-328
            52. 11-beta-hydroxysteroid dehydrogenase 1 [117423]
                1. Human (Homo sapiens) [TaxId: 9606] [117424] (37)
                   SQ P28845
                2. Guinea pig (Cavia porcellus) [TaxId: 10141] [117425] (1)
                   SQ Q6QLL4 23-296
                3. Mouse (Mus musculus) [TaxId: 10090] [141879] (4)
                   SQ P50172 24-298
            53. 17-beta-hydroxysteroid dehydrogenase type XI [117426]
                1. Human (Homo sapiens) [TaxId: 9606] [117427] (1)
                   SQ Q8NBQ5 30-273
            54. UDP-glucuronate decarboxylase 1 [141880]
                1. Human (Homo sapiens) [TaxId: 9606] [141881] (1)
                   SQ Q8NBZ7 87-398
            55. Xylitol dehydrogenase [141882]
                1. Gluconobacter oxydans [TaxId: 442] [141883] (8)
                   SQ Q8GR61 3-262
            56. Peroxisomal trans 2-enoyl CoA reductase [141884]
                1. Human (Homo sapiens) [TaxId: 9606] [141885] (4)
                   SQ Q9BY49 7-303
            57. D(-)-3-hydroxybutyrate dehydrogenase [141886]
                1. Pseudomonas fragi [TaxId: 296] [141887] (3)
                   SQ Q5KST5 1-260
            58. 15-hydroxyprostaglandin dehydrogenase, PGDH [141888]
                1. Human (Homo sapiens) [TaxId: 9606] [141889] (1)
                   SQ P15428 3-256
            59. GDP-mannose-3', 5'-epimerase [141890]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141891] (8)
                   SQ Q93VR3 13-374! SQ Q93VR3 13-375
            60. Bacterial sepiapterin reductase [141892]
                1. Chlorobium tepidum [TaxId: 1097] [141893] (4)
                   SQ Q8KES3 2-241
                   CT0609
            61. Dehydrogenase/reductase SDR family member 6, DHRS6 [141894]
                Oxidoreductase UCPA
                1. Human (Homo sapiens) [TaxId: 9606] [141895] (4)
                   SQ Q9BUT1 1-245
            62. Hypothetical protein TTHA0369 [141896]
                TT0321
                1. Thermus thermophilus [TaxId: 274] [141897] (4)
                   SQ Q5SLC4 2-249
            63. Rhizome secoisolariciresinol dehydrogenase [141898]
                1. Mayapple (Podophyllum peltatum) [TaxId: 35933] [141899] (4)
                   SQ Q94KL8 11-278
            64. Peroxisomal multifunctional enzyme type 2 [141900]
                17-beta-hydroxysteroid dehydrogenase 4
                1. Human (Homo sapiens) [TaxId: 9606] [141901] (6)
                   SQ P51659 2-303
                   the structure of C-terminal domain is also known, PDB entry 1S9C
            65. (s)-1-phenylethanol dehydrogenase [141902]
                1. Azoarcus sp. ebn1 [TaxId: 76114] [141903] (6)
                   SQ Q5P5I4 3-249
            66. TAT-interacting protein TIP30 [141904]
                1. Human (Homo sapiens) [TaxId: 9606] [141905] (1)
                   SQ Q9BUP3 5-236
                2. Mouse (Mus musculus) [TaxId: 10090] [141906] (1)
                   SQ Q9Z2G9 7-236
            67. Retinal dehydrogenase/reductase 3 [141907]
                1. Human (Homo sapiens) [TaxId: 9606] [141908] (16)
                   SQ Q9BPX1 4-253
            68. Erythromycin synthase, eryAI, 1st ketoreductase module [141909]
                tandem repeat of two SDR-like modules resembling a dimer commonly founf in the family; only the second module retains the coenzyme-binding site
                1. Saccharopolyspora erythraea [TaxId: 1836] [141910] (4)
                   SQ Q5UNP6 1448-1656! SQ Q5UNP6 1657-1915
            69. Hypothetical protein PA4017 [141911]
                unknown function; the active site region is blocked by a loop; strong sequence similarity to mammalian TAT-interacting protein TIP30
                1. Pseudomonas aeruginosa [TaxId: 287] [141912] (2)
                   SQ Q9HX10 4-215
            70. Putative carbonyl reductase sniffer [141913]
                1. Caenorhabditis elegans [TaxId: 6239] [141914] (6)
                   SQ P90780 1-250
         3. Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain [51800] (52)
            family members also share a common alpha+beta fold in C-terminal domain
            1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [51801]
               1. Escherichia coli [TaxId: 562] [51802] (13)
                  SQ P06977
               2. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [51803] (14)
               3. Achromobacter xylosoxidans [TaxId: 85698] [89526] (1)
                  formerly Alcaligenes xylosoxidans
               4. Thermus aquaticus [TaxId: 271] [51804] (13)
               5. Thermus thermophilus [TaxId: 274] [102157] (1)
               6. Thermotoga maritima [TaxId: 2336] [51805] (1)
               7. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51806] (1)
               8. Archaeon Methanothermus fervidus [TaxId: 2180] [51807] (1)
               9. Trypanosoma brucei brucei, glycosome [TaxId: 5702] [51808] (1)
               10. Trypanosoma cruzi [TaxId: 5693] [75104] (7)
               11. Leishmania mexicana [TaxId: 5665] [51809] (5)
               12. American lobster (Homarus americanus) [TaxId: 6706] [51810] (2)
               13. South China Sea lobster (Palinurus versicolor) [TaxId: 150436] [51811] (5)
               14. Human (Homo sapiens) [TaxId: 9606] [51812] (1)
               15. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [102158] (1)
               16. Spinach (Spinacia oleracea) [TaxId: 3562] [69409] (24)
                   SQ P19866
               17. Human(Homo sapiens), liver isoform [TaxId: 9606] [141915] (8)
                   SQ P04406 2-150,315-334
               18. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141916] (12)
                   SQ Q8IKK7 4-152,319-335! SQ Q8T6B1 1-152,319-337
               19. Archaeon Pyrococcus horikoshii [TaxId: 53953] [159423] (4)
                   SQ O59494 1-139,302-334
            2. Aspartate beta-semialdehyde dehydrogenase [51813]
               1. Escherichia coli [TaxId: 562] [51814] (4)
                  SQ P00353
               2. Vibrio cholerae [TaxId: 666] [82297] (2)
               3. Haemophilus influenzae [TaxId: 727] [102159] (12)
                  SQ P44801
               4. Streptococcus pneumoniae [TaxId: 1313] [141917] (11)
                  SQ Q8DQ00 2-127,330-357
            3. Acetaldehyde dehydrogenase (acylating) [89527]
               1. Pseudomonas sp. [TaxId: 306] [89528] (1)
            4. Homoserine dehydrogenase [51815]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51816] (4)
                  SQ P31116
            5. Saccharopine reductase [51817]
               1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51818] (3)
            6. Diaminopimelic acid dehydrogenase (DAPDH) [51819]
               1. Corynebacterium glutamicum [TaxId: 1718] [51820] (4)
            7. Dihydrodipicolinate reductase [51821]
               1. Escherichia coli [TaxId: 562] [51822] (5)
               2. Mycobacterium tuberculosis [TaxId: 1773] [102160] (14)
               3. Thermotoga maritima [TaxId: 2336] [110417] (1)
                  SQ Q9X1K8
            8. Myo-inositol 1-phosphate synthase [75105]
               1. Mycobacterium tuberculosis [TaxId: 1773] [75106] (1)
               2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75107] (9)
                  SQ P11986
               3. Archaeoglobus fulgidus [TaxId: 2234] [110418] (1)
                  SQ O28480
               4. Caenorhabditis elegans [TaxId: 6239] [110419] (1)
                  SQ Q18664
            9. Hypothetical protein TM1419 [102161]
               myo-inositol 1-phosphate synthase-related protein
               1. Thermotoga maritima [TaxId: 2336] [102162] (1)
            10. Hypothetical protein TM1643 [75108]
                1. Thermotoga maritima [TaxId: 2336] [75109] (2)
            11. 1-deoxy-D-xylulose-5-phosphate reductoisomerase [69410]
                1. Escherichia coli [TaxId: 562] [69411] (12)
                   SQ P45568
                2. Zymomonas mobilis [TaxId: 542] [110420] (2)
                   SQ Q9X5F2
            12. Biliverdin reductase [51823]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [51824] (3)
            13. Glucose-fructose oxidoreductase, N-terminal domain [51825]
                1. Zymomonas mobilis [TaxId: 542] [51826] (12)
            14. Glucose 6-phosphate dehydrogenase, N-terminal domain [51827]
                1. Leuconostoc mesenteroides [TaxId: 1245] [51828] (9)
                2. Human (Homo sapiens) [TaxId: 9606] [51829] (1)
            15. Virulence factor MviM [110421]
                1. Escherichia coli [TaxId: 562] [110422] (1)
                   SQ P75931
            16. N-acetyl-gamma-glutamyl-phosphate reductase ArgC [110423]
                1. Thermotoga maritima [TaxId: 2336] [110424] (1)
                   SQ Q9X2A2
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117428] (5)
                   SQ O82187 15-359
                3. Salmonella typhimurium [TaxId: 90371] [141918] (1)
                   SQ Q8ZKL8 1-153,309-334
            17. Putative oxidoreductase VCA1048 [110425]
                1. Vibrio cholerae [TaxId: 666] [110426] (1)
                   SQ Q9KKQ4
            18. Probable oxidoreductase At4g09670 [117429]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117430] (1)
                   SQ Q9SZ83
            19. Putative semialdehyde dehydrogenase [141919]
                1. Rice (Oryza sativa) [TaxId: 4530] [141920] (4)
                   SQ Q6AV34 68-218,384-415
            20. Galactose/lactose metabolism regulatory protein GAL80 [141921]
                1. Yeast (Kluyveromyces lactis) [TaxId: 28985] [141922] (9)
                   SQ Q06433 2-154,374-457
            21. Usg-1 protein homolog PA3116 [141923]
                1. Pseudomonas aeruginosa [TaxId: 287] [141924] (1)
                   SQ O87014 3-129,320-336
            22. Hypothetical protein TM0312 [141925]
                1. Thermotoga maritima [TaxId: 2336] [141926] (2)
                   SQ Q9WYE8 4-131,276-328
         4. Formate/glycerate dehydrogenases, NAD-domain [51830] (14)
            this domain interrupts the other domain which defines family
            1. Formate dehydrogenase [51831]
               1. Pseudomonas sp., strain 101 [TaxId: 306] [51832] (2)
            2. Putative formate dehydrogenase [51833]
               1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [51834] (1)
            3. Transcription corepressor CtbP [82298]
               C-terminal binding protein 1; a dehydrogenase
               1. Human (Homo sapiens), Ctbp1 [TaxId: 9606] [82299] (1)
               2. Rat (Rattus norvegicus), Ctbp3 [TaxId: 10116] [89529] (2)
            4. D-2-hydroxyisocaproate dehydrogenase [51835]
               1. Lactobacillus casei [TaxId: 1582] [51836] (1)
            5. D-glycerate dehydrogenase [51837]
               1. Hyphomicrobium methylovorum [TaxId: 84] [51838] (1)
            6. Phosphoglycerate dehydrogenase [51839]
               has additional C-terminal domain of the ferredoxin fold
               1. Escherichia coli [TaxId: 562] [51840] (18)
               2. Mycobacterium tuberculosis [TaxId: 1773] [141927] (2)
                  SQ P0A544 98-281
            7. D-lactate dehydrogenase [51841]
               1. Lactobacillus helveticus [TaxId: 1587] [51842] (3)
            8. L-alanine dehydrogenase [51843]
               1. Phormidium lapideum [TaxId: 32060] [51844] (3)
            9. Nicotinamide nucleotide transhydrogenase dI component [63937]
               L-alanine dehydrogenase homologue
               1. Rhodospirillum rubrum [TaxId: 1085] [63938] (28)
            10. S-adenosylhomocystein hydrolase [51845]
                1. Human (Homo sapiens) [TaxId: 9606] [51846] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [51847] (17)
                3. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117431] (1)
                   SQ P50250
         5. Siroheme synthase N-terminal domain-like [75110] (2)
            1. Siroheme synthase CysG, domain 1 [102163]
               1. Salmonella typhimurium [TaxId: 90371] [102164] (3)
            2. Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain [75111]
               involved in siroheme synthesis
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75112] (1)
         6. LDH N-terminal domain-like [51848] (33)
            1. Malate dehydrogenase [51849]
               1. Pig (Sus scrofa) [TaxId: 9823] [51850] (3)
               2. Sorghum (Sorghum vulgare), chloroplast [TaxId: 4558] [51851] (1)
               3. Flaveria bidentis, chloroplast [TaxId: 4224] [51852] (1)
               4. Escherichia coli [TaxId: 562] [51853] (8)
               5. Thermus flavus [TaxId: 274] [51854] (2)
               6. Thermus thermophilus [TaxId: 274] [82300] (9)
                  identical sequence to that from the Thermus flavus enzyme
               7. Archaeon Haloarcula marismortui [TaxId: 2238] [51855] (17)
               8. Aquaspirillum arcticum [TaxId: 87645] [51856] (3)
               9. Chloroflexus aurantiacus [TaxId: 1108] [69415] (7)
                  SQ P80040
               10. Chlorobium tepidum [TaxId: 1097] [69416] (1)
               11. Chlorobium vibrioforme [TaxId: 1098] [69417] (2)
               12. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110427] (2)
                   SQ O08349
            2. L-2-hydroxyisocapronate dehydrogenase, L-HICDH [51857]
               1. Lactobacillus confusus [TaxId: 1583] [51858] (1)
            3. Lactate dehydrogenase [51859]
               1. Pig (Sus scrofa) [TaxId: 9823] [51860] (3)
               2. Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606] [63939] (2)
               3. Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606] [63940] (1)
               4. Mouse (Mus musculus) [TaxId: 10090] [51861] (4)
               5. Dogfish (Squalus acanthias) [TaxId: 7797] [51862] (3)
               6. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [51863] (9)
               7. Plasmodium berghei [TaxId: 5821] [102165] (7)
               8. Toxoplasma gondii [TaxId: 5811] [102166] (4)
               9. Bacillus stearothermophilus [TaxId: 1422] [51864] (9)
               10. Lactobacillus casei [TaxId: 1582] [51865] (1)
               11. Lactobacillus pentosus [TaxId: 1589] [69418] (1)
               12. Bifidobacterium longum, strain am101-2 [TaxId: 216816] [51866] (2)
               13. Thermotoga maritima [TaxId: 2336] [51867] (1)
               14. Clostridium thermocellum [TaxId: 1515] [117432] (1)
                   SQ Q4CDK5
            4. MJ0490, lactate/malate dehydrogenase [63941]
               1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63942] (2)
            5. Alpha-glucosidase AglA [89530]
               1. Thermotoga maritima [TaxId: 2336] [89531] (1)
                  TM1834
            6. Putative alpha-glucosidase TM0752 [102167]
               1. Thermotoga maritima [TaxId: 2336] [102168] (1)
            7. Maltose-6'-phosphate glucosidase GlvA [102169]
               1. Bacillus subtilis [TaxId: 1423] [102170] (1)
                  SQ P54716
            8. 6-phospho-beta-glucosidase [110428]
               1. Bacillus stearothermophilus [TaxId: 1422] [110429] (1)
                  SQ P84135
               2. Thermotoga maritima [TaxId: 2336] [110430] (3)
                  SQ Q9X108
         7. 6-phosphogluconate dehydrogenase-like, N-terminal domain [51868] (26)
            the beta-sheet is extended to 8 strands, order 32145678; strands 7 & 8 are antiparallel to the rest
            C-terminal domains also show some similarity
            1. Class I ketol-acid reductoisomerase (KARI) [89532]
               1. Pseudomonas aeruginosa [TaxId: 287] [89533] (1)
            2. Class II ketol-acid reductoisomerase (KARI) [51869]
               contains additional subdomain at the N-terminus, partly ordered
               1. Spinach (Spinacia oleracea) [TaxId: 3562] [51870] (2)
            3. 6-phosphogluconate dehydrogenase [51871]
               1. Sheep (Ovis orientalis aries) [TaxId: 9940] [51872] (5)
               2. Trypanosoma brucei [TaxId: 5691] [51873] (1)
            4. Hydroxyisobutyrate dehydrogenase [102171]
               1. Thermus thermophilus [TaxId: 274] [102172] (8)
                  structural genomics
               2. Salmonella typhimurium [TaxId: 90371] [110431] (1)
                  SQ Q8ZLV8
               3. Pseudomonas aeruginosa [TaxId: 287] [159424] (1)
                  SQ Q9I5I6 1-162
            5. Mannitol 2-dehydrogenase [82301]
               1. Pseudomonas fluorescens [TaxId: 294] [82302] (2)
            6. Short chain L-3-hydroxyacyl CoA dehydrogenase [51874]
               1. Human (Homo sapiens) [TaxId: 9606] [51875] (11)
               2. Pig (Sus scrofa) [TaxId: 9823] [51876] (1)
            7. Conserved hypothetical protein MTH1747 [75113]
               1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75114] (1)
            8. UDP-glucose dehydrogenase (UDPGDH) [51877]
               1. Streptococcus pyogenes [TaxId: 1314] [51878] (2)
            9. GDP-mannose 6-dehydrogenase [89534]
               1. Pseudomonas aeruginosa [TaxId: 287] [89535] (3)
            10. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [51879]
                1. Arthrobacter, strain 1c [TaxId: 1663] [51880] (1)
            11. Glycerol-3- phosphate dehydrogenase [51881]
                1. Trypanosome (Leishmania mexicana) [TaxId: 5665] [51882] (7)
                2. Archaeoglobus fulgidus [TaxId: 2234] [117433] (1)
                   SQ O29390
            12. Ketopantoate reductase PanE [69419]
                1. Escherichia coli [TaxId: 562] [69420] (5)
            13. Coenzyme F420H2:NADP+ oxidoreductase (FNO) [69421]
                lacks all but the first helix of the C-terminal all-alpha domain
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69422] (2)
            14. Fatty oxidation complex alpha subunit, middle domain [110432]
                1. Pseudomonas fragi [TaxId: 296] [110433] (4)
                   SQ P28793
            15. Pyrroline-5-carboxylate reductase ProC [117434]
                1. Neisseria meningitidis, serogroup B [TaxId: 487] [117435] (2)
                   SQ Q9K1N1
                2. Streptococcus pyogenes [TaxId: 1314] [141928] (10)
                   SQ Q9A1S9 1-152
            16. Prephenate dehydrogenase TyrA [141929]
                1. Aquifex aeolicus [TaxId: 63363] [141930] (4)
                   SQ O67636 30-200
                2. Synechocystis sp. pcc 6803 [TaxId: 1148] [141931] (4)
                   SQ P73906 1-165
                3. Haemophilus influenzae [TaxId: 727] [159425] (2)
                   SQ P43902 92-243
            17. 5,10-methenyltetrahydromethanopterin hydrogenase, HMD [141932]
                1. Archaeon Methanocaldococcus jannaschii [TaxId: 2190] [141933] (1)
                   SQ Q58194 1-242
            18. Hypothetical protein TM1727 [159426]
                ProC structural homologue
                1. Thermotoga maritima [TaxId: 2336] [159427] (2)
                   SQ Q9X250 2-154
         8. Aminoacid dehydrogenase-like, C-terminal domain [51883] (24)
            extra N-terminal helix displaces the C-terminal helix (following strand 6) from its usual position creating a family nicotineamide-binding site
            1. Glutamate dehydrogenase [51884]
               1. Clostridium symbiosum [TaxId: 1512] [51885] (4)
               2. Archaeon Pyrococcus furiosus [TaxId: 2261] [51886] (1)
               3. Archaeon Thermococcus profundus [TaxId: 49899] [63943] (1)
               4. Archaeon Thermococcus litoralis [TaxId: 2265] [51887] (1)
               5. Thermotoga maritima [TaxId: 2336] [51888] (3)
               6. Cow (Bos taurus) [TaxId: 9913] [51889] (5)
               7. Human (Homo sapiens) [TaxId: 9606] [75115] (2)
               8. Pyrobaculum islandicum [TaxId: 2277] [117436] (1)
                  SQ Q9Y8I4
            2. Leucine dehydrogenase [51890]
               1. Bacillus sphaericus [TaxId: 1421] [51891] (1)
            3. Phenylalanine dehydrogenase [51892]
               1. Rhodococcus sp., M4 [TaxId: 1831] [51893] (4)
            4. Methylenetetrahydrofolate dehydrogenase/cyclohydrolase [51894]
               the two-domain organization is similar to that of aminoacid dehydrogenases, but both domains are truncated
               1. Human (Homo sapiens) [TaxId: 9606] [51895] (4)
               2. Escherichia coli [TaxId: 562] [51896] (1)
               3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51897] (2)
            5. Methylene-tetrahydromethanopterin dehydrogenase [82303]
               1. Methylobacterium extorquens [TaxId: 408] [82304] (2)
            6. Putative shikimate dehydrogenase YdiB [82305]
               1. Escherichia coli [TaxId: 562] [82306] (3)
            7. Shikimate 5-dehydrogenase-like protein HI0607 [89536]
               1. Haemophilus influenzae [TaxId: 727] [89537] (1)
            8. Shikimate 5-dehydrogenase AroE [89538]
               1. Escherichia coli [TaxId: 562] [89539] (1)
               2. Haemophilus influenzae [TaxId: 727] [102173] (2)
               3. Archaeon Methanococcus jannaschii [TaxId: 2190] [89540] (1)
                  MJ1084
            9. Glutamyl tRNA-reductase middle domain [69413]
               other domains of this protein are distinct from those usually associated with the family domain
               1. Archaeon Methanopyrus kandleri [TaxId: 2320] [69414] (1)
            10. Mitochondrial NAD(P)-dependent malic enzyme [51898]
                includes C-terminal additional subdomains
                1. Human (Homo sapiens) [TaxId: 9606] [51899] (10)
                2. Domestic pigeon (Columba livia) [TaxId: 8932] [75116] (1)
                3. Pig roundworm (Ascaris suum) [TaxId: 6253] [75117] (2)
            11. Malate oxidoreductase (malic enzyme) [110434]
                1. Thermotoga maritima [TaxId: 2336] [110435] (5)
                   SQ Q9WZ12
         9. Potassium channel NAD-binding domain [63944] (4)
            1. Rck domain from putative potassium channel Kch [63945]
               1. Escherichia coli [TaxId: 562] [63946] (1)
            2. Ktn bsu222 [75118]
               1. Bacillus subtilis [TaxId: 1423] [75119] (13)
            3. Ktn Mja218 [75120]
               1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75121] (1)
            4. Potassium channel-related protein MthK [75122]
               1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75123] (9)
         10. Transcriptional repressor Rex, C-terminal domain [102174] (1)
             1. Transcriptional repressor Rex, C-terminal domain [102175]
                forms swapped dimer with C-terminal helices
                1. Thermus aquaticus [TaxId: 271] [102176] (3)
                   SQ Q9X2V5
                   CASP5
         11. CoA-binding domain [51900] (7)
             1. Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain [51901]
                1. Escherichia coli [TaxId: 562] [51902] (18)
                2. Thermus thermophilus [TaxId: 274] [89541] (1)
                3. Pig (Sus scrofa) [TaxId: 9823] [51903] (6)
             2. Hypothetical protein TT1466 [89542]
                putative CoA-binding protein
                1. Thermus thermophilus [TaxId: 274] [89543] (2)
             3. Hypothetical protein PH1109 [141934]
                1. Pyrococcus horikoshii [TaxId: 53953] [141935] (3)
                   SQ O58836 1-142
             4. Acetate-CoA ligase alpha chain, AcdA, N-terminal domain [141936]
                1. Pyrococcus horikoshii [TaxId: 53953] [141937] (2)
                   SQ O58493 1-129
             5. Hypothetical protein PF0725 [141938]
                1. Pyrococcus furiosus [TaxId: 2261] [141939] (1)
                   SQ Q8U2V3 6-121
         12. Ornithine cyclodeaminase-like [110436] (2)
             Pfam 02423; contains additional alpha+beta dimerisation subdomain mostly formed by the N-terminal meander beta-sheet
             1. Archaeal alanine dehydrogenase [110437]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110438] (2)
                   SQ O28608 # Rossmann-fold core (101-292) begins with an N-terminal helix and ends with a beta-strand
             2. Ornithine cyclodeaminase [117437]
                1. Pseudomonas putida [TaxId: 303] [117438] (2)
                   SQ Q88H32
   3. FAD/NAD(P)-binding domain [51904] (1)
      core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
      1. FAD/NAD(P)-binding domain [51905] (8)
         uperfamily
         1. C-terminal domain of adrenodoxin reductase-like [51906] (5)
            1. Trimethylamine dehydrogenase, C-terminal domain [51907]
               N-terminal domain is beta/alpha barrel and the middle domain is alpha/beta Rossmann-fold
               1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51908] (5)
            2. 2,4-dienoyl-CoA reductase, C-terminal domain [102177]
               1. Escherichia coli [TaxId: 562] [102178] (1)
            3. Adrenodoxin reductase of mitochondrial p450 systems [51909]
               1. Cow (Bos taurus) [TaxId: 9913] [51910] (6)
            4. Ferredoxin:NADP reductase FprA [75124]
               1. Mycobacterium tuberculosis [TaxId: 1773] [75125] (2)
            5. Dihydropyrimidine dehydrogenase, domain 3 [51911]
               1. Pig (Sus scrofa) [TaxId: 9823] [51912] (5)
         2. FAD-linked reductases, N-terminal domain [51913] (25)
            C-terminal domain is alpha+beta is common for the family
            1. Cholesterol oxidase of GMC family [51914]
               1. Brevibacterium sterolicum [TaxId: 1702] [51915] (2)
               2. Streptomyces sp. [TaxId: 1931] [51916] (13)
               3. Streptomyces sp. (strain SA-COO) (Streptomyces sp. SA-COO) [TaxId: 74576] [159428] (1)
            2. Glucose oxidase [51924]
               1. Aspergillus niger [TaxId: 5061] [51925] (2)
               2. Penicillium amagasakiense [TaxId: 63559] [51926] (1)
            3. Hydroxynitrile lyase [82307]
               1. Almond (Prunus dulcis) [TaxId: 3755] [82308] (1)
            4. Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), FAD-binding domain [82309]
               1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [82310] (2)
            5. p-Hydroxybenzoate hydroxylase, PHBH [51917]
               1. Pseudomonas fluorescens [TaxId: 294] [51918] (17)
               2. Pseudomonas aeruginosa [TaxId: 287] [51919] (19)
            6. Sarcosine oxidase [51920]
               1. Bacillus sp., strain b0618 [TaxId: 1409] [51921] (18)
            7. Glycine oxidase ThiO [89544]
               1. Bacillus sp. [TaxId: 1409] [89545] (6)
            8. Phenol hydroxylase [51922]
               structurally very similar to PHBH, but contains additional C-terminal domain of the thioredoxin-like fold
               1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [51923] (2)
            9. Polyamine oxidase [51927]
               1. Maize (Zea mays) [TaxId: 4577] [51928] (7)
            10. L-aminoacid oxidase [51929]
                1. Malayan pit viper (Calloselasma rhodostoma) [TaxId: 8717] [51930] (6)
                2. Halys viper (Agkistrodon halys) [TaxId: 8714] [102179] (4)
                   SQ Q90W54 21-504
            11. Monoamine oxidase B [69423]
                1. Human (Homo sapiens) [TaxId: 9606] [69424] (20)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [102180] (27)
            12. N,N-dimethylglycine oxidase [102181]
                1. Arthrobacter globiformis [TaxId: 1665] [102182] (3)
            13. Protoporphyrinogen oxidase [102183]
                1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [102184] (1)
                2. Myxococcus xanthus [TaxId: 34] [159429] (4)
                   SQ P56601 10-306,415-464
            14. Pyranose 2-oxidase [117439]
                1. White-rot fungus (Peniophora sp. SG) [TaxId: 204723] [117440] (19)
                   SQ Q8J136 43-619
            15. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [141940]
                1. Pig (Sus scrofa) [TaxId: 9823] [141941] (4)
                   SQ P55931 27-259,359-505
            16. Dihydroxypyridine hydroxylase DhpH [159430]
                1. Arthrobacter nicotinovorans [TaxId: 29320] [159431] (3)
                   SQ Q93NG3 2-163,292-394
            17. Lysine-specific histone demethylase 1, LSD1 [159432]
                1. Human (Homo sapiens) [TaxId: 9606] [159433] (8)
                   SQ O60341 274-654,764-836
            18. Monooxygenase PhzS [159434]
                1. Pseudomonas aeruginosa [TaxId: 287] [159435] (1)
                   SQ Q9HWG9 4-182,294-402
         3. GDI-like N domain [51931] (3)
            Similar to FAD-linked reductases in both domains but does not bind FAD
            1. Guanine nucleotide dissociation inhibitor, GDI [51932]
               the inhibition function is probably associated with an insert subdomain, residues 120-220
               1. Cow (Bos taurus) [TaxId: 9913] [51933] (3)
               2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110439] (13)
                  SQ P39958 5-446
            2. Rab escort protein 1 [89546]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [89547] (3)
                  SQ P37727
         4. Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain [51934] (7)
            1. L-aspartate oxidase [51935]
               1. Escherichia coli [TaxId: 562] [51936] (3)
            2. Succinate dehydogenase [82311]
               1. Escherichia coli [TaxId: 562] [82312] (2)
            3. Fumarate reductase [51937]
               1. Escherichia coli [TaxId: 562] [51938] (7)
               2. Wolinella succinogenes [TaxId: 844] [51939] (8)
            4. Flavocytochrome c3 (respiratory fumarate reductase) [51940]
               contains additional N-terminal multiheme domain
               1. Shewanella frigidimarina [TaxId: 56812] [51941] (16)
               2. Shewanella putrefaciens [TaxId: 24] [51942] (3)
            5. Adenylylsulfate reductase A subunit [69425]
               1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69426] (2)
         5. FAD/NAD-linked reductases, N-terminal and central domains [51943] (28)
            duplication: both domains have similar folds and functions
            most members of the family contain common C-terminal alpha+beta domain
            1. Glutathione reductase [51944]
               1. Human (Homo sapiens) [TaxId: 9606] [51945] (17)
               2. Plasmodium falciparum [TaxId: 5833] [89548] (1)
               3. Escherichia coli [TaxId: 562] [51946] (4)
            2. Trypanothione reductase [51947]
               1. Crithidia fasciculata [TaxId: 5656] [51948] (6)
               2. Trypanosoma cruzi [TaxId: 5693] [51949] (8)
            3. Mammalian thioredoxin reductase [63947]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [63948] (1)
            4. Thioredoxin reductase [51950]
               lacks the "interface" C-terminal alpha+beta domain
               1. Escherichia coli [TaxId: 562] [51951] (5)
               2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [51952] (1)
            5. Apoptosis-inducing factor (AIF) [75126]
               1. Human (Homo sapiens) [TaxId: 9606] [75127] (1)
               2. Mouse (Mus musculus) [TaxId: 10090] [75128] (1)
            6. Alkyl hydroperoxide reductase subunit F (AhpF), C-terminal domains [51953]
               1. Salmonella typhimurium [TaxId: 90371] [51954] (1)
               2. Escherichia coli [TaxId: 562] [63949] (1)
            7. NADH peroxidase [51955]
               1. Enterococcus faecalis [TaxId: 1351] [51956] (8)
            8. NADH-dependent ferredoxin reductase, BphA4 [51957]
               1. Pseudomonas sp., KKS102 [TaxId: 306] [51958] (2)
            9. Putidaredoxin reductase [102185]
               1. Pseudomonas putida [TaxId: 303] [102186] (2)
            10. Dihydrolipoamide dehydrogenase [51959]
                1. Pseudomonas putida [TaxId: 303] [51960] (1)
                2. Pseudomonas fluorescens [TaxId: 294] [51961] (1)
                3. Azotobacter vinelandii [TaxId: 354] [51962] (1)
                4. Bacillus stearothermophilus [TaxId: 1422] [51963] (1)
                5. Neisseria meningitidis [TaxId: 487] [51964] (2)
                6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63950] (5)
                7. Garden pea (Pisum sativum) [TaxId: 3888] [51965] (1)
                8. Mycobacterium tuberculosis [TaxId: 1773] [117441] (1)
                   SQ O53355
            11. NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase [82313]
                1. Xanthobacter sp., py2 [TaxId: 35809] [82314] (10)
            12. Flavocytochrome c sulfide dehydrogenase, FCSD, flavin-binding subunit [51966]
                has a smaller C-terminal alpha+beta domain instead the "interface" domain
                1. Purple phototrophic bacterium (Chromatium vinosum) [TaxId: 1049] [51967] (1)
            13. Phenylacetone monooxygenase [110440]
                1. Thermobifida fusca [TaxId: 2021] [110441] (1)
                   SQ Q5YS95 # 55% sequence identity; Nocardia farcinica TaxID:37329
            14. NADH oxidase /nitrite reductase [117442]
                1. Pyrococcus furiosus [TaxId: 2261] [117443] (1)
                   SQ Q8U1K9
            15. Flavin-dependent monoxygenase SPBP16F5.08c [117444]
                1. Schizosaccharomyces pombe [TaxId: 4896] [117445] (13)
                   SQ Q9HFE4
         6. Thi4-like [141942] (2)
            Pfam 01946; stand-alone, moderately decorated domain
            1. Thiazole biosynthetic enzyme Thi4 [141943]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141944] (2)
                  SQ P32318 16-326
                  mitochondrial
               2. Thale cress(Arabidopsis thaliana) [TaxId: 3702] [141945] (1)
                  SQ Q38814 51-328
                  chloroplast
         7. GidA-like [141946] (1)
            part of Pfam 01266
            1. GidA-related protein TTHA1897 [141947]
               1. Thermus thermophilus [TaxId: 274] [141948] (1)
                  SQ Q5SH33 2-231
         8. HI0933 N-terminal domain-like [159436] (2)
            N-terminal part of Pfam 03486
            1. Hypothetical protein HI0933 [159437]
               1. Haemophilus influenzae [TaxId: 727] [159438] (1)
                  SQ P44941 1-194,343-401
            2. Flavoprotein BC4706 [159439]
               1. Bacillus cereus [TaxId: 1396] [159440] (1)
                  SQ Q816V9 1-192,362-420
   4. Nucleotide-binding domain [51970] (1)
      3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
      1. Nucleotide-binding domain [51971] (3)
         this superfamily shares the common nucleotide-binding site with and provides a link between the Rossmann-fold NAD(P)-binding and FAD/NAD(P)-binding domains
         uperfamily
         1. N-terminal domain of adrenodoxin reductase-like [51972] (5)
            1. Trimethylamine dehydrogenase, middle domain [51973]
               1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51974] (5)
            2. 2,4-dienoyl-CoA reductase, middle domain [102187]
               1. Escherichia coli [TaxId: 562] [102188] (1)
            3. Adrenodoxin reductase of mitochondrial p450 systems [51975]
               1. Cow (Bos taurus) [TaxId: 9913] [51976] (6)
            4. Ferredoxin:NADP reductase FprA [75129]
               1. Mycobacterium tuberculosis [TaxId: 1773] [75130] (2)
            5. Dihydropyrimidine dehydrogenase, domain 2 [51977]
               1. Pig (Sus scrofa) [TaxId: 9823] [51978] (5)
         2. D-aminoacid oxidase, N-terminal domain [51979] (2)
            This family is probably related to the FAD-linked reductases and shares with them the C-terminal domain fold
            1. D-aminoacid oxidase, N-terminal domain [51980]
               1. Pig (Sus scrofa) [TaxId: 9823] [51981] (6)
               2. Rhodotorula gracilis [TaxId: 5286] [51982] (4)
         3. UDP-galactopyranose mutase, N-terminal domain [69427] (2)
            domain structure is similar to that of D-aminoacid oxidase
            1. UDP-galactopyranose mutase, N-terminal domain [69428]
               1. Escherichia coli [TaxId: 562] [69429] (1)
               2. Klebsiella pneumoniae [TaxId: 573] [117446] (3)
                  SQ Q48485
   5. MurCD N-terminal domain [51983] (1)
      3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
      1. MurCD N-terminal domain [51984] (1)
         uperfamily
         1. MurCD N-terminal domain [51985] (3)
            1. UDP-N-acetylmuramate-alanine ligase MurC [82315]
               1. Thermotoga maritima [TaxId: 2336] [82316] (1)
                  TM0231
               2. Haemophilus influenzae [TaxId: 727] [89549] (4)
            2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [51986]
               1. Escherichia coli [TaxId: 562] [51987] (11)
   6. 7-stranded beta/alpha barrel [51988] (3)
      variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
      1. Glycosyl hydrolases family 6, cellulases [51989] (1)
         uperfamily
         1. Glycosyl hydrolases family 6, cellulases [51990] (5)
            Pfam 01341
            1. Cellulase E2 [51991]
               1. Thermomonospora fusca, strain yx [TaxId: 2021] [51992] (2)
            2. Cellobiohydrolase II (Cel6) [51993]
               1. Trichoderma reesei, Cel6a [TaxId: 51453] [51994] (7)
               2. Humicola insolens, Cel6a [TaxId: 34413] [51995] (9)
               3. Humicola insolens, Cel6b [TaxId: 34413] [51996] (1)
            3. Putative cellulase Rv0062 (Cel6, CelA1) [117447]
               1. Mycobacterium tuberculosis [TaxId: 1773] [117448] (4)
                  SQ Q79G13 88-380
      2. PHP domain-like [89550] (2)
         uperfamily
         1. PHP domain [89551] (2)
            putative phosphoesterase domain; contains trinuclear metal-binding site; some similarity to the metallohydrolases of TIM-barrel fold
            1. Hypothetical protein YcdX [89552]
               1. Escherichia coli [TaxId: 562] [89553] (3)
                  SQ P75914
            2. Hypothetical protein TM0559 [141949]
               1. Thermotoga maritima [TaxId: 2336] [141950] (6)
                  SQ Q9WZ29 5-233
         2. RNase P subunit p30 [110442] (1)
            Pfam 01876
            1. Ribonuclease P protein component 3, Rnp3 [110443]
               1. Pyrococcus horikoshii [TaxId: 53953] [110444] (3)
                  SQ O59543 # PH1877
      3. Glycoside hydrolase/deacetylase [88713] (8)
         in the different families beta-barrels are similarly distorted but may vary in the number of strands
         uperfamily
         1. 4-alpha-glucanotransferase, N-terminal domain [89554] (1)
            family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
            1. 4-alpha-glucanotransferase, N-terminal domain [89555]
               1. Archaeon Thermococcus litoralis [TaxId: 2265] [89556] (3)
         2. alpha-mannosidase [88714] (2)
            family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
            1. Golgi alpha-mannosidase II [88715]
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [88716] (46)
                  SQ Q24451 94-1107
            2. Lysosomal alpha-mannosidase [89557]
               the single-chain precursor is processed into 5 peptides; heavily glycosylated
               1. Cow (Bos taurus) [TaxId: 9913] [89558] (1)
         3. AmyC N-terminal domain-like [102189] (2)
            1. Hypothetical protein TT1467, N-terminal domain [102190]
               1. Thermus thermophilus [TaxId: 274] [102191] (1)
            2. Alpha-amylase AmyC [141951]
               1. Thermotoga maritima [TaxId: 2336] [141952] (1)
                  SQ A1GKL6 1-404
         4. NodB-like polysaccharide deacetylase [89559] (6)
            variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=6, S=8; strand order 123456
            1. Probable polysaccharide deacetylase PdaA [89560]
               1. Bacillus subtilis [TaxId: 1423] [89561] (7)
            2. Chitin deacetylase [141953]
               1. Bean anthracnose fungus (Colletotrichum lindemuthianum) [TaxId: 290576] [141954] (1)
                  SQ Q6DWK3 29-248
            3. Xylanase XynA C-terminal domain [141955]
               1. Clostridium thermocellum [TaxId: 1515] [141956] (2)
                  SQ O87119 480-683
            4. Putative polysaccharide deacetylase BA0424 [141957]
               1. Bacillus anthracis [TaxId: 1392] [141958] (1)
                  SQ Q81Z49 54-258
            5. Peptidoglycan GlcNAc deacetylase C-terminal domain [141959]
               1. Streptococcus pneumoniae [TaxId: 1313] [141960] (2)
                  SQ Q8DP63 268-463
            6. Acetyl-xylan esterase [141961]
               1. Streptomyces lividans [TaxId: 1916] [141962] (2)
                  SQ Q54413 42-233
         5. LamB/YcsF-like [117449] (3)
            Pfam 03746
            1. Hypothetical protein YbgL [117450]
               1. Escherichia coli [TaxId: 562] [117451] (1)
                  SQ P75746
            2. Hypothetical protein PH0986 [117452]
               1. Pyrococcus horikoshii [TaxId: 53953] [117453] (1)
                  SQ O58714
            3. Hypothetical protein TTHB195 [141963]
               1. Thermus thermophilus [TaxId: 274] [141964] (1)
                  SQ Q53WG6 1-250
         6. PA1517-like [141965] (1)
            seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel NodB-like family; member of the same Pfam family (Pfam 01522)
            1. Hypothetical protein PA1517 [141966]
               1. Pseudomonas aeruginosa [TaxId: 287] [141967] (8)
                  SQ Q9I3J6 4-304
         7. Divergent polysaccharide deacetylase [141968] (1)
            Pfam 04748
            1. Hypothetical protein BH1492 [141969]
               1. Bacillus halodurans [TaxId: 86665] [141970] (1)
                  SQ Q9KCS7 31-254
         8. YdjC-like [159441] (1)
            Pfam 04794
            1. Uncharacterized protein EF3048 [159442]
               1. Enterococcus faecalis [TaxId: 1351] [159443] (2)
                  SQ P59745 2-262
   7. PFL-like glycyl radical enzymes [51997] (1)
      contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
      1. PFL-like glycyl radical enzymes [51998] (5)
         duplication: the N- and C-terminal halves have similar topologies
         uperfamily
         1. PFL-like [51999] (2)
            Pfam 02901; except the C-terminal ~100 residues covered by Pfam 01228
            1. Pyruvate formate-lyase, PFL [52000]
               1. Escherichia coli [TaxId: 562] [52001] (8)
            2. Glycerol dehydratase DhaB1 [110445]
               1. Clostridium butyricum [TaxId: 1492] [110446] (3)
                  SQ Q8GEZ8
         2. R1 subunit of ribonucleotide reductase, C-terminal domain [52002] (2)
            1. R1 subunit of ribonucleotide reductase, C-terminal domain [52003]
               1. Escherichia coli [TaxId: 562] [52004] (8)
               2. Salmonella typhimurium [TaxId: 90371] [110447] (6)
                  SQ Q08698
         3. B12-dependent (class II) ribonucleotide reductase [75131] (1)
            1. B12-dependent (class II) ribonucleotide reductase [75132]
               1. Lactobacillus leichmannii [TaxId: 28039] [75133] (1)
         4. Class III anaerobic ribonucleotide reductase NRDD subunit [52005] (1)
            1. Class III anaerobic ribonucleotide reductase NRDD subunit [52006]
               1. Bacteriophage T4 [TaxId: 10665] [52007] (5)
         5. SP0239-like [159444] (1)
            Pfam 05167; DUF771
            1. Uncharacterized protein SP0239 [159445]
               1. Streptococcus pneumoniae [TaxId: 1313] [159446] (2)
                  SQ Q97ST4 1-440
   8. The "swivelling" beta/beta/alpha domain [52008] (10)
      3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
      this domain is thought to be mobile in most multi-domain proteins known to contain it
      1. Phosphohistidine domain [52009] (2)
         contains barrel, closed, n=7, S=10
         uperfamily
         1. Pyruvate phosphate dikinase, central domain [52010] (3)
            1. Pyruvate phosphate dikinase, central domain [52011]
               1. Clostridium symbiosum [TaxId: 1512] [52012] (8)
               2. Trypanosoma brucei [TaxId: 5691] [75134] (1)
               3. Maize (Zea mays) [TaxId: 4577] [141971] (2)
                  SQ P11155 454-588
         2. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52013] (1)
            1. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52014]
               contains 4-helical insert domain, residues 22-144
               1. Escherichia coli [TaxId: 562] [52015] (11)
      2. RraA-like [89562] (1)
         structural similarity and possible distant homology to the phosphohistidine domain of pyruvate phosphate dikinase
         uperfamily
         1. RraA-like [89563] (4)
            aka MenG-like; characterized as regulator of RNase E activity A (RraA) that globally modulates RNA abundance in E. coli
            1. Hypothetical protein Rv3853 [89564]
               RraA homologue; (mis)annotated as a probable MenG-like demethylmenaquinone methyltransferase
               1. Mycobacterium tuberculosis [TaxId: 1773] [89565] (1)
            2. Regulator of RNase E activity RraA (MenG) [102192]
               1. Escherichia coli [TaxId: 562] [102193] (1)
            3. Hypothetical protein VC2366 [102194]
               RraA homologue
               1. Vibrio cholerae [TaxId: 666] [102195] (1)
            4. Demethylmenaquinone methyltransferase [102196]
               as (mis)annotated in the PDB entry; RraA homologue
               1. Thermus thermophilus [TaxId: 274] [102197] (1)
      3. Putative cyclase [102198] (1)
         contains mixed beta-sheet barrel, closed n=7, S=10
         uperfamily
         1. Putative cyclase [102199] (2)
            Pfam 04199; COG1878: predicted metal-dependent hydrolase
            1. Unnamed protein [102200]
               not in the sequence database yet; closest homologue is TTE1006 from Thermoanaerobacter tengcongensis
               1. Bacillus stearothermophilus [TaxId: 1422] [102201] (1)
                  conflict: annotated in PDB as from Escherichia coli
            2. Hypothetical protein MJ0783 [141972]
               1. Methanococcus jannaschii [TaxId: 2190] [141973] (1)
                  SQ Q58193 1-186
      4. LeuD/IlvD-like [52016] (3)
         contains mixed beta-sheet barrel, closed n=7, S=10
         uperfamily
         1. LeuD-like [52017] (5)
            Pfam 00694; permutation of the domain order in the proteins containing this family domain
            1. Aconitase A, C-terminal domain [52018]
               other three domains have alpha/beta folds
               1. Pig (Sus scrofa) [TaxId: 9823] [52019] (6)
               2. Cow (Bos taurus) [TaxId: 9913] [52020] (9)
            2. Aconitase B, second N-terminal domain [75135]
               1. Escherichia coli [TaxId: 562] [75136] (1)
            3. Isopropylmalate isomerase LeuD [117454]
               3-isopropylmalate dehydratase small subunit
               1. Pyrococcus horikoshii [TaxId: 53953] [117455] (1)
                  SQ O59393
            4. ron-responsive element binding protein 1, C-terminal domain [141974]
               1. Human (Homo sapiens) [TaxId: 9606] [141975] (3)
                  SQ P21399 631-889
         2. IlvD/EDD C-terminal domain-like [141976] (1)
            C-terminal part of Pfam 00920
            1. 6-phosphogluconate dehydratase EDD [141977]
               1. Shewanella oneidensis [TaxId: 70863] [141978] (2)
                  SQ Q8EEA0 419-608
         3. AF0055-like [141979] (1)
            PF01989; DUF126; probable link between the LeuD-like and Phosphohistidine domain superfamilies (sequence similarity crosshits)
            1. Hypothetical protein AF0055 [141980]
               1. Archaeoglobus fulgidus [TaxId: 2234] [141981] (1)
                  SQ O30181 1-132
      5. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52021] (1)
         uperfamily
         1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52022] (1)
            1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52023]
               1. Escherichia coli [TaxId: 562] [52024] (10)
                  SQ P00907
      6. Swiveling domain of dehydratase reactivase alpha subunit [82317] (1)
         uperfamily
         1. Swiveling domain of dehydratase reactivase alpha subunit [82318] (2)
            1. Swiveling domain of the glycerol dehydratase reactivase alpha subunit [82319]
               1. Klebsiella pneumoniae [TaxId: 573] [82320] (1)
            2. Diol dehydratase-reactivating factor large subunit DdrA [141982]
               1. Klebsiella oxytoca [TaxId: 571] [141983] (4)
                  SQ O68195 93-254
      7. PA domain [52025] (1)
         uperfamily
         1. PA domain [52026] (2)
            1. Transferrin receptor ectodomain, apical domain [52027]
               1. Human (Homo sapiens) [TaxId: 9606] [52028] (4)
            2. Glutamate carboxypeptidase II [141984]
               1. Human (Homo sapiens) [TaxId: 9606] [141985] (17)
                  SQ Q04609 118-350
      8. GroEL apical domain-like [52029] (2)
         uperfamily
         1. GroEL-like chaperone, apical domain [52030] (4)
            1. GroEL, A domain [52031]
               1. Escherichia coli [TaxId: 562] [52032] (22)
               2. Paracoccus denitrificans [TaxId: 266] [69430] (1)
               3. Thermus thermophilus [TaxId: 274] [52033] (3)
                  SQ P61491
               4. Mycobacterium tuberculosis, GroEL2 [TaxId: 1773] [117456] (1)
                  SQ P0A520 60-514
         2. Group II chaperonin (CCT, TRIC), apical domain [52034] (4)
            1. Thermosome, A-domain [52035]
               1. Archaeon Thermoplasma acidophilum, alpha chain [TaxId: 2303] [100946] (4)
               2. Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679] [102202] (4)
               3. Archaeon Thermoplasma acidophilum, beta chain [TaxId: 2303] [100947] (3)
               4. Mouse (Mus musculus), gamma chain [TaxId: 10090] [75137] (2)
      9. FumA C-terminal domain-like [117457] (1)
         uperfamily
         1. FumA C-terminal domain-like [117458] (1)
            Pfam 05683
            1. Fumarate hydratase class I beta subunit [117459]
               1. Archaeoglobus fulgidus [TaxId: 2234] [117460] (1)
                  SQ O29167 # AF1098
      10. LD-carboxypeptidase A C-terminal domain-like [141986] (1)
          uperfamily
          1. LD-carboxypeptidase A C-terminal domain-like [141987] (1)
             C-terminal half of Pfam 02016
             1. LD-carboxypeptidase A, C-terminal domain [141988]
                1. Pseudomonas aeruginosa [TaxId: 287] [141989] (8)
                   SQ Q9HTZ1 152-307! SQ Q9HTZ1 170-307
   9. Barstar-like [52037] (2)
      2 layers, a/b; parallel beta-sheet of 3 strands, order 123
      1. Barstar-related [52038] (1)
         uperfamily
         1. Barstar-related [52039] (2)
            1. Barstar (barnase inhibitor) [52040]
               1. Bacillus amyloliquefaciens [TaxId: 1390] [52041] (23)
            2. Hypothetical protein YhcO [141990]
               1. Escherichia coli [TaxId: 562] [141991] (2)
                  SQ P64618 1-90
      2. Ribosomal protein L32e [52042] (1)
         uperfamily
         1. Ribosomal protein L32e [52043] (1)
            contains irregular N-terminal extension to the common fold
            1. Ribosomal protein L32e [52044]
               1. Archaeon Haloarcula marismortui [TaxId: 2238] [52045] (58)
                  SQ P12736
   10. MurF and HprK N-domain-like [63417] (2)
       core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core.
       1. MurE/MurF N-terminal domain [63418] (1)
          binds UDP group
          uperfamily
          1. MurE/MurF N-terminal domain [63419] (2)
             1. UDP-N-acetylmuramyl tripeptide synthetase MurE [63951]
                1. Escherichia coli [TaxId: 562] [63952] (1)
             2. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [63420]
                1. Escherichia coli [TaxId: 562] [63421] (1)
       2. HprK N-terminal domain-like [75138] (2)
          probable phosphatase
          uperfamily
          1. HPr kinase/phoshatase HprK N-terminal domain [75139] (2)
             1. HPr kinase/phoshatase HprK N-terminal domain [75140]
                1. Staphylococcus xylosus [TaxId: 1288] [75141] (1)
                2. Mycoplasma pneumoniae [TaxId: 2104] [82321] (1)
          2. DRTGG domain [159447] (1)
             Pfam 07085
             1. Hypothetical protein AF1212 [159448]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159449] (2)
                   SQ O29056 206-329
   11. Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [52046] (3)
       2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies
       1. RNI-like [52047] (3)
          regular structure consisting of similar repeats
          uperfamily
          1. 28-residue LRR [52048] (4)
             1. Ribonuclease inhibitor [52049]
                duplication: consists of 16 repeats
                1. Pig (Sus scrofa) [TaxId: 9823] [52050] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [52051] (7)
             2. Tropomodulin C-terminal domain [82322]
                duplication: consists of 5 repeats
                1. Chicken (Gallus gallus) [TaxId: 9031] [82323] (1)
                2. nematode (Caenorhabditis elegans) [TaxId: 6239] [89566] (1)
          2. Rna1p (RanGAP1), N-terminal domain [52052] (1)
             1. Rna1p (RanGAP1), N-terminal domain [52053]
                GTPase-activating protein for SpI1, ortologue of Ran
                duplication: consists of 11 repeats
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [52054] (5)
          3. Cyclin A/CDK2-associated p19, Skp2 [52055] (1)
             1. Cyclin A/CDK2-associated p19, Skp2 [52056]
                1. Human (Homo sapiens) [TaxId: 9606] [52057] (4)
       2. L domain-like [52058] (8)
          less regular structure consisting of variable repeats
          uperfamily
          1. Internalin LRR domain [52059] (3)
             capped at the N-end with a truncated EF-hand subdomain
             1. Internalin A [82324]
                1. Listeria monocytogenes [TaxId: 1639] [82325] (7)
             2. Internalin B [52060]
                1. Listeria monocytogenes [TaxId: 1639] [52061] (9)
             3. Internalin H [69431]
                1. Listeria monocytogenes [TaxId: 1639] [69432] (1)
          2. Leucine rich effector protein YopM [69433] (1)
             1. Leucine rich effector protein YopM [69434]
                1. Yersinia pestis [TaxId: 632] [69435] (2)
          3. Ngr ectodomain-like [75142] (6)
             1. von Willebrand factor binding domain of glycoprotein Ib alpha [75143]
                1. Human (Homo sapiens) [TaxId: 9606] [75144] (9)
             2. Reticulon 4 receptor (Nogo-66 receptor, Ngr) [89567]
                1. Human (Homo sapiens) [TaxId: 9606] [89568] (2)
             3. Slit [117461]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [117462] (1)
                   SQ P24014 542-733
             4. Decorin [117463]
                1. Cow (Bos taurus) [TaxId: 9913] [117464] (3)
                   SQ P21793 52-356
             5. High affinity nerve growth factor receptor, N-terminal domain [141992]
                1. Human (Homo sapiens) [TaxId: 9606] [141993] (2)
                   SQ P04629 36-191
             6. Follicle-stimulating hormone receptor [159450]
                1. Human (Homo sapiens) [TaxId: 9606] [159451] (1)
                   SQ P23945 18-259
          4. Polygalacturonase inhibiting protein PGIP [89569] (1)
             1. Polygalacturonase inhibiting protein PGIP [89570]
                1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [89571] (1)
          5. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52062] (1)
             1. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52063]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52064] (2)
          6. mRNA export factor tap [52065] (1)
             1. mRNA export factor tap [52066]
                1. Human (Homo sapiens) [TaxId: 9606] [52067] (8)
          7. U2A'-like [52068] (1)
             duplication: consists of 5-6 partly irregular repeats
             1. Splicesomal U2A' protein [52069]
                1. Human (Homo sapiens) [TaxId: 9606] [52070] (1)
          8. L domain [52071] (6)
             1. Type 1 insulin-like growth factor receptor extracellular domain [52072]
                1. Human (Homo sapiens) [TaxId: 9606] [52073] (1)
                   L1 and L2 domains
             2. Receptor protein-tyrosine kinase Erbb-3 extracellular domain [75145]
                1. Human (Homo sapiens) [TaxId: 9606] [75146] (1)
             3. EGF receptor extracellular domain [82326]
                1. Human (Homo sapiens) [TaxId: 9606] [82327] (15)
             4. Protooncoprotein Her2 extracellular domain [82328]
                1. Human (Homo sapiens) [TaxId: 9606] [82329] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [82330] (1)
             5. Insulin receptor [159452]
                1. Human (Homo sapiens) [TaxId: 9606] [159453] (2)
                   SQ P06213 31-183! SQ P06213 339-494
       3. Outer arm dynein light chain 1 [52075] (1)
          (beta-beta-alpha)n superhelix
          uperfamily
          1. Outer arm dynein light chain 1 [52076] (1)
             1. Outer arm dynein light chain 1 [52077]
                1. Green algae (Chlamydomonas reinhardtii) [TaxId: 3055] [52078] (2)
   12. Ribosomal proteins L15p and L18e [52079] (1)
       core: three turns of irregular (beta-beta-alpha)n superhelix
       1. Ribosomal proteins L15p and L18e [52080] (1)
          uperfamily
          1. Ribosomal proteins L15p and L18e [52081] (5)
             1. Ribosomal protein L15 (L15p) [52082]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [52083] (40)
                   SQ P12737
                2. Escherichia coli [TaxId: 562] [141994] (29)
                   SQ P02413 1-144
                3. Thermus thermophilus [TaxId: 274] [159454] (11)
                   SQ Q72I23 5-150
                4. Deinococcus radiodurans [TaxId: 1299] [159455] (6)
                   SQ Q9RSK9 4-144
             2. Ribosomal protein L18e [52084]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [52085] (40)
                   SQ P12733
   13. SpoIIaa-like [52086] (2)
       core: 4 turns of a (beta-alpha)n superhelix
       1. CRAL/TRIO domain [52087] (1)
          uperfamily
          1. CRAL/TRIO domain [52088] (3)
             Pfam 00650
             1. C-terminal domain of phosphatidylinositol transfer protein sec14p [52089]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52090] (1)
             2. Alpha-tocopherol transfer protein [102203]
                1. Human (Homo sapiens) [TaxId: 9606] [102204] (3)
             3. Supernatant protein factor (SPF), middle domain [102205]
                Sec14-like protein 2; contains extra C-terminal beta-sandwich domain
                1. Human (Homo sapiens) [TaxId: 9606] [102206] (2)
                   SQ O76054
       2. SpoIIaa-like [52091] (2)
          uperfamily
          1. Anti-sigma factor antagonist SpoIIaa [52092] (4)
             1. Anti-sigma factor antagonist SpoIIaa [52093]
                1. Bacillus sphaericus [TaxId: 1421] [63953] (3)
                2. Bacillus subtilis [TaxId: 1423] [52094] (2)
                3. Bacillus stearothermophilus [TaxId: 1422] [110448] (4)
                   SQ O32726 # 90% sequence identity
                4. Thermotoga maritima [TaxId: 2336] [110449] (3)
                   SQ Q9X1F5; TM1442
          2. Sfri0576-like [159456] (2)
             significant structural variability despite high sequence similarity
             1. Uncharacterized protein Shew3102 [159457]
                1. Shewanella loihica [TaxId: 359303] [159458] (2)
                   SQ A3QHM0 1-125
             2. Hypothetical protein Sfri0576 [159459]
                1. Shewanella frigidimarina [TaxId: 56812] [159460] (2)
                   SQ Q087X8 2-126
   14. ClpP/crotonase [52095] (1)
       core: 4 turns of (beta-beta-alpha)n superhelix
       1. ClpP/crotonase [52096] (4)
          uperfamily
          1. Clp protease, ClpP subunit [52097] (5)
             1. Clp protease, ClpP subunit [52098]
                1. Escherichia coli [TaxId: 562] [52099] (55)
                2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [141995] (7)
                   SQ Q16740 57-249
                3. Plasmodium falciparum [TaxId: 5833] [141996] (7)
                   SQ O97252 177-366
                4. Mycobacterium tuberculosis [TaxId: 1773] [141997] (21)
                   SQ P0A526 15-193
                5. Streptococcus pneumoniae [TaxId: 1313] [141998] (7)
                   SQ P63788 2-193
          2. Tail specific protease, catalytic domain [52100] (3)
             includes N-terminal all-alpha subdomain
             1. Photosystem II D1 C-terminal processing protease [68935]
                1. Algae (Scenedesmus obliquus) [TaxId: 3088] [52102] (4)
             2. Tricorn protease [69436]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69437] (4)
             3. Interphotoreceptor retinoid-binding protein IRBP [69438]
                very similar to the tail-specific protease domain; lacks the PDZ insertion domain and hydrolytic activity
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [69439] (1)
          3. Crotonase-like [52103] (17)
             1. 4-Chlorobenzoyl-CoA dehalogenase [52104]
                1. Pseudomonas sp., strain CBS-3 [TaxId: 306] [52105] (2)
             2. Enoyl-CoA hydratase (crotonase) [52106]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52107] (4)
                2. Thermus thermophilus [TaxId: 274] [102207] (1)
             3. Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase) [52108]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52109] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63954] (4)
                3. Rat (Rattus norvegicus), mitochondrial [TaxId: 10116] [117465] (1)
                   SQ P23965
                4. Human (Homo sapiens), mitochondrial [TaxId: 9606] [141999] (3)
                   SQ P42126 44-292
             4. Naphthoate synthase MenB [102208]
                1. Mycobacterium tuberculosis [TaxId: 1773] [102209] (4)
                   SQ O06414 18-285
             5. AUH protein [69440]
                an RNA-binding homologue of enoyl-CoA hydratase
                1. Human (Homo sapiens) [TaxId: 9606] [69441] (1)
             6. Methylmalonyl CoA decarboxylase [52110]
                1. Escherichia coli [TaxId: 562] [52111] (2)
             7. 6-oxo camphor hydrolase [82331]
                1. Rhodococcus erythropolis [TaxId: 1833] [82332] (2)
                   SQ Q93TU6
             8. Fatty oxidation complex alpha subunit, N-terminal domain [110450]
                1. Pseudomonas fragi [TaxId: 296] [110451] (4)
                   SQ P28793
             9. Probable enoyl-CoA hydratase TTHA0218 [142000]
                1. Thermus thermophilus [TaxId: 274] [142001] (6)
                   SQ Q5SLS5 2-264
             10. Chromodomain protein CDY2A [142002]
                 1. Human (Homo sapiens) [TaxId: 9606] [142003] (6)
                    SQ Q9Y6F7 284-541
             11. Carbapenem biosynthes protein CarB [142004]
                 1. Pectobacterium carotovorum [TaxId: 554] [142005] (12)
                    SQ Q9XB60 1-230
             12. Peroxisomal 3,2-trans-enoyl-CoA isomerase [142006]
                 1. Human (Homo sapiens) [TaxId: 9606] [142007] (3)
                    SQ O75521 103-347
             13. Chromodomain protein CDY1, C-terminal domain [142008]
                 1. Human (Homo sapiens) [TaxId: 9606] [142009] (3)
                    SQ Q9Y6F8 282-532
          4. Biotin dependent carboxylase carboxyltransferase domain [89572] (8)
             Pfam 01039
             the active site is formed by two different homologous subunits or domains of this fold
             1. Acetyl-coenzyme A carboxylase [89573]
                duplication: consists of two similar structural domains forming a functional domain of a larger multifunctional enzyme
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89574] (7)
                   SQ Q00955 1482-2196
             2. Methylmalonyl-CoA carboxyltransferase (transcarboxylase 12S) [89575]
                1. Propionibacterium freudenreichii [TaxId: 1744] [89576] (2)
             3. Glutaconyl-CoA decarboxylase A subunit [102210]
                1. Acidaminococcus fermentans [TaxId: 905] [102211] (1)
             4. Propionyl-CoA carboxylase complex B subunit, PccB [117466]
                1. Streptomyces coelicolor [TaxId: 1902] [117467] (4)
                   SQ Q9X4K7
                2. Mycobacterium tuberculosis [TaxId: 1773] [142010] (12)
                   SQ P96885 20-277! SQ P96885 278-548
                3. Thermotoga maritima [TaxId: 2336] [142011] (12)
                   SQ Q9WZH5 1-251! SQ Q9WZH5 252-515
             5. Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha, AccA [142012]
                1. Escherichia coli [TaxId: 562] [142013] (1)
                   SQ P0ABD5 4-319
             6. Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD [142014]
                1. Escherichia coli [TaxId: 562] [142015] (1)
                   SQ P0A9Q6 23-285
   15. BRCT domain [52112] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. BRCT domain [52113] (5)
          Pfam 00533
          uperfamily
          1. BRCT domain [63955] (2)
             1. Breast cancer associated protein, BRCA1 [63956]
                duplication: tandem repeat of BRCT domain
                1. Human (Homo sapiens) [TaxId: 9606] [63957] (25)
                   SQ P38398 1649-1863
                2. Rat (Rattus norvegicus) [TaxId: 10116] [75147] (3)
          2. 53BP1 [75148] (1)
             1. 53BP1 [75149]
                1. Human (Homo sapiens) [TaxId: 9606] [75150] (2)
          3. DNA-repair protein XRCC1 [52114] (1)
             1. DNA-repair protein XRCC1 [52115]
                1. Human (Homo sapiens) [TaxId: 9606] [52116] (1)
          4. DNA ligase [52117] (2)
             1. DNA ligase III alpha [63958]
                1. Human (Homo sapiens) [TaxId: 9606] [63959] (2)
             2. NAD+-dependent DNA ligase, domain 4 [52118]
                1. Thermus thermophilus [TaxId: 274] [100975] (1)
          5. DNA topoisomerase II binding protein 1, TopBP1 [117468] (1)
             1. DNA topoisomerase II binding protein 1, TopBP1 [117469]
                1. Human (Homo sapiens) [TaxId: 9606] [117470] (1)
                   SQ Q92547 326-444
   16. Lumazine synthase [52120] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. Lumazine synthase [52121] (1)
          uperfamily
          1. Lumazine synthase [52122] (7)
             1. Lumazine synthase [52123]
                1. Bacillus subtilis [TaxId: 1423] [52124] (11)
                   beta-subunit of the lumazine synthase/riboflavin synthase complex; 60 subunits form an icosahedral shell
                2. Brucella abortus [TaxId: 235] [52125] (1)
                3. Aquifex aeolicus [TaxId: 63363] [69442] (5)
                4. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [52126] (1)
                5. Spinach (Spinacia oleracea) [TaxId: 3562] [52127] (1)
                6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63960] (1)
                7. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [75151] (7)
   17. Uracil-DNA glycosylase-like [52140] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. Uracil-DNA glycosylase-like [52141] (4)
          uperfamily
          1. Uracil-DNA glycosylase [52142] (5)
             1. Uracil-DNA glycosylase [52143]
                1. Human (Homo sapiens) [TaxId: 9606] [52144] (11)
                2. Atlantic cod (Gadus morhua) [TaxId: 8049] [102212] (1)
                3. Herpes simplex virus type 1 [TaxId: 10298] [52145] (4)
                4. Escherichia coli [TaxId: 562] [52146] (12)
                5. Epstein-Barr virus [TaxId: 10376] [159461] (2)
                   SQ Q777D9 26-255
          2. Mug-like [52147] (4)
             1. G:T/U mismatch-specific DNA glycosylase, Mug [52148]
                1. Escherichia coli [TaxId: 562] [52149] (4)
             2. Thermophilic uracil-DNA glycosylase [89577]
                1. Thermotoga maritima [TaxId: 2336] [89578] (2)
                   gene TM0511
                2. Thermus thermophilus [TaxId: 274] [102213] (2)
             3. G/T mismatch-specific thymine DNA glycosylase [159462]
                1. Human (Homo sapiens) [TaxId: 9606] [159463] (2)
                   SQ Q13569 117-132
          3. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89579] (1)
             1. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89580]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [89581] (3)
          4. AF0587 domain-like [159464] (1)
             a middle domain in the founder protein
             1. Uncharacterized protein AF0587 [159465]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159466] (1)
                   SQ O29668 244-383
   18. Creatininase [102214] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. Creatininase [102215] (1)
          uperfamily
          1. Creatininase [102216] (1)
             1. Creatininase [102217]
                1. Pseudomonas putida [TaxId: 303] [102218] (4)
   19. DNA polymerase III psi subunit [102219] (1)
       3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
       1. DNA polymerase III psi subunit [102220] (1)
          uperfamily
          1. DNA polymerase III psi subunit [102221] (1)
             1. DNA polymerase III psi subunit [102222]
                1. Escherichia coli [TaxId: 562] [102223] (1)
   20. Initiation factor IF2/eIF5b, domain 3 [52155] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. Initiation factor IF2/eIF5b, domain 3 [52156] (1)
          uperfamily
          1. Initiation factor IF2/eIF5b, domain 3 [52157] (1)
             1. Initiation factor IF2/eIF5b, domain 3 [52158]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52159] (3)
   21. Aminoacid dehydrogenase-like, N-terminal domain [53222] (1)
       core: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134
       1. Aminoacid dehydrogenase-like, N-terminal domain [53223] (5)
          uperfamily
          1. Aminoacid dehydrogenases [53224] (10)
             dimerisation domain; contains additional structures including two extra N-terminal strands in the beta-sheet
             1. Glutamate dehydrogenase [53225]
                1. Clostridium symbiosum [TaxId: 1512] [53226] (4)
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [53227] (1)
                3. Archaeon Thermococcus profundus [TaxId: 49899] [64106] (1)
                4. Archaeon Thermococcus litoralis [TaxId: 2265] [53228] (1)
                5. Thermotoga maritima [TaxId: 2336] [53229] (3)
                6. Cow (Bos taurus) [TaxId: 9913] [53230] (5)
                7. Human (Homo sapiens) [TaxId: 9606] [75252] (2)
                8. Pyrobaculum islandicum [TaxId: 2277] [117471] (1)
                   SQ Q9Y8I4
             2. Leucine dehydrogenase [53231]
                1. Bacillus sphaericus [TaxId: 1421] [53232] (1)
             3. Phenylalanine dehydrogenase [53233]
                1. Rhodococcus sp., M4 [TaxId: 1831] [53234] (4)
          2. Tetrahydrofolate dehydrogenase/cyclohydrolase [53235] (3)
             1. Tetrahydrofolate dehydrogenase/cyclohydrolase [53236]
                the two-domain organization is similar to that of aminoacid dehydrogenases, but both domains are truncated
                1. Human (Homo sapiens) [TaxId: 9606] [53237] (4)
                2. Escherichia coli [TaxId: 562] [53238] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53239] (2)
          3. Methylene-tetrahydromethanopterin dehydrogenase [82333] (1)
             1. Methylene-tetrahydromethanopterin dehydrogenase [82334]
                1. Methylobacterium extorquens [TaxId: 408] [82335] (2)
          4. Shikimate dehydrogenase-like [82336] (5)
             1. Putative shikimate dehydrogenase YdiB [82337]
                1. Escherichia coli [TaxId: 562] [82338] (3)
             2. Shikimate 5-dehydrogenase-like protein HI0607 [89582]
                1. Haemophilus influenzae [TaxId: 727] [89583] (1)
             3. Shikimate 5-dehydrogenase AroE [89584]
                1. Escherichia coli [TaxId: 562] [89585] (1)
                2. Haemophilus influenzae [TaxId: 727] [102224] (2)
                3. Archaeon Methanococcus jannaschii [TaxId: 2190] [89586] (1)
                   MJ1084
          5. Malic enzyme N-domain [53240] (4)
             Pfam 00390; decorated with additional structures; includes N-terminal additional subdomains and extra N-terminal strand
             1. Mitochondrial NAD(P)-dependent malic enzyme [53241]
                1. Human (Homo sapiens) [TaxId: 9606] [53242] (10)
                2. Domestic pigeon (Columba livia) [TaxId: 8932] [75253] (1)
                3. Pig roundworm (Ascaris suum) [TaxId: 6253] [75254] (2)
             2. Malate oxidoreductase (malic enzyme) [110452]
                1. Thermotoga maritima [TaxId: 2336] [110453] (5)
                   SQ Q9WZ12
   22. Toprim domain [110454] (1)
       3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
       1. Toprim domain [110455] (1)
          this domain is also present in several multidomain proteins that are not split in scop yet: scop_sf 56712, scop_sf 56719, scop_sf 56726, scop_sf 56731
          uperfamily
          1. Toprim domain [110456] (2)
             Pfam 01751
             1. Hypothetical protein aq_2086 [110457]
                1. Aquifex aeolicus [TaxId: 63363] [110458] (1)
                   SQ O67859
             2. Hypothetical protein RBSTP2199 [142016]
                B. subtilis YusF homolog
                1. Bacillus stearothermophilus [TaxId: 1422] [142017] (6)
                   SQ Q5KVJ9 1-114
   23. AtpF-like [159467] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
       1. AtpF-like [159468] (1)
          1. AtpF-like [159469] (2)
             Pfam 01990; segment-swapping in some members
             1. V-type ATP synthase subunit F, AtpF [159470]
                1. Thermus thermophilus [TaxId: 274] [159471] (6)
                   SQ P74903 1-104
                2. Archaeoglobus fulgidus [TaxId: 2234] [159472] (2)
                   SQ O29102 4-79
   24. Ribosomal protein L13 [52160] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
       1. Ribosomal protein L13 [52161] (1)
          uperfamily
          1. Ribosomal protein L13 [52162] (5)
             1. Ribosomal protein L13 [52163]
                synonym: 50S ribosomal protein L13p, HMAL13
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82339] (1)
                2. Archaeon Haloarcula marismortui [TaxId: 2238] [52164] (44)
                   SQ P29198
                3. Thermus thermophilus [TaxId: 274] [159473] (10)
                   SQ P60488 1-139
                4. Escherichia coli [TaxId: 562] [159474] (29)
                   SQ P02410 1-140
                5. Deinococcus radiodurans [TaxId: 1299] [159475] (6)
                   SQ Q9RXY1 30-171
   25. Ribosomal protein L4 [52165] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
       1. Ribosomal protein L4 [52166] (1)
          uperfamily
          1. Ribosomal protein L4 [52167] (5)
             1. Ribosomal protein L4 [52168]
                synonym: 50S ribosomal protein L4e, HMAL4, HL6
                1. Thermotoga maritima [TaxId: 2336] [52169] (1)
                2. Archaeon Haloarcula marismortui [TaxId: 2238] [52170] (46)
                   SQ P12735
                3. Thermus thermophilus [TaxId: 274] [159476] (7)
                   SQ Q5SHN9 1-208
                4. Escherichia coli [TaxId: 562] [159477] (29)
                   SQ P60723 1-201
                5. Deinococcus radiodurans [TaxId: 1299] [159478] (6)
                   SQ Q9RXK1 2-198
   26. Nqo1 FMN-binding domain-like [142018] (1)
       3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
       1. Nqo1 FMN-binding domain-like [142019] (1)
          uperfamily
          1. Nqo1 FMN-binding domain-like [142020] (1)
             N-terminal part of Pfam 01512
             1. NADH-quinone oxidoreductase chain 1, Nqo1 [142021]
                1. Thermus thermophilus [TaxId: 274] [142022] (4)
                   SQ Q56222 7-249
   27. Flavodoxin-like [52171] (15)
       3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
       1. CheY-like [52172] (7)
          uperfamily
          1. CheY-related [52173] (32)
             1. CheY protein [52174]
                1. Escherichia coli [TaxId: 562] [52175] (35)
                   SQ P06143
                2. Salmonella typhimurium [TaxId: 90371] [52176] (18)
                3. Thermotoga maritima [TaxId: 2336] [52177] (5)
                   SQ Q56312
                4. Sinorhizobium meliloti, CheY2 [TaxId: 382] [102225] (2)
                   SQ Q52884
             2. Nitrate/nitrite response regulator (NarL), receiver domain [52178]
                1. Escherichia coli [TaxId: 562] [52179] (2)
             3. NTRC receiver domain [52180]
                1. Salmonella typhimurium [TaxId: 90371] [52181] (6)
             4. Transcriptional regulatory protein FixJ, receiver domain [52182]
                1. Rhizobium meliloti [TaxId: 382] [52183] (4)
             5. Transcriptional regulatory protein DctD, receiver domain [52184]
                1. Sinorhizobium meliloti [TaxId: 382] [52185] (3)
             6. Sporulation response regulator Spo0A [52186]
                1. Bacillus stearothermophilus [TaxId: 1422] [52187] (2)
             7. Sporulation response regulator Spo0F [52188]
                1. Bacillus subtilis [TaxId: 1423] [52189] (11)
                   SQ P06628
             8. Methylesterase CheB, N-terminal domain [52190]
                1. Salmonella typhimurium [TaxId: 90371] [52191] (1)
             9. PhoB receiver domain [52192]
                1. Thermotoga maritima [TaxId: 2336] [69445] (1)
                2. Escherichia coli [TaxId: 562] [52193] (7)
             10. PhoP receiver domain [82340]
                 1. Bacillus subtilis [TaxId: 1423] [82341] (1)
                 2. Escherichia coli [TaxId: 562] [159479] (3)
                    SQ P23836 1-119
             11. Response regulator DrrB [89587]
                 1. Thermotoga maritima [TaxId: 2336] [89588] (1)
             12. Response regulator for cyanobacterial phytochrome [75152]
                 1. Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148] [75153] (2)
                 2. Calothrix sp. pcc 7601, RcpA [TaxId: 1188] [102226] (1)
                 3. Calothrix sp. pcc 7601, RcpB [TaxId: 1188] [102227] (1)
             13. Cell division response regulator DivK [82342]
                 1. Caulobacter crescentus [TaxId: 155892] [82343] (5)
             14. Response regulator Sin1 [102228]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102229] (3)
             15. Transcriptional activator sigm54 (NtrC1), N-terminal domain [102230]
                 1. Aquifex aeolicus [TaxId: 63363] [102231] (2)
             16. DNA-binding response regulator MicA, N-terminal domain [102232]
                 1. Streptococcus pneumoniae [TaxId: 1313] [102233] (11)
             17. Probable two-component system transcriptional regulator Rv1626 [110464]
                 contains extra C-terminal all-alpha subdomain (144-20), 3-helical bundle
                 1. Mycobacterium tuberculosis [TaxId: 1773] [110465] (2)
                    SQ O06143
             18. Response regulator PleD, receiver domain [117472]
                 duplication: tandem repeat of 2 CheY-like domains
                 1. Caulobacter crescentus [TaxId: 155892] [117473] (5)
                    SQ Q9A5I5
             19. Sensor kinase protein RcsC, C-terminal domain [142023]
                 1. Escherichia coli [TaxId: 562] [142024] (2)
                    SQ P14376 817-949
             20. Transcriptional regulatory protein KdpE, N-terminal domain [142025]
                 1. Escherichia coli [TaxId: 562] [142026] (4)
                    SQ P21866 2-120
             21. Response regulatory protein StyR, N-terminal domain [142027]
                 1. Pseudomonas fluorescens [TaxId: 294] [142028] (2)
                    SQ O30989 3-130
             22. Hypothetical protein BH3024 [142029]
                 1. Bacillus halodurans [TaxId: 86665] [142030] (1)
                    SQ Q9K8I2 2-119
             23. Transcriptional regulatory protein PrrA, N-terminal domain [142031]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [142032] (4)
                    SQ P0A5Z6 7-127
             24. TorCAD operon transcriptional regulator TorD, N-terminal domain [142033]
                 1. Escherichia coli [TaxId: 562] [142034] (4)
                    SQ P38684 2-121
             25. Aerobic respiration control protein ArcA, N-terminal domain [142035]
                 1. Escherichia coli [TaxId: 562] [142036] (4)
                    SQ P0A9Q1 2-122
          2. Receiver domain of the ethylene receptor [52194] (1)
             1. Receiver domain of the ethylene receptor [52195]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [52196] (1)
          3. Positive regulator of the amidase operon AmiR [52197] (1)
             1. Positive regulator of the amidase operon AmiR [52198]
                contains coiled coil and small all-alpha subdomains in the C-terminal extension
                1. Pseudomonas aeruginosa [TaxId: 287] [52199] (1)
          4. Ornithine decarboxylase N-terminal "wing" domain [52252] (1)
             1. Ornithine decarboxylase N-terminal "wing" domain [52253]
                1. Lactobacillus sp., strain 30a [TaxId: 1591] [52254] (2)
          5. N-terminal domain of the circadian clock protein KaiA [82344] (1)
             lacks canonical receiver domains features
             1. N-terminal domain of the circadian clock protein KaiA [82345]
                1. Synechococcus elongatus [TaxId: 32046] [82346] (3)
                   SQ Q79PF6
          6. RcsC linker domain-like [142037] (1)
             PfamB 016190; probable rudiment CheY-like domain; precedes the C-terminal CheY-related domain of similar structure
             1. Sensor kinase protein RcsC [142038]
                1. Escherichia coli [TaxId: 562] [142039] (2)
                   SQ P14376 700-816
          7. AF1403 C-terminal domain-like [142040] (1)
             1. Hypothetical protein AF1403, C-terminal domain [142041]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [142042] (3)
                   SQ O28869 79-217
       2. Toll/Interleukin receptor TIR domain [52200] (1)
          uperfamily
          1. Toll/Interleukin receptor TIR domain [52201] (2)
             1. Toll-like receptor 1, TLR1 [52202]
                1. Human (Homo sapiens) [TaxId: 9606] [52203] (1)
             2. Toll-like receptor 2, TLR2 [52204]
                1. Human (Homo sapiens) [TaxId: 9606] [52205] (3)
       3. Hypothetical protein MTH538 [52206] (1)
          uperfamily
          1. Hypothetical protein MTH538 [52207] (1)
             1. Hypothetical protein MTH538 [52208]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52209] (1)
       4. Succinyl-CoA synthetase domains [52210] (1)
          uperfamily
          1. Succinyl-CoA synthetase domains [52211] (6)
             contain additional N-terminal strand "0", antiparallel to strand 2
             1. Succinyl-CoA synthetase, alpha-chain, C-terminal domain [52212]
                1. Escherichia coli [TaxId: 562] [52213] (18)
                2. Thermus thermophilus [TaxId: 274] [89589] (1)
                3. Pig (Sus scrofa) [TaxId: 9823] [52214] (6)
             2. Succinyl-CoA synthetase, beta-chain, C-terminal domain [52215]
                1. Escherichia coli [TaxId: 562] [52216] (18)
                2. Pig (Sus scrofa) [TaxId: 9823] [52217] (6)
             3. Acetate-CoA ligase alpha chain, AcdA, domains 2 and 3 [142043]
                duplication: tandem repeat of two similar domains, structurally and functionally related to the C-terminal domains of Succinyl-CoA synthetase subunits; the first domain (2) is related to the alpha-chain domain, whereas the second domain (3) is related to the beta-chain domain
                1. Pyrococcus horikoshii [TaxId: 53953] [142044] (4)
                   SQ O58493 130-290! SQ O58493 291-453
                   PH0766
       5. Flavoproteins [52218] (8)
          uperfamily
          1. Flavodoxin-related [52219] (13)
             binds FMN
             1. Flavodoxin [52220]
                1. Chondrus crispus [TaxId: 2769] [52221] (1)
                2. Desulfovibrio vulgaris [TaxId: 881] [52222] (25)
                   SQ P00323
                3. Anabaena, pcc 7119 and 7120 [TaxId: 1163] [52223] (7)
                4. Escherichia coli [TaxId: 562] [52224] (2)
                5. Synechococcus elongatus PCC 7942 [TaxId: 1140] [52225] (10)
                6. Clostridium beijerinckii [TaxId: 1520] [52226] (16)
                7. Helicobacter pylori [TaxId: 210] [69446] (1)
                8. Megasphaera elsdenii [TaxId: 907] [142045] (1)
                   SQ P00321 1-137
                9. Azotobacter vinelandii [TaxId: 354] [142046] (2)
                   SQ P00324 1-179
             2. FMN-binding domain of the cytochrome P450bm-3 [52227]
                1. Bacillus megaterium [TaxId: 1404] [52228] (1)
             3. Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain [52229]
                1. Desulfovibrio gigas [TaxId: 879] [52230] (1)
             4. ROO-like flavoprotein TM0755, C-terminal domain [110466]
                1. Thermotoga maritima [TaxId: 2336] [110467] (1)
                   SQ Q9WZL4
             5. Nitric oxide reductase C-terminal domain [142047]
                1. Moorella thermoacetica [TaxId: 1525] [142048] (12)
                   SQ Q9FDN7 251-399
          2. Cytochrome p450 reductase N-terminal domain-like [52231] (4)
             1. NADPH-cytochrome p450 reductase, N-terminal domain [52232]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52233] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [52234] (1)
             2. Nitric oxide (NO) synthase FMN domain [110468]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [110469] (1)
                   SQ P29476 750-1413
             3. Sulfite reductase alpha-component CysJ N-terminal domain [142049]
                1. Escherichia coli [TaxId: 562] [142050] (1)
                   SQ P38038 63-208
          3. Quinone reductase [52235] (6)
             binds FAD
             1. NAD(P)H:quinone reductase [52236]
                1. Mouse (Mus musculus) [TaxId: 10090] [52237] (1)
                2. Rat (Rattus rattus) [TaxId: 10117] [52238] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [52239] (16)
             2. Quinone reductase type 2 (menadione reductase) [52240]
                1. Human (Homo sapiens) [TaxId: 9606] [52241] (24)
             3. ACP phosphodiesterase AcpD [110470]
                evolved new enzymatic activity
                1. Escherichia coli [TaxId: 562] [110471] (8)
                   SQ P41407
                2. Salmonella typhimurium [TaxId: 90371] [110472] (1)
                   SQ Q8XFP4
          4. Hypothetical protein SP1951 [102234] (1)
             1. Hypothetical protein SP1951 [102235]
                1. (Streptococcus pneumoniae) [TaxId: 1313] [102236] (3)
          5. Hypothetical protein YwqN [102237] (1)
             1. Hypothetical protein YwqN [102238]
                Trp repressor binding protein
                1. Bacillus subtilis [TaxId: 1423] [102239] (1)
          6. NADPH-dependent FMN reductase [89590] (4)
             Pfam 03358
             1. Azobenzene reductase [89591]
                1. Bacillus subtilis [TaxId: 1423] [89592] (5)
                   YhdA gene product
             2. Hypothetical protein Ylr011wp [110473]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110474] (1)
                   SQ Q07923
             3. Hypothetical protein PA1204 [110475]
                1. Pseudomonas aeruginosa [TaxId: 287] [110476] (2)
                   SQ Q9I4D4 5-167
             4. Putative arsenical resistance protein [142051]
                1. Shigella flexneri [TaxId: 623] [142052] (4)
                   SQ Q7UC03 1-233
          7. Flavoprotein NrdI [110477] (1)
             1. Flavoprotein NrdI [110478]
                1. Bacillus subtilis [TaxId: 1423] [110479] (1)
                   SQ P50618
          8. WrbA-like [117474] (3)
             1. Trp repressor binding protein WrbA [117475]
                1. Deinococcus radiodurans [TaxId: 1299] [117476] (9)
                   SQ Q9RYU4
                2. Pseudomonas aeruginosa [TaxId: 287] [142053] (5)
                   SQ Q9I509 3-198! SQ Q9I509 4-196
             2. Flavodoxin FldA [142054]
                1. Aquifex aeolicus [TaxId: 63363] [142055] (6)
                   SQ O67866 1-184
       6. Cobalamin (vitamin B12)-binding domain [52242] (1)
          uperfamily
          1. Cobalamin (vitamin B12)-binding domain [52243] (6)
             1. Methionine synthase, C-terminal domain [52244]
                1. Escherichia coli [TaxId: 562] [52245] (4)
             2. Glutamate mutase, small subunit [52246]
                1. Clostridium tetanomorphum [TaxId: 1553] [52247] (3)
                2. Clostridium cochlearium [TaxId: 1494] [52248] (4)
             3. Methylmalonyl-CoA mutase alpha subunit, C-terminal domain [88717]
                active subunit; binds B12
                1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88718] (8)
             4. Methylmalonyl-CoA mutase beta subunit, C-terminal domain [88719]
                inactive subunit
                1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88720] (8)
             5. D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain [117477]
                most similar to the glutamate mutase subunit
                1. Clostridium sticklandii [TaxId: 1511] [117478] (1)
                   SQ Q9ZFE5
       7. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52255] (1)
          uperfamily
          1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52256] (4)
             1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52257]
                1. Escherichia coli [TaxId: 562] [52258] (3)
                2. Thermotoga maritima [TaxId: 2336] [89593] (1)
                   TM0446
                3. Acetobacter aceti [TaxId: 435] [110480] (5)
                   SQ Q72LC1
                4. Bacillus anthracis [TaxId: 1392] [117479] (1)
                   SQ Q81ZH8
       8. SGNH hydrolase [52266] (9)
          uperfamily
          1. Esterase [52267] (1)
             1. Esterase [52268]
                1. Streptomyces scabies [TaxId: 1930] [52269] (3)
          2. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52270] (1)
             1. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52271]
                includes irregular N- and C-terminal extensions
                1. Influenza C virus [TaxId: 11552] [52272] (1)
          3. Acetylhydrolase [52273] (3)
             1. Platelet-activating factor acetylhydrolase [52274]
                1. Cow (Bos taurus), alpha1 [TaxId: 9913] [52275] (6)
                2. Cow (Bos taurus), alpha2 [TaxId: 9913] [88721] (11)
             2. Uncharacterized protein SP1450 [159480]
                Putative platelet activating factor
                1. Streptococcus pneumoniae [TaxId: 1313] [159481] (4)
                   SQ Q97PY9 1-211
          4. Rhamnogalacturonan acetylesterase [52276] (1)
             1. Rhamnogalacturonan acetylesterase [52277]
                1. Fungus (Aspergillus aculeatus) [TaxId: 5053] [52278] (4)
          5. TAP-like [89594] (2)
             1. Thioesterase I, TAP [89595]
                multifunctional enzyme with thioesterase, esterase, protease and lysophospholiase activities
                1. Escherichia coli [TaxId: 562] [89596] (5)
                   SQ P29679 27-205
             2. Lipase/acylhydrolase [142056]
                1. Enterococcus faecalis [TaxId: 1351] [142057] (1)
                   SQ Q839J6 1-195
          6. Hypothetical protein alr1529 [102240] (1)
             1. Hypothetical protein alr1529 [102241]
                putative lipase
                1. Nostoc sp. pcc 7120 [TaxId: 103690] [102242] (5)
          7. Putative acetylxylan esterase-like [142058] (2)
             Pfam 03629 (DUF303); contains a characteristic zinc(less) finger-like insertion after strand 1; lacks the conserved in other families Asn residue
             1. Putative acetylxylan esterase At4g34215 [142059]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142060] (4)
                   SQ Q8L9J9 17-260
             2. Acetylxylan esterase related enzyme [142061]
                1. Clostridium acetobutylicum [TaxId: 1488] [142062] (6)
                   SQ Q97LM8 1-282
          8. YxiM C-terminal domain-like [159482] (1)
             subfamily of Pfam 00657
             1. Hypothetical protein YxiM [159483]
                1. Bacillus subtilis [TaxId: 1423] [159484] (1)
                   SQ P42304 175-382
          9. BT2961-like [159485] (2)
             PfamB 005894;homotrimeric assembly
             1. Uncharacterized protein BT2961 [159486]
                putative lipase
                1. Bacteroides thetaiotaomicron [TaxId: 818] [159487] (6)
                   SQ Q8A3J3 38-285
             2. Uncharacterized protein Lp3323 [159488]
                1. Lactobacillus plantarum [TaxId: 1590] [159489] (3)
                   SQ Q88SR8 18-224
       9. Beta-D-glucan exohydrolase, C-terminal domain [52279] (1)
          uperfamily
          1. Beta-D-glucan exohydrolase, C-terminal domain [52280] (1)
             1. Beta-D-glucan exohydrolase, C-terminal domain [52281]
                interdomain linker forms an additional, N-terminal strand
                1. Barley (Hordeum vulgare) [TaxId: 4513] [52282] (9)
       10. Formate/glycerate dehydrogenase catalytic domain-like [52283] (3)
           uperfamily
           1. Formate/glycerate dehydrogenases, substrate-binding domain [52284] (9)
              this domain is interrupted by the Rossmann-fold domain
              1. Formate dehydrogenase [52285]
                 contains an additional beta-hairpin after the common fold
                 1. Pseudomonas sp., strain 101 [TaxId: 306] [52286] (2)
              2. Putative formate dehydrogenase [52287]
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [52288] (1)
              3. Transcription corepressor CtbP [82347]
                 C-terminal binding protein 1; a dehydrogenase
                 1. Human (Homo sapiens), Ctbp1 [TaxId: 9606] [82348] (1)
                 2. Rat (Rattus norvegicus), Ctbp3 [TaxId: 10116] [89597] (2)
              4. D-2-hydroxyisocaproate dehydrogenase [52289]
                 1. Lactobacillus casei [TaxId: 1582] [52290] (1)
              5. D-glycerate dehydrogenase [52291]
                 1. Hyphomicrobium methylovorum [TaxId: 84] [52292] (1)
              6. Phosphoglycerate dehydrogenase [52293]
                 has additional C-terminal domain of the ferredoxin fold
                 1. Escherichia coli [TaxId: 562] [52294] (18)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [142063] (2)
                    SQ P0A544 2-97,282-315
                    there is an intervening domain between this domain and regulatory (C-terminal) domain
              7. D-lactate dehydrogenase [52295]
                 1. Lactobacillus helveticus [TaxId: 1587] [52296] (3)
           2. L-alanine dehydrogenase-like [52297] (2)
              1. L-alanine dehydrogenase [52298]
                 1. Phormidium lapideum [TaxId: 32060] [52299] (3)
              2. Nicotinamide nucleotide transhydrogenase dI component [63963]
                 L-alanine dehydrogenase homologue
                 1. Rhodospirillum rubrum [TaxId: 1085] [63964] (28)
           3. S-adenosylhomocystein hydrolase [52300] (3)
              1. S-adenosylhomocystein hydrolase [52301]
                 contains additional secondary structures disguising the superfamily fold
                 1. Human (Homo sapiens) [TaxId: 9606] [52302] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [52303] (17)
                 3. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117480] (1)
                    SQ P50250
       11. Type II 3-dehydroquinate dehydratase [52304] (1)
           uperfamily
           1. Type II 3-dehydroquinate dehydratase [52305] (5)
              1. Type II 3-dehydroquinate dehydratase [52306]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [52307] (4)
                 2. Streptomyces coelicolor [TaxId: 1902] [52308] (40)
                 3. Bacillus subtilis [TaxId: 1423] [82349] (1)
                 4. Helicobacter pylori [TaxId: 210] [89598] (14)
                 5. Actinobacillus pleuropneumoniae [TaxId: 715] [102243] (1)
       12. N-(deoxy)ribosyltransferase-like [52309] (3)
           there are similar active site architectures as well as the catalytic mechanisms of functionally characterised members
           uperfamily
           1. N-deoxyribosyltransferase [52310] (3)
              1. Nucleoside 2-deoxyribosyltransferase [52311]
                 class II N-deoxyribosyltransferase
                 1. Lactobacillus leichmannii [TaxId: 28039] [52312] (2)
                 2. Trypanosoma brucei [TaxId: 5691] [142064] (10)
                    SQ Q57VC7 1-152
              2. Purine transdeoxyribosylase [102244]
                 class I N-deoxyribosyltransferase
                 1. Lactobacillus helveticus [TaxId: 1587] [102245] (5)
           2. Hypothetical protein PA1492 [110461] (1)
              lacks the last strand; monomer; predicted deoxyribosyltransferase activity
              1. Hypothetical protein PA1492 [110462]
                 1. Pseudomonas aeruginosa [TaxId: 287] [110463] (1)
                    SQ Q9I3M0
           3. ADP ribosyl cyclase-like [56630] (3)
              contains extra N-terminal all-alpha subdomain
              1. ADP ribosyl cyclase [56631]
                 1. California sea hare (Aplysia californica) [TaxId: 6500] [56632] (5)
                 2. Human (Homo sapiens) [TaxId: 9606] [159490] (2)
                    SQ P28907 45-291
              2. Bone marror stromal cell antigen 1, BST-1/CD157 (ADP ribosyl cyclase-2) [75597]
                 1. Human (Homo sapiens) [TaxId: 9606] [75598] (6)
       13. Ribosomal protein S2 [52313] (1)
           fold elaborated with additional structures
           uperfamily
           1. Ribosomal protein S2 [52314] (3)
              1. Ribosomal protein S2 [52315]
                 1. Thermus thermophilus [TaxId: 274] [52316] (46)
                    SQ P80371
                 2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102246] (2)
                 3. Escherichia coli [TaxId: 562] [159491] (26)
                    SQ P0A7V0 8-225
       14. Precorrin-8X methylmutase CbiC/CobH [63965] (1)
           fold elaborated with additional structures
           uperfamily
           1. Precorrin-8X methylmutase CbiC/CobH [63966] (3)
              1. Precorrin-8x methylmutase [63967]
                 1. Pseudomonas denitrificans [TaxId: 43306] [63968] (2)
                 2. Thermus thermophilus [TaxId: 274] [102247] (1)
              2. Precorrin-8x methylmutase related protein [102248]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102249] (1)
       15. Class I glutamine amidotransferase-like [52317] (9)
           conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
           uperfamily
           1. Class I glutamine amidotransferases (GAT) [52318] (18)
              contains a catalytic Cys-His-Glu triad
              1. GMP synthetase [52319]
                 1. Escherichia coli [TaxId: 562] [52320] (1)
              2. Carbamoyl phosphate synthetase, small subunit C-terminal domain [52321]
                 1. Escherichia coli [TaxId: 562] [52322] (10)
                    SQ P00907
              3. Anthranilate synthase GAT subunit, TrpG [52323]
                 1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [52324] (1)
                 2. Salmonella typhimurium [TaxId: 90371] [63969] (1)
                 3. Serratia marcescens [TaxId: 615] [63970] (2)
              4. GAT subunit, HisH, (or domain) of imidazoleglycerolphosphate synthase HisF [69447]
                 1. Thermotoga maritima [TaxId: 2336] [69448] (3)
                 2. Thermus thermophilus [TaxId: 274] [82350] (1)
                 3. Baker's yeast (Saccharomyces cerevisiae), His7 [TaxId: 4932] [69449] (4)
              5. gamma-glutamyl hydrolase [75154]
                 1. Human (Homo sapiens) [TaxId: 9606] [75155] (1)
              6. Hypothetical protein TM1158 [89599]
                 1. Thermotoga maritima [TaxId: 2336] [89600] (1)
              7. Hypothetical protein YaaE [102250]
                 glutamine amidotransferase of SNO/PDX2 family implicated in pyridoxine biosynthesis
                 1. Bacillus subtilis [TaxId: 1423] [102251] (3)
                 2. Bacillus stearothermophilus [TaxId: 1422] [102252] (1)
              8. CTP synthase PyrG, C-terminal domain [110481]
                 1. Escherichia coli [TaxId: 562] [110482] (1)
                    SQ P08398
                 2. Thermus thermophilus [TaxId: 274] [110483] (3)
                    SQ Q5SIA8
              9. FGAM synthase PurL, amidotransferase domain [110484]
                 1. Salmonella typhimurium [TaxId: 90371] [110485] (1)
                    SQ P74881
              10. GMP synthase subunit A, GuaAA [142065]
                  1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142066] (4)
                     SQ Q9HJM3 1-196
                  2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142067] (1)
                     SQ O59071 1-188
              11. Pyridoxine biosynthesis protein 2, Pdx2 [142068]
                  1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [142069] (2)
                     SQ Q5ND68 2-219
           2. A4 beta-galactosidase middle domain [82351] (1)
              probable non-catalytic branch of the class I GAT family; overall fold is very similar but the active site is not conserved
              1. A4 beta-galactosidase middle domain [82352]
                 1. Thermus thermophilus [TaxId: 274] [82353] (2)
           3. DJ-1/PfpI [52325] (9)
              contains a catalytic triad or dyad different from the class I GAT triad
              1. Intracellular protease [52326]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [52327] (1)
              2. Hypothetical protein YhbO [89601]
                 1. Escherichia coli [TaxId: 562] [89602] (1)
              3. DJ-1 [89603]
                 RNA-binding protein regulatory subunit
                 1. Human (Homo sapiens) [TaxId: 9606] [89604] (20)
                    SQ Q99497
              4. Putative sigma cross-reacting protein 27A (SCRP-27A, EllB) [89606]
                 involved in an early stage of isoprenoid biosynthesis; contains a Cys-Glu putative catalytic dyad
                 1. Escherichia coli [TaxId: 562] [89607] (2)
              5. HSP31 (HchA; YedU) [89609]
                 contains a buried Cys-His-Asp triad within one subunit
                 1. Escherichia coli [TaxId: 562] [89610] (5)
              6. Hypothetical protein Ydr533Cp [102253]
                 contains a buried Cys-His-Glu triad within one subunit
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102254] (4)
              7. GK2698 ortholog [117481]
                 1. Bacillus stearothermophilus [TaxId: 1422] [117482] (1)
                    SQ Q5KWF3; 96% sequence identity; Geobacillus kaustophilus TaxID: 1462
              8. Protein ThiJ (YajL) [142070]
                 1. Escherichia coli [TaxId: 562] [142071] (2)
                    SQ Q46948 2-196
              9. Hypothetical protein Atu0886 [142072]
                 1. Agrobacterium tumefaciens [TaxId: 358] [142073] (3)
                    SQ Q8UGZ9 1-188
           4. Catalase, C-terminal domain [52328] (2)
              1. Catalase, C-terminal domain [52329]
                 1. Escherichia coli, HPII [TaxId: 562] [52330] (14)
                 2. Neurospora crassa [TaxId: 5141] [117483] (1)
                    SQ Q9C168 68-765
           5. Aspartyl dipeptidase PepE [52331] (1)
              probable circular permutation in the common core; contains a catalytic Ser-His-Glu triad
              1. Aspartyl dipeptidase PepE [52332]
                 1. Salmonella typhimurium [TaxId: 90371] [52333] (2)
           6. ThuA-like [110486] (1)
              Pfam 06283; overall fold is very similar the class I GAT family but the putative active site has a different structure
              1. GK2113 homologue [110487]
                 1. Bacillus stearothermophilus [TaxId: 1422] [110488] (1)
                    SQ Q5KY38 # 99% sequence identity (Geobacillus kaustophilus TaxID:1462)
           7. LD-carboxypeptidase A N-terminal domain-like [142074] (1)
              N-terminal half of Pfam 02016
              1. LD-carboxypeptidase A, N-terminal domain [142075]
                 1. Pseudomonas aeruginosa [TaxId: 287] [142076] (8)
                    SQ Q9HTZ1 3-169! SQ Q9HTZ1 5-142! SQ Q9HTZ1 5-169
           8. HTS-like [142077] (1)
              Pfam 04204
              1. Homoserine O-succinyltransferase HTS (MetA) [142078]
                 1. Bacillus cereus [TaxId: 1396] [142079] (1)
                    SQ Q72X44 17-297
           9. STM3548-like [159492] (1)
              Pfam 07090; DUF1355
              1. Putative cytoplasmic protein STM3548 [159493]
                 1. Salmonella typhimurium [TaxId: 90371] [159494] (6)
                    SQ Q8ZLF9 8-253
   28. Methylglyoxal synthase-like [52334] (1)
       3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
       1. Methylglyoxal synthase-like [52335] (3)
          contains a common phosphate-binding site
          uperfamily
          1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52336] (1)
             1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52337]
                1. Escherichia coli [TaxId: 562] [52338] (10)
                   SQ P00968
          2. Methylglyoxal synthase, MgsA [52339] (3)
             1. Methylglyoxal synthase, MgsA [52340]
                1. Escherichia coli [TaxId: 562] [52341] (5)
                2. Thermotoga maritima [TaxId: 2336] [110489] (1)
                   SQ Q9X0R7 #
                3. Thermus thermophilus [TaxId: 274] [142080] (6)
                   SQ Q5SHD6 1-126
          3. Inosicase [63971] (3)
             1. IMP cyclohydrolase domain of bifunctional purine biosynthesis enzyme ATIC [63972]
                1. Chicken (Gallus gallus) [TaxId: 9031] [63973] (4)
                   SQ P31335
                2. Human (Homo sapiens) [TaxId: 9606] [102255] (3)
                3. Thermotoga maritima [TaxId: 2336] [142081] (2)
                   SQ Q9X0X6 1-157
   29. Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1)
       3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
       1. Ferredoxin reductase-like, C-terminal NADP-linked domain [52343] (5)
          binds NADP differently than classical Rossmann-fold
          N-terminal FAD-linked domain contains (6,10) barrel
          uperfamily
          1. Reductases [52344] (13)
             1. Ferredoxin reductase (flavodoxin reductase) [52345]
                1. Spinach (Spinacia oleracea) [TaxId: 3562] [52346] (7)
                2. Garden pea (Pisum sativum) [TaxId: 3888] [52347] (4)
                3. Paprika (Capsicum annuum) [TaxId: 4072] [52348] (1)
                4. Maize (Zea mays), leaf isoform [TaxId: 4577] [52349] (2)
                5. Maize (Zea mays), root isoform [TaxId: 4577] [63974] (1)
                6. Cyanobacterium (Anabaena sp.), pcc 7119 [TaxId: 1167] [52350] (25)
                7. Escherichia coli [TaxId: 562] [52351] (1)
                8. Azotobacter vinelandii [TaxId: 354] [52352] (1)
             2. NAD(P)H:flavin oxidoreductase [52353]
                1. Escherichia coli [TaxId: 562] [52354] (1)
             3. Nitrate reductase [52355]
                1. Corn (Zea mays) [TaxId: 4577] [52356] (3)
             4. cytochrome b5 reductase [52357]
                1. Pig (Sus scrofa), liver [TaxId: 9823] [52358] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [69450] (3)
                   SQ P20070 33-300
                3. Human (Homo sapiens) [TaxId: 9606] [117484] (1)
                   SQ P00387 30-300
          2. Aromatic dioxygenase reductase-like [52359] (3)
             contains additional 2Fe-2S ferredoxin domain at one of the termini
             1. Phthalate dioxygenase reductase [52360]
                1. Pseudomonas cepacia, db01 [TaxId: 292] [52361] (1)
             2. Benzoate dioxygenase reductase [75156]
                1. Acinetobacter sp. [TaxId: 472] [75157] (1)
             3. Methane monooxygenase component C, MmoC [117485]
                1. Methylococcus capsulatus [TaxId: 414] [117486] (1)
                   SQ P22868 99-348 # structure of the N-terminal, 2Fe-2S ferredoxin domain is also known (1JQ4; scop_sp 69669)
          3. Dihydroorotate dehydrogenase B, PyrK subunit [52362] (1)
             contains 2Fe-2S cluster in the C-terminal extension
             1. Dihydroorotate dehydrogenase B, PyrK subunit [52363]
                1. Lactococcus lactis, isozyme B [TaxId: 1358] [52364] (3)
          4. NADPH-cytochrome p450 reductase-like [52365] (3)
             1. NADPH-cytochrome p450 reductase [52366]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52367] (4)
             2. Sulfite reductase flavoprotein [52368]
                1. Escherichia coli [TaxId: 562] [52369] (2)
             3. Neuronal nitric-oxide synthase FAD/NADP+ domain [69451]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [69452] (2)
                   SQ P29476 750-1413
          5. Flavohemoglobin, C-terminal domain [52370] (2)
             contains additional globin domain
             1. Flavohemoglobin, C-terminal domain [52371]
                1. Alcaligenes eutrophus [TaxId: 106590] [52372] (1)
                2. Escherichia coli [TaxId: 562] [75158] (1)
   30. Adenine nucleotide alpha hydrolase-like [52373] (3)
       core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
       1. Nucleotidylyl transferase [52374] (5)
          uperfamily
          1. Class I aminoacyl-tRNA synthetases (RS), catalytic domain [52375] (22)
             contains a conserved all-alpha subdomain at the C-terminal extension
             1. Tyrosyl-tRNA synthetase (TyrRS) [52376]
                1. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [52377] (7)
                2. Staphylococcus aureus [TaxId: 1280] [69453] (4)
                3. Thermus thermophilus [TaxId: 274] [82354] (2)
                4. Archaeon Methanococcus jannaschii [TaxId: 2190] [89611] (3)
                5. Human (Homo sapiens) [TaxId: 9606] [82355] (2)
             2. Tryptophanyl-tRNA synthetase (TrpRS) [52378]
                overall structure is similar to TyrRS
                1. Bacillus stearothermophilus [TaxId: 1422] [52379] (9)
                2. Human (Homo sapiens) [TaxId: 9606] [102256] (16)
                   SQ P23381 94-471
             3. Glutaminyl-tRNA synthetase (GlnRS) [52380]
                1. Escherichia coli [TaxId: 562] [52381] (14)
                2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159495] (2)
             4. Glutamyl-tRNA synthetase (GluRS) [52382]
                Catalytic domain is very similar to that of GlnRS
                1. Thermus thermophilus [TaxId: 274] [52383] (15)
             5. Glutamyl-Q tRNA-Asp synthetase YadB [102257]
                truncated GluRS and GlnRS homologue lacking the anticodon-binding domain; glutamylates the modified base queuosine (Q) of tRNA-Asp
                1. Escherichia coli [TaxId: 562] [102258] (2)
             6. Class I lysyl-tRNA synthetase [75159]
                similar domain organization to GluRS
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75160] (1)
             7. Methionyl-tRNA synthetase (MetRS) [52384]
                1. Thermus thermophilus [TaxId: 274] [52385] (4)
                2. Escherichia coli [TaxId: 562] [52386] (9)
                3. Pyrococcus abyssi [TaxId: 29292] [110490] (1)
                   SQ Q9V011 1-606 # C-domain 616-722 is solved separately: 1MKH
             8. Cysteinyl-tRNA synthetase (CysRS) [75161]
                1. Escherichia coli [TaxId: 562] [75162] (3)
                   SQ P21888
             9. Isoleucyl-tRNA synthetase (IleRS) [52387]
                1. Thermus thermophilus [TaxId: 274] [52388] (3)
                2. Staphylococcus aureus [TaxId: 1280] [52389] (3)
             10. Valyl-tRNA synthetase (ValRS) [52390]
                 1. Thermus thermophilus [TaxId: 274] [52391] (3)
             11. Leucyl-tRNA synthetase (LeuRS) [82356]
                 1. Thermus thermophilus [TaxId: 274] [82357] (3)
                    contains a non-conserved insertion (residues 581-633) that forms a separate subdomain; possible rudiment Zn finger
             12. Arginyl-tRNA synthetase (ArgRS) [52392]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52393] (3)
                 2. Thermus thermophilus [TaxId: 274] [69454] (1)
          2. Cytidylyltransferase [52394] (1)
             1. CTP:glycerol-3-phosphate cytidylyltransferase [52395]
                1. Bacillus subtilis [TaxId: 1423] [52396] (2)
          3. Adenylyltransferase [52397] (13)
             1. Phosphopantetheine adenylyltransferase [52398]
                1. Escherichia coli [TaxId: 562] [52399] (4)
                2. Thermus thermophilus [TaxId: 274] [89612] (1)
                3. Bacillus subtilis [TaxId: 1423] [102259] (1)
                4. Thermotoga maritima [TaxId: 2336] [110491] (1)
                   SQ Q9WZK0
                5. Mycobacterium tuberculosis [TaxId: 1773] [110492] (1)
                   SQ Q50452
             2. Cytosolic NMN/NAMN adenylyltransferase [89613]
                1. Human (Homo sapiens), FKSG76 [TaxId: 9606] [89614] (6)
             3. Nicotinamide mononucleotide (NMN) adenylyltransferase [52400]
                1. Human (Homo sapiens) [TaxId: 9606] [75163] (5)
                2. Archaeon Methanococcus jannaschii [TaxId: 2190] [52401] (1)
                3. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63975] (6)
                4. Bacillus subtilis [TaxId: 1423] [75164] (2)
                5. Escherichia coli [TaxId: 562] [82358] (2)
             4. Transcriptional regulator NadR, NMN-adenylyltransferase domain [75165]
                1. Haemophilus influenzae [TaxId: 727] [75166] (1)
             5. FMN adenylyltransferase domain of bifunctional FAD synthetase [102260]
                1. Thermotoga maritima [TaxId: 2336] [102261] (7)
                   SQ Q9WZW1
                   TM0379
          4. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63976] (3)
             contains C-terminal subdomain similar to one structural repeat of the Creatinase/aminopeptidase family
             1. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63977]
                1. Escherichia coli [TaxId: 562] [63978] (1)
                2. Mycobacterium tuberculosis [TaxId: 1773] [89615] (21)
                3. Thermus thermophilus [TaxId: 274] [89616] (2)
          5. ATP sulfurylase catalytic domain [63979] (5)
             1. ATP sulfurylase catalytic domain [63980]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63981] (8)
                2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [63982] (2)
                3. Sulfur-oxidizing endosymbiont of Riftia pachyptila [TaxId: 35843] [69455] (1)
                   lacks the C-terminal domain
                4. Thermus thermophilus [TaxId: 274] [102262] (1)
                   lacks the C-terminal domain
                5. Human (Homo sapiens) [TaxId: 9606] [142082] (6)
                   SQ O43252 390-624
       2. Adenine nucleotide alpha hydrolases-like [52402] (6)
          share similar mode of ligand (Adenosine group) binding
          can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group
          uperfamily
          1. N-type ATP pyrophosphatases [52403] (13)
             1. GMP synthetase, central domain [52404]
                1. Escherichia coli [TaxId: 562] [52405] (1)
             2. NH3-dependent NAD+-synthetase [52406]
                1. Bacillus subtilis [TaxId: 1423] [52407] (7)
                2. Escherichia coli [TaxId: 562] [142083] (5)
                   SQ P18843 2-275
                3. Helicobacter pylori [TaxId: 210] [142084] (3)
                   SQ O25096 3-257
             3. Asparagine synthetase B, C-terminal domain [52408]
                1. Escherichia coli [TaxId: 562] [52409] (1)
             4. beta-Lactam synthetase [69456]
                Asparagine synthetase B homologue
                1. Streptomyces clavuligerus [TaxId: 1901] [69457] (5)
                2. Pectobacterium carotovorum [TaxId: 554] [102263] (2)
                   carbapenam synthetase CarA
             5. Argininosuccinate synthetase, N-terminal domain [69458]
                1. Escherichia coli [TaxId: 562] [69459] (4)
                2. Thermus thermophilus [TaxId: 274] [75167] (7)
                3. Thermotoga maritima [TaxId: 2336] [110493] (1)
                   SQ Q9X2A1
             6. Putative N-type ATP pyrophosphatase PF0828 [102264]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [102265] (1)
             7. Hypothetical protein PH1257 [142085]
                probable orthologue of PF0828
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142086] (4)
                   SQ O58996 2-227
             8. Queuosine biosynthesis protein QueC [159496]
                1. Erwinia carotovora [TaxId: 554] [159497] (1)
                   SQ Q6D820 1-230
          2. PP-loop ATPase [82359] (2)
             1. tRNA-Ile-lysidine synthetase, TilS, N-terminal domain [82360]
                formerly putative cell cycle protein MesJ
                1. Escherichia coli [TaxId: 562] [82361] (1)
             2. TilS-like protein Aq_1887 [142087]
                1. Aquifex aeolicus [TaxId: 63363] [142088] (10)
                   SQ O67728 1-216
          3. PAPS reductase-like [52410] (2)
             1. Phosphoadenylyl sulphate (PAPS) reductase [52411]
                1. Escherichia coli [TaxId: 562] [52412] (1)
             2. Sulfate adenylyltransferase subunit 2, CysD [142089]
                1. Pseudomonas syringae pv. tomato [TaxId: 323] [142090] (1)
                   SQ Q87WW0 1-211
          4. ETFP subunits [52432] (6)
             alpha/beta heterodimer of homologous subunits; contains additional strands on both edges of the core sheet
             1. Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain [81393]
                contains an additional FAD-binding domain of DHS-like fold
                1. Human (Homo sapiens) [TaxId: 9606] [81389] (4)
                   SQ P13804 20-203
                2. Paracoccus denitrificans [TaxId: 266] [81391] (1)
                3. Methylophilus methylotrophus [TaxId: 17] [82362] (8)
             2. Small, beta subunit of electron transfer flavoprotein ETFP [81394]
                binds AMP
                1. Human (Homo sapiens) [TaxId: 9606] [81390] (4)
                   SQ P38117
                2. Paracoccus denitrificans [TaxId: 266] [81392] (1)
                3. Methylophilus methylotrophus [TaxId: 17] [82363] (8)
          5. Universal stress protein-like [52436] (7)
             Pfam 00582
             1. "Hypothetical" protein MJ0577 [52437]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52438] (1)
             2. Universal stress protein A, UspA [69461]
                1. Haemophilus influenzae [TaxId: 727] [69462] (1)
                   the nucleotide-binding is not known
             3. Hypothetical protein Aq_178 [102266]
                putative universal stress protein
                1. Aquifex aeolicus [TaxId: 63363] [102267] (1)
             4. Hypothetical protein Rv1636 [110494]
                1. Mycobacterium tuberculosis [TaxId: 1773] [110495] (1)
                   SQ O06153
             5. Hypothetical protein TTHA0895 [117487]
                1. Thermus thermophilus [TaxId: 274] [117488] (4)
                   SQ Q5SJV7
             6. Putative ethylene-responsive protein AT3g01520/F4P13_7 [142091]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142092] (6)
                   SQ Q940U0 5-175
             7. Hypothetical protein TTC0031 [159498]
                TT0030
                1. Thermus thermophilus [TaxId: 274] [159499] (2)
                   SQ Q72LM7 2-135
          6. ThiI-like [142093] (2)
             Pfam 02568
             1. Thiamine biosynthesis protein ThiI, C-terminal domain [142094]
                1. Bacillus anthracis [TaxId: 1392] [142095] (1)
                   SQ Q81KU0 174-391
             2. Hypothetical protein PH1313, C-terminal domain [142096]
                overal structure is similar to ThiI
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142097] (2)
                   SQ O59053 176-307
       3. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52413] (1)
          uperfamily
          1. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52414] (2)
             1. UDP-glucose dehydrogenase (UDPGDH), C-terminal (UDP-binding) domain [52415]
                1. Streptococcus pyogenes [TaxId: 1314] [52416] (2)
             2. GDP-mannose 6-dehydrogenase, GDP-binding domain [89617]
                1. Pseudomonas aeruginosa [TaxId: 287] [89618] (3)
   31. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1)
       3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
       1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52418] (1)
          uperfamily
          1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52419] (6)
             1. Thymidine phosphorylase [52420]
                1. Escherichia coli [TaxId: 562] [52421] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [102268] (1)
             2. Pyrimidine nucleoside phosphorylase [52422]
                1. Bacillus stearothermophilus [TaxId: 1422] [52423] (1)
             3. Anthranilate phosphoribosyltransferase (TrpD) [82364]
                1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82365] (14)
                2. Pectobacterium carotovorum [TaxId: 554] [82366] (2)
                3. Thermus thermophilus [TaxId: 274] [102269] (5)
   32. Cryptochrome/photolyase, N-terminal domain [52424] (1)
       3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
       1. Cryptochrome/photolyase, N-terminal domain [52425] (1)
          uperfamily
          1. Cryptochrome/photolyase, N-terminal domain [52426] (5)
             1. DNA photolyase [52427]
                binds a light-harvesting cofactor
                1. Escherichia coli [TaxId: 562] [52428] (1)
                   cofactor is MHTF
                2. Thermus thermophilus [TaxId: 274] [69460] (5)
                3. Synechococcus elongatus [TaxId: 32046] [52429] (7)
                   SQ P05327 1-474
                   cofactor is HDF
             2. Cryptochrome [82367]
                1. Synechocystis sp., pcc 6803 [TaxId: 1143] [82368] (1)
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110496] (2)
                   SQ Q43125 13-497
   33. DsrEFH-like [75168] (1)
       3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215
       1. DsrEFH-like [75169] (2)
          uperfamily
          1. DsrEF-like [75170] (6)
             Pfam 02635
             1. Hypothetical protein YchN [82369]
                1. Escherichia coli [TaxId: 562] [82370] (1)
             2. Hypothetical protein MTH1491 [75171]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75172] (1)
             3. Sulfurtransferase DsrE [142098]
                1. Chromatium vinosum [TaxId: 1049] [142099] (7)
                   SQ O87896 1-130
             4. tRNA 2-thiouridine synthesizing protein D, TusD [142100]
                formerly hypothetical protein YheN
                1. Escherichia coli [TaxId: 562] [142101] (3)
                   SQ P45532 1-128
             5. Intracellular sulfur oxidation protein DsrF [142102]
                1. Chromatium vinosum [TaxId: 1049] [142103] (7)
                   SQ O87897 5-136
             6. tRNA 2-thiouridine synthesizing protein C, TusC [142104]
                formerly hypothetical protein YheM
                1. Escherichia coli [TaxId: 562] [142105] (3)
                   SQ P45531 1-119
          2. DsrH-like [117489] (3)
             Pfam 04077
             1. Hypothetical protein TM0979 [117490]
                1. Thermotoga maritima [TaxId: 2336] [117491] (2)
                   SQ Q9X074
             2. tRNA 2-thiouridine synthesizing protein B, TusB [142106]
                formerly hypothetical protein YheL
                1. Escherichia coli [TaxId: 562] [142107] (3)
                   SQ P45530 1-95
             3. DsrH [142108]
                1. Chromatium vinosum [TaxId: 1049] [142109] (7)
                   SQ O87898 2-102
   34. PIN domain-like [88722] (1)
       3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145
       1. PIN domain-like [88723] (2)
          uperfamily
          1. PIN domain [89619] (7)
             Pfam 01850
             1. Hypothetical protein AF0591 [89620]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89621] (1)
             2. Hypothetical protein PAE2754 [102270]
                1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [102271] (2)
             3. Hypothetical protein AF1683 [117492]
                1. Archaeoglobus fulgidus [TaxId: 2234] [117493] (1)
                   SQ O28590
             4. Trafficking protein B [142110]
                1. Neisseria gonorrhoeae [TaxId: 485] [142111] (9)
                   SQ Q5F882 1-138! SQ Q9RF91 1-138
             5. Hypothetical protein PH0500 [142112]
                1. Pyrococcus horikoshii [TaxId: 53953] [142113] (4)
                   SQ O58236 2-149
             6. Conserved hypothetical protein PAE0151 [142114]
                1. Pyrobaculum aerophilum [TaxId: 13773] [142115] (1)
                   SQ Q8ZZP3 1-130
             7. Hypothetical protein PF0355 [142116]
                PH0500 ortholog
                1. Pyrococcus furiosus [TaxId: 2261] [142117] (4)
                   SQ Q8U3V0 2-148
          2. 5' to 3' exonuclease catalytic domain [53045] (8)
             contains an alpha-helical arch and additional strand 6 antiparallel to the rest; strand order 321456; similarity to the resolvase-like fold
             1. T4 RNase H [53046]
                1. Bacteriophage T4 [TaxId: 10665] [53047] (2)
             2. 5' to 3' exonuclease domain of DNA polymerase Taq [53048]
                1. Thermus aquaticus [TaxId: 271] [53049] (4)
             3. T5 5'-exonuclease [53050]
                1. Bacteriophage T5 [TaxId: 10726] [53051] (4)
             4. Flap endonuclease-1 (Fen-1 nuclease) [53052]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53053] (2)
                2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82436] (1)
                3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53055] (1)
                4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102272] (2)
                5. Human (Homo sapiens) [TaxId: 9606] [142118] (3)
                   SQ P39748 2-217
   35. Ribose/Galactose isomerase RpiB/AlsB [89622] (1)
       3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topological similarity to a part of the arginase/deacetylase fold
       1. Ribose/Galactose isomerase RpiB/AlsB [89623] (1)
          uperfamily
          1. Ribose/Galactose isomerase RpiB/AlsB [89624] (3)
             1. Alternate ribose 5-phosphate isomerase B, RpiB [89625]
                1. Escherichia coli [TaxId: 562] [89626] (1)
                2. Mycobacterium tuberculosis [TaxId: 1773] [102273] (18)
                   SQ Q79FD7
                   Rv2465c
             2. Putative sugar-phosphate isomerase [89627]
                1. Thermotoga maritima [TaxId: 2336] [89628] (1)
                   TM1080
   36. EreA/ChaN-like [159500] (1)
       Core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order:51423;
       1. EreA/ChaN-like [159501] (3)
          there are four conserved residues in the putative active site: two His and two Glu
          1. ChaN-like [159502] (1)
             Pfam 04187; DUF399; Ferric uptake regulator CjrA
             1. Heme transport protein ChaN [159503]
                1. Campylobacter jejuni [TaxId: 197] [159504] (1)
                   SQ Q0PBW2 27-281
          2. PMT domain-like [159505] (1)
             This is the second from the PMT C-terminus; it retains the superfamily fold and the active site mainchain conformation but lacks the conserved in the other two families His and Glu residues
             1. Dermonecrotic toxin, ToxA [159506]
                Synonym: Mitogenic toxin PMT
                1. Pasteurella multocida [TaxId: 747] [159507] (4)
                   SQ P17452 875-1093
          3. EreA-like [159508] (2)
             Pfam 05139; Erythromycin esterase-like; the superfamily core is decorated with insertion of a four-helical bundle and a C-terminal alpha+beta extension
             1. Succinoglycan biosynthesis protein BC3120 [159509]
                1. Bacillus cereus [TaxId: 1396] [159510] (3)
                   SQ Q81BN2 40-442
             2. Succinoglycan biosynthesis protein BC3205 [159511]
                1. Bacillus cereus [TaxId: 1396] [159512] (1)
                   SQ Q81BF7 33-445
   37. alpha/beta knot [75216] (1)
       core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot
       1. alpha/beta knot [75217] (8)
          known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
          all known members have dimeric structures
          uperfamily
          1. YbeA-like [82371] (4)
             Pfam 02590
             1. Hypothetical protein YbeA [82372]
                1. Escherichia coli [TaxId: 562] [82373] (1)
             2. Hypothetical protein TM0844 [102274]
                1. Thermotoga maritima [TaxId: 2336] [102275] (1)
             3. Hypothetical protein SAV0024/SA0023 [102276]
                1. Staphylococcus aureus [TaxId: 1280] [102277] (1)
             4. Hypothetical protein YydA [110497]
                1. Bacillus subtilis [TaxId: 1423] [110498] (1)
                   SQ Q45601
          2. tRNA(m1G37)-methyltransferase TrmD [89629] (3)
             fold and dimerisation mode are similar to those of the YbeA-like family; contains additional C-terminal all-alpha subdomain
             1. tRNA(m1G37)-methyltransferase TrmD [89630]
                1. Haemophilus influenzae [TaxId: 727] [89631] (4)
                2. Aquifex aeolicus [TaxId: 63363] [102278] (1)
                3. Escherichia coli [TaxId: 562] [110499] (1)
                   SQ P07020
          3. SpoU-like RNA 2'-O ribose methyltransferase [75218] (4)
             contains extra strand (3) in the parallel beta-sheet, order 321546
             1. tRNA (Gm18) methyltransferase TrmH [102279]
                1. Thermus thermophilus [TaxId: 274] [102280] (1)
             2. Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) [82374]
                1. Haemophilus influenzae [TaxId: 727] [82375] (2)
             3. RrmA (RrmH), C-terminal domain [75219]
                23S rRNA methyltransferase; proposed gene names are as appear in the original publication (and the PDB entry)
                1. Thermus thermophilus [TaxId: 274] [75220] (1)
             4. RlmB, C-terminal domain [82376]
                23S rRNA G2251 2'O-methytransferase
                1. Escherichia coli [TaxId: 562] [82377] (1)
          4. Hypothetical protein MTH1 (MT0001), dimerisation domain [75221] (1)
             contains extra strand (3) in the parallel beta-sheet, order 321546; interrupted by an insert OB-fold domain
             1. Hypothetical protein MTH1 (MT0001), dimerisation domain [75222]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75223] (1)
          5. YggJ C-terminal domain-like [89632] (3)
             contains extra strand (3) in the parallel beta-sheet, order 321546; similar dimerisation to the MTH1 domain
             1. Hypothetical protein HI0303 [89633]
                1. Haemophilus influenzae [TaxId: 727] [89634] (2)
             2. Hypothetical protein YqeU [102281]
                1. Bacillus subtilis [TaxId: 1423] [102282] (1)
             3. Hypothetical protein TTHA0657 (TT1575) [117494]
                1. Thermus thermophilus [TaxId: 274] [117495] (3)
                   SQ Q5SKI6
          6. EMG1/NEP1-like [159513] (2)
             Pfam 03587; structurally most similar to the AF1056-like family, but more decorated
             1. Ribosome biogenesis protein NEP1 [159514]
                1. Methanococcus jannaschii [TaxId: 2190] [159515] (6)
                   SQ Q57977 2-205
             2. Essential for mitotic growth 1, EMG1 [159516]
                1. Saccharomyces cerevisiae [TaxId: 4932] [159517] (2)
                   SQ Q06287 23-251
          7. AF1056-like [159518] (2)
             Pfam 04013; DUF358
             1. Uncharacterized protein AF1056 [159519]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159520] (2)
                   SQ O29206 95-288
             2. Uncharacterized protein VCA1059 [159521]
                1. Vibrio cholerae [TaxId: 666] [159522] (2)
                   SQ Q9KKP3 1-201
          8. AF0751-like [159523] (1)
             Pfam 01994; DUF127
             1. Uncharacterized protein AF0751 [159524]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159525] (2)
                   SQ O29507 1-167
   38. PreATP-grasp domain [52439] (1)
       3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
       possible rudiment form of Rossmann-fold domain
       1. PreATP-grasp domain [52440] (8)
          precedes the ATP-grasp domain common to all superfamily members, can contain a substrate-binding function
          uperfamily
          1. BC N-terminal domain-like [52441] (8)
             1. Biotin carboxylase (BC), N-terminal domain [52442]
                subunit of acetyl-CoA and pyruvate carboxylases
                1. Escherichia coli [TaxId: 562] [52443] (13)
                2. Aquifex aeolicus [TaxId: 63363] [102283] (1)
             2. Glycinamide ribonucleotide synthetase (GAR-syn), N-domain [52444]
                1. Escherichia coli [TaxId: 562] [52445] (1)
                2. Thermotoga maritima [TaxId: 2336] [110500] (1)
                   SQ Q9X0X7
             3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), N-domain [52446]
                1. Escherichia coli [TaxId: 562] [52447] (6)
             4. Glycinamide ribonucleotide transformylase PurT, N-domain [52448]
                1. Escherichia coli [TaxId: 562] [52449] (7)
             5. Carbamoyl phosphate synthetase (CPS), large subunit PreATP-grasp domains [52450]
                duplication: CPS large subunit contains two full BC-like lobes: carboxyphosphate and carbamoyl phosphate domains
                1. Escherichia coli [TaxId: 562] [52451] (10)
                   SQ P00968
             6. Acetyl-CoA carboxylase, BC-N subdomain [117496]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117497] (2)
                   SQ Q00955 13-566
          2. D-Alanine ligase N-terminal domain [52452] (3)
             1. D-Ala-D-Ala ligase, N-domain [52453]
                1. Escherichia coli, gene ddlB [TaxId: 562] [52454] (3)
             2. D-alanine:D-lactate ligase VanA, N-domain [52455]
                1. Leuconostoc mesenteroides, Ddl2 [TaxId: 1245] [52456] (1)
                2. Enterococcus faecium [TaxId: 1352] [63983] (1)
          3. Lysine biosynthesis enzyme LysX, N-terminal domain [102284] (1)
             1. Lysine biosynthesis enzyme LysX, N-terminal domain [102285]
                1. Thermus thermophilus [TaxId: 274] [102286] (2)
          4. Prokaryotic glutathione synthetase, N-terminal domain [52457] (1)
             1. Prokaryotic glutathione synthetase, N-terminal domain [52458]
                1. Escherichia coli [TaxId: 562] [52459] (4)
          5. Eukaryotic glutathione synthetase, substrate-binding domain [52460] (2)
             circularly permuted version of prokaryotic enzyme
             1. Eukaryotic glutathione synthetase, substrate-binding domain [52461]
                1. Human (Homo sapiens) [TaxId: 9606] [52462] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82378] (2)
          6. Synapsin domain [52463] (3)
             1. Synapsin I [52464]
                1. Cow (Bos taurus) [TaxId: 9913] [52465] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [102287] (2)
             2. Synapsin II [89635]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [89636] (2)
          7. Glutathionylspermidine synthase substrate-binding domain-like [142119] (1)
             central part of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
             1. Glutathionylspermidine synthase, synthetase domain [142120]
                1. Escherichia coli [TaxId: 562] [142121] (10)
                   SQ P0AES0 379-496
          8. PurP N-terminal domain-like [159526] (3)
             Pfam 06849; DUF1246
             1. 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP [159527]
                1. Pyrococcus furiosus [TaxId: 2261] [159528] (12)
                   SQ Q8U0R7 1-99
                2. Thermococcus kodakaraensis [TaxId: 311400] [159529] (3)
                   SQ Q5JD28 2-97
                3. Methanocaldococcus jannaschii [TaxId: 2190] [159530] (4)
                   SQ Q57600 1-123
   39. DHS-like NAD/FAD-binding domain [52466] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
       1. DHS-like NAD/FAD-binding domain [52467] (6)
          binds cofactor molecules in the opposite direction than classical Rossmann fold
          uperfamily
          1. Deoxyhypusine synthase, DHS [52468] (1)
             1. Deoxyhypusine synthase, DHS [52469]
                1. Human (Homo sapiens) [TaxId: 9606] [52470] (4)
                   SQ P49366
          2. C-terminal domain of the electron transfer flavoprotein alpha subunit [52471] (3)
             lacks strand 3; shares the FAD-binding mode with the pyruvate oxidase domain
             1. C-terminal domain of the electron transfer flavoprotein alpha subunit [52472]
                1. Human (Homo sapiens) [TaxId: 9606] [52473] (3)
                2. Paracoccus denitrificans [TaxId: 266] [52474] (1)
                3. Methylophilus methylotrophus [TaxId: 17] [82379] (6)
          3. Pyruvate oxidase and decarboxylase, middle domain [52475] (12)
             N-terminal domain is Pyr module, and C-terminal domain is PP module of thiamin diphosphate-binding fold
             1. Pyruvate oxidase [52476]
                binds FAD
                1. Lactobacillus plantarum [TaxId: 1590] [52477] (12)
                2. Aerococcus viridans [TaxId: 1377] [142122] (4)
             2. Pyruvate decarboxylase [52478]
                rudiment domain with a variant fold, lacks FAD-binding
                1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [52479] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52480] (2)
                3. Zymomonas mobilis [TaxId: 542] [52481] (1)
             3. Indole-3-pyruvate decarboxylase [89637]
                1. Enterobacter cloacae [TaxId: 550] [89638] (1)
             4. Benzoylformate decarboxylase [52482]
                1. Pseudomonas putida [TaxId: 303] [52483] (12)
                   SQ P20906
             5. Acetohydroxyacid synthase catalytic subunit [69463]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69464] (6)
                   SQ P07342 84-687
                2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142123] (6)
                   SQ P17597 281-459
             6. Catabolic acetolactate synthase [102288]
                1. Klebsiella pneumoniae [TaxId: 573] [102289] (3)
             7. Carboxyethylarginine synthase [102290]
                1. Streptomyces clavuligerus [TaxId: 1901] [102291] (11)
             8. Oxalyl-CoA decarboxylase [142124]
                1. Oxalobacter formigenes [TaxId: 847] [142125] (12)
                   SQ P40149 195-369
          4. Transhydrogenase domain III (dIII) [52484] (3)
             binds NADP, shares with the pyruvate oxidase FAD-binding domain a common ADP-binding mode
             1. Transhydrogenase domain III (dIII) [52485]
                1. Human (Homo sapiens) [TaxId: 9606] [52486] (4)
                2. Cow (Bos taurus) [TaxId: 9913] [52487] (1)
                3. Rhodospirillum rubrum [TaxId: 1085] [52488] (17)
          5. Sir2 family of transcriptional regulators [63984] (7)
             silent information regulator 2; contains insertion of a rubredoxin-like zinc finger domain
             1. AF1676, Sir2 homolog (Sir2-AF1?) [63985]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [63986] (6)
             2. AF0112, Sir2 homolog (Sir2-AF2) [82380]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [82381] (7)
             3. NAD-dependent deacetylase CobB [102292]
                1. Escherichia coli [TaxId: 562] [102293] (1)
             4. Sirt2 histone deacetylase [63987]
                1. Human (Homo sapiens) [TaxId: 9606] [63988] (1)
             5. Hst2 [102294]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102295] (5)
                   SQ P53686 1-293
             6. NAD-dependent deacetylase NpdA [142126]
                1. Thermotoga maritima [TaxId: 2336] [142127] (10)
                   SQ Q9WYW0 1-245
             7. NAD-dependent deacetylase sirtuin-5 [142128]
                1. Human (Homo sapiens) [TaxId: 9606] [142129] (6)
                   SQ Q9NXA8 36-302
          6. ACDE2-like [142130] (1)
             Pfam 02552
             1. Acetyl-CoA decarbonylase/synthase complex epsilon subunit 2, ACDE2 [142131]
                1. Archaeoglobus fulgidus [TaxId: 2234] [142132] (4)
                   SQ O30273 17-174
   40. Tubulin nucleotide-binding domain-like [52489] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
       1. Tubulin nucleotide-binding domain-like [52490] (1)
          uperfamily
          1. Tubulin, GTPase domain [52491] (9)
             1. Cell-division protein FtsZ [52492]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52493] (7)
                   SQ Q57816 23-360
                2. Pseudomonas aeruginosa [TaxId: 287] [89639] (2)
                3. Mycobacterium tuberculosis [TaxId: 1773] [110501] (7)
                   SQ O08378
                4. Thermotoga maritima [TaxId: 2336] [117498] (1)
                   SQ O08398 22-335
             2. Tubulin alpha-subunit [52494]
                1. Pig (Sus scrofa) [TaxId: 9823] [52495] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [63989] (5)
                3. Prosthecobacter dejongeii [TaxId: 48465] [159531] (3)
                   SQ Q8GCC5 3-246
                   bacterial tubulin BtubA
             3. Tubulin beta-subunit [52496]
                1. Pig (Sus scrofa) [TaxId: 9823] [52497] (1)
                2. Cow (Bos taurus) [TaxId: 9913] [63990] (9)
                   SQ P02550 ! SQ P02554
   41. Isochorismatase-like hydrolases [52498] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
       1. Isochorismatase-like hydrolases [52499] (1)
          uperfamily
          1. Isochorismatase-like hydrolases [100948] (7)
             1. N-carbamoylsarcosine amidohydrolase [52501]
                1. Arthrobacter sp. [TaxId: 1667] [52502] (1)
             2. Pyrazinamidase/nicotinamidase [69465]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [69466] (2)
             3. Phenazine biosynthesis protein PhzD [89643]
                1. Pseudomonas aeruginosa [TaxId: 287] [89644] (2)
             4. YcaC [52504]
                octameric hydrolase of unknown specificity
                1. Escherichia coli [TaxId: 562] [52505] (1)
             5. Hypothetical protein YecD [102298]
                1. Escherichia coli [TaxId: 562] [102299] (1)
             6. Ribonuclease MAR1 [110502]
                1. Leishmania donovani [TaxId: 5661] [110503] (1)
                   SQ O77166 # 89% sequence identity; Leishmania tarentolae TaxID:5689
                2. Leishmania major [TaxId: 5664] [117499] (1)
                   SQ Q4QGT7 # ! Structural genomics target
   42. Dipeptide transport protein [63991] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain
       1. Dipeptide transport protein [63992] (1)
          uperfamily
          1. Dipeptide transport protein [63993] (1)
             1. Zn-dependent D-aminopeptidase DppA [63994]
                1. Bacillus subtilis [TaxId: 1423] [63995] (1)
   43. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52506] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
       1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52507] (1)
          uperfamily
          1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52508] (5)
             Pfam 02441; formerly DFP, DNA/pantothenate metabolism flavoprotein family
             1. 4'-phosphopantothenoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a) [52509]
                involved in signal transduction; binds FMN
                1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52510] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [102300] (1)
                   hypothetical protein mds018
             2. Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD [63996]
                binds FMN
                1. Staphylococcus epidermidis [TaxId: 1282] [63997] (2)
             3. MrsD [102301]
                binds FAD
                1. Bacillus sp. hil-y85/54728 [TaxId: 69002] [102302] (1)
             4. Probable aromatic acid decarboxylase Pad1 [117500]
                1. Escherichia coli O157:H7 [TaxId: 83334] [117501] (1)
                   SQ Q9X728
   44. HAD-like [56783] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
       1. HAD-like [56784] (25)
          usually contains an insertion (sub)domain after strand 1
          uperfamily
          1. Probable phosphatase YrbI [69467] (1)
             the insertion subdomain is a beta-hairpin involved into tetramerisation
             1. Probable phosphatase YrbI [69468]
                1. Haemophilus influenzae, HI1679 [TaxId: 727] [69469] (2)
          2. HAD-related [56785] (3)
             the insertion subdomain is a 4-helical bundle
             1. L-2-Haloacid dehalogenase, HAD [56786]
                1. Pseudomonas sp., strain YL [TaxId: 306] [56787] (4)
                2. Xanthobacter autotrophicus [TaxId: 280] [56788] (4)
             2. Hypothetical protein PH0459 [142133]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142134] (1)
                   SQ O58216 1-230
          3. beta-Phosphoglucomutase-like [75173] (9)
             the insertion subdomain is a 4-helical bundle
             1. beta-Phosphoglucomutase [75174]
                1. Lactococcus lactis [TaxId: 1358] [75175] (8)
             2. Phosphatase YniC [110504]
                1. Escherichia coli [TaxId: 562] [110505] (1)
                   SQ P77247
             3. Phosphoglycolate phosphatase [142135]
                1. Lactobacillus plantarum [TaxId: 1590] [142136] (1)
                   SQ Q88YA8 1-207
             4. N-acylneuraminate-9-phosphatase NANP [142137]
                1. Mouse (Mus musculus) [TaxId: 10090] [142138] (1)
                   SQ Q9CPT3 1-247
             5. Hypothetical protein SP2064 [142139]
                1. Streptococcus pneumoniae [TaxId: 1313] [142140] (4)
                   SQ Q97NG6 3-206
             6. Hypothetical protein Atu0790 [142141]
                1. Agrobacterium tumefaciens [TaxId: 358] [142142] (1)
                   SQ Q8UH93 3-224
             7. Phosphoglycolate phosphatase Gph [142143]
                1. Haemophilus somnus [TaxId: 731] [142144] (2)
                   SQ Q0I1W8 1-224
             8. predicted phosphatase SP0104 [142145]
                1. Streptococcus pneumoniae [TaxId: 1313] [142146] (1)
                   SQ Q97T51 1-210
             9. Hypothetical protein CT1708 [142147]
                1. Chlorobium tepidum [TaxId: 1097] [142148] (1)
                   SQ Q8KBS5 2-229
          4. YihX-like [56789] (3)
             the insertion subdomain is a 4-helical bundle
             1. Epoxide hydrolase, N-terminal domain [56790]
                has a lipid phosphatase activity
                1. Mouse (Mus musculus) [TaxId: 10090] [56791] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [102303] (6)
             2. Putative phosphatase YihX [142149]
                1. Escherichia coli [TaxId: 562] [142150] (1)
                   SQ P0A8Y3 1-197
          5. Phosphonoacetaldehyde hydrolase-like [56792] (2)
             the insertion subdomain is a 4-helical bundle
             1. Phosphonoacetaldehyde hydrolase [56793]
                1. Bacillus cereus [TaxId: 1396] [56794] (6)
                   SQ O31156
             2. Putative hydrolase SP0805 [142151]
                1. Streptococcus pneumoniae [TaxId: 1313] [142152] (1)
                   SQ Q97RK1 4-190
          6. Phosphoserine phosphatase [64511] (2)
             the insertion subdomain is a 4-helical bundle
             1. Phosphoserine phosphatase [64512]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64513] (6)
                2. Human (Homo sapiens) [TaxId: 9606] [89645] (3)
          7. 5'(3')-deoxyribonucleotidase (dNT-2) [82382] (1)
             the insertion subdomain is a 4-helical bundle; dephosphorylates dUMP and dTMP
             1. 5'(3')-deoxyribonucleotidase (dNT-2) [82383]
                1. Human (Homo sapiens) [TaxId: 9606] [82384] (12)
          8. Homoserine kinase ThrH [102304] (1)
             the insertion subdomain is a rudiment 4-helical bundle
             1. Homoserine kinase ThrH [102305]
                1. Pseudomonas aeruginosa [TaxId: 287] [102306] (2)
          9. Class B acid phosphatase, AphA [102307] (2)
             the insertion subdomain is a helical hairpin
             1. Class B acid phosphatase, AphA [102308]
                1. Escherichia coli [TaxId: 562] [102309] (15)
                   SQ P32697 27-237
                2. Salmonella typhimurium [TaxId: 90371] [142153] (12)
                   SQ P58683 30-237
          10. Hypothetical protein MW1667 (SA1546) [102310] (1)
              the insertion subdomain is multi-helical
              1. Hypothetical protein MW1667 (SA1546) [102311]
                 1. Staphylococcus aureus [TaxId: 1280] [102312] (1)
          11. phosphatase domain of polynucleotide kinase [82385] (2)
              no insertion subdomains
              1. Polynucleotide kinase, phosphatase domain [82386]
                 1. Bacteriophage T4 [TaxId: 10665] [82387] (16)
              2. 5' polynucleotide kinase-3' phosphatase, middle domain [142154]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142155] (2)
                    SQ Q9JLV6 144-338
          12. Predicted hydrolases Cof [82388] (13)
              contains an alpha+beta subdomain inserted into a new site after strand 3
              1. Phosphoglycolate phosphatase, PGPase [82389]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [82390] (2)
                 2. Pyrococcus horikoshii [TaxId: 53953] [117502] (1)
                    SQ O50129 # PH1421
              2. Hypothetical protein YwpJ [89646]
                 1. Bacillus subtilis [TaxId: 1423] [89647] (1)
              3. Hypothetical protein TM0651 [102313]
                 1. Thermotoga maritima [TaxId: 2336] [102314] (1)
              4. Hypothetical protein YidA [102315]
                 1. Escherichia coli [TaxId: 562] [102316] (1)
              5. Sugar phosphatase SupH (YbiV) [117503]
                 1. Escherichia coli [TaxId: 562] [117504] (3)
                    SQ P75792
              6. Putative mannosyl-3-phosphoglycerate phosphatase MPGP (YedP) [117505]
                 1. Escherichia coli [TaxId: 562] [117506] (1)
                    SQ P76329 4-235
                 2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142156] (2)
                    SQ O58690 1-243
              7. Sugar-phosphate phosphatase BT4131 [142157]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [142158] (3)
                    SQ Q8A090 2-261
              8. Phosphomannomutase 2 [142159]
                 1. Human (Homo sapiens) [TaxId: 9606] [142160] (2)
                    SQ O15305 4-246
              9. Phosphomannomutase 1 [142161]
                 1. Human (Homo sapiens) [TaxId: 9606] [142162] (2)
                    SQ Q92871 12-256
              10. Sucrose-phosphatase Slr0953 [142163]
                  1. Synechocystis sp. pcc 6803 [TaxId: 1148] [142164] (9)
                     SQ P74325 1-244
              11. PFL1270w orthologue [142165]
                  1. Plasmodium vivax [TaxId: 5855] [142166] (4)
                     SQ Q8I5F4 11-293
          13. NagD-like [102317] (6)
              duplication: consists of two segment-swapped domains of this fold; this results in the insertion of a circularly permuted domain after strand 3, analogously to the Cof family
              1. Hypothetical protein TM1742 [102318]
                 putative NagD protein
                 1. Thermotoga maritima [TaxId: 2336] [102319] (2)
              2. Putative phosphatase SMU.1415c [117507]
                 1. Streptococcus mutans [TaxId: 1309] [117508] (1)
                    SQ Q8DTD6
              3. Hypothetical protein SPy1043 [142167]
                 1. Streptococcus pyogenes [TaxId: 1314] [142168] (1)
                    SQ Q99ZW4 2-254
              4. NagD [142169]
                 1. Escherichia coli [TaxId: 562] [142170] (1)
                    SQ P0AF24 1-250
              5. Putative hydrolase SP1407 [142171]
                 1. Streptococcus pneumoniae [TaxId: 1313] [142172] (1)
                    SQ Q97Q24 3-255
              6. Putative hydrolase EF1188 [142173]
                 1. Enterococcus faecalis [TaxId: 1351] [142174] (2)
                    SQ Q836C7 4-256
          14. Meta-cation ATPase, catalytic domain P [81656] (2)
              interrupted by a large insertion, domain N
              1. Calcium ATPase, catalytic domain P [81655]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81654] (17)
                    SQ P04191
              2. Cation-transporting ATPase [142175]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [142176] (3)
                    SQ O29777 416-434,548-663
          15. Trehalose-phosphatase [110506] (1)
              Pfam 02358; contains an insert alpha+beta subdomain; similar overall fold to the Cof family
              1. Trehalose-6-phosphate phosphatase related protein [110507]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [110508] (1)
                    SQ Q9HIW7
          16. NLI interacting factor-like phosphatase [110509] (1)
              Pfam 03031; NIF; the insertion subdomain is a 3-stranded beta-sheet;
              1. Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1, NRAMP1 [110510]
                 1. Human (Homo sapiens) [TaxId: 9606] [110511] (2)
                    SQ Q9GZU7 76-256
          17. Magnesium-dependent phosphatase-1, Mdp1 [117509] (1)
              the insertion subdomain is a 3-stranded beta-sheet different from the NIF family
              1. Magnesium-dependent phosphatase-1, Mdp1 [117510]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117511] (2)
                    SQ Q9D967
          18. Hypothetical protein VC0232 [117512] (1)
              contains a deletion in the common fold; segment-swapped tetramer
              1. Hypothetical protein VC0232 [117513]
                 1. Vibrio cholerae [TaxId: 666] [117514] (1)
                    SQ Q9KVB4
          19. Histidinol phosphatase-like [142177] (3)
              no insertion subdomains
              1. Histidine biosynthesis bifunctional protein HisB, phosphatase domain [142178]
                 1. Escherichia coli [TaxId: 562] [142179] (10)
                    SQ Q9S5G5 3-163
              2. Hypothetical protein Mll2559 [159532]
                 1. Mesorhizobium loti [TaxId: 381] [159533] (1)
                    SQ Q98I56 8-216
              3. D,D-heptose 1,7-bisphosphate phosphatase GmhB [159534]
                 1. Escherichia coli [TaxId: 562] [159535] (4)
                    SQ P63228 4-185
          20. MtnX-like [142180] (1)
              Pfam 06888; the insertion subdomain is a rudiment 4-helical bundle
              1. 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX [142181]
                 1. Bacillus subtilis [TaxId: 1423] [142182] (2)
                    SQ O31667 2-227
          21. Pyrimidine 5'-nucleotidase (UMPH-1) [142183] (2)
              Pfam 05822; the insertion subdomain is a rudiment 4-helical bundle
              1. Cytosolic 5'-nucleotidase III [142184]
                 1. Human (Homo sapiens) [TaxId: 9606] [142185] (2)
                    SQ Q9H0P0 64-336
                 2. Mouse (Mus musculus) [TaxId: 10090] [159536] (1)
                    SQ Q9D020 7-297
          22. Enolase-phosphatase E1 [142186] (2)
              the insertion subdomain is a 4-helical bundle
              1. Protein UTR4 [142187]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142188] (4)
                    SQ P32626 17-241
              2. E-1 enzyme [142189]
                 1. Human(Homo sapiens) [TaxId: 9606] [142190] (2)
                    SQ Q9UHY7 4-256
          23. 5' nucleotidase-like [142191] (1)
              Pfam 05761; the insertion domain cosists of 3-helical bundle and a pseudo beta-barrel; contains extra C-terminal long alpha hairpin subdomain (scop_cf 46556)
              1. Cytosolic IMP-GMP specific 5'-nucleotidase [142192]
                 1. Legionella pneumophila [TaxId: 446] [142193] (1)
                    SQ Q5ZZB6 2-459
          24. AF1437-like [159537] (1)
              the insertion subdomain is a rudiment 4-helical bundle; extra alpha-hairpin insertion after strand 3
              1. Hypothetical protein AF1437 [159538]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [159539] (1)
                    SQ O28835 1-308
          25. BT0820-like [159540] (1)
              PfamB 073209; deletion in the common fold; segment-swapped dimer
              1. Hypothetical protein BT0820 [159541]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [159542] (1)
                    SQ Q8A9J5 1-122
   45. NagB/RpiA/CoA transferase-like [100949] (1)
       core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
       1. NagB/RpiA/CoA transferase-like [100950] (8)
          uperfamily
          1. NagB-like [52513] (3)
             share a common phosphate-binding site with the RpiA family
             1. Glucosamine 6-phosphate deaminase/isomerase NagB [52514]
                1. Escherichia coli [TaxId: 562] [52515] (10)
                2. Human (Homo sapiens) [TaxId: 9606] [102320] (1)
             2. 6-phosphogluconolactonase [102321]
                1. Thermotoga maritima [TaxId: 2336] [102322] (2)
                   SQ Q9X0N8 # TM1154
          2. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75176] (4)
             share a common phosphate-binding site with the NagB-like family; part of sheet is folded upon itself and forms a barrel-like structure like the CoA transferase subunits
             1. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75177]
                1. Escherichia coli [TaxId: 562] [75178] (3)
                2. Haemophilus influenzae [TaxId: 727] [82391] (1)
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75179] (2)
                4. Thermus thermophilus [TaxId: 274] [110512] (3)
                   SQ Q72J47
          3. CoA transferase beta subunit-like [74657] (3)
             catalytic subunit: similar active site structure to the NagB and RpiA families; mixed beta-sheet of 7 strands, order 4321567; strand 3 is antiparallel to the rest
             1. Glutaconate:CoA transferase beta [53320]
                1. Acidaminococcus fermentans [TaxId: 905] [53321] (1)
             2. Succinate:CoA transferase, C-terminal domain [82466]
                1. Pig (Sus scrofa) [TaxId: 9823] [82467] (13)
             3. Putative enzyme YdiF C-terminal domain [142194]
                1. Escherichia coli [TaxId: 562] [142195] (12)
                   SQ P37766 283-529
          4. CoA transferase alpha subunit-like [74656] (6)
             parallel beta-sheet of 7 strands, order 4321567
             1. Glutaconate:CoA transferase alpha [53318]
                1. Acidaminococcus fermentans [TaxId: 905] [53319] (1)
             2. Acetate:CoA transferase alpha [75257]
                1. Escherichia coli [TaxId: 562] [75258] (1)
             3. Succinate:CoA transferase, N-terminal domain [82464]
                1. Pig (Sus scrofa) [TaxId: 9823] [82465] (13)
             4. Putative citrate lyase alpha chain, citF2 [117515]
                duplication: consists of two topologically similar domains
                1. Salmonella typhimurium [TaxId: 90371] [117516] (1)
                   SQ Q8ZRY1
             5. Acetyl-CoA hydrolase (PA5445) [142196]
                duplication: consists of two topologically similar domains; overall similarity to CitF2
                1. Pseudomonas aeruginosa [TaxId: 287] [142197] (4)
                   SQ Q9HTC2 224-497! SQ Q9HTC2 3-223
             6. Putative enzyme YdiF N-terminal domain [142198]
                1. Escherichia coli [TaxId: 562] [142199] (12)
                   SQ P37766 4-276
          5. IF2B-like [110513] (5)
             Pfam 01008; contains extra N-terminal alpha+beta domain (1-126); beta(3)-alpha(5); 3 layers: b/a/a
             1. Probable methylthioribose-1-phosphate isomerase TM0911 [110514]
                1. Thermotoga maritima [TaxId: 2336] [110515] (1)
                   SQ Q9X013
             2. Putative methylthioribose-1-phosphate isomerase Ypr118W [110516]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110517] (1)
                   SQ Q06489
             3. Putative eIF-2B delta-subunit [110518]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110519] (1)
                   SQ O29877 # AF0370
             4. Putative eIF-2B subunit 2-like protein PH0440 [117517]
                1. Pyrococcus horikoshii [TaxId: 53953] [117518] (1)
                   SQ O58185
             5. Initiation factor 2b [159543]
                1. Leishmania major [TaxId: 5664] [159544] (2)
                   SQ Q4Q0R9 133-506,133-506
          6. Methenyltetrahydrofolate synthetase [110520] (3)
             Pfam 01812; 5-FTHF cyclo-ligase
             1. Hypothetical protein aq_1731 [110521]
                1. Aquifex aeolicus [TaxId: 63363] [110522] (1)
                   SQ O67621
             2. 5,10-methenyltetrahydrofolate synthetase homolog MPN348 [110523]
                1. Mycoplasma pneumoniae [TaxId: 2104] [110524] (3)
                   SQ P75430
             3. Hypothetical protein TTHA1611 [117519]
                1. Thermus thermophilus [TaxId: 274] [117520] (1)
                   SQ Q5SHW9 1-175
          7. YkgG-like [142200] (1)
             Pfam 02589; DUF162
             1. Hypothetical protein DR1909 [142201]
                1. Deinococcus radiodurans [TaxId: 1299] [142202] (1)
                   SQ Q9RT57 38-212
          8. SorC sugar-binding domain-like [159545] (5)
             Pfam 04198
             1. Transcriptional regulator PSPTO2395 [159546]
                1. Pseudomonas syringae [TaxId: 317] [159547] (1)
                   SQ Q883G8 59-316
             2. Transcriptional regulator SP0247 [159548]
                1. Streptococcus pneumoniae [TaxId: 1313] [159549] (1)
                   SQ Q97SS7 56-317
             3. Transcriptional regulator EF1965 [159550]
                1. Enterococcus faecalis [TaxId: 1351] [159551] (1)
                   SQ Q833I7 95-341
             4. Sor-operon regulator SorC [159552]
                1. Shigella flexneri [TaxId: 623] [159553] (4)
                   SQ Q83PA8 61-315
             5. Central glycolytic gene regulator CggR [159554]
                formerly hypothetical protein YvbQ
                1. Bacillus subtilis [TaxId: 1423] [159555] (10)
                   SQ O32253 89-338
   46. Hypothetical protein MTH777 (MT0777) [75180] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
       1. Hypothetical protein MTH777 (MT0777) [75181] (1)
          uperfamily
          1. Hypothetical protein MTH777 (MT0777) [75182] (1)
             1. Hypothetical protein MTH777 (MT0777) [75183]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75184] (1)
   47. Thiamin pyrophosphokinase, catalytic domain [63998] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156
       1. Thiamin pyrophosphokinase, catalytic domain [63999] (1)
          uperfamily
          1. Thiamin pyrophosphokinase, catalytic domain [64000] (2)
             1. Thiamin pyrophosphokinase, catalytic domain [64001]
                1. Mouse (Mus musculus) [TaxId: 10090] [64002] (2)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64003] (1)
   48. Undecaprenyl diphosphate synthase [64004] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156
       1. Undecaprenyl diphosphate synthase [64005] (1)
          the sheet topology is similar to those of the N-terminal domain of phosphoglycerate kinase and carbamate kinase
          uperfamily
          1. Undecaprenyl diphosphate synthase [64006] (2)
             1. Undecaprenyl diphosphate synthase [64007]
                1. Micrococcus luteus [TaxId: 1270] [64008] (1)
                2. Escherichia coli [TaxId: 562] [64009] (15)
   49. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102323] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456
       1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102324] (1)
          the sheet topology is similar to those of the Periplasmic binding protein-like I domains
          uperfamily
          1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102325] (1)
             1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102326]
                1. Archaeon Methanopyrus kandleri [TaxId: 2320] [102327] (28)
   50. Thiamin diphosphate-binding fold (THDP-binding) [52517] (1)
       3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
       1. Thiamin diphosphate-binding fold (THDP-binding) [52518] (8)
          there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
          two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
          uperfamily
          1. Pyruvate oxidase and decarboxylase Pyr module [88724] (12)
             the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpha/beta domain of Rossmann-like topology
             1. Pyruvate decarboxylase [88725]
                1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88726] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88727] (2)
                3. Zymomonas mobilis [TaxId: 542] [88728] (1)
             2. Indole-3-pyruvate decarboxylase [89648]
                1. Enterobacter cloacae [TaxId: 550] [89649] (1)
             3. Pyruvate oxidase [88729]
                1. Lactobacillus plantarum [TaxId: 1590] [88730] (12)
                2. Aerococcus viridans [TaxId: 1377] [142203] (4)
             4. Benzoylformate decarboxylase [88731]
                1. Pseudomonas putida [TaxId: 303] [88732] (12)
                   SQ P20906
             5. Acetohydroxyacid synthase catalytic subunit [88733]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88734] (6)
                   SQ P07342 84-687
                2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142204] (6)
                   SQ P17597 86-280
             6. Catabolic acetolactate synthase [102328]
                1. Klebsiella pneumoniae [TaxId: 573] [102329] (3)
             7. Carboxyethylarginine synthase [102330]
                1. Streptomyces clavuligerus [TaxId: 1901] [102331] (11)
             8. Oxalyl-CoA decarboxylase [142205]
                1. Oxalobacter formigenes [TaxId: 847] [142206] (12)
                   SQ P40149 7-194
          2. TK-like Pyr module [88735] (5)
             different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
             1. Transketolase (TK), Pyr module [88736]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88737] (7)
                2. Maize (Zea mays) [TaxId: 4577] [88738] (1)
                3. Escherichia coli [TaxId: 562] [89650] (7)
                4. Leishmania mexicana mexicana [TaxId: 44270] [117521] (1)
                   SQ Q8MPM3
             2. Pyruvate dehydrogenase E1 component, Pyr module [88739]
                E1A and E1B fused together in a single-chain protein
                1. Escherichia coli [TaxId: 562] [88740] (14)
          3. Branched-chain alpha-keto acid dehydrogenase Pyr module [88741] (6)
             parent family to TK and PFOR
             heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
             1. Branched-chain alpha-keto acid dehydrogenase, Pyr module [88742]
                1. Human (Homo sapiens) [TaxId: 9606] [88743] (21)
                   SQ P21953 52-392
                2. Thermus thermophilus [TaxId: 274] [102332] (4)
             2. 2-oxoisovalerate dehydrogenase (E1B), Pyr module [88744]
                chain A is alpha-subunit and chain B is beta-subunit
                1. Pseudomonas putida [TaxId: 303] [88745] (5)
             3. E1-beta subunit of pyruvate dehydrogenase, Pyr module [69472]
                1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69473] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [89653] (3)
             4. Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain [117522]
                1. Bacillus stearothermophilus [TaxId: 1422] [117523] (2)
                   SQ P21874
          4. PFOR Pyr module [88746] (1)
             domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
             1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain I [88747]
                1. Desulfovibrio africanus [TaxId: 873] [88748] (17)
          5. Pyruvate oxidase and decarboxylase PP module [88749] (12)
             the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpa/beta domain of Rossmann-like topology
             1. Pyruvate decarboxylase [88750]
                1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88751] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88752] (2)
                3. Zymomonas mobilis [TaxId: 542] [88753] (1)
             2. Indole-3-pyruvate decarboxylase [89654]
                1. Enterobacter cloacae [TaxId: 550] [89655] (1)
             3. Pyruvate oxidase [88754]
                1. Lactobacillus plantarum [TaxId: 1590] [88755] (12)
                2. Aerococcus viridans [TaxId: 1377] [142207] (4)
             4. Benzoylformate decarboxylase [88756]
                1. Pseudomonas putida [TaxId: 303] [88757] (12)
                   SQ P20906
             5. Acetohydroxyacid synthase catalytic subunit [88758]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88759] (6)
                   SQ P07342 84-687
                2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142208] (6)
                   SQ P17597 460-667
             6. Catabolic acetolactate synthase [102333]
                1. Klebsiella pneumoniae [TaxId: 573] [102334] (3)
             7. Carboxyethylarginine synthase [102335]
                1. Streptomyces clavuligerus [TaxId: 1901] [102336] (11)
             8. Oxalyl-CoA decarboxylase [142209]
                1. Oxalobacter formigenes [TaxId: 847] [142210] (12)
                   SQ P40149 370-552
          6. TK-like PP module [88760] (5)
             different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
             1. Transketolase (TK), PP module [88761]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88762] (7)
                2. Maize (Zea mays) [TaxId: 4577] [88763] (1)
                3. Escherichia coli [TaxId: 562] [89656] (7)
                4. Leishmania mexicana mexicana [TaxId: 44270] [117524] (1)
                   SQ Q8MPM3
             2. Pyruvate dehydrogenase E1 component, PP module [88764]
                E1A and E1B fused together in a single-chain protein
                1. Escherichia coli [TaxId: 562] [88765] (14)
          7. Branched-chain alpha-keto acid dehydrogenase PP module [88766] (5)
             parent family to TK and PFOR
             heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
             1. Branched-chain alpha-keto acid dehydrogenase, PP module [88767]
                1. Human (Homo sapiens) [TaxId: 9606] [88768] (23)
                   SQ P12694 52-445
                2. Thermus thermophilus [TaxId: 274] [102337] (4)
             2. E1-beta subunit of pyruvate dehydrogenase (PP module) [89651]
                1. Human (Homo sapiens) [TaxId: 9606] [89652] (3)
             3. 2-oxoisovalerate dehydrogenase (E1B), PP module [88769]
                chain A is alpha-subunit and chain B is beta-subunit
                1. Pseudomonas putida [TaxId: 303] [88770] (5)
             4. Pyruvate dehydrogenase E1-alpha, PdhA [117525]
                1. Bacillus stearothermophilus [TaxId: 1422] [117526] (2)
                   SQ P21873
          8. PFOR PP module [88771] (1)
             domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
             1. Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI [88772]
                1. Desulfovibrio africanus [TaxId: 873] [88773] (17)
   51. P-loop containing nucleoside triphosphate hydrolases [52539] (1)
       3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
       1. P-loop containing nucleoside triphosphate hydrolases [52540] (24)
          division into families based on beta-sheet topologies
          uperfamily
          1. Nucleotide and nucleoside kinases [52541] (46)
             parallel beta-sheet of 5 strands, order 23145
             1. Guanylate kinase [52542]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52543] (3)
                2. Mouse (Mus musculus) [TaxId: 10090] [82393] (1)
                3. Escherichia coli [TaxId: 562] [102338] (18)
                4. Mycobacterium tuberculosis [TaxId: 1773] [102339] (5)
                   Rv1389
             2. Guanylate kinase-like domain of Cask [69474]
                1. Human (Homo sapiens) [TaxId: 9606] [69475] (1)
             3. Guanylate kinase-like domain of Psd-95 [69476]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [69477] (3)
             4. Uridylate kinase [52544]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52545] (2)
             5. Deoxynucleoside monophosphate kinase [52546]
                contains insert 4-helical bundle subdomain, residues 35-145
                1. Bacteriophage T4 [TaxId: 10665] [52547] (2)
             6. Deoxyribonucleoside kinase [69478]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [69479] (37)
             7. Deoxycytidine kinase [89657]
                1. Human (Homo sapiens) [TaxId: 9606] [89658] (13)
             8. Deoxyguanosine kinase [69480]
                1. Human (Homo sapiens) [TaxId: 9606] [69481] (8)
             9. CMP kinase [52548]
                1. Escherichia coli [TaxId: 562] [52549] (6)
                2. Streptococcus pneumoniae [TaxId: 1313] [110525] (1)
                   SQ Q97PK6
             10. UMP/CMP kinase [52550]
                 1. Dictyostelium discoideum [TaxId: 44689] [52551] (6)
                 2. Human (Homo sapiens) [TaxId: 9606] [110526] (1)
                    SQ P30085
             11. Thymidine kinase [52552]
                 contains insert all-alpha subdomain, res. 251-322
                 1. Herpes simplex virus type 1, different strains [TaxId: 10298] [52553] (22)
                    SQ P03176 46-375
                 2. Equine herpesvirus type 4 [TaxId: 10331] [102340] (4)
                 3. Varicella-zoster virus [TaxId: 10335] [89659] (1)
             12. Adenylate kinase [52554]
                 1. Pig (Sus scrofa) [TaxId: 9823] [52555] (1)
                 2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [52556] (1)
                 3. Archaeon Methanococcus voltae [TaxId: 2188] [89660] (1)
                 4. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [89661] (1)
                 5. Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913] [52557] (1)
                    contains a rudiment "zinc-finger" subdomain, residue 125-161
                 6. Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913] [52558] (2)
                    contains a rudiment "zinc-finger" subdomain, residue 147-176
                 7. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52559] (4)
                    contains a rudiment "zinc-finger" subdomain, residue 131-168
                 8. Escherichia coli [TaxId: 562] [52560] (6)
                    contains a rudiment "zinc-finger" subdomain, residue 122-156
                 9. Maize (Zea mays) [TaxId: 4577] [52561] (1)
                 10. Bacillus stearothermophilus [TaxId: 1422] [52562] (3)
                     contains a zinc-finger subdomain, residues 126-160
                 11. Bacillus subtilis [TaxId: 1423] [102341] (1)
                     contains a zinc-finger subdomain, residues 126-160
                 12. Bacillus globisporus [TaxId: 1459] [102342] (1)
                     contains a zinc-finger subdomain, residues 126-160
                 13. Mycobacterium tuberculosis [TaxId: 1773] [102343] (2)
                     contains no zinc finger-like insertion
                 14. Human (Homo sapiens), isoenzyme 6 [TaxId: 9606] [117527] (1)
                     SQ Q9Y3D8
             13. Thymidylate kinase [52563]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52564] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [64010] (20)
                 3. Escherichia coli [TaxId: 562] [52565] (2)
                 4. Mycobacterium tuberculosis [TaxId: 1773] [69482] (13)
             14. Dephospho-CoA kinase [75187]
                 1. Haemophilus influenzae [TaxId: 727] [75188] (1)
                 2. Escherichia coli [TaxId: 562] [82394] (5)
                 3. Thermus thermophilus [TaxId: 274] [102344] (1)
                    TT1252
             15. Transcriptional regulator NadR, ribosylnicotinamide kinase domain [75189]
                 1. Haemophilus influenzae [TaxId: 727] [75190] (1)
             16. Polynucleotide kinase, kinase domain [75191]
                 1. Bacteriophage T4 [TaxId: 10665] [75192] (17)
             17. Guanylate kinase-like domain of the L-type calcium channel [110527]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110528] (4)
                    SQ P54288 234-451
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [110529] (3)
                    SQ P54287 38-362
             18. Probable kinase LmjF30.1890 [117528]
                 1. Leishmania major [TaxId: 5664] [117529] (1)
                    SQ Q4Q7A6
             19. Hypothetical protein YorR [142211]
                 1. Bacillus subtilis [TaxId: 1423] [142212] (2)
                    SQ O31896 2-165
             20. 5' polynucleotide kinase-3' phosphatase, C-terminal domain [142213]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142214] (2)
                    SQ Q9JLV6 351-522
          2. Shikimate kinase (AroK) [52566] (4)
             similar to the nucleotide/nucleoside kinases but acts on different substrate
             1. Shikimate kinase (AroK) [52567]
                1. Escherichia coli [TaxId: 562] [75193] (1)
                2. Erwinia chrysanthemi [TaxId: 556] [52568] (3)
                3. Mycobacterium tuberculosis [TaxId: 1773] [75194] (24)
                   SQ P95014
                4. Campylobacter jejuni [TaxId: 197] [102345] (1)
          3. Chloramphenicol phosphotransferase [52569] (1)
             similar to the nucleotide/nucleoside kinases but acts on different substrate
             1. Chloramphenicol phosphotransferase [52570]
                1. Streptomyces venezuelae [TaxId: 54571] [52571] (6)
          4. Gluconate kinase [75195] (1)
             similar to the nucleotide/nucleoside kinases
             1. Gluconate kinase [75196]
                1. Escherichia coli [TaxId: 562] [75197] (6)
          5. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82395] (1)
             similar to the nucleotide/nucleoside kinases; extra N- and C-terminal structures
             1. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82396]
                1. Streptococcus pyogenes [TaxId: 1314] [82397] (1)
          6. Adenosine-5'phosphosulfate kinase (APS kinase) [52572] (2)
             1. Adenosine-5'phosphosulfate kinase (APS kinase) [52573]
                1. Fungus (Penicillium chrysogenum) [TaxId: 5076] [52574] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [142215] (6)
                   SQ O43252 34-228
          7. ATP sulfurylase C-terminal domain [64011] (2)
             1. ATP sulfurylase C-terminal domain [64012]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64013] (7)
                2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [64014] (2)
          8. PAPS sulfotransferase [52575] (15)
             Pfam 00685
             similar to the nucleotide/nucleoside kinases but transfer sulphate group
             1. Estrogen sulfotransferase (STE, sult1e1) [52576]
                1. Mouse (Mus musculus) [TaxId: 10090] [52577] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [75198] (2)
             2. Hydroxysteroid sulfotransferase sult2a1 [52578]
                1. Human (Homo sapiens) [TaxId: 9606] [52579] (3)
             3. Aryl sulfotransferase sult1a [102346]
                1. Human (Homo sapiens) [TaxId: 9606] [102347] (3)
             4. Aryl sulfotransferase sult1a3 [52580]
                1. Human (Homo sapiens) [TaxId: 9606] [52581] (3)
             5. Pregnenolone sulfotransferase sult2b1a [102348]
                1. Human (Homo sapiens) [TaxId: 9606] [102349] (1)
                   cytosolic enzyme
             6. Cholesterol sulfotransferase sult2b1b [102350]
                1. Human (Homo sapiens) [TaxId: 9606] [102351] (3)
                   cytosolic enzyme
             7. Putative steroid sulfotransferase rarO47 [102352]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102353] (2)
             8. Heparan sulfate N-deacetylase/N-sulfotransferase domain [52582]
                1. Human (Homo sapiens) [TaxId: 9606] [52583] (1)
             9. Heparan sulfate 3-O-sulfotransferase [102354]
                1. Mouse (Mus musculus) [TaxId: 10090] [102355] (1)
                   SQ O35310 48-311
             10. Retinol dehydratase [64015]
                 1. Fall armyworm (Spodoptera frugiperda) [TaxId: 7108] [64016] (2)
             11. Stf0 sulfotransferase [110530]
                 1. Mycobacterium smegmatis [TaxId: 1772] [110531] (1)
                    SQ P84151
             12. Heparan sulfate glucosamine 3-O-sulfotransferase 3 [110532]
                 1. Human (Homo sapiens) [TaxId: 9606] [110533] (2)
                    SQ Q9Y663 139-406 # isoform 3A1; 100% sequence identity to isoform 3B1 domain (SQ Q9Y662 133-390)
             13. Thyroid hormone sulfotransferase Sult1b1 [117530]
                 1. Human (Homo sapiens) [TaxId: 9606] [117531] (1)
                    SQ O43704
             14. Sulfotransferase Sult1c2 [159556]
                 1. Human (Homo sapiens) [TaxId: 9606] [159557] (2)
                    SQ O00338 12-296
          9. Phosphoribulokinase/pantothenate kinase [52584] (5)
             1. Phosphoribulokinase [52585]
                1. Rhodobacter sphaeroides [TaxId: 1063] [52586] (1)
             2. Pantothenate kinase PanK [52587]
                has a circularly permuted fold compared to the phosphoribulokinase fold
                1. Escherichia coli [TaxId: 562] [52588] (3)
                   SQ P15044
             3. Hypothetical protein Ygr205W [102356]
                close structural similarity to PanK
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102357] (1)
             4. Hypothetical protein rbstp0775 [102358]
                structural similarity to PanK
                1. Bacillus stearothermophilus [TaxId: 1422] [102359] (1)
             5. Uridine-cytidine kinase 2 [102360]
                1. Human (Homo sapiens) [TaxId: 9606] [102361] (7)
          10. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52589] (2)
              1. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52590]
                 bifunctional enzyme
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [52591] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [82398] (1)
          11. G proteins [52592] (118)
              core: mixed beta-sheet of 6 strands, order 231456; strand 2 is antiparallel to the rest
              1. cH-p21 Ras protein [52593]
                 1. Human (Homo sapiens) [TaxId: 9606] [52594] (57)
                    SQ Q6P716
              2. Rac [52595]
                 1. Human (Homo sapiens) [TaxId: 9606] [52596] (23)
              3. Ras-related protein RalA [89662]
                 1. Human (Homo sapiens) [TaxId: 9606] [89663] (7)
                 2. Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490] [117532] (3)
                    SQ P63320 # 100% identical to the mouse and rat orthologs (SQ P63321 P63322)
              4. Rap1A [52597]
                 1. Human (Homo sapiens) [TaxId: 9606] [52598] (2)
              5. Rap2a [52599]
                 1. Human (Homo sapiens) [TaxId: 9606] [52600] (3)
              6. Rab3a [52601]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [52602] (2)
              7. Rab5a [82399]
                 1. Human (Homo sapiens) [TaxId: 9606] [82400] (11)
                    SQ P20339 18-182
              8. Rab5c [52603]
                 1. Mouse (Mus musculus) [TaxId: 10090] [52604] (4)
              9. Rab6 [52605]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [52606] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [142216] (1)
                    SQ P20340 13-176
              10. Rab11a [102362]
                  1. Human (Homo sapiens) [TaxId: 9606] [102363] (13)
                  2. Saccharomyces cerevisiae [TaxId: 4932] [159558] (4)
              11. Rab-related protein Sec4 [52607]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52608] (5)
              12. Rab-related protein ypt7p [75199]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75200] (2)
              13. Ran [52609]
                  1. Dog (Canis familiaris) [TaxId: 9615] [52610] (6)
                     SQ P62825
                  2. Human (Homo sapiens) [TaxId: 9606] [52611] (7)
              14. RhoA [52612]
                  1. Human (Homo sapiens) [TaxId: 9606] [52613] (14)
                     SQ P61586 2-181
              15. RhoE (RND3) [75201]
                  1. Mouse (Mus musculus) [TaxId: 10090] [75202] (2)
              16. ADP-ribosylation factor [52614]
                  1. Human (Homo sapiens), ARF1 [TaxId: 9606] [52615] (14)
                     SQ P32889
                  2. Rat (Rattus norvegicus), ARF1 [TaxId: 10116] [52616] (2)
                  3. Human (Homo sapiens), ARF6 [TaxId: 9606] [52617] (6)
                  4. Mouse (Mus musculus), ARL3 [TaxId: 10090] [52618] (2)
                  5. Mouse (Mus musculus), ARL2 [TaxId: 10090] [75203] (3)
                  6. Baker's yeast (Saccharomyces cerevisiae), ARF2 [TaxId: 4932] [82401] (1)
                  7. Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932] [82402] (1)
                  8. Human (Homo sapiens), ARL1 [TaxId: 9606] [102364] (2)
                  9. Human (Homo sapiens), ARF4 [TaxId: 9606] [142217] (2)
                     SQ P18085 3-177
                  10. Human (Homo sapiens), ARL5A [TaxId: 9606] [142218] (3)
                      SQ Q9Y689 2-178
                  11. Human (Homo sapiens), ARL8A [TaxId: 9606] [142219] (1)
                      SQ Q96BM9 18-181
                  12. Human (Homo sapiens) [TaxId: 9606] [142220] (1)
                      SQ P84085 6-179
                  13. Human (Homo sapiens), ARL5B [TaxId: 9606] [142221] (1)
                      SQ Q96KC2 6-173
                  14. Human(Homo sapiens), ARL8B [TaxId: 9606] [142222] (1)
                      SQ Q9NVJ2 18-182
              17. SAR1 [69483]
                  1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [69484] (3)
                  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82403] (2)
                  3. Human (Homo sapiens) [TaxId: 9606] [142223] (2)
                     SQ Q9NR31 13-198
              18. CDC42 [52619]
                  1. Human (Homo sapiens) [TaxId: 9606] [52620] (21)
                  2. Mus musculus [TaxId: 10090] [159559] (2)
              19. Ypt51 [52621]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52622] (1)
              20. Chloroplast protein translocon GTPase Toc34 [69485]
                  1. Garden pea (Pisum sativum) [TaxId: 3888] [69486] (1)
              21. Signal recognition particle receptor beta-subunit [89664]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89665] (1)
                  2. Mouse (Mus musculus) [TaxId: 10090] [142224] (2)
                     SQ P47758 63-269
              22. Transducin (alpha subunit) [52623]
                  common fold is interrupted with an all-alpha domain
                  1. Cow (Bos taurus) [TaxId: 9913] [52624] (15)
                     SQ P04896 39-388
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [52625] (33)
                     SQ P10824
                  3. Mouse (Mus musculus) [TaxId: 10090] [142225] (6)
                     SQ P21279 38-66,184-354! SQ P27600 53-81,204-370! SQ P27601 47-75,202-372
                  4. Homo sapiens [TaxId: 9606] [159560] (4)
              23. Elongation factor Tu (EF-Tu), N-terminal (G) domain [52626]
                  1. Escherichia coli [TaxId: 562] [52627] (10)
                     SQ P02990
                  2. Thermus aquaticus [TaxId: 271] [52628] (4)
                  3. Thermus thermophilus [TaxId: 274] [52629] (9)
                  4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [52630] (2)
                     SQ P49410 56-452
              24. Elongation factor eEF-1alpha, N-terminal (G) domain [52631]
                  eukaryotic and archaeal homologue of EF-Tu
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52632] (6)
                  2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69487] (2)
                     SQ P35021
              25. Elongation factor G (EF-G), N-terminal (G) domain [52633]
                  has internal nucleotide exchange factor built in as an insertion subdomain
                  1. Thermus thermophilus [TaxId: 274] [52634] (9)
                     residues 160-252 comprise insertion subdomain
                  2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142226] (2)
                     SQ Q5SI76 1-267
                     TTHA1498
              26. Elongation factor 2 (eEF-2), N-terminal (G) domain [82404]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82405] (22)
                     SQ P32324
              27. Initiation factor IF2/eIF5b, N-terminal (G) domain [52635]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52636] (3)
              28. Initiation factor eIF2 gamma subunit, N-terminal (G) domain [75204]
                  includes rubredoxin-like zinc finger insert domain, res. 56-83, similar that of the Nop10-like family (scop_fa 144211)
                  1. Archaeon Pyrococcus abyssi [TaxId: 29292] [75205] (5)
                  2. Archaeon Methanococcus jannaschii [TaxId: 2190] [102365] (1)
                  3. Sulfolobus solfataricus [TaxId: 2287] [142227] (6)
                     SQ Q980A5 2-206
              29. GTPase Era, N-terminal domain [52637]
                  1. Escherichia coli [TaxId: 562] [52638] (3)
                  2. Thermus thermophilus [TaxId: 274] [117533] (1)
                     SQ Q5SM23
              30. Probable tRNA modification GTPase TrmE (MnmE), G domain [102366]
                  1. Escherichia coli [TaxId: 562] [102367] (11)
              31. Probable GTPase Der, N-terminal and middle domains [82406]
                  member of EngA subfamily of GTPases; contains two G domains
                  1. Thermotoga maritima [TaxId: 2336] [82407] (1)
              32. Obg GTP-binding protein middle domain [82408]
                  1. Bacillus subtilis [TaxId: 1423] [82409] (1)
                  2. Thermus thermophilus [TaxId: 274] [102368] (1)
                     TT1381
              33. YchF GTP-binding protein N-terminal domain [82410]
                  Member of the Obg family of GTPases; contains an alpha-hairpin insert subdomain
                  1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82411] (1)
                  2. Haemophilus influenzae [TaxId: 727] [89666] (1)
                     HI0393
              34. Probable GTPase EngB [89667]
                  1. Escherichia coli [TaxId: 562] [89668] (1)
                  2. Bacillus subtilis [TaxId: 1423] [110534] (3)
                     SQ P38424
              35. Probable GTPase YlqF [89669]
                  naturally occurring circular permutation of G-domain; includes C-terminal all-alpha subdomain
                  1. Bacillus subtilis [TaxId: 1423] [89670] (1)
              36. Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain [52639]
                  1. Human (Homo sapiens) [TaxId: 9606] [52640] (2)
              37. Dynamin G domain [69488]
                  the family common core is decorated with large insertions
                  1. Dictyostelium discoideum [TaxId: 44689] [69489] (2)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [142228] (1)
                     SQ P21575 6-304
                     Dynamin-1
              38. Eukaryotic peptide chain release factor ERF2, G domain [110535]
                  1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110536] (3)
                     SQ O74718
              39. Rab9a [110537]
                  1. Dog (Canis familiaris) [TaxId: 9615] [110538] (1)
                     SQ P24408
                  2. Human (Homo sapiens) [TaxId: 9606] [110539] (1)
                     SQ P51151 2-175 # 100% sequence identity do the dog protein (SQ P24408 2-175)
                  3. Mouse (Mus musculus) [TaxId: 10090] [142229] (1)
                     SQ Q9R0M6 4-175
              40. Rab7 [110540]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [110541] (4)
                     SQ P09527
                  2. Human (Homo sapiens) [TaxId: 9606] [142230] (5)
                     SQ P51149 7-182
              41. Probable GTPase EngC (YjeQ), C-terminal domain [110542]
                  circularly permuted G-domain similar to B. sutilis YlqF; distinct extra C-terminal all-alpha subdomain
                  1. Thermotoga maritima [TaxId: 2336] [110543] (1)
                     SQ Q9X242 # TM1717
                  2. Bacillus subtilis [TaxId: 1423] [117534] (1)
                     SQ O34530
              42. GTPase Ytp1 [110544]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110545] (2)
                     SQ P01123
              43. Interferon-inducible GTPase [110546]
                  G domain is inserted in all-alpha domain
                  1. Mouse (Mus musculus) [TaxId: 10090] [110547] (5)
                     SQ Q9QZ85 # all-alpha domain (14-68,252-415)
              44. TrmE GTPase domain [117535]
                  1. Thermotoga maritima [TaxId: 2336] [117536] (2)
                     SQ Q9WYA4
              45. Elongation factor SelB, N-terminal domain [117537]
                  1. Methanococcus maripaludis [TaxId: 39152] [117538] (3)
                     SQ Q8J307
              46. Rab23 [142231]
                  1. Mouse (Mus musculus) [TaxId: 10090] [142232] (2)
                     SQ P35288 8-171
              47. Rab18 [142233]
                  1. Human (Homo sapiens) [TaxId: 9606] [142234] (1)
                     SQ Q9NP72 2-178
              48. Rab31 [142235]
                  1. Human (Homo sapiens) [TaxId: 9606] [142236] (1)
                     SQ Q13636 3-167
              49. Rab11b [142237]
                  1. Human (Homo sapiens) [TaxId: 9606] [142238] (2)
                     SQ Q15907 7-181
              50. Rab30 [142239]
                  1. Human (Homo sapiens) [TaxId: 9606] [142240] (1)
                     SQ Q15771 5-175
              51. Rab1a [142241]
                  1. Human (Homo sapiens) [TaxId: 9606] [142242] (1)
                     SQ P62820 7-175
              52. RhoB [142243]
                  1. Human (Homo sapiens) [TaxId: 9606] [142244] (1)
                     SQ P62745 4-185
              53. RhoC [142245]
                  1. Human (Homo sapiens) [TaxId: 9606] [142246] (2)
                     SQ P08134 1-179
              54. Rab4a [142247]
                  1. Human (Homo sapiens) [TaxId: 9606] [142248] (5)
                     SQ P20338 2-172! SQ P20338 4-172! SQ P20338 4-184
              55. Centaurin gamma 1, G domain [142249]
                  1. Human (Homo sapiens) [TaxId: 9606] [142250] (1)
                     SQ Q99490 402-576
              56. GTP-binding protein PH0525 [142251]
                  Member of the Obg family of GTPases; contains an alpha-hairpin insert subdomain
                  1. Pyrococcus horikoshii [TaxId: 53953] [142252] (1)
                     SQ O58261 1-319
              57. Rab-22a [142253]
                  1. Mouse (Mus musculus) [TaxId: 10090] [142254] (2)
                     SQ P35285 2-167! SQ P35285 2-168
              58. Rac3 [142255]
                  1. Human (Homo sapiens) [TaxId: 9606] [142256] (2)
                     SQ P60763 3-177
              59. GTP-binding protein engB [142257]
                  1. Pyrococcus horikoshii [TaxId: 53953] [142258] (3)
                     SQ O57939 28-211
                     PH0200
              60. Rab26 [142259]
                  1. Human (Homo sapiens) [TaxId: 9606] [142260] (1)
                     SQ Q9ULW5 58-227
              61. RhoQ [142261]
                  1. Human (Homo sapiens) [TaxId: 9606] [142262] (2)
                     SQ P17081 1-185
              62. Rab27b [142263]
                  1. Human (Homo sapiens) [TaxId: 9606] [142264] (2)
                     SQ O00194 4-189
              63. Rab2a [142265]
                  1. Human (Homo sapiens) [TaxId: 9606] [142266] (4)
                     SQ P61019 2-170
              64. di-Ras2 [142267]
                  1. Human (Homo sapiens) [TaxId: 9606] [142268] (2)
                     SQ Q96HU8 6-176
              65. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain [142269]
                  1. Pseudomonas syringae pv. tomato [TaxId: 323] [142270] (1)
                     SQ Q87WW1 16-237
              66. Rab14 [142271]
                  1. Human (Homo sapiens) [TaxId: 9606] [142272] (2)
                     SQ P61106 7-174
              67. r-Ras [142273]
                  1. Human (Homo sapiens) [TaxId: 9606] [142274] (1)
                     SQ P10301 24-196
              68. GTP-binding protein RheB [142275]
                  1. Human (Homo sapiens) [TaxId: 9606] [142276] (3)
                     SQ Q15382 3-169
              69. di-Ras1 [142277]
                  1. Human (Homo sapiens) [TaxId: 9606] [142278] (4)
                     SQ O95057 4-176
              70. Rab-33b [142279]
                  1. Mouse (Mus musculus) [TaxId: 10090] [142280] (2)
                     SQ O35963 32-196
              71. r-Ras2 [142281]
                  1. Human (Homo sapiens) [TaxId: 9606] [142282] (2)
                     SQ P62070 10-180
              72. Ras-related protein M-Ras (XRas) [142283]
                  1. Mouse (Mus musculus) [TaxId: 10090] [142284] (2)
                     SQ O08989 10-178
              73. Rab21 [142285]
                  1. Human (Homo sapiens) [TaxId: 9606] [142286] (10)
                     SQ Q9UL25 16-182
              74. Rab2b [142287]
                  1. Human (Homo sapiens) [TaxId: 9606] [142288] (1)
                     SQ Q8WUD1 4-176
              75. GTP-binding protein GEM [142289]
                  1. Human (Homo sapiens) [TaxId: 9606] [142290] (1)
                     SQ P55040 73-244
              76. Ras-like estrogen-regulated growth inhibitor, RERG [142291]
                  1. Human (Homo sapiens) [TaxId: 9606] [142292] (1)
                     SQ Q96A58 5-172
              77. Rab8a [142293]
                  1. Mouse (Mus musculus) [TaxId: 10090] [142294] (2)
                     SQ P55258 3-175
              78. Rad [142295]
                  1. Human (Homo sapiens) [TaxId: 9606] [142296] (2)
                     SQ P55042 91-258
          12. Motor proteins [52641] (15)
              1. Myosin S1, motor domain [52642]
                 common fold is interrupted with some all-alpha subdomains
                 1. Chicken (Gallus gallus), pectoral muscle [TaxId: 9031] [52643] (4)
                 2. Chicken (Gallus gallus), Va isoform [TaxId: 9031] [102369] (3)
                 3. Bay scallop (Aequipecten irradians) [TaxId: 31199] [52644] (11)
                    SQ P24733 3-836 ! SQ P24733 6-837
                 4. Dictyostelium discoideum [TaxId: 44689] [52645] (18)
                 5. Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689] [75206] (1)
                    lacks the SH3-like insert domain
              2. Kinesin [52646]
                 1. Human (Homo sapiens) [TaxId: 9606] [52647] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [52648] (2)
                 3. Mouse (Mus musculus), kif1a [TaxId: 10090] [64017] (12)
                    SQ P33173 3-355
                 4. Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606] [64018] (34)
                 5. Mouse (Mus musculus), kif2c [TaxId: 10090] [102370] (2)
                 6. Neurospora crassa [TaxId: 5141] [69490] (1)
                 7. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102371] (1)
              3. Kinesin motor Ncd (non-claret disjunctional) [52649]
                 contains coiled-coil neck
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [52650] (3)
                 2. Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932] [52651] (5)
                    kinesin-like protein
              4. Kinesin heavy chain-like protein [110548]
                 1. Potato (Solanum tuberosum) [TaxId: 4113] [110549] (5)
                    SQ Q41460 884-1252
          13. Nitrogenase iron protein-like [52652] (29)
              core: parallel beta-sheet of 7 strands; order 3241567
              1. Dethiobiotin synthetase [52653]
                 1. Escherichia coli [TaxId: 562] [52654] (13)
              2. Adenylosuccinate synthetase, PurA [52655]
                 common fold is interrupted by an all-alpha subdomain, residues 100-200
                 1. Escherichia coli [TaxId: 562] [52656] (24)
                 2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52657] (1)
                 3. Bread wheat (Triticum aestivum) [TaxId: 4565] [52658] (1)
                 4. Mouse (Mus musculus) [TaxId: 10090] [69491] (9)
                 5. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102372] (1)
              3. Formyltetrahydrofolate synthetase [52659]
                 modified P-loop; there are many insertions in the common fold
                 1. Moorella thermoacetica [TaxId: 1525] [52660] (3)
              4. Nitrogenase iron protein [52661]
                 1. Azotobacter vinelandii [TaxId: 354] [52662] (19)
                 2. Clostridium pasteurianum [TaxId: 1501] [52663] (1)
              5. Cell division regulator MinD [64019]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64020] (1)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [64021] (2)
                 3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [64022] (1)
              6. GTPase domain of the signal sequence recognition protein Ffh [52664]
                 1. Thermus aquaticus [TaxId: 271] [52665] (25)
                 2. Archaeon Acidianus ambivalens [TaxId: 2283] [64023] (2)
                 3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [102373] (2)
              7. GTPase domain of the signal recognition particle receptor FtsY [52666]
                 1. Escherichia coli [TaxId: 562] [52667] (2)
                 2. Thermus aquaticus [TaxId: 271] [102374] (8)
                 3. Thermotoga maritima [TaxId: 2336] [110550] (1)
                    SQ Q9WZ40
              8. Arsenite-translocating ATPase ArsA [52668]
                 Duplication: consists of two domains of this fold arranged as the NIP subunits in the dimer
                 1. Escherichia coli [TaxId: 562] [52669] (4)
              9. Hypothetical protein YjiA, N-terminal domain [89671]
                 homologue of the cobalamin biosynthesis protein CobW
                 1. Escherichia coli [TaxId: 562] [89672] (1)
              10. Molybdopterin-guanine dinucleotide biosynthesis protein MobB [89673]
                  forms segment-swapped dimer
                  1. Escherichia coli [TaxId: 562] [89674] (2)
                  2. Bacillus stearothermophilus [TaxId: 1422] [117539] (1)
                     SQ Q5L1X2 # 91% sequence identity
              11. CTP synthase PyrG, N-terminal domain [110551]
                  1. Escherichia coli [TaxId: 562] [110552] (1)
                     SQ P08398
                  2. Thermus thermophilus [TaxId: 274] [110553] (3)
                     SQ Q5SIA8
                  3. Human (Homo sapiens) [TaxId: 9606] [159561] (2)
                     SQ Q5VW67 1-273
              12. ATP(GTP)-binding protein PAB0955 [142297]
                  PYRAB14380; belongs to Pfam 03029
                  1. Pyrococcus abyssi [TaxId: 29292] [142298] (9)
                     SQ Q9UYR9 30-273
              13. Hypothetical protein TM0796 [142299]
                  member of Pfam 07755; DUF1611; contains extra N-terminal alpha/beta fold of Rossmann-fold topology, parallel beta-sheet, strand order 312456
                  1. Thermotoga maritima [TaxId: 2336] [142300] (2)
                     SQ Q9WZQ3 1-338
              14. LAO/AO transport system kinase ArgK [159562]
                  member of Pfam 03308; contains extra N-terminal 3-helical bundle and extra C-terminal helical dimerisation domain
                  1. Escherichia coli [TaxId: 562] [159563] (1)
                     SQ P27254 1-327
              15. Metallochaperone MeaB [159564]
                  ArgK-like (sub)family; Pfam 03308
                  1. Methylobacterium extorquens [TaxId: 408] [159565] (4)
                     SQ Q8RPA0 5-327
          14. RecA protein-like (ATPase-domain) [52670] (29)
              core: mixed beta-sheet of 8 strands, order 32451678; strand 7 is antiparallel to the rest
              1. RecA protein, ATPase-domain [52671]
                 C-terminal domain is alpha+beta
                 1. Escherichia coli [TaxId: 562] [52672] (7)
                    SQ P0A7G6 P03017
                 2. Mycobacterium tuberculosis [TaxId: 1773] [52673] (6)
                 3. Mycobacterium smegmatis [TaxId: 1772] [89675] (4)
                 4. Deinococcus radiodurans [TaxId: 1299] [117540] (1)
                    SQ P42443 15-341
              2. Gene 4 protein (g4p, DNA primase), helicase domain [52674]
                 1. Bacteriophage T7 [TaxId: 10760] [52675] (7)
              3. Hexameric replicative helicase repA [52676]
                 1. Escherichia coli [TaxId: 562] [52677] (3)
              4. Bacterial conjugative coupling protein TrwB [69492]
                 1. Escherichia coli [TaxId: 562] [69493] (5)
              5. Hexameric traffic ATPase, HP0525 [52719]
                 type II/IV secretion system protein; includes N-terminal alpha+beta domain of a profilin-like topology
                 1. Helicobacter pylori [TaxId: 210] [52720] (6)
              6. Extracellular secretion NTPase EpsE [102375]
                 type II/IV secretion system protein; overall structure is similar to HP0525
                 1. Vibrio cholerae [TaxId: 666] [102376] (2)
              7. DNA repair protein Rad51, catalytic domain [82412]
                 1. Human (Homo sapiens) [TaxId: 9606] [82413] (1)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102377] (1)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110554] (1)
                    SQ P25454 81-395
                 4. Archaeon Methanococcus voltae [TaxId: 2188] [110555] (8)
                    SQ O73948
              8. Central domain of alpha subunit of F1 ATP synthase [88774]
                 1. Cow (Bos taurus) [TaxId: 9913] [88775] (18)
                    SQ P19483
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [88776] (2)
                 3. Bacillus sp., strain ps3 [TaxId: 1409] [88777] (1)
                 4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88778] (2)
              9. Central domain of beta subunit of F1 ATP synthase [88779]
                 1. Cow (Bos taurus) [TaxId: 9913] [88780] (12)
                    SQ P00829
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [88781] (8)
                 3. Bacillus sp., strain ps3 [TaxId: 1409] [88782] (1)
                 4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88783] (2)
              10. Transcription termination factor Rho, ATPase domain [89676]
                  1. Escherichia coli [TaxId: 562] [89677] (10)
                     SQ P03002
              11. Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU [52682]
                  lacks the last strand 8
                  1. Salmonella typhimurium [TaxId: 90371] [52683] (2)
              12. ATP:corrinoid adenosyltransferase CobA [52684]
                  lacks the two last strands
                  1. Salmonella typhimurium [TaxId: 90371] [52685] (3)
              13. Meiotic recombination protein DMC1/LIM15 homolog [110556]
                  1. Human (Homo sapiens) [TaxId: 9606] [110557] (1)
                     SQ Q14565
              14. Circadian clock protein KaiC [110558]
                  duplication: contains two copies of this domain
                  1. Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140] [110559] (25)
                     SQ Q79PF4 14-497
              15. NTPase P4 [117541]
                  contains extra N-terminal subdomain (~100 residues): [contains pseudo beta-barrel]
                  1. Bacteriophage phi-12 [TaxId: 161736] [117542] (8)
                     SQ Q94M05
              16. Hypothetical kinase-like protein Aq_1292 [142301]
                  member of Pfam 03266 (DUF265)
                  1. Aquifex aeolicus [TaxId: 63363] [142302] (1)
                     SQ O67322 1-178
              17. Cancer-related NTPase, C1orf57 [159566]
                  member of Pfam 03266; DUF265
                  1. Human (Homo sapiens) [TaxId: 9606] [159567] (1)
                     SQ Q5TDE9 2-190
          15. Bacterial cell division inhibitor SulA [89678] (1)
              homologous to RecA but lacks its P-loop motif; the fold is C-terminally truncated; 5-stranded parallel beta-sheet, order: 15423
              1. Hypothetical protein PA3008 [89679]
                 1. Pseudomonas aeruginosa [TaxId: 287] [89680] (2)
          16. ABC transporter ATPase domain-like [52686] (29)
              there are two additional subdomains inserted into the central core that has a RecA-like topology
              1. ATP-binding subunit of the histidine permease [52687]
                 1. Salmonella typhimurium [TaxId: 90371] [52688] (1)
              2. Branched chain aminoacid ABC transporter [75207]
                 1. Thermotoga maritima, TM1139 [TaxId: 2336] [75208] (1)
              3. MJ1267 [64025]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64026] (3)
              4. MJ0796 [64027]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64028] (2)
              5. Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain [102378]
                 1. Mouse (Mus musculus) [TaxId: 10090] [102379] (8)
                    SQ P26361 390-670
                 2. Human (Homo sapiens) [TaxId: 9606] [117543] (2)
                    SQ P13569 389-671
              6. Peptide transporter Tap1, C-terminal ABC domain [64029]
                 1. Human (Homo sapiens) [TaxId: 9606] [64030] (1)
              7. Maltose transport protein MalK, N-terminal domain [52689]
                 1. Archaeon Thermococcus litoralis [TaxId: 2265] [52690] (1)
                 2. Escherichia coli [TaxId: 562] [102380] (13)
              8. Glucose transport protein GlcV, N-terminal domain [89681]
                 1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89682] (5)
              9. ABC transporter involved in vitamin B12 uptake, BtuD [75209]
                 1. Escherichia coli [TaxId: 562] [75210] (1)
              10. Haemolysin B ATP-binding protein [89683]
                  1. Escherichia coli [TaxId: 562] [89684] (3)
              11. Multidrug resistance ABC transporter MsbA, C-terminal domain [89685]
                  a low-resolution structure of the E. coli MsbA in an open conformation is also available (f.35.1.1)
                  1. Vibrio cholerae [TaxId: 666] [89686] (1)
                  2. Salmonella typhimurium [TaxId: 90371] [159568] (12)
                     SQ P63359 329-581
              12. Multidrug resistance ABC transporter LmrA, C-terminal domain [102381]
                  1. Lactococcus lactis [TaxId: 1358] [102382] (1)
              13. Rad50 [52691]
                  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [52692] (4)
              14. Smc head domain [52693]
                  1. Thermotoga maritima [TaxId: 2336] [52694] (1)
                  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117544] (1)
                     SQ P32908 2-214,1024-1223
                  3. Pyrococcus furiosus [TaxId: 2261] [117545] (2)
                     SQ Q877I1 1-167,1012-1173
              15. Cell division protein MukB [52695]
                  1. Escherichia coli [TaxId: 562] [52696] (1)
              16. DNA repair protein MutS, the C-terminal domain [52697]
                  1. Thermus aquaticus [TaxId: 271] [52698] (4)
                  2. Escherichia coli [TaxId: 562] [52699] (10)
                     SQ P23909 2-800
              17. Putative ABC transporter PF0895 [110560]
                  1. Pyrococcus furiosus [TaxId: 2261] [110561] (1)
                     SQ Q8U2E3
              18. Hypothetical protein PH0022, N-terminal domain [117546]
                  1. Pyrococcus horikoshii [TaxId: 53953] [117547] (2)
                     SQ O57758
              19. Putative ABC transporter TM0544 [117548]
                  1. Thermotoga maritima [TaxId: 2336] [117549] (1)
                     SQ Q9WZ14
              20. Putative multidrug export ATP-binding/permease protein SAV1866 [142303]
                  1. Staphylococcus aureus [TaxId: 1280] [142304] (4)
                     SQ Q99T13 324-578
              21. Molybdate/tungstate import ATP-binding protein WtpC (ModC) [159569]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [159570] (4)
                     SQ O30144 1-240
              22. Methionine import ATP-binding protein MetN [159571]
                  1. Escherichia coli [TaxId: 562] [159572] (4)
                     SQ P30750 1-240
              23. Sulfate/molybdate ABC transporter, ATP-binding protein [159573]
                  1. Methanosarcina acetivorans [TaxId: 2214] [159574] (2)
                     SQ Q8TTZ3 1-229
          17. Tandem AAA-ATPase domain [81268] (27)
              duplication: tandem repeat of two RecA-like (AAA) domains
              1. DEXX box DNA helicase [52701]
                 each AAA domain contains an all-alpha insert subdomain
                 1. Bacillus stearothermophilus, PcrA [TaxId: 1422] [52702] (5)
                 2. Escherichia coli, RepD [TaxId: 562] [52703] (1)
              2. Putative DEAD box RNA helicase [52704]
                 homologous to eIF4a and UvrB
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52705] (1)
              3. Probable DEAD box RNA helicase YqfR [102383]
                 1. Bacillus stearothermophilus [TaxId: 1422] [102384] (1)
              4. RecQ helicase domain [102385]
                 1. Escherichia coli [TaxId: 562] [102386] (2)
              5. DEAD box RNA helicase rck/p54 [102387]
                 1. Human (Homo sapiens) [TaxId: 9606] [102388] (1)
              6. RecG helicase domain [69494]
                 1. Thermotoga maritima [TaxId: 2336] [69495] (1)
              7. Initiation factor 4a [52706]
                 homologous to UvrB
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52707] (5)
                 2. Human (Homo sapiens) [TaxId: 9606] [142305] (2)
                    SQ P60842 21-238
                    4A-I
              8. Nucleotide excision repair enzyme UvrB [52708]
                 contains large insertions in the first AAA domain
                 1. Thermus thermophilus [TaxId: 274] [52709] (2)
                 2. Bacillus caldotenax [TaxId: 1395] [52710] (7)
                    SQ P56981
              9. Translocation ATPase SecA, nucleotide-binding domains [82414]
                 a pre-protein crosslinking domain inserted in the first AAA domain
                 1. Bacillus subtilis [TaxId: 1423] [82415] (4)
                    SQ P28366
                 2. Mycobacterium tuberculosis [TaxId: 1773] [89687] (2)
              10. Spliceosome RNA helicase BAT1 (UAP56) [110562]
                  1. Human (Homo sapiens) [TaxId: 9606] [110563] (5)
                     SQ Q13838 45-428
              11. Exodeoxyribonuclease V beta chain (RecB), N-terminal domain [117550]
                  each AAA domain contains an all-alpha insert subdomain
                  1. Escherichia coli [TaxId: 562] [117551] (1)
                     SQ P08394
              12. Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain [117552]
                  each AAA domain contains an all-alpha insert subdomain
                  1. Escherichia coli [TaxId: 562] [117553] (1)
                     SQ P07648
              13. Exodeoxyribonuclease V alpha chain (RecD) [117554]
                  contains extra N-terminal alpha+beta (sub)domain (~100 residues)
                  1. Escherichia coli [TaxId: 562] [117555] (1)
                     SQ P04993
              14. putative ATP-dependent RNA helicase VlgB [142306]
                  1. Flatworm (Dugesia japonica) [TaxId: 6161] [142307] (2)
                     SQ O97032 164-401
              15. putative ATP-dependent RNA helicase PF2015 [142308]
                  separate structures of other domains are known: the middle nuclease domain (scop_sp 89718) and the C-terminal RuvA-like HhH domain (PDB 1x2i)
                  1. Pyrococcus furiosus [TaxId: 2261] [142309] (2)
                     SQ Q8TZH8 2-201! SQ Q8TZH8 202-487
              16. ATP-dependent RNA helicase DDX25 [142310]
                  1. Human (Homo sapiens) [TaxId: 9606] [142311] (4)
                     SQ Q9UHL0 307-474
              17. Helicase of the SNF2/Rad54 hamily [142312]
                  1. Sulfolobus solfataricus [TaxId: 2287] [142313] (8)
                     SQ Q97XQ7 432-661! SQ Q97XQ7 662-802! SQ Q97XQ7 663-802
              18. Probable ATP-dependent RNA helicase DDX48 [142314]
                  Eukaryotic translation initiation factor 4A isoform 3
                  1. Human (Homo sapiens) [TaxId: 9606] [142315] (10)
                     SQ P38919 22-243! SQ P38919 244-411
              19. Rad54-like, Rad54L [142316]
                  1. Zebra fish (Danio rerio) [TaxId: 7955] [142317] (2)
                     SQ Q7ZV09 390-735! SQ Q7ZV09 92-389
              20. DNA repair protein RAD25 [142318]
                  shares with the DNA helicase UvsW (scop_fa 102396) extra N-terminal alpha+beta subdomain that might be related to the DNA repair protein MutS domain I (scop_sf 55271)
                  1. Archaeoglobus fulgidus [TaxId: 2234] [142319] (10)
                     SQ O29889 237-436! SQ O29889 238-434! SQ O29889 3-236! SQ O29889 4-209
              21. Transcription-repair coupling factor, TRCF [142320]
                  similar to UvrB in the N-terminal part and DEAD helicases in the C-terminal part; also contains CarD-like domain in the middle and TRCF domain at the C-terminus
                  1. Escherichia coli [TaxId: 562] [142321] (10)
                     SQ P30958 2-348! SQ P30958 26-333! SQ P30958 349-465! SQ P30958 546-778! SQ P30958 779-989
              22. Putative ATP-dependent RNA helicase DHH1 [142322]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142323] (2)
                     SQ P39517 252-422! SQ P39517 46-251
              23. Hel308 helicase [159575]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [159576] (4)
          18. Extended AAA-ATPase domain [81269] (34)
              fold is similar to that of RecA, but lacks the last two strands, followed by a family-specific Arg-finger domain
              1. gamma subunit of DNA polymerase III, N-domain [64031]
                 1. Escherichia coli [TaxId: 562] [64032] (3)
                    SQ P06710 5-368
                 2. Thermotoga maritima [TaxId: 2336] [142324] (1)
                    SQ Q9WZM9 11-208
              2. delta prime subunit of DNA polymerase III, N-domain [52711]
                 contains additional alpha-helical domain after the family specific domains
                 1. Escherichia coli [TaxId: 562] [52712] (6)
                    SQ P28631
              3. delta subunit of DNA polymerase III, N-domain [64033]
                 1. Escherichia coli [TaxId: 562] [64034] (5)
                    SQ P28630
              4. Replication factor C [64035]
                 contains additional alpha-helical domain after the family specific domains
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64036] (1)
              5. Chromosomal replication initiation factor DnaA [82416]
                 contains TrpR-like DNA-binding domain after the family specific domains
                 1. Aquifex aeolicus [TaxId: 63363] [82417] (5)
              6. Holliday junction helicase RuvB [52713]
                 contains "winged helix" DNA-binding domain after the family specific domains
                 1. Thermus thermophilus [TaxId: 274] [52714] (3)
                 2. Thermotoga maritima [TaxId: 2336] [64037] (6)
              7. Transcriptional activator sigm54 (NtrC1), C-terminal domain [102389]
                 1. Aquifex aeolicus [TaxId: 63363] [102390] (2)
              8. CDC6, N-domain [52715]
                 contains "winged helix" DNA-binding domain after the family specific domains
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [52716] (1)
              9. Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein [52717]
                 1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [52718] (2)
              10. Membrane fusion ATPase VCP/p97 [64038]
                  1. Mouse (Mus musculus) [TaxId: 10090] [64039] (4)
              11. AAA domain of cell division protein FtsH [82418]
                  ATP-dependent protease
                  1. Escherichia coli [TaxId: 562] [82419] (1)
                  2. Thermus thermophilus [TaxId: 274] [82420] (4)
                  3. Thermotoga maritima [TaxId: 2336] [142325] (12)
                     SQ Q9WZ49 150-402
              12. HslU [52721]
                  ATPase subunit of ATP-dependent protease
                  1. Escherichia coli [TaxId: 562] [52722] (10)
                  2. Haemophilus influenzae [TaxId: 727] [52723] (6)
              13. ClpX [102391]
                  ATPase subunit of ATP-dependent protease
                  1. Helicobacter pylori [TaxId: 210] [102392] (1)
              14. ATPase domain of protease Lon (La) [102393]
                  1. Escherichia coli [TaxId: 562] [102394] (1)
              15. ClpA, an Hsp100 chaperone, AAA+ modules [82421]
                  duplication: two AAA+ modules; the first module is structurally similar to the CDC6 module whereas the second module to the HslU module
                  1. Escherichia coli [TaxId: 562] [82422] (2)
                     SQ Q83LR6
              16. ClpB, AAA+ modules [75211]
                  ATPase subunit of ATP-dependent protease; similar domain organization to ClpA
                  1. Thermus thermophilus [TaxId: 274] [102395] (1)
                  2. Escherichia coli [TaxId: 562] [75212] (1)
              17. ATPase subunit of magnesium chelatase, BchI [64040]
                  1. Rhodobacter capsulatus [TaxId: 1061] [64041] (1)
              18. Papillomavirus large T antigen helicase domain [89688]
                  1. Simian virus 40 [TaxId: 10633] [89689] (16)
                     SQ P03070 265-627
              19. Rep 40 protein helicase domain [110564]
                  1. Adeno-associated virus 2, AAV2 [TaxId: 10804] [110565] (2)
                     SQ P03132 225-490
              20. Replication factor C1 [110566]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110567] (1)
                     SQ P38630 295-696
              21. Replication factor C4 [110568]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110569] (1)
                     SQ P40339
              22. Replication factor C3 [110570]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110571] (1)
                     SQ P38629
              23. Replication factor C2 [110572]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110573] (1)
                     SQ P40348
              24. Replication factor C5 [110574]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110575] (1)
                     SQ P38251
              25. Replication protein E1 helicase domain [110576]
                  1. Human papillomavirus type 18 [TaxId: 333761] [110577] (1)
                     SQ P06789 428-629 # structure of the origin-binding domain (210-354) is also known, 1r9w (scop_sp 103119)
              26. CDC6-like protein APE0152, N-terminal domain [117556]
                  1. Aeropyrum pernix [TaxId: 56636] [117557] (2)
                     SQ Q9YFU8
              27. Archaeal ATPase SSO1545 [142326]
                  member of Pfam 01637 family; overall structural similarity to the archael CDC6-like protein APE0102
                  1. Sulfolobus solfataricus [TaxId: 2287] [142327] (2)
                     SQ Q97Y08 1-283
              28. CED-4, NB-ARC domain [159577]
                  belongs to Pfam 00931
                  1. Caenorhabditis elegans [TaxId: 6239] [159578] (1)
                     SQ P30429 109-385
          19. RNA helicase [52724] (3)
              duplication: consists of two similar domains, one binds NTP and the other binds RNA; also contains an all-alpha subdomain in the C-terminal extension
              1. HCV helicase domain [52725]
                 1. Human hepatitis C virus (HCV), different isolates [TaxId: 11103] [52726] (6)
              2. Dengue virus helicase [142328]
                 1. Dengue virus type 2 [TaxId: 11060] [142329] (8)
                    SQ Q91H74 1653-1957! SQ Q91H74 1958-2093
              3. YFV helicase domain [142330]
                 1. Yellow fever virus [TaxId: 11089] [142331] (2)
                    SQ P19901 1669-1842! SQ P19901 1843-2107
          20. Helicase-like "domain" of reverse gyrase [69496] (1)
              1. Helicase-like "domain" of reverse gyrase [69497]
                 contains a mobile insertion of LEM/SAP-like HeH motif, residues 354-423
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69498] (2)
          21. DNA helicase UvsW [102396] (1)
              contains extra N-terminal alpha+beta subdomain
              1. DNA helicase UvsW [102397]
                 1. Bacteriophage T4 [TaxId: 10665] [102398] (1)
          22. YjeE-like [75213] (1)
              mixed beta-sheet; order 234156(0), strands 2 and 6 are antiparallel to the rest
              1. Hypothetical protein HI0065 [75214]
                 1. Haemophilus influenzae [TaxId: 727] [75215] (2)
          23. Type II thymidine kinase [117558] (3)
              N-terminal part of Pfam 00265; parallel beta-sheet of 6 strands, order 324516; topological similarity to the RecA-like proteins, especially CobA (scop_pr 52684)
              1. Thymidine kinase, TK1, N-terminal domain [117559]
                 1. Human (Homo sapiens) [TaxId: 9606] [117560] (3)
                    SQ P04183 18-191
                 2. Ureaplasma urealyticum [TaxId: 2130] [117561] (8)
                    SQ Q9PPP5 11-211
                 3. Clostridium acetobutylicum [TaxId: 1488] [117562] (1)
                    SQ Q97F65
          24. Atu3015-like [142332] (2)
              unknown function; similar to the nucleotide/nucleoside kinases
              1. Hypothetical protein BH3686 [142333]
                 annotated as putative gluconate kinase by NESG
                 1. Bacillus halodurans [TaxId: 86665] [142334] (1)
                    SQ Q9K6P2 1-176
              2. Hypothetical protein Atu3015 [142335]
                 1. Agrobacterium tumefaciens [TaxId: 358] [142336] (1)
                    SQ Q8UBK1 6-181
   52. PTS IIb component [52727] (1)
       3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
       1. PTS IIb component [52728] (1)
          uperfamily
          1. PTS IIb component [52729] (2)
             1. Fructose permease, subunit IIb [52730]
                1. Bacillus subtilis [TaxId: 1423] [52731] (1)
             2. Sorbose permease subunit IIb , EIIb-sor [89690]
                1. Klebsiella pneumoniae [TaxId: 573] [89691] (1)
   53. DNA polymerase III chi subunit [102399] (1)
       3 layers, a/b/a; parallel beta-sheet of 7 strands, order 7165243
       1. DNA polymerase III chi subunit [102400] (1)
          structural similarity and possible evolutionary relationship to the AAA domain; lacks the P-loop motif
          uperfamily
          1. DNA polymerase III chi subunit [102401] (1)
             1. DNA polymerase III chi subunit [102402]
                1. Escherichia coli [TaxId: 562] [102403] (1)
   54. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1)
       3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
       1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52733] (1)
          uperfamily
          1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52734] (2)
             1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52735]
                1. Salmonella typhimurium [TaxId: 90371] [52736] (28)
                2. Thermus thermophilus [TaxId: 274] [82423] (1)
   55. CofD-like [142337] (1)
       3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (scop_cf 52732)
       1. CofD-like [142338] (1)
          uperfamily
          1. CofD-like [142339] (2)
             Pfam 01933; UPF0052
             1. LPPG:FO 2-phospho-L-lactate transferase CofD [142340]
                1. Methanosarcina mazei [TaxId: 2209] [142341] (1)
                   SQ Q8PVT6 1-309
             2. Hypothetical protein BH3568 [142342]
                1. Bacillus halodurans [TaxId: 86665] [142343] (4)
                   SQ Q9K706 2-312
   56. MCP/YpsA-like [102404] (1)
       3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567
       1. MCP/YpsA-like [102405] (2)
          uperfamily
          1. MoCo carrier protein-like [102406] (6)
             Pfam 03641
             1. Hypothetical protein TM1055 [102407]
                1. Thermotoga maritima [TaxId: 2336] [102408] (1)
                   structural genomics; NESG target VT76
             2. Hypothetical protein YvdD [102409]
                1. Bacillus subtilis [TaxId: 1423] [102410] (1)
             3. Hypothetical protein TT1887 (TTHA0294) [117563]
                1. Thermus thermophilus [TaxId: 274] [117564] (1)
                   SQ Q5SLJ9
             4. Hypothetical protein TT1465 (TTHA1644) [117565]
                1. Thermus thermophilus [TaxId: 274] [117566] (1)
                   SQ Q5SHT6
             5. Hypothetical protein At5g11950 [117567]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117568] (3)
                   SQ Q84MC2
             6. Hypothetical protein At2g37210/T2N18.3 [142344]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142345] (4)
                   SQ Q8L8B8 8-190
          2. YpsA-like [159579] (1)
             Pfam 06908; DUF1273; lacking the last strand 7; different set of conserved residues in the putative active site than in the MoCo carrier protein-like family
             1. Hypothetical protein YpsA [159580]
                1. Bacillus subtilis [TaxId: 1423] [159581] (1)
                   SQ P50838 1-177
   57. Methylesterase CheB, C-terminal domain [52737] (1)
       3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
       1. Methylesterase CheB, C-terminal domain [52738] (1)
          uperfamily
          1. Methylesterase CheB, C-terminal domain [52739] (1)
             1. Methylesterase CheB, C-terminal domain [52740]
                1. Salmonella typhimurium [TaxId: 90371] [52741] (2)
   58. Subtilisin-like [52742] (1)
       3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
       1. Subtilisin-like [52743] (2)
          uperfamily
          1. Subtilases [52744] (18)
             1. Subtilisin [52745]
                1. Bacillus subtilis, carlsberg [TaxId: 1423] [52746] (6)
                2. Bacillus subtilis, E [TaxId: 1423] [52747] (1)
                3. Bacillus licheniformis [TaxId: 1402] [52748] (17)
                4. Bacillus lentus, savinase (TM) [TaxId: 1467] [52749] (2)
                   SQ P29600
                5. Bacillus lentus [TaxId: 1467] [52750] (11)
                6. Bacillus amyloliquefaciens, Novo/BPN' [TaxId: 1390] [52751] (52)
                   SQ P00782 108-382
             2. Messentericopeptidase [52752]
                1. Bacillus mesentericus [TaxId: 1408] [52753] (1)
             3. M-proteinase [52754]
                1. Bacillus sp., strain ksm-k16 [TaxId: 1409] [52755] (2)
                   SQ Q99405 112-380
             4. Serine protease PB92 (subtilisin PB92) [52756]
                1. Bacillus alcalophilus [TaxId: 1445] [52757] (2)
                   identical sequence to Bacillus lentus, TaxId: 1467
             5. Thermostable serine protease [52758]
                1. Bacillus sp., AK.1 [TaxId: 1409] [52759] (1)
             6. Sphericase [75224]
                1. Bacillus sphaericus [TaxId: 1421] [75225] (3)
             7. Thermitase [52760]
                1. Thermoactinomyces vulgaris [TaxId: 2026] [52761] (4)
             8. Proteinase K [52762]
                1. Fungus (Tritirachium album), strain limber [TaxId: 37998] [52763] (28)
                   SQ P06873
             9. Kexin, N-terminal domain [89692]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89693] (4)
             10. Furin, N-terminal domain [89694]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89695] (1)
             11. Alkaline serine protease kp-43, N-terminal domain [110578]
                 1. Bacillus sp. KSM-KP43 [TaxId: 109322] [110579] (3)
                    SQ Q93UV9 207-640
             12. Fervidolysin [117569]
                 1. Fervidobacterium pennivorans [TaxId: 93466] [117570] (1)
                    SQ Q93LQ6
             13. Alkaline serine protease Apa1 [117571]
                 1. Pseudoalteromonas sp. AS-11 [TaxId: 247492] [117572] (1)
                    SQ Q65Z69 145-579
          2. Serine-carboxyl proteinase, SCP [52764] (3)
             elaborated with additional structures
             1. Serine-carboxyl proteinase, SCP [52765]
                1. Pseudomonas sp., sedolisin [TaxId: 306] [52766] (9)
                2. Bacillus novosp. MN-32, kumamolisin [TaxId: 198803] [75226] (7)
                   SQ Q8RR56 ! SQ Q8RR56
                3. Alicyclobacillus sendaiensis, kumamolisin-as [TaxId: 192387] [102411] (3)
                   SQ Q8GB88
   59. Indigoidine synthase A-like [110580] (1)
       core: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756
       1. Indigoidine synthase A-like [110581] (1)
          uperfamily
          1. Indigoidine synthase A-like [110582] (1)
             Pfam 04227
             1. Hypothetical protein TM1464 [110583]
                1. Thermotoga maritima [TaxId: 2336] [110584] (1)
                   SQ Q9X1H5
   60. Arginase/deacetylase [52767] (1)
       3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
       1. Arginase/deacetylase [52768] (2)
          uperfamily
          1. Arginase-like amidino hydrolases [52769] (8)
             Pfam 00491
             1. Arginase [52770]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52771] (51)
                   SQ P07824
                2. Human (Homo sapiens), isoform II, mitochondrial [TaxId: 9606] [102412] (1)
                3. Bacillus caldovelox [TaxId: 33931] [52772] (5)
                4. Human (Homo sapiens) [TaxId: 9606] [142346] (16)
                   SQ P05089 5-313
                5. Trypanosoma cruzi [TaxId: 5693] [142347] (1)
                   SQ Q4DSA0 5-302
             2. Proclavaminate amidino hydrolase [75227]
                1. Streptomyces clavuligerus [TaxId: 1901] [75228] (2)
             3. Agmatinase [110585]
                1. Deinococcus radiodurans [TaxId: 1299] [110586] (3)
                   SQ Q9RZ04 # DRA0149
             4. Formimidoylglutamase HutG [117573]
                1. Vibrio cholerae [TaxId: 666] [117574] (1)
                   SQ Q9KSQ2
          2. Histone deacetylase, HDAC [52773] (3)
             1. HDAC homologue [52774]
                1. Aquifex aeolicus [TaxId: 63363] [52775] (3)
             2. Histone deacetylase 8, HDAC8 [110587]
                1. Human (Homo sapiens) [TaxId: 9606] [110588] (5)
                   SQ Q9BY41 13-375 ! SQ Q9BY41
             3. Histone deacetylase 7, HDAC7 [159582]
                HDAC7a
                1. Human (Homo sapiens) [TaxId: 9606] [159583] (9)
                   SQ Q8WUI4 515-900
   61. Alpha-2,3/8-sialyltransferase CstII [102413] (1)
       3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678
       1. Alpha-2,3/8-sialyltransferase CstII [102414] (1)
          uperfamily
          1. Alpha-2,3/8-sialyltransferase CstII [102415] (1)
             1. Alpha-2,3/8-sialyltransferase CstII [102416]
                1. Campylobacter jejuni [TaxId: 197] [102417] (2)
   62. Cell-division inhibitor MinC, N-terminal domain [64042] (1)
       beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest
       1. Cell-division inhibitor MinC, N-terminal domain [64043] (1)
          uperfamily
          1. Cell-division inhibitor MinC, N-terminal domain [64044] (1)
             1. Cell-division inhibitor MinC, N-terminal domain [64045]
                1. Thermotoga maritima [TaxId: 2336] [64046] (1)
   63. DTD-like [69499] (1)
       beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC
       1. DTD-like [69500] (1)
          active form is a dimer
          uperfamily
          1. DTD-like [69501] (3)
             Pfam 02580
             1. D-Tyr tRNAtyr deacylase, DTD [69502]
                formerly hypothetical protein YihZ
                1. Escherichia coli [TaxId: 562] [69503] (1)
                2. Haemophilus influenzae [TaxId: 727] [89696] (1)
                   YihZ homologue HI0670
             2. probable eukaryotic D-amino acid tRNA deacylase [110589]
                1. Leishmania major [TaxId: 5664] [110590] (1)
                   SQ P84066
   64. CoA-dependent acyltransferases [52776] (1)
       core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
       1. CoA-dependent acyltransferases [52777] (3)
          uperfamily
          1. CAT-like [52778] (5)
             trimeric enzymes with the active sites being located in between subunits
             1. Chloramphenicol acetyltransferase, CAT [52779]
                1. Escherichia coli [TaxId: 562] [52780] (8)
                   SQ P00483
                2. Shigella flexneri [TaxId: 623] [52781] (1)
             2. Dihydrolipoamide acetyltransferase [52782]
                1. Azotobacter vinelandii [TaxId: 354] [52783] (9)
                2. Bacillus stearothermophilus [TaxId: 1422] [52784] (1)
             3. Dihydrolipoamide succinyltransferase [52785]
                1. Escherichia coli [TaxId: 562] [52786] (3)
          2. Choline/Carnitine O-acyltransferase [82424] (4)
             Pfam 00755; monomeric enzyme containing tandem repeat of two CAT subunit-like domains
             1. Carnitine acetyltransferase [82425]
                relative spatial position of the domains is similar to the monomers in CAT trimer
                1. Mouse (Mus musculus) [TaxId: 10090] [82426] (18)
                   SQ P47934
                2. Human (Homo sapiens) [TaxId: 9606] [89697] (2)
             2. Choline O-acetyltransferase [110591]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [110592] (3)
                   SQ P32738
             3. Peroxisomal carnitine O-octanoyltransferase, COT [117575]
                1. Mouse (Mus musculus) [TaxId: 10090] [117576] (4)
                   SQ Q9DC50 11-612
          3. NRPS condensation domain (amide synthase) [75229] (2)
             Pfam 00668; functional domain of multifunctional enzyme containing tandem repeat of two CAT subunit-like domains
             1. VibH [75230]
                relative spatial position of the domains is similar to the monomers in CAT trimer
                1. Vibrio cholerae [TaxId: 666] [75231] (1)
             2. Polyketide synthase associated protein 5, PapA5 [110593]
                1. Mycobacterium tuberculosis [TaxId: 1773] [110594] (1)
                   SQ P96208
   65. Phosphotyrosine protein phosphatases I-like [52787] (2)
       3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
       1. Phosphotyrosine protein phosphatases I [52788] (1)
          share the common active site structure with the family II
          uperfamily
          1. Low-molecular-weight phosphotyrosine protein phosphatases [52789] (7)
             1. Tyrosine phosphatase [52790]
                1. Cow (Bos taurus) [TaxId: 9913] [52791] (7)
                2. Human (Homo sapiens) [TaxId: 9606] [52792] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52793] (3)
                4. Tritrichomonas foetus [TaxId: 5724] [110595] (1)
                   SQ O00810
             2. Arsenate reductase ArsC [69504]
                also has a phosphotyrosine phosphatase activity
                1. Staphylococcus aureus [TaxId: 1280] [69505] (8)
                   SQ P30330
                2. Bacillus subtilis [TaxId: 1423] [69506] (3)
                3. Archaeoglobus fulgidus [TaxId: 2234] [117577] (1)
                   SQ O28910
       2. PTS system IIB component-like [52794] (2)
          uperfamily
          1. PTS system, Lactose/Cellobiose specific IIB subunit [52795] (2)
             Pfam 02302
             1. Enzyme IIB-cellobiose [52796]
                of the phosphoenol-pyruvate dependent phosphotransferase system
                1. Escherichia coli [TaxId: 562] [52797] (3)
             2. PTS system mannitol-specific EIICBA component [110596]
                1. Escherichia coli [TaxId: 562] [110597] (1)
                   SQ P00550 375-471
          2. PTS system, Fructose specific IIB subunit-like [159584] (2)
             Pfam 02379
             1. Fructose-specific enzyme IIABC component FruA, middle domain [159585]
                1. Bacillus subtilis [TaxId: 1423] [159586] (1)
                   SQ P71012 171-273
             2. Mannose-specific enzyme IIBCA component ManP, N-terminal domain [159587]
                1. Bacillus subtilis [TaxId: 1423] [159588] (1)
                   SQ O31645 2-104
   66. (Phosphotyrosine protein) phosphatases II [52798] (1)
       core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
       1. (Phosphotyrosine protein) phosphatases II [52799] (5)
          share with the family I the common active site structure with a circularly permuted topology
          uperfamily
          1. Dual specificity phosphatase-like [52800] (10)
             1. VH1-related dual-specificity phosphatase, VHR [52801]
                1. Human (Homo sapiens) [TaxId: 9606] [52802] (2)
             2. Mapk phosphatase [52803]
                1. Human (Homo sapiens), pyst1 (mkp3) [TaxId: 9606] [52804] (1)
                2. Human (Homo sapiens), pac-1 [TaxId: 9606] [75232] (1)
             3. Phoshphoinositide phosphatase Pten (Pten tumor suppressor), N-terminal domain [52818]
                1. Human (Homo sapiens) [TaxId: 9606] [52819] (1)
             4. Proline directed phosphatase CDC14b2 [89698]
                duplication: consists of two structurally similar domains with the catalytic site being in the C-terminal domain
                1. Human (Homo sapiens) [TaxId: 9606] [89699] (3)
             5. Protein tyrosine phosphatase type IVa [102418]
                1. Human (Homo sapiens), pr-3 [TaxId: 9606] [102419] (2)
                   SQ O75365 1-162 # 99% sequence identity
                2. Human (Homo sapiens), pr-1 [TaxId: 9606] [117578] (1)
                   SQ Q93096 9-160
             6. mRNA capping enzyme, triphosphatase domain [64047]
                1. Mouse (Mus musculus) [TaxId: 10090] [64048] (2)
             7. Kinase associated phosphatase (kap) [64049]
                1. Human (Homo sapiens) [TaxId: 9606] [64050] (2)
             8. Putative phosphatase At1g05000 [117579]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117580] (3)
                   SQ Q9ZVN4 52-201
          2. Higher-molecular-weight phosphotyrosine protein phosphatases [52805] (12)
             has an extension to the beta-sheet of 3 antiparallel strands before strand 4
             1. Tyrosine phosphatase [52806]
                1. Human (Homo sapiens), 1B [TaxId: 9606] [52807] (92)
                   SQ P18031 2-300 ! SQ P18031 1-298 ! SQ P18031 2-299
                2. Human (Homo sapiens), mu [TaxId: 9606] [52808] (1)
                   receptor protein tyrosine phosphatase mu, domain 1
                3. Mouse (Mus musculus) [TaxId: 10090] [52809] (1)
                   receptor protein tyrosine phosphatase alpha, domain 1
                4. Human (Homo sapiens), shp-2 [TaxId: 9606] [52810] (1)
                5. Human (Homo sapiens), shp-1 [TaxId: 9606] [52811] (2)
                6. Mouse (Mus musculus), ptp-sl/br7 [TaxId: 10090] [64051] (1)
                7. Human (Homo sapiens), T-cell [TaxId: 9606] [75233] (1)
                   non-receptor type 2
             2. Protein-tyrosine phosphatase YopH, catalytic domain [100952]
                1. Yersinia enterocolitica [TaxId: 630] [52812] (13)
             3. SptP tyrosine phosphatase, catalytic domain [52813]
                1. Salmonella typhimurium [TaxId: 90371] [52814] (2)
             4. RPTP Lar [52815]
                duplication: tandem repeat of the phosphatase domain
                1. Human (Homo sapiens) [TaxId: 9606] [52816] (1)
             5. Protein-tyrosine phosphatase alpha [102420]
                1. Mouse (Mus musculus) [TaxId: 10090] [102421] (1)
             6. Tyrosine-protein phosphatase, non-receptor type 13 (PTPL1) [117581]
                1. Human (Homo sapiens) [TaxId: 9606] [117582] (1)
                   SQ Q12923 2170-2477 # structure of a PDZ domain (1361-1456) is also known (scop_sp 50169)
          3. Myotubularin-like phosphatases [102422] (1)
             common fold is decorated with additional structures
             1. Myotubularin-related protein 2, C-terminal domain [102423]
                1. Human (Homo sapiens) [TaxId: 9606] [102424] (4)
          4. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117583] (1)
             1. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117584]
                1. Selenomonas ruminantium [TaxId: 971] [117585] (13)
                   SQ Q7WUJ1 34-346
          5. Mycobacterial PtpB-like [142348] (1)
             1. Phosphotyrosine protein phosphatase PtpB [142349]
                1. Mycobacterium tuberculosis [TaxId: 1773] [142350] (3)
                   SQ P96830 4-275
   67. Rhodanese/Cell cycle control phosphatase [52820] (1)
       3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
       1. Rhodanese/Cell cycle control phosphatase [52821] (4)
          Pfam 00581
          the active site structure is similar to those of the families I and II protein phosphatases; the topology can be related by a different circular permutation to the family I topology
          uperfamily
          1. Cell cycle control phosphatase, catalytic domain [52822] (4)
             1. CDC25a [52823]
                1. Human (Homo sapiens) [TaxId: 9606] [52824] (1)
             2. CDC25b [52825]
                1. Human (Homo sapiens) [TaxId: 9606] [52826] (15)
             3. Erk2 binding domain of Mapk phosphatase mkp-3 [69507]
                1. Human (Homo sapiens) [TaxId: 9606] [69508] (1)
             4. Dual specificity phosphatase Cdc25 [110598]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110599] (1)
                   SQ Q8GY31
          2. Single-domain sulfurtransferase [69509] (3)
             1. Sulfurtransferase GlpE [69510]
                single-domain rhodanese
                1. Escherichia coli [TaxId: 562] [69511] (2)
             2. Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) [102425]
                1. Wolinella succinogenes [TaxId: 844] [102426] (1)
             3. Thiosulfate sulfurtransferase/Senescence-associated protein [110600]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110601] (1)
                   SQ Q39129
          3. Multidomain sulfurtransferase (rhodanese) [52827] (6)
             duplication: consists of two domains of this fold
             1. Rhodanese [52828]
                1. Cow (Bos taurus) [TaxId: 9913] [52829] (7)
             2. Sulfurtransferase [52830]
                1. Azotobacter vinelandii [TaxId: 354] [52831] (3)
                2. Thermus thermophilus [TaxId: 274] [110602] (1)
                   SQ Q5SJI0
             3. 3-mercaptopyruvate sulfurtransferase [102427]
                1. Leishmania major [TaxId: 5664] [102428] (1)
                2. Escherichia coli [TaxId: 562] [102429] (1)
             4. Thiosulfate sulfurtransferase PA2603 [142351]
                1. Pseudomonas aeruginosa [TaxId: 287] [142352] (4)
                   SQ Q9I0N4 105-240! SQ Q9I0N4 241-370! SQ Q9I0N4 371-527! SQ Q9I0N4 4-104
          4. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117586] (1)
             1. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117587]
                1. Human (Homo sapiens) [TaxId: 9606] [117588] (4)
                   SQ P40818 174-317
   68. Thioredoxin fold [52832] (2)
       core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
       1. Thioredoxin-like [52833] (23)
          uperfamily
          1. Thioltransferase [52834] (31)
             1. Thioredoxin [52835]
                1. Escherichia coli [TaxId: 562] [52836] (31)
                   SQ P00274 ! SQ P00581
                2. Anabaena sp., pcc 7120 [TaxId: 1167] [52837] (1)
                   thioredoxin H
                3. Chlamydomonas reinhardtii [TaxId: 3055] [52838] (4)
                4. Alicyclobacillus acidocaldarius, formerly Bacillus acidocaldarius [TaxId: 405212] [52839] (4)
                   SQ P80579
                5. Spinach (Spinacia oleracea), thioredoxin F [TaxId: 3562] [52840] (2)
                6. Spinach (Spinacia oleracea), thioredoxin M [TaxId: 3562] [52841] (3)
                7. Human (Homo sapiens) [TaxId: 9606] [52842] (26)
                8. Trypanosoma brucei [TaxId: 5691] [102430] (1)
                9. Malarial parasite (Plasmodium falciparum) [TaxId: 5833] [102431] (1)
                10. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110603] (1)
                    SQ P29448 #
                11. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [117589] (4)
                    SQ Q9V429
                12. European aspen (Populus tremula), thioredoxin H [TaxId: 113636] [117590] (1)
                    SQ Q8S3L3
             2. Glutaredoxin (Grx, thioltransferase) [52843]
                1. Bacteriophage T4 [TaxId: 10665] [52844] (4)
                2. Escherichia coli [TaxId: 562] [52845] (4)
                3. Escherichia coli, Grx3 [TaxId: 562] [52846] (2)
                4. Pig (Sus scrofa) [TaxId: 9823] [52847] (1)
                5. Human (Homo sapiens) [TaxId: 9606] [52848] (2)
             3. C-terminal, Grx domain of Hybrid-Prx5 [89700]
                1. Haemophilus influenzae [TaxId: 727] [89701] (1)
                   HI0572
             4. Glutaredoxin-like NRDH-redoxin [64052]
                1. Escherichia coli [TaxId: 562] [64053] (1)
                2. Corynebacterium ammoniagenes [TaxId: 1697] [102432] (1)
             5. MJ0307, thioredoxin/glutaredoxin-like protein [64054]
                single-domain PDI
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64055] (1)
             6. MTH807, thioredoxin/glutaredoxin-like protein [102433]
                behaves as true thioredoxin; probable MJ0307 ortholog
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102434] (1)
             7. MTH985, a thioredoxin [69512]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69513] (1)
             8. Thioredoxin-like protein, N-terminal domain [64056]
                1. Human (Homo sapiens) [TaxId: 9606] [64057] (1)
             9. Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma) [102435]
                1. Escherichia coli [TaxId: 562] [102436] (8)
             10. Thioredoxin-like protein p19, TLP19 [110604]
                 1. Human (Homo sapiens) [TaxId: 9606] [110605] (1)
                    SQ O95881 23-172
             11. Hypothetical protein XCC2852 [110606]
                 1. Xanthomonas campestris [TaxId: 339] [110607] (2)
                    SQ Q8P6W3
             12. Thioredoxin-like protein 2 [117591]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117592] (1)
                    SQ Q9CQM9 241-336
             13. Thioredoxin-like structure containing protein C330018D20Rik [117593]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117594] (1)
                    SQ Q9CWB7 21-107
             14. Hypothetical protein PA1234 [142353]
                 1. Pseudomonas aeruginosa [TaxId: 287] [142354] (1)
                    SQ Q9I4A4 1-166
             15. Bacterocin transport accessory protein Bta [142355]
                 1. Streptococcus pneumoniae [TaxId: 1313] [142356] (1)
                    SQ Q97PU4 1-115
          2. PDI-like [52849] (6)
             duplication: contains two tandem repeats of this fold
             1. Protein disulfide isomerase, PDI [52850]
                1. Human (Homo sapiens) [TaxId: 9606] [52851] (3)
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [52852] (1)
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [89702] (1)
                   glutaredoxin-like protein
                4. Fungi (Humicola insolens) [TaxId: 34413] [142357] (2)
                   SQ P55059 227-355! SQ P55059 350-459
                5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142358] (4)
                   SQ P17967 142-239! SQ P17967 23-141! SQ P17967 240-364! SQ P17967 365-504
             2. Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain [52853]
                1. Salmonella typhimurium [TaxId: 90371] [52854] (9)
          3. Calsequestrin [52855] (1)
             duplication: contains three tandem repeats of this fold
             1. Calsequestrin [52856]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [52857] (1)
          4. DsbA-like [100953] (4)
             contains an all-alpha subdomain insertion
             1. Disulfide-bond formation facilitator (DsbA) [100954]
                the insert subdomain is a 4-helical bundle
                1. Escherichia coli [TaxId: 562] [100955] (22)
                2. Vibrio cholerae [TaxId: 666] [100956] (1)
                   TcpG, periplasmic enzyme required for the maturation of secreted virulence factors
             2. Mitochondrial class kappa glutathione S-transferase [102437]
                contains larger and less compact insertion in the common fold than DsbA
                1. Rat (Rattus norvegicus) [TaxId: 10116] [102438] (1)
             3. Hypothetical protein EF0770 [142359]
                1. Enterococcus faecalis [TaxId: 1351] [142360] (1)
                   SQ Q837R1 1-172
          5. Glutathione S-transferase (GST), N-terminal domain [52862] (44)
             1. Class pi GST [81358]
                1. Human (Homo sapiens) [TaxId: 9606] [52864] (49)
                2. Pig (Sus scrofa) [TaxId: 9823] [52865] (1)
                3. Mouse (Mus musculus) [TaxId: 10090] [52866] (12)
                4. Onchocerca volvulus [TaxId: 6282] [117595] (2)
                   SQ P46427
             2. Class mu GST [81359]
                1. Human (Homo sapiens) [TaxId: 9606] [52867] (29)
                   SQ P09488 ! SQ P28161
                2. Rat (Rattus norvegicus) [TaxId: 10116] [52868] (16)
                3. Chicken (Gallus gallus) [TaxId: 9031] [52869] (2)
             3. Class alpha GST [81360]
                1. Human (Homo sapiens), (a1-1) [TaxId: 9606] [52870] (29)
                   SQ P08263
                2. Rat (Rattus norvegicus), (a1-1) [TaxId: 10116] [52871] (2)
                3. Mouse (Mus musculus), (a1-1) [TaxId: 10090] [52872] (2)
                4. Mouse (Mus musculus), (a1-4) [TaxId: 10090] [52873] (2)
                5. Mouse (Mus musculus), (a2-2) [TaxId: 10090] [89703] (1)
                6. Schistosoma japonicum [TaxId: 6182] [52878] (14)
                   SQ P08515
                7. Blood fluke (Schistosoma haematobium) [TaxId: 6185] [89704] (12)
                8. Fasciola hepatica [TaxId: 6192] [52879] (2)
             4. Class theta GST [81361]
                1. Human (Homo sapiens) [TaxId: 9606] [52874] (3)
             5. Class sigma GST [81362]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52875] (1)
                   synonym: hematopoietic prostaglandin D synthase
                2. Human (Homo sapiens) [TaxId: 9606] [89705] (33)
                   SQ O60760
                   synonym: hematopoietic prostaglandin D synthase
                3. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [82427] (1)
                4. Squid (Ommastrephes sloani pacificus) [TaxId: 6634] [52876] (2)
                5. Heligmosomoides polygyrus [TaxId: 6339] [110608] (1)
                   SQ Q9NJQ6 # Fragment
             6. Class omega GST [81363]
                1. Human (Homo sapiens) [TaxId: 9606] [52877] (1)
             7. Class zeta GST [81364]
                1. Human (Homo sapiens) [TaxId: 9606] [64058] (1)
                   maleylacetoacetate isomerase
                2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [64059] (1)
             8. Class delta GST [81366]
                formerly a part of class theta enzymes
                1. Mosquito (Anopheles dirus b), isozyme 1-3 [TaxId: 123217] [75234] (1)
                2. Mosquito (Anopheles dirus b), isozyme 1-4 [TaxId: 123217] [75235] (1)
                3. Mosquito (Anopheles dirus b), isozyme 1-5 [TaxId: 123217] [102439] (1)
                4. Mosquito (Anopheles dirus b), isozyme 1-6 [TaxId: 123217] [102440] (1)
                5. African malaria mosquito (Anopheles gambiae), isozyme 1-6 [TaxId: 7165] [102441] (1)
             9. Class tau GST [81365]
                1. Aegilops tauschii, also known as Triticum tauschii [TaxId: 37682] [75236] (1)
                2. Rice (Oryza sativa) [TaxId: 4530] [89706] (1)
             10. Class phi GST [81367]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52880] (2)
                 2. Maize (Zea mays), type I [TaxId: 4577] [52881] (2)
                 3. Maize (Zea mays), type III [TaxId: 4577] [52882] (1)
             11. Class beta GST [81368]
                 1. Escherichia coli [TaxId: 562] [52883] (3)
                 2. Proteus mirabilis [TaxId: 584] [52884] (2)
                 3. Sphingomonas paucimobilis [TaxId: 13689] [52885] (1)
             12. Pf GST [102442]
                 cannot be assigned to any of the known GST classes
                 1. Malarial parasite (Plasmodium falciparum) [TaxId: 5833] [102443] (5)
             13. Glutaredoxin 2 [64060]
                 similar to class zeta enzymes
                 1. Escherichia coli [TaxId: 562] [64061] (1)
             14. Yeast prion protein ure2p, nitrogen regulation fragment [52886]
                 similar to class phi enzymes
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52887] (8)
             15. GST-like domain of elongation factor 1-gamma [82428]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82429] (1)
             16. Chloride intracellular channel 1 (clic1) [69514]
                 similar to class theta enzymes; the N-domain undergoes a redox-controlled structural transition
                 1. Human (Homo sapiens) [TaxId: 9606] [69515] (4)
             17. Hypothetical protein AGR_pAT_752p/Atu5508 [142361]
                 putative glutathione S-transferase
                 1. Agrobacterium tumefaciens [TaxId: 358] [142362] (2)
                    SQ Q7D2W7 1-87
             18. Microsomal prostaglandin E synthase-2 [142363]
                 1. Crab-eating macaque (Macaca fascicularis) [TaxId: 9541] [142364] (8)
                    SQ Q9N0A4 100-212
          6. Phosducin [52888] (2)
             1. Phosducin [52889]
                the transducin beta subunit-binding subdomain is an irregular array of helices in the N-terminal extension
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52890] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [52891] (1)
          7. ERP29 N domain-like [52892] (2)
             1. Endoplasmic reticulum protein ERP29, N-terminal domain [52893]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [52894] (1)
             2. Windbeutel, N-terminal domain [102444]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102445] (8)
          8. spliceosomal protein U5-15Kd [52895] (1)
             1. spliceosomal protein U5-15Kd [52896]
                1. Human (Homo sapiens) [TaxId: 9606] [52897] (5)
          9. SH3BGR (SH3-binding, glutamic acid-rich protein-like) [102446] (1)
             related to glutaredoxin 1 (GRX1) but lacks both conserved cysteine residues
             1. SH3BGRL3 [102447]
                1. Mouse (Mus musculus) [TaxId: 10090] [102448] (2)
                   SQ Q91VW3
          10. KaiB-like [102449] (2)
              Pfam 07689; contains members with alternative folds
              1. Circadian oscillation regulator KaiB [102450]
                 the differently folded C-terminal half facilitates oligomerization
                 1. Cyanobacterium (Nostoc sp.) pcc 7120 [TaxId: 1180] [102451] (1)
              2. Adaptive-response sensory-kinase SasA, N-terminal domain [117596]
                 has a canonical thioredoxin fold
                 1. Synechococcus elongatus [TaxId: 32046] [117597] (2)
                    SQ Q06904 19-109 # 97% sequence identity
          11. DsbC/DsbG C-terminal domain-like [52898] (3)
              elaborated common fold
              1. Disulfide bond isomerase, DsbC, C-terminal domain [52899]
                 1. Escherichia coli [TaxId: 562] [52900] (5)
                    SQ P21892
                 2. Haemophilus influenzae [TaxId: 727] [110609] (1)
                    SQ P45111 20-228
              2. Thiol:disulfide interchange protein DsbG, C-terminal domain [110610]
                 1. Escherichia coli [TaxId: 562] [110611] (8)
                    SQ P77202
          12. Glutathione peroxidase-like [52901] (42)
              1. Glutathione peroxidase [52902]
                 contains many insertions in the common fold
                 1. Cow (Bos taurus) [TaxId: 9913] [52903] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [142365] (2)
                    SQ P07203 12-195
              2. Tryparedoxin I [52904]
                 1. Crithidia fasciculata [TaxId: 5656] [52905] (8)
                 2. Trypanosoma brucei brucei [TaxId: 5702] [89707] (1)
              3. Tryparedoxin II [64062]
                 1. Crithidia fasciculata [TaxId: 5656] [64063] (6)
              4. Tryparedoxin peroxidase (thioredoxin peroxidase homologue) [64064]
                 1. Crithidia fasciculata [TaxId: 5656] [64065] (1)
                 2. Trypanosoma cruzi [TaxId: 5693] [117598] (1)
                    SQ O96763
              5. Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin) [52906]
                 1. Norway rat (Rattus norvegicus) [TaxId: 10116] [52907] (1)
                    heme-binding protein 23, HBP23
                 2. Human (Homo sapiens) [TaxId: 9606] [52908] (1)
                 3. Plasmodium yoelii [TaxId: 5861] [142366] (1)
                    SQ Q86SB2 8-177
              6. Peroxiredoxin 5 [64066]
                 1. Human (Homo sapiens) [TaxId: 9606] [64067] (10)
                    SQ P30044
              7. 1-Cys peroxiredoxin [52909]
                 1. Human (Homo sapiens) [TaxId: 9606] [52910] (1)
                 2. Plasmodium yoelii yoelii [TaxId: 73239] [117599] (1)
                    SQ Q7RGR1
                 3. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [142367] (2)
                    SQ Q5MYR6 60-238
              8. Alkyl hydroperoxide reductase AhpC [69516]
                 1. Salmonella typhimurium [TaxId: 90371] [69517] (26)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [142368] (3)
                    SQ Q7BHK8 2-170
                 3. Amphibacillus xylanus [TaxId: 1449] [142369] (10)
                    SQ O87200 2-167
              9. N-terminal, Prx domain of Hybrid-Prx5 [89708]
                 1. Haemophilus influenzae [TaxId: 727] [89709] (1)
                    HI0572
              10. Probable thiol peroxidase PsaD [89710]
                  1. Streptococcus pneumoniae [TaxId: 1313] [89711] (1)
              11. Thiol peroxidase Tpx [102452]
                  1. Escherichia coli [TaxId: 562] [102453] (1)
                  2. Haemophilus influenzae [TaxId: 727] [102454] (1)
                     HI0751
                  3. Mycobacterium tuberculosis [TaxId: 1773] [117600] (3)
                     SQ P66952
              12. Membrane-anchored thioredoxin-like protein TlpA, soluble domain [64068]
                  1. Bradyrhizobium japonicum [TaxId: 375] [64069] (1)
              13. Thioredoxin-like protein CcmG (CycY, DsbE) [75237]
                  1. Bradyrhizobium japonicum [TaxId: 375] [75238] (1)
                  2. Escherichia coli [TaxId: 562] [142370] (1)
                     SQ P0AA86 49-184
              14. Thiol-disulfide oxidoreductase ResA [102455]
                  1. Bacillus subtilis [TaxId: 1423] [102456] (6)
              15. Soluble secreted antigen MPT53 [102457]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [102458] (1)
              16. Thioredoxin-like protein Sco1 (YpmQ), soluble domain [102459]
                  1. Bacillus subtilis [TaxId: 1423] [102460] (3)
                  2. Human (Homo sapiens) [TaxId: 9606] [142371] (5)
                     SQ O75880 138-297
                  3. Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932] [142372] (8)
                     SQ P23833 111-262
              17. Phenol hydroxylase, C-terminal domain [52911]
                  1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [52912] (2)
              18. Peroxiredoxin [117601]
                  1. Aeropyrum pernix [TaxId: 56636] [117602] (50)
                     SQ Q9Y9L0 # APE2278
              19. thiol:disulfide oxidoreductase YkuV [142373]
                  1. Bacillus subtilis [TaxId: 1423] [142374] (2)
                     SQ O31699 1-143
              20. Lipoprotein DsbF [142375]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [142376] (1)
                     SQ O53924 47-180
              21. Bacterioferritin comigratory protein [142377]
                  1. Archaeon Aeropyrum pernix [TaxId: 56636] [142378] (12)
                     SQ Q9YA14 4-163
              22. Plant peroxiredoxin [142379]
                  1. Western balsam poplar(Populus trichocarpa) [TaxId: 3694] [142380] (4)
                     SQ Q8S3L0 1-162
              23. Putative peroxiredoxin Rv2238c/MT2298 [142381]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [142382] (6)
                     SQ P65688 1-153
              24. Thioredoxin reductase TsaA [142383]
                  1. Helicobacter pylori [TaxId: 210] [142384] (10)
                     SQ P56876 1-170
              25. Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain [142385]
                  1. Neisseria meningitidis serogroup A [TaxId: 65699] [142386] (3)
                     SQ Q9JWM8 33-175
              26. Peroxiredoxin dot5 [142387]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142388] (1)
                     SQ P40553 59-214
              27. Probable thiol-disulfide isomerase/thioredoxin TTHA0593 [142389]
                  1. Thermus thermophilus [TaxId: 274] [142390] (2)
                     SQ Q5SKQ0 2-188
              28. Peroxiredoxin-3 (AOP-1, SP-22) [142391]
                  1. Cow (Bos taurus) [TaxId: 9913] [142392] (12)
                     SQ P35705 63-220
          13. Thioredoxin-like 2Fe-2S ferredoxin [52918] (1)
              1. Thioredoxin-like 2Fe-2S ferredoxin [52919]
                 1. Aquifex aeolicus [TaxId: 63363] [52920] (4)
          14. ArsC-like [69518] (3)
              Pfam 03960
              1. Arsenate reductase ArsC [69519]
                 1. Escherichia coli [TaxId: 562] [69520] (3)
              2. Hypothetical protein PA3664 (YffB) [117603]
                 1. Pseudomonas aeruginosa [TaxId: 287] [117604] (1)
                    SQ Q9HXX5
              3. Regulatory protein Spx [142393]
                 1. Bacillus subtilis [TaxId: 1423] [142394] (1)
                    SQ O31602 1-114
          15. Txnl5-like [110612] (2)
              Pfam 06110
              1. Putative 42-9-9 protein (thioredoxin containing protein Txnl5) [110613]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110614] (1)
                    SQ Q9D0Y4
                 2. Human (Homo sapiens) [TaxId: 9606] [110615] (1)
                    SQ Q9BRA2
          16. YuzD-like [117605] (1)
              Pfam 07315
              1. Hypothetical protein SA0798 [117606]
                 1. Staphylococcus aureus [TaxId: 1280] [117607] (1)
                    SQ Q7A6J8
          17. YKR049C-like [142395] (1)
              Pfam 07955; DUF1687; contains an all-alpha insert subdomain
              1. Hypothetical protein YKR049C [142396]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142397] (1)
                    SQ P36141 1-133
          18. Atu2684-like [142398] (1)
              Pfam 06764; DUF1223; contains extra C-terminal domain of Immunoglobulin-like fold (scop_cf 48725), intimately associated with the N-terminal thioredixin-like domain and contributing to the active site
              1. Hypothetical protein Atu2684 [142399]
                 1. Agrobacterium tumefaciens [TaxId: 358] [142400] (1)
                    SQ Q8UC14 38-262
          19. HyaE-like [142401] (2)
              Pfam 07449; have evolved a different function; contains no conserved cysteine residues
              1. Hydrogenase-1 operon protein HyaE [142402]
                 1. Escherichia coli [TaxId: 562] [142403] (1)
                    SQ P19931 1-132
                 2. Salmonella typhimurium [TaxId: 90371] [142404] (5)
                    SQ Q8ZP25 7-125
          20. NQO2-like [142405] (1)
              complex I 24 kDa subunit; contains 2Fe-2S cluster in the active site; includes extra N-terminal four-helical bundle
              1. NADH-quinone oxidoreductase chain 2, NQO2 [142406]
                 1. Thermus thermophilus [TaxId: 274] [142407] (4)
                    SQ Q56221 2-179
          21. Mitochondrial ribosomal protein L51/S25/CI-B8 domain [142408] (1)
              Pfam 05047; "minimalized" version of the thioredoxin-like fold; variable positions for cysteine residues in the putative active site
              1. NADH-ubiquinone oxidoreductase b8 subunit, CI-B8 [142409]
                 1. Human (Homo sapiens) [TaxId: 9606] [142410] (1)
                    SQ O43678 14-98
          22. Selenoprotein W-related [142411] (3)
              Pfam 05169; "minimalized" version of the thioredoxin-like fold
              1. Selenoprotein sep15 [142412]
                 1. Drosophila melanogaster [TaxId: 7227] [142413] (1)
                    SQ Q9VVJ7 62-178
              2. Hypothetical protein Atu0228 [142414]
                 1. Agrobacterium tumefaciens [TaxId: 358] [142415] (4)
                    SQ Q8UIR5 4-89
              3. Selenoprotein M [142416]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142417] (1)
                    SQ Q8VHC3 25-144
          23. UAS domain [159589] (1)
              SMART 00594
              1. UBX domain-containing protein 7 [159590]
                 1. Human (Homo sapiens) [TaxId: 9606] [159591] (1)
                    SQ O94888 131-270
       2. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52913] (1)
          uperfamily
          1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52914] (1)
             1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52915]
                1. Escherichia coli [TaxId: 562] [52916] (2)
   69. Peptidyl-tRNA hydrolase II [102461] (1)
       3 layers: a/b/a; mixed beta-sheet of 4 strands, order 2143, strand 4 is antiparallel to the rest
       1. Peptidyl-tRNA hydrolase II [102462] (1)
          uperfamily
          1. Peptidyl-tRNA hydrolase II [102463] (4)
             Pfam 01981; UPF0099
             1. Bit1 (Cgi-147) [102464]
                Peptidyl-tRNA hydrolase; involved in apoptosis
                1. Human (Homo sapiens) [TaxId: 9606] [102465] (1)
             2. Hypothetical protein TA0108 [102466]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102467] (1)
             3. Hypothetical protein AF2095 [117608]
                1. Archaeoglobus fulgidus [TaxId: 2234] [117609] (3)
                   SQ O28185
             4. Hypothetical protein Atu0240 [159592]
                1. Agrobacterium tumefaciens [TaxId: 358] [159593] (2)
                   SQ Q8UIQ3 1-135
   70. TK C-terminal domain-like [52921] (1)
       3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
       1. TK C-terminal domain-like [52922] (3)
          uperfamily
          1. Transketolase C-terminal domain-like [52923] (5)
             1. Transketolase (TK), C-domain [52924]
                two N-terminal domains are PP and Pyr modules of thiamin-binding fold
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52925] (7)
                2. Maize (Zea mays) [TaxId: 4577] [82430] (1)
                3. Escherichia coli [TaxId: 562] [89712] (7)
                4. Leishmania mexicana mexicana [TaxId: 44270] [117610] (1)
                   SQ Q8MPM3
             2. Pyruvate dehydrogenase E1 component, C-domain [75239]
                E1A and E1B fused together in a single-chain protein
                1. Escherichia coli [TaxId: 562] [75240] (14)
          2. Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain [52926] (6)
             1. Branched-chain alpha-keto acid dehydrogenase [52927]
                1. Human (Homo sapiens) [TaxId: 9606] [52928] (21)
                   SQ P21953 52-392
                2. Thermus thermophilus [TaxId: 274] [102468] (4)
             2. 2-oxoisovalerate dehydrogenase E1b, C-domain [52929]
                1. Pseudomonas putida [TaxId: 303] [52930] (5)
             3. E1-beta subunit of pyruvate dehydrogenase, C-domain [69521]
                1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69522] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [89713] (3)
             4. Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain [117611]
                1. Bacillus stearothermophilus [TaxId: 1422] [117612] (2)
                   SQ P21874
          3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52931] (1)
             1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52932]
                1. Desulfovibrio africanus [TaxId: 873] [52933] (17)
   71. Pyruvate kinase C-terminal domain-like [52934] (2)
       3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
       1. PK C-terminal domain-like [52935] (2)
          uperfamily
          1. Pyruvate kinase, C-terminal domain [52936] (6)
             1. Pyruvate kinase, C-terminal domain [52937]
                1. Cat (Felis catus) [TaxId: 9685] [52938] (1)
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [52939] (14)
                3. Human (Homo sapiens) [TaxId: 9606] [82431] (4)
                4. Leishmania mexicana [TaxId: 5665] [52940] (8)
                5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52941] (2)
                6. Escherichia coli [TaxId: 562] [52942] (3)
          2. MTH1675-like [110616] (2)
             PfamB 019040; probable flavoenzyme, binds FMN; the phosphoribityl group binds in the equivalent site to the binding site of the PK allosteric regulator FBP
             1. Hypothetical protein MTH1675 [110617]
                1. Methanobacterium thermoautotrophicum [TaxId: 145262] [110618] (1)
                   SQ O27711
             2. Hypothetical protein AF0103 [117613]
                1. Archaeoglobus fulgidus [TaxId: 2234] [117614] (1)
                   SQ O30133
       2. ATP synthase (F1-ATPase), gamma subunit [52943] (1)
          contains an antiparallel coiled coil formed by N- and C-terminal extensions to the common fold
          uperfamily
          1. ATP synthase (F1-ATPase), gamma subunit [52944] (3)
             1. ATP synthase (F1-ATPase), gamma subunit [52945]
                1. Cow (Bos taurus) [TaxId: 9913] [52946] (14)
                   SQ P05631
                2. Rat (Rattus norvegicus) [TaxId: 10116] [52947] (2)
                3. Escherichia coli [TaxId: 562] [64070] (1)
   72. Anticodon-binding domain-like [52953] (6)
       3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
       1. Class II aaRS ABD-related [52954] (2)
          uperfamily
          1. Anticodon-binding domain of Class II aaRS [52955] (13)
             1. Histidyl-tRNA synthetase (HisRS), C-terminal domain [52956]
                1. Escherichia coli [TaxId: 562] [52957] (7)
                2. Staphylococcus aureus [TaxId: 1280] [52958] (1)
                3. Thermus thermophilus [TaxId: 274] [52959] (3)
                4. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142418] (2)
                   SQ Q9HLX5 330-426
             2. Glycyl-tRNA synthetase (GlyRS), C-terminal domain [52960]
                1. Thermus thermophilus [TaxId: 274] [52961] (3)
             3. Threonyl-tRNA synthetase (ThrRS), C-terminal domain [52962]
                1. Escherichia coli [TaxId: 562] [52963] (5)
                2. Staphylococcus aureus [TaxId: 1280] [102469] (2)
             4. Prolyl-tRNA synthetase (ProRS) domain [64071]
                1. Thermus thermophilus [TaxId: 274] [64072] (4)
                2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [89714] (4)
                3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [89715] (1)
             5. The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain [64073]
                1. Mouse (Mus musculus) [TaxId: 10090] [64074] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [142419] (4)
                   SQ Q9UHN1 369-485
             6. Nuclear receptor coactivator 5 (KIAA1637) [110619]
                1. Human (Homo sapiens) [TaxId: 9606] [110620] (1)
                   SQ Q9HCD5 197-313
          2. Brix domain [142420] (2)
             Pfam 04427; tandem repeat of two ABD-like structural repeats, which are associated together with the formation of single beta-sheet, folded into half-barrel
             1. Probable ribosomal biogenesis protein [142421]
                comprises stand-alone brix domain
                1. Methanobacterium thermoautotrophicum [TaxId: 145262] [142422] (2)
                   SQ O26776 1-154
                   MTH680
                2. Archaeon Aeropyrum pernix [TaxId: 56636] [142423] (1)
                   SQ Q9YC08 13-192
                   APE1443
       2. TolB, N-terminal domain [52964] (1)
          uperfamily
          1. TolB, N-terminal domain [52965] (1)
             1. TolB, N-terminal domain [52966]
                1. Escherichia coli [TaxId: 562] [52967] (10)
       3. B12-dependent dehydatase associated subunit [52968] (2)
          uperfamily
          1. Diol dehydratase, beta subunit [52969] (2)
             contains additional structures in the C-terminal extension
             1. Diol dehydratase, beta subunit [52970]
                1. Klebsiella oxytoca [TaxId: 571] [52971] (7)
                2. Klebsiella pneumoniae [TaxId: 573] [82432] (2)
          2. Dehydratase-reactivating factor beta subunit [82433] (2)
             1. Glycerol dehydratase reactivase, beta subunit [82434]
                1. Klebsiella pneumoniae [TaxId: 573] [82435] (1)
             2. Diol dehydratase-reactivating factor small subunit DdrB [142424]
                1. Klebsiella oxytoca [TaxId: 571] [142425] (4)
                   SQ O68196 5-112
       4. ITPase-like [52972] (3)
          formerly Maf/Ham1; elaborated with additional structures inserted in the common fold
          uperfamily
          1. ITPase (Ham1) [52973] (5)
             Pfam 01725
             1. XTP pyrophosphatase [52974]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52975] (2)
                   MJ0226
                2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102470] (6)
                   PH1917
             2. Hypothetical protein YggV [75242]
                annotated as putative ribosomal protein
                1. Escherichia coli [TaxId: 562] [75243] (1)
             3. Putative inosine/xanthosine triphosphate pyrophosphatase TM0159 [117615]
                1. Thermotoga maritima [TaxId: 2336] [117616] (1)
                   SQ Q9WY06
             4. Inosine triphosphate pyrophosphatase, ITPase [142426]
                1. Human (Homo sapiens) [TaxId: 9606] [142427] (11)
                   SQ Q9BY32 1-194
          2. Maf-like [52976] (2)
             1. Maf protein [52977]
                1. Bacillus subtilis [TaxId: 1423] [52978] (2)
             2. Maf homologue Tb11.01.5890 [142428]
                1. Trypanosoma brucei [TaxId: 5691] [142429] (1)
                   SQ Q382A9 3-203
          3. YjjX-like [110621] (3)
             Pfam 01931
             1. Hypothetical protein YjjX [110622]
                1. Salmonella typhimurium [TaxId: 90371] [110623] (1)
                   SQ P39432
                2. Escherichia coli [TaxId: 562] [142430] (8)
                   SQ P39411 1-170
             2. Hypothetical protein VC0702 [142431]
                1. Vibrio cholerae [TaxId: 666] [142432] (6)
                   SQ Q9KU27 9-181
       5. CinA-like [142433] (1)
          uperfamily
          1. CinA-like [142434] (1)
             Pfam 02464
             1. Competence/damage-inducible protein CinA [142435]
                1. Agrobacterium tumefaciens [TaxId: 358] [142436] (2)
                   SQ Q8UFF5 1-167
       6. XCC0632-like [159594] (2)
          short crossover loop between strands 2 and 3; the antiparallel part of the beta-sheet (strands 3, 4 and 5) and the C-terminal helix are quite long
          1. NLBH-like [159595] (1)
             Pfam 05211; Neuraminyllactose-binding hemagglutinin
             1. Hypothetical protein HP0492 [159596]
                1. Helicobacter pylori [TaxId: 210] [159597] (1)
                   SQ O25234 51-271
          2. XCC0632-like [159598] (1)
             Pfam 03886; DUF330
             1. Hypothetical protein XCC0632 [159599]
                1. Xanthomonas campestris pv. campestris [TaxId: 340] [159600] (8)
                   SQ Q8PCT0 32-209
   73. MTH938-like [64075] (1)
       core: 3 layers, b+a/b/a ; the central mixed sheet of 5 strands: order 21534; strand 2 is antiparallel to the rest
       1. MTH938-like [64076] (1)
          uperfamily
          1. MTH938-like [64077] (5)
             1. Hypothetical protein MT938 (MTH938) [64078]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [64079] (1)
             2. Hypothetical protein RPA2829 [142437]
                1. Rhodopseudomonas palustris [TaxId: 1076] [142438] (1)
                   SQ Q6N5Y9 1-127
             3. Hypothetical outer membrane protein BH05650 [142439]
                1. Bartonella henselae [TaxId: 38323] [142440] (1)
                   SQ Q8RIU4 11-128
             4. Hypothetical protein PH1505 [142441]
                1. Pyrococcus horikoshii [TaxId: 53953] [142442] (1)
                   SQ O59174 1-118
             5. Hypothetical protein PTD015 (C11orf67) [142443]
                1. Human (Homo sapiens) [TaxId: 9606] [142444] (4)
                   SQ Q9H7C9 2-122
   74. Restriction endonuclease-like [52979] (4)
       core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
       1. Restriction endonuclease-like [52980] (33)
          uperfamily
          1. Restriction endonuclease EcoRI [52981] (1)
             1. Restriction endonuclease EcoRI [52982]
                1. Escherichia coli [TaxId: 562] [52983] (7)
          2. Restriction endonuclease EcoRV [52984] (1)
             1. Restriction endonuclease EcoRV [52985]
                1. Escherichia coli [TaxId: 562] [52986] (31)
          3. Restriction endonuclease BamHI [52987] (1)
             1. Restriction endonuclease BamHI [52988]
                1. Bacillus amyloliquefaciens [TaxId: 1390] [52989] (5)
          4. Restriction endonuclease BglI [52990] (1)
             1. Restriction endonuclease BglI [52991]
                1. Bacillus subtilis [TaxId: 1423] [52992] (1)
          5. Restriction endonuclease BglII [52993] (1)
             1. Restriction endonuclease BglII [52994]
                1. Bacillus subtilis [TaxId: 1423] [52995] (3)
          6. Restriction endonuclease BstyI [102471] (1)
             1. Restriction endonuclease BstyI [102472]
                local sequence similarity to BglII
                1. Geobacillus stearothermophilus [TaxId: 1422] [102473] (5)
          7. Restriction endonuclease PvuII [52996] (1)
             1. Restriction endonuclease PvuII [52997]
                1. Proteus vulgaris [TaxId: 585] [52998] (9)
          8. Cfr10I/Bse634I [52999] (2)
             1. Restriction endonuclease Cfr10I [53000]
                1. Citrobacter freundii [TaxId: 546] [53001] (1)
             2. Restriction endonuclease Bse634I [69523]
                1. Bacillus stearothermophilus [TaxId: 1422] [69524] (1)
          9. Restriction endonuclease MunI [53002] (1)
             1. Restriction endonuclease MunI [53003]
                1. Mycoplasma, unidentified species [TaxId: 2093] [53004] (1)
          10. Restriction endonuclease NaeI [53005] (1)
              1. Restriction endonuclease NaeI [53006]
                 1. Nocardia aerocolonigenes [TaxId: 68170] [53007] (2)
          11. Restriction endonuclease NgoIV [53008] (1)
              1. Restriction endonuclease NgoIV [53009]
                 1. Neisseria gonorrhoeae [TaxId: 485] [53010] (1)
          12. Restriction endonuclease BsobI [53011] (1)
              1. Restriction endonuclease BsobI [53012]
                 1. Bacillus stearothermophilus [TaxId: 1422] [53013] (1)
          13. Restriction endonuclease HincII [69525] (1)
              1. Restriction endonuclease HincII [69526]
                 1. Haemophilus influenzae [TaxId: 727] [69527] (12)
                    SQ P17743 ! SQ P44413
          14. Restriction endonuclease FokI, C-terminal (catalytic) domain [53014] (1)
              1. Restriction endonuclease FokI, C-terminal (catalytic) domain [53015]
                 1. Flavobacterium okeanokoites [TaxId: 244] [53016] (2)
          15. Type II restriction endonuclease catalytic domain [102474] (1)
              1. Restriction endonuclease EcoRII, C-terminal domain [102475]
                 1. Escherichia coli [TaxId: 562] [102476] (1)
          16. lambda exonuclease [53017] (1)
              1. lambda exonuclease [53018]
                 1. Bacteriophage lambda [TaxId: 10710] [53019] (1)
          17. DNA mismatch repair protein MutH from [53020] (1)
              1. DNA mismatch repair protein MutH from [53021]
                 1. Escherichia coli [TaxId: 562] [53022] (2)
          18. Very short patch repair (VSR) endonuclease [53023] (1)
              1. Very short patch repair (VSR) endonuclease [53024]
                 1. Escherichia coli [TaxId: 562] [53025] (3)
          19. TnsA endonuclease, N-terminal domain [53026] (1)
              1. TnsA endonuclease, N-terminal domain [53027]
                 a catalytic component of the tn7 transposition system
                 1. Escherichia coli [TaxId: 562] [53028] (2)
                    SQ P13988
          20. Endonuclease I (Holliday junction resolvase) [53029] (1)
              1. Endonuclease I (Holliday junction resolvase) [53030]
                 forms dimer by swapping the common core elements
                 1. Bacteriophage T7 [TaxId: 10760] [53031] (3)
          21. Hjc-like [64080] (3)
              Pfam 01870
              1. Archaeal Holliday junction resolvase Hjc [64081]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64082] (2)
                 2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [64083] (1)
              2. Holliday-junction resolvase SSO1176 [117617]
                 1. Sulfolobus solfataricus [TaxId: 2287] [117618] (2)
                    SQ Q97YX6
          22. XPF/Rad1/Mus81 nuclease [89716] (3)
              1. Putative ATP-dependent RNA helicase Hef, nuclease domain [89717]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89718] (4)
              2. DNA excision repair protein ERCC-1 [142445]
                 1. Human (Homo sapiens) [TaxId: 9606] [142446] (3)
                    SQ P07992 99-227
              3. XPF endonuclease [142447]
                 1. Aeropyrum pernix [TaxId: 56636] [142448] (6)
                    SQ Q9YC15 16-148
          23. Restriction endonuclease MspI [110624] (1)
              1. Restriction endonuclease MspI [110625]
                 1. Moraxella sp. [TaxId: 479] [110626] (3)
                    SQ P11405
          24. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117619] (1)
              related to the RecC domain
              1. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117620]
                 1. Escherichia coli [TaxId: 562] [117621] (1)
                    SQ P08394
          25. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117622] (1)
              related to the RecB domain
              1. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117623]
                 1. Escherichia coli [TaxId: 562] [117624] (1)
                    SQ P07648
          26. Hypothetical protein VC1899 [117625] (1)
              contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
              1. Hypothetical protein VC1899 [117626]
                 1. Vibrio cholerae [TaxId: 666] [117627] (1)
                    SQ Q9KQU9 # d1 (1-156); d2 (161-249); putative catalytic domain d3 (250-383)
          27. Hypothetical protein TT1808 (TTHA1514) [117628] (1)
              Pfam 05685; DUF820
              1. Hypothetical protein TT1808 (TTHA1514) [117629]
                 1. Thermus thermophilus [TaxId: 274] [117630] (1)
                    SQ Q5SI60
          28. RecU-like [117631] (2)
              Pfam 03838
              1. Recombination protein U (RecU)/PBP related factor A (PrfA) [117632]
                 1. Bacillus subtilis [TaxId: 1423] [117633] (1)
                    SQ P39792 34-196
                 2. Bacillus stearothermophilus [TaxId: 1422] [117634] (1)
                    SQ Q5KXY4 31-198 # 99% sequence identity; Geobacillus kaustophilus TaxID: 1462
          29. Restriction endonuclease EcoO109IR [117635] (1)
              1. Restriction endonuclease EcoO109IR [117636]
                 1. Escherichia coli [TaxId: 562] [117637] (2)
                    SQ Q9RPJ3
          30. MRR-like [117638] (1)
              Pfam 04471
              1. Hypothetical protein AF1548, N-terminal domain [117639]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [117640] (1)
                    SQ 28724
          31. PA4535-like [142449] (1)
              contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix
              1. Hypothetical protein PA4535 [142450]
                 1. Pseudomonas aeruginosa [TaxId: 287] [142451] (1)
                    SQ Q9HVP2 1-209
          32. XisH-like [159601] (2)
              Pfam 08814
              1. FdxN element excision controlling factor protein [159602]
                 1. Nostoc punctiforme [TaxId: 272131] [159603] (1)
                 2. Anabaena variabilis [TaxId: 1172] [159604] (2)
                    SQ Q3M7W6 4-139
          33. YaeQ-like [159605] (2)
              Pfam 07152; contains extra N- and C-terminal beta-structures forming additional five-stranded beta-sheet; retains the PD motif in the putative active site
              1. Hypothetical protein XAC2396 [159606]
                 1. Xanthomonas axonopodis pv. citri [TaxId: 92829] [159607] (2)
                    SQ Q8PJY1 4-182
              2. Hypothetical protein PSPTO1487 [159608]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [159609] (1)
                    SQ Q886T9 2-180
       2. tRNA-intron endonuclease catalytic domain-like [53032] (1)
          uperfamily
          1. tRNA-intron endonuclease catalytic domain-like [53033] (3)
             1. Tetrameric tRNA splicing endonuclease, C-terminal domain [53034]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53035] (1)
             2. Dimeric tRNA splicing endonuclease, domains 2 and 4 [102477]
                duplication: one subunit consists of two tetrameric tRNA splicing endonuclease subunit-like repeats
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102478] (11)
             3. tRNA-splicing endonuclease subunit Sen15 [159610]
                1. Human (Homo sapiens) [TaxId: 9606] [159611] (2)
                   SQ Q8WW01 36-157
       3. Eukaryotic RPB5 N-terminal domain [53036] (1)
          uperfamily
          1. Eukaryotic RPB5 N-terminal domain [53037] (1)
             1. Eukaryotic RPB5 N-terminal domain [53038]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53039] (26)
                   SQ P20434; part of multichain biological unit
       4. TBP-interacting protein-like [159612] (1)
          contains extra C-terminal alpha+beta domain of complex fold with an embeded C2H2 zinc-finger
          1. TBP-interacting protein-like [159613] (1)
             PfamB 059845 (N-terminal domain) and Pfam B059846 (C-terminal region)
             1. TBP-interacting protein [159614]
                1. Thermococcus kodakaraensis [TaxId: 311400] [159615] (1)
                   SQ Q9V2W6 1-218
                   TK1172
   75. Resolvase-like [53040] (2)
       Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
       1. Resolvase-like [53041] (1)
          uperfamily
          1. gamma,delta resolvase, catalytic domain [53042] (1)
             1. gamma,delta resolvase, catalytic domain [53043]
                1. Escherichia coli [TaxId: 562] [53044] (13)
       2. beta-carbonic anhydrase, cab [53056] (1)
          uperfamily
          1. beta-carbonic anhydrase, cab [53057] (4)
             1. beta-carbonic anhydrase [53058]
                1. Pea (Pisum sativum) [TaxId: 3888] [53059] (1)
                2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [64084] (1)
                3. Escherichia coli [TaxId: 562] [64085] (5)
                   SQ P61517
                4. Red alga (Porphyridium purpureum) [TaxId: 35688] [53060] (1)
                   duplication: consists of two similar domains
   76. PTS system fructose IIA component-like [53061] (1)
       3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
       1. PTS system fructose IIA component-like [53062] (2)
          active dimer is formed by strand 5 swapping
          uperfamily
          1. EIIA-man component-like [53063] (2)
             1. IIA domain of mannose transporter, IIA-Man [53064]
                1. Escherichia coli [TaxId: 562] [53065] (7)
             2. PTS system, IIA subunit [159616]
                1. Enterococcus faecalis [TaxId: 1351] [159617] (2)
                   SQ Q838I6 1-132
          2. DhaM-like [159618] (2)
             probable link between the PTS system fructose IIA component-like superfamily and the DAK1/DegV-like superfamily (scop_sf 82549)
             1. Uncharacterized protein EF1359 [159619]
                1. Enterococcus faecalis [TaxId: 1351] [159620] (6)
                   SQ Q835L8 1-132
             2. PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM [159621]
                1. Lactococcus lactis [TaxId: 1358] [159622] (4)
                   SQ Q9CIV6 1-123
   77. Ribonuclease H-like motif [53066] (7)
       3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
       1. Actin-like ATPase domain [53067] (14)
          duplication contains two domains of this fold
          uperfamily
          1. Actin/HSP70 [53068] (14)
             1. Heat shock protein 70kDa, ATPase fragment [53069]
                1. Cow (Bos taurus) [TaxId: 9913] [53070] (51)
                2. Human (Homo sapiens) [TaxId: 9606] [53071] (14)
                3. Escherichia coli, gene dnaK [TaxId: 562] [53072] (1)
             2. Actin [53073]
                1. Cow (Bos taurus) [TaxId: 9913] [53074] (68)
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53075] (20)
                   SQ P02568 ! SQ 02568
                3. Chicken (Gallus gallus) [TaxId: 9031] [82437] (1)
                   sequence identical to the rabbit actin
                4. Nematode (Caenorhabditis elegans) [TaxId: 6239] [64086] (1)
                5. Dictyostelium discoideum [TaxId: 44689] [53076] (6)
                6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53077] (2)
             3. Prokaryotic actin homolog MreB [64087]
                1. Thermotoga maritima [TaxId: 2336] [64088] (3)
             4. Actin-related protein 3, Arp3 [69528]
                part of Arp2/3 complex
                1. Cow (Bos taurus) [TaxId: 9913] [69529] (17)
                   SQ P61158
             5. Actin-related protein 2, Arp2 [69530]
                part of Arp2/3 complex
                1. Cow (Bos taurus) [TaxId: 9913] [69531] (3)
                   SQ P61160 143-350 # 100% sequence identity
             6. Cell division protein FtsA [53078]
                1. Thermotoga maritima [TaxId: 2336] [53079] (2)
             7. Plasmid segregation protein ParM [82438]
                1. Escherichia coli [TaxId: 562] [82439] (14)
          2. BadF/BadG/BcrA/BcrD-like [64089] (5)
             1. Hydroxyglutaryl-CoA dehydratase component A [64090]
                1. Acidaminococcus fermentans [TaxId: 905] [64091] (1)
             2. Hypothetical protein PG1100 [142452]
                1. Porphyromonas gingivalis [TaxId: 837] [142453] (2)
                   SQ Q7MVG4 1-107! SQ Q7MVG4 108-283
             3. Probable N-acetylglucosamine kinase CV2896 [142454]
                1. Chromobacterium violaceum [TaxId: 536] [142455] (4)
                   SQ Q7NU07 122-292! SQ Q7NU07 8-121
             4. Hypothetical protein BT3618 [142456]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [142457] (12)
                   SQ Q8A1P1 107-280! SQ Q8A1P1 3-106
             5. N-acetylglucosamine kinase, NAGK [142458]
                1. Human (Homo sapiens) [TaxId: 9606] [142459] (16)
                   SQ Q9UJ70 1-117! SQ Q9UJ70 118-344
          3. Acetokinase-like [53080] (3)
             1. Acetate kinase [53081]
                1. Archaeon Methanosarcina thermophila [TaxId: 2210] [53082] (6)
                   SQ P38502 1-399
             2. butyrate kinase 2 [142460]
                1. Thermotoga maritima [TaxId: 2336] [142461] (18)
                   SQ Q9X278 1-172! SQ Q9X278 173-375
             3. Propionate kinase [142462]
                1. Salmonella typhimurium [TaxId: 90371] [142463] (10)
                   SQ O06961 193-397! SQ O06961 4-192
          4. ATPase domain of dehydratase reactivase alpha subunit [82440] (2)
             1. ATPase domain of the glycerol dehydratase reactivase alpha subunit [82441]
                includes the insert and linker domains
                1. Klebsiella pneumoniae [TaxId: 573] [82442] (1)
             2. Diol dehydratase-reactivating factor large subunit DdrA [142464]
                1. Klebsiella oxytoca [TaxId: 571] [142465] (8)
                   SQ O68195 1-92,255-403! SQ O68195 404-606
          5. Hexokinase [53083] (5)
             1. Hexokinase [53084]
                1. Baker's yeast (Saccharomyces cerevisiae), pII [TaxId: 4932] [64092] (1)
                2. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [53085] (1)
             2. Glucokinase [102479]
                Hexokinase D
                1. Human (Homo sapiens) [TaxId: 9606] [102480] (2)
             3. Mammalian type I hexokinase [53086]
                further duplication: consists of two very similar lobes
                1. Human (Homo sapiens) [TaxId: 9606] [53087] (5)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [53088] (1)
          6. Glycerol kinase [53089] (2)
             1. Glycerol kinase [53090]
                1. Escherichia coli [TaxId: 562] [53091] (28)
                2. Enterococcus casseliflavus [TaxId: 37734] [117641] (2)
                   SQ O34153 5-491
          7. Glucokinase [110627] (1)
             Pfam 02685
             1. Glucokinase Glk [110628]
                1. Escherichia coli [TaxId: 562] [110629] (2)
                   SQ P46880 P0A6V8
          8. Ppx/GppA phosphatase [110630] (2)
             Pfam 02541
             1. Exopolyphosphatase Ppx [110631]
                1. Aquifex aeolicus [TaxId: 63363] [110632] (6)
                   SQ O67040
                2. Escherichia coli [TaxId: 562] [142466] (12)
                   SQ P0AFL6 11-134! SQ P0AFL6 135-311
          9. YeaZ-like [110633] (2)
             Pfam 00814; ubiquitous cytoplasmic protein; annotated as Glycoprotease (Peptidase_M22 family) on the basis of one member's known extracellular activity
             1. Hypothetical protein YeaZ [110634]
                1. Escherichia coli [TaxId: 562] [110635] (1)
                   SQ P76256
             2. Hypothetical protein TM0874 [142467]
                1. Thermotoga maritima [TaxId: 2336] [142468] (4)
                   SQ Q9WZX7 1-103! SQ Q9WZX7 104-193
          10. ROK [110636] (8)
              Pfam 00480
              1. Inorganic polyphosphate/ATP-glucomannokinase PPGMK [110637]
                 1. Arthrobacter sp. KM [TaxId: 184230] [110638] (1)
                    SQ Q7WT42 11-263 # Fragment
              2. Putative fructokinase YhdR [117642]
                 1. Bacillus subtilis [TaxId: 1423] [117643] (1)
                    SQ O05510
              3. N-acetylglucosamine kinase [142469]
                 Transcriptional regulator, XylR-related
                 1. Thermotoga maritima [TaxId: 2336] [142470] (2)
                    SQ Q9X0V1 200-368! SQ Q9X0V1 72-199
                    TM1224
              4. N-acetylmannosamine kinase NanK [142471]
                 1. Escherichia coli [TaxId: 562] [142472] (4)
                    SQ P45425 1-119! SQ P45425 120-289
              5. Mlc protein [142473]
                 Making large colonies protein
                 1. Escherichia coli [TaxId: 562] [142474] (12)
                    SQ P50456 211-406! SQ P50456 82-210
              6. Putative regulator protein YcfX [142475]
                 1. Salmonella typhimurium [TaxId: 90371] [142476] (2)
                    SQ Q8ZPZ9 1-117! SQ Q8ZPZ9 118-303
              7. Hypothetical protein SP2142 [142477]
                 1. Streptococcus pneumoniae [TaxId: 1313] [142478] (2)
                    SQ Q97NB0 1-114! SQ Q97NB0 115-289
              8. Transcriptional regulator VC2007 [142479]
                 1. Vibrio cholerae [TaxId: 666] [142480] (2)
                    SQ Q9KQJ1 209-405! SQ Q9KQJ1 81-208
          11. Cyto-EpsL domain [117644] (1)
              N-terminal part of Pfam 05134
              1. Cytoplasmic domain of general secretion pathway protein L, EpsL [117645]
                 1. Vibrio cholerae [TaxId: 666] [117646] (7)
                    SQ P45782 6-244
          12. Ta0583-like [142481] (1)
              1. Hypothetical protein Ta0583 [142482]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142483] (10)
                    SQ Q9HKL4 1-164! SQ Q9HKL4 165-325
          13. CoaX-like [142484] (3)
              Pfam 03309; Bordetella pertussis Bvg accessory factor family, Baf
              1. Type III pantothenate kinase, CoaX [142485]
                 1. Thermotoga maritima [TaxId: 2336] [142486] (48)
                    SQ Q9WZY5 1-118! SQ Q9WZY5 119-245
                 2. Pseudomonas aeruginosa [TaxId: 287] [142487] (8)
                    SQ Q9HWC1 1-114! SQ Q9HWC1 115-248
                 3. Campylobacter jejuni [TaxId: 197] [142488] (4)
                    SQ Q5HW73 1-82! SQ Q5HW73 83-208
          14. Fumble-like [159623] (3)
              Pfam 03630; type II pantothenate kinase-like
              1. Pantothenate kinase 3, PANK3 [159624]
                 1. Human (Homo sapiens) [TaxId: 9606] [159625] (8)
                    SQ Q9H999 12-152! SQ Q9H999 157-368
              2. Type II pantothenate kinase, CoaW [159626]
                 1. Staphylococcus aureus [TaxId: 1280] [159627] (2)
                    SQ Q8NVG0 1-267
              3. Pantothenate kinase 1, PANK1 [159628]
                 1. Human (Homo sapiens) [TaxId: 9606] [159629] (4)
                    SQ Q8TE04 236-381! SQ Q8TE04 382-593
       2. Creatinase/prolidase N-terminal domain [53092] (1)
          uperfamily
          1. Creatinase/prolidase N-terminal domain [53093] (4)
             1. Creatinase [53094]
                1. Pseudomonas putida [TaxId: 303] [53095] (1)
                2. Actinobacillus sp. [TaxId: 41114] [75244] (1)
             2. Aminopeptidase P [53096]
                synonym: Xaa-Pro dipeptidase, prolidase
                1. Escherichia coli [TaxId: 562] [53097] (37)
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102481] (1)
       3. Ribonuclease H-like [53098] (14)
          consists of one domain of this fold
          uperfamily
          1. Ribonuclease H [53099] (11)
             1. RNase H (RNase HI) [53100]
                1. Escherichia coli [TaxId: 562] [53101] (37)
                   SQ P0A7Y4
                2. Thermus thermophilus [TaxId: 274] [53102] (1)
                3. synthetic, Escherichia coli/Thermus thermophilus chimera [69532] (1)
             2. Class II ribonuclease H (RNase HII) [53103]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53104] (1)
                2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64093] (2)
                3. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [64094] (2)
                4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [110639] (2)
                   SQ O59351
                5. Thermotoga maritima [TaxId: 2336] [142489] (1)
                   SQ Q9X017 1-221
             3. HIV RNase H (Domain of reverse transcriptase) [53105]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [53106] (88)
                   SQ P04585 159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ P03366 186-725 # chain A coverage; chain B coverage: 156-584 ! SQ P04585 158-698 # chain A coverage; chain B is shorter: 159-595
                2. Human immunodeficiency virus type 2 [TaxId: 11709] [82443] (1)
             4. BH0863-like Ribonuclease H [142490]
                new class of RNase H
                1. Bacillus halodurans [TaxId: 86665] [142491] (15)
                   SQ Q9KEI9 61-193! SQ Q9KEI9 62-193
                   BH0863
          2. Retroviral integrase, catalytic domain [53107] (3)
             1. Retroviral integrase, catalytic domain [53108]
                1. Rous sarcoma virus RSV [TaxId: 11886] [53109] (21)
                2. Human immunodeficiency virus type 1 [TaxId: 11676] [53110] (19)
                3. Simian immunodeficiency virus [TaxId: 11723] [53111] (1)
          3. mu transposase, core domain [53112] (1)
             1. mu transposase, core domain [53113]
                1. Bacteriophage mu [TaxId: 10677] [53114] (2)
          4. Transposase inhibitor (Tn5 transposase) [53115] (1)
             1. Transposase inhibitor (Tn5 transposase) [53116]
                contains additional all-alpha subdomains in both N- and C-terminal regions
                1. Escherichia coli [TaxId: 562] [53117] (6)
          5. DnaQ-like 3'-5' exonuclease [53118] (26)
             contains Pfam 00929
             1. Exonuclease domain of prokaryotic DNA polymerase [53119]
                part of Klenow fragment, KF
                1. Escherichia coli [TaxId: 562] [53120] (14)
                2. Thermus aquaticus [TaxId: 271] [53121] (13)
                3. Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] [53122] (45)
                   SQ Q45458 298-876 # 88% sequence identity ! SQ Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
             2. Exonuclease domain of T7 DNA polymerase [53123]
                1. Bacteriophage T7 [TaxId: 10760] [53124] (16)
                   SQ P00581
             3. Exonuclease domain of family B DNA polymerases [53125]
                elaborated with additional structures and the N-terminal subdomain
                1. Escherichia coli [TaxId: 562] [102482] (1)
                   DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
                2. Bacteriophage T4 [TaxId: 10665] [53126] (2)
                   additional N-terminal subdomain contains rudimental OB-fold
                3. Bacteriophage RB69 [TaxId: 12353] [53127] (27)
                   additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
                4. Archaeon Thermococcus gorgonarius [TaxId: 71997] [53128] (3)
                   additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
                5. Archaeon Thermococcus sp., 9on-7 [TaxId: 35749] [53129] (1)
                   additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
                6. Archaeon Desulfurococcus tok [TaxId: 108142] [53130] (2)
                   additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
                7. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [53131] (2)
                   SQ P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
                   additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
                8. Sulfolobus solfataricus [TaxId: 2287] [117647] (1)
                   SQ P26811 40-864
             4. N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444]
                1. Escherichia coli [TaxId: 562] [82445] (5)
             5. Exonuclease I [53132]
                also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region
                1. Escherichia coli [TaxId: 562] [53133] (1)
                2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159630] (3)
             6. Oligoribonuclease [89719]
                1. Haemophilus influenzae [TaxId: 727] [89720] (1)
                   HI1715
                2. Escherichia coli [TaxId: 562] [142492] (6)
                   SQ P0A784 1-180
             7. Hypothetical protein AT5G06450 [102483]
                forms a ring-shaped hexamer; function unknown
                1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [102484] (7)
             8. Exonuclease ERI1 [117648]
                1. Human (Homo sapiens) [TaxId: 9606] [117649] (1)
                   SQ Q8IV48 122-321
             9. Exonuclease domain of phi29 DNA polymerase [117650]
                1. Bacteriophage phi-29 [TaxId: 10756] [117651] (18)
                   SQ P03680
             10. Interferon-stimulated gene 20 kDa protein, ISG20 [117652]
                 1. Human (Homo sapiens) [TaxId: 9606] [117653] (1)
                    SQ Q96AZ6 6-178
             11. Exosome complex exonuclease RRP6 [142493]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142494] (4)
                    SQ Q12149 129-420
             12. Ribonuclease D, catalytic domain [142495]
                 1. Escherichia coli [TaxId: 562] [142496] (1)
                    SQ P09155 1-193
             13. Ribonuclease T [142497]
                 1. Pseudomonas aeruginosa [TaxId: 287] [142498] (2)
                    SQ Q9HY82 19-220
             14. Three prime repair exonuclease 2, TREX2 [142499]
                 1. Human (Homo sapiens) [TaxId: 9606] [142500] (2)
                    SQ Q9BQ50 44-271
             15. Three prime repair exonuclease 1, TREX1 [159631]
                 1. Mouse (Mus musculus) [TaxId: 10090] [159632] (18)
                    SQ Q91XB0 5-234! SQ Q91XB0 9-234
          6. RuvC resolvase [53134] (1)
             1. RuvC resolvase [53135]
                Holliday junction-specific endonuclease
                1. Escherichia coli [TaxId: 562] [53136] (1)
          7. Mitochondrial resolvase ydc2 catalytic domain [69533] (1)
             1. Mitochondrial resolvase ydc2 catalytic domain [69534]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [69535] (1)
          8. Putative Holliday junction resolvase RuvX [102485] (3)
             1. Hypothetical protein YqgF (RuvX) [102486]
                1. Escherichia coli [TaxId: 562] [102487] (3)
             2. Hypothetical protein YrrK (RuvX) [102488]
                1. Bacillus subtilis [TaxId: 1423] [102489] (1)
             3. Hypothetical protein, YqgF homologue [102490]
                1. Thermus thermophilus [TaxId: 274] [102491] (1)
          9. CAF1-like ribonuclease [102492] (2)
             1. Pop2 RNase D domain [102493]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102494] (1)
             2. CCR4-NOT transcription complex subunit 7, CAF1 [159633]
                1. Human (Homo sapiens) [TaxId: 9606] [159634] (1)
                   SQ Q9UIV1 11-262
          10. PIWI domain [110640] (3)
              Pfam 02171
              1. Argonaute homologue PF0537 [110641]
                 includes the middle domain
                 1. Pyrococcus furiosus [TaxId: 2261] [110642] (3)
                    SQ Q8U3D2
              2. Argonaute homologue Aq_1447 [142501]
                 includes the middle domain
                 1. Aquifex aeolicus [TaxId: 63363] [142502] (6)
                    SQ O67434 315-706
              3. Hypothetical protein AF1318 [142503]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [142504] (5)
                    SQ O28951 11-427
          11. TM1739-like [142505] (1)
              Pfam 04251; DUF430; particular similarity to the PIWI domain family
              1. Hypothetical protein TM1739 [142506]
                 1. Thermotoga maritima [TaxId: 2336] [142507] (2)
                    SQ Q9X261 1-301
          12. Hermes transposase-like [142508] (1)
              1. Transposase Hermes, catalytic domain [142509]
                 1. House fly (Musca domestica) [TaxId: 7370] [142510] (1)
                    SQ Q25442 163-609
          13. Tex RuvX-like domain-like [159635] (1)
              1. Transcriptional accessory factor Tex [159636]
                 1. Pseudomonas aeruginosa [TaxId: 287] [159637] (3)
                    SQ Q9HTY8 325-473
          14. Prp8 beta-finger domain-like [159638] (2)
              1. Pre-mRNA-splicing factor 8, Prp8 [159639]
                 1. Human (Homo sapiens) [TaxId: 9606] [159640] (3)
                    SQ Q6P2Q9 1760-2016! SQ Q6P2Q9 1771-1989
                 2. Saccharomyces cerevisiae [TaxId: 4932] [159641] (5)
                    SQ P33334 1833-2087! SQ P33334 1835-2087
       4. Translational machinery components [53137] (2)
          uperfamily
          1. Ribosomal protein L18 and S11 [53138] (7)
             1. Ribosomal protein L18 (L18p) [53139]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [53140] (40)
                   SQ P14123
                2. Thermus thermophilus [TaxId: 274] [75245] (7)
                3. Bacillus stearothermophilus [TaxId: 1422] [102495] (1)
                4. Escherichia coli [TaxId: 562] [159642] (29)
                   SQ P0C018 1-117
                5. Deinococcus radiodurans [TaxId: 1299] [159643] (6)
                   SQ Q9RSL2 8-111
             2. Ribosomal protein S11 [53141]
                1. Thermus thermophilus [TaxId: 274] [53142] (46)
                   SQ P80376
                2. Escherichia coli [TaxId: 562] [159644] (24)
                   SQ P0A7R9 12-128
          2. ERF1/Dom34 middle domain-like [53143] (3)
             1. Middle domain of eukaryotic peptide chain release factor subunit 1, ERF1 [53144]
                1. Human (Homo sapiens) [TaxId: 9606] [53145] (2)
             2. Dom34 [159645]
                1. Saccharomyces cerevisiae [TaxId: 4932] [159646] (3)
                   SQ P33309 136-277
             3. Cell division protein pelota [159647]
                1. Thermoplasma acidophilum [TaxId: 2303] [159648] (1)
                   SQ Q9HJ74 127-243
       5. Nitrogenase accessory factor-like [53146] (2)
          uperfamily
          1. MTH1175-like [53147] (3)
             1. Hypothetical protein MTH1175 [53148]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [53149] (1)
             2. Hypothetical protein TM1816 [82446]
                1. Thermotoga maritima [TaxId: 2336] [82447] (2)
                   SQ Q9X2D6 1-115
             3. Hypothetical protein TM1290 [110643]
                1. Thermotoga maritima [TaxId: 2336] [110644] (1)
                   SQ Q9X116
          2. Nitrogenase accessory factor [102496] (1)
             capable of binding the iron molybdenum cofactor, FeMo-co
             1. NafY core domain [102497]
                1. Azotobacter vinelandii [TaxId: 354] [102498] (1)
       6. DNA repair protein MutS, domain II [53150] (1)
          uperfamily
          1. DNA repair protein MutS, domain II [53151] (2)
             1. DNA repair protein MutS, domain II [53152]
                1. Thermus aquaticus [TaxId: 271] [53153] (4)
                2. Escherichia coli [TaxId: 562] [53154] (10)
                   SQ P23909 2-800
       7. Methylated DNA-protein cysteine methyltransferase domain [53155] (1)
          uperfamily
          1. Methylated DNA-protein cysteine methyltransferase domain [53156] (3)
             1. Ada DNA repair protein [53157]
                1. Escherichia coli [TaxId: 562] [53158] (1)
             2. O6-alkylguanine-DNA alkyltransferase [53159]
                1. Human (Homo sapiens) [TaxId: 9606] [53160] (9)
                   SQ P16455 6-176
                2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [53161] (1)
   78. Phosphorylase/hydrolase-like [53162] (8)
       core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
       1. HybD-like [53163] (2)
          the HybD fold coincides with the consensus core structure
          uperfamily
          1. Hydrogenase maturating endopeptidase HybD [53164] (1)
             1. Hydrogenase maturating endopeptidase HybD [53165]
                1. Escherichia coli [TaxId: 562] [53166] (1)
          2. Germination protease [64095] (1)
             elaborated with the N-terminal alpha+beta subdomain and the insertion all-alpha dimerisation subdomain
             1. Germination protease [64096]
                1. Bacillus megaterium [TaxId: 1404] [64097] (1)
       2. Purine and uridine phosphorylases [53167] (1)
          complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8
          uperfamily
          1. Purine and uridine phosphorylases [53168] (18)
             1. Purine nucleoside phosphorylase, PNP [53169]
                1. Human (Homo sapiens) [TaxId: 9606] [53170] (17)
                   SQ P00491
                2. Cow (Bos taurus) [TaxId: 9913] [53171] (20)
                   SQ P55859
                3. Escherichia coli [TaxId: 562] [53172] (19)
                4. Vibrio cholerae [TaxId: 666] [102499] (2)
                5. Cellulomonas sp. [TaxId: 40001] [53173] (2)
                6. Mycobacterium tuberculosis [TaxId: 1773] [64098] (3)
                7. Thermus thermophilus [TaxId: 274] [89721] (4)
                8. Thermotoga maritima [TaxId: 2336] [117654] (1)
                   SQ Q9X1T2
                9. Bacillus anthracis [TaxId: 1392] [117655] (3)
                   SQ Q81T09
             2. Uridine phosphorylase [53176]
                1. Escherichia coli [TaxId: 562] [53177] (40)
                   also includes the PDB entry (1rxs) where protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
                2. Salmonella typhimurium [TaxId: 90371] [117656] (1)
                   SQ P0A1F6
             3. Putative uridine phosphorylase [102500]
                1. Plasmodium falciparum [TaxId: 5833] [102501] (4)
             4. 5'-deoxy-5'-methylthioadenosine phosphorylase [53174]
                1. Human (Homo sapiens) [TaxId: 9606] [53175] (5)
                   SQ Q13126
                2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69536] (9)
                3. Sulfolobus tokodaii [TaxId: 111955] [117657] (1)
                   SQ Q975C3
             5. 5'-Methylthioadenosine/S-Adenosylhomocysteine nucleosidase [82448]
                1. Escherichia coli [TaxId: 562] [82449] (8)
             6. AMP nucleosidase [110645]
                contains extra N-terminal oligomerisation (sub)domain (8-153)
                1. Escherichia coli [TaxId: 562] [110646] (4)
                   SQ P15272
                2. Bacteroides thetaiotaomicron [TaxId: 818] [117658] (1)
                   SQ Q7MVU1
       3. Peptidyl-tRNA hydrolase-like [53178] (1)
          uperfamily
          1. Peptidyl-tRNA hydrolase-like [53179] (2)
             1. Peptidyl-tRNA hydrolase [53180]
                1. Escherichia coli [TaxId: 562] [53181] (1)
             2. Chloroplast group II intron splicing factor Crs2 [102502]
                1. Maize (Zea mays) [TaxId: 4577] [102503] (3)
       4. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53182] (1)
          uperfamily
          1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53183] (4)
             1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53184]
                1. Archaeon Thermococcus litoralis [TaxId: 2265] [53185] (1)
                2. Bacillus amyloliquefaciens [TaxId: 1390] [53186] (1)
                3. Archaeon Pyrococcus furiosus [TaxId: 2261] [64099] (2)
                4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75246] (1)
       5. Zn-dependent exopeptidases [53187] (9)
          core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest
          uperfamily
          1. Pancreatic carboxypeptidases [53188] (10)
             1. Carboxypeptidase A [53189]
                1. Cow (Bos taurus) [TaxId: 9913] [53190] (30)
                2. Pig (Sus scrofa) [TaxId: 9823] [53191] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [53192] (7)
                4. Cotton bollworm (Helicoverpa armigera) [TaxId: 29058] [75247] (1)
             2. Carboxypeptidase B [53193]
                1. Pig (Sus scrofa) [TaxId: 9823] [53194] (54)
                2. Human (Homo sapiens) [TaxId: 9606] [75248] (2)
                3. Cow (Bos taurus) [TaxId: 9913] [53195] (1)
                4. Corn earworm (Helicoverpa zea) [TaxId: 7113] [142511] (2)
                   SQ Q3T905 117-428
             3. Carboxypeptidase D, catalytic domain [53196]
                1. Crested duck (Lophonetta specularioides) [TaxId: 8836] [53197] (2)
             4. Carboxypeptidase M, catalytic domain [102504]
                1. Human (Homo sapiens) [TaxId: 9606] [102505] (1)
          2. Carboxypeptidase T [53198] (1)
             1. Carboxypeptidase T [53199]
                1. Thermoactinomyces vulgaris [TaxId: 2026] [53200] (1)
          3. Leucine aminopeptidase, C-terminal domain [53201] (2)
             1. Leucine aminopeptidase, C-terminal domain [53202]
                1. Cow (Bos taurus) [TaxId: 9913] [53203] (9)
                2. Escherichia coli, PepA [TaxId: 562] [75249] (1)
          4. Bacterial dinuclear zinc exopeptidases [53204] (19)
             1. Aminopeptidase [53205]
                1. Aeromonas proteolytica [TaxId: 671] [53206] (13)
                   SQ Q01693
                   synonym: Vibrio proteolyticus
                2. Streptomyces griseus [TaxId: 1911] [53207] (11)
             2. Aminopeptidase PepV [82450]
                unspecific amino dipeptidase
                1. Lactobacillus delbrueckii [TaxId: 1584] [82451] (1)
             3. Carboxypeptidase G2, catalytic domain [53208]
                1. Pseudomonas sp., strain rs-16 [TaxId: 306] [53209] (1)
             4. Peptidase T (tripeptidase), catalytic domain [75250]
                1. Salmonella typhimurium [TaxId: 90371] [75251] (1)
                2. Escherichia coli [TaxId: 562] [102506] (1)
             5. Peptidase-like beta-alanine synthase, catalytic domain [102507]
                1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [102508] (2)
             6. Succinyl-diaminopimelate desuccinylase, catalytic domain [102509]
                1. Neisseria meningitidis [TaxId: 487] [102510] (1)
             7. Aminoacylase-1, catalytic domain [102511]
                1. Human (Homo sapiens) [TaxId: 9606] [102512] (1)
             8. Hypothetical protein YsdC, catalytic domain [102513]
                contains insert beta-barrel domain
                1. Bacillus subtilis [TaxId: 1423] [102514] (1)
             9. Putative endoglucanase TM1048, catalytic domain [102515]
                contains insert beta-barrel domain
                1. Thermotoga maritima [TaxId: 2336] [102516] (1)
             10. Frv operon protein FrvX, catalytic domain [117659]
                 1. Pyrococcus horikoshii [TaxId: 53953] [117660] (3)
                    SQ O59196 # PH1527
             11. Probable aminopeptidase ApeA [117661]
                 contains insert beta-barrel domain
                 1. Borrelia burgdorferi [TaxId: 139] [117662] (1)
                    SQ Q45055
             12. IAA-amino acid hydrolase, catalytic domain [117663]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [117664] (2)
                    SQ P54970 37-428
             13. Deblocking aminopeptidase YhfE [142512]
                 contains insert beta-barrel domain
                 1. Bacillus cereus [TaxId: 1396] [142513] (16)
                    SQ Q81HB5 3-73,187-348
                    BC0901
             14. Allantoate amidohydrolase AllC catalytic domain [142514]
                 1. Escherichia coli [TaxId: 562] [142515] (4)
                    SQ P77425 2-210,328-411
             15. Endoglucanase TM1049 [142516]
                 1. Thermotoga maritima [TaxId: 2336] [142517] (1)
                    SQ Q9X0D9 1-64,149-339
             16. Protein YxeP [142518]
                 1. Bacillus subtilis [TaxId: 1423] [142519] (2)
                    SQ P54955 4-177,293-379
             17. Aminopeptidase YpdE [142520]
                 1. Shigella flexneri [TaxId: 623] [142521] (6)
                    SQ Q83K87 1-66,148-345
                    hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)
          5. FolH catalytic domain-like [53210] (2)
             1. Transferrin receptor ectodomain, protease-like domain [53211]
                1. Human (Homo sapiens) [TaxId: 9606] [53212] (4)
             2. Glutamate carboxypeptidase II FOLH1 [142522]
                Folate hydrolase 1, FolH homologue
                1. Human (Homo sapiens) [TaxId: 9606] [142523] (17)
                   SQ Q04609 57-117,351-593
          6. N-acetylmuramoyl-L-alanine amidase-like [102517] (2)
             1. N-acetylmuramoyl-L-alanine amidase CwlV [102518]
                1. Paenibacillus polymyxa [TaxId: 1406] [102519] (1)
             2. Endolysin Ply, catalytic domain [142524]
                1. Bacteriophage Psa [TaxId: 171618] [142525] (1)
                   SQ Q8W5Y8 1-180
          7. AstE/AspA-like [142526] (6)
             Pfam 04952; Succinylglutamate desuccinylase / Aspartoacylase family; contains extra C-terminal domain, new variant of the Barrel-sandwich hybrid fold (scop_cf 51229)
             1. Succinylglutamate desuccinylase AstE [142527]
                1. Vibrio cholerae [TaxId: 666] [142528] (1)
                   SQ Q9KSL4 3-342
                2. Vibrio parahaemolyticus [TaxId: 670] [142529] (2)
                   SQ Q87Q40 4-342
                3. Escherichia coli [TaxId: 562] [142530] (2)
                   SQ P76215 1-322
                4. Chromobacterium violaceum [TaxId: 536] [142531] (1)
                   SQ Q7NU26 2-332
             2. Aspartoacylase AspA [159649]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [159650] (1)
                   SQ Q6AZ03 4-310
                2. Human (Homo sapiens) [TaxId: 9606] [159651] (1)
                   SQ P45381 9-310
          8. Glutaminyl-peptide cyclotransferase-like [142532] (1)
             part of Pfam 04389
             1. Glutaminyl-peptide cyclotransferase, QPCT [142533]
                Glutaminyl cyclase
                1. Human (Homo sapiens) [TaxId: 9606] [142534] (16)
                   SQ Q16769 33-361
          9. FGase-like [159652] (2)
             Pfam 05013; N-formylglutamate amidohydrolase
             1. N-formylglutamate amidohydrolase [159653]
                1. Ralstonia eutropha [TaxId: 106590] [159654] (2)
                   SQ Q46VW8 10-289
             2. Hypothetical protein Atu2144 [159655]
                1. Agrobacterium tumefaciens [TaxId: 358] [159656] (8)
                   SQ Q8UDI1 6-257
       6. LigB-like [53213] (1)
          circular permutation of the common fold, most similar to the PNP fold
          uperfamily
          1. LigB-like [53214] (2)
             1. LigB subunit of an aromatic-ring-opening dioxygenase LigAB [53215]
                1. Pseudomonas paucimobilis [TaxId: 13689] [53216] (2)
             2. Uncharacterized protein YgiD [159657]
                1. Escherichia coli [TaxId: 562] [159658] (1)
                   SQ P24197 14-271
       7. AF0625-like [142535] (1)
          contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
          uperfamily
          1. AF0625-like [142536] (2)
             Pfam 04414; DUF516, binds magnesium ion and pyrophosphate in the putative active site
             1. Hypothetical protein PH0006 [142537]
                1. Pyrococcus horikoshii [TaxId: 53953] [142538] (3)
                   SQ O57774 1-274
             2. Hypothetical protein AF0625 [142539]
                1. Archaeoglobus fulgidus [TaxId: 2234] [142540] (1)
                   SQ O29630 1-278
       8. Cgl1923-like [159659] (1)
          1. Cgl1923-like [159660] (1)
             Pfam 01908; DUF75
             1. Hypothetical protein Cgl1923 [159661]
                1. Corynebacterium glutamicum [TaxId: 1718] [159662] (3)
                   SQ Q8NP93 6-274
   79. Molybdenum cofactor biosynthesis proteins [53217] (1)
       3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
       1. Molybdenum cofactor biosynthesis proteins [53218] (2)
          uperfamily
          1. MogA-like [53219] (8)
             1. MogA [53220]
                1. Escherichia coli [TaxId: 562] [53221] (2)
                2. Shewanella oneidensis [TaxId: 70863] [142541] (12)
                   SQ Q8EKM7 2-174
             2. MoaB [89722]
                1. Escherichia coli [TaxId: 562] [89723] (2)
                   SQ P30746
                2. Bacillus cereus [TaxId: 1396] [142542] (3)
                   SQ Q816R0 12-166
             3. Gephyrin N-terminal domain [64100]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [64101] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [64102] (1)
                   the human neuroreceptor anchoring protein
             4. Plant CNX1 G domain [69537]
                gephyrin homologue
                1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [69538] (6)
                   SQ Q39054 464-623
             5. Putative molybdenum cofactor biosynthesis protein DIP0503 [142543]
                1. Corynebacterium diphtheriae [TaxId: 1717] [142544] (1)
                   SQ Q6NJA6 1-163
          2. MoeA central domain-like [64103] (5)
             1. MoeA, central domain [64104]
                1. Escherichia coli [TaxId: 562] [64105] (27)
                2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102520] (1)
                3. Pyrococcus furiosus [TaxId: 2261] [117665] (1)
                   SQ Q8U034
                4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117666] (1)
                   SQ O59354
             2. Gephyrin, domain 5 [110647]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [110648] (4)
                   SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
   80. CobE/GbiG C-terminal domain-like [159663] (1)
       3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32154; strand 5 is antiparallel to the rest
       1. CobE/GbiG C-terminal domain-like [159664] (1)
          probably involved in deacylation steps in both anaerobic and aerobic pathways of cobalamin biosynthesis
          1. CobE/GbiG C-terminal domain-like [159665] (3)
             C-terminal part of Pfam 01890 (CbiG); corresponds to standalone protein CobE in the aerobic pathway; also includes resent structure 3BY5
             1. Cobalamin biosynthesis protein CobE [159666]
                predicted to facilitate the deacylation of precorrin-5 intermediate; this step can proceed non-enzymatically in vitro
                1. Agrobacterium tumefaciens [TaxId: 358] [159667] (1)
                   SQ A9CHC6 8-130
                   CobE orthologue Atu2797/ChiG; typo in the (mis)annotation
                2. Pseudomonas aeruginosa [TaxId: 287] [159668] (1)
                   SQ Q9HZQ0 1-139
             2. Cobalamin biosynthesis protein G, CbiG [159669]
                1. Sulfolobus solfataricus [TaxId: 2287] [159670] (2)
                   SQ Q97WD0 215-335
   81. CbiG N-terminal domain-like [159671] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands, order 213456, strand 5 is antiparallel to the rest
       1. CbiG N-terminal domain-like [159672] (1)
          probable biological unit is a homodimer; putative active site is formed by residues from both subunits
          1. CbiG N-terminal domain-like [159673] (1)
             N-terminal part of Pfam 01890; also includes variable linker domain to CobE-like C-terminal domain; the linker domain may be in a rudimentary form or missing
             1. Cobalamin biosynthesis protein G, CbiG [159674]
                1. Sulfolobus solfataricus [TaxId: 2287] [159675] (2)
                   SQ Q97WD0 8-215
   82. Bacterial fluorinating enzyme, N-terminal domain [102521] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands; order: 213546, strand 5 is antiparallel to the rest; topological similarity to the MogA-like family fold
       1. Bacterial fluorinating enzyme, N-terminal domain [102522] (1)
          uperfamily
          1. Bacterial fluorinating enzyme, N-terminal domain [102523] (1)
             1. 5'-fluoro-5'-deoxyadenosine synthase [102524]
                1. Streptomyces cattleya [TaxId: 29303] [102525] (41)
   83. Caspase-like [52128] (1)
       3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest
       1. Caspase-like [52129] (2)
          mature protein may be composed of two chains folded in a single domain
          uperfamily
          1. Caspase catalytic domain [52130] (7)
             1. Apopain (caspase-3, cpp32) [52131]
                1. Human (Homo sapiens) [TaxId: 9606] [52132] (31)
             2. Interleukin-1beta converting enzyme (a cysteine protease) [52133]
                1. Human (Homo sapiens) [TaxId: 9606] [52134] (14)
                   SQ P29466 125-297,317-404
             3. Caspase-1 [102526]
                1. Fall armyworm (Spodoptera frugiperda) [TaxId: 7108] [102527] (1)
             4. Caspase-2 [102528]
                1. Human (Homo sapiens) [TaxId: 9606] [102529] (1)
             5. Caspase-7 [63961]
                1. Human (Homo sapiens) [TaxId: 9606] [63962] (9)
                   SQ P55210 57-303
             6. Caspase-8 [52135]
                1. Human (Homo sapiens) [TaxId: 9606] [52136] (6)
             7. Caspase-9 [69443]
                1. Human (Homo sapiens) [TaxId: 9606] [69444] (2)
          2. Gingipain R (RgpB), N-terminal domain [52137] (1)
             contains extra N-terminal alpha/beta subdomain
             1. Gingipain R (RgpB), N-terminal domain [52138]
                Arginine-specific cysteine proteinase
                1. Porphyromonas gingivalis [TaxId: 837] [52139] (1)
   84. Macro domain-like [52948] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 is antiparallel to the rest
       1. Macro domain-like [52949] (2)
          uperfamily
          1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52950] (2)
             1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52951]
                1. Cow (Bos taurus) [TaxId: 9913] [52952] (9)
                2. Escherichia coli, PepA [TaxId: 562] [75241] (1)
                   involved in Xer site-specific recombination; probable DNA-binding domain
          2. Macro domain [89724] (7)
             found in different proteins, including macro-H2a histone and the Appr-1"-p processing enzyme
             1. Hypothetical protein AF1521 [89725]
                contains extra N-terminal strand
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89726] (4)
                   SQ O28751
             2. Hypothetical protein YmbD [102530]
                1. Escherichia coli [TaxId: 562] [102531] (1)
             3. Hypothetical protein Ymr087W [110654]
                contains structural variations at both termini
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110655] (3)
                   SQ Q04299
             4. Hypothetical protein BT1257 [142545]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [142546] (3)
                   SQ Q8A8B0 2-155
             5. Histone macro-H2a1.1 [142547]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [142548] (4)
                   SQ Q02874 180-370
                2. Human (Homo sapiens) [TaxId: 9606] [142549] (8)
                   SQ O75367 179-367! SQ O75367 181-371
             6. Replicase polyprotein 1ab [142550]
                1. SARS coronavirus [TaxId: 227859] [142551] (4)
                   SQ P59641 1002-1169
   85. MurD-like peptide ligases, peptide-binding domain [53243] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
       1. MurD-like peptide ligases, peptide-binding domain [53244] (2)
          uperfamily
          1. MurCDEF C-terminal domain [53245] (5)
             1. UDP-N-acetylmuramate-alanine ligase MurC [82452]
                1. Thermotoga maritima [TaxId: 2336] [82453] (1)
                   TM0231
                2. Haemophilus influenzae [TaxId: 727] [89727] (4)
             2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [53246]
                1. Escherichia coli [TaxId: 562] [53247] (11)
             3. UDP-N-acetylmuramyl tripeptide synthetase MurE [64107]
                1. Escherichia coli [TaxId: 562] [64108] (1)
             4. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [53248]
                1. Escherichia coli [TaxId: 562] [53249] (1)
          2. Folylpolyglutamate synthetase, C-terminal domain [53250] (2)
             1. Folylpolyglutamate synthetase, C-terminal domain [53251]
                1. Lactobacillus casei [TaxId: 1582] [53252] (7)
                2. Thermotoga maritima [TaxId: 2336] [102532] (1)
                   TM0166
   86. Phosphoglycerate mutase-like [53253] (1)
       core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
       1. Phosphoglycerate mutase-like [53254] (3)
          uperfamily
          1. Cofactor-dependent phosphoglycerate mutase [53255] (8)
             1. Phosphoglycerate mutase [53256]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53257] (7)
                2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64109] (1)
                3. Escherichia coli [TaxId: 562] [64110] (2)
                4. Human (Homo sapiens) [TaxId: 9606] [110656] (13)
                   SQ P07738
                5. Mycobacterium tuberculosis [TaxId: 1773] [117667] (1)
                   SQ Q11140
                6. Plasmodium falciparum [TaxId: 5833] [117668] (1)
                   SQ Q8IIG6
             2. Broad specificity phosphatase PhoE (YhfR) [69539]
                1. Bacillus stearothermophilus [TaxId: 1422] [69540] (3)
             3. Alpha-ribazole-5'-phosphate phosphatase [117669]
                1. Thermus thermophilus [TaxId: 274] [117670] (2)
                   SQ Q53WB3
          2. Histidine acid phosphatase [53258] (7)
             1. Prostatic acid phosphatase [53259]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [53260] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [53261] (4)
             2. Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase) [53263]
                1. Aspergillus ficuum [TaxId: 5058] [53264] (1)
                2. Aspergillus niger [TaxId: 5061] [53265] (1)
                3. Escherichia coli [TaxId: 562] [53266] (6)
                4. Aspergillus fumigatus [TaxId: 5085] [110657] (5)
                   SQ O00092 30-464 ! SQ O00092
             3. Glucose-1-phosphatase [102533]
                1. Escherichia coli [TaxId: 562] [102534] (1)
          3. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53267] (2)
             1. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53268]
                bifunctional enzyme
                1. Rat (Rattus norvegicus) [TaxId: 10116] [53269] (8)
                2. Human (Homo sapiens) [TaxId: 9606] [82454] (1)
   87. PRTase-like [53270] (1)
       core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
       1. PRTase-like [53271] (2)
          uperfamily
          1. Phosphoribosyltransferases (PRTases) [53272] (36)
             1. Xanthine-guanine PRTase (XPRTase) [53273]
                1. Escherichia coli [TaxId: 562] [53274] (5)
                2. Thermoanaerobacter tengcongensis [TaxId: 119072] [142552] (2)
                   SQ Q8R7L0 3-180
             2. Hypoxanthine-guanine-xanthine PRTase [53275]
                1. Tritrichomonas foetus [TaxId: 5724] [53276] (1)
                2. Toxoplasma gondii [TaxId: 5811] [53277] (5)
                3. Leishmania tarentolae [TaxId: 5689] [110658] (1)
                   SQ Q9NJI5
             3. Glutamine PRPP amidotransferase, C-terminal domain [53278]
                1. Bacillus subtilis [TaxId: 1423] [53279] (2)
                2. Escherichia coli [TaxId: 562] [53280] (5)
             4. Guanine PRTase [53281]
                1. Giardia lamblia [TaxId: 5741] [53282] (2)
             5. Hypoxanthine-guanine PRTase (HGPRTase) [53283]
                1. Human (Homo sapiens) [TaxId: 9606] [53284] (7)
                2. Plasmodium falciparum [TaxId: 5833] [53285] (1)
                3. Thermoanaerobacter tengcongensis [TaxId: 119072] [117671] (1)
                   SQ Q8R7L0
             6. Hypoxanthine PRTase [53286]
                1. Trypanosoma cruzi [TaxId: 5693] [53287] (9)
                   SQ Q27796
                2. Escherichia coli [TaxId: 562] [75255] (3)
                3. Salmonella typhimurium [TaxId: 90371] [89728] (1)
             7. Adenine PRTase [53288]
                1. Leishmania donovani [TaxId: 5661] [53289] (4)
                2. Leishmania tarentolae [TaxId: 5689] [102535] (1)
                3. Giardia lamblia [TaxId: 5741] [82455] (2)
                4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69541] (2)
                5. Human (Homo sapiens) [TaxId: 9606] [102536] (7)
             8. Orotate PRTase [53290]
                1. Salmonella typhimurium [TaxId: 90371] [53291] (3)
                2. Escherichia coli [TaxId: 562] [53292] (1)
                3. Streptococcus pyogenes [TaxId: 1314] [142553] (2)
                   SQ Q9A076 1-208
             9. Uracil PRTase, Upp [53293]
                1. Bacillus caldolyticus [TaxId: 1394] [75256] (1)
                2. Thermotoga maritima [TaxId: 2336] [102538] (1)
                   TM0721
                3. Toxoplasma gondii [TaxId: 5811] [53295] (6)
                4. Thermus thermophilus [TaxId: 274] [142554] (4)
                   SQ Q72J35 1-208
                5. Sulfolobus solfataricus [TaxId: 2287] [142555] (20)
                   SQ Q980Q4 2-216
             10. Pyrimidine operon regulator PyrR [109612]
                 bifunctional protein; contains the uracil PRTase and Pyr RNA-binding activities
                 1. Bacillus subtilis [TaxId: 1423] [53294] (2)
                 2. Thermus thermophilus [TaxId: 274] [102537] (1)
                    TT1027
                 3. Bacillus caldolyticus [TaxId: 1394] [110659] (7)
                    SQ P41007
                 4. Mycobacterium tuberculosis [TaxId: 1773] [117672] (1)
                    SQ P71807
             11. Pur operon repressor (PurR), C-terminal domain [102539]
                 1. Bacillus subtilis [TaxId: 1423] [102540] (2)
             12. Putative phosphoribosyltransferase TT1426 (TTHA1462) [117673]
                 1. Thermus thermophilus [TaxId: 274] [117674] (1)
                    SQ Q5SIB2
             13. Xanthine phosphoribosyltransferase [142556]
                 1. Bacillus subtilis [TaxId: 1423] [142557] (6)
                    SQ P42085 1-191
             14. Putative phosphoribosyltransferase TTHA1613 [142558]
                 putative APRTase in UniProt
                 1. Thermus thermophilus [TaxId: 274] [142559] (5)
                    SQ Q5SHW7 2-175
             15. Pprobable purine phosphoribosyltransferase PH0095 [142560]
                 1. Pyrococcus horikoshii [TaxId: 53953] [142561] (12)
                    SQ O57827 1-153
          2. Phosphoribosylpyrophosphate synthetase-like [53296] (3)
             duplication: consists of two domains of this fold
             1. Phosphoribosylpyrophosphate synthetase [53297]
                1. Bacillus subtilis [TaxId: 1423] [53298] (3)
                2. Methanocaldococcus jannaschii [TaxId: 2190] [142562] (16)
                   SQ Q58761 1-155! SQ Q58761 156-284
             2. PRPP synthetase-associated protein 1 [142563]
                1. Human (Homo sapiens) [TaxId: 9606] [142564] (12)
                   SQ Q14558 167-350! SQ Q14558 7-166
   88. vWA-like [53299] (1)
       core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
       1. vWA-like [53300] (5)
          uperfamily
          1. Integrin A (or I) domain [53301] (12)
             1. Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) [53302]
                1. Human (Homo sapiens) [TaxId: 9606] [53303] (23)
                   SQ P20701 153-334
             2. von Willebrand factor A3 domain, vWA3 [53304]
                1. Human (Homo sapiens) [TaxId: 9606] [53305] (4)
             3. von Willebrand factor A1 domain, vWA1 [53306]
                1. Human (Homo sapiens) [TaxId: 9606] [53307] (9)
                2. Mouse (Mus musculus) [TaxId: 10090] [159676] (1)
                   SQ Q8CIZ8 1270-1465
             4. Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit) [53308]
                1. Human (Homo sapiens) [TaxId: 9606] [53309] (9)
             5. Integrin alpha1-beta1 [53310]
                1. Human (Homo sapiens) [TaxId: 9606] [53311] (3)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [53312] (4)
             6. Integrin alpha2-beta1 [53313]
                1. Human (Homo sapiens) [TaxId: 9606] [53314] (3)
                   SQ P17301 172-364
             7. Integrin alpha-x beta2 [82456]
                Leukocyte adhesion glycoprotein P150,95 alpha chain
                1. Human (Homo sapiens) [TaxId: 9606] [82457] (1)
             8. Integrin beta A domain [69542]
                1. Human (Homo sapiens) [TaxId: 9606] [69543] (5)
                   SQ P05106 27-716 ! SQ P05106 27-466
             9. Complement factor B domain [102541]
                1. Human (Homo sapiens) [TaxId: 9606] [102542] (5)
                   SQ P00751 268-764
             10. Capillary morphogenesis protein 2 domain [102543]
                 Anthrax toxin receptor 2
                 1. Human (Homo sapiens) [TaxId: 9606] [102544] (3)
                    SQ P58335 41-210
          2. Trunk domain of Sec23/24 [82458] (2)
             1. Sec23 [82459]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82460] (3)
             2. Sec24 [82461]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82462] (4)
          3. Ku70 subunit N-terminal domain [100959] (1)
             1. Ku70 subunit N-terminal domain [100960]
                1. Human (Homo sapiens) [TaxId: 9606] [100961] (2)
          4. Ku80 subunit N-terminal domain [100962] (1)
             1. Ku80 subunit N-terminal domain [100963]
                1. Human (Homo sapiens) [TaxId: 9606] [100964] (2)
          5. RoRNP C-terminal domain-like [142565] (1)
             1. 60-kda SS-A/Ro ribonucleoprotein, RoRNP [142566]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [142567] (5)
                   SQ P42700 364-537
   89. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53322] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
       1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53323] (1)
          uperfamily
          1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53324] (1)
             1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53325]
                also includes linker domain IV
                1. Desulfovibrio africanus [TaxId: 873] [53326] (17)
   90. RbsD-like [102545] (1)
       3 layers: a/b/a; mixed beta-sheet of 6 strands, order 251634; strand 6 is antiparallel to the rest
       1. RbsD-like [102546] (1)
          uperfamily
          1. RbsD-like [102547] (2)
             1. Ribose transport protein RbsD [102548]
                1. Bacillus subtilis [TaxId: 1423] [102549] (4)
             2. Hypothetical protein Atu2016 [159677]
                1. Agrobacterium tumefaciens [TaxId: 358] [159678] (1)
                   SQ Q8UDV3 1-147
   91. FabD/lysophospholipase-like [52150] (1)
       core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
       1. FabD/lysophospholipase-like [52151] (3)
          uperfamily
          1. FabD-like [52152] (2)
             the superfamily common core covers almost all of the family fold
             1. Catalytic domain of malonyl-CoA ACP transacylase FabD [52153]
                1. Escherichia coli [TaxId: 562] [52154] (1)
                2. Streptomyces coelicolor A3(2) [TaxId: 100226] [82463] (1)
          2. Lysophospholipase [53645] (1)
             common core is decorated with many additional structures; mixed beta-sheet of 9 strands, order 654321798; strands 4, 6 and 8 are antiparallel to the rest
             1. Cytosolic phospholipase A2 catalytic domain [53646]
                1. Human (Homo sapiens) [TaxId: 9606] [53647] (1)
          3. Patatin [89729] (1)
             plant proteins; structurally and functionally related to animal cytosolic phospholipase A2
             1. Patatin [89730]
                1. Heartleaf nightshade (Solanum cardiophyllum) [TaxId: 160510] [89731] (1)
   92. L-sulfolactate dehydrogenase-like [89732] (1)
       core: 3 layers, a/b/a; mixed sheet of 7 strands, order 1237456; strands 1, 6 and 7 are antiparallel to the rest
       1. L-sulfolactate dehydrogenase-like [89733] (1)
          topological similarity to the domain 2 of TM1585
          uperfamily
          1. L-sulfolactate dehydrogenase-like [89734] (3)
             Pfam 02615; type II malate/L-lactate dehydrogenase;
             1. 2,3-diketogulonate oxidoreductase (YiaK) [89735]
                1. Escherichia coli [TaxId: 562] [89736] (2)
             2. L-sulfolactate dehydrogenase [102550]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [102551] (1)
             3. Ureidoglycolate dehydrogenase AllD [117675]
                1. Escherichia coli [TaxId: 562] [117676] (1)
                   SQ P77555
   93. Formyltransferase [53327] (1)
       3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
       1. Formyltransferase [53328] (1)
          uperfamily
          1. Formyltransferase [53329] (7)
             1. Glycinamide ribonucleotide transformylase, GART [53330]
                1. Escherichia coli [TaxId: 562] [53331] (12)
                2. Human (Homo sapiens) [TaxId: 9606] [82468] (22)
             2. Methionyl-tRNAfmet formyltransferase [53332]
                1. Escherichia coli [TaxId: 562] [53333] (2)
                2. Clostridium thermocellum [TaxId: 1515] [117677] (1)
                   SQ Q4HJX2 47% sequence identity
                   Structural genomics target; GI:67850689
             3. 10-formyltetrahydrofolate dehydrogenase domain 1 [102552]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [102553] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [142568] (2)
                   SQ O75891 1-203
             4. Polymyxin resistance protein ArnA, N-terminal domain [142569]
                1. Escherichia coli [TaxId: 562] [142570] (9)
                   SQ P77398 1-200! SQ P77398 1-203
   94. S-adenosyl-L-methionine-dependent methyltransferases [53334] (1)
       core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
       1. S-adenosyl-L-methionine-dependent methyltransferases [53335] (57)
          uperfamily
          1. COMT-like [53336] (3)
             1. Catechol O-methyltransferase, COMT [53337]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [53338] (6)
             2. COMT domain-containing protein 1, COMTD1 [142571]
                1. Human (Homo sapiens) [TaxId: 9606] [142572] (2)
                   SQ Q86VU5 44-262
             3. Caffeoyl-CoA O-methyltransferase [142573]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [142574] (8)
                   SQ Q40313 21-247
          2. Plant O-methyltransferase, C-terminal domain [64111] (5)
             1. Chalcone O-methyltransferase [64112]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [64113] (2)
             2. Isoflavone O-methyltransferase [64114]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [64115] (2)
             3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [75259]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [75260] (2)
             4. Aclacinomycin-10-hydroxylase RdmB [102554]
                evolved a different function; binds SAM and SAH
                1. Streptomyces purpurascens [TaxId: 1924] [102555] (4)
                   SQ Q54527
             5. Carminomycin 4-O-methyltransferase [110660]
                1. Streptomyces peucetius [TaxId: 1950] [110661] (2)
                   SQ Q06528
          3. RNA methyltransferase FtsJ [53339] (1)
             1. RNA methyltransferase FtsJ [53340]
                1. Escherichia coli [TaxId: 562] [53341] (2)
          4. Fibrillarin homologue [53342] (3)
             1. Fibrillarin homologue [53343]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53344] (2)
                2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89737] (1)
                   AF2087
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102556] (2)
          5. rRNA methyltransferase RlmA [102557] (1)
             1. rRNA methyltransferase RlmA [102558]
                23S rRNA N1-G745 methyltransferase
                1. Escherichia coli [TaxId: 562] [102559] (1)
          6. rRNA methyltransferase AviRa [89738] (1)
             1. rRNA methyltransferase AviRa [89739]
                1. Streptomyces viridochromogenes [TaxId: 1938] [89740] (2)
          7. rRNA adenine dimethylase-like [88784] (5)
             1. rRNA adenine dimethylase [53363]
                contains additional all-alpha C-terminal domain (res.181-248)
                1. Streptococcus pneumoniae, Ermam [TaxId: 1313] [53364] (1)
                2. Bacillus subtilis, Ermc' [TaxId: 1423] [53365] (5)
             2. Transcription factor sc-mtTFB [69555]
                overall structure is very similar to those of Ermc' and Ermam
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69556] (1)
             3. High level kasugamycin resistance protein KsgA [110662]
                1. Escherichia coli [TaxId: 562] [110663] (1)
                   SQ P06992
             4. Probable dimethyladenosine transferase [142575]
                1. Human (Homo sapiens) [TaxId: 9606] [142576] (2)
                   SQ Q9UNQ2 36-313
          8. mRNA cap methylase [88785] (3)
             1. Polymerase regulatory subunit VP39 [53361]
                1. Vaccinia virus [TaxId: 10245] [53362] (19)
             2. An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5 [89741]
                structurally and functionally similar to VP39
                1. Flavivirus (Dengue virus type 2) [TaxId: 12637] [89742] (3)
                   SQ P12823 2495-2756
                2. Dengue virus 2 [TaxId: 11060] [159679] (5)
          9. mRNA cap (Guanine N-7) methyltransferase [102560] (1)
             mRNA capping enzyme
             1. mRNA cap (Guanine N-7) methyltransferase [102561]
                1. Fungus (Encephalitozoon cuniculi) [TaxId: 6035] [102562] (7)
          10. Hypothetical protein MJ0882 [53345] (1)
              1. Hypothetical protein MJ0882 [53346]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53347] (1)
          11. Hypothetical protein HI0319 (YecO) [69544] (1)
              1. Hypothetical protein HI0319 (YecO) [69545]
                 1. Haemophilus influenzae [TaxId: 727] [69546] (1)
                    structural genomics
          12. Glycine N-methyltransferase [53348] (3)
              1. Glycine N-methyltransferase [53349]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [53350] (16)
                 2. Human (Homo sapiens) [TaxId: 9606] [110664] (1)
                    SQ Q14749
                 3. Mouse (Mus musculus) [TaxId: 10090] [110665] (2)
                    SQ Q9QXF8
          13. Arylamine N-methyltransferase [69547] (2)
              1. Phenylethanolamine N-methyltransferase, PNMTase [69548]
                 1. Human (Homo sapiens) [TaxId: 9606] [69549] (21)
              2. Indolethylamine N-methyltransferase, INMT [142577]
                 1. Human (Homo sapiens) [TaxId: 9606] [142578] (1)
                    SQ O95050 5-261
          14. Histamine methyltransferase [75261] (1)
              1. Histamine methyltransferase [75262]
                 1. Human (Homo sapiens) [TaxId: 9606] [75263] (12)
          15. Hypothetical Protein YjhP [82469] (1)
              1. Hypothetical Protein YjhP [82470]
                 1. Escherichia coli [TaxId: 562] [82471] (1)
          16. Salicylic acid carboxyl methyltransferase (SAMT) [102563] (1)
              1. Salicylic acid carboxyl methyltransferase (SAMT) [102564]
                 1. Clarkia breweri [TaxId: 36903] [102565] (1)
          17. Thiopurine S-methyltransferase [102566] (2)
              1. Thiopurine S-methyltransferase [102567]
                 1. Pseudomonas syringae [TaxId: 317] [102568] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [142579] (3)
                    SQ P51580 17-245
          18. Leucine carboxy methyltransferase Ppm1 [102569] (1)
              1. Leucine carboxy methyltransferase Ppm1 [102570]
                 involved in the regulation of protein phosphatase 2a activity
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102571] (7)
          19. Precorrin-6Y methyltransferase (CbiT) [82472] (1)
              1. Precorrin-6Y methyltransferase (CbiT) [82473]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [82474] (5)
                    MTH146
          20. MraW-like putative methyltransferases [82475] (2)
              1. TM0872, methyltransferase domain [82476]
                 contains an inserted alpha helical subdomain
                 1. Thermotoga maritima [TaxId: 2336] [82477] (2)
                 2. Thermus thermophilus [TaxId: 274] [117678] (1)
                    SQ Q5SJD8
          21. N5-glutamine methyltransferase, HemK [89743] (2)
              1. N5-glutamine methyltransferase, HemK [89744]
                 contains an N-terminal alpha helical subdomain; res. 13-84
                 1. Thermotoga maritima [TaxId: 2336] [89745] (5)
                    SQ Q9WYV8
                 2. Escherichia coli [TaxId: 562] [110666] (2)
                    SQ P37186
          22. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89746] (2)
              1. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89747]
                 a non-SET domain nucleosomal histone methyltransferase
                 1. Human (Homo sapiens) [TaxId: 9606] [89748] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110667] (1)
                    SQ Q04089 176-581
          23. Guanidinoacetate methyltransferase [69550] (2)
              1. Guanidinoacetate methyltransferase [69551]
                 a template structure of protein arginine methyltransferase
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [69552] (5)
                    SQ P10868
                 2. Human (Homo sapiens) [TaxId: 9606] [142580] (3)
                    SQ Q14353 8-236
          24. Arginine methyltransferase [53351] (4)
              lacks the last two strands of the common fold replaced with a beta-sandwich oligomerisation subdomain
              1. Arginine methyltransferase, HMT1 [53352]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53353] (1)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [64116] (1)
              2. Protein arginine N-methyltransferase 1, PRMT1 [89749]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [89750] (3)
              3. Protein arginine N-methyltransferase 3, PRMT3 [142581]
                 1. Human (Homo sapiens) [TaxId: 9606] [142582] (1)
                    SQ O60678 221-531
          25. Protein-L-isoaspartyl O-methyltransferase [53354] (5)
              topological variant; strand order 3214567; strand 6 is antiparallel to the rest
              1. Protein-L-isoaspartyl O-methyltransferase [68927]
                 1. Thermotoga maritima [TaxId: 2336] [68928] (1)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [69553] (4)
                 3. Human (Homo sapiens) [TaxId: 9606] [69554] (2)
                 4. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102572] (1)
                 5. Sulfolobus tokodaii [TaxId: 111955] [110668] (1)
                    SQ Q972K9
          26. Glucose-inhibited division protein B (GidB) [75264] (2)
              1. Glucose-inhibited division protein B (GidB) [75265]
                 function unknown
                 1. Escherichia coli [TaxId: 562] [75266] (1)
                 2. Bacillus subtilis [TaxId: 1423] [117679] (1)
                    SQ P25813
          27. tRNA(1-methyladenosine) methyltransferase-like [64117] (4)
              contains additional N-terminal beta-sandwich domain
              1. Probable methyltransferase Rv2118c [64118]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [64119] (1)
              2. Hypothetical protein TM0748 [102573]
                 1. Thermotoga maritima [TaxId: 2336] [102574] (1)
              3. Hypothetical protein FLJ20628 [142583]
                 1. Human (Homo sapiens) [TaxId: 9606] [142584] (2)
                    SQ Q9BVS5 149-472
              4. Hypothetical protein Ta0852 [142585]
                 forms dimer similar to half-tetramer of the other members but with swapped N-terminal domains; variant topology of the N-terminal domain
                 1. Thermoplasma acidophilum [TaxId: 2303] [142586] (1)
                    SQ Q9HJW1 6-255
          28. NOL1/NOP2/sun [102575] (3)
              Pfam 01189; contains additional N-terminal 3-helical and ferredoxin-like domains
              1. Hypothetical methyltransferase PH1374 [102576]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102577] (1)
              2. Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), C-terminal domain [110669]
                 1. Escherichia coli [TaxId: 562] [110670] (2)
                    SQ P36929
              3. NOL1R [142587]
                 1. Human (Homo sapiens) [TaxId: 9606] [142588] (1)
                    SQ Q96P11 133-425
          29. Ribosomal protein L11 methyltransferase PrmA [102578] (1)
              contains additional N-terminal ferredoxin-like domain
              1. PrmA-like protein TTHA0656 (TT0836) [102579]
                 1. Thermus thermophilus [TaxId: 274] [102580] (12)
          30. (Uracil-5-)-methyltransferase [102581] (1)
              Pfam 05958
              1. rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain [102582]
                 includes an iron-sulfur cluster-binding, alpha+beta sudbomain
                 1. Escherichia coli [TaxId: 562] [102583] (3)
          31. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53357] (1)
              contains additional N-terminal all-alpha domain, res. 11-91
              1. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53358]
                 1. Salmonella typhimurium [TaxId: 90371] [53359] (2)
          32. C5 cytosine-specific DNA methylase, DCM [88786] (3)
              1. DNA methylase HhaI [53367]
                 1. Haemophilus haemolyticus [TaxId: 726] [53368] (20)
                    SQ P05102
              2. DNA methylase HaeIII [53371]
                 1. Haemophilus aegyptius [TaxId: 197575] [53372] (1)
              3. DNMT2 [53375]
                 an enigmatic DNA methyltransferase homologue from mitochondria
                 1. Human (Homo sapiens) [TaxId: 9606] [53376] (1)
          33. DNA methylase TaqI, N-terminal domain [88787] (1)
              1. DNA methylase TaqI, N-terminal domain [53369]
                 1. Thermus aquaticus [TaxId: 271] [53370] (18)
          34. N6 adenine-specific DNA methylase, DAM [88788] (2)
              1. DNA methylase DpnM [53373]
                 1. Streptococcus pneumoniae [TaxId: 1313] [53374] (1)
              2. DNA methylase T4DAM [102584]
                 1. Bacteriophage T4 [TaxId: 10665] [102585] (14)
          35. Type II DNA methylase [53377] (3)
              circularly permuted version of the common fold
              1. m.PvuII N4 cytosine-specific DNA methyltransferase [53378]
                 1. Proteus vulgaris [TaxId: 585] [53379] (1)
              2. m.RsrI N6 adenosine-specific DNA methyltransferase [53380]
                 1. Rhodobacter sphaeroides [TaxId: 1063] [53381] (5)
              3. Methyltransferase mboII [75267]
                 1. Moraxella bovis [TaxId: 476] [75268] (1)
          36. Spermidine synthase [69557] (7)
              contains additional N-terminal tetramerisation all-beta domain, res. 1-71
              1. Spermidine synthase [69558]
                 polyamine aminopropyltransferase
                 1. Thermus thermophilus [TaxId: 274] [102586] (1)
                 2. Thermotoga maritima [TaxId: 2336] [69559] (2)
                 3. Bacillus subtilis [TaxId: 1423] [82478] (1)
                 4. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117680] (5)
                    SQ Q9ZUB3
                 5. Caenorhabditis elegans [TaxId: 6239] [142589] (2)
                    SQ Q9U2F0 3-314
                 6. Human (Homo sapiens) [TaxId: 9606] [142590] (8)
                    SQ P19623 15-300
              2. Putative spermidine synthetase PF0127 (SpeE) [82479]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82480] (1)
          37. Mycolic acid cyclopropane synthase [69560] (6)
              1. CmaA1 [69561]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [69562] (3)
              2. CmaA2 [116723]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [116724] (1)
              3. PccA [75269]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [75270] (1)
              4. Methoxy mycolic acid synthase 2, Mma2 [117681]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [117682] (1)
                    SQ P72026 33-317
              5. Methoxy mycolic acid synthase 4, Mma4 [142591]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [142592] (2)
                    SQ Q79FX8 22-301
              6. Putative sarcosine dimethylglycine methyltransferase [159680]
                 sequence similarity to other families with less structural similarity
                 1. Red algae (Galdieria sulphuraria) [TaxId: 130081] [159681] (1)
          38. Ta1320-like [89751] (2)
              1. Hypothetical protein Ta1320 [89752]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89753] (1)
              2. Hypothetical protein PH1948 [142593]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142594] (4)
                    SQ O59611 4-204
          39. UbiE/COQ5-like [110671] (5)
              Pfam 01209
              1. Hypothetical protein BH2331 [110672]
                 1. Bacillus halodurans [TaxId: 86665] [110673] (1)
                    SQ Q9KAF6
              2. Possible histamine N-methyltransferase TM1293 [110674]
                 1. Thermotoga maritima [TaxId: 2336] [110675] (1)
                    SQ Q9X119
              3. Hypothetical protein YcgJ [117683]
                 1. Bacillus subtilis [TaxId: 1423] [117684] (3)
                    SQ O31474
              4. Hypothetical methyltransferase TM1389 [142595]
                 1. Thermotoga maritima [TaxId: 2336] [142596] (2)
                    SQ Q9X1A9 1-246
              5. Hypothetical protein ECA1738 [159682]
                 1. Erwinia carotovora [TaxId: 554] [159683] (6)
                    SQ Q6D6E7 21-249
          40. AD-003 protein-like [117685] (2)
              Pfam 05891; DUF858
              1. Hypothetical protein Lmaj004091aaa (LmjF30.0810) [117686]
                 1. Leishmania major [TaxId: 5664] [117687] (1)
                    SQ Q4Q7M2
              2. Adrenal gland protein AD-003 (C9orf32) [142597]
                 1. Human (Homo sapiens) [TaxId: 9606] [142598] (2)
                    SQ Q9BV86 1-222
          41. CAC2371-like [117688] (3)
              similar overall fold to the Glycine N-methyltransferase (scop_fa 53348) and mRNA cap (Guanine N-7) methyltransferase (scop_fa 102560) families
              1. Putative methyltransferase CAC2371 [117689]
                 1. Clostridium acetobutylicum [TaxId: 1488] [117690] (1)
                    SQ Q97GJ5
              2. Hypothetical protein PH0226 [142599]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142600] (2)
                    SQ O57965 2-227
              3. Hypothetical methyltransferase PH1305 [142601]
                 the beta-sheet insertion makes trimerization subdomain
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142602] (3)
                    SQ O59000 1-251
          42. TehB-like [142603] (1)
              Pfam 03848; overall structural similarity to Thiopurine S-methyltransferase (Pfam 05724)
              1. Putative methyltransferase TehB [142604]
                 Tellurite resistance protein
                 1. Salmonella typhimurium [TaxId: 90371] [142605] (2)
                    SQ Q8ZPC3 1-198
                    sequence similarity to Hypothetical methyltransferase PH1305 of the CAC2371-like family (scop_fa 117688)
          43. N-6 DNA Methylase-like [142606] (3)
              Pfam 02384; contains C-terminal extension to the canonical fold and extra N-terminal all-alpha domain similar to the insert domain of the DAM family (scop_fa 88788)
              1. Hypothetical protein Lmo1582 [142607]
                 1. Listeria monocytogenes [TaxId: 1639] [142608] (1)
                    SQ Q8Y6U9 2-329
              2. M.EcoKI [142609]
                 contains extra C-terminal structured region
                 1. Escherichia coli [TaxId: 562] [142610] (2)
                    SQ P08957 4-527
              3. Type I restriction enzyme StySJI M protein [159684]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [159685] (2)
                    SQ Q89Z59 9-433
          44. YhhF-like [142611] (5)
              Pfam 03602
              1. Putative methylase EF2452 [142612]
                 1. Enterococcus faecalis [TaxId: 1351] [142613] (2)
                    SQ Q831P8 1-182
              2. Methyltransferase TTHA0928 [142614]
                 1. Thermus thermophilus [TaxId: 274] [142615] (1)
                    SQ Q5SJT0 15-185
              3. Putative methylase HI0767 [142616]
                 YhhF homologue
                 1. Haemophilus influenzae [TaxId: 727] [142617] (1)
                    SQ P44869 11-193
              4. Putative methyltransferase SPy1538 [142618]
                 1. Streptococcus pyogenes [TaxId: 1314] [142619] (2)
                    SQ Q99YU1 28-179
              5. Methylase YhhF [142620]
                 1. Escherichia coli [TaxId: 562] [142621] (6)
                    SQ P0ADX9 10-192
          45. Met-10+ protein-like [142622] (1)
              Pfam 02475; contains extra N-terminal alpha+beta domain: beta(2)-alpha-beta(2); mixed beta-sheet; order: 1234; cf scop_fold 102740
              1. Hypothetical protein PH0793 [142623]
                 1. Pyrococcus horikoshii [TaxId: 53953] [142624] (1)
                    SQ O58523 19-278
          46. Nsp15 N-terminal domain-like [142625] (2)
              rudiment methyltransferase fold that probably has lost the enzymatic activity; contains extra N-terminal alpha+beta subdomain
              1. Nsp15 [142626]
                 1. Murine hepatitis virus, MHV [TaxId: 11138] [142627] (2)
                    SQ P16342 6504-6697! SQ P16342 6697-6872
                 2. SARS coronavirus [TaxId: 227859] [142628] (11)
                    SQ Q6VA80 6619-6774
          47. BC2162-like [142629] (1)
              contains extra helical regions inserted after strands 5 and 6 of the canonical fold
              1. Methyltransferase BC2162 [142630]
                 1. Bacillus cereus [TaxId: 1396] [142631] (2)
                    SQ Q81E32 13-293
          48. CmcI-like [142632] (1)
              Pfam 04989; may have evolved different enzymatic activity
              1. Cephalosporin hydroxylase CmcI [142633]
                 1. Streptomyces clavuligerus [TaxId: 1901] [142634] (34)
                    SQ O85726 2-233
          49. hypothetical RNA methyltransferase [142635] (4)
              C-terminal part of Pfam 03602; similar to (Uracil-5-)-methyltransferase (Pfam 05958)
              1. Putative methyltransferase Atu0340 [142636]
                 there is no associated PUA domain; rudiment extra N-terminal subdomain
                 1. Agrobacterium tumefaciens [TaxId: 358] [142637] (3)
                    SQ Q8UIF7 1-309
              2. Hypothetical protein TTHA1280, middle and C-terminal domains [142638]
                 1. Thermus thermophilus [TaxId: 274] [142639] (10)
                    SQ Q5SIT4 65-382
              3. Hypothetical protein SMu776, middle and C-terminal domains [142640]
                 1. Streptococcus mutans [TaxId: 1309] [142641] (1)
                    SQ Q8DUW5 69-385
              4. Hypothetical protein PH1915, middle and C-terminal domains [142642]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142643] (2)
                    SQ O59578 73-396
          50. RPA4359-like [142644] (1)
              Pfam 02636; DUF185
              1. Hypothetical protein RPA4359 [142645]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [142646] (2)
                    SQ Q6N1P6 2-366
          51. TrmB-like [142647] (2)
              Pfam 02390
              1. tRNA (guanine-N(7)-)-methyltransferase TrmB [142648]
                 1. Streptococcus pneumoniae [TaxId: 1313] [142649] (2)
                    SQ P67506 8-211
                 2. Bacillus subtilis [TaxId: 1423] [142650] (2)
                    SQ O34522 10-213
          52. Methyltransferase 10 domain [142651] (1)
              Pfam 05971; DUF890
              1. Methyltransferase 10 domain containing protein METT10D [142652]
                 1. Human (Homo sapiens) [TaxId: 9606] [142653] (3)
                    SQ Q86W50 42-291
          53. YhiQ-like [159686] (3)
              Pfam 04445; DUF548; contains extra N-terminal alpha+beta subdomain [beta-alpha-beta(4)]
              1. Hypothetical protein YhiQ [159687]
                 1. Escherichia coli [TaxId: 562] [159688] (1)
                    SQ P68568 1-250
                 2. Salmonella typhimurium [TaxId: 90371] [159689] (1)
                    SQ Q9X6G2 1-252
                 3. Shigella flexneri [TaxId: 623] [159690] (1)
                    SQ Q7UAV7 1-250
          54. FkbM-like [159691] (1)
              contains extra N-terminal alpha/beta and all-alpha subdomains
              1. Methyltransferase FkbM [159692]
                 1. Methylobacillus flagellatus [TaxId: 405] [159693] (1)
                    SQ Q1GXX6 14-408
          55. ML2640-like [159694] (1)
              Pfam 02409; O-methyltransferase N-terminus (DUF142); most similar structure to the Leucine carboxy methyltransferase Ppm1 family
              1. Putative methyltransferase ML2640 [159695]
                 1. Mycobacterium leprae [TaxId: 1769] [159696] (4)
                    SQ Q9CCZ4 8-310
          56. TRM1-like [159697] (1)
              Pfam 02005; contains extra C-terminal alpha+beta subdomain
              1. N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1 [159698]
                 1. Pyrococcus horikoshii [TaxId: 53953] [159699] (5)
                    SQ O59493 3-377
          57. LPG1296-like [159700] (1)
              Pfam 04378; DUF519
              1. Uncharacterized protein LPG1296 [159701]
                 involved in catabolism of external DNA
                 1. Legionella pneumophila [TaxId: 446] [159702] (1)
                    SQ Q5ZVZ2 14-284
   95. LmbE-like [102587] (1)
       3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest; topological similarity to SAM-dependent methyltransferases
       1. LmbE-like [102588] (1)
          uperfamily
          1. LmbE-like [102589] (2)
             putative deacetylases
             1. 1D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase MshD [102590]
                1. Mycobacterium tuberculosis [TaxId: 1773] [102591] (2)
                   gene Rv1170
             2. Hypothetical protein TT1542 [102592]
                1. Thermus thermophilus [TaxId: 274] [102593] (1)
   96. PLP-dependent transferase-like [53382] (3)
       main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
       1. PLP-dependent transferases [53383] (9)
          uperfamily
          1. AAT-like [53384] (28)
             1. Aspartate aminotransferase, AAT [53385]
                1. Chicken (Gallus gallus), mitochondria [TaxId: 9031] [53386] (15)
                2. Chicken (Gallus gallus), cytosolic form [TaxId: 9031] [53387] (3)
                3. Pig (Sus scrofa), cytosolic form [TaxId: 9823] [53388] (2)
                4. Baker's yeast (Saccharomyces cerevisiae), cytosolic form [TaxId: 4932] [53389] (1)
                5. Escherichia coli [TaxId: 562] [53390] (65)
                   SQ P00509
                6. Thermus thermophilus [TaxId: 274] [53391] (9)
                7. Phormidium lapideum [TaxId: 32060] [82481] (1)
                8. Thermotoga maritima [TaxId: 2336] [89754] (1)
                   TM1255
             2. Aromatic aminoacid aminotransferase, AroAT [53392]
                1. Paracoccus denitrificans [TaxId: 266] [53393] (12)
                2. Escherichia coli [TaxId: 562] [53394] (1)
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [64120] (3)
             3. Tyrosine aminotransferase (TAT) [53395]
                1. Trypanosoma cruzi [TaxId: 5693] [53396] (1)
             4. Histidinol-phosphate aminotransferase HisC [64121]
                1. Escherichia coli [TaxId: 562] [64122] (6)
                2. Thermotoga maritima [TaxId: 2336] [102594] (8)
                   SQ Q9X0D0
                   TM1040
             5. L-threonine-O-3-phosphate decarboxylase CobD [69563]
                1. Salmonella enterica [TaxId: 28901] [69564] (4)
             6. Low-specificity threonine aldolase [64123]
                1. Thermotoga maritima [TaxId: 2336] [64124] (8)
                2. Leishmania major [TaxId: 5664] [110676] (1)
                   SQ O15839
             7. Alliinase [82482]
                cysteine sulphoxide lyase
                1. Garlic (Allium sativum) [TaxId: 4682] [82483] (6)
             8. Glutamine aminotransferase [110677]
                1. Thermus thermophilus [TaxId: 274] [110678] (3)
                   SQ Q75WK2
             9. Putative methionine aminotransferase YdbL [110679]
                1. Escherichia coli [TaxId: 562] [110680] (1)
                   SQ P77806
             10. Kynurenine--oxoglutarate transaminase I [110681]
                 1. Human (Homo sapiens) [TaxId: 9606] [110682] (3)
                    SQ Q16773
                 2. Yellowfever mosquito (Aedes aegypti) [TaxId: 7159] [142654] (8)
                    SQ Q95VY4 61-477
             11. Putative aminotransferase TM1131 [117691]
                 1. Thermotoga maritima [TaxId: 2336] [117692] (1)
                    SQ Q9X0L5
             12. Putative alanine aminotransferase [117693]
                 1. Pyrococcus furiosus [TaxId: 2261] [117694] (1)
                    SQ Q9P9M8
             13. Multiple substrate aminotransferase, MSAT [142655]
                 1. Thermococcus profundus [TaxId: 49899] [142656] (1)
                    SQ Q9V2W5 13-415
             14. Hypothetical aminotransferase PH0207 [142657]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142658] (1)
                    SQ O57946 26-428
             15. Phenylserine aldolase PSALD [142659]
                 most similar to the low-specificity threonine aldolase
                 1. Pseudomonas putida [TaxId: 303] [142660] (1)
                    SQ Q59IT3 7-351
             16. AAT homologue TM1698 [142661]
                 1. Thermotoga maritima [TaxId: 2336] [142662] (6)
                    SQ Q9X224 4-392
          2. Beta-eliminating lyases [53397] (4)
             1. Tyrosine phenol-lyase [53398]
                1. Citrobacter intermedius [TaxId: 66695] [53399] (2)
                2. Erwinia herbicola [TaxId: 549] [102595] (1)
             2. Tryptophan indol-lyase (tryptophanase) [53400]
                1. Proteus vulgaris [TaxId: 585] [53401] (1)
                2. Escherichia coli [TaxId: 562] [159703] (7)
                   SQ P0A853 5-471! SQ Q8XB34 5-471
          3. Pyridoxal-dependent decarboxylase [69565] (3)
             1. DOPA decarboxylase [69566]
                1. Pig (Sus scrofa) [TaxId: 9823] [69567] (2)
             2. Glutamate decarboxylase beta, GadB [102596]
                1. Escherichia coli [TaxId: 562] [102597] (14)
             3. Glutamate decarboxylase alpha, GadA [117695]
                1. Escherichia coli [TaxId: 562] [117696] (1)
                   SQ P69908
          4. Cystathionine synthase-like [53402] (24)
             1. Cystathionine beta-lyase, CBL [53403]
                1. Escherichia coli [TaxId: 562] [53404] (6)
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [64125] (1)
             2. Cystathionine gamma-synthase, CGS [53405]
                1. Escherichia coli [TaxId: 562] [53406] (1)
                2. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [53407] (4)
             3. Cystathionine gamma-lyase (CYS3) [82484]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82485] (1)
             4. Methionine gamma-lyase, MGL [64126]
                1. Trichomonas vaginalis, MGL1 [TaxId: 5722] [64127] (2)
                2. Pseudomonas putida [TaxId: 303] [75271] (8)
                   SQ P13254
                3. Trichomonas vaginalis, MGL2 [TaxId: 5722] [110683] (1)
                   SQ O15565
                4. Citrobacter freundii [TaxId: 546] [142663] (1)
                   SQ Q84AR1 2-398
             5. Modulator in mal gene expression, MalY [53408]
                1. Escherichia coli [TaxId: 562] [53409] (1)
             6. Cystalysin [53410]
                PLP-dependent haemolytic enzyme
                1. Treponema denticola [TaxId: 158] [53411] (2)
             7. NifS-like protein/selenocysteine lyase [53412]
                1. Thermotoga maritima [TaxId: 2336] [53413] (2)
                2. Escherichia coli [TaxId: 562] [53414] (5)
                   gene product CsdB
             8. Cysteine desulfurase IscS [89755]
                1. Escherichia coli [TaxId: 562] [89756] (1)
             9. Alanine-glyoxylate aminotransferase [89757]
                1. Human (Homo sapiens) [TaxId: 9606] [89758] (2)
                2. Cyanobacteria (Nostoc sp. pcc 7120) [TaxId: 103690] [102598] (1)
                   alr1004
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142664] (1)
                   SQ P43567 3-384
             10. Subgroup IV putative aspartate aminotransferase [102599]
                 1. Thermus thermophilus [TaxId: 274] [102600] (1)
             11. Kynureninase [102601]
                 1. Pseudomonas fluorescens [TaxId: 294] [102602] (1)
             12. 2-aminoethylphosphonate transaminase [82486]
                 1. Salmonella typhimurium [TaxId: 90371] [82487] (1)
             13. Cystine C-S lyase C-des [53415]
                 1. Synechocystis sp. [TaxId: 1143] [53416] (4)
             14. Probable cysteine desulfurase SufS [110684]
                 1. Synechocystis sp. PCC 6803 [TaxId: 1148] [110685] (1)
                    SQ Q55793 # slr0077
             15. O-acetyl-L-homoserine sulfhydrylase [142665]
                 1. Thermus thermophilus [TaxId: 274] [142666] (2)
                    SQ Q93I77 1-421
             16. 3-hydroxykynurenine transaminase [142667]
                 1. Malaria mosquito (Anopheles gambiae) [TaxId: 7165] [142668] (8)
                    SQ Q4LAM2 2-389
          5. GABA-aminotransferase-like [53417] (27)
             formerly omega-Aminoacid:pyruvate aminotransferase-like
             1. Dialkylglycine decarboxylase [53418]
                1. Pseudomonas cepacia [TaxId: 292] [53419] (16)
             2. Glutamate-1-semialdehyde aminomutase (aminotransferase) [53420]
                1. Synechococcus sp., strain GR6 [TaxId: 1131] [53421] (3)
                2. Synechococcus elongatus [TaxId: 32046] [142669] (1)
                   SQ Q8DLK8 45-437
             3. Ornithine aminotransferase [53422]
                1. Human (Homo sapiens) [TaxId: 9606] [53423] (10)
                2. Plasmodium yoelii yoelii [TaxId: 73239] [142670] (6)
                   SQ Q7RT90 7-410
             4. 4-aminobutyrate aminotransferase, GABA-aminotransferase [53424]
                1. Pig (Sus scrofa) [TaxId: 9823] [53425] (3)
                2. Escherichia coli [TaxId: 562] [110686] (14)
                   SQ P22256
             5. Phosphoserine aminotransferase, PSAT [53426]
                1. Bacillus circulans, subsp. alkalophilus [TaxId: 1397] [53427] (4)
                   SQ Q59196
                2. Escherichia coli [TaxId: 562] [53428] (2)
                3. Bacillus alcalophilus [TaxId: 1445] [117697] (19)
                   SQ Q9RME2
             6. Serine hydroxymethyltransferase [53429]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53430] (6)
                   SQ P07511
                2. Mouse (Mus musculus) [TaxId: 10090] [53431] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [53432] (1)
                4. Escherichia coli [TaxId: 562] [53433] (2)
                5. Bacillus stearothermophilus [TaxId: 1422] [75272] (7)
                6. Human (Homo sapiens), mitochondrial [TaxId: 9606] [142671] (1)
                   SQ P34897 42-504
             7. 3-amino-5-hydroxybenzoic acid synthase (AHBA synthase) [53434]
                1. Amycolatopsis mediterranei [TaxId: 33910] [53435] (2)
             8. Aminotransferase ArnB [82488]
                4-amino-4-deoxy-L-arabinose liposaccharide modifying enzyme
                1. Salmonella typhimurium [TaxId: 90371] [82489] (3)
             9. 2-amino-3-ketobutyrate CoA ligase [64128]
                1. Escherichia coli [TaxId: 562] [64129] (1)
             10. PLP-dependent acyl-CoA synthase (8-amino-7-oxonanoate synthase, AONS) [53436]
                 1. Escherichia coli [TaxId: 562] [53437] (4)
             11. Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA [53438]
                 synonym: 7,8-diaminopelargonic acid synthase
                 1. Escherichia coli [TaxId: 562] [53439] (11)
             12. 1-aminocyclopropane-1-carboxylate synthase (ACC synthase) [53440]
                 1. Apple (Malus domestica) [TaxId: 3750] [53441] (4)
                 2. Tomato (Lycopersicon esculentum) [TaxId: 4081] [64130] (2)
             13. Aminotransferase homolog WlaK (PglE, Cj1121c) [102603]
                 1. Campylobacter jejuni [TaxId: 197] [102604] (3)
             14. Spore coat polysaccharide biosynthesis protein C [142672]
                 1. Helicobacter pylori [TaxId: 210] [142673] (6)
                    SQ O25130 2-372
             15. Acetylornithine/acetyl-lysine aminotransferase ArgD [142674]
                 1. Thermus thermophilus [TaxId: 274] [142675] (6)
                    SQ Q93R93 9-395
             16. 5-aminolevulinate synthase [142676]
                 1. Rhodobacter capsulatus [TaxId: 1061] [142677] (12)
                    SQ P18079 2-397
          6. Ornithine decarboxylase major domain [53444] (1)
             1. Ornithine decarboxylase major domain [53445]
                1. Lactobacillus sp., strain 30a [TaxId: 1591] [53446] (2)
          7. Glycine dehydrogenase subunits (GDC-P) [142678] (2)
             Pfam 02347
             1. Glycine dehydrogenase (decarboxylating) subunit 1 [142679]
                1. Thermus thermophilus [TaxId: 274] [142680] (10)
                   SQ Q5SKW8 1-437
             2. Glycine dehydrogenase subunit 2 (P-protein) [142681]
                1. Thermus thermophilus [TaxId: 274] [142682] (10)
                   SQ Q5SKW7 2-472
          8. SelA-like [142683] (1)
             Pfam 03841
             1. Hypothetical protein MJ0158 [142684]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [142685] (2)
                   SQ Q57622 9-374
          9. SepSecS-like [159704] (3)
             Pfam 05889
             1. Selenocysteinyl-tRNA synthase (SepSecS) [159705]
                1. Mouse (Mus musculus) [TaxId: 10090] [159706] (3)
                   SQ Q6P6M7 23-467
                2. Archaeoglobus fulgidus [TaxId: 2234] [159707] (4)
                   SQ O30207 8-371
                3. Methanococcus maripaludis [TaxId: 39152] [159708] (4)
                   SQ Q6LZM9 1-434
       2. PhnH-like [159709] (1)
          single domain protein of similar topology to the core domain of PLP-transferases
          1. PhnH-like [159710] (1)
             Pfam 05845; Bacterial phosphonate metabolism protein (PhnH)
             1. Phosphonate metabolism protein PhnH [159711]
                1. Escherichia coli [TaxId: 562] [159712] (1)
                   SQ P16686 12-194
       3. Dhaf3308-like [159713] (1)
          not known to bind PLP cofactor; the extra N-terminal subdomain has a enolase N-terminal domain-like fold (scop_cf 54825)
          1. Dhaf3308-like [159714] (1)
             Pfam 04016; DUF364
             1. Hypothetical protein Dhaf_3308 [159715]
                1. Desulfitobacterium hafniense [TaxId: 49338] [159716] (2)
                   SQ Q18YZ7 1-251
   97. Nucleotide-diphospho-sugar transferases [53447] (1)
       3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
       1. Nucleotide-diphospho-sugar transferases [53448] (19)
          uperfamily
          1. Spore coat polysaccharide biosynthesis protein SpsA [53449] (1)
             1. Spore coat polysaccharide biosynthesis protein SpsA [53450]
                1. Bacillus subtilis [TaxId: 1423] [53451] (5)
          2. beta 1,4 galactosyltransferase (b4GalT1) [53452] (1)
             1. beta 1,4 galactosyltransferase (b4GalT1) [53453]
                1. Cow (Bos taurus) [TaxId: 9913] [53454] (22)
                   SQ P08037 131-402
          3. Galactosyltransferase LgtC [53458] (1)
             1. Galactosyltransferase LgtC [53459]
                1. Neisseria meningitidis [TaxId: 487] [53460] (3)
                   SQ Q93EK7
          4. Glycogenin [75273] (1)
             1. Glycogenin [75274]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [75275] (10)
          5. alpha-1,3-galactosyltransferase-like [64131] (3)
             1. alpha-1,3-galactosyltransferase catalytic domain [64132]
                1. Cow (Bos taurus) [TaxId: 9913] [64133] (23)
                   SQ P14769
             2. Glycosyltransferase A catalytic domain [75276]
                involved in blood group antigen biosynthesis
                1. Human (Homo sapiens) [TaxId: 9606] [75277] (19)
                   SQ P16442 64-345
             3. Glycosyltransferase B [75278]
                involved in blood group antigen biosynthesis
                1. Human (Homo sapiens) [TaxId: 9606] [75279] (18)
          6. UDP-glucose pyrophosphorylase [53461] (6)
             1. N-acetylglucosamine 1-phosphate uridyltransferase GlmU, N-terminal domain [53462]
                1. Escherichia coli [TaxId: 562] [53463] (9)
                2. Streptococcus pneumoniae [TaxId: 1313] [64134] (5)
             2. UDP-N-acetylglucosamine pyrophosphorylase [75280]
                1. Human (Homo sapiens), AGX1 [TaxId: 9606] [75281] (2)
                2. Human (Homo sapiens), AGX2 [TaxId: 9606] [82490] (2)
                3. Mouse (Mus musculus), AGX2 [TaxId: 10090] [117698] (1)
                   SQ Q91YN5
             3. UDP-glucose pyrophosphorylase 2 (UDPGP 2) [142686]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142687] (8)
                   SQ Q9M9P3 6-383
          7. glucose-1-phosphate thymidylyltransferase [53464] (6)
             1. RmlA (RfbA) [53465]
                1. Pseudomonas aeruginosa [TaxId: 287] [53466] (7)
                2. Salmonella enterica [TaxId: 28901] [64135] (5)
                3. Escherichia coli [TaxId: 562] [69568] (3)
                4. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89759] (1)
             2. RffH [82491]
                1. Escherichia coli [TaxId: 562] [82492] (1)
             3. Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain [142688]
                1. Potato (Solanum tuberosum) [TaxId: 4113] [142689] (12)
                   SQ P23509 80-386
          8. 1,3-glucuronyltransferase [53467] (2)
             1. 1,3-Glucuronyltransferase I (glcAT-I) [53468]
                1. Human (Homo sapiens) [TaxId: 9606] [53469] (4)
             2. Beta-1,3-glucuronyltransferase 1, GlcAT-P [110687]
                1. Human (Homo sapiens) [TaxId: 9606] [110688] (3)
                   SQ Q9P2W7
          9. N-acetylglucosaminyltransferase I [64136] (1)
             1. N-acetylglucosaminyltransferase I [64137]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [64138] (7)
          10. Exostosin [89760] (1)
              1. Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2) [89761]
                 1. Mouse (Mus musculus) [TaxId: 10090] [89762] (4)
          11. Molybdenum cofactor biosynthesis protein MobA [53470] (1)
              1. Molybdenum cofactor biosynthesis protein MobA [53471]
                 1. Escherichia coli [TaxId: 562] [53472] (8)
          12. Cytidylytransferase [68901] (12)
              1. 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) [64140]
                 1. Escherichia coli [TaxId: 562] [64141] (6)
                 2. Neisseria gonorrhoeae [TaxId: 485] [102605] (2)
                 3. Thermotoga maritima [TaxId: 2336] [117699] (1)
                    SQ Q9X1B3
                 4. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142690] (1)
                    SQ P69834 75-300
              2. CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase [64143]
                 1. Escherichia coli, KpsU [TaxId: 562] [64144] (8)
                    capsule-specific enzyme
                 2. Escherichia coli, KdsB [TaxId: 562] [102606] (1)
                 3. Haemophilus influenzae [TaxId: 727] [102607] (2)
              3. CTP:phosphocholine cytidylytransferase LicC [69569]
                 1. Streptococcus pneumoniae [TaxId: 1313] [69570] (2)
              4. CMP acylneuraminate synthetase [53456]
                 a sialic acid activating synthetase
                 1. Neisseria meningitidis [TaxId: 487] [53457] (2)
                 2. Mouse (Mus musculus) [TaxId: 10090] [102608] (1)
              5. Glucose-1-phosphate cytidylyltransferase RfbF [110689]
                 1. Salmonella typhimurium [TaxId: 90371] [110690] (2)
                    SQ P26396 2-257
              6. IspD/IspF bifunctional enzyme, CDP-me synthase domain [117700]
                 1. Campylobacter jejuni [TaxId: 197] [117701] (2)
                    SQ Q9PM68
          13. Glycolipid 2-alpha-mannosyltransferase [102609] (1)
              1. Glycolipid 2-alpha-mannosyltransferase [102610]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102611] (3)
          14. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117702] (1)
              1. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117703]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117704] (1)
                    SQ O08912
          15. MGS-like [142691] (1)
              contains extra C-terminal all-alpha subdomain: 5 helices, orthogonal array
              1. Mannosylglycerate synthase, MGS [142692]
                 1. Rhodothermus marinus [TaxId: 29549] [142693] (28)
                    SQ Q9RFR0 2-382
          16. TTHA0179-like [159717] (1)
              1. Uncharacterized protein TTHA0179 [159718]
                 1. Thermus thermophilus [TaxId: 274] [159719] (1)
                    SQ Q5SLW4 1-231
          17. mannose-1-phosphate guanylyl transferase [159720] (1)
              1. Putative mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase TTHA1750 [159721]
                 1. Thermus thermophilus [TaxId: 274] [159722] (1)
                    SQ Q5SHI0 1-268
          18. MM2497-like [159723] (1)
              Pfam 01983; DUF121
              1. Hypothetical protein MM2497 [159724]
                 1. Methanosarcina mazei [TaxId: 2209] [159725] (2)
                    SQ Q8PU52 1-208
          19. Glycosylating toxin catalytic domain-like [159726] (3)
              contains Glycosyltransferase sugar-binding region containing DXD motif, Pfam 04488
              1. Cytotoxin L [159727]
                 1. Clostridium sordellii [TaxId: 1505] [159728] (9)
                    SQ Q46342 1-542
              2. Alpha-toxin [159729]
                 1. Clostridium novyi [TaxId: 1542] [159730] (1)
                    SQ Q46149 2-541
              3. Toxin B [159731]
                 1. Clostridium difficile [TaxId: 1496] [159732] (2)
                    SQ P18177 1-542
   98. RibA-like [142694] (1)
       3 layers: a/b/a; mixed beta-sheet of 7 strands, order 1235467, strands 1 and 3 are antiparallel to the rest; partial topological similarity to some alpha/beta hydrolases (scop_cf 53473)
       1. RibA-like [142695] (1)
          uperfamily
          1. RibA-like [142696] (1)
             Pfam 00925; GTP cyclohydrolase II
             1. GTP cyclohydrolase II, RibA [142697]
                1. Escherichia coli [TaxId: 562] [142698] (3)
                   SQ P0A7I7 1-174
   99. Activating enzymes of the ubiquitin-like proteins [69571] (1)
       3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
       1. Activating enzymes of the ubiquitin-like proteins [69572] (2)
          transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins
          the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
          uperfamily
          1. Molybdenum cofactor biosynthesis protein MoeB [69573] (1)
             1. Molybdenum cofactor biosynthesis protein MoeB [69574]
                1. Escherichia coli [TaxId: 562] [69575] (3)
          2. Ubiquitin activating enzymes (UBA) [89763] (2)
             the common fold is elaborated with additional (sub)domains
             1. UBA3 [89764]
                a subunit of the heterodimeric E1 enzyme for NEDD8; contains an all-alpha insert subdomain of the FF-like fold (residues 210-288) and an extra C-terminal alpha+beta subdomain (partly disordered)
                1. Human (Homo sapiens) [TaxId: 9606] [89765] (11)
                   SQ Q8TBC4 33-458
             2. Amyloid beta precursor protein-binding protein 1, APPBP1 [89766]
                a subunit of the heterodimeric E1 enzyme for NEDD8; contains a large insertion (residues 170-487) that can be divided into 3 units similar to the UBA3 insertion
                1. Human (Homo sapiens) [TaxId: 9606] [89767] (18)
                   SQ Q13564
   100. alpha/beta-Hydrolases [53473] (1)
        core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
        1. alpha/beta-Hydrolases [53474] (41)
           many members have left-handed crossover connection between strand 8 and additional strand 9
           uperfamily
           1. Acetylcholinesterase-like [53475] (11)
              1. Acetylcholinesterase [53476]
                 1. Pacific electric ray (Torpedo californica) [TaxId: 7787] [53477] (79)
                    SQ P04058 25-556
                 2. Electric eel (Electrophorus electricus) [TaxId: 8005] [53478] (3)
                 3. Mouse (Mus musculus) [TaxId: 10090] [53479] (31)
                 4. Human (Homo sapiens) [TaxId: 9606] [53480] (2)
                 5. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [53481] (3)
              2. Butyryl cholinesterase [102612]
                 1. Human (Homo sapiens) [TaxId: 9606] [102613] (9)
              3. Bile-salt activated lipase (cholesterol esterase) [53482]
                 1. Cow (Bos taurus) [TaxId: 9913] [53483] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [53484] (2)
              4. Mammalian carboxylesterase (liver carboxylesterase I) [75282]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [75283] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [89768] (48)
              5. Thermophilic para-nitrobenzyl esterase (PNB esterase) [53485]
                 1. Bacillus subtilis [TaxId: 1423] [53486] (3)
           2. Carboxylesterase [53487] (9)
              1. Carboxylesterase [53488]
                 bacterial homologue of human hormone sensitive lipase
                 1. Bacillus subtilis, brefeldin A esterase [TaxId: 1423] [53489] (1)
                 2. Alicyclobacillus acidocaldarius [TaxId: 405212] [53490] (3)
                    SQ Q7SIG1
                 3. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69576] (1)
              2. Feruloyl esterase domain of the cellulosomal xylanase z [69577]
                 1. Clostridium thermocellum [TaxId: 1515] [69578] (2)
              3. Feruloyl esterase domain of the cellulosomal xylanase y [69579]
                 1. Clostridium thermocellum [TaxId: 1515] [69580] (8)
              4. Heroin esterase [82493]
                 1. Rhodococcus sp. [TaxId: 1831] [82494] (2)
              5. Enterochelin esterase, catalytic domain [142699]
                 1. Shigella flexneri [TaxId: 623] [142700] (1)
                    SQ Q83SB9 151-397
                 2. Shigella flexneri 2a str. 2457T [TaxId: 198215] [159733] (10)
              6. Uncharacterized protein TM1040_2492 [159734]
                 1. Silicibacter sp. tm1040 [TaxId: 292414] [159735] (4)
                    SQ Q1GDP2 1-261
           3. Mycobacterial antigens [53491] (4)
              1. Antigen 85b [53492]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [53493] (2)
              2. Antigen 85c [53494]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [53495] (3)
                    SQ P31953
              3. Antigen pt51/mpb51 [102614]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [102615] (1)
              4. Antigen 85a [110691]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [110692] (1)
                    SQ P17944 43-330
           4. Hypothetical protein TT1662 [102616] (1)
              1. Hypothetical protein TT1662 [102617]
                 1. Thermus thermophilus [TaxId: 274] [102618] (1)
           5. PepX catalytic domain-like [69581] (4)
              1. Bacterial cocaine esterase N-terminal domain [69582]
                 1. Rhodococcus sp. mb1 [TaxId: 51612] [69583] (4)
              2. Alpha-amino acid ester hydrolase [89769]
                 1. Xanthomonas citri [TaxId: 346] [89770] (1)
                 2. Acetobacter pasteurianus [TaxId: 438] [102619] (29)
              3. X-Prolyl dipeptidyl aminopeptidase PepX, middle domain [82495]
                 1. Lactococcus lactis [TaxId: 1358] [82496] (1)
           6. Prolyl oligopeptidase, C-terminal domain [53496] (1)
              N-terminal domain is a 7-bladed beta-propeller
              1. Prolyl oligopeptidase, C-terminal domain [53497]
                 1. Pig (Sus scrofa) [TaxId: 9823] [53498] (16)
                    SQ P23687
           7. DPP6 catalytic domain-like [82497] (3)
              N-terminal domain is a 8-bladed beta-propeller
              1. Dipeptidyl peptidase IV/CD26, C-terminal domain [82498]
                 1. Human (Homo sapiens) [TaxId: 9606] [82499] (58)
                    SQ P27487 39-776 ! SQ P27487 ! SQ P27487
                 2. Pig (Sus scrofa) [TaxId: 9823] [89771] (76)
              2. Dipeptidyl aminopeptidase-like protein 6, DPP6, C-terminal domain [117705]
                 1. Human (Homo sapiens) [TaxId: 9606] [117706] (1)
                    SQ P42658 127-849
           8. Serine carboxypeptidase-like [53499] (5)
              1. Serine carboxypeptidase II [53500]
                 1. Wheat (Triticum vulgare) [TaxId: 4565] [53501] (5)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53502] (3)
                 3. Baker's yeast (Saccharomyces cerevisiae), kex1(delta)p [TaxId: 4932] [53503] (1)
                    prohormone-processing carboxypeptidase
              2. Human 'protective protein', HPP [53504]
                 synonyms: cathepsin A, carboxypeptidase L
                 1. Human (Homo sapiens) [TaxId: 9606] [53505] (1)
              3. Hydroxynitrile lyase [82500]
                 a novel cyanogenic enzyme
                 1. Sorghum (Sorghum bicolor) [TaxId: 4558] [82501] (1)
           9. Gastric lipase [53506] (2)
              1. Gastric lipase [53507]
                 1. Human (Homo sapiens) [TaxId: 9606] [53508] (1)
                 2. Dog (Canis familiaris) [TaxId: 9615] [75284] (1)
           10. Proline iminopeptidase-like [53509] (3)
               1. Proline iminopeptidase [53510]
                  1. Xanthomonas campestris, pv. citri [TaxId: 339] [53511] (1)
               2. Proline aminopeptidase [81303]
                  1. Serratia marcescens [TaxId: 615] [81304] (4)
                     SQ O32449
               3. Tricorn interacting factor F1 [82502]
                  1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [82503] (3)
           11. Acetyl xylan esterase-like [82504] (2)
               Pfam 05448; AXE1
               1. Cephalosporin C deacetylase [82505]
                  1. Bacillus subtilis [TaxId: 1423] [82506] (3)
               2. Acetyl xylan esterase TM0077 [110693]
                  1. Thermotoga maritima [TaxId: 2336] [110694] (1)
                     SQ Q9WXT2
           12. Haloalkane dehalogenase [53513] (3)
               1. Haloalkane dehalogenase [53514]
                  1. Xanthobacter autotrophicus [TaxId: 280] [53515] (17)
                  2. Rhodococcus sp. [TaxId: 1831] [53516] (3)
                  3. Sphingomonas paucimobilis, UT26, LinB [TaxId: 13689] [53517] (12)
           13. Dienelactone hydrolase [53518] (2)
               1. Dienelactone hydrolase [53519]
                  1. Pseudomonas sp., B13 [TaxId: 306] [53520] (1)
                  2. Pseudomonas putida [TaxId: 303] [53521] (1)
           14. Carbon-carbon bond hydrolase [53522] (4)
               closely related to the Proline iminopeptidase-like family
               1. 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (BPHD) [53523]
                  1. Rhodococcus sp., strain rha1 [TaxId: 1831] [53524] (1)
                  2. Burkholderia xenovorans [TaxId: 36873] [159736] (4)
                     SQ P47229 4-286
               2. Meta-cleavage product hydrolase CumD [82507]
                  2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
                  1. Pseudomonas fluorescens [TaxId: 294] [82508] (9)
                     SQ P96965 3-273
               3. Meta cleavage compound hydrolase CarC [89772]
                  involved in carbazole degradation
                  1. Janthinobacterium sp. J3 [TaxId: 213804] [89773] (1)
           15. Biotin biosynthesis protein BioH [82509] (1)
               1. Biotin biosynthesis protein BioH [82510]
                  1. Escherichia coli [TaxId: 562] [82511] (1)
           16. Aclacinomycin methylesterase RdmC [102620] (1)
               1. Aclacinomycin methylesterase RdmC [102621]
                  1. Streptomyces purpurascens [TaxId: 1924] [102622] (2)
           17. Carboxylesterase/lipase [102623] (1)
               1. Carboxylesterase Est [102624]
                  1. Bacillus stearothermophilus [TaxId: 1422] [102625] (2)
                     SQ Q06174
           18. Epoxide hydrolase [53525] (4)
               1. Mammalian epoxide hydrolase, C-terminal domain [53526]
                  1. Mouse (Mus musculus) [TaxId: 10090] [53527] (4)
                  2. Human (Homo sapiens) [TaxId: 9606] [102626] (6)
               2. Bacterial epoxide hydrolase [53528]
                  1. Agrobacterium radiobacter [TaxId: 358] [53529] (1)
                  2. Aspergillus niger [TaxId: 5061] [53530] (1)
           19. Haloperoxidase [53531] (7)
               1. Bromoperoxidase A2 [53532]
                  1. Streptomyces aureofaciens [TaxId: 1894] [53533] (2)
               2. Bromoperoxidase A1 [53534]
                  1. Streptomyces aureofaciens [TaxId: 1894] [53535] (1)
               3. Chloroperoxidase T [53536]
                  1. Streptomyces aureofaciens [TaxId: 1894] [53537] (2)
               4. Chloroperoxidase L [53538]
                  1. Streptomyces lividans [TaxId: 1916] [53539] (1)
               5. Chloroperoxidase F [53540]
                  1. Pseudomonas fluorescens [TaxId: 294] [53541] (1)
               6. Gamma-lactamase [102627]
                  haloperoxidase homologue
                  1. Aureobacterium sp. [TaxId: 51671] [102628] (2)
               7. Arylesterase [110695]
                  haloperoxidase homologue
                  1. Pseudomonas fluorescens [TaxId: 294] [110696] (1)
                     SQ P22862
           20. Thioesterases [53542] (3)
               1. Myristoyl-ACP-specific thioesterase [53543]
                  1. Vibrio harveyi [TaxId: 669] [53544] (1)
               2. Palmitoyl protein thioesterase 1 [53545]
                  1. Cow (Bos taurus) [TaxId: 9913] [53546] (3)
               3. Palmitoyl protein thioesterase 2 [102629]
                  1. Human (Homo sapiens) [TaxId: 9606] [102630] (1)
           21. Carboxylesterase/thioesterase 1 [53547] (5)
               1. Carboxylesterase [53548]
                  1. Pseudomonas fluorescens [TaxId: 294] [53549] (2)
                  2. Bacillus cereus [TaxId: 1396] [159737] (3)
                     SQ Q81AD5 1-202
                     similar fold and function to the Pseudomonas fluorescens enzyme despite low sequence identity
               2. Acyl protein thioesterase 1 [53550]
                  1. Human (Homo sapiens) [TaxId: 9606] [53551] (1)
               3. Uncharacterized protein Mll8374 [159738]
                  1. Mesorhizobium loti [TaxId: 381] [159739] (2)
                     SQ Q983D6 7-215
               4. Uncharacterized protein Atu2452 [159740]
                  1. Agrobacterium tumefaciens [TaxId: 358] [159741] (2)
                     SQ A9CHT9 1-203
           22. Ccg1/TafII250-interacting factor B (Cib) [75285] (1)
               1. Ccg1/TafII250-interacting factor B (Cib) [75286]
                  1. Human (Homo sapiens) [TaxId: 9606] [75287] (1)
           23. A novel bacterial esterase [53552] (1)
               1. A novel bacterial esterase [53553]
                  1. Alcaligenes sp. [TaxId: 512] [53554] (1)
           24. Lipase [53555] (1)
               1. Lipase [53556]
                  1. Streptomyces exfoliatus [TaxId: 1905] [53557] (1)
           25. Fungal lipases [53558] (12)
               1. Triacylglycerol lipase [53559]
                  1. Yeast (Candida antarctica), form b [TaxId: 34362] [53560] (11)
                  2. Rhizomucor miehei [TaxId: 4839] [53561] (4)
                  3. Penicillium camembertii [TaxId: 5075] [53562] (1)
                  4. Thermomyces lanuginosus, formerly Humicola lanuginosa [TaxId: 5541] [53563] (7)
                  5. Rhizopus niveus [TaxId: 4844] [53564] (1)
                  6. Rhizopus delemar [TaxId: 64495] [53565] (1)
               2. Feruloyl esterase A [102631]
                  Triacylglycerol lipase homologue
                  1. Aspergillus niger [TaxId: 5061] [102632] (7)
                     SQ O42807 23-281
               3. Type-B carboxylesterase/lipase [53566]
                  1. Fungus (Geotrichum candidum), ATCC 34614 [TaxId: 27317] [53567] (1)
                  2. Fungus (Candida rugosa), formerly Cylindracea [TaxId: 5481] [53568] (7)
                  3. Candida rugosa, lipase 2 isoform [TaxId: 5481] [89774] (1)
                  4. Candida cylindracea, cholesterol esterase [TaxId: 44322] [53569] (2)
               4. Esterase EstA [110697]
                  1. Aspergillus niger [TaxId: 5061] [110698] (1)
                     SQ Q6ED33
           26. Bacterial lipase [53570] (7)
               lack the first two strands of the common fold
               1. Lipase A [64145]
                  minimal alpha/beta hydrolase fold;
                  1. Bacillus subtilis [TaxId: 1423] [64146] (16)
                     SQ P37957 34-212
               2. Lipase [53571]
                  1. Pseudomonas glumae, also known as Pseudomonas gladioli [TaxId: 337] [53572] (2)
                  2. Burkholderia cepacia, formerly Pseudomonas cepacia [TaxId: 292] [63399] (7)
                  3. Pseudomonas aeruginosa [TaxId: 287] [53575] (1)
                  4. Chromobacterium viscosum [TaxId: 42739] [53576] (3)
               3. Lipase L1 [75288]
                  1. Bacillus stearothermophilus [TaxId: 1422] [75289] (1)
                  2. Bacillus stearothermophilus, P1 [TaxId: 1422] [82512] (1)
                     the first thermostable bacterial lipase
           27. Pancreatic lipase, N-terminal domain [53577] (6)
               1. Pancreatic lipase, N-terminal domain [53578]
                  contains additional, colipase-binding domain
                  1. Horse (Equus caballus) [TaxId: 9796] [53579] (1)
                  2. Pig (Sus scrofa) [TaxId: 9823] [53580] (1)
                  3. Human (Homo sapiens) [TaxId: 9606] [53581] (3)
                  4. Guinea pig (Cavia porcellus) [TaxId: 10141] [53582] (1)
                  5. Dog (Canis familiaris) [TaxId: 9615] [53583] (1)
                     pancreatic lipase related protein 1
                  6. Rat (Rattus norvegicus) [TaxId: 10116] [53584] (1)
                     pancreatic lipase related protein 2
           28. Hydroxynitrile lyase-like [53585] (3)
               1. Hydroxynitrile lyase [53586]
                  1. Rubber tree (Hevea brasiliensis) [TaxId: 3981] [53587] (19)
                     SQ P52704
                  2. Cassava (Manihot esculenta) [TaxId: 3983] [53588] (7)
               2. Salicylic acid-binding protein 2 (SABP2) [117707]
                  1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [117708] (3)
                     SQ Q6RYA0
           29. Thioesterase domain of polypeptide, polyketide and fatty acid synthases [69584] (4)
               Pfam 00975
               1. Erythromycin polyketide synthase [69585]
                  synonym: 6-deoxyerythronolide synthase
                  1. Saccharopolyspora erythraea [TaxId: 1836] [69586] (2)
               2. Picromycin polyketide synthase [82513]
                  1. Streptomyces venezuelae [TaxId: 54571] [82514] (9)
               3. Surfactin synthetase, SrfA [75290]
                  1. Bacillus subtilis [TaxId: 1423] [75291] (1)
               4. Fatty acid synthase [117709]
                  1. Human (Homo sapiens) [TaxId: 9606] [117710] (1)
                     SQ P49327 2212-2496
           30. Cutinase-like [52260] (3)
               minimal alpha/beta hydrolase lacking peripheral secondary structures; similar to a flavodoxin-like fold
               1. Cutinase [52261]
                  1. Fungus (Fusarium solani), subsp. pisi [TaxId: 169388] [52262] (39)
               2. Acetylxylan esterase [52263]
                  1. Penicillium purpurogenum [TaxId: 28575] [52264] (3)
                  2. Trichoderma reesei [TaxId: 51453] [52265] (1)
           31. YdeN-like [110699] (1)
               Pfam 06821; DUF1234; lack the first two strands of the common fold
               1. Hypothetical protein YdeN [110700]
                  1. Bacillus subtilis [TaxId: 1423] [110701] (1)
                     SQ P96671
           32. Putative serine hydrolase Ydr428c [110702] (1)
               1. Putative serine hydrolase Ydr428c [110703]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110704] (1)
                     SQ Q04066
           33. Acylamino-acid-releasing enzyme, C-terminal donain [117711] (1)
               closely related to the prolyl peptidase and DPP6 domains (scop_fa 53496 and 82497)
               1. Acylamino-acid-releasing enzyme, C-terminal donain [117712]
                  1. Aeropyrum pernix [TaxId: 56636] [117713] (12)
                     SQ Q9YBQ2
           34. Hypothetical esterase YJL068C [117714] (1)
               part of Pfam 00756
               1. Hypothetical esterase YJL068C [117715]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117716] (1)
                     SQ P40363
           35. Hypothetical protein VC1974 [117717] (1)
               1. Hypothetical protein VC1974 [117718]
                  1. Vibrio cholerae [TaxId: 666] [117719] (1)
                     SQ Q9KQM4
           36. Atu1826-like [159742] (2)
               1. XC6422 protein [159743]
                  XCC0260 orthologue
                  1. Xanthomonas campestris [TaxId: 339] [159744] (1)
                     SQ Q8PDS5 3-220
               2. Hypothetical protein Atu1826 [159745]
                  1. Agrobacterium tumefaciens [TaxId: 358] [159746] (2)
                     SQ Q8UED4 2-219
           37. PHB depolymerase-like [159747] (1)
               1. Polyhydroxybutyrate depolymerase [159748]
                  1. Penicillium funiculosum [TaxId: 28572] [159749] (2)
           38. IroE-like [159750] (1)
               1. Enterobactin and salmochelin hydrolase IroE [159751]
                  1. Escherichia coli [TaxId: 562] [159752] (2)
                     SQ Q6KD95 41-305
           39. TTHA1544-like [159753] (1)
               minimal hydrolase fold (one strand less than the cutinase-like family); there is neither catalytic triad, nor nucleopilic residue in the elbow motif
               1. Hypothetical protein TTHA1544 [159754]
                  1. Thermus thermophilus [TaxId: 274] [159755] (2)
                     SQ Q5SI36 2-123
           40. O-acetyltransferase [159756] (3)
               1. Acetyl-CoA:deacetylcephalosporin C acetyltransferase CefG [159757]
                  1. Acremonium chrysogenum [TaxId: 5044] [159758] (36)
                     SQ P39058 66-441
               2. Homoserine O-acetyltransferase [159759]
                  1. Leptospira interrogans [TaxId: 173] [159760] (1)
                     SQ Q8F4I0 5-366
                  2. Haemophilus influenzae [TaxId: 727] [159761] (1)
                     SQ P45131 2-358
           41. 2,6-dihydropseudooxynicotine hydrolase-like [159762] (1)
               Pfam 06500; DUF1100
               1. 2,6-dihydropseudooxynicotine hydrolase [159763]
                  1. Arthrobacter nicotinovorans [TaxId: 29320] [159764] (1)
                     SQ Q93NG6 8-367
   101. Nucleoside hydrolase [53589] (1)
        core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
        1. Nucleoside hydrolase [53590] (1)
           uperfamily
           1. Nucleoside hydrolase [53591] (4)
              1. Inosine-uridine nucleoside N-ribohydrolase, IU-NH [53592]
                 1. Crithidia fasciculata [TaxId: 5656] [53593] (2)
              2. Nucleoside hydrolase [53594]
                 1. Leishmania major [TaxId: 5664] [53595] (1)
              3. Inosine-adenosine-guanosine preferring nucleoside hydrolase [69587]
                 1. Trypanosoma vivax [TaxId: 5699] [69588] (9)
              4. Pyrimidine nucleoside hydrolase YeiK [102633]
                 1. Escherichia coli [TaxId: 562] [102634] (5)
   102. Dihydrofolate reductase-like [53596] (1)
        3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
        1. Dihydrofolate reductase-like [53597] (2)
           uperfamily
           1. Dihydrofolate reductases [53598] (12)
              1. Dihydrofolate reductase, prokaryotic type [53599]
                 1. Escherichia coli [TaxId: 562] [53600] (46)
                 2. Lactobacillus casei [TaxId: 1582] [53601] (8)
                 3. Mycobacterium tuberculosis [TaxId: 1773] [53602] (4)
                 4. Thermotoga maritima [TaxId: 2336] [53603] (2)
                 5. Haloferax volcanii [TaxId: 2246] [53604] (1)
                 6. Bacteriophage T4 [TaxId: 10665] [102635] (1)
              2. Dihydrofolate reductases, eukaryotic type [53605]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [53606] (8)
                 2. Human (Homo sapiens) [TaxId: 9606] [53607] (27)
                 3. Fungus (Pneumocystis carinii) [TaxId: 4754] [53608] (14)
                 4. Yeast (Candida albicans) [TaxId: 5476] [53609] (9)
              3. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, DFR domain [53610]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [88963] (3)
                 2. Cryptosporidium hominis [TaxId: 237895] [102636] (7)
                    SQ Q5CGA3 Q27552
           2. RibD C-terminal domain-like [142701] (3)
              Pfam 01872
              1. Riboflavin biosynthesis protein RibD [142702]
                 1. Bacillus subtilis [TaxId: 1423] [142703] (8)
                    SQ P17618 146-359
                 2. Thermotoga maritima [TaxId: 2336] [142704] (1)
                    SQ Q9X2E8 148-345
              2. HTP reductase [142705]
                 monofunctional 5-amino-6-(5-phosphoribosylamino)uracil reductase
                 1. Methanococcus jannaschii [TaxId: 2190] [142706] (6)
                    SQ Q58085 6-224
   103. Ribokinase-like [53612] (3)
        core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
        potential superfamily: members of this fold have similar functions but different ATP-binding sites
        1. Ribokinase-like [53613] (5)
           has extra strand located between strands 2 and 3
           uperfamily
           1. Thiamin biosynthesis kinases [53620] (4)
              1. Hydroxyethylthiazole kinase (THZ kinase, ThiK) [53621]
                 1. Bacillus subtilis [TaxId: 1423] [53622] (5)
                 2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102637] (1)
              2. 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) [69589]
                 1. Salmonella typhimurium [TaxId: 90371] [69590] (2)
                 2. Thermus thermophilus [TaxId: 274] [89775] (1)
           2. YjeF C-terminal domain-like [75292] (2)
              1. Hypothetical protein YxkO [75293]
                 1. Bacillus subtilis [TaxId: 1423] [75294] (1)
              2. Hypothetical protein TM0922, C-terminal domain [142707]
                 YjeF homolog
                 1. Thermotoga maritima [TaxId: 2336] [142708] (1)
                    SQ Q9X024 212-489
           3. PfkB-like kinase [82515] (2)
              includes a variety of carbohydrate and pyrimidine kinases
              1. Pyridoxal kinase [82516]
                 1. Sheep (Ovis aries) [TaxId: 9940] [82517] (8)
              2. Pyridoxamine kinase [102638]
                 1. Escherichia coli [TaxId: 562] [102639] (2)
                    SQ P77150
           4. Ribokinase-like [53614] (13)
              1. Ribokinase [53615]
                 1. Escherichia coli [TaxId: 562] [53616] (5)
                 2. Thermotoga maritima [TaxId: 2336] [110706] (1)
                    SQ Q9X055
                 3. Human (Homo sapiens) [TaxId: 9606] [142709] (2)
                    SQ Q9H477 15-322
              2. 2-keto-3-deoxygluconate kinase [75295]
                 1. Thermotoga maritima, TM0067 [TaxId: 2336] [75296] (2)
                 2. Thermus thermophilus [TaxId: 274] [102640] (4)
              3. Hypothetical protein TM0415 [102641]
                 1. Thermotoga maritima [TaxId: 2336] [102642] (1)
              4. Putative sugar kinase TM0828 [82518]
                 1. Thermotoga maritima [TaxId: 2336] [82519] (2)
              5. Adenosine kinase [53617]
                 1. Human (Homo sapiens) [TaxId: 9606] [53618] (5)
                 2. Toxoplasma gondii [TaxId: 5811] [53619] (10)
              6. Aminoimidazole riboside kinase [117720]
                 1. Salmonella typhimurium [TaxId: 90371] [117721] (3)
                    SQ Q8ZKR2
              7. Tagatose-6-phosphate kinase LacC [142710]
                 1. Enterococcus faecalis [TaxId: 1351] [142711] (4)
                    SQ Q833W9 1-313
              8. Fructose 1-phosphate kinase FruB [142712]
                 1. Bacillus halodurans [TaxId: 86665] [142713] (2)
                    SQ Q9KEM5 1-306
              9. Hypothetical fructokinase ST2478 [142714]
                 1. Sulfolobus tokodaii [TaxId: 111955] [142715] (18)
                    SQ Q96XN9 2-309
           5. ADP-specific Phosphofructokinase/Glucokinase [64147] (3)
              Pfam 04587
              1. ADP-dependent glucokinase [64148]
                 1. Archaeon Thermococcus litoralis [TaxId: 2265] [64149] (2)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102643] (1)
              2. ADP-specific phosphofructokinase [110707]
                 1. Pyrococcus horikoshii [TaxId: 53953] [110708] (1)
                    SQ O59355 # PH1645
        2. MurD-like peptide ligases, catalytic domain [53623] (2)
           has extra strand located between strands 1 and 2
           uperfamily
           1. MurCDEF [53624] (5)
              1. UDP-N-acetylmuramate-alanine ligase MurC [82520]
                 1. Thermotoga maritima [TaxId: 2336] [82521] (1)
                    TM0231
                 2. Haemophilus influenzae [TaxId: 727] [89776] (4)
              2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [53625]
                 1. Escherichia coli [TaxId: 562] [53626] (11)
              3. UDP-N-acetylmuramyl tripeptide synthetase MurE [64150]
                 1. Escherichia coli [TaxId: 562] [64151] (1)
              4. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [53627]
                 1. Escherichia coli [TaxId: 562] [53628] (1)
           2. Folylpolyglutamate synthetase [53629] (2)
              1. Folylpolyglutamate synthetase [53630]
                 1. Lactobacillus casei [TaxId: 1582] [53631] (7)
                 2. Thermotoga maritima [TaxId: 2336] [102644] (1)
                    TM0166
        3. CoaB-like [102645] (1)
           combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest
           uperfamily
           1. CoaB-like [102646] (2)
              Pfam 04127
              1. Phosphopantothenoylcysteine synthetase [102647]
                 1. Human (Homo sapiens) [TaxId: 9606] [102648] (1)
              2. Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (CoaB) [117722]
                 1. Escherichia coli [TaxId: 562] [117723] (4)
                    SQ P24285 181-404
   104. YjeF N-terminal domain-like [64152] (1)
        3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest
        1. YjeF N-terminal domain-like [64153] (1)
           possible circular permutation of the ribokinase-like fold (of the YjeF C-terminal domain)
           uperfamily
           1. YjeF N-terminal domain-like [64154] (2)
              1. Hypothetical protein YNL200c (YNU0_YEAST) [64155]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64156] (1)
              2. Hypothetical protein TM0922, N-terminal domain [142716]
                 YjeF homolog
                 1. Thermotoga maritima [TaxId: 2336] [142717] (1)
                    SQ Q9X024 1-211
   105. Carbamate kinase-like [53632] (1)
        3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
        1. Carbamate kinase-like [53633] (3)
           the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase
           uperfamily
           1. Carbamate kinase [53634] (2)
              1. Carbamate kinase [53635]
                 1. Enterococcus faecium [TaxId: 1352] [53636] (1)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [53637] (1)
           2. N-acetyl-l-glutamate kinase [75297] (4)
              1. N-acetyl-l-glutamate kinase [75298]
                 1. Escherichia coli [TaxId: 562] [75299] (5)
                 2. Pseudomonas aeruginosa [TaxId: 287] [142718] (12)
                    SQ Q9HTN2 1-300
                 3. Mycobacterium tuberculosis [TaxId: 1773] [142719] (6)
                    SQ P0A4Y6 4-294
                 4. Thermotoga maritima [TaxId: 2336] [142720] (3)
                    SQ Q9X2A4 1-282
           3. PyrH-like [142721] (10)
              part of Pfam 00696
              1. Glutamate 5-kinase [142722]
                 1. Campylobacter jejuni [TaxId: 197] [142723] (4)
                    SQ Q9PJ29 2-251
              2. Aspartokinase [142724]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142725] (2)
                    SQ Q9LYU8 84-387
                 2. Methanococcus jannaschii [TaxId: 2190] [142726] (4)
                    SQ Q57991 2-303
                 3. Escherichia coli [TaxId: 562] [142727] (3)
                    SQ P08660 3-294
                    Lysine-sensitive aspartokinase 3
              3. Uridylate kinase PyrH [142728]
                 1. Streptococcus pyogenes [TaxId: 1314] [142729] (3)
                    SQ P65938 2-239
                 2. Escherichia coli [TaxId: 562] [142730] (12)
                    SQ P0A7E9 4-240
                 3. Pyrococcus furiosus [TaxId: 2261] [142731] (6)
                    SQ Q8U122 1-225
                 4. Archaeoglobus fulgidus [TaxId: 2234] [142732] (2)
                    SQ O28237 1-219
                 5. Haemophilus influenzae [TaxId: 727] [142733] (6)
                    SQ P43890 2-237
                 6. Neisseria meningitidis [TaxId: 487] [142734] (3)
                    SQ P65932 4-239
   106. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64157] (1)
        core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest
        1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64158] (1)
           uperfamily
           1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64159] (1)
              1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64160]
                 1. Bacillus stearothermophilus [TaxId: 1422] [64161] (4)
   107. Alkaline phosphatase-like [53648] (1)
        core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
        1. Alkaline phosphatase-like [53649] (5)
           uperfamily
           1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64162] (1)
              1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64163]
                 1. Bacillus stearothermophilus [TaxId: 1422] [64164] (4)
           2. Alkaline phosphatase [53650] (3)
              common fold is decorated with several large insertions
              1. Alkaline phosphatase [53651]
                 1. Escherichia coli [TaxId: 562] [53652] (33)
                 2. Human (Homo sapiens) [TaxId: 9606] [64165] (5)
                 3. Northern shrimp (Pandalus borealis) [TaxId: 6703] [75300] (3)
                    SQ Q9BHT8 # fragment
           3. Arylsulfatase [53653] (4)
              includes additional C-terminal alpha+beta (sub)domain
              1. Arylsulfatase A [53654]
                 1. Human (Homo sapiens) [TaxId: 9606] [53655] (7)
              2. Arylsulfatase B (4-sulfatase) [53656]
                 1. Human (Homo sapiens) [TaxId: 9606] [53657] (1)
                 2. Pseudomonas aeruginosa [TaxId: 287] [69591] (1)
              3. Steryl-sulfatase [102649]
                 contains membrane-anchoring alpha-hairpin insertion
                 1. Human (Homo sapiens) [TaxId: 9606] [102650] (1)
                    placental estrone/DHEA sulfatase
           4. Phosphonoacetate hydrolase [102651] (1)
              contains alpha+beta subdomain inserted near C-terminus
              1. Phosphonoacetate hydrolase [102652]
                 1. Pseudomonas fluorescens [TaxId: 294] [102653] (1)
           5. DeoB catalytic domain-like [142735] (1)
              Pfam 08342 in the N-terminal part; Pfam 01676 in the C-terminal part; there is an alpha+beta domain between the two parts, inserted in the same location as the substrate-binding domain of 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
              1. Phosphopentomutase DeoB [142736]
                 1. Streptococcus mutans [TaxId: 1309] [142737] (2)
                    SQ Q8DTU0 2-107,227-403
   108. TTHA0583/YokD-like [110709] (1)
        3 layers: a/b/a; mixed beta-sheet of 8 strands, order 78612354; strands 3, 4 and 8 are antiparallel to the rest
        1. TTHA0583/YokD-like [110710] (2)
           uperfamily
           1. Hypothetical protein TT1679 [110711] (1)
              Pfam 04260, DUF436
              1. Hypothetical protein TT1679 [110712]
                 UPF0340 protein TTHA0583
                 1. Thermus thermophilus [TaxId: 274] [110713] (1)
                    SQ P68591
           2. Aminoglycoside 3-N-acetyltransferase-like [159765] (1)
              Pfam 02522; CoA-dependent enzymes
              1. Uncharacterized protein YokD [159766]
                 1. Bacillus subtilis [TaxId: 1423] [159767] (3)
                    SQ O32003 2-271
   109. Glycerol-3-phosphate (1)-acyltransferase [69592] (1)
        3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8 are antiparallel to the rest
        1. Glycerol-3-phosphate (1)-acyltransferase [69593] (1)
           some topological similarity to the dihydrofolate reductase fold
           uperfamily
           1. Glycerol-3-phosphate (1)-acyltransferase [69594] (1)
              1. Glycerol-3-phosphate (1)-acyltransferase [69595]
                 1. Cushaw squash (Cucurbita moschata) [TaxId: 3662] [69596] (2)
   110. AraD/HMP-PK domain-like [53638] (1)
        3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
        1. AraD/HMP-PK domain-like [53639] (2)
           uperfamily
           1. AraD-like aldolase/epimerase [53640] (4)
              metal (zinc)-ion dependent
              1. L-fuculose-1-phosphate aldolase [53641]
                 class II aldolase
                 1. Escherichia coli [TaxId: 562] [53642] (17)
              2. L-ribulose-5-phosphate 4-epimerase [69597]
                 1. Escherichia coli [TaxId: 562] [69598] (2)
              3. L-rhamnulose-1-phosphate aldolase [75301]
                 1. Escherichia coli [TaxId: 562] [75302] (2)
              4. Putative sugar-phosphate aldolase [102654]
                 1. Thermotoga maritima [TaxId: 2336] [102655] (1)
           2. Phosphomethylpyrimidine kinase C-terminal domain-like [159768] (2)
              1. Phosphomethylpyrimidine kinase [159769]
                 1. Pyrococcus furiosus [TaxId: 2261] [159770] (2)
                    SQ Q8U193 268-451
              2. Uncharacterized protein MJ0236 [159771]
                 1. Methanocaldococcus jannaschii [TaxId: 2190] [159772] (4)
                    SQ Q57688 241-420
   111. SurE-like [64166] (1)
        3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7
        1. SurE-like [64167] (1)
           some topological similarity to the N-terminal domain of Glutaminase/Asparaginase family
           uperfamily
           1. SurE-like [64168] (2)
              1. SurE homolog TM1662 [64169]
                 has a phosphatase activity
                 1. Thermotoga maritima [TaxId: 2336] [64170] (4)
              2. SurE homolog PAE2908 (SurE-alpha) [82522]
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [82523] (1)
   112. YerB-like [159773] (1)
        3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4
        1. YerB-like [159774] (1)
           1. YerB-like [159775] (1)
              PfamB 028118
              1. Uncharacterized protein YerB [159776]
                 1. Bacillus subtilis [TaxId: 1423] [159777] (1)
                    SQ O34968 32-327
   113. CdCA1 repeat-like [159778] (1)
        contains two parallel beta-strands of four strands each; the sheets contact each other with edges at a right angle
        1. CdCA1 repeat-like [159779] (1)
           1. CdCA1 repeat-like [159780] (1)
              Pfam 10563
              1. Cadmium-specific carbonic anhydrase CdCA1 [159781]
                 1. Thalassiosira weissflogii [TaxId: 67004] [159782] (6)
                    SQ Q50EL4 1-196! SQ Q50EL4 198-406
   114. Isocitrate/Isopropylmalate dehydrogenase-like [53658] (1)
        consists of two intertwined (sub)domains related by pseudo dyad; duplication
        3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
        1. Isocitrate/Isopropylmalate dehydrogenase-like [53659] (5)
           the constituent families form similar dimers
           uperfamily
           1. Dimeric isocitrate & isopropylmalate dehydrogenases [53660] (13)
              the active site is between the two identical subunits
              1. 3-isopropylmalate dehydrogenase, IPMDH [53661]
                 1. Thermus thermophilus [TaxId: 274] [53662] (14)
                 2. Chimera (Thermus thermophilus) and (Bacillus subtilis) [TaxId: 274] [53663] (2)
                 3. Bacillus coagulans [TaxId: 1398] [53664] (3)
                 4. Thiobacillus ferrooxidans [TaxId: 920] [53665] (1)
                 5. Salmonella typhimurium [TaxId: 90371] [53666] (1)
                 6. Escherichia coli [TaxId: 562] [53667] (1)
                 7. Thermotoga maritima [TaxId: 2336] [110714] (1)
                    SQ Q9WZ26
                 8. Sulfolobus tokodaii [TaxId: 111955] [117724] (1)
                    SQ P50455
                 9. Mycobacterium tuberculosis [TaxId: 1773] [117725] (5)
                    SQ P95313
              2. Isocitrate dehydrogenase, ICDH [53668]
                 1. Escherichia coli [TaxId: 562] [53669] (26)
                 2. Bacillus subtilis [TaxId: 1423] [64171] (1)
              3. NADP-dependent isocitrate dehydrogenase [82524]
                 1. Pig (Sus scrofa) [TaxId: 9823] [82525] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [110715] (2)
                    SQ O75874
           2. PdxA-like [102656] (2)
              Pfam 04166; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PlsX-like and phosphotransacetylase families
              1. 4-hydroxythreonine-4-phosphate dehydrogenase PdxA [102657]
                 pyridoxal phosphate biosynthetic protein
                 1. Escherichia coli [TaxId: 562] [102658] (3)
                 2. Salmonella typhimurium [TaxId: 90371] [102659] (1)
           3. PlsX-like [102660] (2)
              Pfam 02504; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and phosphotransacetylase families
              1. Fatty acid/phospholipid synthesis protein PlsX [102661]
                 1. Bacillus subtilis [TaxId: 1423] [102662] (1)
                 2. Enterococcus faecalis [TaxId: 1351] [110716] (1)
                    SQ Q82ZE8
           4. Phosphotransacetylase [102663] (4)
              Pfam 01515; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and PlsX-like families
              1. Phosphotransacetylase Pta [110717]
                 1. Methanosarcina thermophila [TaxId: 2210] [110718] (5)
                    SQ P38503
                 2. Streptococcus pyogenes [TaxId: 1314] [102665] (1)
                 3. Bacillus subtilis [TaxId: 1423] [117726] (2)
                    SQ P39646
              2. Ethanolamine utilization protein EutD [117727]
                 1. Escherichia coli [TaxId: 562] [117728] (1)
                    SQ P77218 2-323
           5. Monomeric isocitrate dehydrogenase [82526] (1)
              the active site is contained within one subunit between the canonical ICDH fold and a large insert domain that itself is a probable rudiment form of ICDH fold resulted from duplication, domain swapping and deletion
              1. Monomeric isocitrate dehydrogenase [82527]
                 1. Azotobacter vinelandii [TaxId: 354] [82528] (1)
                    the insert region spans residues 150-404
   115. Amidase signature (AS) enzymes [75303] (1)
        possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest
        1. Amidase signature (AS) enzymes [75304] (1)
           uperfamily
           1. Amidase signature (AS) enzymes [75305] (5)
              1. Malonamidase E2 [75306]
                 1. Bradyrhizobium japonicum [TaxId: 375] [75307] (12)
              2. Peptide amidase Pam [82529]
                 1. Stenotrophomonas maltophilia [TaxId: 40324] [82530] (2)
              3. Fatty acid amide hydrolase (oleamide hydrolase) [82531]
                 elaborated fold with additional helices
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [82532] (1)
              4. Glutamyl-tRNA(Gln) amidotransferase subunit A [142738]
                 1. Staphylococcus aureus [TaxId: 1280] [142739] (5)
                    SQ P63488 1-485
                 2. Thermotoga maritima [TaxId: 2336] [142740] (1)
                    SQ Q9X0Z9 1-475
   116. ATC-like [53670] (2)
        consists of two similar domains related by pseudo dyad; duplication
        core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
        1. Aspartate/ornithine carbamoyltransferase [53671] (1)
           uperfamily
           1. Aspartate/ornithine carbamoyltransferase [53672] (11)
              1. Aspartate carbamoyltransferase catalytic subunit [53673]
                 1. Escherichia coli [TaxId: 562] [53674] (94)
                    SQ P00479
                 2. Bacillus subtilis [TaxId: 1423] [53675] (1)
                 3. Archaeon Pyrococcus abyssi [TaxId: 29292] [82533] (1)
                 4. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [110719] (3)
                    SQ Q55338
              2. Ornithine transcarbamoylase [53676]
                 1. Pseudomonas aeruginosa [TaxId: 287] [53677] (2)
                 2. Escherichia coli [TaxId: 562] [53678] (3)
                 3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53679] (2)
                 4. Human (Homo sapiens) [TaxId: 9606] [53680] (4)
                 5. Sheep (Ovis aries) [TaxId: 9940] [102666] (1)
                 6. Thermotoga maritima [TaxId: 2336] [110720] (1)
                    SQ P96108
              3. Transcarbamylase-like protein [75308]
                 1. Bacteroides fragilis [TaxId: 817] [75309] (25)
        2. Aspartate/glutamate racemase [53681] (1)
           uperfamily
           1. Aspartate/glutamate racemase [53682] (3)
              C-terminal extension is added to the N-terminal domain
              1. Glutamate racemase [53683]
                 1. Aquifex pyrophilus [TaxId: 2714] [53684] (2)
              2. Aspartate racemase [75310]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75311] (2)
                 2. Pyrococcus horikoshii OT3 [TaxId: 70601] [159783] (2)
   117. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53685] (1)
        consists of two similar domains related by pseudo dyad; duplication
        core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
        1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53686] (1)
           uperfamily
           1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53687] (22)
              1. Tryptophan synthase, beta-subunit [53688]
                 1. Salmonella typhimurium [TaxId: 90371] [53689] (47)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [142741] (10)
                    SQ Q8U093 1-386
              2. O-acetylserine sulfhydrylase (Cysteine synthase) [53690]
                 1. Salmonella typhimurium [TaxId: 90371] [53691] (3)
                 2. Thermotoga maritima [TaxId: 2336] [75312] (1)
                    TM0665
                 3. Archaeon Aeropyrum pernix [TaxId: 56636] [142742] (2)
                    SQ Q9YBL2 1-382
                 4. Thermus thermophilus [TaxId: 274] [142743] (5)
                    SQ Q5SLE6 1-302
                 5. Escherichia coli, isoform B (CysM) [TaxId: 562] [142744] (8)
                    SQ P16703 2-293
                 6. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142745] (2)
                    SQ P47998 3-322
                 7. Haemophilus influenzae [TaxId: 727] [142746] (1)
                    SQ P45040 2-311
              3. Threonine deaminase [53692]
                 1. Escherichia coli [TaxId: 562] [53693] (1)
                 2. Thermus thermophilus [TaxId: 274] [142747] (4)
                    SQ Q5SLL4 2-311
              4. Threonine synthase [64172]
                 1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [64173] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75313] (1)
                 3. Thermus thermophilus [TaxId: 274] [102667] (3)
                 4. Escherichia coli [TaxId: 562] [142748] (1)
                    SQ P00934 1-428
              5. L-serine dehydratase [102668]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [102669] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [110721] (1)
                    SQ P20132
              6. 1-aminocyclopropane-1-carboxylate deaminase [53694]
                 1. Yeast (Hansenula saturnus) [TaxId: 4906] [53695] (4)
                 2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [89777] (2)
                 3. Pseudomonas sp., strain ACP [TaxId: 306] [110722] (6)
                    SQ Q00740
              7. Cystathionine beta-synthase [64174]
                 PLP-dependent hemoprotein
                 1. Human (Homo sapiens) [TaxId: 9606] [64175] (2)
              8. Hypothetical protein C320.14 (SPCC320.14, SPCC330.15c) [142749]
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [142750] (2)
                    SQ O59791 6-323
   118. SIS domain [53696] (1)
        3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
        1. SIS domain [53697] (3)
           uperfamily
           1. mono-SIS domain [69599] (8)
              dimer of mono-domain subunits
              1. Probable 3-hexulose-6-phosphate isomerase MJ1247 [69600]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [69601] (1)
              2. Hypothetical protein YckF [82534]
                 1. Bacillus subtilis [TaxId: 1423] [82535] (2)
              3. Hypothetical protein HI0754 [89778]
                 1. Haemophilus influenzae [TaxId: 727] [89779] (1)
              4. Hypothetical protein AF1796 [102670]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102671] (1)
              5. Phosphoheptose isomerase GmhA1 [110723]
                 1. Campylobacter jejuni [TaxId: 197] [110724] (1)
                    SQ Q9PNE6
                 2. Vibrio cholerae [TaxId: 666] [110725] (1)
                    SQ Q9KPY2
                 3. Pseudomonas aeruginosa [TaxId: 287] [117729] (1)
                    SQ Q9HVZ0
                 4. Pseudomonas aeruginosa str. PAO1 (Pseudomonas aeruginosa PAO1) [TaxId: 208964] [159784] (4)
           2. double-SIS domain [53698] (4)
              duplication: consists of two SIS domains related by pseudo dyad
              1. Hypothetical protein TM0813 [75314]
                 1. Thermotoga maritima [TaxId: 2336] [75315] (1)
              2. "Isomerase domain" of glucosamine 6-phosphate synthase (GLMS) [53699]
                 1. Escherichia coli [TaxId: 562] [53700] (11)
              3. Glucose-6-phosphate isomerase, conjectural [110726]
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [110727] (4)
                    SQ Q8ZWV0
              4. Glucose-6-phosphate isomerase-like protein TTHA1346 [117730]
                 1. Thermus thermophilus [TaxId: 274] [117731] (1)
                    SQ Q5SIM3
           3. Phosphoglucose isomerase, PGI [53701] (6)
              permutation of the double-SIS domain fold
              1. Phosphoglucose isomerase, PGI [53702]
                 moonlights as neuroleukin, autocrine motility factor, and differentiation mediator
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53703] (8)
                 2. Human (Homo sapiens) [TaxId: 9606] [64176] (5)
                 3. Pig (Sus scrofa) [TaxId: 9823] [75316] (2)
                 4. Bacillus stearothermophilus [TaxId: 1422] [53704] (4)
                 5. Leishmania mexicana [TaxId: 5665] [110728] (2)
                    SQ P42861
                 6. Mouse (Mus musculus) [TaxId: 10090] [117732] (3)
                    SQ P06745
   119. Formate dehydrogenase/DMSO reductase, domains 1-3 [53705] (1)
        contains of two similar intertwined domains related by pseudo dyad; duplication
        core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
        1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53706] (1)
           molybdopterine enzyme
           uperfamily
           1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53707] (12)
              domain 1 (residues 1-55) binds Fe4S4 cluster in FDH but not DMSO reductase
              1. Dimethylsulfoxide reductase (DMSO reductase) [53708]
                 1. Rhodobacter sphaeroides [TaxId: 1063] [53709] (1)
                 2. Rhodobacter capsulatus [TaxId: 1061] [53710] (10)
              2. Formate dehydrogenase H [53711]
                 1. Escherichia coli [TaxId: 562] [53712] (4)
              3. Formate dehydrogenase N, alpha subunit [75317]
                 1. Escherichia coli [TaxId: 562] [75318] (2)
              4. Tungsten containing formate dehydrogenase, large subunit [82536]
                 1. Desulfovibrio gigas [TaxId: 879] [82537] (1)
              5. Trimethylamine N-oxide reductase [53713]
                 1. Shewanella massilia [TaxId: 76854] [53714] (1)
              6. Arsenite oxidase large subunit [53715]
                 1. Alcaligenes faecalis [TaxId: 511] [53716] (2)
              7. Periplasmic nitrate reductase alpha chain [53717]
                 1. Desulfovibrio desulfuricans [TaxId: 876] [53718] (8)
                    dissimilatory nitrate reductase (NAP)
                 2. Rhodobacter sphaeroides [TaxId: 1063] [102672] (1)
              8. Respiratory nitrate reductase 1 alpha chain [102673]
                 1. Escherichia coli [TaxId: 562] [102674] (7)
                    SQ P09152
              9. Transhydroxylase alpha subunit, AthL [110729]
                 1. Pelobacter acidigallici [TaxId: 35816] [110730] (6)
                    SQ P80563
              10. NADH-quinone oxidoreductase chain 3, Nqo3 [142751]
                  1. Thermus thermophilus [TaxId: 274] [142752] (4)
                     SQ Q56223 247-685
   120. ALDH-like [53719] (1)
        consists of two similar domains with 3 layers (a/b/a) each; duplication
        core: parallel beta-sheet of 5 strands, order 32145
        1. ALDH-like [53720] (2)
           binds NAD differently from other NAD(P)-dependent oxidoreductases
           uperfamily
           1. ALDH-like [53721] (14)
              1. Aldehyde reductase (dehydrogenase), ALDH [53722]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [53723] (1)
                 2. Rat (Rattus norvegicus), retinal type II [TaxId: 10116] [53724] (1)
                 3. Cow (Bos taurus), mitochondrial [TaxId: 9913] [53725] (2)
                 4. Human (Homo sapiens), mitochondrial [TaxId: 9606] [53726] (17)
                    SQ P05091
                 5. Sheep (Ovis aries) [TaxId: 9940] [53727] (1)
                 6. Elephant shrew (Elephantulus edwardii) [TaxId: 28737] [89780] (1)
                    cytosolic form; eta-crystallin
                 7. Baltic cod (Gadus callarias) [TaxId: 8053] [53728] (2)
                 8. Streptococcus mutans [TaxId: 1309] [53729] (4)
                 9. Vibrio harveyi [TaxId: 669] [53730] (2)
              2. Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN [82538]
                 1. Archaeon Thermoproteus tenax [TaxId: 2271] [82539] (8)
                    SQ O57693
              3. Gamma-glutamyl phosphate reductase [89781]
                 1. Thermotoga maritima [TaxId: 2336] [89782] (1)
                    TM0293
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110731] (1)
                    SQ P54885
              4. 1-pyrroline-5-carboxylate dehydrogenase [102675]
                 1. Thermus thermophilus [TaxId: 274] [102676] (3)
              5. Putative betaine aldehyde dehydrogenase YdcW [117733]
                 1. Escherichia coli [TaxId: 562] [117734] (2)
                    SQ P77674
           2. L-histidinol dehydrogenase HisD [69602] (1)
              1. L-histidinol dehydrogenase HisD [69603]
                 1. Escherichia coli [TaxId: 562] [69604] (4)
   121. NadA-like [142753] (1)
        duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134
        1. NadA-like [142754] (1)
           uperfamily
           1. NadA-like [142755] (1)
              Pfam 02445
              1. Quinolinate synthetase A, NadA [142756]
                 1. Pyrococcus horikoshii [TaxId: 53953] [142757] (1)
                    SQ O57767 1-298
   122. Aconitase iron-sulfur domain [53731] (1)
        consists of three similar domains with 3 layers (a/b/a) each; duplication
        core: parallel beta-sheet of 5 strands, order 32145
        1. Aconitase iron-sulfur domain [53732] (1)
           uperfamily
           1. Aconitase iron-sulfur domain [53733] (4)
              duplication: consists of three structurally similar subdomains with subdomains 1 and 3 being related by pseudo twofold symmetry
              1. Aconitase A, N-terminal domain [53734]
                 1. Pig (Sus scrofa) [TaxId: 9823] [53735] (6)
                 2. Cow (Bos taurus) [TaxId: 9913] [53736] (9)
              2. Aconitase B, C-terminal domain [75319]
                 1. Escherichia coli [TaxId: 562] [75320] (1)
              3. Iron-responsive element binding protein 1, N-terminal domain [142758]
                 1. Human (Homo sapiens) [TaxId: 9606] [142759] (3)
                    SQ P21399 2-630
   123. Phosphoglucomutase, first 3 domains [53737] (1)
        consists of three similar domains with 3 layers (a/b/a) each; duplication
        core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
        1. Phosphoglucomutase, first 3 domains [53738] (1)
           uperfamily
           1. Phosphoglucomutase, first 3 domains [53739] (3)
              1. Phosphoglucomutase [53740]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53741] (6)
              2. Exocytosis-sensitive phosphoprotein, pp63/parafusin [69605]
                 1. Paramecium tetraurelia [TaxId: 5888] [69606] (2)
              3. Phosphomannomutase/phosphoglucomutase [69607]
                 1. Pseudomonas aeruginosa [TaxId: 287] [69608] (24)
   124. FucI/AraA N-terminal and middle domains [53742] (1)
        consists of two domains of similar topology, 3 layers (a/b/a) each
        Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
        Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
        1. FucI/AraA N-terminal and middle domains [53743] (2)
           uperfamily
           1. L-fucose isomerase, N-terminal and second domains [53744] (1)
              1. L-fucose isomerase, N-terminal and second domains [53745]
                 1. Escherichia coli [TaxId: 562] [53746] (1)
           2. AraA N-terminal and middle domain-like [142760] (1)
              N-terminal part of Pfam 02610
              1. L-arabinose isomerase AraA [142761]
                 1. Escherichia coli [TaxId: 562] [142762] (6)
                    SQ P08202 1-328
   125. YgbK-like [142763] (1)
        consists of two domains with partial topological similarity to the P-loop kinases but without the P-loop motif; the domain association results in the formation of a single mixed beta-sheet of 15 strands
        1. YgbK-like [142764] (1)
           uperfamily
           1. YgbK-like [142765] (1)
              Pfam 07005; DUF1537; the B-fam model-covered region is non-compact in structure and distributed between the two domains
              1. Hypothetical protein HI1011 [142766]
                 1. Haemophilus influenzae [TaxId: 727] [142767] (2)
                    SQ P44093 2-413
   126. Phosphoglycerate kinase [53747] (1)
        consists of two non-similar domains, 3 layers (a/b/a) each
        Domain 1 has parallel beta-sheet of 6 strands, order 342156
        Domain 2 has parallel beta-sheet of 6 strands, order 321456
        1. Phosphoglycerate kinase [53748] (1)
           uperfamily
           1. Phosphoglycerate kinase [53749] (7)
              Domain 2 binds ATP
              1. Phosphoglycerate kinase [53750]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53751] (3)
                 2. Bacillus stearothermophilus [TaxId: 1422] [53752] (1)
                 3. Thermus thermophilus [TaxId: 274] [102677] (1)
                 4. Thermotoga maritima [TaxId: 2336] [53753] (1)
                 5. Trypanosoma brucei [TaxId: 5691] [53754] (2)
                 6. Pig (Sus scrofa) [TaxId: 9823] [64177] (4)
                 7. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [89783] (1)
   127. UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1)
        consists of two non-similar domains with 3 layers (a/b/a) each
        domain 1: parallel beta-sheet of 7 strands, order 3214567
        domain 2: parallel beta-sheet of 6 strands, order 321456
        1. UDP-Glycosyltransferase/glycogen phosphorylase [53756] (11)
           uperfamily
           1. beta-Glucosyltransferase (DNA-modifying) [53757] (1)
              1. beta-Glucosyltransferase (DNA-modifying) [53758]
                 1. Bacteriophage T4 [TaxId: 10665] [53759] (20)
                    SQ P04547
           2. Peptidoglycan biosynthesis glycosyltransferase MurG [53760] (1)
              1. Peptidoglycan biosynthesis glycosyltransferase MurG [53761]
                 UDP-N-acetylglucosamine:N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
                 1. Escherichia coli [TaxId: 562] [53762] (2)
           3. UDP-N-acetylglucosamine 2-epimerase [53763] (3)
              1. UDP-N-acetylglucosamine 2-epimerase [53764]
                 1. Escherichia coli [TaxId: 562] [53765] (2)
                 2. Bacillus subtilis [TaxId: 1423] [102678] (1)
                 3. Thermus thermophilus [TaxId: 274] [102679] (1)
           4. Gtf glycosyltransferase [64178] (3)
              Glycosyltransferase family 28
              1. UDP-glucosyltransferase GtfB [64179]
                 1. Amycolatopsis orientalis [TaxId: 31958] [64180] (1)
              2. TDP-epi-vancosaminyltransferase GtfA [102680]
                 1. Amycolatopsis orientalis [TaxId: 31958] [102681] (2)
              3. TDP-vancosaminyltransferase GftD [110732]
                 1. Amycolatopsis orientalis [TaxId: 31958] [110733] (1)
                    SQ Q9AFC7
           5. ADP-heptose LPS heptosyltransferase II [89784] (1)
              1. ADP-heptose LPS heptosyltransferase II [89785]
                 1. Escherichia coli [TaxId: 562] [89786] (1)
           6. Trehalose-6-phosphate synthase, OtsA [82540] (1)
              family 20 glycosyltransferase; good structural similarity in the active site to the Oligosaccharide phosphorylases
              1. Trehalose-6-phosphate synthase, OtsA [82541]
                 1. Escherichia coli [TaxId: 562] [82542] (3)
           7. Oligosaccharide phosphorylase [53766] (4)
              1. Glycogen phosphorylase [53767]
                 both domains are elaborated with many insertions
                 1. Human (Homo sapiens) [TaxId: 9606] [53768] (17)
                 2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53769] (106)
                    SQ P00489 ! SQ P00489
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53770] (1)
              2. Maltodextrin phosphorylase (MALP) [53771]
                 1. Escherichia coli [TaxId: 562] [53772] (15)
           8. Glycosyl transferases group 1 [110734] (4)
              Pfam 00534
              1. Glycogen synthase 1, GlgA [110735]
                 1. Agrobacterium tumefaciens [TaxId: 358] [110736] (2)
                    SQ P39670
                 2. Pyrococcus abyssi [TaxId: 29292] [142768] (4)
                    SQ Q9V2J8 1-437! SQ Q9V2J8 218-413
              2. First mannosyl transferase WbaZ [142769]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [142770] (1)
                    SQ O30192 173-338
              3. Lipopolysaccharide core biosynthesis protein RfaG [142771]
                 Glucosyltransferase I
                 1. Escherichia coli [TaxId: 562] [142772] (2)
                    SQ P25740 2-371
           9. Sialyltransferase-like [142773] (1)
              1. Alpha-2,3/2,6-sialyltransferase/sialidase [142774]
                 1. Pasteurella multocida [TaxId: 747] [142775] (9)
                    SQ Q15KI8 26-412
           10. UDPGT-like [159785] (4)
               Pfam 00201
               1. UDP glucose:flavonoid 3-o-glucosyltransferase [159786]
                  1. Grape (Vitis vinifera) [TaxId: 29760] [159787] (3)
                     SQ O22304 7-456
               2. Triterpene UDP-glucosyl transferase UGT71G1 [159788]
                  1. Medicago truncatula [TaxId: 3880] [159789] (4)
                     SQ Q5IFH7 3-463
               3. (Iso)flavonoid glycosyltransferase [159790]
                  1. Medicago truncatula [TaxId: 3880] [159791] (1)
                     SQ A6XNC5 8-480
               4. Hydroquinone glucosyltransferase [159792]
                  1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [159793] (3)
                     SQ Q9M156 6-476
           11. FucT-like [159794] (1)
               Pfam 00852; Glycosyltransferase family 10 (fucosyltransferase)
               1. Alpha1,3-fucosyltransferase FucT [159795]
                  1. Helicobacter pylori [TaxId: 210] [159796] (9)
                     SQ O30511 1-349
   128. Glutaminase/Asparaginase [53773] (1)
        consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
        Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
        Domain 2 has parallel beta-sheet of 4 strands, order 1234
        1. Glutaminase/Asparaginase [53774] (1)
           uperfamily
           1. Glutaminase/Asparaginase [53775] (8)
              1. Asparaginase type II [53776]
                 1. Escherichia coli [TaxId: 562] [53777] (7)
                 2. Wolinella succinogenes [TaxId: 844] [53778] (1)
                 3. Erwinia chrysanthemi [TaxId: 556] [53779] (8)
                 4. Vibrio cholerae [TaxId: 666] [159797] (4)
                    SQ Q9KQK3 2-337
              2. Glutaminase-asparaginase [53780]
                 1. Acinetobacter glutaminasificans [TaxId: 474] [53781] (1)
                 2. Pseudomonas sp., 7A [TaxId: 306] [53782] (4)
              3. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [142776]
                 1. Pyrococcus abyssi [TaxId: 29292] [142777] (2)
                    SQ Q9V0T9 76-438
                 2. Methanobacterium thermoautotrophicum [TaxId: 145262] [142778] (2)
                    SQ O26802 84-435
   129. Phosphofructokinase [53783] (1)
        consists of two non-similar domains, 3 layers (a/b/a) each
        Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
        Domain 2 has parallel sheet of 4 strands, order 2314
        1. Phosphofructokinase [53784] (1)
           uperfamily
           1. Phosphofructokinase [53785] (3)
              1. ATP-dependent phosphofructokinase [53786]
                 Domain 1 binds ATP
                 1. Escherichia coli [TaxId: 562] [53787] (2)
                 2. Bacillus stearothermophilus [TaxId: 1422] [53788] (4)
              2. Pyrophosphate-dependent phosphofructokinase [75321]
                 1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [75322] (3)
   130. Tetrapyrrole methylase [53789] (1)
        consists of two non-similar domains
        Domain 1 has parallel sheet of 5 strands, order 32415
        Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
        1. Tetrapyrrole methylase [53790] (1)
           uperfamily
           1. Tetrapyrrole methylase [53791] (10)
              Pfam 00590
              1. Cobalt precorrin-4 methyltransferase CbiF [53792]
                 1. Bacillus megaterium [TaxId: 1404] [53793] (2)
              2. Siroheme synthase CysG, domains 4 and 5 [102682]
                 1. Salmonella typhimurium [TaxId: 90371] [102683] (3)
              3. Diphthine synthase, DphB [102684]
                 diphthamide biosynthesis methyltransferase
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102685] (1)
                 2. Aeropyrum pernix [TaxId: 56636] [117735] (1)
                    SQ Q9YDI2; APE0931
                 3. Pyrococcus horikoshii [TaxId: 53953] [142779] (6)
                    SQ O58456 1-265
              4. Uroporphyrin-III C-methyltransferase (SUMT, UROM, CobA) [117736]
                 1. Pseudomonas denitrificans [TaxId: 43306] [117737] (1)
                    SQ P21631
                 2. Thermus thermophilus [TaxId: 274] [142780] (2)
                    SQ Q53WA2 1-235
              5. Hypothetical protein TTHA0667 [142781]
                 strong sequence similarity to the CysG domain
                 1. Thermus thermophilus [TaxId: 274] [142782] (4)
                    SQ Q5SKH6 2-226
              6. Putative methytransferase BT4190 [142783]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [142784] (4)
                    SQ Q8A031 2-234
              7. Precorrin-6y methylase CbiE [142785]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [142786] (2)
                    SQ O29536 1-195
   131. GckA/TtuD-like [82543] (1)
        consists of two non-similar domains
        Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology
        Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2
        1. GckA/TtuD-like [82544] (1)
           uperfamily
           1. GckA/TtuD-like [82545] (1)
              1. Putative glycerate kinase (hypothetical protein TM1585) [82546]
                 1. Thermotoga maritima [TaxId: 2336] [82547] (2)
   132. DAK1/DegV-like [82548] (1)
        2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order: 2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest]
        1. DAK1/DegV-like [82549] (2)
           domain folds and architecture show some similarity to the tubulin-like GTPases; the nucleotide-binding sites of the Dihydroxyacetone kinase and tubulin families are different
           uperfamily
           1. DegV-like [82550] (2)
              Pfam 02645, DUF194
              1. Hypothetical protein TM841 [82551]
                 reveals fatty acid binding function
                 1. Thermotoga maritima [TaxId: 2336] [82552] (2)
                    SQ Q9X1H9
              2. Hypothetical protein apc36103 [102686]
                 lipid-binding protein; Bacilus subtilis YitS ortholog
                 1. Bacillus stearothermophilus [TaxId: 1422] [102687] (1)
           2. DAK1 [109613] (2)
              Pfam 02733
              1. Dihydroxyacetone kinase subunit K, DhaK [109614]
                 1. Escherichia coli [TaxId: 562] [109615] (4)
                    SQ P76015 20-366
                    gene product YcgT
              2. Dihydroxyacetone kinase [109616]
                 contains additional alpha-helical, ATP-binding domain
                 1. Citrobacter freundii [TaxId: 546] [109617] (2)
   133. DHH phosphoesterases [64181] (1)
        consists of two non-similar domains
        Domain 1 has parallel sheet of 6 strands, order 321456
        Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest
        1. DHH phosphoesterases [64182] (2)
           constituent families have similar domain organization with variable interdomain linker and spatial arrangement of the domains
           uperfamily
           1. Manganese-dependent inorganic pyrophosphatase (family II) [64183] (3)
              1. Manganese-dependent inorganic pyrophosphatase (family II) [64184]
                 1. Streptococcus mutans [TaxId: 1309] [64185] (1)
                 2. Streptococcus gordonii [TaxId: 1302] [69609] (2)
                    SQ P95765
                 3. Bacillus subtilis [TaxId: 1423] [69610] (5)
                    SQ P37487
           2. Exonuclease RecJ [75323] (1)
              1. Exonuclease RecJ [75324]
                 1. Thermus thermophilus [TaxId: 274] [75325] (1)
   134. Glycerate kinase I [110737] (1)
        consists of two different alpha/beta domains; (1) of the Flavodoxin-like fold (scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf 52979), inserted into domain 1
        1. Glycerate kinase I [110738] (1)
           uperfamily
           1. Glycerate kinase I [110739] (1)
              Pfam 02595
              1. Glycerate kinase GlxK [110740]
                 1. Neisseria meningitidis, (serogroup A) [TaxId: 487] [110741] (1)
                    SQ P57098
   135. PEP carboxykinase-like [53794] (1)
        contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
        1. PEP carboxykinase-like [53795] (2)
           uperfamily
           1. PEP carboxykinase C-terminal domain [53796] (4)
              1. Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) [68921]
                 1. Escherichia coli [TaxId: 562] [53798] (10)
                 2. Thermus thermophilus [TaxId: 274] [82553] (7)
                    SQ Q7SIC6
                 3. Trypanosoma cruzi [TaxId: 5693] [69611] (1)
              2. Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing) [69612]
                 1. Human (Homo sapiens) [TaxId: 9606] [69613] (8)
           2. HPr kinase HprK C-terminal domain [64186] (3)
              1. HPr kinase HprK C-terminal domain [64187]
                 1. Lactobacillus casei [TaxId: 1582] [64188] (3)
                 2. Staphylococcus xylosus [TaxId: 1288] [75326] (1)
                 3. Mycoplasma pneumoniae [TaxId: 2104] [82554] (1)
   136. PEP carboxykinase N-terminal domain [68922] (1)
        contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain
        1. PEP carboxykinase N-terminal domain [68923] (1)
           uperfamily
           1. PEP carboxykinase N-terminal domain [68924] (4)
              1. Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) [68925]
                 1. Escherichia coli [TaxId: 562] [68926] (10)
                 2. Thermus thermophilus [TaxId: 274] [82555] (7)
                    SQ Q7SIC6
                 3. Trypanosoma cruzi [TaxId: 5693] [69614] (1)
              2. Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing) [69615]
                 1. Human (Homo sapiens) [TaxId: 9606] [69616] (8)
   137. Chelatase-like [53799] (3)
        duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
        1. Chelatase [53800] (3)
           interdomain linker is short; swapping of C-terminal helices between the two domains
           uperfamily
           1. Ferrochelatase [53801] (3)
              1. Ferrochelatase [53802]
                 1. Bacillus subtilis [TaxId: 1423] [53803] (8)
                 2. Human (Homo sapiens) [TaxId: 9606] [64189] (3)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82556] (2)
           2. Cobalt chelatase CbiK [53804] (1)
              1. Cobalt chelatase CbiK [53805]
                 1. Salmonella typhimurium [TaxId: 90371] [53806] (1)
           3. CbiX-like [110742] (1)
              Pfam 01903; single-domain protein; forms the C-terminal helix-swapped dimer similar to the CbiK subunit
              1. Sirohydrochlorin cobaltochelatase CbiX [110743]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110744] (3)
                    SQ O29537
        2. "Helical backbone" metal receptor [53807] (4)
           contains a long alpha helical insertion in the interdomain linker
           uperfamily
           1. Periplasmic ferric siderophore binding protein FhuD [53808] (1)
              1. Periplasmic ferric siderophore binding protein FhuD [53809]
                 1. Escherichia coli [TaxId: 562] [53810] (4)
           2. TroA-like [53811] (5)
              1. Periplasmic zinc binding protein TroA [53812]
                 1. Treponema pallidum [TaxId: 160] [53813] (2)
              2. Periplasmic zinc binding protein ZnuA [102688]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [102689] (1)
              3. Pneumococcal surface antigen PssA [53814]
                 1. Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] [53815] (1)
              4. Vitamin B12 binding protein BtuF [82557]
                 1. Escherichia coli [TaxId: 562] [82558] (4)
              5. Mn transporter MntC [142787]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [142788] (2)
                    SQ Q79EF9 49-327
           3. Nitrogenase iron-molybdenum protein [53816] (6)
              contains three domains of this fold; "Helical backbone" holds domains 2 and 3
              both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
              1. Nitrogenase iron-molybdenum protein, alpha chain [81402]
                 1. Clostridium pasteurianum [TaxId: 1501] [81396] (1)
                 2. Azotobacter vinelandii [TaxId: 354] [81398] (18)
                 3. Klebsiella pneumoniae [TaxId: 573] [81400] (4)
              2. Nitrogenase iron-molybdenum protein, beta chain [81401]
                 both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
                 1. Clostridium pasteurianum [TaxId: 1501] [81395] (1)
                 2. Azotobacter vinelandii [TaxId: 354] [81397] (18)
                 3. Klebsiella pneumoniae [TaxId: 573] [81399] (4)
           4. TM0189-like [142789] (3)
              Part of Pfam 01497 that include some other superfamily members
              1. Putative iron(III) transporter TM0189 [142790]
                 1. Thermotoga maritima [TaxId: 2336] [142791] (2)
                    SQ Q9WY32 25-358
              2. Enterochelin uptake protein CeuE [142792]
                 1. Campylobacter jejuni [TaxId: 197] [142793] (2)
                    SQ Q0P8Q4 44-330
              3. Iron-uptake system-binding protein FeuA [159798]
                 1. Bacillus subtilis [TaxId: 1423] [159799] (1)
                    SQ P40409 39-315
        3. PrpR receptor domain-like [159800] (1)
           recent PDB entry 2q5c belongs to this superfamily
           1. PrpR receptor domain-like [159801] (1)
              N-terminal domain corresponds to Pfam 06506; C-terminal domain, assigned to Pfam 00158, is distinct from other structures of this Pfam family
              1. Propionate catabolism operon regulatory protein PrpR [159802]
                 1. Escherichia coli [TaxId: 562] [159803] (4)
                    SQ P77743 11-196
   138. HemD-like [69617] (1)
        duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345
        1. HemD-like [69618] (1)
           uperfamily
           1. HemD-like [69619] (2)
              Pfam 02602
              1. Uroporphyrinogen III synthase (U3S, HemD) [69620]
                 1. Human (Homo sapiens) [TaxId: 9606] [69621] (1)
              2. Probable uroporphyrinogen-III synthase [117738]
                 1. Thermus thermophilus [TaxId: 274] [117739] (1)
                    SQ Q5SKH2; TTHA0671
   139. CAC2185-like [142794] (1)
        consists of two non-similar domains, 3 layers (a/b/a) each; d1 has parallel sheet of 4 strands, order 2134; d2 has parallel sheet of 5 strands, order 21345, and antiparallel meander sheet of 3 strands
        1. CAC2185-like [142795] (1)
           uperfamily
           1. CAC2185-like [142796] (1)
              1. Hypothetical protein CAC2185 [142797]
                 1. Clostridium acetobutylicum [TaxId: 1488] [142798] (2)
                    SQ Q97H28 1-305
   140. Periplasmic binding protein-like I [53821] (1)
        consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
        parallel beta-sheet of 6 strands, order 213456
        1. Periplasmic binding protein-like I [53822] (1)
           Similar in architecture to the superfamily II but partly differs in topology
           uperfamily
           1. L-arabinose binding protein-like [53823] (18)
              1. D-ribose-binding protein [53824]
                 1. Escherichia coli, strain k-12 [TaxId: 562] [53825] (6)
              2. L-arabinose-binding protein [53826]
                 1. Escherichia coli [TaxId: 562] [53827] (9)
              3. D-allose-binding protein [53828]
                 1. Escherichia coli [TaxId: 562] [53829] (3)
              4. Galactose/glucose-binding protein [53830]
                 1. Escherichia coli [TaxId: 562] [53831] (6)
                 2. Salmonella typhimurium, strain lt2 [TaxId: 90371] [53832] (3)
              5. Amide receptor/negative regulator of the amidase operon (AmiC) [53833]
                 1. Pseudomonas aeruginosa [TaxId: 287] [53834] (3)
              6. Quorum-sensing signal (autoinducer-2) binding protein LuxP [69622]
                 1. Vibrio harveyi [TaxId: 669] [69623] (4)
              7. Purine repressor (PurR), C-terminal domain [53835]
                 1. Escherichia coli [TaxId: 562] [53836] (24)
              8. Lac-repressor (lacR) core (C-terminal domain) [53837]
                 1. Escherichia coli [TaxId: 562] [53838] (16)
              9. Trehalose repressor, C-terminal domain [53839]
                 1. Escherichia coli [TaxId: 562] [53840] (1)
              10. Leucine-,isoleucine-,valine-binding (LIV) protein [53841]
                  1. Escherichia coli [TaxId: 562] [53842] (1)
              11. Leucine-binding protein [53843]
                  1. Escherichia coli [TaxId: 562] [53844] (4)
              12. Hormone binding domain of the atrial natriuretic peptide receptor [53845]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [53846] (2)
                     SQ P18910 29-454
                  2. Human (Homo sapiens) [TaxId: 9606] [64190] (2)
              13. Metabotropic glutamate receptor subtype 1 [53847]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [53848] (5)
              14. AI-2 receptor LsrB [110745]
                  1. Salmonella typhi [TaxId: 90370] [110746] (2)
                     SQ Q8Z2X8 27-340
              15. Glucose-resistance amylase regulator CcpA, C-terminal domain [117740]
                  1. Bacillus megaterium [TaxId: 1404] [117741] (11)
                     SQ P46828 58-322 ! SQ P46828
              16. YraM C-terminal domain [159804]
                  1. Haemophilus influenzae [TaxId: 727] [159805] (1)
                     SQ P45299 257-573
                     HI1655
   141. Periplasmic binding protein-like II [53849] (1)
        consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
        mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
        1. Periplasmic binding protein-like II [53850] (3)
           Similar in architecture to the superfamily I but partly differs in topology
           uperfamily
           1. Phosphate binding protein-like [53851] (65)
              1. Oligo-peptide binding protein (OPPA) [53852]
                 contains an additional alpha+beta domain inserted in the N-terminal domain
                 1. Salmonella typhimurium [TaxId: 90371] [53853] (32)
                 2. Bacillus subtilis [TaxId: 1423] [142799] (1)
                    SQ P42061 40-543
                 3. Thermotoga maritima [TaxId: 2336] [142800] (2)
                    SQ Q9X0V0 23-557
                    TM1223
              2. Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain [53854]
                 1. Escherichia coli [TaxId: 562] [53855] (5)
              3. Lysine-,arginine-,ornithine-binding (LAO) protein [53856]
                 1. Salmonella typhimurium [TaxId: 90371] [53857] (5)
              4. Sulphate-binding protein [53858]
                 1. Salmonella typhimurium [TaxId: 90371] [53859] (1)
              5. Phosphate-binding protein [53860]
                 1. Escherichia coli [TaxId: 562] [53861] (13)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [110747] (1)
                    SQ P15712
              6. D-maltodextrin-binding protein, MBP [53862]
                 contains a few additional helices in the C-terminal extension; homologous to thiaminase I
                 1. Escherichia coli [TaxId: 562] [53863] (47)
                    SQ P02928
                 2. Alicyclobacillus acidocaldarius [TaxId: 405212] [102690] (3)
                 3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53864] (1)
                 4. Archaeon Thermococcus litoralis [TaxId: 2265] [64191] (1)
                    trehalose maltose-binding protein
                 5. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159806] (1)
              7. Thiaminase I [53865]
                 contains a few additional helices in the C-terminal extension; homologous to MBP
                 1. Paenibacillus thiaminolyticus [TaxId: 49283] [53866] (3)
              8. Ferric-binding protein FbpA [53867]
                 1. Haemophilus influenzae [TaxId: 727] [53868] (5)
                 2. Mannheimia haemolytica [TaxId: 75985] [102691] (3)
                    SQ Q9Z4N6
                 3. Neisseria gonorrhoeae [TaxId: 485] [53869] (4)
                    SQ Q50964 23-331
                 4. Yersinia enterocolitica, YfuA [TaxId: 630] [117742] (1)
                    SQ Q56925 28-338
                 5. Serratia marcescens, SfuA [TaxId: 615] [117743] (1)
                    SQ P21408 32-338
                 6. Campylobacter jejuni [TaxId: 197] [117744] (1)
                    SQ Q9PIV4 17-334
                 7. Bordetella pertussis [TaxId: 520] [117745] (3)
                    SQ Q7VXW9 31-349
              9. Dipeptide-binding protein [53870]
                 similar domain organization to oligopeptide-binding protein, OPPA
                 1. Escherichia coli [TaxId: 562] [53871] (2)
              10. Hypothetical protein YliB [102692]
                  similar domain organization to oligo- and dipeptide-binding protein
                  1. Escherichia coli [TaxId: 562] [102693] (1)
              11. Nickel-binding periplasmic protein NikA [102694]
                  similar domain organization to oligo- and dipeptide-binding protein
                  1. Escherichia coli [TaxId: 562] [102695] (10)
              12. Histidine-binding protein [53872]
                  1. Escherichia coli [TaxId: 562] [53873] (1)
                  2. Salmonella typhimurium [TaxId: 90371] [53874] (1)
              13. Spermidine/putrescine-binding protein PotD [53875]
                  1. Escherichia coli [TaxId: 562] [53876] (2)
              14. Putrescine receptor (PotF) [53877]
                  1. Escherichia coli [TaxId: 562] [53878] (1)
              15. Glutamine-binding protein [53879]
                  1. Escherichia coli [TaxId: 562] [53880] (2)
              16. Glutamate receptor ligand binding core [53881]
                  1. Rat (Rattus norvegicus), GluR2 [TaxId: 10116] [53882] (80)
                  2. Synechocystis sp., GluR0 [TaxId: 1143] [64192] (3)
                  3. Rat (Rattus norvegicus), GluR6 [TaxId: 10116] [142801] (14)
                     SQ P42260 421-544,668-804! SQ P42260 429-544,667-806
                  4. Rat (Rattus norvegicus), GluR5 [TaxId: 10116] [142802] (13)
                     SQ P22756 429-546,667-799! SQ P22756 433-544,682-815
              17. Putative GluR0 ligand binding core [102696]
                  1. Thermus thermophilus [TaxId: 274] [102697] (2)
              18. N-methyl-D-aspartate receptor subunit 1 [89787]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [89788] (9)
                  2. Rat (Rattus norvegicus), subtype 2A [TaxId: 10116] [142803] (2)
                     SQ Q00959 404-539,661-801
              19. ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain [82559]
                  there is an additional C-terminal allosteric domain in some species
                  1. Mycobacterium tuberculosis [TaxId: 1773] [82560] (2)
                  2. Escherichia coli [TaxId: 562] [102698] (2)
                  3. Thermotoga maritima [TaxId: 2336] [102699] (3)
                     SQ Q9X0D2
                  4. Lactococcus lactis [TaxId: 1358] [142804] (8)
                     SQ Q02129 1-204
                  5. Thermus thermophilus [TaxId: 274] [142805] (1)
                     SQ Q5SM15 1-206
              20. Molybdate-binding protein, ModA [53883]
                  1. Escherichia coli [TaxId: 562] [53884] (2)
                  2. Azotobacter vinelandii [TaxId: 354] [53885] (1)
                  3. Archaeoglobus fulgidus [TaxId: 2234] [159807] (4)
                     SQ O30142 32-342
              21. Cofactor-binding fragment of LysR-type protein CysB [53886]
                  1. Klebsiella aerogenes [TaxId: 28451] [53887] (1)
              22. Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain [64193]
                  1. Escherichia coli [TaxId: 562] [64194] (2)
              23. LysR-type regulatory protein CbnR [89789]
                  1. Ralstonia eutropha [TaxId: 106590] [89790] (2)
              24. Alginate-binding periplasmic protein AlgQ2 [69624]
                  1. Sphingomonas sp. [TaxId: 28214] [69625] (2)
              25. Putative lipoprotein (NlpA family) [102700]
                  aka PG110, TpN32
                  1. Staphylococcus aureus [TaxId: 1280] [102701] (1)
                  2. Treponema pallidum [TaxId: 160] [117746] (1)
                     SQ O07950 28-267
              26. Glycine betaine-binding periplasmic protein ProX [102702]
                  1. Escherichia coli [TaxId: 562] [102703] (2)
              27. LysR-type regulatory protein DntR [110748]
                  1. Burkholderia sp. [TaxId: 36773] [110749] (2)
                     SQ Q7WT50 75-301
              28. Osmoprotection protein ProX [110750]
                  functionally related to the bacterial ProX
                  1. Archaeoglobus fulgidus [TaxId: 2234] [110751] (4)
                     SQ O29280 # AF0982
              29. ABC transporter, periplasmic substrate-binding protein VCA0807 [117747]
                  1. Vibrio cholerae [TaxId: 666] [117748] (1)
                     SQ Q9KLD9 26-274
              30. Hypothetical protein TTHA1568 [142806]
                  member of Pfam 02642 (DUF191)
                  1. Thermus thermophilus [TaxId: 274] [142807] (2)
                     SQ Q5SI12 3-272
              31. Alginate-binding periplasmic protein AlgQ1 [142808]
                  1. Sphingomonas sp. [TaxId: 28214] [142809] (3)
                     SQ Q9KWT6 25-514
              32. Hypothetical protein AF1704 [142810]
                  member of Pfam 02642 (DUF191)
                  1. Archaeoglobus fulgidus [TaxId: 2234] [142811] (1)
                     SQ O28569 2-261
              33. Probable LysR-type transcriptional regulator PA0477 [142812]
                  1. Pseudomonas aeruginosa [TaxId: 287] [142813] (4)
                     SQ Q9I641 92-303
              34. Putative amino-acid transporter CjaA [142814]
                  1. Campylobacter jejuni [TaxId: 197] [142815] (2)
                     SQ Q0P9S0 29-276
              35. LysR-type regulatory protein Cbl [142816]
                  1. Escherichia coli [TaxId: 562] [142817] (4)
                     SQ Q47083 88-307
              36. Prephenate dehydratase [159808]
                  1. Staphylococcus aureus [TaxId: 1280] [159809] (2)
                     SQ Q99SX2 1-184
              37. Hypothetical protein SCo4506 [159810]
                  1. Streptomyces coelicolor [TaxId: 1902] [159811] (4)
                     SQ Q9L0T8 6-282
              38. Hypothetical protein YhfZ [159812]
                  1. Shigella flexneri [TaxId: 623] [159813] (1)
                     SQ Q83JA6 1-228
              39. Hypothetical protein DR0370 [159814]
                  1. Deinococcus radiodurans [TaxId: 1299] [159815] (8)
                     SQ Q9RXE3 14-285
              40. PstS-like phosphate-binding protein [159816]
                  1. Human (Homo sapiens) [TaxId: 9606] [159817] (1)
                     SQ P85173 1-376
           2. Transferrin [53888] (11)
              further duplication: composed of two two-domain lobes
              1. Lactoferrin [53889]
                 1. Human (Homo sapiens) [TaxId: 9606] [53890] (23)
                 2. Cow (Bos taurus) [TaxId: 9913] [53891] (44)
                 3. Domestic water buffalo (Bubalus arnee bubalis) [TaxId: 89462] [53892] (2)
                 4. Goat (Capra hircus) [TaxId: 9925] [89791] (1)
                 5. Horse (Equus caballus) [TaxId: 9796] [53893] (8)
                 6. Arabian camel (Camelus dromedarius) [TaxId: 9838] [64195] (2)
              2. Ovotransferrin [53894]
                 1. Duck (Anas platyrhynchos) [TaxId: 8839] [53895] (5)
                 2. Chicken (Gallus gallus) [TaxId: 9031] [53896] (11)
                    SQ P02789
              3. Transferrin [53897]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53898] (6)
                 2. Human (Homo sapiens) [TaxId: 9606] [53899] (17)
                 3. Pig (Sus scrofa) [TaxId: 9823] [69626] (1)
           3. PG0945 N-terminal domain-like [159818] (1)
              truncated to one domain; extra C-terminal region provides dimerisation interface
              1. Uncharacterized protein PG0945 [159819]
                 putative ABC transporter, permease
                 1. Porphyromonas gingivalis [TaxId: 837] [159820] (1)
                    SQ Q7MVU4 48-183
   142. Thiolase-like [53900] (1)
        consists of two similar domains related by pseudo dyad; duplication
        3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
        1. Thiolase-like [53901] (2)
           uperfamily
           1. Thiolase-related [53902] (12)
              1. Thiolase [53903]
                 topology of each domain is similar to the first domain of phosphoglucomutase
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53904] (2)
              2. Biosynthetic thiolase [53905]
                 1. Zoogloea ramigera [TaxId: 350] [53906] (12)
                    SQ P07097
              3. Beta-ketoacyl-ACP synthase I [53907]
                 1. Escherichia coli [TaxId: 562] [53908] (135)
                    SQ P14926
              4. Beta-ketoacyl-ACP synthase II [53909]
                 1. Escherichia coli [TaxId: 562] [53910] (10)
                 2. Synechocystis sp. [TaxId: 1143] [53911] (1)
                 3. Thermus thermophilus [TaxId: 274] [89792] (1)
                 4. Streptococcus pneumoniae [TaxId: 1313] [89793] (4)
                 5. Thale cress (Arabidopsis thaliana), mitochondrial isoform [TaxId: 3702] [117749] (5)
                    SQ Q8L3X9
              5. Actinorhodin polyketide putative beta-ketoacyl synthase 1, KasA [110752]
                 1. Streptomyces coelicolor [TaxId: 1902] [110753] (1)
                    SQ Q02059
              6. Actinorhodin polyketide putative beta-ketoacyl synthase 2, KasB [110754]
                 1. Streptomyces coelicolor [TaxId: 1902] [110755] (1)
                    SQ Q02062
              7. Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase) [110756]
                 1. Pseudomonas fragi [TaxId: 296] [110757] (7)
                    SQ P28790
              8. Beta-ketoadipyl CoA thiolase [117750]
                 1. Thermus thermophilus [TaxId: 274] [117751] (1)
                    SQ Q5SJM1
           2. Chalcone synthase-like [53914] (10)
              1. Chalcone synthase [53915]
                 1. Alfalfa (Medicago sativa) [TaxId: 3879] [53916] (16)
                    SQ P30074
              2. Pyrone synthase (PyS, chalcone synthase 2) [53917]
                 1. Gerbera hybrid cultivar [TaxId: 18101] [53918] (2)
              3. Ketoacyl-ACP synthase III (FabH) [53912]
                 1. Escherichia coli [TaxId: 562] [53913] (15)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [64196] (42)
                 3. Thermus thermophilus [TaxId: 274] [89794] (1)
              4. Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway [82561]
                 1. Streptomyces sp. r1128 [TaxId: 140437] [82562] (1)
              5. Polyketide synthase PKS18 [110758]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [110759] (2)
                    SQ Q79FQ0
              6. 3-hydroxy-3-methylglutaryl CoA synthase MvaS [110760]
                 most similar to FabH
                 1. Staphylococcus aureus [TaxId: 1280] [110761] (5)
                    SQ Q7A3F6
              7. Putative polyketide synthase SCO1206 [110762]
                 1. Streptomyces coelicolor [TaxId: 1902] [110763] (1)
                    SQ Q9FCA7
              8. Dihydropinosylvin synthase [117752]
                 1. Scots pine (Pinus sylvestris) [TaxId: 3349] [117753] (1)
                    SQ Q02323
   143. NIF3 (NGG1p interacting factor 3)-like [102704] (1)
        consist of two intertwined domains; duplication: contains two structural repeats of alpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 is antiparallel to the rest
        1. NIF3 (NGG1p interacting factor 3)-like [102705] (1)
           di-iron binding protein
           uperfamily
           1. NIF3 (NGG1p interacting factor 3)-like [102706] (3)
              Pfam 01784
              1. Hypothetical protein YbgI [102707]
                 1. Escherichia coli [TaxId: 562] [102708] (2)
              2. Nif3-related protein BC4286 [142818]
                 1. Bacillus cereus [TaxId: 1396] [142819] (3)
                    SQ Q818H0 4-373
              3. Hypothetical protein SP1609 [142820]
                 1. Streptococcus pneumoniae [TaxId: 1313] [142821] (3)
                    SQ Q97PK0 1-265
   144. Fe-only hydrogenase [53919] (1)
        consist of two intertwined domains; contains partial duplication
        1. Fe-only hydrogenase [53920] (1)
           uperfamily
           1. Fe-only hydrogenase [53921] (2)
              1. Fe-only hydrogenase, catalytic domain [53922]
                 includes C-terminal region homologous to the smaller subunit of Desulfovidrio hydrogenase
                 1. Clostridium pasteurianum [TaxId: 1501] [53923] (4)
              2. Fe-only hydrogenase larger subunit, C-domain [53924]
                 1. Desulfovibrio desulfuricans [TaxId: 876] [53925] (1)
   145. ComB-like [142822] (1)
        contains of two similar intertwined domains related by pseudo dyad; duplication; core: 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 1423
        1. ComB-like [142823] (1)
           uperfamily
           1. ComB-like [142824] (1)
              Pfam 04029; 2-phosphosulpholactate phosphatase
              1. 2-phosphosulfolactate phosphatase ComB [142825]
                 1. Clostridium acetobutylicum [TaxId: 1488] [142826] (3)
                    SQ Q97E82 1-235
   146. CoA-transferase family III (CaiB/BaiF) [89795] (1)
        consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit
        1. CoA-transferase family III (CaiB/BaiF) [89796] (1)
           uperfamily
           1. CoA-transferase family III (CaiB/BaiF) [89797] (4)
              forms interlocked homodimer of two ring-like subunits
              1. Formyl-CoA transferase [89798]
                 1. Oxalobacter formigenes [TaxId: 847] [89799] (11)
                    SQ O06644
              2. Hypothetical protein YfdW [102709]
                 1. Escherichia coli [TaxId: 562] [102710] (6)
              3. Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB [117754]
                 1. Escherichia coli [TaxId: 562] [117755] (12)
                    SQ P31572
              4. 2-methylacyl-CoA racemase Mcr [142827]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [142828] (24)
                    SQ O06543 2-360
   147. Cytidine deaminase-like [53926] (2)
        core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 1 is antiparallel to the rest
        1. Cytidine deaminase-like [53927] (5)
           contains extra C-terminal strand 5, order 21345
           uperfamily
           1. Cytidine deaminase [53928] (7)
              strand 5 is antiparallel to strand 4
              1. mono-domain cytidine deaminase [75327]
                 1. Bacillus subtilis [TaxId: 1423] [75328] (4)
                    SQ P19079
                 2. Human (Homo sapiens) [TaxId: 9606] [102711] (1)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110764] (1)
                    SQ Q06549
                 4. Bacillus anthracis [TaxId: 1392] [142829] (2)
                    SQ Q81LT6 1-124
                 5. Mouse (Mus musculus) [TaxId: 10090] [142830] (12)
                    SQ P56389 10-146
              2. Two-domain cytidine deaminase [53929]
                 duplication: consists of two similar domains; contains extra helices in the N-terminal domain
                 1. Escherichia coli [TaxId: 562] [53930] (4)
              3. Blasticidin-S deaminase [142831]
                 1. Aspergillus terreus [TaxId: 33178] [142832] (14)
                    SQ P78986 2-126
           2. Deoxycytidylate deaminase-like [89800] (10)
              strand 5 is parallel to strand 4
              1. Cytosine deaminase [89801]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89802] (8)
              2. Guanine deaminase GuaD [110765]
                 1. Bacillus subtilis [TaxId: 1423] [110766] (2)
                    SQ O34598
              3. Deoxycytidylate deaminase [117756]
                 1. Bacteriophage T4 [TaxId: 10665] [117757] (1)
                    SQ P16006
              4. Putative deaminase NE0047 [142833]
                 1. Nitrosomonas europaea [TaxId: 915] [142834] (1)
                    SQ Q82Y41 1-189
              5. Cytidine and deoxycytidylate deaminase CodA [142835]
                 1. Agrobacterium tumefaciens [TaxId: 358] [142836] (2)
                    SQ Q8UHJ4 2-131
              6. Riboflavin biosynthesis protein RibD [142837]
                 1. Bacillus subtilis [TaxId: 1423] [142838] (8)
                    SQ P17618 1-145
                 2. Thermotoga maritima [TaxId: 2336] [142839] (1)
                    SQ Q9X2E8 1-147
              7. tRNA adenosine deaminase TadA [142840]
                 1. Staphylococcus aureus [TaxId: 1280] [142841] (4)
                    SQ Q99W51 1-151
                 2. Escherichia coli [TaxId: 562] [142842] (2)
                    SQ P68398 13-168
                 3. Aquifex aeolicus [TaxId: 63363] [142843] (4)
                    SQ O67050 1-151
           3. Hypothetical protein TM1506 [110651] (1)
              strand 5 is parallel to strand 4
              1. Hypothetical protein TM1506 [110652]
                 1. Thermotoga maritima [TaxId: 2336] [110653] (1)
                    SQ Q9X1J4
           4. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64198] (3)
              duplication: consists of two domains of this fold with extra secondary structures within and in between the two core motifs
              1. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64199]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [64200] (4)
                    SQ P31335
                 2. Human (Homo sapiens) [TaxId: 9606] [102716] (3)
                 3. Thermotoga maritima [TaxId: 2336] [142844] (2)
                    SQ Q9X0X6 158-452
           5. FdhD/NarQ [159821] (1)
              Pfam 02634; contains extra N-terminal beta-hairpin arm, involved in dimerization, and an alpha+beta subdomain of beta-grasp fold (scop_cf 54235)
              1. Uncharacterized protein DP1777 [159822]
                 Related to formate dehydrogenase accessory protein FdhD
                 1. Desulfotalea psychrophila [TaxId: 84980] [159823] (4)
                    SQ Q6AMB9 7-257
        2. JAB1/MPN domain [102712] (1)
           uperfamily
           1. JAB1/MPN domain [102713] (1)
              Pfam 01398; synonyms Mov34, PAD-1;
              1. Hypothetical protein AF2198 [102714]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102715] (2)
4. Alpha and beta proteins (a+b) [53931] (376)
   Mainly antiparallel beta sheets (segregated alpha and beta regions)
   1. Microbial ribonucleases [53932] (1)
      single helix packs against antiparallel beta-sheet
      1. Microbial ribonucleases [53933] (3)
         uperfamily
         1. Bacterial ribonucleases [81307] (5)
            1. Barnase [81305]
               1. Bacillus amyloliquefaciens [TaxId: 1390] [53945] (60)
            2. Binase [81306]
               1. Bacillus intermedius [TaxId: 1400] [53946] (5)
            3. RNase Sa [53935]
               1. Streptomyces aureofaciens [TaxId: 1894] [53936] (22)
                  SQ P05798
            4. Cytotoxic RNase Sa3 [82563]
               1. Streptomyces aureofaciens [TaxId: 1894] [82564] (2)
            5. Ribonuclease Sa2 [110767]
               1. Streptomyces aureofaciens [TaxId: 1894] [110768] (2)
                  SQ Q53752
         2. Fungal ribonucleases [81311] (5)
            1. RNase F1 [53937]
               1. Fusarium moniliforme [TaxId: 117187] [53938] (4)
            2. RNase T1 [53939]
               1. Aspergillus oryzae [TaxId: 5062] [53940] (64)
               2. Aspergillus niger [TaxId: 5061] [53941] (1)
            3. RNase U2 [53942]
               1. Ustilago sphaerogena [TaxId: 5271] [53943] (1)
            4. RNase Ms [53947]
               1. Molsin (Aspergillus saitoi) [TaxId: 5063] [53948] (2)
         3. Ribotoxin [81310] (2)
            the fungal cytotoxic ribonucleases with many insertions in the common fold
            1. Restrictocin [81308]
               1. Fungus (Aspergillus restrictus) [TaxId: 5064] [53952] (4)
            2. alpha-Sarcin [81309]
               1. Fungus (Aspergillus giganteus) [TaxId: 5060] [53953] (2)
   2. Lysozyme-like [53954] (1)
      common alpha+beta motif for the active site region
      1. Lysozyme-like [53955] (11)
         uperfamily
         1. Family 19 glycosidase [53956] (2)
            1. Plant class II chitinase [53957]
               1. Barley (Hordeum vulgare) [TaxId: 4513] [53958] (2)
               2. Jack bean (Canavalia ensiformis) [TaxId: 3823] [53959] (1)
         2. C-type lysozyme [53960] (20)
            1. Lysozyme [53961]
               ubiquitous in a variety of tissues and secretions
               1. Chicken (Gallus gallus) [TaxId: 9031] [53962] (280)
                  SQ P00698
               2. Turkey (Meleagris gallopavo) [TaxId: 9103] [53963] (13)
               3. Guinea fowl (Numida meleagris) [TaxId: 8996] [53964] (2)
               4. Pheasant (Phasianus colchicus) [TaxId: 9054] [53965] (2)
               5. Bobwhite quail (Colinus virginianus) [TaxId: 9014] [53966] (3)
               6. Japanese quail (Coturnix coturnix japonica) [TaxId: 93934] [53967] (1)
               7. Human (Homo sapiens) [TaxId: 9606] [53969] (205)
                  SQ P00695
               8. Horse (Equus caballus), milk [TaxId: 9796] [53970] (1)
               9. Dog (Canis familiaris), milk [TaxId: 9615] [53971] (5)
               10. Mouse (Mus musculus) [TaxId: 10090] [75329] (1)
               11. Australian echidna (Tachyglossus aculeatus) [TaxId: 9261] [53972] (1)
               12. Rainbow trout (Oncorhynchus mykiss) [TaxId: 8022] [53973] (7)
               13. Silkworm (Bombyx mori) [TaxId: 7091] [64201] (1)
               14. Tasar silkworm (Antheraea mylitta) [TaxId: 34739] [69627] (1)
                   induced antibacterial protein
            2. alpha-Lactalbumin [53975]
               expressed only in the lactating mammary gland, strongly binds calcium ion
               1. Yellow baboon (Papio cynocephalus) [TaxId: 9556] [53976] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [53977] (3)
               3. Guinea pig (Cavia porcellus) [TaxId: 10141] [53978] (1)
               4. Goat (Capra hircus) [TaxId: 9925] [53979] (4)
               5. Cow (Bos taurus) [TaxId: 9913] [53980] (9)
               6. Mouse (Mus musculus) [TaxId: 10090] [69628] (15)
         3. Phage lysozyme [53981] (3)
            1. Phage T4 lysozyme [53982]
               1. Bacteriophage T4 [TaxId: 10665] [53983] (446)
                  SQ P00720
                  many mutant structures
            2. Tail-associated lysozyme gp5, catalytic domain [69629]
               1. Bacteriophage T4 [TaxId: 10665] [69630] (1)
            3. Endolysin Lyz [117758]
               1. Bacteriophage P1 [TaxId: 10678] [117759] (2)
                  SQ Q37875 1-185
         4. Lambda lysozyme [53984] (1)
            1. Lambda lysozyme [53985]
               1. Bacteriophage lambda [TaxId: 10710] [53986] (4)
         5. G-type lysozyme [53987] (2)
            1. Lysozyme [53988]
               1. Western graylag goose (Anser anser anser) [TaxId: 8844] [53989] (2)
               2. Australian black swan (Cygnus atratus) [TaxId: 8868] [53990] (2)
         6. Bacterial muramidase, catalytic domain [53991] (2)
            the large N-terminal domain is all-alpha superhelix
            1. 70 kDa soluble lytic transglycosylase, SLT70 [53992]
               1. Escherichia coli [TaxId: 562] [53993] (3)
            2. 36 kDa soluble lytic transglycosylase, SLT35 [53994]
               1. Escherichia coli [TaxId: 562] [53995] (8)
         7. Chitosanase [53996] (2)
            1. Endochitosanase [53997]
               1. Streptomyces sp., strain N174 [TaxId: 1931] [53998] (1)
               2. Bacillus circulans [TaxId: 1397] [53999] (1)
         8. RPF-like [159824] (1)
            Pfam 06737; Transglycosylase-like domain
            1. Probable resuscitation-promoting factor RpfB [159825]
               1. Mycobacterium tuberculosis [TaxId: 1773] [159826] (1)
                  SQ O05594 247-362
         9. NMB1012-like [159827] (2)
            Pfam 05838; predicted lysozyme (DUF847)
            1. Hypothetical protein NMB1012 [159828]
               1. Neisseria meningitidis [TaxId: 487] [159829] (8)
                  SQ Q7DDI9 1-153
            2. Putative secretion activator PG0293 [159830]
               1. Porphyromonas gingivalis [TaxId: 837] [159831] (1)
                  SQ Q7MXB3 1-192
         10. PBP transglycosylase domain-like [159832] (2)
             Pfam 00912; lacking the characteristic beta-sheet; otherwise has a similar fold to the Family 19 glycosidase
             1. Penicillin-binding protein 1a, PBP1a [159833]
                1. Aquifex aeolicus [TaxId: 63363] [159834] (2)
                   SQ O66874 57-243
             2. Penicillin-binding protein 2, PBP2 [159835]
                1. Staphylococcus aureus [TaxId: 1280] [159836] (7)
                   SQ Q2YY56 67-292
         11. PA2222-like [159837] (1)
             PfamB 104465
             1. Hypothetical protein PA2222 [159838]
                1. Pseudomonas aeruginosa [TaxId: 287] [159839] (8)
                   SQ Q9I1P7 4-215
   3. Cysteine proteinases [54000] (1)
      consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
      1. Cysteine proteinases [54001] (22)
         the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet
         uperfamily
         1. Papain-like [54002] (30)
            1. Actinidin [54003]
               1. Chinese gooseberry or kiwifruit (Actinidia chinensis) [TaxId: 3625] [54004] (2)
            2. Papain [54005]
               1. Papaya (Carica papaya) [TaxId: 3649] [54006] (18)
            3. Caricain (protease omega) [54007]
               1. Papaya (Carica papaya) [TaxId: 3649] [54008] (3)
            4. Chymopapain [54009]
               1. Papaya (Carica papaya) [TaxId: 3649] [54010] (1)
            5. Glycyl endopeptidase [54011]
               1. Papaya (Carica papaya) [TaxId: 3649] [54012] (1)
            6. Proline-specific cysteine protease [54013]
               1. Ginger rhizome (Zingiber officinale) [TaxId: 94328] [54014] (1)
            7. Ervatamin B [89803]
               1. Adam's apple (Ervatamia coronaria) [TaxId: 52861] [89804] (1)
            8. Ervatamin C [102717]
               1. East indian rosebay (Ervatamia coronaria) [TaxId: 52861] [102718] (1)
            9. Vignain (bean endopeptidase) [102719]
               1. Castor bean (Ricinus communis) [TaxId: 3988] [102720] (1)
            10. Bleomycin hydrolase [54017]
                DNA-binding protease that has more insertions in the papain-like fold
                1. Baker's yeast (Saccharomyces cerevisiae), Gal6 [TaxId: 4932] [54018] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [54019] (2)
            11. Cruzain [54020]
                1. Trypanosoma cruzi [TaxId: 5693] [54021] (17)
            12. (Pro)cathepsin B [54022]
                1. Human (Homo sapiens) [TaxId: 9606] [54023] (6)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [54024] (4)
                3. Cow (Bos taurus) [TaxId: 9913] [54025] (11)
            13. Cathepsin C (dipeptidyl peptidase I), catalytic domain [75330]
                1. Human (Homo sapiens) [TaxId: 9606] [75331] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [82565] (1)
            14. Cathepsin F [89805]
                1. Human (Homo sapiens) [TaxId: 9606] [89806] (1)
            15. Cathepsin H [81637]
                also contains a disulfide-bound minicathepsin H chain
                1. Pig (Sus scrofa) [TaxId: 9823] [81636] (3)
            16. (Pro)cathepsin K [54028]
                1. Human (Homo sapiens) [TaxId: 9606] [54029] (32)
                   SQ P43235 116-329 ! SQ P43235 115-329
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [142845] (1)
                   SQ P43236 115-329
            17. (Pro)cathepsin L [54026]
                1. Human (Homo sapiens) [TaxId: 9606] [54027] (4)
            18. (Pro)cathepsin S [82566]
                1. Human (Homo sapiens) [TaxId: 9606] [82567] (36)
            19. (Pro)cathepsin V [64202]
                1. Human (Homo sapiens) [TaxId: 9606] [64203] (1)
            20. (Pro)cathepsin X [54031]
                1. Human (Homo sapiens) [TaxId: 9606] [54032] (2)
            21. Staphopain StpA [54033]
                1. Staphylococcus aureus [TaxId: 1280] [54034] (1)
            22. Staphopain SspB [102721]
                1. Staphylococcus aureus [TaxId: 1280] [102722] (4)
                   SQ Q70UQ9 41-393
            23. Streptococcal pyrogenic exotoxin B [54035]
                1. Streptococcus pyogenes [TaxId: 1314] [54036] (2)
                   SQ P00788 31-398
            24. Falcipain 2 [142846]
                1. Plasmodium falciparum [TaxId: 5833] [142847] (6)
                   SQ Q9N6S8 244-484
            25. Major mite fecal allergen der p 1 [142848]
                1. House-dust mite (Dermatophagoides pteronyssinus) [TaxId: 6956] [142849] (3)
                   SQ P08176 19-320! SQ P08176 99-320
         2. Avirulence protein Avrpph3 [102723] (1)
            1. Avirulence protein Avrpph3 [102724]
               1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [102725] (1)
         3. FMDV leader protease [54037] (1)
            1. FMDV leader protease [54038]
               1. Foot-and-mouth disease virus [TaxId: 12110] [54039] (5)
         4. Calpain large subunit, catalytic domain (domain II) [54040] (5)
            1. Calpain large subunit, catalytic domain (domain II) [54041]
               includes the N-terminal 'sequence' domain I
               1. Human (Homo sapiens), M-type [TaxId: 9606] [54042] (2)
               2. Rat (Rattus norvegicus), M-type [TaxId: 10116] [54043] (3)
               3. Rat (Rattus norvegicus), mu-type [TaxId: 10116] [75332] (10)
                  SQ P97571 33-353
               4. Human (Homo sapiens), calpain 9 [TaxId: 9606] [142850] (1)
                  SQ O14815 28-337
               5. Human(Homo sapiens), mu type [TaxId: 9606] [142851] (3)
                  SQ P07384 33-353! SQ P07384 33-354
         5. Transglutaminase core [54044] (6)
            1. Transglutaminase catalytic domain [54045]
               1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [54046] (8)
                  Coagulation factor XIII
               2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [75333] (2)
                  GDP-binding protein
               3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [75334] (8)
               4. Red sea bream (Chrysophrys major) [TaxId: 143350] [64204] (1)
            2. Peptide:N-glycanase 1, PNG1 [142852]
               1. Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932] [142853] (2)
                  SQ Q02890 8-327
               2. Mouse (Mus musculus) [TaxId: 10090] [159840] (2)
                  SQ Q9JI78 164-450
         6. Arylamine N-acetyltransferase [54047] (4)
            fold similar to that of the factor XIII catalytic domain
            1. Arylamine N-acetyltransferase [54048]
               1. Salmonella typhimurium [TaxId: 90371] [54049] (1)
               2. Mycobacterium smegmatis [TaxId: 1772] [75335] (7)
               3. Rhizobium loti [TaxId: 381] [142854] (2)
                  SQ Q98D42 6-275
               4. Pseudomonas aeruginosa [TaxId: 287] [142855] (1)
                  SQ Q9HUY3 1-277
         7. Ubiquitin carboxyl-terminal hydrolase UCH-L [54050] (3)
            1. Ubiquitin carboxyl-terminal hydrolase UCH-l3 [54051]
               1. Human (Homo sapiens) [TaxId: 9606] [54052] (2)
                  SQ P15374
               2. Synthetic, based on Saccharomyces cerevisiae sequence [54053] (1)
            2. Ubiquitin carboxyl-terminal hydrolase isozyme l1 [142856]
               1. Human (Homo sapiens) [TaxId: 9606] [142857] (2)
                  SQ P09936 1-223
         8. Ubiquitin carboxyl-terminal hydrolase, UCH [82568] (5)
            Pfam 00443
            1. Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAUSP) [82569]
               1. Human (Homo sapiens) [TaxId: 9606] [82570] (2)
            2. Ubiquitin carboxyl-terminal hydrolase 6 [110769]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110770] (1)
                  SQ P43593 103-499
            3. Ubiquitin carboxyl-terminal hydrolase 8 [142858]
               1. Human (Homo sapiens) [TaxId: 9606] [142859] (1)
                  SQ P40818 762-1109
            4. Ubiquitin carboxyl-terminal hydrolase 14 [142860]
               1. Human (Homo sapiens) [TaxId: 9606] [142861] (4)
                  SQ P54578 100-482
            5. Ubiquitin carboxyl-terminal hydrolase 2, USP2 [159841]
               1. Human (Homo sapiens) [TaxId: 9606] [159842] (2)
                  SQ O75604 263-600! SQ O75604 264-599
         9. Adenain-like [54054] (5)
            Pfam 02902; Ulp1 protease family
            1. Human adenovirus 2 proteinase, adenain [54055]
               1. Mastadenovirus H2 [TaxId: 10515] [54056] (2)
            2. Ulp1 protease C-terminal domain [54057]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54058] (4)
            3. Sentrin-specific protease 2, SENP2 [110771]
               1. Human (Homo sapiens) [TaxId: 9606] [110772] (8)
                  SQ Q9HC62 366-589
            4. Sentrin-specific protease 8, SENP8 [117760]
               1. Human (Homo sapiens) [TaxId: 9606] [117761] (6)
                  SQ Q96LD8
            5. Sentrin-specific protease 1 [142862]
               1. Human (Homo sapiens) [TaxId: 9606] [142863] (6)
                  SQ Q9P0U3 419-643
         10. Microbial transglutaminase [75336] (1)
             inverted positions of the catalytic triad Asp and His residues
             1. Microbial transglutaminase [75337]
                1. Streptoverticillium mobaraense [TaxId: 35621] [75338] (1)
         11. Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [110773] (1)
             probably the same as Pfam 02338, OTU-like cysteine protease, but 1TFF (SQ Q96DC9) was not detected by the Pfam model
             1. Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [110774]
                1. Human (Homo sapiens) [TaxId: 9606] [110775] (1)
                   SQ Q96DC9
         12. IgG-specific endopeptidase IdeS (Sib38) [117762] (1)
             1. IgG-specific endopeptidase IdeS (Sib38) [117763]
                1. Streptococcus pyogenes [TaxId: 1314] [117764] (1)
                   SQ Q9F1R7 38-339 # SPy0861
         13. Lpg0564-like [142864] (1)
             Pfam 07313, DUF1460; contains new PDB entry 2p1g, annotated as putative xylanase
             1. Hypothetical protein Lpg0564 [142865]
                1. Legionella pneumophila [TaxId: 446] [142866] (1)
                   SQ Q5ZY11 49-352
         14. Phytochelatin synthase [142867] (1)
             Pfam 05023; assosiated Pfam 09328 (DUF1984) is a part of the same functional unit
             1. Primitive phytochelatin synthase [142868]
                1. Nostoc sp. pcc 7120 [TaxId: 103690] [142869] (4)
                   SQ Q8YY76 29-238
         15. CHAP domain [142870] (1)
             Pfam 05257
             1. Glutathionylspermidine synthase, amidase domain [142871]
                1. Escherichia coli [TaxId: 562] [142872] (10)
                   SQ P0AES0 10-200
         16. NlpC/P60 [142873] (1)
             Pfam 00877
             1. Cell wall-associated hydrolase Spr C-terminal domain [142874]
                1. Nostoc punctiforme [TaxId: 272131] [142875] (3)
                   SQ Q8YRR4 87-234
         17. PMT C-terminal domain like [159843] (1)
             displays a minimal thiol-protease fold and its catalytic triad; potential redox regulation: the catalytic cysteine can form a disulfide bond with an N-terminal cysteine
             1. Dermonecrotic toxin, ToxA [159844]
                Synonym: Mitogenic toxin PMT
                1. Pasteurella multocida [TaxId: 747] [159845] (4)
                   SQ P17452 1094-1285
         18. MOA C-terminal domain-like [159846] (1)
             PfamB 070855
             1. Agglutinin MOA [159847]
                1. Fairy-ring mushroom (Marasmius oreades) [TaxId: 181124] [159848] (1)
                   SQ Q8X123 156-293
         19. Atu2299-like [159849] (1)
             Pfam 09641; DUF2026; putative Cys/Ser-His-Asp catalytic triad
             1. Hypothetical protein Atu2299 [159850]
                Serine catalytic nucleophile
                1. Agrobacterium tumefaciens [TaxId: 358] [159851] (1)
                   SQ Q8UD29 1-202
         20. M48USP-like [159852] (1)
             Pfam 04843; Herpesvirus tegument protein, N-terminal conserved region
             1. Tegument protein M48; N-terminal domain [159853]
                1. Murine cytomegalovirus (MCMV) [TaxId: 10366] [159854] (2)
                   SQ A8E1C4 1-232
         21. YiiX-like [159855] (1)
             Pfam 06520; DUF1105; circularly permuted active site residues compare to papain
             1. Hypothetical protein YiiX [159856]
                1. Escherichia coli [TaxId: 562] [159857] (2)
                   SQ Q8X778 19-200
         22. Autophagin-like [159858] (2)
             Pfam 03416
             1. Cysteine protease ATG4A [159859]
                Autophagin-2
                1. Human (Homo sapiens) [TaxId: 9606] [159860] (4)
                   SQ Q8WYN0 26-359
             2. Cysteine protease ATG4B [159861]
                Autophagin-1
                1. Human (Homo sapiens) [TaxId: 9606] [159862] (5)
                   SQ Q9Y4P1 10-373! SQ Q9Y4P1 5-354
   4. His-Me finger endonucleases [54059] (1)
      core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
      1. His-Me finger endonucleases [54060] (6)
         common motif contains conserved histidine residue and metal-binding site
         uperfamily
         1. Endonuclease I [102726] (1)
            1. Periplasmic endonuclease Vvn [102727]
               1. Vibrio vulnificus [TaxId: 672] [102728] (6)
         2. HNH-motif [54061] (2)
            1. DNase domain of colicin E7 [54062]
               1. Escherichia coli [TaxId: 562] [54063] (10)
            2. DNase domain of colicin E9 [54064]
               1. Escherichia coli [TaxId: 562] [54065] (15)
                  SQ P09883 456-581
         3. DNA/RNA non-specific endonuclease [54066] (2)
            the core motif is inserted in a six-stranded meander beta-sheet domain
            1. Sm endonuclease [54067]
               1. Serratia marcescens [TaxId: 615] [54068] (4)
            2. Nuclease NucA [159863]
               1. Anabaena sp., PCC 7120 [TaxId: 1167] [159864] (1)
                  SQ P38446 35-274
         4. Intron-encoded homing endonucleases [54069] (2)
            1. Intron-encoded homing endonuclease I-PpoI [54070]
               1. Physarum polycephalum [TaxId: 5791] [54071] (7)
            2. Intron-encoded homing endonuclease I-HmuI [110776]
               1. Bacteriophage SP01 [TaxId: 10685] [110777] (1)
                  SQ P34081
         5. Recombination endonuclease VII, N-terminal domain [68915] (1)
            1. Recombination endonuclease VII, N-terminal domain [68916]
               1. Bacteriophage T4 [TaxId: 10665] [68917] (7)
         6. Caspase-activated DNase, CAD (DffB, DFF40) [110778] (1)
            1. Caspase-activated DNase, CAD (DffB, DFF40) [110779]
               1. Mouse (Mus musculus) [TaxId: 10090] [110780] (1)
                  SQ O54788 85-329 # structure of the N-terminal, CAD domain (1-87) is solved separately; scop_sp 54282
   5. RNase A-like [54075] (1)
      contains long curved beta-sheet and 3 helices
      1. RNase A-like [54076] (1)
         can be classified as disulfide-rich
         uperfamily
         1. Ribonuclease A-like [54077] (15)
            1. Ribonuclease A (also ribonuclease B, S) [54078]
               1. Cow (Bos taurus) [TaxId: 9913] [54079] (167)
               2. Human (Homo sapiens), des1-7 [TaxId: 9606] [54080] (7)
               3. Rat (Rattus norvegicus) [TaxId: 10116] [54081] (1)
            2. Amphibian cytotoxic ribonuclease [54084]
               1. Frog (Rana pipiens), P-30 [TaxId: 8404] [54083] (3)
               2. Bullfrog (Rana catesbeiana) [TaxId: 8400] [54085] (4)
               3. Bullfrog (Rana catesbeiana), RNase2 [TaxId: 8400] [82571] (1)
               4. Bullfrog (Rana catesbeiana), RNase4 [TaxId: 8400] [75339] (1)
               5. Bullfrog (Rana catesbeiana), RNase6 [TaxId: 8400] [110781] (2)
                  SQ Q9DFY5
            3. Seminal ribonucleasease [54086]
               1. Cow (Bos taurus) [TaxId: 9913] [54087] (12)
                  SQ P00669 27-150
            4. Hybrid between ribonuclease A and seminal ribonuclease [54088]
               1. Cow (Bos taurus) [TaxId: 9913] [54089] (1)
            5. Eosinophil cationic protein (ECP), ribonuclease 3 [54090]
               1. Human (Homo sapiens) [TaxId: 9606] [54091] (3)
            6. Eosinophil-derived neurotoxin (EDN) [64205]
               1. Human (Homo sapiens) [TaxId: 9606] [64206] (12)
            7. Ribonuclease 4 [54092]
               1. Human (Homo sapiens) [TaxId: 9606] [54093] (2)
            8. Angiogenin [54094]
               1. Human (Homo sapiens) [TaxId: 9606] [54095] (19)
               2. Cow (Bos taurus) [TaxId: 9913] [54096] (2)
   6. EndoU-like [142876] (1)
      comprises several helices and two three-stranded antiparallel beta-sheets; similar architecture to the RNase A-like fold (scop_cf 54075)
      1. EndoU-like [142877] (2)
         similarity to the RNase A-like superfamily (scop_sf 54076) extends to the active site location and architecture; the two structural cores of the RNase A and EndoU superfamilies are interrelated by a topological permutation - transposition of two pereferial beta-strands, suggesting possible distant homology of the two superfamilies (and their unification in a hyperfamily)
         uperfamily
         1. Eukaryotic EndoU ribonuclease [142878] (1)
            PfamB 010233; common fold decorated with additional structures
            1. EndoU [142879]
               1. African clawed frog (Xenopus laevis) [TaxId: 8355] [142880] (3)
                  SQ Q8JFY9 6-289
         2. Nsp15 C-terminal domain-like [142881] (2)
            PfamB 001946
            1. Nsp15, C-terminal domain [142882]
               1. SARS coronavirus [TaxId: 227859] [142883] (11)
                  SQ Q6VA80 6620-6774
               2. Murine hepatitis virus, MHV [TaxId: 11138] [142884] (2)
                  SQ P16342 6720-6872
   7. Prion-like [54097] (1)
      beta-alpha-beta-alpha(2); antiparallel beta-ribbon
      1. Prion-like [54098] (1)
         uperfamily
         1. Prion-like [54099] (14)
            1. Prion protein domain [54100]
               1. Mouse (Mus musculus) [TaxId: 10090] [54101] (3)
                  SQ P04925 120-231
               2. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [54102] (1)
               3. Human (Homo sapiens) [TaxId: 9606] [54103] (18)
               4. Cow (Bos taurus) [TaxId: 9913] [54104] (4)
               5. Sheep (Ovis aries) [TaxId: 9940] [102729] (6)
                  SQ P23907 124-234 ! SQ P23907 122-234 ! SQ P23907 127-228
               6. American elk (Cervus elaphus nelsoni) [TaxId: 9864] [117765] (1)
                  SQ 67986 124-234
               7. Chicken (Gallus gallus) [TaxId: 9031] [117766] (1)
                  SQ P27177 132-248
               8. Red-eared slider turtle (Trachemys scripta) [TaxId: 34903] [117767] (1)
                  SQ Q9I9C0 141-248
               9. African clawed frog (Xenopus laevis) [TaxId: 8355] [117768] (1)
                  SQ Q5S1W7 43-171
               10. Cat (Felis silvestris catus) [TaxId: 9685] [117769] (1)
                   SQ O18754 104-214
               11. Dog (Canis familiaris) [TaxId: 9615] [117770] (1)
                   SQ O46501 124-233
               12. Pig (Sus scrofa) [TaxId: 9823] [117771] (1)
                   SQ P49927 125-235
            2. Prion-like protein Doppel [64207]
               1. Human (Homo sapiens) [TaxId: 9606] [82572] (1)
               2. Mouse (Mus musculus) [TaxId: 10090] [64208] (1)
   8. LysM domain [54105] (1)
      beta-alpha(2)-beta; antiparallel strands
      1. LysM domain [54106] (1)
         uperfamily
         1. LysM domain [54107] (2)
            1. Membrane-bound lytic murein transclycosylase D, MltD [54108]
               1. Escherichia coli [TaxId: 562] [54109] (1)
            2. Hypothetical protein YkuD, N-terminal domain [142885]
               1. Bacillus subtilis [TaxId: 1423] [142886] (2)
                  SQ O34816 1-48
   9. gpW/XkdW-like [64209] (2)
      alpha-beta(2)-alpha; antiparallel hairpin
      1. Head-to-tail joining protein W, gpW [64210] (1)
         uperfamily
         1. Head-to-tail joining protein W, gpW [64211] (1)
            1. Head-to-tail joining protein W, gpW [64212]
               1. Bacteriophage lambda [TaxId: 10710] [64213] (1)
      2. XkdW-like [159865] (1)
         different packing of secondary structures than in gpW
         1. XkdW-like [159866] (1)
            Pfam 09636
            1. Phage-like element PbsX protein XkdW [159867]
               1. Bacillus subtilis [TaxId: 1423] [159868] (1)
                  SQ P54342 1-60
   10. Hypothetical protein MTH677 [110782] (1)
       alpha-beta(2)-alpha; 2 layers a/b; antiparallel beta-hairpin
       1. Hypothetical protein MTH677 [110783] (1)
          uperfamily
          1. Hypothetical protein MTH677 [110784] (1)
             1. Hypothetical protein MTH677 [110785]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [110786] (1)
                   SQ O26773
   11. GTF2I-like repeat [117772] (1)
       alpha(2)-beta-alpha-beta-alpha; 2 layers: a/b; antiparallel beta-ribbon
       1. GTF2I-like repeat [117773] (1)
          uperfamily
          1. GTF2I-like repeat [117774] (1)
             Pfam 02946
             1. General transcription factor II-I [117775]
                there are six GTF2I-like repeats in this protein
                1. Mouse (Mus musculus) [TaxId: 10090] [117776] (1)
                   SQ Q9ESZ8
   12. Urease, gamma-subunit [54110] (1)
       alpha(3)-beta(2); antiparallel hairpin
       1. Urease, gamma-subunit [54111] (1)
          uperfamily
          1. Urease, gamma-subunit [54112] (3)
             1. Urease, gamma-subunit [54113]
                1. Klebsiella aerogenes [TaxId: 28451] [54114] (27)
                2. Bacillus pasteurii [TaxId: 1474] [54115] (6)
                3. Helicobacter pylori [TaxId: 210] [69631] (2)
                   fused with beta subunit
   13. IL8-like [54116] (2)
       beta(3)-alpha
       1. Interleukin 8-like chemokines [54117] (1)
          form dimers with different dimerisation modes
          uperfamily
          1. Interleukin 8-like chemokines [54118] (29)
             1. Interleukin-8, IL-8 [54119]
                1. Human (Homo sapiens) [TaxId: 9606] [54120] (9)
             2. Platelet factor 4, PF4 [54121]
                1. Cow (Bos taurus) [TaxId: 9913] [54122] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [54123] (6)
             3. IP-10/CXCL10 [82573]
                1. Human (Homo sapiens) [TaxId: 9606] [82574] (4)
             4. Melanoma growth stimulating activity (MGSA) [54124]
                1. Human (Homo sapiens) [TaxId: 9606] [54125] (3)
             5. IL-8/MGSA chimeric protein CIL-8M [54126]
                IL-8: residues 1-53; MGSA: residues 54-72
                1. Human (Homo sapiens) [TaxId: 9606] [54127] (1)
             6. Macrophage inflammatory protein, MIP [54128]
                has different dimerisation mode
                1. Human (Homo sapiens), 1-beta [TaxId: 9606] [54129] (3)
                2. Human (Homo sapiens), 1-alpha [TaxId: 9606] [54130] (2)
                3. Human (Homo sapiens), ccl20/mip-3a [TaxId: 9606] [75340] (4)
                4. Mouse (Mus musculus), ccl20/mip-3a [TaxId: 10090] [64214] (1)
                5. Kaposi's sarcoma-associated herpesvirus, VMIP-II [TaxId: 37296] [54131] (10)
                   anti-HIV chemokine
             7. RANTES (regulated upon activation, normal T-cell expressed and secreted) [54132]
                has different dimerisation mode
                1. Human (Homo sapiens) [TaxId: 9606] [54133] (9)
                   SQ P13501 25-91
             8. Monocyte chemoattractant protein-1 (MCP-1, MCAF) [54134]
                1. Human (Homo sapiens) [TaxId: 9606] [54135] (9)
             9. Monocyte chemoattractant protein-2 (MCP-2) [54136]
                1. Human (Homo sapiens) [TaxId: 9606] [54137] (1)
             10. CC chemokine I-309 [54138]
                 1. Human (Homo sapiens) [TaxId: 9606] [54139] (1)
             11. Eotaxin [54140]
                 1. Human (Homo sapiens) [TaxId: 9606] [54141] (2)
             12. Eotaxin-2 [54142]
                 1. Human (Homo sapiens) [TaxId: 9606] [54143] (2)
             13. Eotaxin-3 [75341]
                 1. Human (Homo sapiens) [TaxId: 9606] [75342] (2)
             14. Lymphotactin [69632]
                 1. Human (Homo sapiens) [TaxId: 9606] [69633] (2)
             15. Monocyte chemoattractant protein-3 (MCP-3) [54144]
                 1. Human (Homo sapiens) [TaxId: 9606] [54145] (2)
             16. Chemokine domain of fractalkine [54146]
                 1. Human (Homo sapiens) [TaxId: 9606] [54147] (2)
             17. Platelet basic protein, PBP [54148]
                 synonym: Small inducible cytokine B7; Neutrophil-activating peptide-2 (NAP-2), Connective tissue activating peptide-III (CTAP-III)
                 1. Human (Homo sapiens) [TaxId: 9606] [54149] (3)
             18. Stromal cell-derived factor-1 (SDF-1) [54150]
                 1. Human (Homo sapiens) [TaxId: 9606] [54151] (7)
             19. Macrophage inflammatory protein-2 [54152]
                 1. Mouse (Mus musculus) [TaxId: 10090] [54153] (1)
             20. Chemokine hcc-2 (macrophage inflammatory protein-5) [54154]
                 1. Human (Homo sapiens) [TaxId: 9606] [54155] (1)
             21. Gro beta [54156]
                 1. Human (Homo sapiens) [TaxId: 9606] [54157] (1)
             22. Myeloid progenitor inhibitory factor-1 (MPIF-1) [64215]
                 1. Human (Homo sapiens) [TaxId: 9606] [64216] (1)
             23. Thymus and activation-regulated chemokine, TRAC [102730]
                 1. Human (Homo sapiens) [TaxId: 9606] [102731] (2)
             24. Small inducible cytokine b11 (CXCL11/I-TAC) [102732]
                 1. Human (Homo sapiens) [TaxId: 9606] [102733] (1)
       2. PhtA domain-like [142887] (1)
          contains extra N-terminal beta-hairpin, like structurally similar archaeal "histone-like" proteins (scop_fa 54161), but does not adopt its SH3-like barrel fold
          uperfamily
          1. PhtA domain-like [142888] (1)
             Pfam 04270; Streptococcal histidine triad protein
             1. Pneumococcal histidine triad protein A, PhtA [142889]
                1. Streptococcus pneumoniae [TaxId: 1313] [142890] (3)
                   SQ Q97QM8 166-220
   14. DNA-binding domain [54170] (1)
       beta(3)-alpha; 2 layers: alpha/beta
       1. DNA-binding domain [54171] (4)
          uperfamily
          1. DNA-binding domain from tn916 integrase [54172] (1)
             1. DNA-binding domain from tn916 integrase [54173]
                1. Enterococcus faecalis [TaxId: 1351] [54174] (4)
          2. lambda integrase N-terminal domain [75344] (1)
             1. lambda integrase N-terminal domain [75345]
                1. Bacteriophage lambda [TaxId: 10710] [75346] (7)
          3. GCC-box binding domain [54175] (1)
             1. GCC-box binding domain [54176]
                1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [54177] (3)
          4. Methyl-CpG-binding domain, MBD [54178] (3)
             1. Methyl-CpG-binding protein 2, MECP2 [54179]
                1. Human (Homo sapiens) [TaxId: 9606] [54180] (1)
                2. Chicken (Gallus gallus) [TaxId: 9031] [102734] (1)
             2. Methylation-dependent transcriptional repressor MBD1/PCM1 [54181]
                1. Human (Homo sapiens) [TaxId: 9606] [54182] (2)
   15. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54183] (1)
       alpha1-beta3; 2 layers: alpha/beta; order 132
       1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54184] (1)
          duplication: consists of 2 subdomains of this fold
          uperfamily
          1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54185] (1)
             1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54186]
                1. Streptococcus pneumoniae [TaxId: 1313] [54187] (22)
   16. Dodecin subunit-like [88797] (6)
       beta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132
       1. Dodecin-like [89807] (1)
          uperfamily
          1. Dodecin-like [89808] (2)
             Subunit assembly and a probable biological unit is a dodecamer, hence the name
             1. Flavin-binding protein dodecin [89809]
                1. Archaeon Halobacterium salinarum [TaxId: 2242] [89810] (12)
             2. Uncharacterized protein TTHA1431 [159869]
                1. Thermus thermophilus [TaxId: 274] [159870] (62)
                   SQ Q5SIE3 2-67! SQ Q5SIE3 2-68
       2. Amyloid beta a4 protein copper binding domain (domain 2) [89811] (1)
          uperfamily
          1. Amyloid beta a4 protein copper binding domain (domain 2) [89812] (1)
             1. Amyloid beta a4 protein copper binding domain (domain 2) [89813]
                1. Human (Homo sapiens) [TaxId: 9606] [89814] (3)
       3. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88798] (1)
          uperfamily
          1. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88799] (3)
             1. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88800]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88801] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117777] (7)
                   SQ P34087
                3. Human (Homo sapiens) [TaxId: 9606] [142891] (4)
                   SQ P62487 1-77
       4. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117778] (1)
          uperfamily
          1. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117779] (1)
             1. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117780]
                homo-dimerisation domain
                1. Clostridium sticklandii [TaxId: 1511] [117781] (1)
                   SQ Q9ZFE5
       5. YbjQ-like [117782] (1)
          pentamer, beta/alpha-propeller; additional short beta-strands promote oligomeric assembly
          uperfamily
          1. YbjQ-like [117783] (2)
             Pfam 01906; DUF 74, UPF0145
             1. Hypothetical protein YbjQ [117784]
                1. Shigella flexneri [TaxId: 623] [117785] (1)
                   SQ Q83LS2
             2. Hypothetical protein BC1012 [142892]
                1. Bacillus cereus [TaxId: 1396] [142893] (5)
                   SQ Q81H14 1-103
       6. YdgH-like [159871] (1)
          extra N-terminal structures: short strand and short helix; topological similarity to the YbjQ-like superfamily
          1. YdgH-like [159872] (2)
             Pfam 07338; DUF1471
             1. Hypothetical protein STM0082 [159873]
                1. Salmonella typhimurium [TaxId: 90371] [159874] (2)
                   SQ Q7CR88 1-96
             2. Putative periplasmic protein YahO [159875]
                SCH_0407
                1. Salmonella choleraesuis [TaxId: 28901] [159876] (1)
                   SQ Q57SJ8 1-91
   17. Ribosomal proteins S24e, L23 and L15e [54188] (1)
       beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
       1. Ribosomal proteins S24e, L23 and L15e [54189] (3)
          uperfamily
          1. L23p [54190] (4)
             1. Ribosomal protein L23 [54191]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [54192] (62)
                   SQ P12732
                2. Thermus thermophilus [TaxId: 274] [89815] (7)
                3. Deinococcus radiodurans [TaxId: 1299] [159877] (8)
                   SQ Q9RXK0 2-94
                4. Escherichia coli [TaxId: 562] [159878] (28)
                   SQ P02424 1-99
          2. L15e [54193] (1)
             elaborated with additional structures
             1. Ribosomal protein L15e [54194]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [54195] (42)
                   SQ P60618
          3. Ribosomal protein S24e [117786] (4)
             Pfam 01282
             1. Ribosomal protein S24e [117787]
                1. Methanosarcina mazei [TaxId: 2209] [117788] (1)
                   SQ Q8PZ95
                2. Thermoplasma acidophilum [TaxId: 2303] [142894] (1)
                   SQ Q9HJ79 1-98
                3. Methanococcus maripaludis [TaxId: 39152] [142895] (1)
                   SQ P61193 1-102
                4. Pyrococcus abyssi [TaxId: 29292] [159879] (2)
                   SQ Q9UY20 1-93
   18. Ribosome binding domain-like [100965] (2)
       beta-(2)-alpha(2)-beta(2); 2 layers: beta/alpha; antiparallel beta-sheet: order 1243; topological similarity to the common core of ribosomal proteins L23 and L15e
       1. Trigger factor ribosome-binding domain [102735] (1)
          uperfamily
          1. Trigger factor ribosome-binding domain [102736] (2)
             1. Trigger factor ribosome-binding domain [102737]
                1. Escherichia coli [TaxId: 562] [102738] (4)
                   SQ P22257
                2. Vibrio cholerae [TaxId: 666] [110787] (1)
                   SQ Q9KQS5
       2. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100966] (1)
          uperfamily
          1. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100967] (2)
             1. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100968]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102739] (1)
                2. Archaeon Methanococcus jannaschii [TaxId: 2190] [100969] (1)
   19. TFB5-like [142896] (1)
       beta-alpha-beta(2)-alpha; 2 layers, a/b; antiparallel sheet, order: 132; dimerises in solution (PDB 2jnj) via extended N-terminal strand
       1. TFB5-like [142897] (1)
          uperfamily
          1. TFB5-like [142898] (1)
             Pfam 06331
             1. General transcription factor IIH polypeptide 5, TFB5 [142899]
                1. Human (Homo sapiens) [TaxId: 9606] [142900] (1)
                   SQ Q6ZYL4 6-71
   20. Obg GTP-binding protein C-terminal domain [102740] (1)
       beta-(2)-alpha(3)-beta(2); 2 layers: beta/alpha; mixed beta-sheet: order 1234; strands 2 and 3 a parallel to each other
       1. Obg GTP-binding protein C-terminal domain [102741] (1)
          uperfamily
          1. Obg GTP-binding protein C-terminal domain [102742] (1)
             1. Obg GTP-binding protein C-terminal domain [102743]
                1. Thermus thermophilus [TaxId: 274] [102744] (1)
                   TT1381
   21. HIT-like [54196] (2)
       alpha-beta(3)-alpha-beta(2); 3 layers: alpha/beta/alpha
       1. HIT-like [54197] (4)
          uperfamily
          1. HIT (HINT, histidine triad) family of protein kinase-interacting proteins [54198] (7)
             Pfam 01230
             topologically similar to the N-terminal domain of protein kinases
             1. Histidine triad nucleotide-binding protein (HINT) [54199]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [54200] (5)
             2. FHIT (fragile histidine triad protein) [54201]
                1. Human (Homo sapiens) [TaxId: 9606] [54202] (8)
             3. Protein kinase C inhibitor-1, PKCI-1 [54203]
                1. Human (Homo sapiens) [TaxId: 9606] [54204] (6)
             4. NIT-FHIT fusion protein, C-terminal domain [54205]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [54206] (1)
             5. Hit [117789]
                1. Bacillus subtilis [TaxId: 1423] [117790] (1)
                   SQ O07513
             6. Putative hydrolase [117791]
                1. Clostridium thermocellum [TaxId: 1515] [117792] (1)
                   SQ Q4CCR3
             7. Histidine triad protein Mfla2506 [159880]
                1. Methylobacillus flagellatus [TaxId: 405] [159881] (4)
                   SQ Q1GYB6 6-144
          2. Hexose-1-phosphate uridylyltransferase [54207] (2)
             duplication: consists of 2 HIT-like motifs
             binds zinc and iron ions
             1. Galactose-1-phosphate uridylyltransferase [54208]
                1. Escherichia coli [TaxId: 562] [54209] (4)
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110788] (20)
                   SQ Q9FK51
          3. mRNA decapping enzyme DcpS C-terminal domain [102745] (2)
             1. mRNA decapping enzyme DcpS C-terminal domain [102746]
                1. Human (Homo sapiens) [TaxId: 9606] [102747] (14)
                2. Mouse (Mus musculus) [TaxId: 10090] [110789] (1)
                   SQ Q9DAR7
          4. CDH-like [159882] (1)
             Pfam 02611; CDP-diacylglycerol pyrophosphatase; duplication: consists of the N-terminal HIT subdomain and C-terminal rudiment HIT-like subdomain
             1. CDP-diacylglycerol pyrophosphatase CDH [159883]
                1. Escherichia coli [TaxId: 562] [159884] (2)
                   SQ Q8X7A5 31-250
       2. Rotavirus NSP2 fragment, C-terminal domain [75347] (1)
          uperfamily
          1. Rotavirus NSP2 fragment, C-terminal domain [75348] (1)
             1. Rotavirus NSP2 fragment, C-terminal domain [75349]
                1. Simian 11 rotavirus [TaxId: 10923] [75350] (5)
   22. Secretion chaperone-like [69634] (5)
       alpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/beta
       1. Type III secretory system chaperone-like [69635] (2)
          uperfamily
          1. Type III secretory system chaperone [69636] (11)
             the family sequences are very divergent
             1. YopE chaperone SycE [69637]
                1. Yersinia pestis [TaxId: 632] [69638] (3)
                2. Yersinia enterocolitica [TaxId: 630] [75351] (1)
             2. Virulence effector SptP secretion chaperone SicP [69639]
                1. Salmonella typhimurium [TaxId: 90371] [69640] (1)
             3. Secretion chaperone CesT [69641]
                1. Escherichia coli [TaxId: 562] [69642] (1)
             4. Secretion chaperone SigE [69643]
                1. Salmonella enterica [TaxId: 28901] [69644] (1)
             5. Surface presentation of antigens protein SpaK (Spa15) [102748]
                1. Shigella flexneri [TaxId: 623] [102749] (1)
                2. Salmonella typhimurium [TaxId: 90371] [142901] (2)
                   SQ P0A1N0 1-134
             6. Putative YopH chaperone SycH [110790]
                1. Yersinia pestis [TaxId: 632] [110791] (1)
                   SQ Q7ARG9
             7. AvrPphF ORF1, chaperone of AvrPphF ORF2 [110792]
                1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [110793] (1)
                   SQ Q9K2L2 1-125
             8. Chaperone protein YscB [142902]
                1. Yersinia pestis [TaxId: 632] [142903] (1)
                   SQ Q56973 2-127
             9. Chaperone protein SycN [142904]
                1. Yersinia pestis [TaxId: 632] [142905] (1)
                   SQ P61380 2-122
          2. Tll0839-like [159885] (1)
             Pfam 08851; DUF1821; cyanobacterial family of similar subunit and dimer structures to the Type III secretory system chaperone from proteobacteria
             1. Uncharacterized protein Tll0839 [159886]
                1. Synechococcus elongatus [TaxId: 32046] [159887] (2)
                   SQ Q8DKM0 1-152
       2. Arp2/3 complex subunits [69645] (1)
          uperfamily
          1. Arp2/3 complex subunits [69646] (2)
             1. ARPC4 (20 kDa subunit) [69647]
                1. Cow (Bos taurus) [TaxId: 9913] [69648] (10)
                   SQ P59998 # 100% sequence identity
             2. ARPC2 (34 kDa subunit) [69649]
                duplication: tandem repeat of two domains of this fold
                1. Cow (Bos taurus) [TaxId: 9913] [69650] (17)
                   SQ O15144 1-282 # 100% sequence identity
       3. YjbR-like [142906] (1)
          overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
          uperfamily
          1. YjbR-like [142907] (2)
             Pfam 04237; DUF419
             1. Hypothetical protein DR2400 [142908]
                1. Deinococcus radiodurans [TaxId: 1299] [142909] (1)
                   SQ Q9RRT5 2-132
             2. Hypothetical protein YjbR [142910]
                1. Escherichia coli [TaxId: 562] [142911] (1)
                   SQ P0AF50 1-118
       4. YdhG-like [159888] (1)
          some similarity to YjbR-like (scop_sf 136320)
          1. YdhG-like [159889] (2)
             Pfam 08818; DUF1801
             1. Uncharacterized protein LSEI2283 [159890]
                1. Lactobacillus casei [TaxId: 1582] [159891] (2)
                   SQ Q035U5 2-122
             2. Uncharacterized protein YdhG [159892]
                1. Bacillus subtilis [TaxId: 1423] [159893] (2)
                   SQ Q797E6 1-123
       5. YgaC/TfoX-N like [159894] (2)
          overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
          1. YgaC-like [159895] (1)
             Pfam 09400; DUF2002
             1. Putative cytoplasmic protein YgaC [159896]
                1. Salmonella typhimurium [TaxId: 90371] [159897] (1)
                   SQ Q8ZML5 1-112
          2. TfoX N-terminal domain-like [159898] (1)
             Pfam 04993
             1. Hypothetical protein VP1028 [159899]
                1. Vibrio parahaemolyticus [TaxId: 670] [159900] (2)
                   SQ Q87QX1 3-105
   23. DNA-binding domain of intron-encoded endonucleases [64495] (1)
       beta(2)-alpha(2)-beta; 2 layers; 3-stranded antiparallel beta-sheet, order 213; HTH motif; also includes the extra N-terminal, DNA minor groove-binding helix
       1. DNA-binding domain of intron-encoded endonucleases [64496] (1)
          uperfamily
          1. DNA-binding domain of intron-encoded endonucleases [64497] (2)
             1. DNA-binding domain of intron endonuclease I-TevI [64498]
                contains extra N-terminal zinc-finger domain
                1. Bacteriophage T4 [TaxId: 10665] [64499] (2)
                   SQ P13299 149-244
             2. Intron-encoded homing endonuclease I-HmuI [110794]
                1. Bacteriophage SP01 [TaxId: 10685] [110795] (1)
                   SQ P34081
   24. MotA C-terminal domain-like [69651] (1)
       alpha-beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta
       1. DNA-binding C-terminal domain of the transcription factor MotA [69652] (1)
          uperfamily
          1. DNA-binding C-terminal domain of the transcription factor MotA [69653] (1)
             1. DNA-binding C-terminal domain of the transcription factor MotA [69654]
                1. Bacteriophage T4 [TaxId: 10665] [69655] (1)
   25. YktB/PF0168-like [142912] (1)
       alpha-beta(4)-alpha-beta(2)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order: 1234756; half-barrel shape; topological similarity to the MotA C-terminal domain-like fold (scop_cf 69651) and the Secretion chaperone-like fold (scop_cf 69634)
       1. YktB/PF0168-like [142913] (2)
          uperfamily
          1. YktB-like [142914] (1)
             Pfam 06335; DUF1054
             1. Hypothetical protein YktB [142915]
                1. Bacillus subtilis [TaxId: 1423] [142916] (1)
                   SQ Q45498 2-211
          2. PF0168-like [142917] (1)
             1. Hypothetical protein PF0168 [142918]
                1. Pyrococcus furiosus [TaxId: 2261] [142919] (1)
                   SQ Q8U4C0 2-167
   26. Mago nashi protein [89816] (1)
       beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, order: 651234
       1. Mago nashi protein [89817] (1)
          uperfamily
          1. Mago nashi protein [89818] (2)
             1. Mago nashi protein [89819]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89820] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [102750] (6)
   27. WGR domain-like [142920] (1)
       beta(4)-alpha-X-beta; 2 layers, a/b; antiparallel beta-sheet, order 51234; the beta-hairpin insetrion in strand 1 results in the formation of a beta-triangle structure
       1. WGR domain-like [142921] (1)
          uperfamily
          1. WGR domain [142922] (1)
             Pfam 05406; the conserved WGR motif maps to the C-end of strand 3, both large sidechains are exposed
             1. Poly [ADP-ribose] polymerase-1, PARP-1 [142923]
                1. Human (Homo sapiens) [TaxId: 9606] [142924] (1)
                   SQ P09874 517-642
   28. PH1570-like [159901] (1)
       duplication: two beta(4)-alpha structural repeats, related by pseudo twofold symmetry; two extra helices in the linker region; single 8-standed antiparallel beta-sheet, order: 12348765
       1. PH1570-like [159902] (1)
          1. PH1570-like [159903] (1)
             Pfam 09638
             1. Hypothetical protein PH1570 [159904]
                1. Pyrococcus horikoshii [TaxId: 53953] [159905] (2)
                   SQ O59278 1-152
   29. Ribosomal protein S5 domain 2-like [54210] (1)
       core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
       1. Ribosomal protein S5 domain 2-like [54211] (12)
          uperfamily
          1. Translational machinery components [54212] (8)
             1. Elongation factor G (EF-G), domain IV [54213]
                1. Thermus thermophilus [TaxId: 274] [54214] (9)
                2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142925] (2)
                   SQ Q5SI76 448-562
                   TTHA1498
             2. Elongation factor 2 (eEF-2), domain IV [82575]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82576] (22)
                   SQ P32324
             3. Ribosomal protein S5, C-terminal domain [54215]
                1. Bacillus stearothermophilus [TaxId: 1422] [54216] (1)
                2. Thermus thermophilus [TaxId: 274] [54217] (36)
                   SQ P27152 ! SQ P80373
                3. Escherichia coli [TaxId: 562] [159906] (24)
                   SQ P0A7W1 78-158
             4. Ribosomal protein S9 [54218]
                1. Thermus thermophilus [TaxId: 274] [54219] (39)
                   SQ P80374
                2. Escherichia coli [TaxId: 562] [159907] (26)
                   SQ P0A7X3 3-129
          2. RNase P protein [54220] (3)
             1. RNase P protein [54221]
                1. Bacillus subtilis [TaxId: 1423] [54222] (1)
                2. Staphylococcus aureus [TaxId: 1280] [54223] (1)
                3. Thermotoga maritima [TaxId: 2336] [89821] (1)
          3. DNA gyrase/MutL, second domain [54224] (7)
             1. DNA mismatch repair protein MutL [54225]
                1. Escherichia coli [TaxId: 562] [54226] (6)
             2. DNA mismatch repair protein PMS2 [69656]
                1. Human (Homo sapiens) [TaxId: 9606] [69657] (3)
             3. DNA gyrase B [54227]
                1. Escherichia coli [TaxId: 562] [54228] (1)
                2. Thermus thermophilus [TaxId: 274] [75352] (1)
             4. DNA topoisomerase II [102751]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102752] (2)
             5. Topoisomerase IV subunit B [102753]
                1. Escherichia coli [TaxId: 562] [102754] (1)
             6. Topoisomerase VI-B subunit [82577]
                contains an H2TH domain inserted in front of this domain and after the N-terminal ATPase domain
                1. Archaeon Sulfolobus shibatae [TaxId: 2286] [82578] (10)
          4. Hsp90 middle domain [102755] (1)
             related to the DNA gyrase/MutL family; contains extra C-terminal alpha/beta subdomain
             1. Heat shock protein hsp82 [102756]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102757] (3)
          5. Ribonuclease PH domain 1-like [54229] (14)
             1. Ribonuclease PH, domain 1 [102758]
                1. Aquifex aeolicus [TaxId: 63363] [102759] (4)
                2. Pseudomonas aeruginosa [TaxId: 287] [102760] (2)
                3. Bacillus subtilis [TaxId: 1423] [102761] (3)
             2. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 [54230]
                duplication of two-domain units formed by domains 1-2 and 4-5
                1. Streptomyces antibioticus [TaxId: 1890] [54231] (2)
             3. Exosome complex exonuclease RRP42 [159908]
                1. Human (Homo sapiens) [TaxId: 9606] [159909] (1)
                   SQ Q15024 5-191
             4. Exosome complex exonuclease RRP46 [159910]
                1. Human (Homo sapiens) [TaxId: 9606] [159911] (1)
                   SQ Q9NQT4 25-146
             5. Exosome complex exonuclease RRP45 [159912]
                1. Human (Homo sapiens) [TaxId: 9606] [159913] (1)
                   SQ Q86Y41 1-184
             6. Exosome complex exonuclease RRP43 [159914]
                1. Human (Homo sapiens) [TaxId: 9606] [159915] (1)
                   SQ Q96B26 7-187
             7. Exosome complex exonuclease MTR3 [159916]
                1. Human (Homo sapiens) [TaxId: 9606] [159917] (1)
                   SQ Q5RKV6 29-175
             8. Exosome complex exonuclease RRP41 [159918]
                1. Human (Homo sapiens) [TaxId: 9606] [159919] (1)
                   SQ Q9NPD3 7-151
             9. Exosome complex exonuclease 2,ECX2 [159920]
                1. Archaeoglobus fulgidus [TaxId: 2234] [159921] (6)
                   SQ O29756 3-178
                2. Sulfolobus solfataricus [TaxId: 2287] [159922] (51)
                   SQ Q9UXC0 1-191
             10. Exosome complex exonuclease 1, ECX1 [159923]
                 1. Sulfolobus solfataricus [TaxId: 2287] [159924] (50)
                    SQ Q9UXC2 8-155
                 2. Archaeoglobus fulgidus [TaxId: 2234] [159925] (6)
                    SQ O29757 10-153
          6. GHMP Kinase, N-terminal domain [54232] (10)
             1. Galactokinase [102762]
                1. Lactococcus lactis [TaxId: 1358] [102763] (1)
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102764] (1)
                3. Human (Homo sapiens) [TaxId: 9606] [117793] (1)
                   SQ P51570
             2. Homoserine kinase [54233]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [54234] (5)
             3. Mevalonate kinase [75353]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75354] (2)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [75355] (2)
             4. Phosphomevalonate kinase (PMK) [75356]
                1. Streptococcus pneumoniae r6 [TaxId: 171101] [75357] (1)
             5. Mevalonate 5-diphosphate decarboxylase [64219]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64220] (1)
             6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89822]
                1. Thermus thermophilus [TaxId: 274] [89823] (1)
                2. Escherichia coli [TaxId: 562] [102765] (1)
          7. Early switch protein XOL-1, N-terminal domain [89824] (1)
             diverged from the GHMP Kinase family; lost the ATP-binding site
             1. Early switch protein XOL-1, N-terminal domain [89825]
                1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89826] (1)
          8. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89827] (1)
             duplication; there are two structural repeats of this fold; each repeat is elaborated with additional structures forming the active site
             1. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89828]
                1. Aquifex aeolicus [TaxId: 63363] [89829] (34)
                   SQ O67648 3-270
          9. Imidazole glycerol phosphate dehydratase [102766] (3)
             duplication; there are two structural repeats of this fold
             1. Imidazole glycerol phosphate dehydratase [102767]
                1. Fungus (Filobasidiella neoformans) [TaxId: 5207] [102768] (1)
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142926] (32)
                   SQ P34047 159-255! SQ P34047 73-158
                3. Staphylococcus aureus [TaxId: 1280] [142927] (12)
                   SQ P64373 1-84! SQ P64373 85-179
          10. ATP-dependent protease Lon (La), catalytic domain [102769] (2)
              contains extra C-terminal alpha/beta subdomain
              1. ATP-dependent protease Lon (La), catalytic domain [102770]
                 1. Escherichia coli [TaxId: 562] [102771] (2)
                 2. Methanococcus jannaschii [TaxId: 2190] [117794] (1)
                    SQ Q58812 456-640 # MJ1417
          11. YigZ N-terminal domain-like [102772] (2)
              modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand is inserted between strands 3 and 4
              1. Hypothetical protein YigZ, N-terminal domain [102773]
                 1. Escherichia coli [TaxId: 562] [102774] (1)
                    two-domain structure is similar to the C-terminal region of EF-G (domains IV and V)
              2. Hypothetical protein TTHA1053, N-terminal domain [142928]
                 1. Thermus thermophilus [TaxId: 274] [142929] (1)
                    SQ Q5SJF5 2-124
          12. Formaldehyde-activating enzyme, FAE [117795] (1)
              modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand extends beta-sheet antiparallel to strand 3
              1. Formaldehyde-activating enzyme, FAE [117796]
                 1. Methylobacterium extorquens [TaxId: 408] [117797] (2)
                    SQ Q9FA38
   30. beta-Grasp (ubiquitin-like) [54235] (14)
       core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
       1. Ubiquitin-like [54236] (8)
          uperfamily
          1. Ubiquitin-related [54237] (47)
             Pfam 00240
             1. Ubiquitin [54238]
                1. Human (Homo sapiens) [TaxId: 9606] [54239] (102)
                   SQ P62988
                   identical sequence in many other species
                2. Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932] [89830] (7)
                3. Synthetic, based on Saccharomyces cerevisiae sequence [54240] (1)
             2. SUMO-1 (smt3 homologue) [54241]
                1. Human (Homo sapiens) [TaxId: 9606] [54242] (17)
                   SQ Q93068
                2. Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932] [54243] (4)
             3. Nedd8 [54244]
                1. Human (Homo sapiens) [TaxId: 9606] [54245] (7)
                   SQ Q15843
             4. Elongin B [54246]
                1. Human (Homo sapiens) [TaxId: 9606] [54247] (7)
                2. Mouse (Mus musculus) [TaxId: 10090] [142930] (1)
                   SQ P62869 1-98
             5. Rub1 [54248]
                1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [54249] (1)
             6. Ubiquitin-like modifier protein hub1 [82579]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82580] (1)
             7. Ubiquitin-like N-terminal domain of PLIC-2 [75358]
                1. Human (Homo sapiens) [TaxId: 9606] [75359] (1)
             8. Ubiquitin-like domain of parkin [89831]
                1. Human (Homo sapiens) [TaxId: 9606] [89832] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [89833] (2)
             9. Ubiquitin-like domain of Rad23 homolog A (Hhr23a) [102775]
                1. Human (Homo sapiens) [TaxId: 9606] [102776] (4)
             10. Ubiquitin-like domain of Rad23 homolog B (Hhr23B) [102777]
                 1. Human (Homo sapiens) [TaxId: 9606] [102778] (2)
                    SQ P54727 1-82
             11. Ubiquitin-like protein 5, ubl5 [102779]
                 1. Human (Homo sapiens) [TaxId: 9606] [102780] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [102781] (1)
             12. Hypothetical protein At3g01050 [102782]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102783] (1)
             13. Ubiquitin-like protein 3300001g02rik [102784]
                 1. Mouse (Mus musculus) [TaxId: 10090] [102785] (1)
             14. Ubiquitin-like domain of tubulin folding cofactor B [102786]
                 1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102787] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [117798] (1)
                    SQ Q9D1E6 11-92
             15. 1700011n24rik protein [110796]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110797] (1)
                    SQ Q9DAF3 1-89
             16. 8430435i17rik protein [110798]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110799] (1)
                    SQ Q8BGR9 3-79
             17. hypothetical D7wsu128e protein [110800]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110801] (1)
                    SQ Q78JW9 76-157
             18. Splicing factor 3 subunit 1, C-terminal domain [117799]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117800] (1)
                    SQ Q8K4Z5 685-786
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117801] (1)
                    SQ Q8RXF1 683-780; T5E21.13/At1g14650
                 3. Human (Homo sapiens) [TaxId: 9606] [142931] (1)
                    SQ Q15459 704-789
             19. Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 [117802]
                 1. Human (Homo sapiens) [TaxId: 9606] [117803] (1)
                    SQ Q15011 10-90
             20. Ubiquitin carboxyl-terminal hydrolase 14 [117804]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117805] (1)
                    SQ Q9JMA1 3-85
             21. Ubiquitin-like protein 3, Ubl3 [117806]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117807] (1)
                    SQ Q9Z2M6 1-103
             22. 2'-5'-oligoadenylate synthetase-like protein, OASL [117808]
                 1. Human (Homo sapiens) [TaxId: 9606] [117809] (1)
                    SQ Q15646 434-507
             23. Ubiquitin-like protein bab25500 (2010008E23Rik) [117810]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117811] (1)
                    SQ Q9D8C5 163-244
             24. Tubulin-folding protein TbcE [117812]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117813] (1)
                    SQ Q8CIV8 441-524
             25. NEDD8 ultimate buster-1, NUB1 [117814]
                 1. Human (Homo sapiens) [TaxId: 9606] [117815] (1)
                    SQ Q9Y5A7 75-161
             26. SUMO-2 [117816]
                 1. Human (Homo sapiens) [TaxId: 9606] [117817] (13)
                    SQ P61956
             27. Bag-family molecular chaperone regulator-1 [142932]
                 1. Human (Homo sapiens) [TaxId: 9606] [142933] (1)
                    SQ Q99933 72-152
                    the BAG domain structure is also known (scop_sp 63494)
             28. NPL4-like protein 1 [142934]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142935] (1)
                    SQ Q9LYC2 2-95
             29. Interferon-induced 15 kDa protein [142936]
                 1. Human (Homo sapiens) [TaxId: 9606] [142937] (2)
                    SQ P05161 2-77! SQ P05161 78-153
             30. Ubiquitin-like protein smt3a, SUMO-3 [142938]
                 1. Human (Homo sapiens) [TaxId: 9606] [142939] (1)
                    SQ P55854 14-92
             31. DSK2 [142940]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142941] (5)
                    SQ P48510 2-74
             32. Ubiquitin-like protein 7 [142942]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142943] (1)
                    SQ Q91W67 1-94
             33. Ubiquitin-like PHD and RING finger domain-containing protein 2 [142944]
                 1. Human (Homo sapiens) [TaxId: 9606] [142945] (1)
                    SQ Q96PU4 1-76
             34. Ubiquilin-3 [142946]
                 1. Human (Homo sapiens) [TaxId: 9606] [142947] (2)
                    SQ Q9H347 11-104! SQ Q9H347 15-98
             35. Ubiquitin-like PHD and RING finger domain-containing protein 1 [142948]
                 1. Human (Homo sapiens) [TaxId: 9606] [142949] (2)
                    SQ Q96T88 1-76
             36. 4931431F19Rik [142950]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142951] (1)
                    SQ Q9D4I8 14-96
                    structure of the C-terminal UBA domain is also known (PDB 1vej)
             37. Large proline-rich protein BAT3 [142952]
                 1. Human (Homo sapiens) [TaxId: 9606] [142953] (1)
                    SQ P46379 17-89
             38. Dendritic cell-derived ubiquitin-like protein [142954]
                 1. Human (Homo sapiens) [TaxId: 9606] [142955] (1)
                    SQ Q8WUN7 149-228
          2. UBX domain [54250] (5)
             Pfam 00789
             1. Fas-associated factor 1, Faf1 [54251]
                1. Human (Homo sapiens) [TaxId: 9606] [54252] (1)
             2. p47 [64221]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [64222] (3)
             3. Hypothetical protein KIAA0794 [117818]
                1. Human (Homo sapiens) [TaxId: 9606] [117819] (1)
                   SQ O94888 376-487
             4. UBX domain-containing protein 6 (Reproduction 8) [142956]
                1. Mouse (Mus musculus) [TaxId: 10090] [142957] (1)
                   SQ Q9QZ49 182-277
             5. Tether containing UBX domain for GLUT4 (Tug) [142958]
                1. Mouse (Mus musculus) [TaxId: 10090] [142959] (1)
                   SQ Q8VBT9 10-85
          3. GABARAP-like [54253] (5)
             intracellular membrane trafficking and fusion proteins
             1. Golgi-associated ATPase enhancer of 16 kD, Gate-16 [54254]
                1. Cow (Bos taurus) [TaxId: 9913] [54255] (1)
             2. GABA(A) receptor associated protein GABARAP [69658]
                1. Human (Homo sapiens) [TaxId: 9606] [69659] (6)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [75360] (1)
             3. Microtubule-associated proteins 1A/1B light chain 3B [110802]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [110803] (4)
                   SQ Q62625 4-116
                2. Human (Homo sapiens) [TaxId: 9606] [117820] (3)
                   SQ Q9GZQ8
          4. First domain of FERM [54256] (7)
             1. Moesin [54257]
                1. Human (Homo sapiens) [TaxId: 9606] [54258] (3)
                   SQ P26038 4-297
             2. Radixin [54259]
                1. Mouse (Mus musculus) [TaxId: 10090] [54260] (20)
             3. Ezrin [82581]
                1. Human (Homo sapiens) [TaxId: 9606] [82582] (1)
             4. Erythroid membrane protein 4.1R [54261]
                1. Human (Homo sapiens) [TaxId: 9606] [54262] (1)
             5. Merlin [69660]
                the neurofibromatosis 2 tumor suppressor protein
                1. Human (Homo sapiens) [TaxId: 9606] [69661] (1)
                2. Mouse (Mus musculus) [TaxId: 10090] [75361] (1)
             6. Focal adhesion kinase 1 [142960]
                1. Chicken (Gallus gallus) [TaxId: 9031] [142961] (5)
                   SQ Q00944 31-130
          5. Ras-binding domain, RBD [54263] (16)
             contains Pfam 00788 and Pfam 02196
             1. c-Raf1 RBD [54264]
                1. Human (Homo sapiens) [TaxId: 9606] [54265] (3)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [54266] (1)
             2. Ral guanosine-nucleotide exchange factor, RalGDS [54267]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [54268] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [54269] (3)
             3. RalGDS-like factor, Rlf [54270]
                1. Mouse (Mus musculus) [TaxId: 10090] [54271] (1)
             4. Rgl [54272]
                1. Mouse (Mus musculus) [TaxId: 10090] [54273] (1)
             5. Phoshoinositide 3-kinase (PI3K) [54274]
                includes parts of the flanking linkers
                1. Pig (Sus scrofa) [TaxId: 9823] [54275] (5)
                2. Human (Homo sapiens) [TaxId: 9606] [54276] (3)
             6. Protein kinase byr2 [69662]
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [69663] (2)
             7. Regulator of G-protein signaling 14, RGS14 [117821]
                1. Mouse (Mus musculus) [TaxId: 10090] [117822] (1)
                   SQ P97492 366-456
             8. Growth factor receptor-bound protein 7, GRB-7 [117823]
                1. Human (Homo sapiens) [TaxId: 9606] [117824] (1)
                   SQ Q14451 100-186
             9. Rap guanine nucleotide exchange factor 5, RapGEF5 [117825]
                1. Human (Homo sapiens) [TaxId: 9606] [117826] (1)
                   SQ Q92565 241-331
             10. Ras association domain-containing protein 8 [142962]
                 1. Human (Homo sapiens) [TaxId: 9606] [142963] (1)
                    SQ Q8NHQ8 1-83
             11. Afadin [142964]
                 1. Mouse (Mus musculus) [TaxId: 10090] [142965] (1)
                    SQ Q9QZQ1 246-348
                    The FHA domain structure is also known (PDB 1wln)
             12. Phospholipase C-epsilon-1 [142966]
                 contains several Ras-binding domains; some are 'hidden' in the sequence
                 1. Human (Homo sapiens) [TaxId: 9606] [142967] (4)
                    SQ Q9P212 2006-2114! SQ Q9P212 2131-2246! SQ Q9P212 2134-2239
             13. A-Raf proto-oncogene serine/threonine-protein kinase [142968]
                 1. Human (Homo sapiens) [TaxId: 9606] [142969] (1)
                    SQ P10398 19-91
          6. BM-002-like [75362] (3)
             Pfam 03671; UPF0185; this family comprises small uncharacterized proteins including human protein BM-002
             1. Hypothetical protein zk652.3 [75363]
                1. Caenorhabditis elegans [TaxId: 6239] [75364] (1)
             2. Hypothetical protein 1810045k17 [102788]
                1. Mouse (Mus musculus) [TaxId: 10090] [102789] (1)
             3. Ubiquitin-fold modifier 1 [142970]
                1. Human (Homo sapiens) [TaxId: 9606] [142971] (1)
                   SQ P61960 1-83
          7. APG12-like [142972] (1)
             Pfam 04110
             1. Autophagy-related protein 12b (APG12b) [142973]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142974] (2)
                   SQ Q9LVK3 10-93
          8. DIX domain [159926] (1)
             Pfam 00778
             1. Axin 1 [159927]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [159928] (9)
                   SQ O70239 745-827
       2. CAD & PB1 domains [54277] (2)
          contain extra helix; similar heterodimerization modes; possibly related to the ubiquitin-like superfamily
          uperfamily
          1. CAD domain [54278] (5)
             1. Cell death-inducing effector B (CIDE-B), N-terminal domain [54279]
                1. Human (Homo sapiens) [TaxId: 9606] [54280] (1)
             2. Caspase-activated DNase (CAD), DFF40, N-terminal domain [54281]
                1. Mouse (Mus musculus) [TaxId: 10090] [54282] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [64223] (1)
             3. Inhibitor of caspase-activated DNase (ICAD), DFF45, N-terminal domain [54283]
                1. Mouse (Mus musculus) [TaxId: 10090] [54284] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [64224] (1)
          2. PB1 domain [64225] (11)
             Pfam 00564
             forms heterodimers, although not all PB1 domain pairs associate.
             1. Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) [102790]
                1. Human (Homo sapiens) [TaxId: 9606] [102791] (1)
             2. Neutrophil cytosol factor 4 (p40phox component of NADPH oxidase) [102792]
                1. Human (Homo sapiens) [TaxId: 9606] [102793] (1)
             3. Bud emergence mediator Bemp1 [64226]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64227] (2)
             4. Cell division control protein 24, CDC24, C-terminal domain [89834]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89835] (3)
             5. Protein kinase C, iota type [110804]
                1. Human (Homo sapiens) [TaxId: 9606] [110805] (2)
                   SQ P41743 16-98 ! SQ P41743 16-99
             6. Mitogen activated protein kinase kinase 5, Map2k5 [117827]
                1. Mouse (Mus musculus) [TaxId: 10090] [117828] (1)
                   SQ Q9D222 7-107
                2. Human (Homo sapiens) [TaxId: 9606] [142975] (2)
                   SQ Q13163 4-108
             7. Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) [117829]
                1. Human (Homo sapiens) [TaxId: 9606] [117830] (2)
                   SQ Q14596 1-85
             8. Partitioning defective-6 homolog alpha, PAR-6 alpha [117831]
                1. Human (Homo sapiens) [TaxId: 9606] [117832] (1)
                   SQ Q9NPB6 14-95
             9. Mitogen-activated protein kinase kinase kinase 2, MEKK 2 [142976]
                1. Human (Homo sapiens) [TaxId: 9606] [142977] (3)
                   SQ Q9Y2U5 42-123! SQ Q9Y2U5 43-132
             10. Mitogen-activated protein kinase kinase kinase 3, MEKK 3 [142978]
                 1. Human (Homo sapiens) [TaxId: 9606] [142979] (2)
                    SQ Q99759 42-123! SQ Q99759 43-122
       3. MoaD/ThiS [54285] (4)
          possible link between the ubiquitin-like and 2Fe-2S ferredoxin-like superfamilies
          uperfamily
          1. MoaD [54286] (3)
             1. Molybdopterin synthase subunit MoaD [54287]
                1. Escherichia coli [TaxId: 562] [54288] (7)
                2. Pyrococcus furiosus [TaxId: 2261] [110806] (1)
                   SQ Q8U3C7
             2. MoaD-related protein, N-terminal domain [102794]
                1. Thermus thermophilus [TaxId: 274] [102795] (1)
          2. ThiS [54289] (5)
             1. Thiamin biosynthesis sulfur carrier protein ThiS [54290]
                1. Escherichia coli [TaxId: 562] [54291] (3)
                2. Bacillus subtilis [TaxId: 1423] [110807] (1)
                   SQ O31617
             2. Hypothetical protein MTH1743 [69664]
                probable ThiS homologue
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69665] (1)
             3. Hypothetical protein PF1061 [102796]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [102797] (2)
             4. Uncharacterised protein TTHA0675 [159929]
                probable ThiS homologue
                1. Thermus thermophilus [TaxId: 274] [159930] (6)
                   SQ Q5SKG8 1-63
          3. C9orf74 homolog [117833] (1)
             1. C9orf74 homolog [117834]
                1. Mouse (Mus musculus) [TaxId: 10090] [117835] (2)
                   SQ Q9D2P4 #
          4. HI0395-like [159931] (1)
             Pfam 03658; UPF0125
             1. Hypothetical protein HI0395 [159932]
                NTHI0516
                1. Haemophilus influenzae [TaxId: 727] [159933] (2)
                   SQ Q4QNE7 2-78
       4. TGS-like [81271] (2)
          possibly related to the ubiquitin-like and MoaD/ThiS superfamilies; some similarity to the alpha-L RNA-binding motif
          uperfamily
          1. TGS domain [81270] (2)
             1. Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain [55176]
                1. Escherichia coli [TaxId: 562] [55177] (5)
                   SQ P0A8M3
                2. Staphylococcus aureus [TaxId: 1280] [102798] (2)
          2. G domain-linked domain [82583] (3)
             1. YchF GTP-binding protein, C-terminal domain [82584]
                N-terminal domain belongs to the Obg family of GTPases some members of which contain a C-terminal TGS domain
                1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82585] (1)
                2. Haemophilus influenzae [TaxId: 727] [89836] (1)
                   HI0393
             2. GTP-binding protein PH0525 [142980]
                1. Pyrococcus horikoshii [TaxId: 53953] [142981] (1)
                   SQ O58261 320-395
       5. 2Fe-2S ferredoxin-like [54292] (2)
          uperfamily
          1. 2Fe-2S ferredoxin-related [54293] (19)
             1. 2Fe-2S ferredoxin [54294]
                1. Cyanobacterium (Anabaena sp.), pcc 7119 and 7120 [TaxId: 1167] [54295] (12)
                2. Spirulina platensis [TaxId: 118562] [54296] (1)
                3. Cyanobacterium (Aphanothece sacrum) [TaxId: 1122] [54297] (1)
                4. Synechocystis sp., pcc 6803 [TaxId: 1143] [54298] (3)
                5. Synechococcus elongatus [TaxId: 32046] [54299] (3)
                6. Chlorella fusca [TaxId: 3073] [54300] (1)
                7. Equisetum arvense [TaxId: 3258] [54301] (2)
                   SQ P00237 # isoform II
                8. Archaeon Haloarcula marismortui [TaxId: 2238] [54302] (1)
                9. Archaeon Halobacterium halobium [TaxId: 2242] [64228] (2)
                10. Parsley (Petroselinum crispum) [TaxId: 4043] [54303] (1)
                11. Spinach (Spinacia oleracea) [TaxId: 3562] [54304] (1)
                12. Maize (Zea mays) [TaxId: 4577] [54305] (1)
                13. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102799] (1)
                14. Trichomonas vaginalis [TaxId: 5722] [75365] (1)
                15. Rhodobacter capsulatus, ferredoxin VI [TaxId: 1061] [64230] (2)
                16. Pseudomonas putida, putidaredoxin [TaxId: 303] [54307] (18)
                17. Pseudomonas sp., terpredoxin [TaxId: 306] [54309] (1)
             2. Adrenodoxin-like ferredoxin [75366]
                1. Escherichia coli [TaxId: 562] [75367] (1)
             3. Adrenodoxin [54310]
                1. Cow (Bos taurus) [TaxId: 9913] [54311] (7)
          2. 2Fe-2S ferredoxin domains from multidomain proteins [54312] (16)
             1. Fe-only hydrogenase, N-terminal domain [54313]
                1. Clostridium pasteurianum [TaxId: 1501] [54314] (4)
             2. Aldehyde oxidoreductase, N-terminal domain [54315]
                1. Desulfovibrio gigas [TaxId: 879] [54316] (3)
                   SQ Q46509
                2. Desulfovibrio desulfuricans [TaxId: 876] [54317] (1)
             3. Xanthine oxidase, N-terminal domain [54318]
                1. Cow (Bos taurus) [TaxId: 9913] [54319] (7)
                   SQ P80457
             4. Xanthine dehydrogenase chain A, N-terminal domain [69666]
                1. Rhodobacter capsulatus [TaxId: 1061] [69667] (2)
             5. Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain [54320]
                1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [54321] (5)
                2. Hydrogenophaga pseudoflava [TaxId: 47421] [54322] (4)
             6. Phthalate dioxygenase reductase, C-terminal domain [54323]
                two other domains are common to ferredoxin reductase
                1. Pseudomonas cepacia, db01 [TaxId: 292] [54324] (1)
             7. Benzoate dioxygenase reductase, N-terminal domain [75368]
                1. Acinetobacter sp. [TaxId: 472] [75369] (1)
             8. Succinate dehydogenase iron-sulfur protein, N-terminal domain [82586]
                1. Escherichia coli [TaxId: 562] [82587] (3)
             9. Fumarate reductase iron-sulfur protein, N-terminal domain [54325]
                1. Escherichia coli [TaxId: 562] [54326] (7)
                2. Wolinella succinogenes [TaxId: 844] [54327] (8)
             10. Methane monooxygenase reductase N-terminal domain [69668]
                 1. Methylococcus capsulatus [TaxId: 414] [69669] (1)
             11. Quinoline 2-oxidoreductase small subunit QorS, N-domain [110808]
                 1. Pseudomonas putida [TaxId: 303] [110809] (1)
                    SQ P72223
             12. 4-hydroxybenzoyl-CoA reductase gamma subunit HrcC, N-terminal domain [117836]
                 1. Thauera aromatica [TaxId: 59405] [117837] (2)
                    SQ O33818
             13. Nadh-quinone oxidoreductase chain 3, Nqo3, N-terminal domain [142982]
                 1. Thermus thermophilus [TaxId: 274] [142983] (4)
                    SQ Q56223 1-95
       6. Staphylokinase/streptokinase [54328] (1)
          uperfamily
          1. Staphylokinase/streptokinase [54329] (2)
             1. Staphylokinase [54330]
                1. Staphylococcus aureus [TaxId: 1280] [54331] (7)
                   phage-borne; Bacteriophage 42D
             2. Streptokinase [54332]
                duplication: consists of three similar domains
                1. Streptococcus equisimilis [TaxId: 119602] [54333] (5)
       7. Doublecortin (DC) [89837] (1)
          possibly related to the ubiquitin-like superfamily
          uperfamily
          1. Doublecortin (DC) [89838] (2)
             1. Doublecortin-like kinase Dclk [89839]
                KIAA0369; duplication: contains tandem repeat of two DC domains
                1. Human (Homo sapiens) [TaxId: 9606] [89840] (3)
             2. Doublecortin [89841]
                duplication: contains tandem repeat of two DC domains
                1. Human (Homo sapiens) [TaxId: 9606] [89842] (1)
       8. Superantigen toxins, C-terminal domain [54334] (1)
          uperfamily
          1. Superantigen toxins, C-terminal domain [54335] (15)
             1. Staphylococcal enterotoxin A, SEA [54336]
                1. Staphylococcus aureus [TaxId: 1280] [54337] (6)
             2. Staphylococcal enterotoxin C2, SEC2 [54338]
                1. Staphylococcus aureus [TaxId: 1280] [54339] (8)
             3. Toxic shock syndrome toxin-1 (TSST-1) [54340]
                1. Staphylococcus aureus [TaxId: 1280] [54341] (13)
             4. Staphylococcal enterotoxin B, SEB [54342]
                1. Staphylococcus aureus [TaxId: 1280] [54343] (12)
             5. Staphylococcal enterotoxin C3, SEC3 [54344]
                1. Staphylococcus aureus [TaxId: 1280] [54345] (11)
                   SQ P23313
             6. Staphylococcal enterotoxin H, SEH [54346]
                1. Staphylococcus aureus [TaxId: 1280] [54347] (4)
             7. Superantigen-like protein SET3 [75370]
                1. Staphylococcus aureus [TaxId: 1280] [75371] (3)
             8. Streptococcal superantigen Spe-C [54348]
                1. Streptococcus pyogenes [TaxId: 1314] [54349] (3)
             9. Streptococcal superantigen Spe-H [54350]
                1. Streptococcus pyogenes [TaxId: 1314] [54351] (2)
             10. Streptococcal superantigen Smez-2 [54352]
                 1. Streptococcus pyogenes [TaxId: 1314] [54353] (2)
             11. Streptococcal superantigen SSA [54354]
                 1. Streptococcus pyogenes [TaxId: 1314] [54355] (10)
             12. Streptococcal pyrogenic exotoxin A1 [54356]
                 1. Streptococcus pyogenes [TaxId: 1314] [54357] (8)
                    SQ P08095
             13. Exotoxin 1 (SET1, Superantigen-like protein 7) [110810]
                 1. Staphylococcus aureus [TaxId: 1280] [110811] (2)
                    SQ Q9ZFS5 36-231
             14. Streptococcal pyrogenic exotoxin Spe-J [110812]
                 1. Streptococcus pyogenes [TaxId: 1314] [110813] (2)
                    SQ Q7BAE3
             15. Enterotoxin type I [159934]
                 1. Staphylococcus aureus [TaxId: 1280] [159935] (1)
                    SQ Q52T95 87-216
       9. Immunoglobulin-binding domains [54358] (1)
          uperfamily
          1. Immunoglobulin-binding domains [54359] (2)
             1. Immunoglobulin-binding protein G, different constituent domains [54360]
                1. Streptococcus sp., group G [TaxId: 1306] [54361] (30)
             2. Immunoglobulin light chain-binding domain of protein L [54362]
                1. Peptostreptococcus magnus [TaxId: 1260] [54363] (12)
       10. Translation initiation factor IF3, N-terminal domain [54364] (1)
           uperfamily
           1. Translation initiation factor IF3, N-terminal domain [54365] (1)
              1. Translation initiation factor IF3, N-terminal domain [54366]
                 1. Bacillus stearothermophilus [TaxId: 1422] [54367] (1)
       11. Glutamine synthetase, N-terminal domain [54368] (1)
           uperfamily
           1. Glutamine synthetase, N-terminal domain [54369] (2)
              1. Glutamine synthetase, N-terminal domain [54370]
                 1. Salmonella typhimurium [TaxId: 90371] [54371] (18)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [75372] (8)
       12. TmoB-like [110814] (1)
           possibly related to the ubiquitin-like and/or 2Fe-2S ferredoxin-like superfamilies
           uperfamily
           1. TmoB-like [110815] (1)
              Pfam 06234
              1. Toluene, o-xylene monooxygenase oxygenase subunit TouB [110816]
                 1. Pseudomonas stutzeri [TaxId: 316] [110817] (6)
                    SQ O87799
       13. Nqo1 middle domain-like [142984] (1)
           possibly evolved from 2Fe-2S ferredoxins; contains no iron-sulfur cluster
           uperfamily
           1. Nqo1 middle domain-like [142985] (1)
              C-terminal part of Pfam 01512
              1. NADH-quinone oxidoreductase chain 1, Nqo1 [142986]
                 1. Thermus thermophilus [TaxId: 274] [142987] (4)
                    SQ Q56222 250-333
       14. NSP3A-like [159936] (1)
           short helical inserions in the common fold
           1. NSP3A-like [159937] (1)
              1. Nsp3 [159938]
                 1. SARS coronavirus [TaxId: 227859] [159939] (2)
                    SQ P59641 819-930
   31. MM3350-like [159940] (1)
       beta(2)-alpha-beta(4); antiparallel beta-sheet; order: 216534; similar to a ubiquitin-like fold with the extra C-terminal strand inserted in the middle of the beta-sheet
       1. MM3350-like [159941] (1)
          1. MM3350-like [159942] (1)
             Pfam07929; plasmid pRiA4b ORF-3-like protein
             1. Hypothetical protein MM3350 [159943]
                1. Methanosarcina mazei [TaxId: 2209] [159944] (2)
                   SQ Q8PRU3 4-188
   32. WWE domain [117838] (1)
       beta(2)-alpha-beta(4); antiparallel folded beta-sheet (half-barrel), order 216543
       1. WWE domain [117839] (1)
          uperfamily
          1. WWE domain [117840] (2)
             Pfam 02825
             1. RING finger protein 146 (Dactylidin) [117841]
                1. Mouse (Mus musculus) [TaxId: 10090] [117842] (1)
                   SQ Q9CZW6 83-179
             2. Deltex (Dx) [159945]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [159946] (2)
                   SQ Q23985 132-211! SQ Q23985 43-131
   33. FAD-linked reductases, C-terminal domain [54372] (1)
       alpha+beta sandwich
       1. FAD-linked reductases, C-terminal domain [54373] (7)
          N-terminal domain is beta/beta/alpha common fold
          uperfamily
          1. GMC oxidoreductases [54374] (8)
             1. Cholesterol oxidase [54375]
                1. Brevibacterium sterolicum [TaxId: 1702] [54376] (2)
                2. Streptomyces sp. [TaxId: 1931] [54377] (13)
                3. Streptomyces sp. (strain SA-COO) (Streptomyces sp. SA-COO) [TaxId: 74576] [159947] (1)
             2. Glucose oxidase [54391]
                1. Aspergillus niger [TaxId: 5061] [54392] (2)
                2. Penicillium amagasakiense [TaxId: 63559] [54393] (1)
             3. Hydroxynitrile lyase [82588]
                1. Almond (Prunus dulcis) [TaxId: 3755] [82589] (1)
             4. Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), substrate-binding domain [82590]
                1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [82591] (2)
             5. Pyranose 2-oxidase [117843]
                1. White-rot fungus (Peniophora sp. SG) [TaxId: 204723] [117844] (19)
                   SQ Q8J136 43-619
          2. PHBH-like [54378] (5)
             1. p-Hydroxybenzoate hydroxylase (PHBH) [54379]
                1. Pseudomonas fluorescens [TaxId: 294] [54380] (17)
                2. Pseudomonas aeruginosa [TaxId: 287] [54381] (19)
             2. Phenol hydroxylase [54382]
                structurally very similar to PHBH, but contains additional C-terminal domain of the thioredoxin-like fold
                1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [54383] (2)
             3. Monooxygenase PhzS [159948]
                1. Pseudomonas aeruginosa [TaxId: 287] [159949] (1)
                   SQ Q9HWG9 183-293
             4. Dihydroxypyridine hydroxylase DhpH [159950]
                1. Arthrobacter nicotinovorans [TaxId: 29320] [159951] (3)
                   SQ Q93NG3 164-201
          3. D-aminoacid oxidase-like [54384] (4)
             1. D-aminoacid oxidase [54385]
                1. Pig (Sus scrofa) [TaxId: 9823] [54386] (6)
                2. Rhodotorula gracilis [TaxId: 5286] [54387] (4)
             2. Sarcosine oxidase [54388]
                1. Bacillus sp., strain b0618 [TaxId: 1409] [54389] (18)
             3. Glycine oxidase ThiO [89843]
                1. Bacillus sp. [TaxId: 1409] [89844] (6)
          4. UDP-galactopyranose mutase [69670] (2)
             1. UDP-galactopyranose mutase [69671]
                1. Escherichia coli [TaxId: 562] [69672] (1)
                2. Klebsiella pneumoniae [TaxId: 573] [117845] (3)
                   SQ Q48485
          5. L-aminoacid/polyamine oxidase [54394] (9)
             1. Polyamine oxidase [54395]
                1. Maize (Zea mays) [TaxId: 4577] [54396] (7)
             2. L-aminoacid oxidase [54397]
                1. Malayan pit viper (Calloselasma rhodostoma) [TaxId: 8717] [54398] (6)
                2. Halys viper (Agkistrodon halys) [TaxId: 8714] [102800] (4)
                   SQ Q90W54 21-504
             3. Monoamine oxidase B [69673]
                1. Human (Homo sapiens) [TaxId: 9606] [69674] (20)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [102801] (27)
             4. N,N-dimethylglycine oxidase [102802]
                1. Arthrobacter globiformis [TaxId: 1665] [102803] (3)
             5. Protoporphyrinogen oxidase [102804]
                1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [102805] (1)
                2. Myxococcus xanthus [TaxId: 34] [159952] (4)
                   SQ P56601 307-414
             6. Lysine-specific histone demethylase 1, LSD1 [159953]
                1. Human (Homo sapiens) [TaxId: 9606] [159954] (8)
                   SQ O60341 655-763
          6. GDI-like [54399] (3)
             Similar to FAD-linked reductases in both domains but does not bind FAD
             1. Guanine nucleotide dissociation inhibitor, GDI [54400]
                1. Cow (Bos taurus) [TaxId: 9913] [54401] (3)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110818] (7)
                   SQ P39958 5-446
             2. Rab escort protein 1 [89845]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [89846] (3)
                   SQ P37727
          7. Electron transfer flavoprotein-ubiquinone oxidoreductase-like [142988] (1)
             1. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [142989]
                1. Pig (Sus scrofa) [TaxId: 9823] [142990] (4)
                   SQ P55931 260-358
   34. Cystatin-like [54402] (7)
       Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
       1. Cystatin/monellin [54403] (6)
          has a additional strand at the N-terminus
          uperfamily
          1. Monellin [54404] (1)
             1. Monellin, B & A chains together [54405]
                1. Serendipity berry (Dioscoreophyllum cumminsii) [TaxId: 3457] [54406] (12)
          2. Cystatins [54407] (6)
             1. Phytocystatin [54408]
                1. Japanese rice (Oryza sativa), subsp. japonica, oryzacystatin-I [TaxId: 4530] [54409] (1)
             2. Cystatin [54410]
                1. Chicken (Gallus gallus) [TaxId: 9031] [54411] (4)
             3. Cystatin A (stefin A) [54412]
                1. Human (Homo sapiens) [TaxId: 9606] [54413] (9)
             4. Cystatin B (stefin B) [54414]
                1. Human (Homo sapiens) [TaxId: 9606] [54415] (1)
             5. Cystatin C [64231]
                1. Human (Homo sapiens) [TaxId: 9606] [64232] (4)
                   SQ P01034 37-146
             6. Cystatin D [110819]
                1. Human (Homo sapiens) [TaxId: 9606] [110820] (2)
                   SQ P28325 31-142
          3. Cathelicidin motif [82592] (1)
             cathelin-like domain
             1. Cathelicidin motif of protegrin-3 [82593]
                antimicrobial protein
                1. Pig (Sus scrofa) [TaxId: 9823] [82594] (5)
          4. Staphopain B, prodomain [117846] (1)
             1. Staphopain B, prodomain [117847]
                includes additional beta-sheet subdomain, connecting the N-terminal cystatin-like domain to the catalytic domain/mature enzyme
                1. Staphylococcus aureus [TaxId: 1280] [117848] (1)
                   SQ Q70UQ9 41-393
          5. Latexin-like [142991] (1)
             Pfam 06907; duplication: consits of two domains of this fold
             1. Latexin [142992]
                1. Human (Homo sapiens) [TaxId: 9606] [142993] (4)
                   SQ Q9BS40 1-98! SQ Q9BS40 99-217
          6. PepSY-like [159955] (1)
             Pfam 03413; Peptidase propeptide and YPEB domain
             1. Uncharacterized protein YpmB [159956]
                duplication; consist of two similar domains
                1. Bacillus subtilis [TaxId: 1423] [159957] (2)
                   SQ P54396 34-98! SQ P54396 99-161
       2. Amine oxidase N-terminal region [54416] (1)
          uperfamily
          1. Amine oxidase N-terminal region [54417] (5)
             duplication: contains two domains of this fold
             1. Copper amine oxidase, domains 1 and 2 [54418]
                1. Escherichia coli [TaxId: 562] [54419] (11)
                2. Pea seedling (Pisum sativum) [TaxId: 3888] [54420] (2)
                   SQ Q43077
                3. Arthrobacter globiformis [TaxId: 1665] [54421] (91)
                   SQ P46881 9-628
                4. Yeast (Hansenula polymorpha) [TaxId: 4905] [54422] (26)
             2. Lysyl oxidase PplO, domains 1 and 2 [102806]
                1. Yeast (Pichia pastoris) [TaxId: 4922] [102807] (4)
                   SQ Q96X16 43-777
       3. DsbC/DsbG N-terminal domain-like [54423] (1)
          uperfamily
          1. DsbC/DsbG N-terminal domain-like [54424] (3)
             1. Disulfide bond isomerase, DsbC, N-terminal domain [54425]
                1. Escherichia coli [TaxId: 562] [54426] (7)
                   SQ P21892
                2. Haemophilus influenzae [TaxId: 727] [110821] (1)
                   SQ P45111 20-228
             2. Thiol:disulfide interchange protein DsbG, N-terminal domain [110822]
                1. Escherichia coli [TaxId: 562] [110823] (10)
                   SQ P77202
       4. NTF2-like [54427] (30)
          has a beta-alpha(2)-beta insertion after the main helix
          uperfamily
          1. Scytalone dehydratase [54428] (1)
             1. Scytalone dehydratase [54429]
                1. Fungus (Magnaporthe grisea) [TaxId: 148305] [54430] (8)
          2. NTF2-like [54431] (11)
             1. Nuclear transport factor-2 (NTF2) [54432]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [54433] (10)
                   SQ P61972
                2. Human (Homo sapiens) [TaxId: 9606] [75373] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75374] (2)
                4. Cryptosporidium parvum [TaxId: 5807] [159958] (2)
                   SQ Q5CQI4 4-127
             2. NTF2-related export protein 1 (p15) [69675]
                1. Human (Homo sapiens) [TaxId: 9606] [69676] (2)
             3. NTF2-like domain of Tip associating protein, TAP [69677]
                1. Human (Homo sapiens) [TaxId: 9606] [69678] (2)
             4. NTF2-like domain of mRNA export factor MEX67 [89847]
                similar to the TAP domain; forms complex with MTR2 similar to the TAP-p15 complex
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89848] (1)
                   Ypl169C
                2. Yeast (Candida albicans) [TaxId: 5476] [102808] (1)
             5. mRNA transport regulator MTR2 [89849]
                similar to p15; forms complex with MEX67 similar to the TAP-p15 complex
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89850] (1)
                   Ykl186C
                2. Yeast (Candida albicans) [TaxId: 5476] [102809] (2)
             6. UBP3-associated protein BRE5 [159959]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159960] (4)
                   SQ P53741 1-141
          3. Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A [89851] (3)
             1. Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A [89852]
                1. Mouse (Mus musculus) [TaxId: 10090] [89853] (1)
                2. Caenorhabditis elegans [TaxId: 6239] [159961] (7)
                   SQ Q9U6Q0 343-471
                3. Human (Homo sapiens) [TaxId: 9606] [159962] (6)
                   SQ Q8N4I3 387-521
          4. Limonene-1,2-epoxide hydrolase-like [89854] (2)
             1. Limonene-1,2-epoxide hydrolase [89855]
                1. Rhodococcus erythropolis [TaxId: 1833] [89856] (2)
             2. Uncharacterized protein Mb2760 [159963]
                1. Mycobacterium tuberculosis [TaxId: 1773] [159964] (3)
                   SQ Q7TY00 13-144
          5. SnoaL-like polyketide cyclase [102810] (5)
             1. Nogalonic acid methyl ester cyclase SnoaL [102811]
                1. Streptomyces nogalater [TaxId: 38314] [102812] (1)
             2. Aklanonic acid methyl ester cyclase, AknH [159965]
                1. Streptomyces galilaeus [TaxId: 33899] [159966] (8)
                   SQ O52646 2-141
             3. Nogalamycin biosynthesis protein SnoL [159967]
                1. Streptomyces nogalater [TaxId: 38314] [159968] (2)
                   SQ Q9RN64 2-139
             4. Putative hydroxylase AclR [159969]
                1. Streptomyces galilaeus [TaxId: 33899] [159970] (2)
                   SQ Q1XDX7 2-145
             5. Uncharacterized protein BPSS0132 [159971]
                1. Burkholderia pseudomallei [TaxId: 28450] [159972] (1)
                   SQ Q63P16 1-131
          6. PhzA/PhzB-like [102813] (4)
             1. Hypothetical protein YesE [102814]
                1. Bacillus subtilis [TaxId: 1423] [102815] (1)
             2. Uncharacterized protein BTHI0051 [159973]
                1. Burkholderia thailandensis [TaxId: 57975] [159974] (2)
                   SQ Q2T2I4 10-139
             3. Uncharacterized protein Ava2261 [159975]
                1. Anabaena variabilis [TaxId: 1172] [159976] (2)
                   SQ Q3MAV7 1-133
             4. Uncharacterized protein PA3332 [159977]
                1. Pseudomonas aeruginosa [TaxId: 287] [159978] (1)
                   SQ Q9HYR3 1-129
          7. Ketosteroid isomerase-like [54434] (4)
             1. Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI [54435]
                1. Comamonas testosteroni, also known as Pseudomonas testosteroni [TaxId: 285] [54436] (14)
                2. Pseudomonas putida [TaxId: 303] [54437] (23)
                   SQ P07445
             2. Hypothetical protein Rv0760c [142994]
                1. Mycobacterium tuberculosis [TaxId: 1773] [142995] (1)
                   SQ P71817 5-136
                2. Mycobacterium tuberculosis H37Rv [TaxId: 83332] [159979] (10)
          8. Ring hydroxylating beta subunit [54438] (7)
             Pfam 00866
             1. Naphthalene 1,2-dioxygenase beta subunit [54439]
                1. Pseudomonas putida [TaxId: 303] [54440] (16)
                2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [142996] (6)
                   SQ Q7BSK6 6-172
             2. Biphenyl dioxygenase small subunit BphA2 [110824]
                1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [110825] (2)
                   SQ Q53123 11-187
             3. Small subunit of cumene dioxygenase CumA2 [142997]
                1. Pseudomonas fluorescens [TaxId: 294] [142998] (1)
                   SQ Q51744 6-186
             4. Nitrobenzene dioxygenase beta subunit, NBDO-beta [142999]
                1. Comamonas sp. JS765 [TaxId: 58226] [143000] (3)
                   SQ Q8RTL3 1-194
             5. Putative hydroxylase subunit Saro3860 [159980]
                1. Novosphingobium aromaticivorans [TaxId: 48935] [159981] (1)
                   SQ A4XDU4 6-162
             6. Benzoate 1,2-dioxygenase beta subunit BenB [159982]
                1. Burkholderia mallei [TaxId: 13373] [159983] (1)
                   SQ Q62E64 1-163
          9. Penicillin binding protein 2a (PBP2A), N-terminal domain [82595] (1)
             some sequence similarity to KSI
             1. Penicillin binding protein 2a (PBP2A), N-terminal domain [82596]
                1. Staphylococcus aureus [TaxId: 1280] [82597] (5)
                   SQ O54286 27-668
          10. Orange carotenoid protein, C-terminal domain [82598] (1)
              1. Orange carotenoid protein, C-terminal domain [82599]
                 1. Cyanobacteria (Arthrospira maxima) [TaxId: 129910] [82600] (1)
          11. Hypothetical protein egc068 from a soil-derived mobile gene cassette [110826] (1)
              1. Hypothetical protein egc068 from a soil-derived mobile gene cassette [110827]
                 1. uncultured organism [TaxId: 155900] [110828] (1)
                    SQ Q99IU3
          12. PA1314-like [110829] (1)
              COG4460
              1. Hypothetical protein PA1314 [110830]
                 1. Pseudomonas aeruginosa [TaxId: 287] [110831] (1)
                    SQ Q9I430
          13. TIM44-like [143001] (2)
              contains extra N-terminal helices but lacks the beta-hairpin in the superfamily-specific insertion
              1. Translocase of inner mitochondrial membrane TIMM44 (TIM44), C-terminal domain [143002]
                 1. Human (Homo sapiens) [TaxId: 9606] [143003] (1)
                    SQ O43615 270-451
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159984] (1)
                    SQ Q01852 234-425
          14. Sbal0622-like [159985] (1)
              PfamB 002762
              1. Uncharacterized protein Sbal0622 [159986]
                 1. Shewanella baltica [TaxId: 62322] [159987] (12)
                    SQ A3D088 3-126
          15. CHU142-like [159988] (1)
              single domain covered by PfamB 000743 in the N-terminal part and PfamB 000860 in the C-terminal part
              1. Uncharacterized protein CHU142 [159989]
                 1. Cytophaga hutchinsonii [TaxId: 985] [159990] (4)
                    SQ Q11V67 1-122
          16. SO0125-like [159991] (2)
              PfamB 003666
              1. Uncharacterized protein Sfri1973 [159992]
                 1. Shewanella frigidimarina [TaxId: 56812] [159993] (6)
                    SQ Q082J6 23-147
              2. Uncharacterized protein SO0125 [159994]
                 1. Shewanella oneidensis [TaxId: 70863] [159995] (1)
                    SQ Q8EKG8 1-121
          17. SAV4671-like [159996] (1)
              PfamB 000442; uncertain annotation of some members as 3-dehydroquinate dehydratase
              1. Uncharacterized protein SAV4671 [159997]
                 1. Streptomyces avermitilis [TaxId: 33903] [159998] (3)
                    SQ Q82EE4 5-157
          18. BxeB1374-like [159999] (2)
              similar dimer to KSI
              1. Uncharacterized protein ECA3500 [160000]
                 1. Pectobacterium atrosepticum [TaxId: 29471] [160001] (4)
                    SQ Q6D1E8 1-127
              2. Hypothetical protein BxeB1374 [160002]
                 1. Burkholderia xenovorans [TaxId: 36873] [160003] (2)
                    SQ Q13MU9 1-128
          19. Atu0744-like [160004] (1)
              PfamB 003773
              1. Uncharacterized protein Atu0744 [160005]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160006] (2)
                    SQ Q7D0S4 1-117
          20. Rpa4348-like [160007] (2)
              PfamB 000085
              1. Uncharacterized protein BxeB2092 [160008]
                 1. Burkholderia xenovorans [TaxId: 36873] [160009] (1)
                    SQ Q13PU4 1-127
              2. Uncharacterized protein Rpa4348 [160010]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [160011] (1)
                    SQ Q6N1Q6 1-135
          21. Ava4193-like [160012] (1)
              PfamB 183524
              1. Uncharacterized protein Ava4193 [160013]
                 1. Anabaena variabilis [TaxId: 1172] [160014] (4)
                    SQ Q3M5E4 2-129
          22. YybH-like [160015] (1)
              PfamB 052627
              1. Hypothetical protein YybH [160016]
                 1. Bacillus subtilis [TaxId: 1423] [160017] (4)
                    SQ P37496 1-128
          23. PFL3262-like [160018] (1)
              Pfam 07080; DUF1348
              1. Hypothetical protein PFL3262 [160019]
                 1. Pseudomonas fluorescens [TaxId: 294] [160020] (4)
                    SQ Q4KBL6 5-159
          24. Exig0174-like [160021] (1)
              PfamB 092483
              1. Uncharacterized protein Exig0174 [160022]
                 1. Exiguobacterium sibiricum 255-15 [TaxId: 262543] [160023] (2)
                    SQ B1YHC8 5-122
          25. Rv3472-like [160024] (2)
              similar trimer to Scytalone dehydratase
              1. Uncharacterized protein NpunR3134 [160025]
                 1. Nostoc punctiforme [TaxId: 272131] [160026] (3)
                    SQ B2IXS6 1-133
              2. Uncharacterized protein Rv3472 [160027]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [160028] (3)
                    SQ O06337 1-167
          26. VirB8-like [160029] (2)
              Pfam 04335
              1. Type IV secretion system protein VirB8 [160030]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160031] (2)
                    SQ P17798 92-231
                 2. Brucella melitensis [TaxId: 29459] [160032] (5)
                    SQ Q7CEG3 97-235
          27. ECA1476-like [160033] (1)
              single domain covered by PfamB 006272 in the N-terminal part and PfamB 005262 in the C-terminal part
              1. Uncharacterized protein ECA1476 [160034]
                 1. Pectobacterium atrosepticum [TaxId: 29471] [160035] (4)
                    SQ Q6D750 3-134
          28. BaiE/LinA-like [160036] (5)
              PfamB 000019; includes sequences of characterized enzymes BaiE and LinA
              1. Uncharacterized protein Saro2766 [160037]
                 1. Novosphingobium aromaticivorans [TaxId: 48935] [160038] (1)
                    SQ Q2G4M1 2-160
              2. Uncharacterized protein Saro3722 [160039]
                 1. Novosphingobium aromaticivorans [TaxId: 48935] [160040] (1)
                    SQ A4XF70 13-165
              3. Uncharacterized protein Saro1465 [160041]
                 1. Novosphingobium aromaticivorans [TaxId: 48935] [160042] (2)
                    SQ Q2G8B5 1-149
              4. Uncharacterized protein NpunR1993 [160043]
                 1. Nostoc punctiforme [TaxId: 272131] [160044] (1)
                    SQ B2J4W9 9-170
              5. Uncharacterized protein Saro3538 [160045]
                 1. Novosphingobium aromaticivorans [TaxId: 48935] [160046] (6)
                    SQ A4XEN7 1-144
          29. Atu0742-like [160047] (1)
              PfamB 017405
              1. Uncharacterized protein Atu0742 [160048]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160049] (1)
                    SQ A9CJY7 1-123
          30. SEC-C associated NTF2-like domain [160050] (1)
              there is a C-terminal SEC-C motif, also there can be an additional SEC-C like motif at the N-terminus (there is only C-terminal motif in the new entry 2JQ5)
              1. Hypothetical protein Psyc2064 [160051]
                 1. Psychrobacter arcticus [TaxId: 334543] [160052] (1)
                    SQ Q4FPZ7 46-158
       5. Uracil-DNA glycosylase inhibitor protein [54441] (1)
          has an additional strand at the C-terminus and a helix inserted after the first strand
          uperfamily
          1. Uracil-DNA glycosylase inhibitor protein [54442] (2)
             1. Uracil-DNA glycosylase inhibitor protein [54443]
                1. Bacteriophage pbs1 [TaxId: 10683] [54444] (1)
                2. Bacteriophage pbs2 [TaxId: 10684] [54445] (17)
       6. Putative dsDNA mimic [102816] (1)
          elaborated with additional structures; some similarity to Uracil-DNA glycosylase (UGI) and Nuclease A (NuiA) inhibitors
          uperfamily
          1. Putative dsDNA mimic [102817] (1)
             Pfam 04269, DUF440
             1. Hypothetical protein HI1450 [102818]
                putative dsDNA mimic
                1. Haemophilus influenzae [TaxId: 727] [102819] (1)
       7. Pre-PUA domain [88802] (5)
          this domain is found in association with the PUA domain in the C-terminal region of Archaeosine tRNA-guanine transglycosylase and related stand-alone proteins
          uperfamily
          1. Archaeosine tRNA-guanine transglycosylase, C2 domain [88803] (1)
             1. Archaeosine tRNA-guanine transglycosylase, C2 domain [88804]
                the second of the 3 additional C-terminal domains to the TGT-like domain, also includes "linker" C1 domain
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [88805] (4)
          2. Hypothetical protein Ta1423, N-terminal domain [102820] (1)
             1. Hypothetical protein Ta1423, N-terminal domain [102821]
                this protein is related to the C-terminal part (domains C2 and C3) of Archaeosine tRNA-guanine transglycosylase
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102822] (1)
          3. Nip7p homolog, N-terminal domain [110832] (1)
             1. Nip7p homolog, N-terminal domain [110833]
                1. Human (Homo sapiens) [TaxId: 9606] [110834] (2)
                   SQ Q9Y221
          4. Hypothetical protein APE0525, N-terminal domain [143004] (1)
             1. Hypothetical protein APE0525, N-terminal domain [143005]
                1. Archaeon Aeropyrum pernix [TaxId: 56636] [143006] (3)
                   SQ Q9YEQ6 1-90
          5. AF0587 pre C-terminal domain-like [160053] (1)
             PfamB 006016
             1. Uncharacterized protein AF0587 [160054]
                1. Archaeoglobus fulgidus [TaxId: 2234] [160055] (1)
                   SQ O29668 394-459
   35. Nuclease A inhibitor (NuiA) [82601] (1)
       alpha-beta-alpha-beta-alpha(2)-beta(3); antiparallel beta-sheet; order: 15432
       1. Nuclease A inhibitor (NuiA) [82602] (1)
          some structural similarity to Uracil-DNA glycosylase inhibitor and putative dsDNA mimic HI1450 of the cystatin-like fold
          uperfamily
          1. Nuclease A inhibitor (NuiA) [82603] (1)
             1. Nuclease A inhibitor (NuiA) [82604]
                1. Anabaena sp., pcc 7120 [TaxId: 1167] [82605] (3)
   36. Colicin D/E5 nuclease domain [102823] (1)
       alpha(2)-beta(4)-alpha, 2 layers: alpha/beta, antiparallel beta sheet, meander
       1. Colicin D/E5 nuclease domain [102824] (2)
          uperfamily
          1. Colicin D nuclease domain [102825] (1)
             1. Colicin D nuclease domain [102826]
                tRNA-specific ribonuclease
                1. Escherichia coli [TaxId: 562] [102827] (2)
          2. Colicin E5 nuclease domain [143007] (1)
             1. Colicin E5 [143008]
                1. Escherichia coli [TaxId: 562] [143009] (7)
                   SQ P18000 84-177
   37. RelE-like [143010] (1)
       beta-alpha(2)-beta(4), 2 layers; a/b, antiparallel beta-sheet; order 15432
       1. RelE-like [143011] (2)
          Toxin component of plasmid stabilisation system
          uperfamily
          1. YoeB/Txe-like [143012] (1)
             Pfam 06769
             1. Toxin YoeB [143013]
                1. Escherichia coli [TaxId: 562] [143014] (12)
                   SQ P69348 1-84
          2. RelE-like [143015] (2)
             Pfam 05016
             1. Hypothetical protein PHS013 [143016]
                1. Pyrococcus horikoshii [TaxId: 53953] [143017] (2)
                   SQ O73966 1-88
             2. Hypothetical protein HP0894 [143018]
                1. Helicobacter pylori [TaxId: 210] [143019] (1)
                   SQ O25554 1-88
   38. Hypothetical protein SAV1430 [110835] (1)
       beta(3)-alpha-beta(2)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet, order: 12543
       1. Hypothetical protein SAV1430 [110836] (1)
          uperfamily
          1. Hypothetical protein SAV1430 [110837] (1)
             1. Hypothetical protein SAV1430 [110838]
                1. Staphylococcus aureus [TaxId: 1280] [110839] (2)
                   SQ Q99U58
   39. Ns1 effector domain-like [143020] (1)
       beta-X-beta(5)-alpha-beta-alpha; 2 layers: a/b; bifurcated beta-sheet; order 23654[1,7]
       1. Ns1 effector domain-like [143021] (1)
          uperfamily
          1. Ns1 effector domain-like [143022] (1)
             C-terminal part of Pfam 00600
             1. Non-structural protein NS1 C-terminal domain [143023]
                1. Influenza A virus [TaxId: 11320] [143024] (2)
                   SQ Q71QT3 79-205
   40. YbaB-like [82606] (1)
       core: alpha-beta(3)-alpha, 2 layers:alpha/beta, three-stranded antiparallel beta sheet, strand order 123
       1. YbaB-like [82607] (1)
          forms tight dimer of a 3-layer structure: beta/alpha/beta
          uperfamily
          1. YbaB-like [82608] (2)
             Pfam 02575; DUF149; function unknown
             1. Hypothetical upf0133 protein YbaB [89857]
                1. Escherichia coli [TaxId: 562] [89858] (1)
             2. Hypothetical protein HI0442 [82609]
                1. Haemophilus influenzae [TaxId: 727] [82610] (1)
   41. Kinetochore globular domain-like [143025] (1)
       core: alpha-beta(3)-alpha; variant: alpha-beta(4)-alpha(2)
       1. Kinetochore globular domain [143026] (2)
          swapped heterodimer with the N-terminal helices; Spc24-like subunits have the core fold, whereas Spc25-like subunits have a variant fold
          uperfamily
          1. Spc25-like [143027] (1)
             Pfam 08234
             1. Kinetochore protein Spc25 [143028]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143029] (2)
                   SQ P40014 133-221
          2. Spc24-like [143030] (1)
             Pfam 08286
             1. Kinetochore protein Spc24 [143031]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143032] (2)
                   SQ Q04477 155-213! SQ Q04477 156-213
   42. L35p-like [143033] (1)
       core: alpha-beta(3)-alpha; 2layers a/b
       1. L35p-like [143034] (1)
          uperfamily
          1. Ribosomal protein L35p [143035] (3)
             Pfam 01632
             1. Ribosomal protein L35p [143036]
                1. Escherichia coli [TaxId: 562] [143037] (27)
                   SQ P0A7Q1 1-64
                2. Deinococcus radiodurans [TaxId: 1299] [160056] (10)
                   SQ Q9RSW6 2-64
                3. Thermus thermophilus [TaxId: 274] [160057] (5)
                   SQ P80341 1-64
   43. Cell division protein ZapA-like [102828] (1)
       core: beta(2)-alpha(2), 2 layers: alpha/beta; long C-terminal helix forms dimeric parallel and tetrameric antiparallel coiled coils
       1. Cell division protein ZapA-like [102829] (1)
          uperfamily
          1. Cell division protein ZapA-like [102830] (1)
             Pfam 05164; ZapA is a Z-ring associated protein first discovered in B. subtilis (formerly hypothetical protein YshA);
             1. ZapA homologue PA5227 [102831]
                1. Pseudomonas aeruginosa [TaxId: 287] [102832] (2)
                   SQ Q9HTW3
   44. ssDNA-binding transcriptional regulator domain [54446] (1)
       helix-swapped dimer of beta(4)-alpha motifs
       1. ssDNA-binding transcriptional regulator domain [54447] (4)
          uperfamily
          1. Transcriptional coactivator PC4 C-terminal domain [54448] (1)
             dimer of two separate motifs
             1. Transcriptional coactivator PC4 C-terminal domain [54449]
                1. Human (Homo sapiens) [TaxId: 9606] [54450] (5)
          2. Plant transcriptional regulator PBF-2 [75375] (1)
             single-chain domain formed by a tandem repeat of two motifs
             1. Plant transcriptional regulator PBF-2 [75376]
                1. Potato (Solanum tuberosum) [TaxId: 4113] [75377] (1)
          3. PMN2A0962/syc2379c-like [143038] (2)
             Pfam 08848; DUF1818; specific to cyanobacteria; single-chain domain made of two repeats of this structural motif
             1. Hypothetical protein PMN2A_0962 [143039]
                1. Prochlorococcus marinus [TaxId: 1219] [143040] (4)
                   SQ Q46J75 1-122
             2. Hypothetical protein syc2379_c [143041]
                1. Synechococcus sp. pcc 7942 [TaxId: 1140] [143042] (1)
                   SQ Q5MZF1 1-121
          4. Guide RNA binding protein gBP [143043] (2)
             includes PfamB 080318 and PB073991; forms heterooligomers; similar subunit and oligomeric structures to the Plant transcriptional regulator family
             1. GBP21 [143044]
                Mitochondrial RNA binding protein 1, MRP1
                1. Trypanosoma brucei [TaxId: 5691] [143045] (7)
                   SQ P90629 28-173
             2. Guide RNA binding protein gBP25 [143046]
                Mitochondrial RNA-binding protein 2, MRP2
                1. Trypanosoma brucei [TaxId: 5691] [143047] (6)
                   SQ Q952G2 56-221
   45. Photosystem I subunit PsaD [64233] (1)
       beta-BETA(2)-beta-alpha-beta(2); antiparallel sheet: order 2134 packed against helix and BETA-hairpin on the same side; irregular C-terminal tail
       1. Photosystem I subunit PsaD [64234] (1)
          uperfamily
          1. Photosystem I subunit PsaD [64235] (1)
             1. Photosystem I subunit PsaD [64236]
                1. Synechococcus elongatus [TaxId: 32046] [64237] (1)
   46. GINS/PriA/YqbF domain [160058] (1)
       beta(4)-alpha-beta; 3-stranded antiparallel beta-sheet (strands 4,1 and 5) are covered on the same side by the helix and beta hairpin of strands 2 and 3; similarity to the L9 N-domain-like fold (scop_cf 55657) and the PsaD fold (scop_sf 64243)
       1. PriA/YqbF domain [160059] (4)
          associated with known or presumed DNA-binding domains; this superfamily also includes the C-terminal domain of PriA (PDB entry 1zt2)
          1. YqbF N-terminal domain-like [160060] (2)
             1. Hypothetical protein YqbF [160061]
                1. Bacillus subtilis [TaxId: 1423] [160062] (1)
                   SQ P45922 1-49
             2. Mu-like prophage FluMu protein gp35, HI1506 [160063]
                1. Haemophilus influenzae [TaxId: 727] [160064] (1)
                   SQ P44228 1-67
          2. PSF2 N-terminal domain-like [160065] (1)
             N-terminal part of Pfam 04128
             1. DNA replication complex GINS protein PSF2 [160066]
                1. Human (Homo sapiens) [TaxId: 9606] [160067] (7)
                   SQ Q9Y248 1-61
          3. SLD5 C-terminal domain-like [160068] (1)
             C-terminal part of Pfam 05916
             1. GINS complex subunit 4, SLD5 [160069]
                1. Human (Homo sapiens) [TaxId: 9606] [160070] (4)
                   SQ Q9BRT9 166-223
          4. PSF3 N-terminal domain-like [160071] (1)
             N-terminal part of Pfam 06425
             1. GINS complex subunit 3, PSF3 [160072]
                1. Human (Homo sapiens) [TaxId: 9606] [160073] (7)
                   SQ Q9BRX5 1-87
   47. MHC antigen-recognition domain [54451] (1)
       dimeric
       1. MHC antigen-recognition domain [54452] (1)
          uperfamily
          1. MHC antigen-recognition domain [54453] (73)
             1. Class II MHC alpha chain, N-terminal domain [88806]
                1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88807] (1)
                2. Human (Homo sapiens), HLA-DR1 [TaxId: 9606] [88808] (15)
                   SQ P01903 28-207
                3. Human (Homo sapiens), HLA-DR2 [TaxId: 9606] [88809] (8)
                4. Human (Homo sapiens), HLA-DR3 [TaxId: 9606] [88810] (1)
                5. Human (Homo sapiens), HLA-DR4 [TaxId: 9606] [88811] (5)
                6. Human (Homo sapiens), HLA-DQ2 [TaxId: 9606] [102833] (1)
                7. Human (Homo sapiens), HLA-DQ6 [TaxId: 9606] [102834] (1)
                8. Human (Homo sapiens), HLA-DQ8 [TaxId: 9606] [88812] (1)
                9. Mouse (Mus musculus), I-AK [TaxId: 10090] [88813] (3)
                10. Mouse (Mus musculus), I-AU [TaxId: 10090] [89859] (30)
                11. Mouse (Mus musculus), I-EK [TaxId: 10090] [88814] (9)
                12. Mouse (Mus musculus), I-AB [TaxId: 10090] [88815] (2)
                13. Mouse (Mus musculus), I-AD [TaxId: 10090] [88816] (2)
                14. Mouse (Mus musculus), I-A(G7) [TaxId: 10090] [88817] (2)
                15. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88818] (1)
             2. Class II MHC beta chain, N-terminal domain [88819]
                1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88820] (1)
                2. Human (Homo sapiens), HLA-DR1 [TaxId: 9606] [88821] (13)
                3. Human (Homo sapiens), HLA-DR2 [TaxId: 9606] [88822] (16)
                   SQ P04229 30-219
                4. Human (Homo sapiens), HLA-DR3 [TaxId: 9606] [88823] (1)
                5. Human (Homo sapiens), HLA-DR4 [TaxId: 9606] [88824] (18)
                6. Human (Homo sapiens), HLA-DQ2 [TaxId: 9606] [102835] (1)
                7. Human (Homo sapiens), HLA-DQ6 [TaxId: 9606] [102836] (1)
                8. Human (Homo sapiens), HLA-DQ8 [TaxId: 9606] [88825] (1)
                9. Mouse (Mus musculus), I-AK [TaxId: 10090] [88826] (3)
                10. Mouse (Mus musculus), I-AU [TaxId: 10090] [89860] (1)
                11. Mouse (Mus musculus), I-EK [TaxId: 10090] [88827] (9)
                12. Mouse (Mus musculus), I-AB [TaxId: 10090] [88828] (8)
                13. Mouse (Mus musculus), I-AD [TaxId: 10090] [88829] (2)
                14. Mouse (Mus musculus), I-A(G7) [TaxId: 10090] [88830] (6)
                15. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88831] (1)
             3. Class I MHC, alpha-1 and alpha-2 domains [54468]
                1. Human (Homo sapiens), HLA-A2 [TaxId: 9606] [54469] (1)
                2. Human (Homo sapiens), HLA-A2.1 [TaxId: 9606] [54470] (95)
                   SQ P01892 25-298
                3. Human (Homo sapiens), HLA-AW68 [TaxId: 9606] [54472] (3)
                4. Human (Homo sapiens), HLA-B08 [TaxId: 9606] [54473] (7)
                5. Human (Homo sapiens), HLA-B27 [TaxId: 9606] [54471] (8)
                   SQ P03989 25-300
                6. Human (Homo sapiens), HLA-BW44 [TaxId: 9606] [102837] (12)
                   SQ P30481 25-300
                7. Human (Homo sapiens), HLA-B53 [TaxId: 9606] [54474] (31)
                8. Human (Homo sapiens), HLA-B35 [TaxId: 9606] [54475] (5)
                   SQ P30685 25-300
                9. Human (Homo sapiens), HLA-B51 [TaxId: 9606] [54476] (2)
                10. Human (Homo sapiens), HLA-CW3 [TaxId: 9606] [54477] (1)
                11. Human (Homo sapiens), HLA-CW4 [TaxId: 9606] [54478] (2)
                12. Human (Homo sapiens), HLA-E [TaxId: 9606] [54479] (14)
                13. Mouse (Mus musculus), H-2KB [TaxId: 10090] [54481] (40)
                    SQ P01901 22-299
                14. Mouse (Mus musculus), H-2DB [TaxId: 10090] [54482] (18)
                15. Mouse (Mus musculus), H-2M3 [TaxId: 10090] [54483] (1)
                16. Mouse (Mus musculus), H-2LD [TaxId: 10090] [54484] (2)
                17. Mouse (Mus musculus), H-2DD [TaxId: 10090] [54485] (36)
                18. Mouse (Mus musculus), tla(c), H-2 class [TaxId: 10090] [89861] (1)
                19. Mouse (Mus musculus), IB QA-2 [TaxId: 10090] [69680] (1)
                20. Rat (Rattus norvegicus), RT1-AA [TaxId: 10116] [54486] (3)
                21. Human (Homo sapiens), HLA-A11 [TaxId: 9606] [110840] (4)
                    SQ P13746 25-299 # 1A11_HUMAN HLA class I histocompatibility antigen, A-11 alpha chain precursor
                22. Human (Homo sapiens), HLA-A1 [TaxId: 9606] [117849] (1)
                    SQ P30443 25-298 # 1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain precursor
                23. Rhesus monkey (Macaca mulatta) [TaxId: 9544] [160074] (2)
                24. Mouse (Mus musculus), H-2KK [TaxId: 10090] [160075] (3)
                    SQ P04223 22-197
                25. Human (Homo sapiens), HLA-G [TaxId: 9606] [160076] (4)
                    SQ P17693 25-205! SQ P17693 26-205
                26. Mouse (Mus musculus), H-2M10 [TaxId: 10090] [160077] (5)
                27. Mouse (Mus musculus), H-2KD [TaxId: 10090] [160078] (2)
                    SQ P01902 22-202
             4. Hemochromatosis protein Hfe, alpha-1 and alpha-2 domains [88832]
                1. Human (Homo sapiens) [TaxId: 9606] [54480] (2)
             5. Fc (IgG) receptor, alpha-1 and alpha-2 domains [54454]
                class I MHC-related
                1. Rat (Rattus norvegicus) [TaxId: 10116] [54455] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [54493] (1)
             6. CD1, alpha-1 and alpha-2 domains [54456]
                Class I MHC-related
                1. Mouse (Mus musculus) [TaxId: 10090] [54457] (10)
                2. Human (Homo sapiens), CD1b [TaxId: 9606] [75378] (3)
                3. Human (Homo sapiens), CD1a [TaxId: 9606] [102838] (4)
                4. Human (Homo sapiens), CD1d [TaxId: 9606] [160079] (4)
                   SQ P15813 24-201
             7. Zinc-alpha-2-glycoprotein, ZAG [54487]
                fat depleting factor related to class I MHC
                1. Human (Homo sapiens) [TaxId: 9606] [54488] (7)
                   SQ P25311 22-294
             8. Class I MHC homolog [54489]
                gamma, delta T-cell ligand
                1. Human (Homo sapiens), Mic-a [TaxId: 9606] [54490] (2)
                2. Human (Homo sapiens), Mic-b [TaxId: 9606] [75380] (1)
                3. Mouse (Mus musculus), t22 [TaxId: 10090] [54491] (3)
                4. Mouse (Mus musculus), t10 [TaxId: 10090] [102839] (1)
             9. Class I MHC-related molecule Ulbp3 [69681]
                1. Human (Homo sapiens) [TaxId: 9606] [69682] (1)
             10. NK cell ligand RAE-1 beta [69683]
                 1. Mouse (Mus musculus) [TaxId: 10090] [69684] (2)
             11. Endothelial protein C receptor [75381]
                 phospholipid-binding protein
                 1. Human (Homo sapiens) [TaxId: 9606] [75382] (2)
             12. Immunomodulatory protein m144, alpha-1 and alpha-2 domains [110841]
                 1. Murine cytomegalovirus [TaxId: 10366] [110842] (2)
                    SQ Q69G19 27-263 # 95% sequence identity
   48. UBC-like [54494] (1)
       alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
       1. UBC-like [54495] (4)
          uperfamily
          1. UBC-related [54496] (38)
             1. Ubiquitin conjugating enzyme, UBC [54497]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [54498] (1)
                2. Baker's yeast (Saccharomyces cerevisiae), ubc1 [TaxId: 4932] [69685] (3)
                   SQ P21734
                3. Baker's yeast (Saccharomyces cerevisiae), ubc2 (RAD6) [TaxId: 4932] [54499] (1)
                4. Baker's yeast (Saccharomyces cerevisiae), ubc4 [TaxId: 4932] [54500] (1)
                5. Baker's yeast (Saccharomyces cerevisiae), ubc7 [TaxId: 4932] [54501] (1)
                6. Baker's yeast (Saccharomyces cerevisiae), ubc13 [TaxId: 4932] [64239] (3)
                7. Baker's yeast (Saccharomyces cerevisiae), mms2 [TaxId: 4932] [64241] (2)
                8. Human (Homo sapiens), ubc13 [TaxId: 9606] [64240] (5)
                9. Human (Homo sapiens), mms2 [TaxId: 9606] [64242] (3)
                10. Human (Homo sapiens), ubch7 [TaxId: 9606] [54502] (2)
                11. Human (Homo sapiens), ubc9 [TaxId: 9606] [54503] (12)
                    identical sequence in many other species
                12. Human (Homo sapiens), ubch10 [TaxId: 9606] [64243] (1)
                13. Human (Homo sapiens), ubc2b [TaxId: 9606] [102840] (1)
                    E2-17 kDa
                14. Human (Homo sapiens), ubch5b [TaxId: 9606] [102841] (14)
                    SQ P62837
                    E2-17 kDa 2
                15. Clam (Spisula solidissima), E-2C [TaxId: 6584] [54504] (1)
                16. Nematode (Caenorhabditis elegans), E2-19 kDa [TaxId: 6239] [89862] (1)
                17. Nematode (Caenorhabditis elegans), E2-21.5 kDa [TaxId: 6239] [102842] (2)
                18. Human (Homo sapiens), ubch8 [TaxId: 9606] [117850] (1)
                    SQ Q96LR5 54-201
                19. Human(Homo sapiens), E2 S [TaxId: 9606] [143048] (2)
                    SQ Q16763 6-156
                20. Leishmania major [TaxId: 5664] [143049] (3)
                    SQ Q4Q5L3 9-166
                    Ubiquitin carrier protein 4, putative
                21. Human (Homo sapiens), E2 J2 [TaxId: 9606] [143050] (2)
                    SQ Q5T7L1 12-168
                    ubc6 homologue
                22. Human (Homo sapiens), E2 variant 1 [TaxId: 9606] [143051] (5)
                    SQ Q13404 80-221! SQ Q13404 82-220
                23. Human (Homo sapiens), E2 L6 [TaxId: 9606] [143052] (3)
                    SQ O14933 2-151
                24. Human (Homo sapiens), E2 U [TaxId: 9606] [143053] (1)
                    SQ Q5VVX9 1-148
                25. Human (Homo sapiens), E2 D3 [TaxId: 9606] [143054] (5)
                    SQ P61077 1-147
                26. Human (Homo sapiens), E2 H [TaxId: 9606] [143055] (2)
                    SQ P62256 4-155
                27. Human (Homo sapiens), E2 G1 [TaxId: 9606] [143056] (1)
                    SQ P62253 7-131
                28. Human (Homo sapiens), E2 T [TaxId: 9606] [143057] (1)
                    SQ Q9NPD8 1-154
                    Hspc150
                29. Human (Homo sapiens), E2 M [TaxId: 9606] [143058] (2)
                    SQ P61081 27-183
                    the extra N-terminal peptide, bound to the heterodimeric E1 enzyme for NEDD8, can be seen in the PDB entry 1tt5, chains E and F
                30. Toxoplasma gondii [TaxId: 5811] [143059] (1)
                31. Caenorhabditis elegans, E2 2 [TaxId: 6239] [143060] (1)
                    SQ P35129 1-147
                32. Xenopus laevis [TaxId: 8355] [160080] (1)
             2. Ubiquitin-protein ligase W (E2 W) [143061]
                forms segment-swapped dimer
                1. Human (Homo sapiens) [TaxId: 9606] [143062] (2)
                   SQ Q96B02 1-117
             3. Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain [143063]
                ubc1 homologue; also contains the C-terminal UBA domain
                1. Human (Homo sapiens) [TaxId: 9606] [143064] (5)
                   SQ P61086 1-156
                2. Cow (Bos taurus) [TaxId: 9913] [143065] (2)
                   SQ P61085 1-154
             4. Hypothetical protein Tgtwinscan_2721, E2 domain [143066]
                1. Toxoplasma gondii [TaxId: 5811] [143067] (2)
             5. Ubiquitin-conjugating enzyme E2 Q2, C-terminal domain [143068]
                this proteins contains the N-terminal RWD domain
                1. Human (Homo sapiens) [TaxId: 9606] [143069] (1)
                   SQ Q8WVN8 201-362
             6. Putative ubiquitin-conjugating enzyme, E2 domain [143070]
                1. Plasmodium chabaudi [TaxId: 5825] [143071] (1)
                   SQ Q4Y037 88-196
          2. UEV domain [75383] (2)
             1. Tumor susceptibility gene 101 (TSG101) [75384]
                1. Human (Homo sapiens) [TaxId: 9606] [75385] (7)
             2. Vacuolar protein sorting-associated [102843]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102844] (1)
          3. RWD domain [110843] (4)
             Pfam 05773
             1. EIF2-alpha kinase 4 (GCN2-like protein) [110844]
                1. Mouse (Mus musculus) [TaxId: 10090] [110845] (1)
                   SQ Q9QZ05 17-139
             2. E3 ubiquitin-protein ligase RNF25 [160081]
                RING finger protein 25
                1. Human (Homo sapiens) [TaxId: 9606] [160082] (2)
                   SQ Q96BH1 10-125! SQ Q96BH1 10-134
             3. Uncharacterized protein C21orf6 [160083]
                1. Human (Homo sapiens) [TaxId: 9606] [160084] (1)
                   SQ P57060 34-173
             4. RWD domain-containing protein 2 [160085]
                1. Human (Homo sapiens) [TaxId: 9606] [160086] (1)
                   SQ Q9UIY3 1-141
          4. UFC1-like [143072] (1)
             1. Ufm1-conjugating enzyme 1, UFC1 [143073]
                aka cgi-126
                1. Human (Homo sapiens) [TaxId: 9606] [143074] (3)
                   SQ Q9Y3C8 1-167
   49. SAND domain-like [63762] (1)
       core: three short helices packed against a barrel-like beta-sheet; some similarity to the SH3-like fold
       1. SAND domain-like [63763] (2)
          uperfamily
          1. SAND domain [63764] (3)
             1. Nuclear autoantigen Sp100b [63765]
                1. Human (Homo sapiens) [TaxId: 9606] [63766] (1)
             2. Glucocorticoid modulatory element binding protein-1 (Gmeb1) [102845]
                1. Human (Homo sapiens) [TaxId: 9606] [102846] (1)
             3. Putative nuclear protein homolog 5830484a20rik [110846]
                1. Mouse (Mus musculus) [TaxId: 10090] [110847] (1)
                   SQ Q8BVK9 353-433
          2. SMAD4-binding domain of oncoprotein Ski [82611] (1)
             1. SMAD4-binding domain of oncoprotein Ski [82612]
                1. Human (Homo sapiens) [TaxId: 9606] [82613] (1)
   50. NRDP1 C-terminal domain-like [160087] (1)
       alpha-beta-alpha(3)-beta(3); a pseudo barrel beta-sheet of an SH3-like topology, surrounded by helices
       1. NRDP1 C-terminal domain-like [160088] (1)
          1. USP8 interacting domain [160089] (1)
             Pfam 08941
             1. E3 ubiquitin-protein ligase NRDP1 [160090]
                RING finger protein 41
                1. Human (Homo sapiens) [TaxId: 9606] [160091] (6)
                   SQ Q9H4P4 193-317! SQ Q9H4P4 197-317
   51. Coronavirus NSP8-like [143075] (1)
       core: alpha-beta(2)-alpha-beta(4)-alpha-beta; bifurcated barrel-like beta-sheet
       1. Coronavirus NSP8-like [143076] (1)
          uperfamily
          1. Coronavirus NSP8-like [143077] (1)
             1. Nonstructural protein 8, NSP8 [143078]
                contains extra N-terminal helical regions involved in heterooligomerisation with NSP7
                1. SARS coronavirus [TaxId: 227859] [143079] (3)
                   SQ P59641 3961-4111
   52. ParB/Sulfiredoxin [110848] (1)
       beta*-alpha-beta(2)-alpha-beta-alpha; mixed beta sheet forms a partly open barrel: (n*=4, S*=8)
       1. ParB/Sulfiredoxin [110849] (4)
          uperfamily
          1. ParB-like nuclease domain [110850] (1)
             Pfam 02195
             1. Putative partitioning protein ParB/Spo0J [110851]
                1. Thermus thermophilus [TaxId: 274] [110852] (1)
                   SQ Q9LCY0 # Fragment
          2. Hypothetical protein PF0380 [110853] (1)
             contains insert domain (101-200) of an unusual alpha+beta fold beta-alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order 516342; possibly related to Pfam 06245
             1. Hypothetical protein PF0380 [110854]
                1. Pyrococcus furiosus [TaxId: 2261] [110855] (1)
                   SQ Q8U3S5
          3. Atu1540-like [160092] (1)
             Pfam 08857; ParBc_2; contains extra C-terminal all-alpha subdomain
             1. Hypothetical protein Atu1540 [160093]
                1. Agrobacterium tumefaciens [TaxId: 358] [160094] (6)
                   SQ Q8UF59 4-204
          4. Sulfiredoxin-like [160095] (1)
             PfamB 015736
             1. Sulfiredoxin [160096]
                1. Human (Homo sapiens) [TaxId: 9606] [160097] (4)
                   SQ Q9BYN0 17-137! SQ Q9BYN0 28-137! SQ Q9BYN0 30-137
   53. Gamma-glutamyl cyclotransferase-like [110856] (1)
       beta-alpha-beta(4)-alpha-beta(2); contains beta-sheet barrel (n=5, S=8)
       1. Gamma-glutamyl cyclotransferase-like [110857] (1)
          uperfamily
          1. Gamma-glutamyl cyclotransferase-like [110858] (3)
             Pfam 03674
             1. Hypothetical protein LOC223267 [110859]
                1. Mouse (Mus musculus) [TaxId: 10090] [110860] (1)
                   SQ Q923B0
             2. Hypothetical protein PH0828 [117851]
                1. Pyrococcus horikoshii [TaxId: 53953] [117852] (1)
                   SQ O58558
             3. Hypothetical protein YtfP [117853]
                1. Escherichia coli [TaxId: 562] [117854] (1)
                   SQ P0AE48
   54. BB1717-like [143080] (1)
       complex fold with a bifurcated beta-sheet structure surrounded by helices; contains beta-sheet barrel, closed (n=5, S=8)
       1. BB1717-like [143081] (1)
          uperfamily
          1. BB1717-like [143082] (4)
             Pfam 02586; DUF159, COG2135
             1. Hypothetical protein Atu5096 [143083]
                1. Agrobacterium tumefaciens [TaxId: 358] [143084] (3)
                   SQ Q8UKK6 2-244
             2. Phage-related hypothetical protein BB1717 [143085]
                1. Bordetella bronchiseptica [TaxId: 518] [143086] (1)
                   SQ Q7WLM8 2-219
             3. Phage-related hypothetical protein BB2244 [143087]
                1. Bordetella bronchiseptica [TaxId: 518] [143088] (1)
                   SQ Q7WK92 2-218
             4. Hypothetical protein BT1218 [143089]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [143090] (2)
                   SQ Q8A8E9 2-232
   55. SARS Nsp1-like [160098] (1)
       complex alpha+beta fold; contains mixed beta-sheet barrel, n=6, S=10
       1. SARS Nsp1-like [160099] (1)
          1. SARS Nsp1-like [160100] (1)
             1. Nsp1 [160101]
                1. SARS coronavirus [TaxId: 227859] [160102] (2)
                   SQ P59641 13-127
   56. Acetoacetate decarboxylase-like [160103] (1)
       complex fold: contains a 3-layer beta-sheet structure, which is folded in two conjoint barrels capped by helices; one rounded barrel has 7 strands, the other flattened barrel has 9 strands
       1. Acetoacetate decarboxylase-like [160104] (1)
          1. Acetoacetate decarboxylase-like [160105] (2)
             Pfam 06314
             1. Acetoacetate decarboxylase [160106]
                1. Legionella pneumophila [TaxId: 446] [160107] (4)
                   SQ Q5ZXQ9 5-254
                2. Methanoculleus marisnigri [TaxId: 2198] [160108] (4)
                   SQ A3CUL0 1-264
   57. AF0104/ALDC/Ptd012-like [117855] (1)
       duplication: consists of two similar beta-alpha-beta(4) motifs
       1. AF0104/ALDC/Ptd012-like [117856] (3)
          characteristic metal ion (zinc)-binding motif in the putative active site
          uperfamily
          1. Alpha-acetolactate decarboxylase-like [117857] (1)
             Pfam 03306
             1. Hypothetical protein SA2394 [117858]
                1. Staphylococcus aureus [TaxId: 1280] [117859] (1)
                   SQ Q7A3A7
          2. PTD012-like [143091] (1)
             1. Hypothetical protein PTD012 [143092]
                Ester hydrolase C11orf54
                1. Human (Homo sapiens) [TaxId: 9606] [143093] (2)
                   SQ Q9H0W9 3-315
          3. AF0104-like [143094] (2)
             Pfam 03479; DUF296; PD1 domain; plant- and prokaryote conserved (PPC; see new PDB 2DT4)
             1. Hypothetical protein AF0104 [143095]
                1. Archaeoglobus fulgidus [TaxId: 2234] [143096] (3)
                   SQ O30132 1-138
             2. Hypothetical protein STM3071 [143097]
                1. Salmonella typhimurium [TaxId: 90371] [143098] (2)
                   SQ Q8ZM67 6-141
   58. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102847] (1)
       beta(3)-alpha(2)-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other
       1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102848] (1)
          uperfamily
          1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102849] (2)
             1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102850]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [102851] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [117860] (1)
                   SQ Q9UNZ2 171-270
   59. TTHA1013/TTHA0281-like [143099] (1)
       beta(3)-alpha-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other; topological similarity to the SEP domain fold (scop_cf 102847); dimerises via the long C-terminal strand with the formation of a single beta-sheet
       1. TTHA1013/TTHA0281-like [143100] (2)
          uperfamily
          1. TTHA1013-like [143101] (1)
             1. Hypothetical protein TTHA1013 [143102]
                1. Thermus thermophilus [TaxId: 274] [143103] (1)
                   SQ Q5SJJ5 2-72
          2. TTHA0281-like [160109] (1)
             Pfam 03681; UPF0150; alpha-beta(3)-alpha-X
             1. Hypothetical protein TTHA0281 [160110]
                1. Thermus thermophilus [TaxId: 274] [160111] (4)
                   SQ Q5SLL2 3-82
   60. YegP-like [160112] (1)
       comprises two subunits or tandem repeats of beta(3)-alpha-beta motifs; these assemble with the formation of a single beta-sheet and swapping of the C-terminal strands
       1. YegP-like [160113] (1)
          1. YegP-like [160114] (4)
             Pfam 07411; DUF1508
             1. Uncharacterized protein Atu0232 [160115]
                homodimer
                1. Agrobacterium tumefaciens [TaxId: 358] [160116] (2)
                   SQ Q8UIR1 1-62
             2. Uncharacterized protein SO3888 [160117]
                duplication: consists of two repeats
                1. Shewanella oneidensis [TaxId: 70863] [160118] (2)
                   SQ Q8EAL4 1-58! SQ Q8EAL4 59-110
             3. Uncharacterized protein YegP [160119]
                duplication: consists of two repeats
                1. Escherichia coli [TaxId: 562] [160120] (2)
                   SQ P76402 1-58! SQ P76402 59-110
             4. Uncharacterized protein NMB1088 [160121]
                homodimer
                1. Neisseria meningitidis [TaxId: 487] [160122] (8)
                   SQ Q7DDI1 1-56
   61. Diaminopimelate epimerase-like [54505] (1)
       mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
       1. Diaminopimelate epimerase-like [54506] (4)
          duplication: consists of two similar domain swapped with C-terminal strands
          uperfamily
          1. Diaminopimelate epimerase [54507] (1)
             1. Diaminopimelate epimerase [54508]
                1. Haemophilus influenzae [TaxId: 727] [54509] (10)
          2. PhzC/PhzF-like [89863] (4)
             Pfam 02567
             1. Hypothetical protein YddE [89864]
                1. Escherichia coli [TaxId: 562] [89865] (3)
                   SQ P37757
                   structural genomics; NESG target ET25
             2. Hypothetical protein EF0119 [102852]
                1. Enterococcus faecalis [TaxId: 1351] [102853] (1)
             3. Hypothetical protein PA4716 [110861]
                1. Pseudomonas aeruginosa [TaxId: 287] [110862] (1)
                   SQ Q9HV82
             4. Phenazine biosynthesis protein PhzF [117861]
                1. Pseudomonas fluorescens [TaxId: 294] [117862] (6)
                   SQ Q51792
          3. Proline racemase [110863] (1)
             Pfam 05544
             1. Proline racemase [110864]
                1. Brucella melitensis [TaxId: 29459] [110865] (1)
                   SQ Q8YFD6
          4. PA0793-like [160123] (1)
             Pfam 04303; DUF453
             1. Hypothetical protein PA0793 [160124]
                1. Pseudomonas aeruginosa [TaxId: 287] [160125] (2)
                   SQ Q9I5E5 1-182! SQ Q9I5E5 187-395
   62. GFP-like [54510] (1)
       beta-sheet folds into a barrel (n=11, S=14) around the central helix
       1. GFP-like [54511] (2)
          uperfamily
          1. Fluorescent proteins [54512] (6)
             1. Green fluorescent protein, GFP [54513]
                1. Jellyfish (Aequorea victoria) [TaxId: 6100] [54514] (53)
                   SQ P42212
                2. Renilla reniformis [TaxId: 6136] [160126] (4)
                   SQ Q963I9 7-226
             2. Red fluorescent protein (fp583 or dsred(clontech)) [54515]
                1. Coral (Discosoma sp.) [TaxId: 86600] [54516] (2)
             3. Red fluorescent protein fp61 [102854]
                1. Sea anemone (Entacmaea quadricolor) [TaxId: 6118] [102855] (1)
             4. Pocilloporin pigment Rtms5 [89866]
                1. Coral (Montipora efflorescens) [TaxId: 105610] [89867] (2)
             5. GFP-like non-fluorescent chromoprotein FP595 [117863]
                1. Anemonia sulcata [TaxId: 6108] [117864] (1)
                   SQ Q9GZ28 # 95% sequence identity
          2. Domain G2 of nidogen-1 [64244] (1)
             1. Domain G2 of nidogen-1 [64245]
                1. Mouse (Mus musculus) [TaxId: 10090] [64246] (2)
   63. Tubby C-terminal domain-like [54517] (1)
       beta-sheet folds into a barrel (n=12, S=12) around the central helix
       1. Tubby C-terminal domain-like [54518] (2)
          uperfamily
          1. Transcriptional factor tubby, C-terminal domain [54519] (1)
             1. Transcriptional factor tubby, C-terminal domain [54520]
                1. Mouse (Mus musculus) [TaxId: 10090] [54521] (2)
          2. At5g01750-like [143104] (1)
             Pfam 04525; DUF567
             1. Hypothetical protein At5g01750 [143105]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143106] (2)
                   SQ Q9LZX1 24-212
   64. Pili subunits [54522] (1)
       contains very long N-terminal helix, which end is packed against beta-sheet
       1. Pili subunits [54523] (7)
          bacterial filament proteins
          uperfamily
          1. Pilin [54524] (4)
             1. Pilin Gc [109618]
                1. Neisseria gonorrhoeae [TaxId: 485] [54526] (2)
             2. Pilin P1 [109619]
                1. Pseudomonas aeruginosa [TaxId: 287] [64247] (3)
                   SQ P17838 36-147
             3. Type IV Pilin Pak [109620]
                1. Pseudomonas aeruginosa [TaxId: 287] [54527] (8)
             4. Type IVb pilin PilS [110866]
                1. Salmonella typhi [TaxId: 90370] [110867] (1)
                   SQ Q9ZIU9 51-206
          2. TcpA-like pilin [89868] (1)
             common fold is decorated with additional structures
             1. Toxin-coregulated pilus subunit TcpA [89869]
                1. Vibrio cholerae [TaxId: 666] [89870] (1)
          3. Pseudopilin [117865] (1)
             1. Pullulanase secretion protein PulG [117866]
                1. Klebsiella pneumoniae [TaxId: 573] [117867] (1)
                   SQ P15746 32-138
          4. YadA C-terminal domain-like [143107] (1)
             Pfam 03895; trimerizes with the formation of closed beta-barrel (n=12, S=12), wrapped around triple parallel coiled coil
             1. Adhesin Hia [143108]
                1. Haemophilus influenzae [TaxId: 727] [143109] (12)
                   SQ Q48152 1022-1098! SQ Q48152 998-1098
          5. EpsJ-like [160127] (2)
             1. Type II secretory pathway component EpsJ [160128]
                1. Vibrio vulnificus [TaxId: 672] [160129] (4)
                   SQ Q7MPZ0 48-213
             2. Pseudopilin GspJ [160130]
                1. Escherichia coli [TaxId: 562] [160131] (1)
                   SQ Q8VRM4 34-187
          6. GspK pilin-like domain [160132] (1)
             N-terminal and C-terminal regions of Pfam 03934
             1. Pseudopilin GspK [160133]
                1. Escherichia coli [TaxId: 562] [160134] (1)
                   SQ A7ZRI8 38-102,284-324
          7. GSPII I/J protein-like [160135] (2)
             Pfam 02501
             1. Pseudopilin EpsI [160136]
                1. Vibrio vulnificus [TaxId: 672] [160137] (4)
                   SQ Q7MPZ1 63-143
             2. Pseudopilin GspI [160138]
                1. Escherichia coli [TaxId: 562] [160139] (1)
                   SQ Q8VPC3 35-118
   65. Mitochondrial glycoprotein MAM33-like [54528] (1)
       core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
       1. Mitochondrial glycoprotein MAM33-like [54529] (1)
          uperfamily
          1. Mitochondrial glycoprotein MAM33-like [54530] (2)
             1. Acidic mitochondrial matrix protein p32 [54531]
                1. Human (Homo sapiens) [TaxId: 9606] [54532] (1)
             2. Hypothetical protein Lmaj011689 [143110]
                1. Leishmania major [TaxId: 5664] [143111] (6)
                   SQ Q4Q7K6 14-195
   66. NAP-like [143112] (1)
       core: central meander 4-stranded beta-sheet (order: 1234) transversed by a C-terminal helix
       1. NAP-like [143113] (1)
          uperfamily
          1. NAP-like [143114] (2)
             Pfam 00956
             1. Nucleosome assembly protein, NAP [143115]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143116] (3)
                   SQ P25293 70-370
             2. Protein SET [160140]
                Phosphatase 2A inhibitor I2PP2A
                1. Human (Homo sapiens) [TaxId: 9606] [160141] (2)
                   SQ Q01105 1-235
   67. Polo-box domain [82614] (1)
       beta(6)-alpha; antiparallel beta-sheet, meander
       1. Polo-box domain [82615] (2)
          Serine/threonine protein kinase-associated motif embedded in two distinct folds
          uperfamily
          1. Polo-box duplicated region [102856] (1)
             duplication: consists of two polo-box domains; binds phosphothreonine peptide
             1. Serine/threonine-protein kinase plk C-terminal domain [102857]
                1. Human (Homo sapiens) [TaxId: 9606] [102858] (9)
          2. Swapped Polo-box domain [82616] (1)
             beta(5)-alpha-beta; forms swapped dimer with two 6-stranded antiparallel beta sheets; order [6]123[4][5]
             1. Serine/threonine-protein kinase Sak C-terminal domain [82617]
                1. Mouse (Mus musculus) [TaxId: 10090] [82618] (1)
   68. mRNA decapping enzyme DcpS N-terminal domain [102859] (1)
       beta(3)-alpha-beta(3)-alpha; 3 layers a/b/a
       1. mRNA decapping enzyme DcpS N-terminal domain [102860] (1)
          forms swapped dimer with two 6-stranded antiparallel beta sheets; order 1236[5][4]
          uperfamily
          1. mRNA decapping enzyme DcpS N-terminal domain [102861] (2)
             1. mRNA decapping enzyme DcpS N-terminal domain [102862]
                1. Human (Homo sapiens) [TaxId: 9606] [102863] (14)
                2. Mouse (Mus musculus) [TaxId: 10090] [110868] (1)
                   SQ Q9DAR7
   69. Inhibitor of vertebrate lysozyme, Ivy [89871] (1)
       alpha(2)-beta(5)-alpha(2); 3 layers a/b/a; meander beta-sheet
       1. Inhibitor of vertebrate lysozyme, Ivy [89872] (1)
          uperfamily
          1. Inhibitor of vertebrate lysozyme, Ivy [89873] (2)
             1. Inhibitor of vertebrate lysozyme, Ivy [89874]
                formerly hypothetical protein YkfE
                1. Escherichia coli [TaxId: 562] [89875] (2)
                   SQ P45502 31-157
                2. Pseudomonas aeruginosa [TaxId: 287] [89876] (1)
   70. FKBP-like [54533] (3)
       core: beta(2)-alpha-beta(2); antiparallel beta-sheet
       1. FKBP-like [54534] (3)
          uperfamily
          1. FKBP immunophilin/proline isomerase [54535] (24)
             1. FK-506 binding protein (FKBP12), an immunophilin [54536]
                cis-trans prolyl-isomerase
                1. Human (Homo sapiens) [TaxId: 9606] [54537] (33)
                2. Cow (Bos taurus) [TaxId: 9913] [54538] (2)
             2. Calcineurin (FKBP12.6) [54539]
                1. Human (Homo sapiens) [TaxId: 9606] [54540] (1)
                2. Cow (Bos taurus) [TaxId: 9913] [54541] (1)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54542] (1)
             3. FKBP25 [54543]
                1. Human (Homo sapiens) [TaxId: 9606] [54544] (1)
             4. FKB-6, N-terminal domain [102864]
                1. Caenorhabditis elegans [TaxId: 6239] [102865] (1)
             5. FKBP59-I, N-terminal domain [54545]
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [54546] (2)
             6. FKBP52, N-terminal domains [82619]
                1. Human (Homo sapiens) [TaxId: 9606] [82620] (4)
                   SQ Q02790 21-427; contains tandem repeat of two FKPB domains
             7. FKBP51, N-terminal domains [82621]
                duplication: tandem repeat of two FKBP domains
                1. Human (Homo sapiens) [TaxId: 9606] [82622] (1)
                2. Monkey (Saimiri boliviensis) [TaxId: 27679] [82623] (1)
             8. Mitotic rotamase PIN1, domain 2 [54547]
                Domain 1 is a WW-domain
                1. Human (Homo sapiens) [TaxId: 9606] [54548] (7)
                2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [75386] (1)
             9. Parvulin [64248]
                1. Human (Homo sapiens), hpar14 [TaxId: 9606] [64249] (2)
             10. Parvulin 10 (rotamase C) [89877]
                 1. Escherichia coli [TaxId: 562] [89878] (2)
             11. Archaeal FKBP [89879]
                 contains insert all-beta subdomain; dual function: PPI and chaperone-like activities
                 1. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [89880] (1)
             12. Macrophage infectivity potentiator protein (MIP) [64250]
                 contains all-alpha dimerisation subdomain in the N-terminal extension
                 1. Legionella pneumophila [TaxId: 446] [64251] (1)
                 2. Trypanosoma cruzi [TaxId: 5693] [75387] (1)
             13. Peptidyl-prolyl cis-trans isomerase FkpA [102866]
                 similar to MIP; contains all-alpha dimerisation subdomain in the N-terminal extension
                 1. Escherichia coli [TaxId: 562] [102867] (3)
             14. Trigger factor PPIase domain [75388]
                 1. Mycoplasma genitalium [TaxId: 2097] [75389] (1)
                 2. Escherichia coli [TaxId: 562] [89881] (3)
                    SQ P22257
                 3. Vibrio cholerae [TaxId: 666] [110869] (1)
                    SQ Q9KQS5
             15. Porin chaperone SurA, PPIase domains [82624]
                 1. Escherichia coli [TaxId: 562] [82625] (8)
             16. FKBP13 [110870]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110871] (6)
                    SQ Q9SCY2 84-208
          2. GreA transcript cleavage factor, C-terminal domain [54549] (3)
             1. GreA transcript cleavage factor, C-terminal domain [54550]
                N-terminal domain is a long alpha-hairpin
                1. Escherichia coli [TaxId: 562] [54551] (1)
                2. Thermus aquaticus [TaxId: 271] [143117] (3)
                   SQ Q8VQD7 78-156
                3. Thermus thermophilus [TaxId: 274] [143118] (6)
                   SQ Q5SJG6 78-156! SQ Q72JT8 78-156
          3. 3-mercaptopyruvate sulfurtransferase, C-terminal domain [102868] (1)
             1. 3-mercaptopyruvate sulfurtransferase, C-terminal domain [102869]
                1. Leishmania major [TaxId: 5664] [102870] (1)
       2. Colicin E3 immunity protein [54552] (1)
          uperfamily
          1. Colicin E3 immunity protein [54553] (1)
             1. Colicin E3 immunity protein [54554]
                1. Escherichia coli [TaxId: 562] [54555] (5)
       3. Chitinase insertion domain [54556] (1)
          uperfamily
          1. Chitinase insertion domain [54557] (15)
             1. Chitinase A [54558]
                1. Serratia marcescens [TaxId: 615] [54559] (11)
                   SQ P07254 24-563
             2. Chitinase B [54560]
                1. Serratia marcescens [TaxId: 615] [54561] (14)
             3. Psychrophilic chitinase B [82626]
                1. Arthrobacter sp., tad20 [TaxId: 1667] [82627] (1)
             4. Chitinase A1 [75390]
                1. Bacillus circulans [TaxId: 1397] [75391] (1)
             5. Chitinase 1 [54562]
                1. Fungus (Coccidioides immitis) [TaxId: 5501] [54563] (4)
                2. Aspergillus fumigatus [TaxId: 5085] [117868] (26)
                   SQ Q873X9
             6. Chitotriosidase [82628]
                1. Human (Homo sapiens) [TaxId: 9606] [82629] (10)
             7. Signal processing protein (SPC-40, MGP-40) [89882]
                secreted during involution
                1. Goat (Capra hircus) [TaxId: 9925] [89883] (14)
                2. Cow (Bos taurus) [TaxId: 9913] [110872] (1)
                   SQ P30922
                3. Sheep (Ovis aries) [TaxId: 9940] [109621] (12)
                   SQ Q6TMG6
                4. Buffalo (Bubalus bubalis) [TaxId: 89462] [110873] (3)
                   SQ Q7YS85
                5. Pig (Sus scrofa) [TaxId: 9823] [117869] (4)
                   SQ Q5UC99
             8. Chitinase-3 like protein 1 (GP-39, YKL-40) [89884]
                1. Human (Homo sapiens) [TaxId: 9606] [89885] (7)
             9. Chitinase-like lectin ym1 [64252]
                1. Mouse (Mus musculus) [TaxId: 10090] [64253] (2)
             10. Imaginal disc growth factor-2 [75392]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75393] (2)
   71. Ribosomal protein S16 [54564] (1)
       beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
       1. Ribosomal protein S16 [54565] (1)
          uperfamily
          1. Ribosomal protein S16 [54566] (3)
             1. Ribosomal protein S16 [54567]
                1. Thermus thermophilus [TaxId: 274] [54568] (37)
                   SQ P80379
                2. Aquifex aeolicus [TaxId: 63363] [160142] (1)
                   SQ O66523 2-102
                3. Escherichia coli [TaxId: 562] [160143] (26)
                   SQ P0A7T3 1-82
   72. Ribosomal protein S19 [54569] (1)
       alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
       1. Ribosomal protein S19 [54570] (1)
          uperfamily
          1. Ribosomal protein S19 [54571] (2)
             1. Ribosomal protein S19 [54572]
                1. Thermus thermophilus [TaxId: 274] [54573] (38)
                   SQ P80381
                2. Escherichia coli [TaxId: 562] [160144] (26)
                   SQ P0A7U3 2-80
   73. YefM-like [143119] (1)
       core: beta-alpha(2)-beta(2)-alpha; mixed beta-sheet, order:123, strands 1 and 2 are parallel; forms compact dimer with a single beta-sheet;
       1. YefM-like [143120] (1)
          uperfamily
          1. YefM-like [143121] (2)
             antitoxin component of the YefM/YoeB-like system; binds to the toxin component wia extra C-terminal tail, unstructured in the free state, but adopting a RelB-like conformation in the bound state
             1. Antitoxin YefM [143122]
                1. Escherichia coli [TaxId: 562] [143123] (4)
                   SQ P69346 1-55! SQ P69346 1-83
             2. Hypothetical protein NE2111 [143124]
                1. Nitrosomonas europaea [TaxId: 915] [143125] (4)
                   SQ Q82T22 1-51
   74. Ribosomal protein L31e [54574] (1)
       beta-alpha-beta-(alpha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
       1. Ribosomal protein L31e [54575] (1)
          uperfamily
          1. Ribosomal protein L31e [54576] (1)
             1. Ribosomal protein L31e [54577]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [54578] (40)
                   SQ P18138
   75. Allophycocyanin linker chain (domain) [54579] (1)
       beta(2)-alpha-beta; 2 layers: alpha/beta
       1. Allophycocyanin linker chain (domain) [54580] (1)
          uperfamily
          1. Allophycocyanin linker chain (domain) [54581] (1)
             1. Allophycocyanin linker chain (domain) [54582]
                1. Mastigocladus laminosus [TaxId: 83541] [54583] (1)
   76. Cdc48 domain 2-like [54584] (1)
       beta-alpha-beta(3); 2 layers: alpha/beta
       1. Cdc48 domain 2-like [54585] (1)
          uperfamily
          1. Cdc48 domain 2-like [54586] (5)
             1. C-terminal domain of NSF-N, NSF-Nc [54587]
                NSF-N, the N-terminal 'functional' domain of the N-ethylmaleimide sensitive fusion protein, consists of two structural domains
                1. Hamster (Cricetulus griseus) [TaxId: 10029] [54588] (2)
                2. Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932] [54589] (1)
             2. C-terminal domain of VAT-N, VAT-Nc [54590]
                VAT-N is the N-terminal 'functional' domain of the VCP-like ATPase
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [54591] (2)
             3. Membrane fusion atpase p97 domain 2, P97-Nc [64254]
                1. Mouse (Mus musculus) [TaxId: 10090] [64255] (5)
             4. Peroxisome biogenesis factor 1 (PEX-1), domain 2 [110874]
                1. Mouse (Mus musculus) [TaxId: 10090] [110875] (1)
                   SQ Q5BL07 13-179
   77. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54592] (1)
       beta-alpha-beta(3); 2 layers: alpha/beta
       1. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54593] (10)
          uperfamily
          1. Glyoxalase I (lactoylglutathione lyase) [54594] (3)
             duplication: consists of two clear structural repeats each having this fold
             1. Glyoxalase I (lactoylglutathione lyase) [54595]
                1. Human (Homo sapiens) [TaxId: 9606] [54596] (4)
                2. Escherichia coli [TaxId: 562] [54597] (5)
                3. Leishmania major [TaxId: 5664] [143126] (6)
                   SQ Q68RJ8 3-141
                   Trypanothione-dependent glyoxalase i
          2. Antibiotic resistance proteins [54598] (10)
             duplication: consists of two clear structural repeats each having this fold
             subunit fold and dimeric assembly are similar to those of glyoxalase
             1. Bleomycin resistance protein, BRP [54599]
                Active as dimer
                1. Streptomyces verticillus [TaxId: 29309] [54600] (3)
                2. Streptoalloteichus hindustanus [TaxId: 2017] [54601] (2)
                   SQ P17493
                3. Klebsiella pneumoniae [TaxId: 573] [64256] (4)
                   the transposon tn5-encoding bleomycin-binding protein, BlmT
             2. Mitomycin resistance protein D, MRD [75394]
                1. Streptomyces lavendulae [TaxId: 1914] [75395] (6)
             3. Fosfomycin resistance protein A (FosA) [82630]
                1. Pseudomonas aeruginosa [TaxId: 287] [82631] (5)
                2. Serratia marcescens [TaxId: 615] [102871] (1)
                   gene from transposon tn2921
             4. Fosfomycin resistance protein FosX [102872]
                1. Mesorhizobium loti [TaxId: 381] [102873] (1)
             5. Hypothetical protein BC3580 [117870]
                1. Bacillus cereus [TaxId: 1396] [117871] (1)
                   SQ Q81AI8
             6. Hypotheical protein SP0731 [143127]
                1. Streptococcus pneumoniae [TaxId: 1313] [143128] (2)
                   SQ Q97RR3 1-115
             7. Uncharacterized protein Atu1953 [160145]
                1. Agrobacterium tumefaciens [TaxId: 358] [160146] (2)
                   SQ Q8UE11 2-115
          3. Methylmalonyl-CoA epimerase [64257] (1)
             Different association of repeats but a similar dimeric structure to the glyoxalase dimer
             1. Methylmalonyl-CoA epimerase [64258]
                1. Propionibacterium shermanii [TaxId: 1752] [64259] (2)
          4. Hypothetical protein YecM (EC4020) [75396] (1)
             Similar subunit fold is to methylmalonyl-CoA epimerase
             1. Hypothetical protein YecM (EC4020) [75397]
                1. Escherichia coli [TaxId: 562] [75398] (1)
          5. Extradiol dioxygenases [54602] (10)
             duplication: consists of 2 similar domains with 2 repeats in each
             Similar to the Methylmalonyl-CoA epimerase dimer
             1. 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme) [54603]
                1. Pseudomonas sp. [TaxId: 306] [54604] (10)
                2. Burkholderia cepacia, formerly Pseudomonas cepacia [TaxId: 292] [54605] (6)
             2. Catechol 2,3-dioxygenase (metapyrocatechase) [54606]
                1. Pseudomonas putida, mt2 [TaxId: 303] [54607] (1)
             3. Homoprotocatechuate 2,3-dioxygenase [89886]
                1. Arthrobacter globiformis [TaxId: 1665] [89887] (3)
                2. Brevibacterium fuscum [TaxId: 47914] [89888] (43)
             4. 4-hydroxyphenylpyruvate dioxygenase, HppD [54608]
                1. Pseudomonas fluorescens [TaxId: 294] [54609] (1)
                2. Streptomyces avermitilis [TaxId: 33903] [110876] (1)
                   SQ Q53586
                3. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [110877] (4)
                   SQ P93836 33-428 ! SQ P93836 63-459
                4. Human (Homo sapiens) [TaxId: 9606] [110878] (1)
                   SQ P32755
                5. Corn (Zea mays) [TaxId: 4577] [110879] (1)
                   SQ O48604 29-423 # 85% sequence identity
          6. Hypothetical protein BC1747 [110880] (1)
             subunit fold and dimeric assembly are similar to those of glyoxalase
             1. Hypothetical protein BC1747 [110881]
                1. Bacillus cereus (strain ATCC 14579 / DSM 31) [TaxId: 226900] [110882] (1)
                   SQ Q81F54
          7. 3-demethylubiquinone-9 3-methyltransferase [110883] (4)
             Pfam 06983; both variants of dimeric assembly are observed in the family (domain swapping)
             1. Hypothetical protein PA1358 [110884]
                1. Pseudomonas aeruginosa [TaxId: 287] [110885] (1)
                   SQ Q9I3Y6
             2. Hypothetical protein PA2721 [110886]
                1. Pseudomonas aeruginosa [TaxId: 287] [110887] (1)
                   SQ Q9I0C1
             3. Hypothetical protein MW1090 [117872]
                1. Staphylococcus aureus [TaxId: 1280] [117873] (1)
                   SQ Q8NX24
             4. Hypothetical protein PA1353 [117874]
                Family assignment by BLAST; HMM assignment is the Glyoxalase family (Pfam 00903)
                1. Pseudomonas aeruginosa [TaxId: 287] [117875] (1)
                   SQ Q9I3Z1
          8. Hypothetical protein YycE [110888] (1)
             subunit fold and dimeric assembly are similar to those of glyoxalase
             1. Hypothetical protein YycE [110889]
                1. Bacillus subtilis [TaxId: 1423] [110890] (1)
                   SQ P37479
          9. Hypothetical protein At5g48480 [117876] (1)
             subunit fold and dimeric assembly are similar to those of glyoxalase
             1. Hypothetical protein At5g48480 [117877]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117878] (3)
                   SQ Q9LV66 20-154
          10. BC1024-like [143129] (1)
              duplication: consists of 2 similar domains with 2 repeats in each; similar to the glyoxalase dimer
              1. Hypothetical protein BC1024 [143130]
                 1. Bacillus cereus [TaxId: 1396] [143131] (2)
                    SQ Q81H03 1-144! SQ Q81H03 145-314
   78. Chromosomal protein MC1 [102874] (1)
       beta(2)-alpha-beta(3); 2 layers: alpha/beta
       1. Chromosomal protein MC1 [102875] (1)
          uperfamily
          1. Chromosomal protein MC1 [102876] (1)
             1. Chromosomal protein MC1 [102877]
                1. Archaeon Methanosarcina thermophila [TaxId: 2210] [102878] (1)
                   SQ P12770
   79. CPE0013-like [160147] (1)
       beta(2)-alpha-beta(3); mixed, mostly antiparallel beta-sheet, folded in a half-barrel; order:31254; strand 3 is parallel to strand 1 and is shorter than the rest
       1. CPE0013-like [160148] (1)
          1. CPE0013-like [160149] (1)
             Pfam 07892; DUF1667; the founding protein lacks the predicted metal-binding motif, found at the N-termini of other members of the Pfam family
             1. Hypothetical protein CPE0013 [160150]
                1. Clostridium perfringens [TaxId: 1502] [160151] (1)
                   SQ Q8XPF0 1-77
   80. beta-hairpin-alpha-hairpin repeat [74651] (2)
       multiple repeats of beta(2)-alpha(2) motif
       1. Ankyrin repeat [48403] (1)
          repeats organized in elongated structures
          uperfamily
          1. Ankyrin repeat [48404] (20)
             1. Ankyrin-R [82632]
                1. Human (Homo sapiens) [TaxId: 9606] [82633] (1)
             2. 53BP2 [48405]
                1. Human (Homo sapiens) [TaxId: 9606] [48406] (1)
             3. GA bindinig protein (GABP) beta 1 [48407]
                1. Mouse (Mus musculus) [TaxId: 10090] [48408] (1)
             4. Cell cycle inhibitor p19ink4D [48409]
                1. Human (Homo sapiens) [TaxId: 9606] [48410] (2)
                2. Mouse (Mus musculus) [TaxId: 10090] [48411] (1)
             5. p18ink4C(ink6) [48412]
                1. Human (Homo sapiens) [TaxId: 9606] [48413] (6)
             6. Cell cycle inhibitor p16ink4A [48414]
                1. Human (Homo sapiens) [TaxId: 9606] [48415] (4)
                2. Mouse (Mus musculus) [TaxId: 10090] [48416] (1)
             7. I-kappa-B-alpha [48417]
                1. Human (Homo sapiens) [TaxId: 9606] [48418] (2)
             8. bcl-3 [69091]
                a member of the I-kappa-B family
                1. Human (Homo sapiens) [TaxId: 9606] [69092] (2)
             9. Transcription factor inhibitor I-kappa-B-beta, IKBB [82634]
                1. Mouse (Mus musculus) [TaxId: 10090] [82635] (2)
             10. Myotrophin [48419]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [48420] (2)
             11. Swi6 ankyrin-repeat fragment [48421]
                 interrupted by an insertion
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48422] (1)
             12. Pyk2-associated protein beta [48423]
                 1. Mouse (Mus musculus) [TaxId: 10090] [48424] (1)
             13. Neurogenic locus notch receptor domain [102879]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102880] (1)
             14. 26S proteasome non-ATPase regulatory subunit 10, gankyrin [102881]
                 1. Human (Homo sapiens) [TaxId: 9606] [102882] (3)
                    SQ O75832
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102883] (7)
             15. Myosin phosphatase targeting subunit 1, MYPT1 [110891]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [110892] (1)
                    SQ Q90623 1-299
             16. RNase L, 2-5a-dependent ribonuclease [117879]
                 1. Human (Homo sapiens) [TaxId: 9606] [117880] (1)
                    SQ Q05823 21-305
             17. Lin-12 [160152]
                 1. Caenorhabditis elegans [TaxId: 6239] [160153] (1)
                    SQ P14585 1021-1297
       2. Plakin repeat [75399] (1)
          repeats associate forming globular subdomains
          uperfamily
          1. Plakin repeat [75400] (1)
             1. Desmoplakin intermediate filament-binding domains [75401]
                1. Human (Homo sapiens) [TaxId: 9606] [75402] (2)
   81. Proguanylin [89889] (1)
       beta(2)-alpha(3)-beta; two layers: alpha/beta; antiparallel sheet: order 213
       1. Proguanylin [89890] (1)
          uperfamily
          1. Proguanylin [89891] (1)
             1. Proguanylin [89892]
                processing of this protein releases peptide hormone guanylin, structure of which structure is known: see 1gna
                1. Human (Homo sapiens) [TaxId: 9606] [89893] (1)
   82. SecB-like [54610] (1)
       beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
       1. SecB-like [54611] (2)
          uperfamily
          1. Bacterial protein-export protein SecB [54612] (2)
             1. Bacterial protein-export protein SecB [54613]
                1. Haemophilus influenzae [TaxId: 727] [54614] (2)
                2. Escherichia coli [TaxId: 562] [102884] (1)
          2. SP1558-like [160154] (2)
             Pfam 06619; DUF1149
             1. Hypothetical protein SP1558 [160155]
                1. Streptococcus pneumoniae [TaxId: 1313] [160156] (1)
                   SQ Q97PP5 5-128
             2. Hypothetical protein gbs1413 [160157]
                1. Streptococcus agalactiae [TaxId: 1311] [160158] (4)
                   SQ Q8E4I8 1-124
   83. MesJ substrate recognition domain-like [82828] (1)
       beta-alpha(2)-beta(3); 2 layers: a/b; antiparallel beta-sheet, order:1432
       1. MesJ substrate recognition domain-like [82829] (1)
          uperfamily
          1. MesJ substrate recognition domain-like [82830] (2)
             1. tRNA-Ile-lysidine synthetase, TilS, substrate-binding domain [82831]
                formerly putative cell cycle protein MesJ
                1. Escherichia coli [TaxId: 562] [82832] (1)
             2. TilS-like protein Aq_1887 [143132]
                lacks the C-terminal domain of the E. coli homologue
                1. Aquifex aeolicus [TaxId: 63363] [143133] (10)
                   SQ O67728 217-311
   84. FYSH domain [89894] (1)
       beta(2)-alpha(2)-beta(2)-alpha-beta; two layers: alpha/beta; antiparallel sheet: order 51234
       1. FYSH domain [89895] (2)
          uperfamily
          1. Hypothetical protein Yhr087W [89896] (1)
             1. Hypothetical protein Yhr087W [89897]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89898] (1)
          2. Hypothetical protein AF0491, N-terminal domain [110893] (1)
             1. Hypothetical protein AF0491, N-terminal domain [110894]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110895] (2)
                   SQ O29759
   85. VSV matrix protein [75403] (1)
       beta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiled beta-sheet: order of the first 5 strands: 23154
       1. VSV matrix protein [75404] (1)
          uperfamily
          1. VSV matrix protein [75405] (1)
             1. VSV matrix protein [75406]
                1. Vesicular stomatitis virus, VSV [TaxId: 11276] [75407] (1)
   86. DNA-binding domain of Mlu1-box binding protein MBP1 [54615] (1)
       beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
       1. DNA-binding domain of Mlu1-box binding protein MBP1 [54616] (1)
          has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain
          uperfamily
          1. DNA-binding domain of Mlu1-box binding protein MBP1 [54617] (1)
             1. DNA-binding domain of Mlu1-box binding protein MBP1 [54618]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54619] (3)
   87. Heme-binding protein A (HasA) [54620] (1)
       beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
       1. Heme-binding protein A (HasA) [54621] (1)
          uperfamily
          1. Heme-binding protein A (HasA) [54622] (1)
             1. Heme-binding protein A (HasA) [54623]
                1. Serratia marcescens [TaxId: 615] [54624] (6)
   88. Chalcone isomerase [54625] (1)
       beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
       1. Chalcone isomerase [54626] (1)
          uperfamily
          1. Chalcone isomerase [54627] (1)
             1. Chalcone isomerase [54628]
                1. Alfalfa (Medicago sativa) [TaxId: 3879] [54629] (7)
   89. Coproporphyrinogen III oxidase [102885] (1)
       alpha-beta(6)-alpha(2)-beta-alpha(n); 3 layers alpha/beta/alpha; antiparallel sheet: order 1234567
       1. Coproporphyrinogen III oxidase [102886] (1)
          uperfamily
          1. Coproporphyrinogen III oxidase [102887] (2)
             Pfam 01218
             1. Hypothetical protein Lmaj006828 [102888]
                1. Leishmania major [TaxId: 5664] [102889] (7)
             2. Coproporphyrinogen III oxidase [110896]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110897] (4)
                   SQ P11353
   90. Hypothetical protein Ta1206 [102890] (1)
       beta(4)-alpha-beta(2)-alpha(2); mixed, predominately antiparallel beta-sheet, order: 123465, strands 4 and 5 are parallel to each other
       1. Hypothetical protein Ta1206 [102891] (1)
          can be divided into an N-terminal, tetramerisation all-beta subdomain and a C-terminal alpha+beta subdomain related by a circular permutation to the Y-family DNA-polymerase 'fingers' subdomain
          uperfamily
          1. Hypothetical protein Ta1206 [102892] (1)
             1. Hypothetical protein Ta1206 [102893]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102894] (1)
   91. CBS-domain pair [54630] (1)
       duplication: tandem repeat of two beta-X-beta-alpha-beta(2)-alpha motifs of similar sequences; 4 layers: a/b/b/a
       1. CBS-domain pair [54631] (1)
          uperfamily
          1. CBS-domain pair [54632] (24)
             Pfam 00571; pairs of CBS domains dimerize to form a stable globular domain, a.k.a. Bateman domain
             1. Hypothetical protein TM0935 [102895]
                1. Thermotoga maritima [TaxId: 2336] [102896] (1)
             2. Hypothetical protein MTH1622 [102897]
                1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102898] (1)
             3. Hypothetical protein Ta0289 [102899]
                contains extra C-terminal zinc-finger domain
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102900] (3)
             4. Type II inosine monophosphate dehydrogenase CBS domains [54633]
                contains tandem repeat of two CBS domains inserted into the catalytic TIM-barrel domain; may be disordered in the crystals
                1. Human (Homo sapiens), type I [TaxId: 9606] [89899] (1)
                2. Human (Homo sapiens), type II [TaxId: 9606] [54634] (3)
                3. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [64260] (1)
                4. Streptococcus pyogenes [TaxId: 1314] [54635] (1)
             5. Hypothetical protein YkuL [117881]
                1. Bacillus subtilis [TaxId: 1423] [117882] (1)
                   SQ O31698 9-142
             6. Nuclear protein SNF4 [143134]
                duplication: comprises four CBS repeats
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143135] (3)
                   SQ P12904 181-265
             7. Hypothetical protein TM0892, CBS tandem [143136]
                1. Thermotoga maritima [TaxId: 2336] [143137] (2)
                   SQ Q9WZZ4 1-60! SQ Q9WZZ4 61-121
             8. Chloride channel protein, CBS tandem [143138]
                contains additional structures between the two CBS repeats
                1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [143139] (2)
                   SQ P21564 527-606! SQ P21564 691-770
             9. Hypothetical protein VC0737 [143140]
                Putative acetoin utilization protein AcuB
                1. Vibrio cholerae [TaxId: 666] [143141] (2)
                   SQ Q9KTZ3 21-83! SQ Q9KTZ3 93-159
             10. Hypothetical protein Rv2626c [143142]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143143] (4)
                    SQ O06186 2-124
             11. Uncharacterized protein PH1780 [160159]
                 duplication: comprises four CBS repeats
                 1. Pyrococcus horikoshii [TaxId: 53953] [160160] (2)
                    SQ O59416 125-281! SQ O59416 126-281
             12. Uncharacterized protein ST2348 [160161]
                 1. Sulfolobus tokodaii [TaxId: 111955] [160162] (2)
                    SQ Q96Y20 1-127
             13. Magnesium transporter MgtE [160163]
                 1. Thermus thermophilus [TaxId: 274] [160164] (4)
                    SQ Q5SMG8 132-275
                 2. Enterococcus faecalis [TaxId: 1351] [160165] (1)
                    SQ Q830V1 136-262
             14. Uncharacterized protein C1556.08c [160166]
                 consists of 4 CBS units
                 1. Schizosaccharomyces pombe [TaxId: 4896] [160167] (2)
                    SQ Q10343 182-334! SQ Q10343 3-181
             15. Uncharacterized protein PH0107 [160168]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160169] (2)
                    SQ O57847 4-135
             16. Uncharacterized protein SSO3205 [160170]
                 duplication: comprises four CBS repeats
                 1. Sulfolobus solfataricus [TaxId: 2287] [160171] (2)
                    SQ Q97U20 1-135! SQ Q97U20 136-276
             17. Uncharacterized protein NE2398 [160172]
                 1. Nitrosomonas europaea [TaxId: 915] [160173] (4)
                    SQ Q82SE2 1-127
             18. Chloride channel protein 5, ClC-5 [160174]
                 1. Human (Homo sapiens) [TaxId: 9606] [160175] (1)
                    SQ P51795 578-746
             19. 5'-AMP-activated protein kinase subunit gamma-1, AMPKg [160176]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [160177] (6)
                    SQ P80385 182-326! SQ P80385 23-181
             20. Uncharacterized protein PAE2072 [160178]
                 2 CBS domains = 1 Bateman domain; binds two adenosine nucleotides per subunit (one per one CBS repeat)
                 1. Pyrobaculum aerophilum [TaxId: 13773] [160179] (6)
                    SQ Q8ZVX8 2-132
   92. Thioesterase/thiol ester dehydrase-isomerase [54636] (1)
       core: beta-alpha-beta(4); 2 layers: alpha/beta
       1. Thioesterase/thiol ester dehydrase-isomerase [54637] (8)
          uperfamily
          1. 4HBT-like [54638] (18)
             Pfam 03061
             1. 4-hydroxybenzoyl-CoA thioesterase [54639]
                1. Pseudomonas sp., CBS-3 [TaxId: 306] [54640] (4)
             2. Hypothetical protein YbaW [89900]
                1. Escherichia coli [TaxId: 562] [89901] (1)
             3. Hypothetical protein YbgC [102901]
                1. Escherichia coli [TaxId: 562] [102902] (1)
             4. Putative acyl-coa thioester hydrolase HI0827 [102903]
                1. Haemophilus influenzae [TaxId: 727] [102904] (2)
             5. Acyl-CoA hydrolase BH0798 [117883]
                1. Bacillus halodurans [TaxId: 86665] [117884] (1)
                   SQ Q9KEQ1
             6. Hypothetical protein PP0301 [143144]
                1. Pseudomonas putida [TaxId: 303] [143145] (1)
                   SQ Q88R33 1-156
             7. Hypothetical protein XCC1147 [143146]
                1. Xanthomonas campestris pv. campestris [TaxId: 340] [143147] (1)
                   SQ Q8PBH4 5-122
             8. Probable acyl-CoA hydrolase AGR_L_2016 [143148]
                1. Agrobacterium tumefaciens [TaxId: 358] [143149] (6)
                   SQ Q7CTE6 147-262! SQ Q7CTE6 9-143
             9. Probable thioesterase TTHA1846 [143150]
                1. Thermus thermophilus [TaxId: 274] [143151] (4)
                   SQ Q5SH84 1-132
             10. Probable thioesterase TTHA0908 [143152]
                 1. Thermus thermophilus [TaxId: 274] [143153] (4)
                    SQ Q5SJV0 1-132
             11. Hypothetical protein Jann_1972 [143154]
                 1. Jannaschia sp. CCS1 [TaxId: 290400] [143155] (2)
                    SQ Q28QX3 3-161
             12. Hypothetical protein SSO2295 [143156]
                 1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [143157] (4)
                    SQ Q97WD2 1-134
             13. Hypothetical thioesterase PA5185 [143158]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143159] (25)
                    SQ Q9HU04 5-146
             14. Hypothetical protein PMT2055 [143160]
                 1. Prochlorococcus marinus [TaxId: 1219] [143161] (1)
                    SQ Q7V4A7 1-144
             15. Hypothetical protein PA2801 [143162]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143163] (1)
                    SQ Q9I042 5-134
             16. Acyl-coa hydrolase BC2038 [143164]
                 1. Bacillus cereus [TaxId: 1396] [143165] (3)
                    SQ Q81EE4 8-171
             17. Hypothetical protein Jann0674 [160180]
                 1. Jannaschia sp. ccs1 [TaxId: 290400] [160181] (2)
                    SQ Q28UM1 1-143
             18. GK1870 orthologue [160182]
                 Predicted 4-hydroxybenzoyl-CoA thioesterase
                 1. Bacillus stearothermophilus [TaxId: 1422] [160183] (4)
                    SQ Q5KYT1 1-131
          2. beta-Hydroxydecanol thiol ester dehydrase [54641] (1)
             contains two additional beta-strands in the N-terminal extension
             1. beta-Hydroxydecanol thiol ester dehydrase [54642]
                1. Escherichia coli [TaxId: 562] [54643] (4)
          3. Acyl-CoA thioesterase [54644] (2)
             duplication: consists of two domains of this fold
             1. Thioesterase II (TesB) [54645]
                1. Escherichia coli [TaxId: 562] [54646] (1)
             2. Peroxisomal long-chain acyl-CoA thioesterase 1, TES1 [143166]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143167] (4)
                   SQ P41903 13-116
          4. MaoC-like [82636] (7)
             1. (R)-specific enoyl-CoA hydratase [82637]
                involved in polyhydroxyalkanoate (PHA) biosynthesis
                1. Aeromonas caviae [TaxId: 648] [82638] (1)
             2. Monoamine oxidase regulatory protein [102905]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102906] (1)
             3. 2-enoyl-coa hydratase domain of multifunctional peroxisomal hydratase-dehydrogenase-epimerase [102907]
                duplication: consists of two MaoC-like domains; there is a greater structural divergence in the N-terminal domain
                1. Yeast (Candida tropicalis) [TaxId: 5482] [102908] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [143168] (24)
                   SQ P51659 326-479! SQ P51659 480-605
                   the structure of N-terminal, SDR domain is also known, PDB entry 1ZBQ
             4. Hypothetical protein Rv0216/MT0226 [143169]
                duplication: consists of two MaoC-like domains
                1. Mycobacterium tuberculosis [TaxId: 1773] [143170] (2)
                   SQ P96398 186-337! SQ P96398 8-185
             5. Hypothetical protein AF1124 [143171]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143172] (3)
                   SQ O29141 6-159
             6. Hypothetical protein Rv0130 [143173]
                1. Mycobacterium tuberculosis [TaxId: 1773] [143174] (2)
                   SQ P96807 2-150
          5. PaaI/YdiI-like [89902] (16)
             1. Phenylacetic acid degradation protein PaaI [89903]
                1. Escherichia coli [TaxId: 562] [89904] (3)
                2. Thermus thermophilus [TaxId: 274] [102909] (26)
             2. Hypothetical protein HI1161 [89905]
                1. Haemophilus influenzae [TaxId: 727] [89906] (10)
             3. Hypothetical protein YdiI [102910]
                1. Escherichia coli [TaxId: 562] [102911] (3)
             4. Hypothetical protein YbdB [102912]
                1. Escherichia coli [TaxId: 562] [102913] (1)
             5. 4-hydroxybenzoyl CoA thioesterase [102914]
                1. Arthrobacter sp., strain su [TaxId: 1667] [102915] (3)
             6. Hypothetical protein PH1136 [102916]
                1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102917] (1)
             7. Putative thioesterase SO4397 [110898]
                1. Shewanella oneidensis [TaxId: 70863] [110899] (1)
                   SQ Q8E989
             8. Hypothetical protein PA5026 [110900]
                1. Pseudomonas aeruginosa [TaxId: 287] [110901] (1)
                   SQ Q9HUE3
             9. Hypothetical protein PA5202 [143175]
                1. Pseudomonas aeruginosa [TaxId: 287] [143176] (2)
                   SQ Q9HTY7 4-129
             10. Hypothetical protein CC3309 [143177]
                 1. Caulobacter crescentus [TaxId: 155892] [143178] (1)
                    SQ Q9A395 12-153
             11. Hypothetical protein Them2 [143179]
                 1. Mouse (Mus musculus) [TaxId: 10090] [143180] (2)
                    SQ Q9CQR4 13-139
                 2. Human (Homo sapiens) [TaxId: 9606] [143181] (12)
                    SQ Q9NPJ3 19-139! SQ Q9NPJ3 3-138
             12. Hypothetical protein PA1835 [143182]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143183] (2)
                    SQ Q9I2R0 1-145
             13. Transcription factor FapR, C-terminal domain [143184]
                 1. Bacillus subtilis [TaxId: 1423] [143185] (6)
                    SQ O34835 66-186! SQ O34835 73-183
             14. Hypothetical protein RHA1_ro05818 [160184]
                 includes two extra N-terminal helices forming an interlocking four-helical bundle in the dimer
                 1. Rhodococcus sp. RHA1 [TaxId: 101510] [160185] (3)
                    SQ Q0S4E1 7-209
          6. FabZ-like [110902] (2)
             1. (3R)-hydroxymyristoyl ACP dehydrase FabZ [110903]
                1. Pseudomonas aeruginosa [TaxId: 287] [110904] (1)
                   SQ Q9HXY7
                2. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [143186] (8)
                   SQ Q965D7 84-229! SQ Q965D7 94-229
          7. TTHA0967-like [143187] (2)
             contains extra C-terminal helix
             1. Hypothetical protein TTHA0967 [143188]
                1. Thermus thermophilus [TaxId: 274] [143189] (4)
                   SQ Q5SJP1 1-138
             2. Uncharacterized protein TM0581 [160186]
                1. Thermotoga maritima [TaxId: 2336] [160187] (8)
                   SQ Q9WZ50 1-130
          8. Acyl-ACP thioesterase-like [143190] (2)
             Pfam 01643; duplication: consists of two 4HBT-like domains
             1. Acyl-ACP thioesterase [143191]
                1. Bacteroides thetaiotaomicron [TaxId: 818] [143192] (2)
                   SQ Q8A611 1-149! SQ Q8A611 150-257
             2. Putative oleoyl-ACP thioesterase LP0708 [160188]
                1. Lactobacillus plantarum [TaxId: 1590] [160189] (4)
                   SQ Q88YP1 150-258! SQ Q88YP1 3-149
   93. DLC [54647] (1)
       core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
       1. DLC [54648] (1)
          uperfamily
          1. DLC [54649] (4)
             8 kDa dynein light chain, DLC8
             1. Dynein light chain 1 (DLC1) [54650]
                synonym: PIN, a protein inhibitor of neuronal nitric oxide synthase
                1. Human (Homo sapiens) [TaxId: 9606] [54651] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [54652] (5)
                3. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102918] (7)
             2. Dynein light chain 2 (DLC2) [102919]
                1. Mouse (Mus musculus) [TaxId: 10090] [102920] (1)
   94. CI-2 family of serine protease inhibitors [54653] (1)
       alpha+beta sandwich; loop across free side of beta-sheet
       1. CI-2 family of serine protease inhibitors [54654] (1)
          uperfamily
          1. CI-2 family of serine protease inhibitors [54655] (4)
             1. Eglin C [54656]
                1. Leech (Hirudo medicinalis) [TaxId: 6421] [54657] (11)
             2. Chymotrypsin inhibitor CI-2 [54658]
                1. Barley (Hordeum vulgare) [TaxId: 4513] [54659] (29)
                   SQ Q40059 22-84
             3. Trypsin inhibitor V [54660]
                1. Pumpkin (Cucurbita maxima) [TaxId: 3661] [54661] (3)
             4. Trypsin inhibitor LUTI [54662]
                1. Flax (Linum usitatissimum) [TaxId: 4006] [54663] (1)
   95. Integrin beta tail domain [69686] (1)
       alpha-beta-loop-beta(3); loop across free side of beta-sheet
       1. Integrin beta tail domain [69687] (1)
          uperfamily
          1. Integrin beta tail domain [69688] (1)
             1. Integrin beta tail domain [69689]
                1. Human (Homo sapiens) [TaxId: 9606] [69690] (4)
                   SQ P05106 27-716
   96. YcgL-like [160190] (1)
       beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order:3124
       1. YcgL-like [160191] (1)
          1. YcgL-like [160192] (1)
             Pfam 05166
             1. Hypothetical protein YcgL [160193]
                1. Escherichia coli [TaxId: 562] [160194] (1)
                   SQ Q2LD68 1-108
   97. alpha/beta-Hammerhead [54664] (5)
       core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
       1. CO dehydrogenase molybdoprotein N-domain-like [54665] (1)
          uperfamily
          1. CO dehydrogenase molybdoprotein N-domain-like [54666] (8)
             1. Aldehyde oxidoreductase, domain 3 [54667]
                1. Desulfovibrio gigas [TaxId: 879] [54668] (3)
                   SQ Q46509
                2. Desulfovibrio desulfuricans [TaxId: 876] [54669] (1)
             2. Xanthine oxidase, domain 5 (?) [54670]
                1. Cow (Bos taurus) [TaxId: 9913] [54671] (6)
                   SQ P80457
             3. Xanthine dehydrogenase chain B, N-terminal domain [69691]
                1. Rhodobacter capsulatus [TaxId: 1061] [69692] (2)
             4. Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain [54672]
                1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [54673] (6)
                2. Hydrogenophaga pseudoflava [TaxId: 47421] [54674] (2)
             5. Quinoline 2-oxidoreductase large subunit QorL, N-domain [110905]
                1. Pseudomonas putida [TaxId: 303] [110906] (1)
                   SQ P72224
             6. 4-hydroxybenzoyl-CoA reductase alpha subunit HrcA, N-terminal domain [117885]
                1. Thauera aromatica [TaxId: 59405] [117886] (2)
                   SQ O33819
       2. Nicotinate/Quinolinate PRTase N-terminal domain-like [54675] (2)
          uperfamily
          1. NadC N-terminal domain-like [54676] (6)
             1. Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), N-terminal domain [54677]
                1. Salmonella typhimurium [TaxId: 90371] [54678] (1)
                2. Mycobacterium tuberculosis [TaxId: 1773] [54679] (4)
                3. Thermotoga maritima [TaxId: 2336] [89907] (1)
                   TM1645
             2. Nicotinate phosphoribosyltransferase Ta1145 [143193]
                1. Thermoplasma acidophilum [TaxId: 2303] [143194] (1)
                   SQ Q9HJ28 1-119
             3. Nicotinate-nucleotide pyrophosphorylase PF1904 [143195]
                1. Pyrococcus furiosus [TaxId: 2261] [143196] (6)
                   SQ Q8TZS9 1-110
             4. Putative nicotinate phosphoribosyltransferase EF2626 [143197]
                1. Enterococcus faecalis [TaxId: 1351] [143198] (1)
                   SQ Q830Y8 4-140
          2. Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like [110907] (3)
             1. Nicotinate phosphoribosyltransferase, N-terminal domain [110908]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110909] (1)
                   SQ P39683
                2. Agrobacterium tumefaciens [TaxId: 358] [117887] (1)
                   SQ Q8UIS9
                3. Pseudomonas aeruginosa [TaxId: 287] [143199] (4)
                   SQ Q9HW26 2-142
                   NAPRTase 2
       3. Pyrimidine nucleoside phosphorylase C-terminal domain [54680] (1)
          uperfamily
          1. Pyrimidine nucleoside phosphorylase C-terminal domain [54681] (3)
             1. Thymidine phosphorylase [54682]
                1. Escherichia coli [TaxId: 562] [54683] (4)
                2. Human (Homo sapiens) [TaxId: 9606] [102921] (1)
             2. Pyrimidine nucleoside phosphorylase [54684]
                1. Bacillus stearothermophilus [TaxId: 1422] [54685] (1)
       4. Ribosomal protein L16p/L10e [54686] (2)
          uperfamily
          1. Ribosomal protein L10e [54687] (2)
             1. Ribosomal protein L10e [54688]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [54689] (58)
                   SQ P60617
                2. Human (Homo sapiens) [TaxId: 9606] [160195] (2)
                   SQ P27635 40-176
          2. Ribosomal protein L16p [117888] (4)
             Pfam 00252
             1. Ribosomal protein L16p [117889]
                1. Thermotoga maritima [TaxId: 2336] [117890] (1)
                   SQ P60489
                2. Escherichia coli [TaxId: 562] [143200] (29)
                   SQ P0ADY7 1-136
                3. Deinococcus radiodurans [TaxId: 1299] [160196] (6)
                   SQ Q9RXJ5 5-140
                4. Thermus thermophilus [TaxId: 274] [160197] (5)
       5. Molybdopterin synthase subunit MoaE [54690] (1)
          uperfamily
          1. Molybdopterin synthase subunit MoaE [54691] (1)
             1. Molybdopterin synthase subunit MoaE [54692]
                1. Escherichia coli [TaxId: 562] [54693] (5)
   98. POZ domain [54694] (1)
       core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
       1. POZ domain [54695] (2)
          uperfamily
          1. BTB/POZ domain [54696] (6)
             1. Promyelocytic leukaemia zinc finger (PLZF) protein BTB domain [54697]
                1. Human (Homo sapiens) [TaxId: 9606] [54698] (2)
             2. B-cell lymphoma 6 (Bcl6) protein BTB domain [102922]
                1. Human (Homo sapiens) [TaxId: 9606] [102923] (11)
             3. Elongin C [54699]
                1. Human (Homo sapiens) [TaxId: 9606] [54700] (9)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64261] (1)
             4. Cyclin A/CDK2-associated p45, Skp1 [54710]
                1. Human (Homo sapiens) [TaxId: 9606] [54711] (8)
             5. Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D [82639]
                Suppressor of kinetochore protein 1,Scskp1
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82640] (1)
          2. Tetramerization domain of potassium channels [54701] (6)
             1. Shaker potassium channel [54702]
                1. California sea hare (Aplysia californica) [TaxId: 6500] [54703] (5)
             2. akv3.1 voltage-gated potassium channel [54704]
                1. California sea hare (Aplysia californica) [TaxId: 6500] [54705] (1)
             3. KV1.1 [54706]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [54707] (1)
             4. Kv1.2 [54708]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [54709] (3)
             5. Potassium channel kv4.2 [89908]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [89909] (1)
             6. Potassium channel kv4.3 [102924]
                1. Human (Homo sapiens) [TaxId: 9606] [102925] (1)
   99. EF-Ts domain-like [54712] (2)
       beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
       1. Elongation factor Ts (EF-Ts), dimerisation domain [54713] (1)
          comprises two structural repeats of this fold
          uperfamily
          1. Elongation factor Ts (EF-Ts), dimerisation domain [54714] (3)
             1. Elongation factor Ts (EF-Ts), dimerisation domain [63422]
                1. Escherichia coli [TaxId: 562] [54716] (1)
                   duplication: consists of two subdomains of this fold
                2. Thermus thermophilus [TaxId: 274] [54717] (2)
                3. Cow (Bos taurus), mitochondrial [TaxId: 9913] [117891] (1)
                   SQ P43896 56-331
       2. Band 7/SPFH domain [117892] (1)
          beta(2)-alpha(3)-beta
          uperfamily
          1. Band 7/SPFH domain [117893] (1)
             Pfam 01145
             1. Flotillin-2 [117894]
                1. Mouse (Mus musculus) [TaxId: 10090] [117895] (1)
                   SQ Q60634 1-123
   100. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54718] (1)
        alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
        1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54719] (1)
           uperfamily
           1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54720] (19)
              1. Mn superoxide dismutase (MnSOD) [54721]
                 1. Escherichia coli [TaxId: 562] [54722] (12)
                 2. Thermus thermophilus [TaxId: 274] [54723] (2)
                 3. Bacillus halodenitrificans [TaxId: 1482] [75408] (1)
                 4. Anabaena sp. [TaxId: 1167] [75409] (1)
                 5. Human (Homo sapiens) [TaxId: 9606] [54724] (44)
                 6. Aspergillus fumigatus [TaxId: 5085] [69693] (1)
                 7. Deinococcus radiodurans [TaxId: 1299] [117896] (3)
                    SQ Q9RUV2
              2. Fe superoxide dismutase (FeSOD) [54725]
                 1. Pseudomonas ovalis [TaxId: 303] [54726] (2)
                 2. Escherichia coli [TaxId: 562] [54727] (13)
                 3. Mycobacterium tuberculosis [TaxId: 1773] [54728] (5)
                 4. Thermosynechococcus elongatus [TaxId: 146786] [89910] (1)
                 5. Aquifex pyrophilus [TaxId: 2714] [54729] (1)
                 6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [54730] (2)
                    SQ P80857
                 7. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [54731] (1)
                 8. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75410] (1)
                 9. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [102926] (1)
                 10. Cowpea (Vigna unguiculata) [TaxId: 3917] [117897] (1)
                     SQ Q9M7R2 21-245
              3. Cambialistic superoxide dismutase [54732]
                 active with either fe or mn
                 1. Propionibacterium shermanii [TaxId: 1752] [54733] (6)
                 2. Porphyromonas gingivalis [TaxId: 837] [54734] (3)
                    SQ P19665
   101. ClpS-like [54735] (1)
        beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
        1. ClpS-like [54736] (2)
           uperfamily
           1. Ribosomal protein L7/12, C-terminal domain [54737] (3)
              1. Ribosomal protein L7/12, C-terminal domain [54738]
                 1. Escherichia coli [TaxId: 562] [54739] (9)
                 2. Thermotoga maritima [TaxId: 2336] [54740] (4)
                 3. Deinococcus radiodurans [TaxId: 1299] [160198] (1)
                    SQ Q9RST0 52-122
           2. Adaptor protein ClpS (YljA) [82641] (1)
              1. Adaptor protein ClpS (YljA) [82642]
                 1. Escherichia coli [TaxId: 562] [82643] (9)
   102. Hypothetical protein MTH1880 [75411] (1)
        beta-alpha-beta(2)-alpha(2); 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
        1. Hypothetical protein MTH1880 [75412] (1)
           uperfamily
           1. Hypothetical protein MTH1880 [75413] (1)
              1. Hypothetical protein MTH1880 [75414]
                 1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75415] (2)
   103. Ribosomal L11/L12e N-terminal domain [54746] (1)
        beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
        1. Ribosomal L11/L12e N-terminal domain [54747] (1)
           uperfamily
           1. Ribosomal L11/L12e N-terminal domain [54748] (5)
              Pfam 03946
              1. Ribosomal protein L11, N-terminal domain [54749]
                 1. Thermotoga maritima [TaxId: 2336] [54750] (6)
                 2. Deinococcus radiodurans [TaxId: 1299] [160199] (4)
                    SQ Q9RSS7 1-71
                 3. Thermus thermophilus [TaxId: 274] [160200] (19)
                    SQ P36238 1-70! SQ P36238 2-68! SQ P36238 2-70
                 4. Escherichia coli [TaxId: 562] [160201] (29)
                    SQ P0A7J7 1-72
              2. 60S ribosomal protein L12 [117898]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117899] (1)
                    SQ P35979 2-80
   104. Anti-LPS factor/recA domain [54751] (2)
        alpha-beta(3)-alpha(2); 2 layers, alpha/beta
        1. RecA protein, C-terminal domain [54752] (1)
           uperfamily
           1. RecA protein, C-terminal domain [54753] (4)
              1. RecA protein, C-terminal domain [54754]
                 1. Escherichia coli [TaxId: 562] [54755] (8)
                    SQ P0A7G6 P03017
                 2. Mycobacterium tuberculosis [TaxId: 1773] [54756] (6)
                 3. Mycobacterium smegmatis [TaxId: 1772] [89911] (4)
                 4. Deinococcus radiodurans [TaxId: 1299] [117900] (1)
                    SQ P42443 15-341
        2. Anti-lipopolysaccharide factor [54757] (1)
           uperfamily
           1. Anti-lipopolysaccharide factor [54758] (1)
              1. Endotoxin-neutralizing protein [54759]
                 1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [54760] (1)
                    SQ P07086 # ALPS_LIMPO
   105. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54761] (1)
        (beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
        1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54762] (1)
           uperfamily
           1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54763] (4)
              1. Signal recognition particle 9KDa protein, SRP9 [88845]
                 1. Human (Homo sapiens) [TaxId: 9606] [88846] (2)
                 2. Mouse (Mus musculus) [TaxId: 10090] [88847] (1)
              2. Signal recognition particle 14KDa protein, SRP14 [88848]
                 1. Human (Homo sapiens) [TaxId: 9606] [88849] (2)
                 2. Mouse (Mus musculus) [TaxId: 10090] [88850] (1)
   106. dsRBD-like [54767] (5)
        alpha-beta(3)-alpha; 2 layers: alpha/beta
        1. dsRNA-binding domain-like [54768] (3)
           uperfamily
           1. Double-stranded RNA-binding domain (dsRBD) [54769] (15)
              Pfam 00035
              1. Double-stranded RNA-binding protein A, second dsRBD [54770]
                 1. Xenopus laevis [TaxId: 8355] [54771] (1)
              2. Staufen, domain III [54772]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [54773] (2)
              3. dsRNA-dependent protein kinase pkr [54774]
                 contains tandem repeat of two dsRBD
                 1. Human (Homo sapiens) [TaxId: 9606] [54775] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [143201] (2)
                    SQ Q03963 1-85! SQ Q03963 96-181
              4. RNase III, C-terminal domain [54776]
                 1. Thermotoga maritima [TaxId: 2336] [82644] (1)
                 2. Aquifex aeolicus [TaxId: 63363] [102927] (19)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110913] (3)
                    SQ Q02555 364-447 ! SQ Q02555 366-453 ! SQ Q02555 363-443
              5. staufen homolog 2 [110914]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110915] (1)
                    SQ Q9D5N7 3-78
              6. ATP-dependent RNA helicase A, Dhx9 [117901]
                 formerly hypothetical protein bab28848
                 1. Mouse (Mus musculus) [TaxId: 10090] [117902] (2)
                    SQ O70133 4-89, 168-262
              7. tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) [117903]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117904] (1)
                    SQ Q9D7B1 350-464
              8. dsRNA-specific editase 1 [143202]
                 duplication: contains two dsRBD domains
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [143203] (2)
                    SQ P51400 231-301! SQ P51400 74-146
              9. Interferon-inducible double stranded RNA-dependent protein kinase activator A [143204]
                 1. Human (Homo sapiens) [TaxId: 9606] [143205] (1)
                    SQ O75569 32-104
              10. Dgcr8 protein [143206]
                  1. Human (Homo sapiens) [TaxId: 9606] [143207] (1)
                     SQ Q8WYQ5 502-586
              11. TAR RNA-binding protein 2 [143208]
                  duplication: contains three dsRBD
                  1. Human (Homo sapiens) [TaxId: 9606] [143209] (1)
                     SQ Q15633 150-225
              12. Spermatid perinuclear RNA-binding protein [143210]
                  1. Human (Homo sapiens) [TaxId: 9606] [143211] (1)
                     SQ Q96SI9 378-461
           2. The homologous-pairing domain of Rad52 recombinase [82645] (1)
              contains N- and C-terminal extensions to the common fold involved in the oligomerization
              1. The homologous-pairing domain of Rad52 recombinase [82646]
                 forms an undecameric ring structure; binds to ssDNA and dsDNA
                 1. Human (Homo sapiens) [TaxId: 9606] [82647] (2)
           3. Ribosomal S5 protein, N-terminal domain [54778] (3)
              1. Ribosomal S5 protein, N-terminal domain [54779]
                 lacks the N-terminal helix
                 1. Bacillus stearothermophilus [TaxId: 1422] [54780] (1)
                 2. Thermus thermophilus [TaxId: 274] [54781] (36)
                    SQ P27152
                 3. Escherichia coli [TaxId: 562] [160202] (24)
                    SQ P0A7W1 9-77
        2. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54782] (1)
           uperfamily
           1. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54783] (1)
              1. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54784]
                 1. Escherichia coli [TaxId: 562] [54785] (5)
        3. YcfA/nrd intein domain [54786] (3)
           uperfamily
           1. PI-Pfui intein middle domain [54787] (1)
              1. PI-Pfui intein middle domain [54788]
                 contains additional C-terminal helix
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [54789] (1)
           2. YcfA-like [117905] (1)
              Pfam 07927
              1. Hypothetical protein TTHA1913 [117906]
                 1. Thermus thermophilus [TaxId: 274] [117907] (1)
                    SQ Q5SH17
           3. YkfF-like [160203] (1)
              Pfam 06006; DUF905
              1. Hypothetical protein YkfF [160204]
                 1. Escherichia coli [TaxId: 562] [160205] (1)
                    SQ P75677 10-75
        4. Peptidyl-tRNA hydrolase domain-like [110916] (1)
           uperfamily
           1. Peptidyl-tRNA hydrolase domain [110917] (1)
              Pfam 00472; related to domain 3 of the Polypeptide chain release factors RF1 and RF2 (scop_fa 75621)
              1. Ict1 protein [110918]
                 1. Mouse (Mus musculus) [TaxId: 10090] [110919] (1)
                    SQ Q8R035 63-162
        5. Rv2632c-like [143212] (1)
           lacks the N-terminal helix; dimerises via the N-terminal strand and the C-terminal helix with the formation of a single beta-sheet wrapped around an antiparallel coiled coil
           uperfamily
           1. Rv2632c-like [143213] (1)
              1. Hypothetical protein Rv2632c/MT2708 [143214]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143215] (1)
                    SQ P65033 4-87
   107. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110920] (1)
        duplication: consists of two beta(3)-alpha repeats; 3 layers, beta/alpha/beta
        1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110921] (1)
           uperfamily
           1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110922] (1)
              1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110923]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [110924] (1)
                    SQ P96420
   108. NMB0488-like [160206] (1)
        duplication: two beta(3)-alpha motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456, shaped into a half-barrel; helical linker region
        1. NMB0488-like [160207] (1)
           1. NMB0488-like [160208] (1)
              Pfam 07262; DUF1436
              1. Hypothetical protein NMB0488 [160209]
                 1. Neisseria meningitidis [TaxId: 487] [160210] (1)
                    SQ Q9K0T5 1-164
   109. SRP19 [69694] (1)
        beta-alpha-beta(2)-alpha; 2 layers: alpha/beta
        1. SRP19 [69695] (1)
           uperfamily
           1. SRP19 [69696] (3)
              1. SRP19 [69697]
                 1. Human (Homo sapiens) [TaxId: 9606] [69698] (4)
                 2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75416] (2)
                 3. Archaeon Methanococcus jannaschii [TaxId: 2190] [75417] (4)
   110. SufE/NifU [82648] (1)
        alpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
        1. SufE/NifU [82649] (3)
           iron-sulfur cluster assembly proteins
           uperfamily
           1. SufE-like [82650] (2)
              Fe-S metabolism associated domain
              1. SufE (YhnA) [82651]
                 unknown function; probably involved in Fe-S center assembly
                 1. Escherichia coli [TaxId: 562] [82652] (1)
              2. Hypothetical protein YgdK [89912]
                 1. Escherichia coli [TaxId: 562] [89913] (1)
           2. NifU/IscU domain [102928] (4)
              1. NifU-like protein HI0377 [102929]
                 1. Haemophilus influenzae [TaxId: 727] [102930] (2)
                    SQ Q57074
              2. IscU homolog SPy0289 [110925]
                 1. Streptococcus pyogenes [TaxId: 1314] [110926] (1)
                    SQ Q9A1G2
              3. Iron-sulfur cluster protein U (IscU) [117908]
                 1. Mouse (Mus musculus), mitochondrial [TaxId: 10090] [117909] (1)
                    SQ Q9D7P6 45-161
              4. NifU [117910]
                 1. Bacillus subtilis [TaxId: 1423] [117911] (1)
                    SQ O32163
           3. SP1160 C-terminal domain-like [143216] (2)
              1. LplA-like protein SP1160, C-terminal domain [143217]
                 1. Streptococcus pneumoniae [TaxId: 1313] [143218] (1)
                    SQ Q97QP1 242-329
              2. Two-domain LplA, C-terminal domain [160211]
                 1. Escherichia coli [TaxId: 562] [160212] (6)
                    SQ P32099 247-337
   111. FlaG-like [160213] (1)
        alpha(2)-beta(3)-alpha; 2 layers: a/b; antiparallel beta-sheet, order: 123; partial similatity to the dsRBD-like fold(sop_cf 54767)
        1. FlaG-like [160214] (1)
           1. FlaG-like [160215] (1)
              Pfam 03646
              1. Hypothetical protein YvyC [160216]
                 1. Bacillus subtilis [TaxId: 1423] [160217] (1)
                    SQ P39737 1-109
   112. AMPKBI-like [160218] (1)
        comprises 3 short helices and 3-stranded meander beta-sheet; makes extensive intermolecular interactions
        1. AMPKBI-like [160219] (1)
           1. AMPKBI-like [160220] (3)
              Pfam 04739; 5'-AMP-activated protein kinase, beta subunit, complex-interacting region
              1. SIP2 [160221]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [160222] (2)
                    SQ P34164 306-412
              2. 5'-AMP-activated protein kinase subunit beta-2 [160223]
                 1. Human (Homo sapiens) [TaxId: 9606] [160224] (3)
                    SQ O43741 190-272
              3. AMP-activated protein kinase beta subunit [160225]
                 1. Schizosaccharomyces pombe [TaxId: 4896] [160226] (12)
                    SQ P78789 205-297
                    Spcc1919.03c
   113. DNA-binding protein Tfx [89914] (1)
        alpha(3)-beta-alpha(2)-beta(2); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
        1. DNA-binding protein Tfx [89915] (1)
           uperfamily
           1. DNA-binding protein Tfx [89916] (1)
              1. DNA-binding protein Tfx [89917]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89918] (1)
                    MTH916
   114. Eukaryotic type KH-domain (KH-domain type I) [54790] (1)
        beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
        1. Eukaryotic type KH-domain (KH-domain type I) [54791] (1)
           Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
           uperfamily
           1. Eukaryotic type KH-domain (KH-domain type I) [54792] (20)
              an RNA-binding domain
              1. Neuro-oncological ventral antigen 1, nova-1, KH3 [54793]
                 1. Human (Homo sapiens) [TaxId: 9606] [54794] (1)
              2. Neuro-oncological ventral antigen 2, nova-2, KH3 [54795]
                 1. Human (Homo sapiens) [TaxId: 9606] [54796] (2)
              3. Vigilin [54797]
                 1. Human (Homo sapiens) [TaxId: 9606] [54798] (8)
              4. Fragile X protein, KH1 [54799]
                 1. Human (Homo sapiens) [TaxId: 9606] [54800] (1)
              5. HnRNP K, KH3 [54801]
                 1. Human (Homo sapiens) [TaxId: 9606] [54802] (8)
              6. RNA splicing factor 1 [69699]
                 1. Human (Homo sapiens) [TaxId: 9606] [69700] (1)
              7. Far upstream binding element, FBP [75418]
                 1. Human (Homo sapiens) [TaxId: 9606] [75419] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [143219] (2)
                    SQ Q91WJ8 175-255! SQ Q91WJ8 89-168
              8. Hypothetical protein APE0754 [110927]
                 duplication: tandem repeat of two KH-1 domains
                 1. Aeropyrum pernix [TaxId: 56636] [110928] (1)
                    SQ Q9YE16
              9. Tudor and KH domain containing protein, Tdrkh [117912]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117913] (1)
                    SQ Q80VL1 118-208
              10. Poly(RC)-binding protein 2 [143220]
                  contains three KH domains
                  1. Human (Homo sapiens) [TaxId: 9606] [143221] (12)
                     SQ Q15366 11-81
              11. Fragile X mental retardation syndrome related protein 1, FXR1 [143222]
                  1. Human (Homo sapiens) [TaxId: 9606] [143223] (1)
                     SQ P51114 212-289
              12. Poly(RC)-binding protein 1 [143224]
                  1. Human (Homo sapiens) [TaxId: 9606] [143225] (1)
                     SQ Q15365 279-348
              13. Quaking protein A (Xqua) [143226]
                  1. African clawed frog (Xenopus laevis) [TaxId: 8355] [143227] (1)
                     SQ Q32NN2 82-215
              14. Ribosomal RNA-processing protein 4, RRP4 [160227]
                  1. Human (Homo sapiens) [TaxId: 9606] [160228] (1)
                     SQ Q13868 168-293
              15. Exosome complex RNA-binding protein 1, ECR1 [160229]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [160230] (3)
                     SQ O29758 136-219
                  2. Aeropyrum pernix [TaxId: 56636] [160231] (1)
                     SQ Q9YC02 148-234
                  3. Sulfolobus solfataricus [TaxId: 2287] [160232] (2)
                     SQ Q9UXC4 153-221
              16. Ribosomal RNA-processing protein 40, RRP40 [160233]
                  1. Saccharomyces cerevisiae [TaxId: 4932] [160234] (1)
                     SQ Q08285 152-236
                  2. Human (Homo sapiens) [TaxId: 9606] [160235] (1)
                     SQ Q9NQT5 196-275
   115. Alpha-lytic protease prodomain-like [54805] (10)
        core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
        1. Alpha-lytic protease prodomain [54806] (1)
           uperfamily
           1. Alpha-lytic protease prodomain [54807] (1)
              1. Alpha-lytic protease prodomain [54808]
                 duplication: consists of two domains of this fold
                 1. Lysobacter enzymogenes [TaxId: 69] [54809] (3)
        2. GMP synthetase C-terminal dimerisation domain [54810] (1)
           uperfamily
           1. GMP synthetase C-terminal dimerisation domain [54811] (1)
              1. GMP synthetase C-terminal dimerisation domain [54812]
                 1. Escherichia coli [TaxId: 562] [54813] (1)
        3. Prokaryotic type KH domain (KH-domain type II) [54814] (1)
           Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
           uperfamily
           1. Prokaryotic type KH domain (KH-domain type II) [54815] (9)
              1. Ribosomal protein S3 N-terminal domain [54816]
                 1. Thermus thermophilus [TaxId: 274] [54817] (36)
                    SQ P80372
                 2. Mouse (Mus musculus) [TaxId: 10090] [117914] (1)
                    SQ P23396 17-95
                 3. Escherichia coli [TaxId: 562] [160236] (24)
                    SQ P0A7V3 1-105
                 4. Canis lupus familiaris [TaxId: 9615] [160237] (1)
              2. GTPase Era C-terminal domain [54818]
                 1. Escherichia coli [TaxId: 562] [54819] (3)
                 2. Thermus thermophilus [TaxId: 274] [117915] (1)
                    SQ Q5SM23
              3. Transcription factor NusA, C-terminal domains [69701]
                 duplication: tandem repeat of two type II KH-domains
                 1. Thermotoga maritima [TaxId: 2336] [69702] (2)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [69703] (7)
              4. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 [54803]
                 the type of KH-domain fold (II or I) adopted by this domain is not ascertained yet
                 1. Streptomyces antibioticus [TaxId: 1890] [54804] (2)
        4. Probable GTPase Der, C-terminal domain [82653] (1)
           possible distant relative of the Era C-terminal domain lacking the KH motif
           uperfamily
           1. Probable GTPase Der, C-terminal domain [82654] (1)
              1. Probable GTPase Der, C-terminal domain [82655]
                 1. Thermotoga maritima [TaxId: 2336] [82656] (1)
        5. Ribosome-binding factor A, RbfA [89919] (1)
           possible distant homologue of the type I KH domain lacking the KH motif
           uperfamily
           1. Ribosome-binding factor A, RbfA [89920] (5)
              1. Ribosome-binding factor A, RbfA [89921]
                 1. Escherichia coli [TaxId: 562] [89922] (1)
                 2. Haemophilus influenzae [TaxId: 727] [89923] (1)
                    HI1288
                 3. Mycoplasma pneumoniae [TaxId: 2104] [102931] (1)
                 4. Human (Homo sapiens) [TaxId: 9606] [160238] (1)
                    SQ Q8N0V3 86-201
                 5. Thermus thermophilus [TaxId: 274] [160239] (3)
                    SQ Q5SJV1 4-94
        6. YhbC-like, N-terminal domain [75420] (1)
           uperfamily
           1. YhbC-like, N-terminal domain [75421] (1)
              1. Hypothetical protein SP14.3 (SP0552) [75422]
                 1. Streptococcus pneumoniae [TaxId: 1313] [75423] (1)
        7. BolA-like [82657] (1)
           uperfamily
           1. BolA-like [82658] (2)
              Pfam 01722
              1. BolA-like protein [82659]
                 1. Mouse (Mus musculus) [TaxId: 10090] [82660] (1)
              2. Hypothetical protein YrbA [110929]
                 1. Escherichia coli [TaxId: 562] [110930] (1)
                    SQ P43781
        8. Fe-S cluster assembly (FSCA) domain-like [117916] (2)
           similar putative active site with a conserved cysteine residue
           uperfamily
           1. NifU C-terminal domain-like [117917] (3)
              Pfam 01106
              1. HIRA-interacting protein 5, HIRIP5 [117918]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117919] (1)
                    SQ Q9QZ23 106-185
              2. Nitrogen fixation protein NifU homolog SE0630 [117920]
                 1. Staphylococcus epidermidis [TaxId: 1282] [117921] (1)
                    SQ Q8CPV7
              3. NifU-like protein 1, NIFUL1 [143228]
                 1. Rice (Oryza sativa) [TaxId: 4530] [143229] (1)
                    SQ Q84LK7 154-226
           2. PaaD-like [117922] (2)
              Pfam 01883; DUF59
              1. Hypothetical protein TM0487 [117923]
                 1. Thermotoga maritima [TaxId: 2336] [117924] (2)
                    SQ Q9WYV7
              2. Hypothetical protein TTHB138 [143230]
                 1. Thermus thermophilus [TaxId: 274] [143231] (2)
                    SQ Q53W28 6-96
        9. Cation efflux protein cytoplasmic domain-like [160240] (1)
           1. Cation efflux protein cytoplasmic domain-like [160241] (2)
              C=terminal part of Pfam 01545
              1. Putative Zinc transporter CzrB [160242]
                 1. Thermus thermophilus [TaxId: 274] [160243] (3)
                    SQ Q8VLX7 203-284
              2. Ferrous-iron efflux pump FieF (YiiP) [160244]
                 Also able to transport Zn(2+)
                 1. Escherichia coli [TaxId: 562] [160245] (2)
                    SQ P69380 209-290
        10. EspE N-terminal domain-like [160246] (1)
            contains extra C-terminal helix that packs against shorter N-terminal helix
            1. GSPII protein E N-terminal domain-like [160247] (2)
               Pfam 05157 (also includes PfamB 000210)
               1. Type II secretion ATPase XpsE [160248]
                  contains extra N-terminal alpha-helical subdomain, that can form swapped dimers
                  1. Xanthomonas campestris [TaxId: 339] [160249] (2)
                     SQ P31742 1-148! SQ P31742 1-149
               2. General secretion pathway protein E, EpsE [160250]
                  1. Vibrio cholerae [TaxId: 666] [160251] (2)
                     SQ P37093 14-81
   116. Nucleotidyltransferase [81302] (1)
        core: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands: 123
        1. Nucleotidyltransferase [81301] (14)
           uperfamily
           1. Catalytic subunit of bi-partite nucleotidyltransferase [102932] (3)
              insert X in the core is an alpha-helix; minimal nucleotidyltransferase fold
              1. Hypothetical protein HI0073 [102933]
                 nucleotide binding subunit of the HI0073/HI0074 nucleotidyltransferase (see 1jog)
                 1. Haemophilus influenzae [TaxId: 727] [102934] (1)
              2. Unnamed putative nucleotidyltransferase [102935]
                 1. Thermus thermophilus [TaxId: 274] [102936] (1)
                    SQ P83814 # 100% identical to SQ Q72I47 (TTC1285)
              3. Putative nucleotidyltransferase AF0614 [143232]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143233] (2)
                    SQ O29641 1-90
           2. Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [56708] (1)
              insert X in the core is a beta-strand ; mixed 4-stranded sheet, order: 1243
              1. Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [56709]
                 1. Staphylococcus aureus [TaxId: 1280] [56710] (2)
           3. Poly(A) polymerase, PAP, N-terminal domain [81589] (2)
              insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543
              1. Poly(A) polymerase, PAP, N-terminal domain [81588]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81586] (7)
                 2. Cow (Bos taurus) [TaxId: 9913] [81587] (3)
                    SQ P25500 18-497
           4. 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [102937] (1)
              similar overall structure to the first two domains of poly(A) polymerase, PAP
              1. 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [102938]
                 1. Pig (Sus scrofa) [TaxId: 9823] [102939] (1)
           5. Archaeal tRNA CCA-adding enzyme catalytic domain [102940] (1)
              similar overall structure to poly(A) polymerase, PAP
              1. tRNA nucleotidyltransferase, N-terminal domain [102941]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102942] (28)
                    SQ O28126
           6. DNA polymerase beta-like [81300] (5)
              insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543; contains extra C-terminal alpha+beta subdomain
              1. DNA polymerase beta, catalytic (31 kD) fragment [81578]
                 1. Human (Homo sapiens) [TaxId: 9606] [81574] (107)
                    SQ P06746
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [81576] (18)
              2. Terminal deoxynucleotidyl transferase [81581]
                 1. Mouse (Mus musculus) [TaxId: 10090] [81580] (3)
              3. DNA polymerase lambda [102943]
                 1. Human (Homo sapiens) [TaxId: 9606] [102944] (24)
              4. DNA polymerase X [69885]
                 1. African swine fever virus [TaxId: 10497] [69886] (2)
           7. Poly A polymerase head domain-like [82661] (3)
              overlaps with the N-terminal part of Pfam 01743; this family is distinct from eukaryotic PAPs
              insert X in the core is an alpha-beta(2) unit; contains two extra C-terminal strands; mixed 7-stranded sheet, order: 7612543
              1. tRNA CCA-adding enzyme, head domain [82662]
                 1. Bacillus stearothermophilus [TaxId: 1422] [82663] (3)
                 2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [89924] (1)
              2. Poly A polymerase PcnB [110931]
                 1. Aquifex aeolicus [TaxId: 63363] [110932] (1)
                    SQ O66728 443-824
           8. RelA/SpoT domain [102945] (2)
              Pfam 04607; ppGpp-synthetase
              1. Stringent response-like protein RelA domain 2 [102946]
                 1. Streptococcus equisimilis [TaxId: 119602] [102947] (1)
              2. Putative GTP pyrophosphokinase SP1097 [143234]
                 1. Streptococcus pneumoniae [TaxId: 1313] [143235] (2)
                    SQ Q97QV1 1-203
           9. GlnE-like domain [110933] (1)
              Pfam 03710; Pfam coverage excludes the extra N-terminal subdomain but includes a short segment of the next domain 2
              1. Glutamine synthase adenylyltransferase GlnE, N-terminal domain [110934]
                 includes extra N-terminal all-alpha subdomain (2-61) structurally similar to the PABP domain (scop_fa 63571)
                 1. Escherichia coli [TaxId: 562] [110935] (1)
                    SQ P30870 1-437
           10. RNA editing terminal uridyl transferase 2, RET2, catalytic domain [143236] (1)
               contains insert domain of a ferredoxin-like fold
               1. RNA editing terminal uridyl transferase 2, TUTase 2, RET2 [143237]
                  1. Trypanosoma brucei [TaxId: 5691] [143238] (1)
                     SQ Q86MV5 30-288
           11. TM1012-like [143239] (1)
               insert X in the core is an alpha-beta(2) unit; contains extra C-terminal structures; mixed 7-stranded sheet, order: 6712543;
               1. Hypothetical protein TM1012 [143240]
                  1. Thermotoga maritima [TaxId: 2336] [143241] (2)
                     SQ Q9X0A5 1-157! SQ Q9X0A5 2-157
           12. Iojap/YbeB-like [160252] (2)
               Pfam 02410, probably has evolved a different function; closer relationship to the GrpB-like family
               1. Hypothetical protein CV0518 [160253]
                  1. Chromobacterium violaceum [TaxId: 536] [160254] (2)
                     SQ Q7P0P8 1-120
               2. Uncharacterized protein BH1328 [160255]
                  1. Bacillus halodurans [TaxId: 86665] [160256] (2)
                     SQ Q9KD89 2-114
           13. AadK N-terminal domain-like [160257] (1)
               N-terminal part of Pfam 04439; Streptomycin adenylyltransferase; insert X is alpha-beta(2) unit; overall domain architecture is similar to Kanamycin nucleotidyltransferase
               1. Aminoglycoside 6-adenylyltransferase AadK [160258]
                  1. Bacillus subtilis [TaxId: 1423] [160259] (1)
                     SQ P17585 1-135
           14. GrpB-like [160260] (1)
               Pfam 04229, different set of active-site residues
               1. Hypothetical protein GrpB [160261]
                  1. Enterococcus faecalis [TaxId: 1351] [160262] (1)
                     SQ Q837C3 4-170
   117. Nqo5-like [143242] (1)
        core: alpha-beta(2)-alpha-beta(3); 2 layers, a/b; mixed beta-sheet, order 12534, strands 2 and 5 are parallel
        1. Nqo5-like [143243] (1)
           uperfamily
           1. Nqo5-like [143244] (1)
              Globular region is covered by PfamB 121908 from N-end and then by PfamB 000646; contains extra C-terminal unstructured region, corresponding to Pfam 00329
              1. NADH-quinone oxidoreductase chain 5, Nqo5 [143245]
                 1. Thermus thermophilus [TaxId: 274] [143246] (4)
                    SQ Q56219 1-196
   118. Ribosomal protein S3 C-terminal domain [54820] (1)
        alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
        1. Ribosomal protein S3 C-terminal domain [54821] (1)
           uperfamily
           1. Ribosomal protein S3 C-terminal domain [54822] (2)
              1. Ribosomal protein S3 C-terminal domain [54823]
                 1. Thermus thermophilus [TaxId: 274] [54824] (36)
                    SQ P80372
                 2. Escherichia coli [TaxId: 562] [160263] (24)
                    SQ P0A7V3 106-206
   119. Transcription factor NusA, N-terminal domain [69704] (1)
        alpha-beta(3)-alpha-beta-alpha; bifurcated coiled beta-sheet
        1. Transcription factor NusA, N-terminal domain [69705] (1)
           uperfamily
           1. Transcription factor NusA, N-terminal domain [69706] (2)
              1. Transcription factor NusA, N-terminal domain [69707]
                 1. Thermotoga maritima [TaxId: 2336] [69708] (2)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [69709] (1)
   120. Enolase N-terminal domain-like [54825] (1)
        beta(3)-alpha(3); meander and up-and-down bundle
        1. Enolase N-terminal domain-like [54826] (1)
           uperfamily
           1. Enolase N-terminal domain-like [54827] (28)
              C-terminal domain is beta/alpha-barrel
              1. Enolase [54828]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54829] (18)
                 2. European lobster (Homarus vulgaris) [TaxId: 6707] [54830] (2)
                 3. Trypanosoma brucei brucei [TaxId: 5702] [89925] (1)
                 4. Enterococcus hirae [TaxId: 1354] [89926] (1)
                 5. Escherichia coli [TaxId: 562] [69710] (5)
                 6. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110936] (5)
                    SQ P09104
                 7. Streptococcus pneumoniae [TaxId: 1313] [143247] (2)
                    SQ Q8DPS0 1-137
                 8. Trypanosoma brucei [TaxId: 5691] [160264] (6)
              2. D-glucarate dehydratase [54831]
                 1. Pseudomonas putida [TaxId: 303] [54832] (1)
                 2. Escherichia coli [TaxId: 562] [54833] (6)
              3. O-succinylbenzoate synthase [54834]
                 1. Escherichia coli [TaxId: 562] [54835] (7)
              4. Muconate-lactonizing enzyme (cis muconate cycloisomerase) [54836]
                 1. Pseudomonas putida [TaxId: 303] [54837] (5)
              5. Mandelate racemase [54838]
                 1. Pseudomonas putida [TaxId: 303] [54839] (6)
              6. Chlormuconate cycloisomerase [54840]
                 1. Alcaligenes eutrophus [TaxId: 106590] [54841] (2)
                 2. Pseudomonas sp. p51 [TaxId: 65067] [102948] (1)
              7. L-Ala-D/L-Glu epimerase [69711]
                 1. Escherichia coli [TaxId: 562] [69712] (1)
                 2. Bacillus subtilis [TaxId: 1423] [69713] (2)
                    SQ O34508
              8. beta-Methylaspartase [69714]
                 1. Clostridium tetanomorphum [TaxId: 1553] [69715] (2)
                 2. Citrobacter amalonaticus [TaxId: 35703] [69716] (2)
              9. Hypothetical protein Atu3453 [102949]
                 1. Agrobacterium tumefaciens [TaxId: 358] [102950] (1)
              10. N-acylamino acid racemase [110937]
                  1. Amycolatopsis sp. [TaxId: 37632] [110938] (4)
                     SQ Q44244; similar activity to a remotely related O-succinylbenzoate synthase from E. coli
                  2. Deinococcus radiodurans [TaxId: 1299] [110939] (4)
                     SQ Q9RYA6
                  3. Enterococcus faecalis [TaxId: 1351] [117925] (1)
                     SQ Q838J7; EF0450; protein assignment by sequence similarity
                  4. Listeria innocua [TaxId: 1642] [117926] (1)
                     SQ Q927X3; Lin2664; protein assignment by sequence similarity
              11. Hypothetical protein Bll6730 [117927]
                  1. Bradyrhizobium japonicum [TaxId: 375] [117928] (21)
                     SQ Q89FH0
              12. RTS beta protein [117929]
                  1. Xanthomonas campestris pv. campestris [TaxId: 340] [117930] (1)
                     SQ Q8P3K2; extended, mainly helical linker between the domains
              13. Hypothetical protein YitF [143248]
                  1. Bacillus subtilis [TaxId: 1423] [143249] (10)
                     SQ O06741 1-114
              14. Putative dehydratase protein STM2273 [143250]
                  1. Salmonella typhimurium [TaxId: 90371] [143251] (2)
                     SQ Q8ZNH1 1-122
   121. Ribosomal protein L22 [54842] (1)
        beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
        1. Ribosomal protein L22 [54843] (1)
           some topological similarity to prokaryotic ribosomal protein L17
           uperfamily
           1. Ribosomal protein L22 [54844] (5)
              1. Ribosomal protein L22 [54845]
                 1. Thermus aquaticus, subsp. Thermus thermophilus [TaxId: 271] [54846] (6)
                 2. Archaeon Haloarcula marismortui [TaxId: 2238] [54847] (58)
                    SQ P10970
                 3. Deinococcus radiodurans [TaxId: 1299] [160265] (6)
                    SQ Q9RXJ7 8-134
                 4. Escherichia coli [TaxId: 562] [160266] (29)
                    SQ P61175 1-110
                 5. Thermus thermophilus [TaxId: 274] [160267] (6)
   122. Prokaryotic ribosomal protein L17 [64262] (1)
        alpha-beta-alpha(3)-beta(2); 2 layers: alpha/beta;
        1. Prokaryotic ribosomal protein L17 [64263] (1)
           some topological similarity to ribosomal protein L22
           uperfamily
           1. Prokaryotic ribosomal protein L17 [64264] (4)
              1. Prokaryotic ribosomal protein L17 [64265]
                 1. Thermus thermophilus [TaxId: 274] [64266] (11)
                 2. Deinococcus radiodurans [TaxId: 1299] [160268] (6)
                    SQ Q9RSJ5 3-115
                 3. Human (Homo sapiens) [TaxId: 9606] [160269] (1)
                    SQ Q9NRX2 28-136
                 4. Escherichia coli [TaxId: 562] [160270] (27)
                    SQ P02416 1-127
   123. GroEL-intermediate domain like [54848] (1)
        3-helical bundle packed against 3-stranded mixed beta-sheet
        1. GroEL-intermediate domain like [54849] (2)
           uperfamily
           1. GroEL-like chaperone, intermediate domain [54850] (4)
              1. GroEL, I domain [54851]
                 1. Escherichia coli [TaxId: 562] [54852] (15)
                 2. Paracoccus denitrificans [TaxId: 266] [69717] (1)
                 3. Thermus thermophilus [TaxId: 274] [110940] (2)
                    SQ P61491
                 4. Mycobacterium tuberculosis, GroEL2 [TaxId: 1773] [117931] (1)
                    SQ P0A520 60-514
           2. Group II chaperonin (CCT, TRIC), intermediate domain [54853] (3)
              1. Thermosome, I domain [54854]
                 1. Archaeon Thermoplasma acidophilum, alpha chain [TaxId: 2303] [100973] (2)
                 2. Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679] [102951] (4)
                 3. Archaeon Thermoplasma acidophilum, beta chain [TaxId: 2303] [100974] (2)
   124. PX domain [64267] (1)
        beta(3)-alpha(4); meander beta-sheet packed against array of helices; contains Pro-rich stretch
        1. PX domain [64268] (1)
           uperfamily
           1. PX domain [64269] (5)
              Pfam 00787
              1. p40phox NADPH oxidase [69718]
                 1. Human (Homo sapiens) [TaxId: 9606] [69719] (1)
              2. p47phox NADPH oxidase [64270]
                 1. Human (Homo sapiens) [TaxId: 9606] [64271] (3)
              3. Vam7p [75424]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75425] (1)
              4. Sorting nexin grd19 [102952]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102953] (2)
              5. Serine/threonine-protein kinase Sgk3, Cisk [117932]
                 1. Mouse (Mus musculus) [TaxId: 10090] [117933] (2)
                    SQ Q9ERE3 10-125 ! SQ Q9ERE3 11-121
   125. Shew3726-like [160271] (1)
        beta(3)-alpha(n)-beta; 2 layers, a/b; mixed beta-sheet, order 1234, strands 3 and 4 are parallel with a left-handed crossover connection
        1. Shew3726-like [160272] (1)
           1. Shew3726-like [160273] (1)
              Pfam 07369; DUF1488
              1. Hypothetical protein Shew3726 [160274]
                 1. Shewanella loihica [TaxId: 359303] [160275] (1)
                    SQ A3QJE4 1-90
   126. DsrC, the gamma subunit of dissimilatory sulfite reductase [69720] (1)
        beta(3)-alpha(5); meander beta-sheet packed against array of helices
        1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69721] (1)
           uperfamily
           1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69722] (2)
              1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69723]
                 1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69724] (1)
                 2. Desulfovibrio vulgaris [TaxId: 881] [160276] (2)
                    SQ P45573 3-105
   127. DNA damage-inducible protein DinI [54856] (1)
        beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
        1. DNA damage-inducible protein DinI [54857] (1)
           uperfamily
           1. DNA damage-inducible protein DinI [54858] (1)
              1. DNA damage-inducible protein DinI [54859]
                 1. Escherichia coli [TaxId: 562] [54860] (1)
   128. HSP90 C-terminal domain [110941] (1)
        alpha-beta(3)-alpha(3); 2 layers, a/b; mixed beta-sheet, order:132; crossing loops
        1. HSP90 C-terminal domain [110942] (1)
           uperfamily
           1. HSP90 C-terminal domain [110943] (1)
              C-terminal part of Pfam 00183
              1. Chaperone protein HtpG [110944]
                 1. Escherichia coli [TaxId: 562] [110945] (1)
                    SQ P10413 511-624
   129. Ferredoxin-like [54861] (59)
        alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
        1. 4Fe-4S ferredoxins [54862] (6)
           uperfamily
           1. Short-chain ferredoxins [54863] (5)
              contains two 4Fe-4S clusters
              1. Ferredoxin II [54864]
                 1. Peptostreptococcus asaccharolyticus [TaxId: 1258] [54866] (1)
                 2. Clostridium acidurici [TaxId: 1556] [54867] (3)
                 3. Clostridium pasteurianum [TaxId: 1501] [54868] (1)
                 4. Chromatium vinosum [TaxId: 1049] [54869] (1)
                 5. Thauera aromatica [TaxId: 59405] [102954] (1)
           2. 7-Fe ferredoxin [54870] (5)
              has C-terminal extension to the common fold
              1. Ferredoxin [54871]
                 1. Azotobacter vinelandii [TaxId: 354] [54872] (32)
                 2. Bacillus schlegelii [TaxId: 1484] [54873] (4)
                 3. Thermus thermophilus [TaxId: 274] [69725] (1)
              2. Photosystem I iron-sulfur protein PsaC [64272]
                 1. Synechococcus elongatus [TaxId: 32046] [64273] (1)
                 2. Synechococcus sp. pcc 7002 [TaxId: 32049] [75426] (1)
           3. Archaeal ferredoxins [54874] (1)
              1. Ferredoxin [54875]
                 the N-terminal extension to the common fold forms a part of a Zn-binding site
                 1. Archaeon Sulfolobus sp. [TaxId: 2288] [54876] (1)
           4. Single 4Fe-4S cluster ferredoxin [54877] (5)
              contains only one 4Fe-4S cluster
              1. Ferredoxin A [54878]
                 1. Thermotoga maritima [TaxId: 2336] [54879] (2)
              2. Ferredoxin I [54880]
                 1. Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873] [54881] (3)
                 2. Desulfovibrio gigas [TaxId: 879] [54865] (2)
              3. Ferredoxin [54882]
                 1. Bacillus thermoproteolyticus [TaxId: 1427] [54883] (6)
              4. Fe3S4-ferredoxin PF1909 [110946]
                 1. Pyrococcus furiosus [TaxId: 2261] [110947] (2)
                    SQ P29603
           5. Ferredoxin domains from multidomain proteins [54884] (15)
              members of this "family" may be more closely related to other ferredoxins than to each other
              1. Fe-only hydrogenase, second domain [54885]
                 1. Clostridium pasteurianum [TaxId: 1501] [54886] (4)
              2. Fe-only hydrogenase larger subunit, N-domain [54887]
                 1. Desulfovibrio desulfuricans [TaxId: 876] [54888] (1)
              3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain V [54889]
                 1. Desulfovibrio africanus [TaxId: 873] [54890] (17)
              4. Dihydropyrimidine dehydrogenase, C-terminal domain [54891]
                 includes linker from domain 4
                 1. Pig (Sus scrofa) [TaxId: 9823] [54892] (5)
              5. Adenylylsulfate reductase B subunit [69726]
                 includes N-terminal partly folded tail
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69727] (10)
              6. Formate dehydrogenase N, iron-sulfur (beta) subunit [75427]
                 1. Escherichia coli [TaxId: 562] [75428] (2)
              7. Tungsten containing formate dehydrogenase, small subunit [82664]
                 1. Desulfovibrio gigas [TaxId: 879] [82665] (1)
              8. Respiratory nitrate reductase 1 beta chain [102955]
                 1. Escherichia coli [TaxId: 562] [102956] (7)
                    SQ P11349
              9. Transhydroxylase beta subunit, BthL, N-terminal domain [110948]
                 1. Pelobacter acidigallici [TaxId: 35816] [110949] (6)
                    SQ P80564
              10. NADH-quinone oxidoreductase chain 9, Nqo9 [143252]
                  1. Thermus thermophilus [TaxId: 274] [143253] (4)
                     SQ Q56224 26-179
              11. NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 [143254]
                  1. Thermus thermophilus [TaxId: 274] [143255] (4)
                     SQ Q56223 96-246
              12. DsrB insert domain [160277]
                  1. Desulfovibrio vulgaris [TaxId: 881] [160278] (2)
                     SQ P45575 209-277
                  2. Archaeoglobus fulgidus [TaxId: 2234] [160279] (2)
                     SQ Q59110 197-261
              13. DsrA insert domain [160280]
                  1. Desulfovibrio vulgaris [TaxId: 881] [160281] (2)
                     SQ P45574 242-322
                  2. Archaeoglobus fulgidus [TaxId: 2234] [160282] (2)
                     SQ Q59109 240-305
           6. ETF-QO domain-like [143256] (1)
              Pfam 05187; Electron transfer flavoprotein-ubiquinone oxidoreductase; contains single Fe4-S4 cluster
              1. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [143257]
                 1. Pig (Sus scrofa) [TaxId: 9823] [143258] (4)
                    SQ P55931 506-607
        2. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1)
           uperfamily
           1. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54894] (2)
              1. Aspartate carbamoyltransferase [54895]
                 1. Escherichia coli [TaxId: 562] [54896] (59)
                    SQ P00478
                 2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [110950] (2)
        3. Protease propeptides/inhibitors [54897] (3)
           uperfamily
           1. Pancreatic carboxypeptidase, activation domain [54898] (6)
              1. Procarboxypeptidase A [54899]
                 1. Pig (Sus scrofa) [TaxId: 9823] [54900] (1)
                 2. Cow (Bos taurus) [TaxId: 9913] [54901] (1)
                 3. Human (Homo sapiens) [TaxId: 9606] [54902] (4)
                    procarboxypeptidase A2
                 4. Cotton bollworm (Helicoverpa armigera) [TaxId: 29058] [75429] (1)
              2. Procarboxypeptidase B [54903]
                 1. Pig (Sus scrofa) [TaxId: 9823] [54904] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [75430] (1)
           2. Subtilase propeptides/inhibitors [54905] (4)
              decorated with additional structure
              1. Subtilisin prosegment [54906]
                 1. Bacillus amyloliquefaciens [TaxId: 1390] [54907] (1)
                 2. Bacillus subtilis [TaxId: 1423] [54908] (1)
              2. Proteinase A inhibitor 1, POIA1 [69728]
                 1. Oyster mushroom (Pleurotus ostreatus) [TaxId: 5322] [69729] (2)
              3. Pro-kumamolisin activation domain [110951]
                 1. Bacillus sp. MN-32 [TaxId: 198803] [110952] (1)
                    SQ Q8RR56
           3. Prohormone convertase 1 pro-domain [75431] (1)
              1. Prohormone convertase 1 pro-domain [75432]
                 1. Mouse (Mus musculus) [TaxId: 10090] [75433] (1)
        4. Dimeric alpha+beta barrel [54909] (23)
           dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
           uperfamily
           1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82666] (1)
              1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82667]
                 1. Streptomyces coelicolor [TaxId: 1902] [82668] (5)
           2. Plant stress-induced protein [89927] (3)
              1. Hypothetical protein AT3G17210.1 [89928]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [89929] (3)
              2. Hypothetical protein AT5G22580 [102957]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102958] (1)
              3. Boiling stable protein 1 [110953]
                 1. European aspen (Populus tremula) [TaxId: 113636] [110954] (2)
                    SQ Q9AR79
           3. PG130-like [102959] (5)
              subfamily of Pfam 03992
              1. Hypothetical protein TT1380 [102960]
                 1. Thermus thermophilus [TaxId: 274] [102961] (1)
              2. Hypothetical protein PG130 (SAV0165) [110955]
                 1. Staphylococcus aureus [TaxId: 1280] [110956] (3)
                    SQ Q99X56
              3. Hypothetical protein BC2969 [110957]
                 1. Bacillus cereus [TaxId: 1396] [110958] (1)
                    SQ Q81C15
              4. Hypothetical protein IsdG [117934]
                 1. Staphylococcus aureus [TaxId: 1280] [117935] (1)
                    SQ Q8NX62
              5. Hypothetical protein YqjZ [160283]
                 1. Bacillus subtilis [TaxId: 1423] [160284] (1)
                    SQ P54563 3-110
           4. Hypothetical protein YjcS [102962] (1)
              1. Hypothetical protein YjcS [102963]
                 1. Bacillus subtilis [TaxId: 1423] [102964] (1)
           5. YciI-like [102965] (1)
              structural similarity to MLI extends to the active site cavity location
              1. Hypothetical protein HI0828 [102966]
                 1. Haemophilus influenzae [TaxId: 727] [102967] (1)
           6. Muconalactone isomerase, MLI [54910] (1)
              decamer: pentamer of dimers
              1. Muconalactone isomerase, MLI [54911]
                 1. Pseudomonas putida [TaxId: 303] [54912] (10)
           7. Lrp/AsnC-like transcriptional regulator C-terminal domain [69733] (4)
              octamer: tetramer of dimers
              1. LprA [69734]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [69735] (1)
              2. Putative transcriptional regulator PH1519 [102968]
                 archaeal feast/famine regulatory protein
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102969] (3)
                    identical sequence to Pyrococcus sp. ot3 protein
              3. Transcriptional regulator LrpC [143259]
                 1. Bacillus subtilis [TaxId: 1423] [143260] (8)
                    SQ P96582 64-140
              4. Regulatory protein AsnC [143261]
                 1. Escherichia coli [TaxId: 562] [143262] (2)
                    SQ P0ACI6 67-152
           8. Polyketide synthesis cyclase [110959] (1)
              Pfam 04673
              1. Tetracenomycin polyketide synthesis protein TcmI [110960]
                 1. Streptomyces glaucescens [TaxId: 1907] [110961] (1)
                    SQ P39890
           9. DGPF domain (Pfam 04946) [110962] (1)
              there is the putative active site cavity in the equivalent location location to the MLI and YciI active sites
              1. Hypothetical protein PA1349 [110963]
                 1. Pseudomonas aeruginosa [TaxId: 287] [110964] (1)
                    SQ Q9I3Z5
           10. Chlorite dismutase-like [110965] (2)
               Pfam 06778; duplication: consists of two similar domains; forms a pentamer similar to the MLI decamer
               1. YwfI homologue [110966]
                  1. Bacillus stearothermophilus [TaxId: 1422] [110967] (1)
                     SQ Q5KUD5 # 98% sequence identity; Geobacillus kaustophilus TaxID:1462
               2. Polyketide synthase CurD homologue TTHA1714/TTC1352 [110968]
                  1. Thermus thermophilus [TaxId: 274] [110969] (1)
                     SQ Q5SHL6
           11. PA3566-like [110970] (5)
               subfamily of Pfam 03992
               1. Hypothetical protein PA3566 [110971]
                  1. Pseudomonas aeruginosa [TaxId: 287] [110972] (1)
                     SQ Q9HY51
               2. Hypothetical protein YgiN [117936]
                  1. Escherichia coli [TaxId: 562] [117937] (2)
                     SQ P0ADU2 P40718
               3. Hypothetical protein Rv0793 [117938]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [117939] (1)
                     SQ O86332
               4. Hypothetical protein NE2512 [160285]
                  1. Nitrosomonas europaea [TaxId: 915] [160286] (4)
                     SQ Q82S47 1-100
               5. Hypothetical protein NE0621 [160287]
                  1. Nitrosomonas europaea [TaxId: 915] [160288] (8)
                     SQ Q82WP3 1-98
           12. Hypothetical protein YdhR [117940] (1)
               1. Hypothetical protein YdhR [117941]
                  1. Escherichia coli [TaxId: 562] [117942] (5)
                     SQ P77225
           13. NIPSNAP [117943] (2)
               Pfam 07978
               1. Hypothetical protein Atu4242 [117944]
                  1. Agrobacterium tumefaciens [TaxId: 358] [117945] (9)
                     SQ Q8U857
               2. Hypothetical protein Atu5224 [143263]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143264] (8)
                     SQ Q8UK99 1-104
           14. Dyp-type peroxidase-like [143265] (3)
               Pfam 04261
               1. Hypothetical protein BT1219 [143266]
                  1. Bacteroides thetaiotaomicron [TaxId: 818] [143267] (1)
                     SQ Q8A8E8 8-316
               2. Decolorizing peroxidase DyP [143268]
                  1. Geotrichum candidum [TaxId: 27317] [143269] (2)
                     SQ Q8WZK8 60-498
                     species assignment from the UniProt sequence (Id 100%); 2d3q species is Thanatephorus cucumeris
               3. Melanin biosynthesis protein TyrA [143270]
                  1. Shewanella oneidensis [TaxId: 70863] [143271] (2)
                     SQ Q8EIU4 5-311
           15. EthD-like [143272] (1)
               Pfam 07110
               1. Hypothetical protein BH0200 [143273]
                  1. Bacillus halodurans [TaxId: 86665] [143274] (2)
                     SQ Q9KGB0 4-106
           16. Atu0297-like [143275] (1)
               Pfam 07045; DUF1330
               1. Hypothetical protein Atu0297 [143276]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143277] (2)
                     SQ Q8UIJ7 1-95
           17. SOR-like [143278] (1)
               Pfam 07682; duplication: consists of two similar domains
               1. Sulfur oxygenase reductase SOR [143279]
                  1. Acidianus ambivalens [TaxId: 2283] [143280] (1)
                     SQ P29082 2-308
           18. YbaA-like [160289] (1)
               Pfam 07237; DUF1428
               1. Hypothetical protein YbaA [160290]
                  1. Shigella flexneri [TaxId: 623] [160291] (2)
                     SQ P0AAQ9 1-117
           19. MmlI-like [160292] (1)
               Pfam 09448; Methylmuconolactone methyl-isomerase
               1. Hypothetical protein Reut_A1503 [160293]
                  1. Ralstonia eutropha [TaxId: 106590] [160294] (2)
                     SQ Q471R3 1-108
           20. Marine metagenome family DABB2 [160295] (1)
               1. Hypothetical protein GOS_3280838 [160296]
                  1. environmental samples [160297] (2)
           21. YiiL-like [160298] (1)
               Pfam 05336; DUF718
               1. L-rhamnose mutarotase YiiL [160299]
                  1. Escherichia coli [TaxId: 562] [160300] (4)
                     SQ P32156 1-104
           22. Marine metagenome family DABB1 [160301] (2)
               1. Hypothetical protein GOS_7213774 [160302]
                  1. environmental samples [160303] (6)
                     marine metagenome
               2. Hypothetical protein GOS_2359375 [160304]
                  1. environmental samples [160305] (4)
                     marine metagenome
           23. Marine metagenome family DABB3 [160306] (1)
               duplication: consists of two similar domains; forms a pentamer similar to the Chlorite dismutase-like pentamer and the MLI decamer
               1. Uncharacterized protein GOS_2596953 [160307]
                  1. environmental samples [160308] (5)
        5. GlnB-like [54913] (5)
           form timeric structures with the orthogonally packed beta-sheets
           uperfamily
           1. Prokaryotic signal transducing protein [54914] (8)
              1. PII (product of glnB) [54915]
                 trimer with orthogonal packing of beta-sheets around the threefold axis
                 1. Escherichia coli [TaxId: 562] [54916] (2)
                 2. Herbaspirillum seropedicae [TaxId: 964] [89930] (1)
                 3. Cyanobacteria (Synechococcus sp.) pcc 7942 [TaxId: 1131] [102970] (1)
                 4. Cyanobacteria (Synechococcus sp.) pcc pcc 6803 [TaxId: 1131] [102971] (1)
                 5. Thermus thermophilus [TaxId: 274] [102972] (5)
                    SQ P83820
              2. PII-homolog GlnK [54917]
                 1. Escherichia coli [TaxId: 562] [54918] (8)
                 2. Shigella flexneri [TaxId: 623] [160309] (1)
                    SQ P0AC58 1-112
              3. Hypothetical protein TTHA0516 [143281]
                 1. Thermus thermophilus [TaxId: 274] [143282] (3)
                    SQ Q5SKX7 1-100
           2. Divalent ion tolerance proteins CutA (CutA1) [75434] (7)
              1. Cut A1 [89931]
                 1. Thermus thermophilus [TaxId: 274] [89932] (2)
                 2. Escherichia coli [TaxId: 562] [102973] (1)
                 3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102974] (15)
                    SQ O58720
                 4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89933] (1)
              2. Hypothetical protein TM1056 [75435]
                 1. Thermotoga maritima [TaxId: 2336] [75436] (3)
              3. Mammalian CutA-like protein [102975]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [102976] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [117946] (7)
                    SQ O60888 40-146
           3. DUF190/COG1993 [89934] (1)
              1. Hypothetical protein TM0021 [89935]
                 1. Thermotoga maritima [TaxId: 2336] [89936] (1)
           4. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [88851] (2)
              1. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [82669]
                 binds allosteric inhibitor histidine
                 1. Mycobacterium tuberculosis [TaxId: 1773] [82670] (2)
                 2. Escherichia coli [TaxId: 562] [102977] (2)
           5. RPA1041-like [160310] (1)
              PF09413; DUF2007; provisional superfamily assignment based on a single monomeric solution structure
              1. Hypothetical protein RPA1041 [160311]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [160312] (1)
                    SQ Q6NAY9 1-75
                    missannotated in PDB 2HFV as Pseudomonas aeruginosa
        6. SEA domain [82671] (1)
           uperfamily
           1. SEA domain [82672] (1)
              1. SEA domain from the hypothetical protein homologous to mucin 16 [82673]
                 1. Mouse (Mus musculus) [TaxId: 10090] [82674] (1)
        7. Nucleoside diphosphate kinase, NDK [54919] (1)
           uperfamily
           1. Nucleoside diphosphate kinase, NDK [54920] (20)
              1. Nucleoside diphosphate kinase, NDK [54921]
                 1. Human (Homo sapiens) [TaxId: 9606] [54922] (14)
                 2. Human (Homo sapiens), NDK4 [TaxId: 9606] [54923] (1)
                 3. Human (Homo sapiens), NDKA [TaxId: 9606] [75437] (5)
                 4. Cow (Bos taurus) [TaxId: 9913] [54924] (2)
                 5. Dictyostelium discoideum [TaxId: 44689] [54925] (27)
                 6. Drosophila melanogaster [TaxId: 7227] [54926] (2)
                 7. Myxococcus xanthus [TaxId: 34] [54927] (3)
                 8. Mycobacterium tuberculosis [TaxId: 1773] [75438] (1)
                 9. Bacillus halodenitrificans [TaxId: 1482] [89937] (1)
                 10. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117947] (1)
                     SQ Q8ID43
                 11. Pea (Pisum sativum) [TaxId: 3888] [117948] (1)
                     SQ Q9SP13 81-231
                 12. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117949] (1)
                     SQ P39207
                 13. Thale cress (Arabidopsis thaliana), chloroplast NDK2 [TaxId: 3702] [117950] (2)
                     SQ O64903 79-231
                 14. Human(Homo sapiens), NDK3 [TaxId: 9606] [143283] (3)
                     SQ Q13232 18-169
                 15. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143284] (12)
                     SQ O58429 3-155
                 16. Rice(Oryza sativa) [TaxId: 4530] [143285] (12)
                     SQ Q07661 1-148
                 17. Mimivirus [TaxId: 315393] [143286] (8)
                     SQ Q5UQL3 2-137
                 18. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [143287] (3)
                     SQ Q8ZWY4 2-183
                 19. Archaeon Halobacterium salinarum [TaxId: 2242] [143288] (15)
                     SQ P61136 4-158
                 20. Thermus thermophilus [TaxId: 274] [143289] (6)
                     SQ Q5SLV5 1-137
        8. RNA-binding domain, RBD [54928] (5)
           uperfamily
           1. Canonical RBD [54929] (71)
              1. Nuclear ribonucleoprotein A1 (RNP A1, UP1) [54930]
                 duplication: contains two domains of this fold
                 1. Human (Homo sapiens) [TaxId: 9606] [54931] (14)
                    SQ P09651 7-188
              2. Nuclear ribonucleoprotein D0 (AUF1) [75439]
                 1. Human (Homo sapiens) [TaxId: 9606] [75440] (3)
              3. Splicesomal U1A protein [54932]
                 duplication: contains two domains of this fold
                 1. Human (Homo sapiens) [TaxId: 9606] [54933] (38)
                    SQ P09012 1-97 ! SQ P09012 4-98 ! SQ P09012 1-98
                 2. Drosophila melanogaster [TaxId: 7227] [160313] (3)
                    SQ P43332 1-104! SQ P43332 134-216
              4. Splicing factor U2B'' [54934]
                 1. Human (Homo sapiens) [TaxId: 9606] [54935] (1)
              5. Splicing factor U2AF 65 KDa subunit [54936]
                 1. Human (Homo sapiens) [TaxId: 9606] [54937] (4)
              6. Sex-lethal protein [54938]
                 1. Drosophila melanogaster [TaxId: 7227] [54939] (4)
              7. Hu antigen C (Huc) [54940]
                 1. Mouse (Mus musculus) [TaxId: 10090] [54941] (3)
              8. Hu antigen D (Hud) [54942]
                 1. Human (Homo sapiens) [TaxId: 9606] [54943] (2)
              9. Heterogeneous nuclear ribonucleoprotein d0 [54944]
                 1. Human (Homo sapiens) [TaxId: 9606] [54945] (2)
              10. Neural RNA-binding protein Musashi-1 [54946]
                  1. Mouse (Mus musculus) [TaxId: 10090] [54947] (2)
              11. Poly(A)-binding protein [54948]
                  1. Human (Homo sapiens) [TaxId: 9606] [54949] (1)
              12. Polypyrimidine tract-binding protein [54950]
                  1. Human (Homo sapiens) [TaxId: 9606] [54951] (9)
                     SQ P26599 54-141, 177-284, 335-531
              13. Nucleolin [54952]
                  1. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [54953] (4)
              14. CBP20, 20KDa nuclear cap-binding protein [64274]
                  1. Human (Homo sapiens) [TaxId: 9606] [64275] (6)
              15. RNA-binding protein 8 [89938]
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89939] (3)
                     CG8781 protein
                  2. Human (Homo sapiens) [TaxId: 9606] [102978] (6)
                     RBM8A, Y14
              16. Lupus LA protein [89940]
                  1. Human (Homo sapiens) [TaxId: 9606] [89941] (13)
              17. Nuclear factor Aly [102979]
                  1. Mouse (Mus musculus) [TaxId: 10090] [102980] (1)
              18. Musashi-1 [102981]
                  1. Mouse (Mus musculus) [TaxId: 10090] [102982] (1)
              19. Cleavage stimulation factor, 64 kda subunit [102983]
                  1. Human (Homo sapiens) [TaxId: 9606] [102984] (1)
              20. Synaptojanin 2 [102985]
                  1. Human (Homo sapiens) [TaxId: 9606] [102986] (1)
              21. Heterogeneous nuclear ribonucleoprotein L-like [117951]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117952] (1)
                     SQ Q921F4 116-207
              22. Calcipressin-1 [117953]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117954] (1)
                     SQ Q9JHG6 14-103
              23. Heterogeneous nuclear ribonucleoprotein H' [117955]
                  1. Human (Homo sapiens) [TaxId: 9606] [117956] (2)
                     SQ P55795 103-193; 280-369
              24. TAR DNA-binding protein 43, TDP-43 [117957]
                  1. Human (Homo sapiens) [TaxId: 9606] [117958] (2)
                     SQ Q13148 193-267
              25. RNA-binding protein Raly (Autoantigen p542) [117959]
                  1. Human (Homo sapiens) [TaxId: 9606] [117960] (1)
                     SQ Q9UKM9 1-97
              26. Heterogeneous nuclear ribonucleoproteins C1/C2 [117961]
                  1. Human (Homo sapiens) [TaxId: 9606] [117962] (1)
                     SQ P07910 8-92
              27. Probable RNA-binding protein KIAA1579 [117963]
                  1. Human (Homo sapiens) [TaxId: 9606] [117964] (1)
                     SQ Q9HCJ3 71-145
              28. Splicing factor, arginine/serine-rich 9 (SFRS9) [117965]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117966] (1)
                     SQ Q9D0B0 104-188
              29. Poly(A)-specific ribonuclease PARN [117967]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117968] (1)
                     SQ Q8VDG3 430-516; structure of the R3H domain (162-248) is also known (scop_sp 111031)
              30. Probable RNA-binding protein 19, Rbm19 [117969]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117970] (4)
                     SQ Q8R3C6 399-484; 581-678
              31. Putative RNA-binding protein 15B, Rbm15b [117971]
                  1. Mouse (Mus musculus) [TaxId: 10090] [117972] (1)
                     SQ Q6PHZ5 81-164
              32. Eukaryotic translation initiation factor 4B [117973]
                  1. Human (Homo sapiens) [TaxId: 9606] [117974] (1)
                     SQ P23588 88-178
              33. HIV Tat-specific factor 1 [143290]
                  1. Human (Homo sapiens) [TaxId: 9606] [143291] (1)
                     SQ O43719 256-354
              34. Ataxin-2-binding protein 1 [143292]
                  1. Human (Homo sapiens) [TaxId: 9606] [143293] (1)
                     SQ Q9NWB1 109-196
              35. E3 ubiquitin protein ligase CNOT4 [143294]
                  CCR4-NOT transcription complex subunit 4
                  1. Mouse (Mus musculus) [TaxId: 10090] [143295] (1)
                     SQ Q8BT14 101-198
              36. RNA-binding protein 41, RBM41 [143296]
                  1. Human (Homo sapiens) [TaxId: 9606] [143297] (1)
                     SQ Q96IZ5 291-392
              37. Nucleolysin TIAR [143298]
                  1. Human (Homo sapiens) [TaxId: 9606] [143299] (2)
                     SQ Q01085 1-90! SQ Q01085 187-282
              38. Cold-inducible RNA-binding protein [143300]
                  1. Human (Homo sapiens) [TaxId: 9606] [143301] (1)
                     SQ Q14011 1-90
              39. Negative elongation factor E, NELF-E [143302]
                  1. Human (Homo sapiens) [TaxId: 9606] [143303] (3)
                     SQ P18615 257-335! SQ P18615 258-341
              40. Eukaryotic translation initiation factor 3 subunit 4 [143304]
                  1. Human (Homo sapiens) [TaxId: 9606] [143305] (1)
                     SQ O75821 231-320
              41. Matrin 3 [143306]
                  1. Mouse (Mus musculus) [TaxId: 10090] [143307] (2)
                     SQ Q8K310 390-478! SQ Q8K310 478-576
              42. Ribonucleoprotein PTB-binding 1, Raver-1 [143308]
                  1. Mouse (Mus musculus) [TaxId: 10090] [143309] (1)
                     SQ Q9CW46 61-135
              43. Peptidyl-prolyl cis-trans isomerase E, N-terminal domain [143310]
                  1. Human (Homo sapiens) [TaxId: 9606] [143311] (1)
                     SQ Q9UNP9 1-89
              44. Arginine/serine-rich splicing factor 10 [143312]
                  1. Human (Homo sapiens) [TaxId: 9606] [143313] (1)
                     SQ P62995 109-191
              45. RNA-binding protein 9 [143314]
                  1. Human (Homo sapiens) [TaxId: 9606] [143315] (1)
                     SQ O43251 110-202
              46. Pre-mRNA branch site protein p14 [143316]
                  1. Human (Homo sapiens) [TaxId: 9606] [143317] (4)
                     SQ Q9Y3B4 12-125
              47. Splicing factor 3B subunit 4 [143318]
                  1. Human (Homo sapiens) [TaxId: 9606] [143319] (2)
                     SQ Q15427 102-184! SQ Q15427 4-96
              48. RNA-binding motif, single-stranded-interacting protein 2, RBMS2 [143320]
                  1. Human (Homo sapiens) [TaxId: 9606] [143321] (1)
                     SQ Q15434 58-129
              49. RNA-binding protein UBP1 [143322]
                  1. Trypanosoma cruzi [TaxId: 5693] [143323] (1)
                     SQ Q967R0 1-139
              50. Limkain-b1, LKAP [143324]
                  KIAA0430
                  1. Human (Homo sapiens) [TaxId: 9606] [143325] (1)
                     SQ Q9Y4F3 788-870
              51. APOBEC1 stimulating protein [143326]
                  1. Human (Homo sapiens) [TaxId: 9606] [143327] (1)
                     SQ Q9NQ94 223-308
              52. Hypothetical protein FLJ20273 [143328]
                  1. Human (Homo sapiens) [TaxId: 9606] [143329] (1)
                     SQ Q8NI52 150-245
              53. Nucleoporin 35 [143330]
                  1. Mouse (Mus musculus) [TaxId: 10090] [143331] (4)
                     SQ Q8R4R6 169-249
              54. Polypyrimidine tract-binding protein 2, PTBP2 [143332]
                  1. Human (Homo sapiens) [TaxId: 9606] [143333] (1)
                     SQ Q9UKA9 51-138
              55. Alkylation repair AlkB homolog 8, ALKBH8 [143334]
                  1. Human (Homo sapiens) [TaxId: 9606] [143335] (1)
                     SQ Q96BT7 25-125
              56. CUG triplet repeat RNA-binding protein 1 [143336]
                  1. Human (Homo sapiens) [TaxId: 9606] [143337] (1)
                     SQ Q92879 383-484
              57. U4/U6 snRNA-associated-splicing factor PRP24 [143338]
                  contains three RBDs
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143339] (24)
                     SQ P49960 116-196! SQ P49960 206-291! SQ P49960 41-115
              58. RNA-binding protein EWS [143340]
                  1. Human (Homo sapiens) [TaxId: 9606] [143341] (1)
                     SQ Q01844 353-453
              59. Heterogeneous nuclear ribonucleoproteins A2/B1 [143342]
                  1. Human (Homo sapiens) [TaxId: 9606] [143343] (1)
                     SQ P22626 1-103
              60. IGF-II mRNA-binding protein 2 isoform A [143344]
                  1. Human (Homo sapiens) [TaxId: 9606] [143345] (1)
                     SQ Q9Y6M1 2-81
              61. Splicing factor, arginine/serine-rich 1, SFRS1 [143346]
                  1. Human (Homo sapiens) [TaxId: 9606] [143347] (3)
                     SQ Q07955 1-95
                  2. Mouse (Mus musculus) [TaxId: 10090] [143348] (1)
                     SQ Q6PDM2 112-206
              62. RNA-binding protein 12 [143349]
                  3rd RBD
                  1. Human (Homo sapiens) [TaxId: 9606] [143350] (2)
                     SQ Q9NTZ6 412-523! SQ Q9NTZ6 536-638
                  2. Mouse (Mus musculus) [TaxId: 10090] [143351] (1)
                     SQ Q8R4X3 917-1002
              63. RNA binding protein 23 [143352]
                  1. Human (Homo sapiens) [TaxId: 9606] [143353] (1)
                     SQ Q86U06 148-248
              64. Non-POU domain-containing octamer-binding protein, NonO [143354]
                  1. Mouse (Mus musculus) [TaxId: 10090] [143355] (1)
                     SQ Q99K48 68-153
              65. RNA-binding motif, single-stranded-interacting protein 1, RBMS1 [143356]
                  1. Human (Homo sapiens) [TaxId: 9606] [143357] (1)
                     SQ P29558 123-223
              66. RNA-binding protein 28 [143358]
                  1. Mouse (Mus musculus) [TaxId: 10090] [143359] (1)
                     SQ Q8CGC6 316-413
              67. RNA-binding region containing protein 1 [143360]
                  1. Human (Homo sapiens) [TaxId: 9606] [143361] (1)
                     SQ Q9H0Z9 1-103
           2. Non-canonical RBD domain [54954] (1)
              1. mRNA export factor tap [54955]
                 1. Human (Homo sapiens) [TaxId: 9606] [54956] (5)
           3. Splicing factor U2AF subunits [64276] (1)
              1. U2AF35 (35 KDa subunit) [64277]
                 1. Human (Homo sapiens) [TaxId: 9606] [64278] (1)
           4. Smg-4/UPF3 [102987] (1)
              Pfam 03467
              1. RNA processing protein UPF3x, RRM domain [102988]
                 1. Human (Homo sapiens) [TaxId: 9606] [102989] (1)
           5. GUCT domain [160314] (1)
              Pfam 08152
              1. ATP-dependent RNA helicase DDX50 [160315]
                 1. Human (Homo sapiens) [TaxId: 9606] [160316] (1)
                    SQ Q9BQ39 575-659
        9. Viral DNA-binding domain [54957] (1)
           uperfamily
           1. Viral DNA-binding domain [54958] (6)
              1. Papillomavirus-1 E2 protein [54959]
                 forms dimers with subunit beta-sheets making (8,12) barrel
                 1. Bovine papillomavirus type 1 [TaxId: 10559] [54960] (3)
                 2. Human papillomavirus type 31 [TaxId: 10585] [54961] (2)
                 3. Human papillomavirus type 16 [TaxId: 333760] [54962] (5)
                    SQ P03120 286-365
                 4. Human papillomavirus type 18 [TaxId: 333761] [54963] (2)
                 5. Human papillomavirus type 6a [TaxId: 37122] [102990] (11)
              2. Epstein barr virus nuclear antigen-1 (ebna1) [54964]
                 DNA-binding mode differs from that of E2 protein
                 1. Epstein-Barr virus [TaxId: 10376] [54965] (2)
        10. RuBisCO, large subunit, small (N-terminal) domain [54966] (1)
            C-terminal domain is beta/alpha barrel
            uperfamily
            1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54967] (12)
               1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54968]
                  1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [54969] (5)
                  2. Spinach (Spinacia oleracea) [TaxId: 3562] [54970] (11)
                  3. Galdieria partita [TaxId: 83374] [54971] (2)
                  4. Chlamydomonas reinhardtii [TaxId: 3055] [69730] (74)
                  5. Alcaligenes eutrophus [TaxId: 106590] [54972] (1)
                  6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [54973] (16)
                  7. Rhodospirillum rubrum [TaxId: 1085] [54974] (5)
                  8. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [69731] (1)
                  9. Chlorobium tepidum [TaxId: 1097] [117975] (3)
                     SQ Q8KBL4 1-428
                  10. Rice (Oryza sativa) [TaxId: 4530] [117976] (1)
                      SQ P12089
                  11. Archaeon Halothiobacillus neapolitanus [TaxId: 927] [143362] (1)
                      SQ O85040 16-142
                  12. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143363] (10)
                      SQ O58677 8-133
        11. Acylphosphatase/BLUF domain-like [54975] (2)
            uperfamily
            1. Acylphosphatase-like [54976] (6)
               1. Acylphosphatase [54977]
                  1. Cow (Bos taurus) [TaxId: 9913] [54978] (1)
                  2. Horse (Equus caballus) [TaxId: 9796] [54979] (1)
                  3. Pyrococcus horikoshii [TaxId: 53953] [110973] (2)
                     SQ P84142
                  4. Thermus thermophilus [TaxId: 274] [117977] (1)
                     SQ Q5SKS6
               2. Hydrogenase maturation protein HypF N-terminal domain (HypF-ACP) [82675]
                  1. Escherichia coli [TaxId: 562] [82676] (2)
               3. Acylphosphatase 2 (Cg18505) [110974]
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110975] (1)
                     SQ Q9VF36
            2. BLUF domain [143364] (3)
               Pfam 04940; sensors of blue-light using FAD
               1. Blue light receptor BlrB [143365]
                  1. Rhodobacter sphaeroides [TaxId: 1063] [143366] (2)
                     SQ Q3IYE4 1-136
               2. Sensor of blue light AppA [143367]
                  1. Rhodobacter sphaeroides [TaxId: 1063] [143368] (4)
                     SQ Q53119 17-130! SQ Q53119 5-125
               3. Hypothetical protein Tll0078 [143369]
                  1. Thermosynechococcus elongatus [TaxId: 146786] [143370] (10)
                     SQ Q8DMN3 2-143
        12. EF-G C-terminal domain-like [54980] (3)
            uperfamily
            1. EF-G/eEF-2 domains III and V [54981] (3)
               domain III structure is lacking some of the superfamily characters and is often disordered in crystals
               1. Elongation factor G (EF-G) [54982]
                  domain III is seen in 1FNM but disordered in the most of other PDB entries
                  1. Thermus thermophilus [TaxId: 274] [54983] (12)
                  2. Thermus thermophilus, EF-G-2 [TaxId: 274] [143371] (4)
                     SQ Q5SI76 371-447! SQ Q5SI76 563-658
                     TTHA1498
               2. Elongation factor 2 (eEF-2) [82677]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82678] (41)
                     SQ P32324
            2. YigZ C-terminal domain-like [102991] (2)
               similar to EF-G domain V; N-terminal domain shares structural similarity with the EF-G domain IV
               1. Hypothetical protein YigZ, C-terminal domain [102992]
                  1. Escherichia coli [TaxId: 562] [102993] (1)
               2. Hypothetical protein TTHA1053, C-terminal domain [143372]
                  1. Thermus thermophilus [TaxId: 274] [143373] (1)
                     SQ Q5SJF5 125-191
            3. Hypothetical protein AF0491, C-terminal domain [110976] (1)
               1. Hypothetical protein AF0491, C-terminal domain [110977]
                  1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110978] (2)
                     SQ O29759
        13. eEF-1beta-like [54984] (1)
            uperfamily
            1. eEF-1beta-like [54985] (3)
               1. Guanine nucleotide exchange factor (GEF) domain from elongation factor-1 beta [54986]
                  1. Human (Homo sapiens) [TaxId: 9606] [54987] (1)
                  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54988] (6)
               2. aEF-1beta [54989]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [54990] (1)
        14. eEF1-gamma domain [89942] (1)
            elaborated with additional structures
            uperfamily
            1. eEF1-gamma domain [89943] (1)
               1. Elongation factor 1-gamma C-terminal domain [89944]
                  1. Human (Homo sapiens) [TaxId: 9606] [89945] (1)
        15. Anticodon-binding domain of PheRS [54991] (1)
            uperfamily
            1. Anticodon-binding domain of PheRS [54992] (1)
               1. Phenylalanyl-tRNA synthetase [54993]
                  1. Thermus thermophilus [TaxId: 274] [54994] (9)
                     identical sequence to Thermus aquaticus, TaxId: 271
        16. Ribosomal protein S6 [54995] (1)
            uperfamily
            1. Ribosomal protein S6 [54996] (4)
               1. Ribosomal protein S6 [54997]
                  1. Thermus thermophilus [TaxId: 274] [54998] (54)
                     SQ P23370
                  2. Thermotoga maritima [TaxId: 2336] [117978] (1)
                     SQ Q9WZ72
                  3. Escherichia coli [TaxId: 562] [160317] (24)
                     SQ P02358 1-100
                  4. Aquifex aeolicus [TaxId: 63363] [160318] (1)
                     SQ O66474 3-108
        17. Ribosomal protein S10 [54999] (1)
            uperfamily
            1. Ribosomal protein S10 [55000] (2)
               1. Ribosomal protein S10 [55001]
                  1. Thermus thermophilus [TaxId: 274] [55002] (45)
                     SQ P80375
                  2. Escherichia coli [TaxId: 562] [160319] (24)
                     SQ P0A7R5 5-102
        18. N-utilization substance G protein NusG, N-terminal domain [82679] (1)
            uperfamily
            1. N-utilization substance G protein NusG, N-terminal domain [82680] (2)
               1. N-utilization substance G protein NusG, N-terminal domain [82681]
                  1. Aquifex aeolicus [TaxId: 63363] [82682] (4)
                     interrupted by an insert beta-sandwich domain
                  2. Thermus thermophilus [TaxId: 274] [102994] (1)
        19. PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2)
            uperfamily
            1. Poly(A) polymerase, PAP, C-terminal domain [55004] (2)
               1. Poly(A) polymerase, PAP, C-terminal domain [55005]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55006] (7)
                  2. Cow (Bos taurus) [TaxId: 9913] [55007] (3)
                     SQ P25500 18-497
            2. Archaeal tRNA CCA-adding enzyme [102995] (1)
               decorated fold with a large insertion
               1. tRNA nucleotidyltransferase, C-terminal domain [102996]
                  1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102997] (28)
                     SQ O28126
        20. HMA, heavy metal-associated domain [55008] (1)
            uperfamily
            1. HMA, heavy metal-associated domain [55009] (12)
               1. Mercuric ion binding protein MerP [55010]
                  1. Shigella flexneri [TaxId: 623] [55011] (3)
                  2. Ralstonia metallidurans CH34 [TaxId: 266264] [110979] (1)
                     SQ O66016 Q58AI1 Q5NUU9 Q6UP70 Q7BRH5 Q7BRH6 Q7X3A5 # 100% identity
               2. Potential copper-translocating P-type ATPase CopA (YvgX) [75441]
                  duplication: contains tandem repeat of two HMA domains in the N-terminal region
                  1. Bacillus subtilis [TaxId: 1423] [75442] (6)
               3. Metal ion-transporting ATPase ZntA, N-terminal domain [82683]
                  1. Escherichia coli [TaxId: 562] [82684] (2)
               4. Copper transporter domain ccc2a [64279]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64280] (3)
               5. Menkes copper-transporting ATPase [55012]
                  1. Human (Homo sapiens) [TaxId: 9606] [55013] (7)
               6. ATX1 metallochaperone protein (ATOX1) [55014]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55015] (5)
                  2. Human (Homo sapiens), HAH1 [TaxId: 9606] [55016] (5)
                     SQ O00244
               7. Copper chaperone [55017]
                  1. Enterococcus hirae [TaxId: 1354] [55018] (1)
                  2. Bacillus subtilis, CopZ [TaxId: 1423] [69736] (4)
                  3. Synechocystis sp. pcc 6803, Scatx1 [TaxId: 1148] [102998] (1)
               8. Copper chaperone for superoxide dismutase, N-terminal domain [55019]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55020] (2)
        21. Urease metallochaperone UreE, C-terminal domain [69737] (1)
            uperfamily
            1. Urease metallochaperone UreE, C-terminal domain [69738] (2)
               1. Urease metallochaperone UreE, C-terminal domain [69739]
                  1. Klebsiella aerogenes [TaxId: 28451] [69740] (3)
                  2. Bacillus pasteurii [TaxId: 1474] [69741] (2)
        22. ACT-like [55021] (14)
            regulatory domain linked to a wide range of metabolic enzymes
            uperfamily
            1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55022] (2)
               1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55023]
                  1. Escherichia coli [TaxId: 562] [55024] (18)
                  2. Mycobacterium tuberculosis [TaxId: 1773] [143374] (2)
                     SQ P0A544 451-528
                     there is an intervening domain between the substrate-binding domain and this domain
            2. Allosteric threonine deaminase C-terminal domain [55025] (1)
               1. Allosteric threonine deaminase C-terminal domain [55026]
                  duplication: consists of two homologous domains
                  1. Escherichia coli [TaxId: 562] [55027] (1)
            3. Phenylalanine metabolism regulatory domain [55028] (2)
               1. Phenylalanine hydroxylase N-terminal domain [55029]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [55030] (2)
               2. Prephenate dehydratase C-terminal domain [160320]
                  1. Staphylococcus aureus [TaxId: 1280] [160321] (2)
                     SQ Q99SX2 185-264
            4. Nickel responsive regulator NikR, C-terminal domain [102999] (2)
               1. Nickel responsive regulator NikR, C-terminal domain [103000]
                  1. Escherichia coli [TaxId: 562] [103001] (21)
                  2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143375] (12)
                     SQ O58316 51-132
            5. Glycine cleavage system transcriptional repressor [110980] (1)
               tandem repeat of two ACT-like domains; swapped domain dimer
               1. putative transcriptional repressor VC2159 [110981]
                  1. Vibrio cholerae [TaxId: 666] [110982] (1)
                     SQ Q9KQ45
            6. IlvH-like [143376] (3)
               Duplication: tandem repeat of two ACT-like domains; dimer, the N- and C-terminal domains have different dimerisation modes
               1. Acetolactate synthase small subunit, IlvH [143377]
                  1. Thermotoga maritima [TaxId: 2336] [143378] (2)
                     SQ Q9WZ19 5-82! SQ Q9WZ19 83-165
                  2. Escherichia coli [TaxId: 562] [143379] (4)
                     SQ P00894 2-77! SQ P00894 78-163
                  3. Nitrosomonas europaea [TaxId: 915] [143380] (8)
                     SQ Q82UZ2 1-77! SQ Q82UZ2 78-163
            7. SP0238-like [143381] (1)
               stand-alone protein; dimer, the dimerization interface is formed by parallel packing of the subunit beta-sheets
               1. UPF0237 protein SP0238 [143382]
                  1. Streptococcus pneumoniae [TaxId: 1313] [143383] (3)
                     SQ P67382 1-83
            8. Atu0741-like [143384] (1)
               duplication: tandem repeat of two ACT-like domains; contains strand invasion of extra N-terminal strand into the C-terminal domain beta-sheet; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
               1. Hypothetical protein Atu0741 [143385]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143386] (2)
                     SQ Q8UHE1 2-61! SQ Q8UHE1 62-127
            9. VC0802-like [143387] (1)
               duplication: tandem repeat of two ACT-like domains; contains circular permutation (the C-terminal strand replacement with extra N-terminal strand); dimerizes with the formation of orthogonally packed intersubunit beta-sheets
               1. Hypothetical protein VC0802 [143388]
                  1. Vibrio cholerae [TaxId: 666] [143389] (8)
                     SQ Q9KTT6 2-67! SQ Q9KTT6 68-131
            10. Aspartokinase allosteric domain-like [143390] (3)
                duplication: tandem repeat of two ACT-like domains; similar subunit and oligomeric structures to the VC0802-like family
                1. Aspartokinase [143391]
                   1. Methanococcus jannaschii [TaxId: 2190] [143392] (8)
                      SQ Q57991 304-403! SQ Q57991 404-470
                   2. Escherichia coli [TaxId: 562] [143393] (6)
                      SQ P08660 295-385! SQ P08660 386-449
                      Lysine-sensitive aspartokinase 3
                   3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143394] (4)
                      SQ Q9LYU8 388-478! SQ Q9LYU8 479-553
            11. BT0572-like [143395] (1)
                duplication: tandem repeat of two ACT-like domains; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
                1. Hypothetical protein BT0572 [143396]
                   1. Bacteroides thetaiotaomicron [TaxId: 818] [143397] (4)
                      SQ Q8AA93 1-70! SQ Q8AA93 71-141
            12. AF1403 N-terminal domain-like [143398] (1)
                dimerizes with the formation of a single intersubunit beta-sheet
                1. Hypothetical protein AF1403, N-terminal domain [143399]
                   1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143400] (3)
                      SQ O28869 2-78
            13. NIL domain-like [160322] (4)
                Pfam 09383
                1. Methionine import ATP-binding protein MetN [160323]
                   1. Vibrio parahaemolyticus [TaxId: 670] [160324] (2)
                      SQ Q87RS1 248-344
                   2. Escherichia coli [TaxId: 562] [160325] (6)
                      SQ P30750 241-343! SQ P30750 247-343
                2. Methionine import ATP-binding protein MetN2 [160326]
                   1. Enterococcus faecalis [TaxId: 1351] [160327] (1)
                      SQ Q831K6 256-345
                   2. Staphylococcus aureus [TaxId: 1280] [160328] (3)
                      SQ Q99VG8 247-341
            14. TM1266-like [160329] (1)
                PfamB 015436; stand-alone tetrameric protein; there are single beta-sheet dimers, whose beta-sheets are packed in parallel fasion in the tetramer
                1. Hypothetical protein TM1266 [160330]
                   1. Thermotoga maritima [TaxId: 2336] [160331] (4)
                      SQ Q9X0Z3 2-81
        23. Bacterial exopeptidase dimerisation domain [55031] (1)
            uperfamily
            1. Bacterial exopeptidase dimerisation domain [55032] (9)
               1. Carboxypeptidase G2 [55033]
                  dimerisation mode is similar to that of 1PSD domain
                  1. Pseudomonas sp., strain rs-16 [TaxId: 306] [55034] (1)
               2. Peptidase T (tripeptidase) [75443]
                  1. Salmonella typhimurium [TaxId: 90371] [75444] (1)
                  2. Escherichia coli [TaxId: 562] [103002] (1)
               3. Peptidase-like beta-alanine synthase [103003]
                  1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [103004] (2)
               4. Succinyl-diaminopimelate desuccinylase [103005]
                  1. Neisseria meningitidis [TaxId: 487] [103006] (1)
               5. IAA-amino acid hydrolase [117979]
                  apparently monomeric
                  1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [117980] (2)
                     SQ P54970 37-428
               6. Aminopeptidase PepV [82685]
                  contains insert sudbomain 205-292 mimicking the other half of the family-specific dimer
                  1. Lactobacillus delbrueckii [TaxId: 1584] [82686] (1)
               7. Allantoate amidohydrolase AllC [143401]
                  1. Escherichia coli [TaxId: 562] [143402] (4)
                     SQ P77425 211-327
               8. Protein YxeP [143403]
                  dimeric protein closely related to IAA-amino acid hydrolase
                  1. Bacillus subtilis [TaxId: 1423] [143404] (2)
                     SQ P54955 178-292
        24. NAD-binding domain of HMG-CoA reductase [55035] (1)
            uperfamily
            1. NAD-binding domain of HMG-CoA reductase [55036] (2)
               1. NAD-binding domain of HMG-CoA reductase [55037]
                  1. Human (Homo sapiens) [TaxId: 9606] [55038] (9)
                  2. Pseudomonas mevalonii [TaxId: 32044] [55039] (5)
                     SQ P13702 4-377
        25. Molybdenum cofactor biosynthesis protein C, MoaC [55040] (1)
            uperfamily
            1. Molybdenum cofactor biosynthesis protein C, MoaC [55041] (1)
               1. Molybdenum cofactor biosynthesis protein C, MoaC [55042]
                  1. Escherichia coli [TaxId: 562] [55043] (2)
        26. TRADD, N-terminal domain [55044] (1)
            uperfamily
            1. TRADD, N-terminal domain [55045] (1)
               1. TRADD, N-terminal domain [55046]
                  1. Human (Homo sapiens) [TaxId: 9606] [55047] (2)
        27. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1)
            uperfamily
            1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55049] (2)
               1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55050]
                  1. Escherichia coli [TaxId: 562] [55051] (1)
                  2. Streptomyces coelicolor A3(2) [TaxId: 100226] [82687] (1)
        28. CheY-binding domain of CheA [55052] (1)
            uperfamily
            1. CheY-binding domain of CheA [55053] (2)
               1. CheY-binding domain of CheA [55054]
                  1. Escherichia coli [TaxId: 562] [55055] (6)
                  2. Thermotoga maritima [TaxId: 2336] [110983] (1)
                     SQ Q56310 175-260
                     structurally distinct from the E.coli domain and possesses a different CheY-binding mode
        29. D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1)
            uperfamily
            1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75446] (4)
               1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75447]
                  1. Escherichia coli [TaxId: 562] [75448] (3)
                  2. Haemophilus influenzae [TaxId: 727] [82688] (1)
                  3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75449] (2)
                  4. Thermus thermophilus [TaxId: 274] [110984] (3)
                     SQ Q72J47
        30. Killer toxin KP6 alpha-subunit [55056] (1)
            uperfamily
            1. Killer toxin KP6 alpha-subunit [55057] (1)
               1. Killer toxin KP6 alpha-subunit [55058]
                  1. Smut fungus (Ustilago maydis) [TaxId: 5270] [55059] (1)
        31. Hypothetical protein VC0424 [89946] (1)
            uperfamily
            1. Hypothetical protein VC0424 [89947] (1)
               1. Hypothetical protein VC0424 [89948]
                  1. Vibrio cholerae [TaxId: 666] [89949] (1)
        32. Hypothetical protein TT1725 [103007] (1)
            uperfamily
            1. Hypothetical protein TT1725 [103008] (1)
               1. Hypothetical protein TT1725 [103009]
                  1. Thermus thermophilus [TaxId: 274] [103010] (1)
                     structural genomics
        33. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82689] (1)
            the last strand of the fold is flipped away and involved in oligomerisation
            uperfamily
            1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82690] (1)
               1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82691]
                  1. Escherichia coli [TaxId: 562] [82692] (14)
        34. GHMP Kinase, C-terminal domain [55060] (7)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. Galactokinase [103011] (3)
               1. Galactokinase [103012]
                  1. Lactococcus lactis [TaxId: 1358] [103013] (1)
                  2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103014] (1)
                  3. Human (Homo sapiens) [TaxId: 9606] [117981] (1)
                     SQ P51570
            2. Homoserine kinase [55061] (1)
               1. Homoserine kinase [55062]
                  1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55063] (5)
            3. Mevalonate kinase [75450] (2)
               1. Mevalonate kinase [75451]
                  1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75452] (2)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [75453] (2)
            4. Phosphomevalonate kinase (PMK) [75454] (1)
               1. Phosphomevalonate kinase (PMK) [75455]
                  1. Streptococcus pneumoniae r6 [TaxId: 171101] [75456] (1)
            5. Mevalonate 5-diphosphate decarboxylase [64281] (1)
               1. Mevalonate 5-diphosphate decarboxylase [64282]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64283] (1)
            6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89950] (2)
               1. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89951]
                  1. Thermus thermophilus [TaxId: 274] [89952] (1)
                  2. Escherichia coli [TaxId: 562] [103015] (1)
            7. Early switch protein XOL-1 [89953] (1)
               lost the ATP-binding site
               1. Early switch protein XOL-1 [89954]
                  primary determinant of sexual fate in C. elegans
                  1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89955] (1)
        35. Translational regulator protein regA [55064] (1)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. Translational regulator protein regA [55065] (1)
               1. Translational regulator protein regA [55066]
                  1. Bacteriophage T4 [TaxId: 10665] [55067] (1)
        36. Peptide methionine sulfoxide reductase [55068] (1)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. Peptide methionine sulfoxide reductase [55069] (3)
               1. Peptide methionine sulfoxide reductase [55070]
                  1. Cow (Bos taurus) [TaxId: 9913] [55071] (2)
                  2. Escherichia coli [TaxId: 562] [55072] (2)
                  3. Mycobacterium tuberculosis [TaxId: 1773] [89956] (1)
        37. Nucleotide cyclase [55073] (2)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. Adenylyl and guanylyl cyclase catalytic domain [55074] (5)
               Pfam 00211
               structurally similar to the "palm" domain of DNA/RNA polymerase superfamily
               1. Type II adenylyl cyclase C2 domain [55075]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [55076] (5)
                     SQ P26769 879-1077
               2. Adenylyl cyclase VC1, domain C1a [55077]
                  1. Dog (Canis familiaris) [TaxId: 9615] [55078] (11)
                     SQ P30803 458-646
               3. Adenylyl cyclase IIC1, domain C2a [55079]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [55080] (7)
               4. Receptor-type monomeric adenylyl cyclase [55081]
                  1. Trypanosome (Trypanosoma brucei), different isoform [TaxId: 5691] [55082] (2)
               5. Adenylate cyclase CyaC [117982]
                  1. Spirulina platensis [TaxId: 118562] [117983] (6)
                     SQ O32393 1004-1200
            2. GGDEF domain [117984] (1)
               Pfam 00990; less decorated than the adenylyl/guanylyl cyclase domain
               1. Response regulator PleD, C-terminal domain [117985]
                  Diguanylate cyclase
                  1. Caulobacter crescentus [TaxId: 155892] [117986] (3)
                     SQ Q9A5I5
        38. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55084] (2)
               1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55085]
                  1. Escherichia coli [TaxId: 562] [55086] (19)
                     SQ P26281
                  2. Haemophilus influenzae [TaxId: 727] [55087] (1)
        39. Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1)
            common fold is elaborated with additional secondary structures
            uperfamily
            1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69743] (1)
               1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69744]
                  1. Archaeon Methanopyrus kandleri [TaxId: 2320] [69745] (1)
        40. MTH1187/YkoF-like [89957] (2)
            uperfamily
            1. MTH1187-like [89958] (5)
               Pfam 01910; two domains form a single beta-sheet dimer; two dimers pack sheet-to-sheet in a tetramer; contains extra C-terminal helix
               1. Hypothetical protein MTH1187 [89959]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89960] (1)
               2. Hypothetical protein YB1001C [89961]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89962] (1)
               3. Hypothetical protein TM0486 [110985]
                  1. Thermotoga maritima [TaxId: 2336] [110986] (1)
                     SQ Q9WYV6
               4. Hypothetical protein BC0424 [143405]
                  1. Bacillus cereus [TaxId: 1396] [143406] (2)
                     SQ Q81IG4 1-101
               5. Hypothetical protein SP2199 [143407]
                  1. Streptococcus pneumoniae [TaxId: 1313] [143408] (4)
                     SQ Q97N67 1-90
            2. Putative thiamin/HMP-binding protein YkoF [110987] (1)
               duplication: one subunit consists of two domains assembled as in the MHT1178-like dimer
               1. Putative thiamin/HMP-binding protein YkoF [110988]
                  1. Bacillus subtilis [TaxId: 1423] [110989] (3)
                     SQ O34911
        41. Methyl-coenzyme M reductase subunits [55088] (2)
            each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
            uperfamily
            1. Methyl-coenzyme M reductase gamma chain [55089] (3)
               1. Methyl-coenzyme M reductase gamma chain [55090]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55091] (5)
                  2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55092] (1)
                  3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55093] (1)
            2. Methyl-coenzyme M reductase alpha and beta chain N-terminal domain [55094] (6)
               C-terminal domain is all-alpha
               1. Alpha chain [55095]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55096] (5)
                  2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55097] (1)
                  3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55098] (1)
               2. Beta chain [55099]
                  1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55100] (5)
                  2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55101] (1)
                  3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55102] (1)
        42. FAD-linked oxidases, C-terminal domain [55103] (4)
            duplication: contains two subdomains of this fold
            uperfamily
            1. Vanillyl-alcohol oxidase-like [55104] (2)
               1. Vanillyl-alcohol oxidase [55105]
                  1. Fungus (Penicillium simplicissimum) [TaxId: 69488] [55106] (16)
                     SQ P56216
               2. Flavoprotein subunit of p-cresol methylhydroxylase [55107]
                  the other subunit is a short-chain cytochrome c
                  1. Pseudomonas putida [TaxId: 303] [55108] (5)
            2. D-lactate dehydrogenase [55109] (1)
               1. D-lactate dehydrogenase [55110]
                  1. Escherichia coli [TaxId: 562] [55111] (1)
            3. Cholesterol oxidase [64284] (1)
               1. Cholesterol oxidase [64285]
                  1. Brevibacterium sterolicum [TaxId: 1702] [64286] (2)
            4. Cytokinin dehydrogenase 1 [110990] (1)
               1. Cytokinin dehydrogenase 1 [110991]
                  1. Maize (Zea mays) [TaxId: 4577] [110992] (4)
                     SQ Q9T0N8
        43. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1)
            duplication: contains two subdomains of this fold
            uperfamily
            1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55113] (3)
               1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55114]
                  1. Archaeon Methanopyrus kandleri [TaxId: 2320] [55115] (17)
                  2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75457] (1)
                  3. Archaeon Methanosarcina barkeri [TaxId: 2208] [75458] (1)
        44. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1)
            duplication: contains two subdomains of this fold
            uperfamily
            1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55117] (1)
               1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55118]
                  1. Pig (Sus scrofa) [TaxId: 9823] [55119] (1)
        45. Nitrite/Sulfite reductase N-terminal domain-like [55124] (2)
            duplication: contains two subdomains of this fold
            uperfamily
            1. Duplicated SiR/NiR-like domains 1 and 3 [55125] (3)
               1. Sulfite reductase, domains 1 and 3 [55126]
                  1. Escherichia coli [TaxId: 562] [55127] (12)
               2. Ferredoxin--nitrite reductase, NIR [160332]
                  1. Spinach (Spinacia oleracea) [TaxId: 3562] [160333] (2)
                     SQ P05314 378-462! SQ P05314 54-206
               3. Sulfite reductase NirA [160334]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [160335] (8)
                     SQ P71753 10-161! SQ P71753 327-406
            2. DsrA/DsrB N-terminal-domain-like [160336] (4)
               Dissimilatory sulfite reductase is a heterodimer of homologous DsrA and DsrB subunits, the assembly of which is similar to the architecture of duplicated sulfite reductase CysI
               1. Dissimilatory sulfite reductase subunit alpha, DsrA [160337]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [160338] (2)
                     SQ Q59109 2-418
                  2. Desulfovibrio vulgaris [TaxId: 881] [160339] (2)
                     SQ P45574 2-437
               2. Dissimilatory sulfite reductase subunit beta, DsrB [160340]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [160341] (2)
                     SQ Q59110 4-122
                  2. Desulfovibrio vulgaris [TaxId: 881] [160342] (2)
                     SQ P45575 2-381
        46. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82693] (1)
            duplication: the N- and C-terminal halves of the whole proteins are structurally similar; each half contains two domains of this fold
            uperfamily
            1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82694] (1)
               1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82695]
                  PN2 and PC2 subdomains are interrupted by the inserted subdomains DN and DC, respectively
                  1. Escherichia coli [TaxId: 562] [82696] (6)
        47. YajQ-like [89963] (1)
            duplication: consists of two domains of this fold swapped with their N-terminal strands
            uperfamily
            1. YajQ-like [89964] (1)
               1. Hypothetical protein HI1034 [89965]
                  1. Haemophilus influenzae [TaxId: 727] [89966] (1)
        48. eIF-2-alpha, C-terminal domain [110993] (1)
            uperfamily
            1. eIF-2-alpha, C-terminal domain [110994] (2)
               1. eIF-2-alpha, C-terminal domain [110995]
                  1. Human (Homo sapiens) [TaxId: 9606] [110996] (1)
                     SQ P05198
                  2. Sulfolobus solfataricus [TaxId: 2287] [143409] (3)
                     SQ Q97Z79 176-264
        49. Sporulation related repeat [110997] (1)
            duplication: one domain contains two repeats of similar sequence and structure
            uperfamily
            1. Sporulation related repeat [110998] (1)
               Pfam 05036; SPOR
               1. Cell division protein FtsN [110999]
                  1. Escherichia coli [TaxId: 562] [111000] (1)
                     SQ P29131 243-319
        50. CRISPR-associated protein [117987] (1)
            duplication: contains two subdomains of this fold
            uperfamily
            1. CRISPR-associated protein [117988] (1)
               1. Hypothetical protein TTHB192 [117989]
                  1. Thermus thermophilus [TaxId: 274] [117990] (1)
                     SQ Q53WG9
        51. YbeD/HP0495-like [117991] (2)
            uperfamily
            1. YbeD-like [117992] (1)
               Pfam 04359; DUF493
               1. Hypothetical protein ybeD [117993]
                  1. Escherichia coli [TaxId: 562] [117994] (1)
                     SQ P0A8J4
            2. HP0495-like [160343] (1)
               PfamB 045675
               1. Hypothetical protein HP0495 [160344]
                  1. Helicobacter pylori [TaxId: 210] [160345] (2)
                     SQ O25237 1-86
        52. DOPA-like [143410] (1)
            probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
            uperfamily
            1. DOPA dioxygenase-like [143411] (1)
               Pfam 08883
               1. Putative dioxygenase BxeB0224 [143412]
                  Bxeno_B2751
                  1. Burkholderia xenovorans [TaxId: 36873] [143413] (6)
                     SQ Q13JM0 1-115
        53. CcmK-like [143414] (1)
            contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
            uperfamily
            1. CcmK-like [143415] (3)
               Pfam 00936; BMC domain
               1. Major carboxysome shell protein 1A, CsoS1A [143416]
                  1. Halothiobacillus neapolitanus [TaxId: 927] [143417] (2)
                     SQ P45689 5-97
               2. Carboxysome shell protein CcmK4 [143418]
                  1. Synechocystis sp. PCC 6803 [TaxId: 1148] [143419] (9)
                     SQ P73407 3-106
               3. Carboxysome shell protein CcmK2 [143420]
                  1. Synechocystis sp. PCC 6803 [TaxId: 1148] [143421] (12)
                     SQ P72761 1-101
        54. Transposase IS200-like [143422] (1)
            contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
            uperfamily
            1. Transposase IS200-like [143423] (3)
               Pfam 01797
               1. Putative transposase SSO1474 [143424]
                  1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [143425] (4)
                     SQ Q97Y68 2-131
               2. ISHP608 transposase [143426]
                  1. Helicobacter pylori [TaxId: 210] [143427] (14)
                     SQ Q933Z0 4-133
               3. Putative transposase DR0177 [143428]
                  1. Deinococcus radiodurans [TaxId: 1299] [143429] (2)
                     SQ Q9RXX8 1-130
        55. TTP0101/SSO1404-like [143430] (1)
            contains extra C-terminal beta-strand that integrates into the beta-sheet of the other subunit in the homodimer, a probable biological unit of this superfamily
            uperfamily
            1. TTP0101/SSO1404-like [143431] (3)
               Pfam 02647; DUF196; this family includes recent structure of SSO1404 (PDB entry 2IVY)
               1. Hypothetical protein TTP0101 (TT1823) [143432]
                  1. Thermus thermophilus [TaxId: 274] [143433] (1)
                     SQ Q746F4 2-83
               2. Hypothetical protein PF1117 [160346]
                  1. Pyrococcus furiosus [TaxId: 2261] [160347] (1)
                     SQ Q8U1T8 1-84
               3. Hypothetical protein SSO1404 [160348]
                  predicted DNA repair associated protein
                  1. Sulfolobus solfataricus [TaxId: 2287] [160349] (2)
                     SQ Q97YC2 2-89
        56. Rnp2-like [160350] (1)
            contains extra C-terminal helix
            1. Rpp14/Pop5-like [160351] (2)
               Pfam 01900
               1. RNase P protein component 2, Rnp2 [160352]
                  1. Pyrococcus horikoshii [TaxId: 53953] [160353] (2)
                     SQ O59150 3-120
                  2. Pyrococcus furiosus [TaxId: 2261] [160354] (5)
                     SQ Q8U151 15-120
        57. Bacterial polysaccharide co-polymerase-like [160355] (1)
            Decorated common fold with extra helical regions, which facilitate oligomerization
            1. FepE-like [160356] (3)
               the ferredoxin-like fold resides mainly on in the N-terminal part that corresponds to Pfam 02706 (Wzz)
               1. Chain length determinant protein WzzB [160357]
                  1. Salmonella typhimurium [TaxId: 90371] [160358] (5)
                     SQ Q04866 54-292
               2. Lipopolysaccharide biosynthesis protein WzzE [160359]
                  1. Escherichia coli [TaxId: 562] [160360] (8)
                     SQ P0AG01 54-318
               3. Enterochelin transport protein FepE [160361]
                  1. Escherichia coli [TaxId: 562] [160362] (12)
                     SQ Q8XBV8 64-330! SQ Q8XBV8 65-330
        58. MTH889-like [160363] (1)
            assembles into hexameric ring-like structures with the formation of a singe beta-barrel sheet of 24 strands
            1. MTH889-like [160364] (2)
               Pfam 02680; DUF211, COG1888
               1. Uncharacterized protein MTH889 [160365]
                  1. Methanobacterium thermoautotrophicum [TaxId: 145262] [160366] (7)
                     SQ O26975 3-95
               2. Uncharacterized protein AF1549 [160367]
                  1. Archaeoglobus fulgidus [TaxId: 2234] [160368] (14)
                     SQ O28723 1-91
        59. Ribosomal protein L10-like [160369] (1)
            consists of globular N-terminal domain, structurally similar to NDK, and the L7/L12-binding C-terminal alpha-helical tail
            1. Ribosomal protein L10-like [160370] (1)
               Pfam 00466; covers globular domain only
               1. Ribosomal protein L10 [160371]
                  see also scop_pr 64661 for a partial structure in the ribosome
                  1. Thermotoga maritima [TaxId: 2336] [160372] (3)
                     SQ P29394 1-177
   130. PurS-like [109622] (1)
        consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
        1. PurS-like [82697] (2)
           segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit
           uperfamily
           1. PurS subunit of FGAM synthetase [82698] (3)
              1. PurS subunit of FGAM synthetase [82699]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [82700] (1)
                    MTH169
                 2. Bacillus subtilis [TaxId: 1423] [111001] (2)
                    SQ P12049 # YexA
                 3. Thermotoga maritima [TaxId: 2336] [117995] (1)
                    SQ Q9X0X1
           2. FGAM synthase PurL, PurS-like domain [111002] (1)
              duplication: consists of 2 structural repeats of the PurS subunit fold, assembled like the PurS dimer
              1. FGAM synthase PurL, PurS-like domain [111003]
                 1. Salmonella typhimurium [TaxId: 90371] [111004] (1)
                    SQ P74881
   131. RplX-like [160373] (1)
        beta(2)-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 213; some structural similarity to the PurS subunit/repeat (scop_cf 109622)
        1. RplX-like [160374] (1)
           similar structural motif to the Ribosomal S24e family (scop_fa 117786); possible structural permutation
           1. RplX-like [160375] (1)
              Pfam 01911
              1. Ribosomal protein LX, RplX [160376]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [160377] (1)
                    SQ O27647 1-78
   132. Dystroglycan, domain 2 [111005] (1)
        beta-alpha-beta-X-beta(2)-alpha(2)-beta; antiparallel beta-sheet, order 24153; topological similarity to the ferredoxin-like fold (scop_cf 54861)
        1. Dystroglycan, domain 2 [111006] (1)
           uperfamily
           1. Dystroglycan, domain 2 [111007] (1)
              1. Dystroglycan, domain 2 [111008]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111009] (1)
                    SQ Q62165 58-303
   133. Pseudouridine synthase [100877] (1)
        consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
        1. Pseudouridine synthase [55120] (4)
           the active site is the most conserved structural region of the superfamily and is located between the subdomains
           uperfamily
           1. Pseudouridine synthase I TruA [55121] (1)
              1. Pseudouridine synthase I TruA [55122]
                 1. Escherichia coli [TaxId: 562] [55123] (10)
           2. Pseudouridine synthase II TruB [69746] (5)
              contains C-terminal PUA domain
              1. Pseudouridine synthase II TruB [69747]
                 1. Escherichia coli [TaxId: 562] [69748] (3)
                 2. Thermotoga maritima [TaxId: 2336] [103016] (8)
                 3. Mycobacterium tuberculosis [TaxId: 1773] [103017] (1)
                 4. Archaeon Pyrococcus furiosus [TaxId: 2261] [143434] (4)
                    SQ Q7LWY0 5-249
                 5. Archaeon Methanococcus jannaschii [TaxId: 2190] [143435] (1)
                    SQ Q57612 17-246
           3. Pseudouridine synthase RsuA/RluD [75459] (4)
              contains N-terminal alpha-L RNA-binding motif
              1. Ribosomal small subunit pseudouridine 516 synthase RsuA [75460]
                 1. Escherichia coli [TaxId: 562] [75461] (3)
                 2. Haemophilus influenzae [TaxId: 727] [103018] (1)
              2. Ribosomal large subunit pseudouridine synthase D, RluD [103019]
                 1. Escherichia coli [TaxId: 562] [103020] (3)
                    SQ P33643
              3. Ribosomal large subunit pseudouridine synthase C, RluC [111010]
                 1. Escherichia coli [TaxId: 562] [111011] (1)
                    SQ P23851
           4. tRNA pseudouridine synthase TruD [103021] (1)
              natural circular permutation in the catalytic domain; insertion of the family-specific alpha+beta subdomain
              1. tRNA pseudouridine synthase TruD [103022]
                 1. Escherichia coli [TaxId: 562] [103023] (3)
                    SQ Q57261
                    family-specific insert subdomain: res. 158-301
   134. SP0830-like [160378] (1)
        duplication: two beta-alpha-beta(2)-alpha-beta-alpha motifs are organized in ferredoxin-like subdomains swapped with the extra C-terminal helices
        1. SP0830-like [160379] (1)
           1. SP0830-like [160380] (1)
              Pfam 08002; DUF1697
              1. Hypothetical protein SP0830 [160381]
                 1. Streptococcus pneumoniae [TaxId: 1313] [160382] (4)
                    SQ Q97RI5 1-180
   135. Folate-binding domain [103024] (1)
        duplication: consists of two beta(2)-alpha-beta(3)-alpha subdomains swapped with the first strands
        1. Folate-binding domain [103025] (2)
           some topological similarity to Formylmethanofuran:tetrahydromethanopterin formyltransferase
           uperfamily
           1. Aminomethyltransferase folate-binding domain [103026] (5)
              1. N,N-dimethylglycine oxidase domain 3 [103027]
                 1. Arthrobacter globiformis [TaxId: 1665] [103028] (3)
              2. Hypothetical protein YgfZ, N-terminal domain [103029]
                 1. Escherichia coli [TaxId: 562] [103030] (2)
                    SQ P39179
              3. Glycine cleavage system T protein, GcvT [111012]
                 1. Thermotoga maritima [TaxId: 2336] [111013] (4)
                    SQ Q9WY54
                 2. Escherichia coli [TaxId: 562] [111014] (1)
                    SQ P27248
                 3. Pyrococcus horikoshii [TaxId: 53953] [117996] (1)
                    SQ O58888
           2. TrmE formyl-THF-binding domain [117997] (1)
              dimeric biological unit; one subunit domain corresponds to one "unswapped" subdomain of the other family
              1. TrmE formyl-THF-binding domain [117998]
                 1. Thermotoga maritima [TaxId: 2336] [117999] (2)
                    SQ Q9WYA4
   136. THUMP domain [143436] (1)
        contains mixed 8-stranded beta-sheet, folded into a half-barrel and covered with 4 helices on the outside; order 32148756; strands 5, 6 and 7 are parallel
        1. THUMP domain-like [143437] (3)
           predicted RNA-binding function
           uperfamily
           1. THUMP domain [143438] (2)
              Pfam 02926
              1. Thiamine biosynthesis protein ThiI, N-terminal domain [143439]
                 1. Bacillus anthracis [TaxId: 1392] [143440] (1)
                    SQ Q81KU0 3-173
              2. Hypothetical protein PH1313, N-terminal domain [143441]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143442] (2)
                    SQ O59053 1-175
           2. PAE0736-like [143443] (1)
              orphan protein; rudiment, disulfide-stabilized form of THUMP domain fold
              1. Hypothetical protein PAE0736 [143444]
                 1. Pyrobaculum aerophilum [TaxId: 13773] [143445] (2)
                    SQ Q8ZYK2 1-98
           3. Minimal THUMP [160383] (1)
              subfamily of Pfam 02926; 4 stranded mixed beta-sheet with 2 helices on one side and a crossover loop on the other side
              1. THUMP domain-containing protein 1 [160384]
                 1. Human (Homo sapiens) [TaxId: 9606] [160385] (1)
                    SQ Q9NXG2 170-254
   137. AMMECR1-like [143446] (1)
        duplication; contains two beta(2)-alpha-beta(2) structural repeats, swapped with C-terminal strands; extra N-terminal helix and C-terminal strand
        1. AMMECR1-like [143447] (1)
           uperfamily
           1. AMMECR1-like [143448] (3)
              Pfam 01871
              1. Hypothetical protein MM0484 [143449]
                 1. Methanosarcina mazei [TaxId: 2209] [143450] (4)
                    SQ Q8PZK8 1-199
              2. Hypothetical protein PH0010 [143451]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143452] (1)
                    SQ O57770 3-205
              3. Hypothetical protein ST0229 [143453]
                 1. Sulfolobus tokodaii [TaxId: 111955] [143454] (1)
                    SQ Q976G0 3-227
   138. NosL/MerB-like [160386] (1)
        unusual fold; comprises two structural repeats of beta(2)-alpha-beta motifs, forming separate beta-sheets; probable duplication
        1. NosL/MerB-like [160387] (2)
           1. NosL-like [160388] (1)
              Pfam 05573
              1. NosL [160389]
                 1. Achromobacter cycloclastes [TaxId: 223] [160390] (2)
                    SQ O68481 53-178
           2. MerB-like [160391] (1)
              Pfam 03243
              1. Alkylmercury lyase MerB [160392]
                 1. Escherichia coli [TaxId: 562] [160393] (1)
                    SQ P77072 81-212
   139. YehU-like [118000] (1)
        beta-alpha(2)-beta(2)-alpha; 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
        1. YehU-like [118001] (1)
           uperfamily
           1. YehU-like [118002] (1)
              Pfam 06794; UPF0270
              1. Hypothetical UPF0270 protein PA3463 [118003]
                 1. Pseudomonas aeruginosa [TaxId: 287] [118004] (1)
                    SQ Q9HYE3
   140. Hypothetical protein YwqG [103031] (1)
        duplication: contains two similar beta-x-beta(4) motifs swapped with the first strands
        1. Hypothetical protein YwqG [103032] (1)
           uperfamily
           1. Hypothetical protein YwqG [103033] (1)
              1. Hypothetical protein YwqG [103034]
                 1. Bacillus subtilis [TaxId: 1423] [103035] (1)
   141. VC0467-like [143455] (1)
        complex fold; contains bifurcated beta-sheet structure folded into pseudo barrel
        1. VC0467-like [143456] (1)
           uperfamily
           1. VC0467-like [143457] (5)
              Pfam 02622; DUF179
              1. Hypothetical protein DIP2367 [143458]
                 1. Corynebacterium diphtheriae [TaxId: 1717] [143459] (2)
                    SQ Q6NEA9 1-191! SQ Q6NEA9 1-193
              2. Hypothetical protein HD1794 [143460]
                 1. Haemophilus ducreyi [TaxId: 730] [143461] (1)
                    SQ Q7VKS7 1-186
              3. Hypothetical protein VC0467 [143462]
                 1. Vibrio cholerae [TaxId: 666] [143463] (2)
                    SQ Q9KUP8 1-177! SQ Q9KUP8 1-179
              4. Hypothetical protein ACIAD0353 [143464]
                 1. Acinetobacter sp. ADP1 [TaxId: 62977] [143465] (1)
                    SQ Q6FF54 5-179
              5. Hypotheical protein SO3346 [143466]
                 1. Shewanella oneidensis [TaxId: 70863] [143467] (1)
                    SQ Q8EBZ9 1-187
   142. Lesion bypass DNA polymerase (Y-family), little finger domain [100878] (1)
        beta-alpha-beta(2)-alpha-beta; antiparallel beta-sheet: order 1423; "reversed" ferredoxin-like topology
        1. Lesion bypass DNA polymerase (Y-family), little finger domain [100879] (1)
           uperfamily
           1. Lesion bypass DNA polymerase (Y-family), little finger domain [100880] (7)
              1. DinB homolog (DBH) [100881]
                 1. Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287] [100882] (62)
                 2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [100883] (2)
                 3. Sulfolobus acidocaldarius Brock et al. 1972 (Sulfolobus acidocaldarius) [TaxId: 2285] [160394] (3)
              2. DNA polymerase eta [100884]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [100885] (5)
              3. DNA polymerase IV [103036]
                 1. Escherichia coli [TaxId: 562] [103037] (1)
              4. DNA polymerase iota [111015]
                 1. Human (Homo sapiens) [TaxId: 9606] [111016] (8)
                    SQ Q9UNA4
              5. DNA polymerase kappa [111017]
                 1. Human (Homo sapiens) [TaxId: 9606] [111018] (1)
                    SQ Q9UBT6 71-517
   143. ImmE5-like [143468] (1)
        alpha-beta(2)-alpha-beta; 2 layers, a/b; antiparallel beta-sheet, order 213
        1. ImmE5-like [143469] (1)
           uperfamily
           1. ImmE5-like [143470] (1)
              1. Colicin E5 immunity protein ImmE5 [143471]
                 1. Escherichia coli [TaxId: 562] [143472] (2)
                    SQ P13476 1-83
   144. Ribosomal protein L30p/L7e [55128] (1)
        core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity to the ferredoxin-like fold
        1. Ribosomal protein L30p/L7e [55129] (1)
           uperfamily
           1. Ribosomal protein L30p/L7e [55130] (4)
              1. Prokaryotic ribosomal protein L30 [55131]
                 short-chain member of the family
                 1. Thermus thermophilus [TaxId: 274] [55132] (11)
                 2. Escherichia coli [TaxId: 562] [160395] (29)
                    SQ P02430 1-58
                 3. Deinococcus radiodurans [TaxId: 1299] [160396] (6)
                    SQ Q9RSL0 1-55
              2. Archaeal L30 (L30a) [55133]
                 long-chain member of the family; contains additional C-terminal (sub)domain
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [55134] (40)
                    SQ P14121
   145. Chorismate lyase-like [64287] (1)
        duplication of alpha(2)-beta(3) motif; antiparallel beta sheet, order 123654
        1. Chorismate lyase-like [64288] (3)
           uperfamily
           1. Chorismate lyase [64289] (1)
              1. Chorismate lyase [64290]
                 1. Escherichia coli [TaxId: 562] [64291] (10)
                    SQ P26602
           2. UTRA domain [143473] (10)
              Pfam 07702
              1. Probable transcriptional regulator PhnF, receptor domain [143474]
                 1. Escherichia coli [TaxId: 562] [143475] (2)
                    SQ P16684 84-241
              2. Transcriptional regulator EF1328 [160397]
                 1. Enterococcus faecalis [TaxId: 1351] [160398] (4)
                    SQ Q835P8 93-235
              3. Histidine utilization repressor HutC [160399]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [160400] (8)
                    SQ Q87UX0 109-249
              4. Trehalose operon transcriptional repressor TreR [160401]
                 formerly YfxA
                 1. Bacillus subtilis [TaxId: 1423] [160402] (1)
                    SQ P39796 95-238
              5. Putative transcriptional regulator BB3683 [160403]
                 1. Bordetella bronchiseptica [TaxId: 518] [160404] (4)
                    SQ Q7WD95 98-259
              6. Hypothetical protein SA0254 [160405]
                 1. Staphylococcus aureus [TaxId: 1280] [160406] (2)
                    SQ Q7A7U1 73-233
              7. Hypothetical transcriptional regulator YurK [160407]
                 1. Bacillus subtilis [TaxId: 1423] [160408] (2)
                    SQ O32152 86-238
              8. Putative transcriptional regulator SCO6256 [160409]
                 1. Streptomyces coelicolor [TaxId: 1902] [160410] (1)
                    SQ Q9RKT6 66-245
              9. Transcriptional regulator Cgl0157/Cg0196 [160411]
                 1. Corynebacterium glutamicum [TaxId: 1718] [160412] (3)
                    SQ Q8NTZ4 106-253
              10. Transcriptional regulator YydK [160413]
                  1. Bacillus subtilis [TaxId: 1423] [160414] (3)
                     SQ Q45591 89-233
           3. AF1396-like [160415] (1)
              Pfam 01947; DUF98
              1. Hypothetical protein AF1396 [160416]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [160417] (6)
                    SQ O28875 1-160
   146. YdfO-like [160418] (1)
        duplication: two alpha(2)-beta(3) motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456
        1. YdfO-like [160419] (1)
           1. YdfO-like [160420] (1)
              Pfam 07166; DUF1398
              1. Hypothetical protein YdfO [160421]
                 1. Escherichia coli [TaxId: 562] [160422] (1)
                    SQ P76156 2-128
   147. TM1622-like [143476] (1)
        alpha-beta(3)-alpha-beta(4)-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 1237654
        1. TM1622-like [143477] (1)
           uperfamily
           1. TM1622-like [143478] (1)
              1. Hypothetical protein TM1622 [143479]
                 annotated in PDB as GTP binding regulator
                 1. Thermotoga maritima [TaxId: 2336] [143480] (1)
                    SQ Q9X1V7 25-154
   148. BH3703-like [160423] (1)
        alpha-beta(3)-alpha-beta(2)-alpha(2); antiparallel beta-sheet, order:32145; duplication: two alpha-beta(2) structural repeats are arranged with pseudo twofold symmetry
        1. BH3703-like [160424] (1)
           1. BH3703-like [160425] (1)
              Pfam 04634; DUF600
              1. Uncharacterized protein BH3703 [160426]
                 1. Bacillus halodurans [TaxId: 86665] [160427] (2)
                    SQ Q9K6M5 1-166
   149. Probable bacterial effector-binding domain [55135] (1)
        duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
        1. Probable bacterial effector-binding domain [55136] (4)
           uperfamily
           1. Gyrase inhibitory protein GyrI (SbmC, YeeB) [75462] (1)
              1. Gyrase inhibitory protein GyrI (SbmC, YeeB) [75463]
                 1. Escherichia coli [TaxId: 562] [75464] (1)
           2. Multidrug-binding domain of transcription activator BmrR [55137] (1)
              1. Multidrug-binding domain of transcription activator BmrR [55138]
                 1. Bacillus subtilis [TaxId: 1423] [55139] (9)
                    SQ P39075
           3. Rob transcription factor, C-terminal domain [55140] (1)
              1. Rob transcription factor, C-terminal domain [55141]
                 1. Escherichia coli [TaxId: 562] [55142] (1)
           4. SOUL heme-binding protein [143481] (1)
              Pfam 04832
              1. Heme-binding protein 1 [143482]
                 p22HBP
                 1. Mouse (Mus musculus) [TaxId: 10090] [143483] (2)
                    SQ Q9R257 1-190! SQ Q9R257 7-190
   150. CheC-like [103038] (1)
        duplication: tandem repeat of two intertwined alpha-beta-(X)-beta(2) motifs
        1. CheC-like [103039] (1)
           uperfamily
           1. CheC-like [103040] (2)
              Pfam 04509
              1. Chemotaxis protein CheX [103041]
                 1. Thermotoga maritima [TaxId: 2336] [103042] (2)
                    SQ Q9X1V3
                    TM1618
              2. Chemotaxis protein CheC [118005]
                 1. Thermotoga maritima [TaxId: 2336] [118006] (3)
                    SQ Q9X006 # TM0904
   151. LigT-like [55143] (1)
        duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
        1. LigT-like [55144] (4)
           uperfamily
           1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [55145] (1)
              1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [55146]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [55147] (3)
           2. 2'-5' RNA ligase LigT [89967] (1)
              1. 2'-5' RNA ligase LigT [89968]
                 1. Thermus thermophilus [TaxId: 274] [89969] (1)
                    TT0787
           3. 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [103043] (1)
              1. 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [103044]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [103045] (1)
           4. Atu0111-like [143484] (1)
              1. Putative phosphoesterase Atu0111 [143485]
                 1. Agrobacterium tumefaciens [TaxId: 358] [143486] (1)
                    SQ Q8UJ27 6-237
   152. Pepsin inhibitor-3 [55148] (1)
        duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
        1. Pepsin inhibitor-3 [55149] (1)
           uperfamily
           1. Pepsin inhibitor-3 [55150] (1)
              1. Pepsin inhibitor-3 [55151]
                 1. Pig roundworm (Ascaris suum) [TaxId: 6253] [55152] (2)
   153. CYTH-like phosphatases [55153] (1)
        duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
        1. CYTH-like phosphatases [55154] (2)
           uperfamily
           1. mRNA triphosphatase CET1 [55155] (1)
              Pfam 02940
              1. mRNA triphosphatase CET1 [55156]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55157] (2)
           2. CYTH domain [118007] (4)
              Pfam 01928
              1. Hypothetical protein PF0863 [118008]
                 1. Pyrococcus furiosus [TaxId: 2261] [118009] (1)
                    SQ Q8U2H2 2-171
              2. Putative adenylate cyclase VP1760 [143487]
                 1. Vibrio parahaemolyticus [TaxId: 670] [143488] (2)
                    SQ Q87NV8 8-181
              3. Hypothetical protein NE1496 [143489]
                 shape-shifter; open beta-sheet instead of beta-barrel
                 1. Nitrosomonas europaea [TaxId: 915] [143490] (2)
                    SQ Q82UI9 2-151
              4. Thiamine-triphosphatase (ThTPase) [160428]
                 1. Mouse (Mus musculus) [TaxId: 10090] [160429] (1)
                    SQ Q8JZL3 2-224
   154. Antiparallel beta/alpha barrel (PT-barrel) [143491] (1)
        tandem repeat of five alpha(2)-beta(2) motifs; antiparallel beta-sheet barrel, closed; n=10, S=10; order 123456789A; there is a channel along the barrel axis
        1. Prenyltransferase-like [143492] (1)
           the barrel channel harbours the substrate-binding site
           uperfamily
           1. Prenyltransferase-like [143493] (1)
              1. Aromatic prenyltransferase [143494]
                 1. Streptomyces sp. CL190 [TaxId: 93372] [143495] (4)
                    SQ Q4R2T2 3-303
   155. eIF1-like [55158] (2)
        beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
        1. eIF1-like [55159] (1)
           uperfamily
           1. eIF1-like [55160] (2)
              1. Eukaryotic translation initiation factor eIF-1 (SUI1) [55161]
                 1. Human (Homo sapiens) [TaxId: 9606] [55162] (1)
              2. YciH [55163]
                 1. Escherichia coli [TaxId: 562] [55164] (1)
        2. TM1457-like [118010] (1)
           forms a homodimer via alpha-helical interface
           uperfamily
           1. TM1457-like [118011] (4)
              Pfam 04327; DUF464
              1. Hypothetical protein TM1457 [118012]
                 1. Thermotoga maritima [TaxId: 2336] [118013] (1)
                    SQ Q9X1G8
              2. Hypothetical protein SAV1646 [160430]
                 1. Staphylococcus aureus [TaxId: 1280] [160431] (2)
                    SQ Q931Q2 1-106
              3. Hypothetical protein SP1106 [160432]
                 1. Streptococcus pneumoniae [TaxId: 1313] [160433] (2)
                    SQ Q97QU3 1-112
              4. Hypothetical protein Smu.848 [160434]
                 1. Streptococcus mutans [TaxId: 1309] [160435] (6)
                    SQ Q8DUQ5 1-111
   156. Hedgehog/DD-peptidase [55165] (1)
        alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
        1. Hedgehog/DD-peptidase [55166] (5)
           zinc-binding motif
           uperfamily
           1. Muramoyl-pentapeptide carboxypeptidase [55167] (1)
              1. Zn2+ DD-carboxypeptidase C-terminal catalytic domain [55168]
                 1. Streptomyces albus G [TaxId: 1962] [55169] (1)
           2. MepA-like [111019] (1)
              1. D-alanyl-D-alanine-endopeptidase MepA [111020]
                 1. Escherichia coli [TaxId: 562] [111021] (2)
                    SQ P14007
           3. VanX-like [111022] (1)
              Pfam 01427
              1. D-Ala-D-Ala dipeptidase VanX [111023]
                 1. Enterococcus faecium [TaxId: 1352] [111024] (1)
                    SQ Q06241
           4. Hedgehog (development protein), N-terminal signaling domain [55170] (2)
              1. Sonic hedgehog [55171]
                 1. Mouse (Mus musculus) [TaxId: 10090] [55172] (3)
              2. Hedgehog [143496]
                 lacks the conserved metal ion-binding site
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143497] (4)
                    SQ Q02936 50-198
           5. VanY-like [160436] (1)
              Pfam 02557
              1. L-alanyl-D-glutamate peptidase Ply [160437]
                 1. Listeria phage A500 [TaxId: 40522] [160438] (3)
                    SQ Q37979 1-148
   157. Alpha-L RNA-binding motif [55173] (1)
        alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
        1. Alpha-L RNA-binding motif [55174] (5)
           common motif in otherwise different folds
           uperfamily
           1. Ribosomal protein S4 [55178] (3)
              has a RRF/tRNA synthetase additional domain-like fold
              1. Ribosomal protein S4 [55179]
                 also contains a Zn-binding N-terminal subdomain
                 1. Thermus thermophilus [TaxId: 274] [55180] (45)
                 2. Bacillus stearothermophilus [TaxId: 1422] [55181] (2)
                 3. Escherichia coli [TaxId: 562] [160439] (26)
                    SQ P0A7V8 1-205
           2. Heat shock protein 15 kD [55182] (1)
              there are additional C-terminal structures
              1. Heat shock protein 15 kD [55183]
                 ribosome-binding protein
                 1. Escherichia coli [TaxId: 562] [55184] (2)
           3. Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [75465] (2)
              there are additional N-terminal structures
              1. Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [75466]
                 1. Thermus thermophilus [TaxId: 274] [82701] (2)
                 2. Bacillus stearothermophilus [TaxId: 1422] [75467] (1)
           4. YbcJ-like [103046] (1)
              overall topological similarity to the TyrRS C-domain
              1. Hypothetical protein YbcJ [103047]
                 1. Escherichia coli [TaxId: 562] [103048] (1)
           5. Pseudouridine synthase RsuA N-terminal domain [75468] (2)
              1. Pseudouridine synthase RsuA N-terminal domain [75469]
                 1. Escherichia coli [TaxId: 562] [75470] (3)
                 2. Haemophilus influenzae [TaxId: 727] [103049] (1)
   158. RRF/tRNA synthetase additional domain-like [55185] (4)
        core: alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
        1. ThrRS/AlaRS common domain [55186] (2)
           putative editing domain found in the N-terminal part of ThrRS, the C-terminal of AlaRS, and as a stand-alone protein; probable circular permutation of LuxS (d.185.1.2)
           uperfamily
           1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain [55187] (2)
              1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain [55188]
                 1. Escherichia coli [TaxId: 562] [55189] (5)
                    SQ P0A8M3
                 2. Staphylococcus aureus [TaxId: 1280] [103050] (2)
           2. AlaX-like [103051] (2)
              1. Hypothetical protein PH0574 [103052]
                 stand-alone protein related to the AlaRS domain
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103053] (7)
                    SQ P27248
              2. AlaX-M trans-editing enzyme, C-terminal domain [160440]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160441] (1)
                    SQ O57848 88-216
        2. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55190] (1)
           uperfamily
           1. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55191] (2)
              1. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55192]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55193] (3)
                 2. Thermus thermophilus [TaxId: 274] [69749] (1)
        3. Ribosome recycling factor, RRF [55194] (1)
           uperfamily
           1. Ribosome recycling factor, RRF [55195] (7)
              1. Ribosome recycling factor, RRF [55196]
                 1. Thermotoga maritima [TaxId: 2336] [55197] (1)
                 2. Thermus thermophilus [TaxId: 274] [55198] (9)
                 3. Escherichia coli [TaxId: 562] [64292] (5)
                 4. Aquifex aeolicus [TaxId: 63363] [64293] (1)
                 5. Vibrio parahaemolyticus [TaxId: 670] [89970] (1)
                 6. Mouse (Mus musculus), mitochondrial [TaxId: 10090] [118014] (1)
                    SQ Q9D6S7 116-186
                 7. Mycobacterium tuberculosis [TaxId: 1773] [160442] (3)
                    SQ Q10794 2-184
        4. General secretion pathway protein M, EpsM [103054] (1)
           uperfamily
           1. General secretion pathway protein M, EpsM [103055] (1)
              1. General secretion pathway protein M, EpsM [103056]
                 1. Vibrio cholerae [TaxId: 666] [103057] (1)
   159. LuxS/MPP-like metallohydrolase [63410] (1)
        core: beta-alpha-beta(2)-alpha(2); 2 layers: alpha/beta
        1. LuxS/MPP-like metallohydrolase [63411] (2)
           Share the same "active site motif" HxxEH located in the first core helix, but differ in one of the zinc-binding residues
           uperfamily
           1. Autoinducer-2 production protein LuxS [64294] (4)
              contains additional N-terminal strand; possible relationships to the putative editing domain of ThrRS (d.67.1)
              1. Autoinducer-2 production protein LuxS [64295]
                 S-ribosylhomocysteinase
                 1. Bacillus subtilis [TaxId: 1423] [64296] (6)
                 2. Deinococcus radiodurans [TaxId: 1299] [64297] (5)
                 3. Haemophilus influenzae [TaxId: 727] [64298] (2)
                 4. Helicobacter pylori [TaxId: 210] [64299] (1)
           2. MPP-like [63412] (10)
              Common fold elaborated with many additional structures; duplication: each family member consists of two similar domains of beta(2)-alpha(2)-beta(2)-alpha(5)-beta structure, but only the N-terminal domain of MPP beta chain binds the catalytic metal
              1. Mitochondrial processing peptidase (MPP) beta chain [64300]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64301] (4)
              2. Mitochondrial processing peptidase (MPP) alpha chain [64302]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64303] (4)
              3. Cytochrome bc1 core subunit 1 [63408]
                 1. Cow (Bos taurus) [TaxId: 9913] [55997] (26)
                    SQ P31800
                 2. Chicken (Gallus gallus) [TaxId: 9031] [55998] (3)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64304] (14)
              4. Cytochrome bc1 core subunit 2 [63409]
                 1. Cow (Bos taurus) [TaxId: 9913] [56000] (12)
                    SQ P23004
                 2. Chicken (Gallus gallus) [TaxId: 9031] [56001] (17)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64305] (14)
              5. Presequence protease 1, PREP1 [143498]
                 duplication: comprises four domains of this fold; similar to the MPP alpha-beta heterodimer
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143499] (8)
                    SQ Q9LJL3 100-356! SQ Q9LJL3 357-624! SQ Q9LJL3 625-882! SQ Q9LJL3 883-1078
              6. Protease III [143500]
                 duplication: comprises four domains of this fold
                 1. Escherichia coli [TaxId: 562] [143501] (4)
                    SQ P05458 24-263! SQ P05458 264-503! SQ P05458 504-732! SQ P05458 733-960
   160. IF3-like [55199] (8)
        beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
        1. Translation initiation factor IF3, C-terminal domain [55200] (1)
           uperfamily
           1. Translation initiation factor IF3, C-terminal domain [55201] (3)
              1. Translation initiation factor IF3, C-terminal domain [55202]
                 1. Bacillus stearothermophilus [TaxId: 1422] [55203] (1)
                 2. Escherichia coli [TaxId: 562] [55204] (1)
                 3. Thermus thermophilus [TaxId: 274] [64306] (1)
        2. YhbY-like [75471] (1)
           uperfamily
           1. YhbY-like [75472] (3)
              Pfam 01985
              1. hypothetical protein YhbY [75473]
                 1. Escherichia coli [TaxId: 562] [75474] (1)
              2. YhbY homologue HI1333 [82702]
                 1. Haemophilus influenzae [TaxId: 727] [82703] (1)
              3. Hypothetical protein SAV1595 [111025]
                 1. Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280] [111026] (1)
                    SQ Q99TQ4
        3. SirA-like [64307] (1)
           uperfamily
           1. SirA-like [88852] (4)
              predicted redox protein, regulator of disulfide bond formation
              1. SirA [64309]
                 implicated in cell division
                 1. Escherichia coli [TaxId: 562] [64310] (1)
                    formerly hypothetical protein YhhP
              2. Hypothetical protein Ta1170/Ta1414 [89971]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89972] (1)
              3. hypothetical protein YedF (EC005) [75475]
                 1. Escherichia coli [TaxId: 562] [75476] (1)
              4. Hypothetical protein TM0983 [69751]
                 1. Thermotoga maritima [TaxId: 2336] [69752] (1)
        4. AlbA-like [82704] (2)
           uperfamily
           1. DNA-binding protein AlbA [82705] (4)
              1. DNA-binding protein AlbA [82706]
                 an archaeal chromatin protein modulated by acetylation, a Sir2 substrate
                 1. Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287] [82707] (4)
                    gene SSO0962 (AlbA1)
                 2. Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287] [103058] (5)
                    gene SSO6877 (AlbA2)
                 3. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103059] (2)
                    gene AF1956
                 4. Archaeon Methanococcus jannaschii [TaxId: 2190] [103060] (1)
           2. Hypothetical protein At2g34160 [111027] (1)
              1. Hypothetical protein At2g34160 [111028]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111029] (3)
                    SQ O22969 19-117
        5. C-terminal domain of ProRS [64586] (1)
           contains a metal (zinc)-binding site
           uperfamily
           1. C-terminal domain of ProRS [64587] (3)
              1. C-terminal domain of ProRS [64588]
                 1. Thermus thermophilus [TaxId: 274] [64589] (4)
                 2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [89973] (4)
                 3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [89974] (1)
        6. R3H domain [82708] (1)
           possibly lacks the N-terminal strand of the common fold
           uperfamily
           1. R3H domain [82709] (3)
              Pfam 01424; predicted nucleic acid-binding domain
              1. SmuBP-2 [82710]
                 1. Human (Homo sapiens) [TaxId: 9606] [82711] (1)
              2. Poly(A)-specific ribonuclease PARN [111030]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111031] (1)
                    SQ Q8VDG3 162-248; structure of an RNA-binding domain (430-516) is also known: 1WHV
              3. R3H domain protein KIAA1002 [118015]
                 1. Human (Homo sapiens) [TaxId: 9606] [118016] (1)
                    SQ Q9Y2K5 133-343
        7. EPT/RTPC-like [55205] (2)
           uperfamily
           1. RNA 3'-terminal phosphate cyclase, RPTC [55206] (1)
              duplication: 3 repeats of this fold are packed together around the pseudo threefold axis
              1. RNA 3'-terminal phosphate cyclase, RPTC [55207]
                 also contains an insert alpha+beta domain of the thioredoxin-like topology
                 1. Escherichia coli [TaxId: 562] [55208] (2)
           2. Enolpyruvate transferase, EPT [55209] (4)
              duplication: 6 repeats of this fold are organized in two RPTC-like domains
              1. UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ) [55210]
                 1. Escherichia coli [TaxId: 562] [55211] (2)
                 2. Enterobacter cloacae [TaxId: 550] [55212] (11)
                    SQ P33038
              2. 5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase [55213]
                 1. Escherichia coli [TaxId: 562] [55214] (12)
                    SQ P07638
                 2. Streptococcus pneumoniae [TaxId: 1313] [103061] (3)
        8. SMR domain-like [160443] (1)
           1. Smr domain [160444] (1)
              Pfam 01713
              1. Nedd4-binding protein 2 [160445]
                 1. Human (Homo sapiens) [TaxId: 9606] [160446] (1)
                    SQ Q86UW6 1688-1770
   161. PUG domain-like [143502] (1)
        alpha(2)-beta-alpha(2)-beta(2)-alpha; cluster of helices with a small antiparallel beta-sheet on one side; order 132; topological similarity to the fold of an extended R3H domain (PDB 1whr)
        1. PUG domain-like [143503] (1)
           uperfamily
           1. PUG domain [143504] (2)
              SMART 00580; domain in protein kinases, N-glycanases and other nuclear proteins
              1. N-glycanase 1, N-terminal domain [143505]
                 1. Mouse (Mus musculus) [TaxId: 10090] [143506] (1)
                    SQ Q9JI78 1-119
                 2. Human (Homo sapiens) [TaxId: 9606] [143507] (2)
                    SQ Q96IV0 11-109
   162. PG1857-like [160447] (1)
        alpha-beta-alpha-beta(2)-alpha(3); 3 layers, a/b/a; antiparallel beta-sheet, order: 132
        1. PG1857-like [160448] (1)
           1. PG1857-like [160449] (1)
              Pfam 09633; DUF2023
              1. Hypothetical protein PG1857 [160450]
                 1. Porphyromonas gingivalis [TaxId: 837] [160451] (2)
                    SQ Q7MTT4 4-114
   163. PB2 C-terminal domain-like [160452] (1)
        alpha-beta-alpha-X-alpha-beta(2); 3 layers, a/b/a; antiparallel beta-sheet, order 132; connection between helices 2 and 3 runs over the edge of the beta-sheet
        1. PB2 C-terminal domain-like [160453] (1)
           1. PB2 C-terminal domain-like [160454] (1)
              C-terminal part of Pfam 00604
              1. Polymerase basic protein 2, BP2 [160455]
                 1. Influenza A virus [TaxId: 11320] [160456] (3)
                    SQ P31345 685-759
   164. Ribosome binding protein Y (YfiA homologue) [69753] (1)
        beta-alpha-beta(3)-alpha; 2 layers; mixed sheet 1234, strand 3 is antiparallel to the rest
        1. Ribosome binding protein Y (YfiA homologue) [69754] (1)
           uperfamily
           1. Ribosome binding protein Y (YfiA homologue) [69755] (3)
              1. Ribosome binding protein Y (YfiA homologue) [69756]
                 Ribosome associated factor; cold-shock response protein
                 1. Haemophilus influenzae [TaxId: 727] [69757] (1)
                    HI0257
                 2. Escherichia coli [TaxId: 562] [82712] (2)
                 3. Thermus thermophilus [TaxId: 274] [160457] (4)
                    SQ Q5SIS0 1-95
   165. TolA/TonB C-terminal domain [74652] (1)
        beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit in non-swapped monomer
        1. TolA/TonB C-terminal domain [74653] (2)
           uperfamily
           1. TolA [55217] (2)
              contains extra N-terminal helix
              1. TolA [55218]
                 1. Escherichia coli [TaxId: 562] [55219] (2)
                 2. Pseudomonas aeruginosa [TaxId: 287] [75477] (1)
           2. TonB [64326] (1)
              isolated domain can form different segment-swapped dimers depending on the fragment length
              1. TonB [64327]
                 1. Escherichia coli [TaxId: 562] [64328] (7)
                    SQ P02929 150-239
   166. Yeast killer toxins [55220] (1)
        beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
        1. Yeast killer toxins [55221] (2)
           uperfamily
           1. Virally encoded KP4 toxin [55222] (1)
              1. Virally encoded KP4 toxin [55223]
                 1. Ustilago maydis, P4 strain [TaxId: 5270] [55224] (1)
           2. SMK toxin [55225] (1)
              1. SMK toxin [55226]
                 cleaved into alpha and beta chains
                 1. Halotolerant yeast (Pichia farinosa) [TaxId: 4920] [55227] (2)
   167. Cell division protein MinE topological specificity domain [55228] (1)
        dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
        1. Cell division protein MinE topological specificity domain [55229] (1)
           uperfamily
           1. Cell division protein MinE topological specificity domain [55230] (1)
              1. Cell division protein MinE topological specificity domain [55231]
                 1. Escherichia coli [TaxId: 562] [55232] (1)
   168. Hypothetical protein YoaG [103062] (1)
        dimer of beta(2)-alpha motifs ; 2 layers, alpha/beta; reverse MinE topology
        1. Hypothetical protein YoaG [103063] (1)
           uperfamily
           1. Hypothetical protein YoaG [103064] (1)
              1. Hypothetical protein YoaG [103065]
                 1. Escherichia coli [TaxId: 562] [103066] (1)
   169. BLRF2-like [160458] (1)
        homodimer of alpha(2)-beta motif; also includes extra N-terminal helix of variable position
        1. BLRF2-like [160459] (1)
           1. BLRF2-like [160460] (1)
              Pfam 05812; Herpesvirus BLRF2 protein
              1. Uncharacterized protein BQLF2 [160461]
                 1. Murid herpesvirus 4 [TaxId: 33708] [160462] (6)
                    SQ P88989 7-102
   170. Nucleocapsid protein dimerization domain [103067] (1)
        dimer of alpha-beta(2)-alpha motifs ; 2 layers, alpha/beta
        1. Nucleocapsid protein dimerization domain [103068] (2)
           uperfamily
           1. Arterivirus nucleocapsid protein [103069] (2)
              1. Arterivirus nucleocapsid protein [103070]
                 1. PRRSV (Porcine reproductive and respiratory syndrome virus) [TaxId: 28344] [103071] (1)
                 2. Equine arteritis virus [TaxId: 11047] [160463] (4)
                    SQ Q66526 50-105
           2. Coronavirus nucleocapsid protein [143508] (2)
              C-terminal part of Pfam 00937
              1. Coronavirus nucleocapsid protein [143509]
                 1. Avian infectious bronchitis virus [TaxId: 11120] [143510] (12)
                    SQ P32923 222-333! SQ P32923 226-332! SQ Q4ZJS4 218-326
                    different strains
                 2. SARS coronavirus [TaxId: 227859] [143511] (12)
                    SQ P59595 270-366
   171. Cyanase C-terminal domain [55233] (1)
        intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
        1. Cyanase C-terminal domain [55234] (1)
           uperfamily
           1. Cyanase C-terminal domain [55235] (1)
              active form is a decamer formed by five dimers
              1. Cyanase C-terminal domain [55236]
                 1. Escherichia coli [TaxId: 562] [55237] (22)
   172. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82713] (1)
        Intertwined pseudo hexamer of an alpha+beta motif
        1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82714] (1)
           duplication: the N- and C-terminal halves of the whole proteins are structurally similar
           uperfamily
           1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82715] (1)
              1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82716]
                 1. Escherichia coli [TaxId: 562] [82717] (6)
   173. RuBisCO, small subunit [55238] (1)
        alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
        1. RuBisCO, small subunit [55239] (1)
           uperfamily
           1. RuBisCO, small subunit [55240] (8)
              1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [55241]
                 1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [55242] (5)
                 2. Spinach (Spinacia oleracea) [TaxId: 3562] [55243] (11)
                 3. Galdieria partita [TaxId: 83374] [55244] (2)
                 4. Chlamydomonas reinhardtii [TaxId: 3055] [69758] (74)
                 5. Alcaligenes eutrophus [TaxId: 106590] [55245] (1)
                 6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [55246] (16)
                 7. Rice (Oryza sativa) [TaxId: 4530] [118017] (1)
                    SQ P18567
                 8. Halothiobacillus neapolitanus [TaxId: 927] [143512] (1)
                    SQ P45686 3-110
   174. DCoH-like [55247] (5)
        beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
        1. PCD-like [55248] (1)
           has additional alpha helix at the N-terminus
           uperfamily
           1. PCD-like [55249] (3)
              Pfam 01329
              1. Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) [55250]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [55251] (4)
                 2. Thermus thermophilus [TaxId: 274] [103072] (2)
              2. DcoH-like protein DCoH2 [118018]
                 1. Mouse (Mus musculus) [TaxId: 10090] [118019] (1)
                    SQ Q9CZL5
        2. C-terminal domain of arginine repressor [55252] (1)
           forms trimers with three closely packed beta-sheets
           uperfamily
           1. C-terminal domain of arginine repressor [55253] (3)
              1. C-terminal domain of arginine repressor [55254]
                 1. Escherichia coli [TaxId: 562] [55255] (3)
                 2. Bacillus stearothermophilus [TaxId: 1422] [55256] (2)
                 3. Bacillus subtilis [TaxId: 1423] [69759] (4)
        3. RBP11-like subunits of RNA polymerase [55257] (2)
           form homo and heterodimers
           uperfamily
           1. RBP11/RpoL [64311] (2)
              1. RPB11 [64312]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64313] (25)
                    SQ P38902; part of multichain biological unit
              2. DNA-directed RNA polymerase subunit L, RpoL [118020]
                 1. Thermoplasma acidophilum [TaxId: 2303] [118021] (1)
                    SQ Q9HIC5
           2. RNA polymerase alpha subunit dimerisation domain [55258] (4)
              1. RNA polymerase alpha [55259]
                 1. Escherichia coli [TaxId: 562] [55260] (1)
                 2. Thermus aquaticus [TaxId: 271] [64314] (7)
                 3. Thermus thermophilus [TaxId: 274] [75478] (30)
                    SQ Q9Z9H6; part of multichain biological unit
              2. RPB3 [64315]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64316] (25)
                    SQ P16370; part of multichain biological unit
        4. GAD domain-like [55261] (2)
           uperfamily
           1. GAD domain [55262] (4)
              has additional structures inserted in the common fold loops
              1. Prokaryotic AspRS, insert domain [55263]
                 1. Escherichia coli [TaxId: 562] [55264] (3)
                 2. Thermus thermophilus, AspRS-1 [TaxId: 274] [55265] (3)
              2. Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain [143513]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [143514] (2)
                    SQ O26803 271-395
                 2. Pyrococcus abyssi [TaxId: 29292] [143515] (2)
                    SQ Q9V0U0 277-407
           2. PH0730 C-terminal domain-like [160464] (1)
              1. Hypothetical protein PH0730 [160465]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160466] (1)
                    SQ O58461 97-213
        5. PH0987 N-terminal domain-like [160467] (1)
           1. PH0987 N-terminal domain-like [160468] (1)
              corresponds to the N-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
              1. Uncharacterized protein PH0987 [160469]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160470] (1)
                    SQ O58715 2-85
   175. TRCF domain-like [143516] (1)
        beta-alpha(3)-beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed beta sheet, order 12354, strands 1 and 2 are parallel; some topological similarity to the DCoH-like fold (scop_cf 55247)
        1. TRCF domain-like [143517] (1)
           uperfamily
           1. TRCF domain [143518] (1)
              Pfam 03461
              1. Transcription-repair coupling factor, TRCF, C-terminal domain [143519]
                 1. Escherichia coli [TaxId: 562] [143520] (2)
                    SQ P30958 990-1147
   176. NMB0513-like [160471] (1)
        alpha(3)-beta(2)-alpha-beta(2); some similarity to the "winged helix" DNA-binding domain fold
        1. NMB0513-like [160472] (1)
           1. NMB0513-like [160473] (1)
              C-terminal part corresponds to Pfam 04591, DUF596
              1. Hypothetical protein NMB0513 [160474]
                 1. Neisseria meningitidis [TaxId: 487] [160475] (1)
                    SQ Q9K0R7 1-131
   177. PA1123-like [160476] (1)
        irregular array of short helices and two three-stranded beta-sheets
        1. PA1123-like [160477] (1)
           1. PA1123-like [160478] (1)
              Pfam 09634; DUF2025
              1. Hypothetical protein PA1123 [160479]
                 1. Pseudomonas aeruginosa [TaxId: 287] [160480] (1)
                    SQ Q9I4L2 1-106
   178. Hypothetical protein Yml108w [100886] (1)
        beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta; mixed beta-sheet 2143, strands 1 and 4 are parallel
        1. Hypothetical protein Yml108w [89975] (1)
           uperfamily
           1. Hypothetical protein Yml108w [89976] (1)
              1. Hypothetical protein Yml108w [89977]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89978] (1)
   179. MutS N-terminal domain-like [55266] (2)
        beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
        1. tRNA-intron endonuclease N-terminal domain-like [55267] (1)
           uperfamily
           1. tRNA-intron endonuclease N-terminal domain-like [55268] (2)
              1. Tetrameric tRNA splicing endonuclease, N-terminal domain [55269]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55270] (1)
              2. Dimeric tRNA splicing endonuclease, domains 1 and 3 [103073]
                 duplication: one subunit consists of two tetrameric tRNA splicing endonuclease subunit-like repeats
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103074] (11)
        2. DNA repair protein MutS, domain I [55271] (1)
           uperfamily
           1. DNA repair protein MutS, domain I [55272] (2)
              1. DNA repair protein MutS, domain I [55273]
                 1. Thermus aquaticus [TaxId: 271] [55274] (3)
                 2. Escherichia coli [TaxId: 562] [55275] (10)
                    SQ P23909 2-800
   180. GYF/BRK domain-like [55276] (2)
        beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
        1. GYF domain [55277] (1)
           uperfamily
           1. GYF domain [55278] (2)
              Pfam 02213
              1. GYF domain from cd2bp2 protein [55279]
                 1. Human (Homo sapiens) [TaxId: 9606] [55280] (5)
              2. Hypothetical rotein At5g08430 [118022]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118023] (1)
                    SQ Q9FT92 444-508; structure of the N-terminal SWIB domain (25-112) is also known (scop_sp 101202)
        2. BRK domain-like [160481] (1)
           1. BRK domain-like [160482] (2)
              Pfam 07533; TCH domain
              1. Chromodomain-helicase-dna-binding protein 8, CHD8 [160483]
                 1. Human (Homo sapiens) [TaxId: 9606] [160484] (2)
                    SQ Q9HCK8 2024-2093! SQ Q9HCK8 2028-2085
              2. Chromodomain-helicase-DNA-binding protein 7, CHD7 [160485]
                 1. Human (Homo sapiens) [TaxId: 9606] [160486] (3)
                    SQ Q9P2D1 1799-1852! SQ Q9P2D1 1801-1860! SQ Q9P2D1 1869-1953
   181. GTP cyclohydrolase I feedback regulatory protein, GFRP [69760] (1)
        beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta, antiparallel beta-sheet: order 342165
        1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69761] (1)
           uperfamily
           1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69762] (1)
              1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69763]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [69764] (4)
                    SQ P70552
   182. RL5-like [55281] (1)
        beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
        1. RL5-like [55282] (2)
           uperfamily
           1. Ribosomal protein L5 [55283] (5)
              1. Ribosomal protein L5 [55284]
                 synonym: 50S ribosomal protein L5p, HMAL5, HL13
                 1. Bacillus stearothermophilus [TaxId: 1422] [64317] (1)
                 2. Thermus thermophilus [TaxId: 274] [82718] (6)
                 3. Archaeon Haloarcula marismortui [TaxId: 2238] [55285] (40)
                    SQ P14124
                 4. Deinococcus radiodurans [TaxId: 1299] [160487] (6)
                    SQ Q9RXJ0 3-179
                 5. Escherichia coli [TaxId: 562] [160488] (29)
                    SQ P62399 1-178
           2. SSO1042-like [160489] (4)
              Pfam 01877; DUF54
              1. Hypothetical protein SSo1042 [160490]
                 1. Sulfolobus solfataricus [TaxId: 2287] [160491] (2)
                    SQ Q97Z89 3-144
              2. Hypothetical protein AF2318 [160492]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [160493] (4)
                    SQ O27966 3-143
              3. Hypothetical protein SSO0741 [160494]
                 1. Sulfolobus solfataricus [TaxId: 2287] [160495] (1)
                    SQ Q9UXC9 4-144
              4. Hypotheical protein MJ1564 [160496]
                 1. Methanocaldococcus jannaschii [TaxId: 2190] [160497] (1)
                    SQ Q58959 1-133
   183. RPB5-like RNA polymerase subunit [55286] (1)
        core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
        1. RPB5-like RNA polymerase subunit [55287] (1)
           uperfamily
           1. RPB5 [55288] (3)
              1. RNA polymerase subunit RBP5 (RNA polymerase subunit H) [55289]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55290] (1)
                 2. Archaeon Methanococcus jannaschii [TaxId: 2190] [55291] (1)
              2. Eukaryotic RPB5 C-terminal domain [55292]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55293] (26)
                    SQ P20434; part of multichain biological unit
   184. Bacillus chorismate mutase-like [55297] (9)
        core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
        1. YjgF-like [55298] (2)
           forms trimers with three closely packed beta-sheets; possibly related to the IspF (d.79.5) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
           uperfamily
           1. YjgF/L-PSP [55299] (15)
              some members possess an endoribonuclease activity inhibiting mRNA translation
              1. Conserved 'hypothetical' protein YjgF [55300]
                 1. Escherichia coli [TaxId: 562] [55301] (1)
                 2. Haemophilus influenzae [TaxId: 727] [82719] (1)
                    YjgF homologue HI0719
              2. Hypothetical protein YjgH [103075]
                 1. Escherichia coli [TaxId: 562] [103076] (1)
              3. Purine regulatory protein YabJ [55302]
                 1. Bacillus subtilis [TaxId: 1423] [55303] (1)
                 2. Clostridium thermocellum [TaxId: 1515] [118024] (1)
                    SQ Q4CI45
              4. Highdosage growth inhibitor YER057cp (YEO7_YEAST) [64319]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64320] (1)
              5. 14.5 kda translational inhibitor protein, L-PSP [89979]
                 mammalian tumor associated antigen UK114
                 1. Human (Homo sapiens) [TaxId: 9606] [89980] (1)
                 2. Goat (Capra hircus) [TaxId: 9925] [103077] (1)
                 3. Rat (Rattus norvegicus) [TaxId: 10116] [103078] (1)
                    Perchloric acid soluble protein
              6. Hypothetical protein ST0811 [143521]
                 1. Sulfolobus tokodaii [TaxId: 111955] [143522] (2)
                    SQ Q973T6 1-124
              7. Putative endonuclease APE1501 [143523]
                 1. Aeropyrum pernix [TaxId: 56636] [143524] (1)
                    SQ Q9YBU8 4-119
              8. Putative protein synthesis inhibitor TM0215 [143525]
                 1. Thermotoga maritima [TaxId: 2336] [143526] (2)
                    SQ Q9WY58 2-127
              9. Hypothetical protein SPy2060 [143527]
                 1. Streptococcus pyogenes [TaxId: 1314] [143528] (12)
                    SQ Q99XS4 3-122
              10. Putative translation intiation inhibitor TTHA0137 [143529]
                  1. Thermus thermophilus [TaxId: 274] [143530] (13)
                     SQ Q5SM06 1-124
              11. Hypothetical protein SO1960 [160498]
                  1. Shewanella oneidensis [TaxId: 70863] [160499] (3)
                     SQ Q8EFL1 2-153
           2. Chorismate mutase [55304] (3)
              1. Chorismate mutase [55305]
                 1. Bacillus subtilis [TaxId: 1423] [55306] (6)
                 2. Thermus thermophilus [TaxId: 274] [89981] (3)
                 3. Clostridium thermocellum [TaxId: 1515] [118025] (1)
                    SQ Q5KXU6 5-114 # 53% sequence identity
        2. IpsF-like [69765] (1)
           forms trimers with three closely packed beta-sheets; possible link between the YjgF-like (d.79.1) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
           uperfamily
           1. IpsF-like [69766] (5)
              1. 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF [69767]
                 1. Escherichia coli [TaxId: 562] [69768] (11)
                    SQ P62617 ! SQ P36663
                 2. Haemophilus influenzae [TaxId: 727] [75479] (3)
                 3. Thermus thermophilus [TaxId: 274] [82720] (4)
                 4. Shewanella oneidensis [TaxId: 70863] [118026] (1)
                    SQ Q8EBR3
              2. IspD/ispF bifunctional enzyme, MECDP synthase domain [118027]
                 1. Campylobacter jejuni [TaxId: 197] [118028] (2)
                    SQ Q9PM68
        3. Tubulin C-terminal domain-like [55307] (1)
           uperfamily
           1. Tubulin, C-terminal domain [55308] (9)
              1. Cell-division protein FtsZ [55309]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55310] (7)
                    SQ Q57816 23-360
                 2. Pseudomonas aeruginosa [TaxId: 287] [89982] (2)
                 3. Mycobacterium tuberculosis [TaxId: 1773] [111032] (7)
                    SQ O08378
                 4. Thermotoga maritima [TaxId: 2336] [118029] (1)
                    SQ O08398 22-335
              2. Tubulin alpha-subunit [55311]
                 1. Pig (Sus scrofa) [TaxId: 9823] [55312] (3)
                 2. Cow (Bos taurus) [TaxId: 9913] [64321] (6)
                    SQ P02550
                 3. Prosthecobacter dejongeii [TaxId: 48465] [160500] (3)
                    SQ Q8GCC5 253-432
                    bacterial tubulin BtubA
              3. Tubulin beta-subunit [55313]
                 1. Pig (Sus scrofa) [TaxId: 9823] [55314] (1)
                 2. Cow (Bos taurus) [TaxId: 9913] [64322] (8)
                    SQ P02554
        4. L30e-like [55315] (3)
           uperfamily
           1. L30e/L7ae ribosomal proteins [55316] (11)
              1. Eukaryotic ribosomal protein L30 (L30e) [55317]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55318] (4)
                    SQ P14120
                 2. Archaeon Thermococcus celer [TaxId: 2264] [89986] (8)
              2. Ribosomal protein L7ae [55319]
                 1. Archaeon Pyrococcus abyssi [TaxId: 29292] [103081] (2)
                 2. Archaeon Haloarcula marismortui [TaxId: 2238] [55320] (58)
                    SQ P12743
                 3. Archaeon Methanococcus jannaschii [TaxId: 2190] [111033] (3)
                    SQ P54066
                 4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111034] (1)
                    SQ O29494 # AF0764
                 5. Aeropyrum pernix [TaxId: 56636] [160501] (1)
                    SQ Q9YAX7 4-127
                 6. Pyrococcus furiosus [TaxId: 2261] [160502] (1)
                    SQ Q8U160 3-123
                 7. Cryptosporidium parvum [TaxId: 5807] [160503] (1)
                    SQ Q7YYQ3 17-131
              3. Spliceosomal 15.5kd protein [55321]
                 1. Human (Homo sapiens) [TaxId: 9606] [55322] (4)
              4. Small nuclear ribonucleoprotein-associated protein 1, Snu13p [160504]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [160505] (3)
                    SQ P39990 1-126! SQ P39990 2-126
           2. RNA 2'-O ribose methyltransferase substrate binding domain [75480] (2)
              1. RrmA (RrmH), N-terminal domain [75481]
                 23S rRNA methyltransferase; proposed gene names are as appear in the original publication (and the PDB entry)
                 1. Thermus thermophilus [TaxId: 274] [75482] (1)
              2. RlmB, N-terminal domain [82721]
                 23S rRNA G2251 2'O-methytransferase
                 1. Escherichia coli [TaxId: 562] [82722] (1)
           3. ERF1/Dom34 C-terminal domain-like [55323] (4)
              1. C-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55324]
                 contains a large insertion forming a separate (sub)domain
                 1. Human (Homo sapiens) [TaxId: 9606] [55325] (1)
              2. Cell division protein pelota [160506]
                 1. Human (Homo sapiens) [TaxId: 9606] [160507] (1)
                    SQ Q9BRX2 261-371
                 2. Thermoplasma acidophilum [TaxId: 2303] [160508] (1)
                    SQ Q9HJ74 244-338
              3. Dom34 [160509]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [160510] (3)
                    SQ P33309 278-381
        5. PurM N-terminal domain-like [55326] (1)
           uperfamily
           1. PurM N-terminal domain-like [55327] (6)
              1. Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain [55328]
                 1. Escherichia coli [TaxId: 562] [55329] (1)
              2. Phosphoribosylformylglycinamidine synthase II, domains 1 and 3 [103082]
                 duplication: tandem repeats of two PurM-like units arranged like the PurM subunits in the dimer
                 1. Thermotoga maritima [TaxId: 2336] [103083] (17)
                    TM1246
              3. FGAM synthase PurL, PurM-like module, N1 and N2 domains [111035]
                 1. Salmonella typhimurium [TaxId: 90371] [111036] (1)
                    SQ P74881
              4. Thiamine monophosphate kinase (ThiL) N-terminal domain [118030]
                 1. Aquifex aeolicus [TaxId: 63363] [118031] (9)
                    SQ O67883
              5. Selenide, water dikinase SelD [160511]
                 1. Aquifex aeolicus [TaxId: 63363] [160512] (7)
                    SQ O67139 1-154! SQ O67139 28-154
              6. Hydrogenase expression/formation protein HypE [160513]
                 1. Thermococcus kodakaraensis [TaxId: 311400] [160514] (2)
                    SQ Q5JII7 41-155
        6. Holliday junction resolvase RusA [103084] (1)
           uperfamily
           1. Holliday junction resolvase RusA [103085] (1)
              1. Holliday junction resolvase RusA [103086]
                 1. Escherichia coli [TaxId: 562] [103087] (1)
        7. OmpA-like [103088] (1)
           uperfamily
           1. OmpA-like [103089] (3)
              Pfam 00691
              1. Peptidoglycan-associated lipoprotein, PAL, periplasmic domain [103090]
                 1. Escherichia coli [TaxId: 562] [103091] (5)
                 2. Haemophilus influenzae [TaxId: 727] [143531] (1)
                    SQ P10324 20-153
              2. Outer membrane protein class 4, RmpM, C-terminal domain [103092]
                 1. Neisseria meningitidis [TaxId: 487] [103093] (1)
        8. YueI-like [160515] (1)
           1. YueI-like [160516] (1)
              Pfam 07997; DUF1694
              1. Uncharacterized protein YueI [160517]
                 1. Bacillus subtilis [TaxId: 1423] [160518] (2)
                    SQ O32092 3-130
        9. BB2672-like [160519] (1)
           contains extra N-terminal strand and a beta-hairpin insertion between strands 3 and 4 that packs against the main beta-sheet
           1. BB2672-like [160520] (2)
              Pam 06684; DUF1185
              1. Uncharacterized protein BB2672 [160521]
                 1. Bordetella bronchiseptica [TaxId: 518] [160522] (3)
                    SQ Q7WJ28 2-192
              2. Uncharacterized protein SPO0826 [160523]
                 1. Silicibacter pomeroyi [TaxId: 89184] [160524] (1)
                    SQ Q5LV76 3-171
   185. YjbQ-like [111037] (1)
        beta(2)-alpha-beta(2)-alpha(2)-beta(3); contains a beta-sandwich: 7 strands in 2 sheets; trimerizes with orthogonally packed beta-sheets
        1. YjbQ-like [111038] (1)
           uperfamily
           1. YjbQ-like [111039] (4)
              Pfam 01894
              1. B.subtilis YugU ortolog CAC0907 [111040]
                 1. Clostridium acetobutylicum [TaxId: 1488] [111041] (2)
                    SQ Q97KL0
              2. Hypothetical protein BH3498 [118032]
                 1. Bacillus halodurans [TaxId: 86665] [118033] (1)
                    SQ Q9K772
              3. Hypothetical protein TM0723 [118034]
                 1. Thermotoga maritima [TaxId: 2336] [118035] (1)
                    SQ Q9WZI2
              4. Hypothetical protein SSO2532 [118036]
                 1. Sulfolobus solfataricus [TaxId: 2287] [118037] (1)
                    SQ Q97VS8
   186. Tautomerase/MIF [55330] (1)
        (beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
        generally forms trimers with three closely packed beta-sheets
        1. Tautomerase/MIF [55331] (6)
           uperfamily
           1. 4-oxalocrotonate tautomerase-like [55332] (5)
              dimer of beta-alpha-beta subunits: may assemble further in hexamer (trimer of the dimers)
              1. 4-oxalocrotonate tautomerase [55333]
                 1. Pseudomonas sp., DmpI [TaxId: 306] [55334] (1)
                 2. Pseudomonas putida, XylH [TaxId: 303] [55335] (4)
              2. Trans-3-chloroacrylic acid dehalogenase alpha-subunit, CaaD1 [103094]
                 forms heterohexamer with beta-subunit
                 1. Pseudomonas pavonaceae [TaxId: 47881] [103095] (1)
              3. Trans-3-chloroacrylic acid dehalogenase beta-subunit, CaaD2 [103096]
                 forms heterohexamer with alpha-subunit
                 1. Pseudomonas pavonaceae [TaxId: 47881] [103097] (1)
              4. 4-oxalocrotonate tautomerase homologue YdcE [82723]
                 forms stable dimer without further oligomerisation
                 1. Escherichia coli [TaxId: 562] [82724] (3)
           2. 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) [55336] (1)
              1. 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) [55337]
                 1. Escherichia coli [TaxId: 562] [55338] (1)
           3. MIF-related [55339] (6)
              1. Microphage migration inhibition factor (MIF) [55340]
                 synonym: glycosylation-inhibiting factor (GIF)
                 1. Human (Homo sapiens) [TaxId: 9606] [55341] (20)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [55342] (1)
                 3. Mouse (Mus musculus) [TaxId: 10090] [55343] (5)
                 4. Trichinella spiralis [TaxId: 6334] [64323] (1)
                 5. African clawed frog (Xenopus laevis) [TaxId: 8355] [111042] (1)
                    SQ Q76BK2
              2. D-dopachrome tautomerase [55344]
                 1. Human (Homo sapiens) [TaxId: 9606] [55345] (1)
           4. Hypothetical protein HI1388.1 [103098] (1)
              lacks the N-terminal proline
              1. Hypothetical protein HI1388.1 [103099]
                 1. Haemophilus influenzae [TaxId: 727] [103100] (1)
           5. VC0714-like [111043] (1)
              1. Hypothetical protein VC0714 [111044]
                 1. Vibrio cholerae [TaxId: 666] [111045] (1)
                    SQ Q9KU16
           6. MSAD-like [143532] (1)
              1. Malonate semialdehyde decarboxylase, MSAD [143533]
                 1. Pseudomonas pavonaceae [TaxId: 47881] [143534] (14)
                    SQ Q9EV83 2-130! SQ Q9EV83 2-230
   187. FwdE/GAPDH domain-like [55346] (4)
        core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
        1. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain [55347] (5)
           N-terminal domain is the classic Rossmann-fold
           uperfamily
           1. GAPDH-like [55348] (29)
              has many additional secondary structures
              1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [55349]
                 1. Escherichia coli [TaxId: 562] [55350] (13)
                    SQ P06977
                 2. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [55351] (14)
                 3. Achromobacter xylosoxidans [TaxId: 85698] [89987] (1)
                    formerly Alcaligenes xylosoxidans
                 4. Thermus aquaticus [TaxId: 271] [55352] (13)
                 5. Thermus thermophilus [TaxId: 274] [103101] (1)
                 6. Thermotoga maritima [TaxId: 2336] [55353] (1)
                 7. Archaeon Sulfolobus solfataricus [TaxId: 2287] [55354] (1)
                 8. Archaeon Methanothermus fervidus [TaxId: 2180] [55355] (1)
                 9. Trypanosoma brucei brucei, glycosome [TaxId: 5702] [55356] (1)
                 10. Trypanosoma cruzi [TaxId: 5693] [75483] (7)
                 11. Leishmania mexicana [TaxId: 5665] [55357] (5)
                 12. American lobster (Homarus americanus) [TaxId: 6706] [55358] (2)
                 13. South China Sea lobster (Palinurus versicolor) [TaxId: 150436] [55359] (5)
                 14. Human (Homo sapiens) [TaxId: 9606] [55360] (1)
                 15. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [103102] (1)
                 16. Spinach (Spinacia oleracea) [TaxId: 3562] [69769] (24)
                     SQ P19866
                 17. Human(Homo sapiens), liver isoform [TaxId: 9606] [143535] (8)
                     SQ P04406 151-314
                 18. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [143536] (12)
                     SQ Q8IKK7 153-318! SQ Q8T6B1 153-318
                 19. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143537] (4)
                     SQ O59494 140-301
              2. Aspartate beta-semialdehyde dehydrogenase [55361]
                 1. Escherichia coli [TaxId: 562] [55362] (4)
                    SQ P00353
                 2. Vibrio cholerae [TaxId: 666] [82725] (2)
                 3. Haemophilus influenzae [TaxId: 727] [103103] (12)
                    SQ P44801
                 4. Streptococcus pneumoniae [TaxId: 1313] [143538] (11)
                    SQ Q8DQ00 128-329
              3. Acetaldehyde dehydrogenase (acylating) [89988]
                 1. Pseudomonas sp. [TaxId: 306] [89989] (1)
              4. N-acetyl-gamma-glutamyl-phosphate reductase ArgC [111046]
                 1. Thermotoga maritima [TaxId: 2336] [111047] (1)
                    SQ Q9X2A2
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118038] (5)
                    SQ O82187 15-359
                 3. Salmonella typhimurium [TaxId: 90371] [143539] (1)
                    SQ Q8ZKL8 154-308
              5. Putative semialdehyde dehydrogenase [143540]
                 1. Rice (Oryza sativa) [TaxId: 4530] [143541] (4)
                    SQ Q6AV34 219-383
              6. Usg-1 protein homolog PA3116 [143542]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143543] (1)
                    SQ O87014 130-319
           2. Homoserine dehydrogenase-like [55363] (2)
              1. Homoserine dehydrogenase [55364]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55365] (4)
                    SQ P31116
              2. Saccharopine reductase [55366]
                 contains an alpha-helical subdomain inserted in the common fold and other additional secondary structures
                 1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [55367] (3)
           3. Dihydrodipicolinate reductase-like [55368] (12)
              1. Diaminopimelic acid dehydrogenase (DAPDH) [55369]
                 distantly related to dihydrodipicolinate reductase
                 larger alpha+beta subdomain substitutes for one helix and one strand of the common fold
                 1. Corynebacterium glutamicum [TaxId: 1718] [55370] (4)
              2. Dihydrodipicolinate reductase [55371]
                 1. Escherichia coli [TaxId: 562] [55372] (5)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [103104] (14)
                 3. Thermotoga maritima [TaxId: 2336] [111048] (1)
                    SQ Q9X1K8
              3. Myo-inositol 1-phosphate synthase [75484]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [75485] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75486] (9)
                    SQ P11986
                 3. Archaeoglobus fulgidus [TaxId: 2234] [111049] (1)
                    SQ O28480
                 4. Caenorhabditis elegans [TaxId: 6239] [111050] (1)
                    SQ Q18664
              4. Hypothetical protein TM1419 [103105]
                 myo-inositol 1-phosphate synthase-related protein
                 1. Thermotoga maritima [TaxId: 2336] [103106] (1)
              5. Hypothetical protein TM1643 [75487]
                 1. Thermotoga maritima [TaxId: 2336] [75488] (2)
              6. 1-deoxy-D-xylulose-5-phosphate reductoisomerase [69770]
                 1. Escherichia coli [TaxId: 562] [69771] (12)
                    SQ P45568
                 2. Zymomonas mobilis [TaxId: 542] [111051] (2)
                    SQ Q9X5F2
           4. Biliverdin reductase [55373] (1)
              1. Biliverdin reductase [55374]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [55375] (3)
           5. Glucose 6-phosphate dehydrogenase-like [55376] (8)
              has many additional secondary structures
              1. Glucose-fructose oxidoreductase [55377]
                 very similar to the glucose 6-phosphate dehydrogenase domain
                 1. Zymomonas mobilis [TaxId: 542] [55378] (12)
              2. Glucose 6-phosphate dehydrogenase [55379]
                 1. Leuconostoc mesenteroides [TaxId: 1245] [55380] (9)
                 2. Human (Homo sapiens) [TaxId: 9606] [55381] (1)
              3. Virulence factor MviM [111052]
                 1. Escherichia coli [TaxId: 562] [111053] (1)
                    SQ P75931
              4. Putative oxidoreductase VCA1048 [111054]
                 1. Vibrio cholerae [TaxId: 666] [111055] (1)
                    SQ Q9KKQ4
              5. Probable oxidoreductase At4g09670 [118039]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118040] (1)
                    SQ Q9SZ83
              6. Hypothetical protein TM0312 [143544]
                 1. Thermotoga maritima [TaxId: 2336] [143545] (2)
                    SQ Q9WYE8 132-275
              7. Galactose/lactose metabolism regulatory protein GAL80 [143546]
                 1. Yeast (Kluyveromyces lactis) [TaxId: 28985] [143547] (9)
                    SQ Q06433 155-373
        2. Serine metabolism enzymes domain [143548] (2)
           contains extra C-terminal beta-hairpin
           uperfamily
           1. Serine dehydratase beta chain-like [143549] (1)
              Pfam 03315
              1. L-serine dehydratase SdhL, N-terminal domain [143550]
                 1. Legionella pneumophila [TaxId: 446] [143551] (3)
                    SQ Q5ZXE1 17-161
           2. SerA intervening domain-like [143552] (1)
              PfamB 001360; this domain is found in some but not all D-3-phosphoglycerate dehydrogenases (SerA) and related enzymes
              1. D-3-phosphoglycerate dehydrogenase SerA [143553]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143554] (2)
                    SQ P0A544 316-450
        3. FwdE-like [143555] (1)
           contains extra N-terminal and C-terminal structures
           uperfamily
           1. FwdE-like [143556] (2)
              Pfam 02663; Tungsten formylmethanofuran dehydrogenase, subunit E, FwdE, is a stand-alone domain of this fold
              1. FwdE-like protein DSY1837 (Dhaf_2201) [143557]
                 1. Desulfitobacterium hafniense [TaxId: 49338] [143558] (2)
                    SQ Q24WG6 3-151
              2. Uncharacterized protein Ta1109 [160525]
                 1. Thermoplasma acidophilum [TaxId: 2303] [160526] (1)
                    SQ Q9HJ63 1-168
        4. V-type ATPase subunit E-like [160527] (1)
           extra N-terminal helix and extra C-terminal helix form dimerisation subdomain
           1. V-type ATPase subunit E [160528] (1)
              Pfam 01991
              1. V-type ATP synthase subunit E [160529]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160530] (3)
                    SQ O57724 81-198
   188. Ava3019-like [160531] (1)
        alpha(2)-beta-alpha-beta(4); 2 layers, a/b; antiparallel beta-sheet, order: 32145; similarity to the insert domain of Glucose 6-phosphate dehydrogenase-like family (sop_fa 55376)
        1. Ava3019-like [160532] (1)
           1. Ava3019-like [160533] (1)
              Pfam 08854; DUF1824
              1. Uncharacterized protein Ava3019 [160534]
                 1. Anabaena variabilis [TaxId: 1172] [160535] (3)
                    SQ Q3M8Q7 8-138
   189. Hypothetical protein PF0899 [111056] (1)
        alpha-beta-alpha-beta(4); 2 layers: a/b; mixed beta-sheet, order 23145, strands 1 and 3 are parallel; similar to the GAPDH C-terminal domain-like fold (scop_cf 55346)
        1. Hypothetical protein PF0899 [111057] (1)
           possibly related to Major capsid protein gp5 (scop_sf 56563)63566
           uperfamily
           1. Hypothetical protein PF0899 [111058] (1)
              1. Hypothetical protein PF0899 [111059]
                 1. Pyrococcus furiosus [TaxId: 2261] [111060] (1)
                    SQ Q8U2E0
   190. Major capsid protein gp5 [56562] (1)
        unusual fold; contains PF0899-like core, decorated with additional structure
        1. Major capsid protein gp5 [56563] (1)
           possibly related to the hypothetical protein PF0899 superfamily (scop_sf 111057)
           uperfamily
           1. Major capsid protein gp5 [56564] (1)
              1. Major capsid protein gp5 [56565]
                 1. Bacteriophage HK97 [TaxId: 37554] [56566] (21)
   191. MK0786-like [143559] (1)
        alpha(2)-beta(4); 2 layers: a/b; antiparallel beta-sheet, order 1234 (meander)
        1. MK0786-like [143560] (1)
           probable biological unit is a teramer; all subunit interfaces are provided by helices
           uperfamily
           1. MK0786-like [143561] (2)
              single domain; the N-terminal half is covered by Pfam 04036 (DUF372) and the C-terminal half by Pfam 04038 (DUF381)
              1. Hypothetical protein PTO0218 [143562]
                 1. Picrophilus torridus [TaxId: 82076] [143563] (6)
                    SQ Q6L2J9 1-120
              2. Hypothetical protein MK0786 [143564]
                 1. Methanopyrus kandleri [TaxId: 2320] [143565] (4)
                    SQ Q8TX89 7-119
   192. YkuJ-like [143566] (1)
        alpha-beta(4)-alpha; 2 layers a/b; antiparallel beta-sheet, order 1234
        1. YkuJ-like [143567] (1)
           uperfamily
           1. YkuJ-like [143568] (1)
              1. Hypothetical protein YkuJ [143569]
                 1. Bacillus subtilis [TaxId: 1423] [143570] (2)
                    SQ O34588 2-79
   193. N domain of copper amine oxidase-like [55382] (5)
        alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
        1. Copper amine oxidase, domain N [55383] (1)
           uperfamily
           1. Copper amine oxidase, domain N [55384] (1)
              1. Copper amine oxidase, domain N [55385]
                 non-conserved N-terminal domain
                 1. Escherichia coli [TaxId: 562] [55386] (11)
        2. Frataxin/Nqo15-like [55387] (2)
           uperfamily
           1. Frataxin-like [55388] (3)
              iron homeostasis proteins
              1. C-terminal domain of frataxin [55389]
                 protein responsible for Friedreich ataxia
                 1. Human (Homo sapiens) [TaxId: 9606] [55390] (2)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143571] (2)
                    SQ Q07540 52-174! SQ Q07540 61-172
              2. CyaY [55391]
                 1. Escherichia coli [TaxId: 562] [55392] (4)
                    SQ P27838
           2. Nqo15-like [143572] (1)
              overall structural similarity to the frataxin-like family
              1. NADH-quinone oxidoreductase subunit 15, Nqo15 [143573]
                 1. Thermus thermophilus [TaxId: 274] [143574] (4)
                    SQ Q5SKZ7 3-129
        3. Hypothetical protein c14orf129, hspc210 [103107] (1)
           uperfamily
           1. Hypothetical protein c14orf129, hspc210 [103108] (1)
              Pfam 05303
              1. Hypothetical protein c14orf129, hspc210 [103109]
                 1. Human (Homo sapiens) [TaxId: 9606] [103110] (1)
        4. GAS2 domain-like [143575] (1)
           this superfamily may include the most C-terminal domain of IBP39 (scop_fa 103410); the preceeding (middle) domain of IBP39 may be split and reassigned to the EF-hand superfamily (scop_sf 47473)
           uperfamily
           1. GAS2 domain [143576] (1)
              Pfam 02187
              1. Growth-arrest-specific protein 2, GAS2 [143577]
                 1. Mouse (Mus musculus) [TaxId: 10090] [143578] (1)
                    SQ P11862 200-284
        5. GK1464-like [143579] (1)
           dimer; pseudo barrel; the true dimeric barrel formation requires swapping of the C-ternimal beta-alpha units
           uperfamily
           1. GK1464-like [143580] (1)
              1. Hypothetical protein, GK1464 ortholog [143581]
                 MCSG target ID: APC35702
                 1. Bacillus stearothermophilus [TaxId: 1422] [143582] (2)
                    SQ Q5KZY7 1-100
   194. Aha1/BPI domain-like [55393] (2)
        core: [beta]-alpha-beta(5)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, meander
        1. Activator of Hsp90 ATPase, Aha1 [103111] (1)
           consists of a single domain of this fold
           uperfamily
           1. Activator of Hsp90 ATPase, Aha1 [103112] (1)
              1. Activator of Hsp90 ATPase, Aha1 [103113]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103114] (2)
        2. Bactericidal permeability-increasing protein, BPI [55394] (1)
           duplication: consists of two clear structural repeats of this fold also containing an extra C-terminal beta-hairpin
           uperfamily
           1. Bactericidal permeability-increasing protein, BPI [55395] (1)
              1. Bactericidal permeability-increasing protein, BPI [55396]
                 1. Human (Homo sapiens) [TaxId: 9606] [55397] (2)
   195. SpoVG-like [160536] (1)
        beta(5)-alpha; comprises a coiled antiparallel beta-sheet (order: 12345) packed against the C-terminal helix; the extensions of strands 4 and 5 form an isolated beta-hairpin
        1. SpoVG-like [160537] (1)
           probable biological unit is a hexamer (trimer of dimers)
           1. SpoVG-like [160538] (2)
              Pfam 04026
              1. Putative septation protein SpoVG [160539]
                 1. Bacillus subtilis [TaxId: 1423] [160540] (6)
                    SQ P28015 1-92
                 2. Staphylococcus epidermidis [TaxId: 1282] [160541] (4)
                    SQ Q8CML1 1-84! SQ Q8CML1 1-87
   196. Subtilisin inhibitor [55398] (1)
        alpha+beta sandwich
        1. Subtilisin inhibitor [55399] (1)
           uperfamily
           1. Subtilisin inhibitor [55400] (2)
              1. Subtilisin inhibitor [55401]
                 1. Streptomyces lividans [TaxId: 1916] [55402] (3)
                 2. Streptomyces albogriseolus, s-3253 [TaxId: 1887] [55403] (2)
   197. RNA bacteriophage capsid protein [55404] (1)
        6-standed beta-sheet followed with 2 helices; meander
        1. RNA bacteriophage capsid protein [55405] (1)
           uperfamily
           1. RNA bacteriophage capsid protein [55406] (5)
              1. MS2 virus coat protein [55407]
                 1. Bacteriophage MS2 [TaxId: 12022] [55408] (48)
                    SQ P03612
              2. GA coat protein [55409]
                 1. Bacteriophage GA [TaxId: 12018] [55410] (2)
              3. fr coat protein [55411]
                 1. Bacteriophage FR [TaxId: 12017] [55412] (2)
              4. Qbeta coat protein [55413]
                 1. Bacteriophage Qbeta [TaxId: 39803] [55414] (1)
              5. PP7 coat protein [55415]
                 1. Bacteriophage PP7 [TaxId: 12023] [55416] (1)
   198. eIF4e-like [55417] (1)
        beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
        1. eIF4e-like [55418] (2)
           uperfamily
           1. Translation initiation factor eIF4e [55419] (3)
              1. Translation initiation factor eIF4e [55420]
                 messenger RNA 5' cap-binding protein
                 1. Mouse (Mus musculus) [TaxId: 10090] [55421] (7)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55422] (2)
                 3. Homo sapiens [TaxId: 9606] [160542] (6)
           2. BLES03-like [143583] (1)
              the N-terminal strand is missing, but there extra C-terminal strands in the beta-sheet
              1. Basophilic leukemia expressed protein BLES03 [143584]
                 1. Human (Homo sapiens) [TaxId: 9606] [143585] (4)
                    SQ Q9H3H3 17-250
   199. CO dehydrogenase flavoprotein C-domain-like [55423] (2)
        core: beta(3,4)-alpha(3); alpha+beta sandwich
        1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55424] (1)
           both first two domains are of same beta/beta/alpha fold
           uperfamily
           1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55425] (22)
              1. Glutathione reductase [55426]
                 1. Human (Homo sapiens) [TaxId: 9606] [55427] (17)
                 2. Plasmodium falciparum [TaxId: 5833] [89990] (1)
                 3. Escherichia coli [TaxId: 562] [55428] (4)
              2. Trypanothione reductase [55429]
                 1. Crithidia fasciculata [TaxId: 5656] [55430] (6)
                 2. Trypanosoma cruzi [TaxId: 5693] [55431] (6)
              3. Mammalian thioredoxin reductase [64329]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [64330] (1)
              4. Apoptosis-inducing factor (AIF) [75489]
                 contains a large loop insertion in this domain
                 1. Human (Homo sapiens) [TaxId: 9606] [75490] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [75491] (1)
              5. NADH peroxidase [55432]
                 1. Enterococcus faecalis [TaxId: 1351] [55433] (8)
              6. NADH-dependent ferredoxin reductase, BphA4 [55434]
                 1. Pseudomonas sp., KKS102 [TaxId: 306] [55435] (2)
              7. Putidaredoxin reductase [103115]
                 1. Pseudomonas putida [TaxId: 303] [103116] (2)
              8. Dihydrolipoamide dehydrogenase [55436]
                 1. Pseudomonas putida [TaxId: 303] [55437] (1)
                 2. Pseudomonas fluorescens [TaxId: 294] [55438] (1)
                 3. Azotobacter vinelandii [TaxId: 354] [55439] (1)
                 4. Bacillus stearothermophilus [TaxId: 1422] [55440] (1)
                 5. Neisseria meningitidis [TaxId: 487] [55441] (2)
                 6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64331] (3)
                 7. Garden pea (Pisum sativum) [TaxId: 3888] [55442] (1)
                 8. Mycobacterium tuberculosis [TaxId: 1773] [118041] (1)
                    SQ O53355
              9. NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase [82726]
                 1. Xanthobacter sp., py2 [TaxId: 35809] [82727] (6)
              10. Flavocytochrome c sulfide dehydrogenase, FCSD, flavin-binding subunit [55443]
                  rudiment "interface" domain of smaller size; beta(3)-alpha
                  1. Purple phototrophic bacterium (Chromatium vinosum) [TaxId: 1049] [55444] (1)
              11. NADH oxidase /nitrite reductase [118042]
                  1. Pyrococcus furiosus [TaxId: 2261] [118043] (1)
                     SQ Q8U1K9
        2. CO dehydrogenase flavoprotein C-terminal domain-like [55447] (1)
           uperfamily
           1. CO dehydrogenase flavoprotein C-terminal domain-like [55448] (6)
              1. Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain [55449]
                 1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [55450] (7)
                 2. Hydrogenophaga pseudoflava [TaxId: 47421] [55451] (2)
              2. Xanthine oxidase, domain 4 (?) [55452]
                 1. Cow (Bos taurus) [TaxId: 9913] [55453] (7)
                    SQ P80457
              3. Xanthine dehydrogenase chain A, domain 4 [69772]
                 1. Rhodobacter capsulatus [TaxId: 1061] [69773] (2)
              4. Quinoline 2-oxidoreductase medium subunit QorM [111061]
                 1. Pseudomonas putida [TaxId: 303] [111062] (1)
                    SQ P72222
              5. 4-hydroxybenzoyl-CoA reductase beta subunit HrcB, C-terminal domain [118044]
                 1. Thauera aromatica [TaxId: 59405] [118045] (2)
                    SQ O33820
   200. SRF-like [55454] (1)
        alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
        1. SRF-like [55455] (1)
           uperfamily
           1. SRF-like [55456] (4)
              1. Serum response factor (SRF) core [55457]
                 1. Human (Homo sapiens) [TaxId: 9606] [55458] (3)
              2. MCM1 transcriptional regulator [55459]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55460] (1)
              3. Myocyte enhancer factor Mef2a core [55461]
                 1. Human (Homo sapiens) [TaxId: 9606] [55462] (2)
              4. Myocyte enhancer factor Mef2b core [103117]
                 1. Human (Homo sapiens) [TaxId: 9606] [103118] (2)
                    SQ Q02080 2-91
   201. Origin of replication-binding domain, RBD-like [55463] (1)
        alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel sheet 41325
        1. Origin of replication-binding domain, RBD-like [55464] (5)
           uperfamily
           1. The origin DNA-binding domain of SV40 T-antigen [55465] (1)
              1. The origin DNA-binding domain of SV40 T-antigen [55466]
                 1. Simian virus 40, Sv40 [TaxId: 10633] [55467] (14)
           2. DNA-binding domain of REP protein [82728] (1)
              1. DNA-binding domain of REP protein [82729]
                 1. Geminivirus (Tomato yellow leaf curl virus - sardinia) [TaxId: 123735] [82730] (2)
           3. Replication initiation protein E1 [64332] (2)
              1. Replication initiation protein E1 [64333]
                 1. Bovine papillomavirus [TaxId: 10571] [64334] (3)
                 2. Human papillomavirus type 18 [TaxId: 333761] [103119] (1)
           4. Replication protein Rep, nuclease domain [75492] (1)
              1. Replication protein Rep, nuclease domain [75493]
                 1. Adeno-associated virus, aav-5 [TaxId: 272636] [75494] (3)
           5. Relaxase domain [103120] (2)
              circular permutation of the common fold
              1. F factor TraI relaxase [103121]
                 1. Escherichia coli [TaxId: 562] [103122] (1)
              2. TrwC relaxase [103123]
                 1. Escherichia coli [TaxId: 562] [103124] (5)
   202. SARS receptor-binding domain-like [143586] (1)
        core: 3 layers, a/b/a; antiparallel beta-sheet of 5 strands, order 13542
        1. SARS receptor-binding domain-like [143587] (1)
           uperfamily
           1. SARS receptor-binding domain-like [143588] (1)
              part of PfamB 000266
              1. Spike protein S1 [143589]
                 1. SARS coronavirus [TaxId: 227859] [143590] (9)
                    SQ P59594 320-502! SQ P59594 321-512! SQ P59594 323-502
   203. Hut operon positive regulatory protein HutP [111063] (1)
        alpha(2)-beta-alpha(2)-beta(3); 3 layers: a/b/a; antiparallel beta-sheet: order 1234
        1. Hut operon positive regulatory protein HutP [111064] (1)
           uperfamily
           1. Hut operon positive regulatory protein HutP [111065] (1)
              1. Hut operon positive regulatory protein HutP [111066]
                 an RNA-binding antitermination protein
                 1. Bacillus subtilis [TaxId: 1423] [111067] (23)
                    SQ P10943
   204. Hypothetical protein yfbM [111068] (1)
        beta-alpha(2)-beta-alpha(2)-beta(2)-alpha(n)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 21543
        1. Hypothetical protein yfbM [111069] (1)
           uperfamily
           1. Hypothetical protein yfbM [111070] (1)
              1. Hypothetical protein yfbM [111071]
                 1. Escherichia coli [TaxId: 562] [111072] (1)
                    SQ P76483
   205. TTHA1528-like [143591] (1)
        beta-alpha-beta(3)-alpha-beta-alpha(2)-beta; 3 layers: a/b/a; mixed beta-sheet, order: 143256, parallel strands' pairs are 1-4 and 2-5
        1. TTHA1528-like [143592] (1)
           uperfamily
           1. TTHA1528-like [143593] (1)
              1. Hypothetical protein TTHA1528 (TT1805) [143594]
                 1. Thermus thermophilus [TaxId: 274] [143595] (2)
                    SQ Q5SI52 1-127
   206. YojJ-like [143596] (1)
        alpha-beta-X-beta-alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; 7-stranded mixed beta-sheet, order 2431567; strands 1 and 3 are parallel to each other
        1. YojJ-like [143597] (1)
           uperfamily
           1. YojJ-like [143598] (1)
              Pfam 02457; DUF147
              1. Hypothetical protein BC4920 (YojJ) [143599]
                 contains extra N-terminal hairpin of long helices; possible membrane spanning region
                 1. Bacillus cereus [TaxId: 1396] [143600] (3)
                    SQ Q812L9 1-201
   207. STIV B116-like [143601] (1)
        subunit fold consists of mixed 5-stranded beta-sheet, order:31452, strand 5 is antiparallel to the rest, with 3 helices on one side; dimerises with the formation of a single 10-stranded beta-sheet; strand 2 is in the dimer interface
        1. STIV B116-like [143602] (1)
           uperfamily
           1. STIV B116-like [143603] (2)
              1. Hypothetical protein B116 [143604]
                 1. Sulfolobus turreted icosahedral virus, STIV [TaxId: 269145] [143605] (2)
                    SQ Q6Q0K9 2-116
              2. Afv3-109 [143606]
                 1. Acidianus filamentous virus 1 [TaxId: 235266] [143607] (2)
   208. Bacillus phage protein [111073] (1)
        alpa-beta(3)-alpha-beta(3)-alpha; 3 layers: b/a/b, 3-helical bundle flanked by two 3-stranded meander beta-sheets
        1. Bacillus phage protein [111074] (1)
           uperfamily
           1. Bacillus phage protein [111075] (1)
              1. Bacillus phage protein [111076]
                 1. Bacillus cereus [TaxId: 1396] [111077] (1)
                    SQ Q81EU2; 100% sequence identity to a Bacteriophage phBC6A51 protein
   209. FMN-dependent nitroreductase-like [55468] (1)
        core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
        1. FMN-dependent nitroreductase-like [55469] (2)
           uperfamily
           1. NADH oxidase/flavin reductase [55470] (11)
              1. NADH oxidase [55471]
                 1. Thermus thermophilus, HB8 [TaxId: 274] [55472] (1)
              2. Flavin reductase P (NADPH:FMN oxidoreductase) [55473]
                 1. Vibrio harveyi [TaxId: 669] [55474] (2)
                 2. Vibrio fischeri [TaxId: 668] [55475] (5)
              3. Oxygen-insensitive NAD(P)H nitroreductase [55476]
                 1. Enterobacter cloacae [TaxId: 550] [55477] (4)
                 2. Escherichia coli, minor form, NfnB [TaxId: 562] [55478] (17)
                 3. Escherichia coli, major form, NfsA [TaxId: 562] [55479] (1)
              4. Hypothetical oxidoreductase SP0622 [143608]
                 1. Streptococcus pneumoniae [TaxId: 1313] [143609] (4)
                    SQ Q97S03 1-201
              5. Hypothetical protein Smu.260 [143610]
                 1. Streptococcus mutans [TaxId: 1309] [143611] (6)
                    SQ Q8DW21 2-200
              6. Hypothetical oxidoreductase BC1844 [143612]
                 1. Bacillus cereus [TaxId: 1396] [143613] (1)
                    SQ Q81EW9 2-200
              7. Hypothetical oxidoreductase YcnD [143614]
                 1. Bacillus subtilis [TaxId: 1423] [143615] (1)
                    SQ P94424 1-249
              8. NAD(P)H-flavin oxidoreductase Atu0013 [143616]
                 1. Agrobacterium tumefaciens [TaxId: 358] [143617] (2)
                    SQ Q8UJB5 1-200
           2. Putative nitroreductase TM1586 [111078] (1)
              duplication: consists of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site
              1. Putative nitroreductase TM1586 [111079]
                 1. Thermotoga maritima [TaxId: 2336] [111080] (1)
                    SQ Q9X1S2
   210. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55480] (1)
        alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
        1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55481] (1)
           uperfamily
           1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55482] (1)
              1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55483]
                 1. Human (Homo sapiens) [TaxId: 9606] [55484] (1)
   211. EscU C-terminal domain-like [160543] (1)
        alpha-beta(3)-alpha-beta-alpha(2); 3 layers, a/b/a; mixed beta-sheet, order: 4123, strand 2 is antiparallel to the rest
        1. EscU C-terminal domain-like [160544] (1)
           1. EscU C-terminal domain-like [160545] (3)
              C-terminal part of Pfam 01312; self-cleaving type III secretion protein domain
              1. Type III secretion proteins EscU [160546]
                 1. Escherichia coli [TaxId: 562] [160547] (8)
                    SQ Q9AJ26 237-345! SQ Q9AJ26 244-262,263-343! SQ Q9AJ26 245-262,263-343! SQ Q9AJ26 245-345! SQ Q9AJ26 246-262,263-345! SQ Q9AJ26 246-345
              2. Surface presentation of antigens protein SpaS [160548]
                 1. Shigella flexneri [TaxId: 623] [160549] (1)
                    SQ P0A1M8 237-257,258-338
                 2. Salmonella typhimurium [TaxId: 90371] [160550] (1)
                    SQ P40702 239-258,259-346
   212. Zincin-like [55485] (2)
        contains mixed beta sheet with connection over free side of the sheet
        1. Metalloproteases ("zincins"), catalytic domain [55486] (17)
           uperfamily
           1. Zinc protease [55487] (1)
              single domain
              1. Zinc protease [55488]
                 1. Streptomyces caespitosus [TaxId: 53502] [55489] (2)
           2. Fungal zinc peptidase [64335] (2)
              single domain with insertions in the common fold
              1. Fungal zinc peptidase [64336]
                 1. Grifola frondosa [TaxId: 5627] [64337] (4)
                 2. Aspergillus oryzae, deuterolysin [TaxId: 5062] [69774] (1)
           3. Thermolysin-like [55490] (4)
              includes alpha-helical C-terminal domain characteristic for the family
              1. Elastase [63413]
                 1. Pseudomonas aeruginosa [TaxId: 287] [55492] (2)
                    SQ P14756 198-495
              2. Thermolysin [63414]
                 1. Bacillus thermoproteolyticus [TaxId: 1427] [55494] (59)
                    SQ P00800
              3. Neutral protease [63415]
                 1. Bacillus cereus, strain dsm 3101 [TaxId: 1396] [55496] (2)
              4. Aureolysin [63416]
                 1. Staphylococcus aureus [TaxId: 1280] [55498] (1)
           4. Leukotriene A4 hydrolase catalytic domain [64338] (1)
              adopts thermolysin-like fold
              1. Leukotriene A4 hydrolase catalytic domain [64339]
                 1. Human (Homo sapiens) [TaxId: 9606] [64340] (15)
                    SQ P09960
           5. Neutral endopeptidase (neprilysin) [55502] (1)
              1. Neutral endopeptidase (neprilysin) [55503]
                 contains thermolysin-like catalytic domain (residues 419-749)
                 the N-terminal half of the structure is multihelical
                 1. Human (Homo sapiens) [TaxId: 9606] [55504] (6)
                    SQ P08473 54-749
           6. Neurolysin-like [55505] (6)
              combines M2, M3 and M32 families of metalloproteases
              the N-terminal half of the structure is multihelical; the C-terminal half contains the thermolysin-like catalytic domain
              1. Neurolysin (endopeptidase 24.16, thimet oligopeptidase) [55506]
                 M3 family member; the thermolysin-like catalytic domain consists of residues 352-674
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [55507] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [111081] (1)
                    SQ P52888
              2. Thermostable carboxypeptidase 1 [82731]
                 M32 (Taq) family member; overall fold is similar to that of neurolysin but is less elaborated
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82732] (3)
              3. Angiotensin converting enzyme, ACE [82733]
                 M2 family member; overall fold is similar to that of neurolysin but is less elaborated
                 1. Human (Homo sapiens) [TaxId: 9606] [82734] (5)
                    SQ P22966
                 2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89991] (3)
              4. Angiotensin converting enzyme 2, ACE2 [103125]
                 1. Human (Homo sapiens) [TaxId: 9606] [103126] (4)
           7. Anthrax toxin lethal factor, N- and C-terminal domains [69775] (1)
              1. Anthrax toxin lethal factor, N- and C-terminal domains [69776]
                 duplication: each domain adopts a thermolysin-like fold, but the proteolytic activity resides only in the C-terminal domain
                 1. Bacillus anthracis [TaxId: 1392] [69777] (12)
           8. Leishmanolysin [55499] (1)
              1. Leishmanolysin [55500]
                 the catalytic domain is N-terminal (residues 100-272)
                 the rest of structure will be classified in future releases
                 1. Leishmania major [TaxId: 5664] [55501] (1)
           9. Serralysin-like metalloprotease, catalytic (N-terminal) domain [55508] (4)
              characteristic HEXXHXXGXXH motif and Met located near C-terminus
              1. Metalloprotease [55509]
                 the rest of protein is all-beta sandwich containing a parallel beta-helix
                 1. Pseudomonas aeruginosa [TaxId: 287] [55510] (3)
                    alkaline protease
                 2. Serratia marcescens [TaxId: 615] [55511] (4)
                    Serralysin
                 3. Erwinia chrysanthemi [TaxId: 556] [82735] (5)
                    Protease C
                 4. Pseudomonas sp., tac ii 18 [TaxId: 306] [82736] (8)
                    psychrophilic alkaline protease
           10. Clostridium neurotoxins, catalytic domain [55512] (4)
               1. Botulinum neurotoxin [55513]
                  1. Clostridium botulinum, serotype A [TaxId: 1491] [55514] (15)
                     SQ P10845 1-419
                  2. Clostridium botulinum, serotype B [TaxId: 1491] [55515] (18)
                  3. Clostridium botulinum, serotype E [TaxId: 1491] [111082] (2)
                     SQ Q00496 1-421
                  4. Clostridium butyricum [TaxId: 1492] [160551] (2)
           11. Astacin [55516] (1)
               1. Astacin [55517]
                  1. European fresh water crayfish (Astacus astacus) [TaxId: 6715] [55518] (8)
           12. Reprolysin-like [55519] (8)
               Pfam 01421
               1. Snake venom metalloprotease [55520]
                  1. Eastern diamondback rattlesnake (Crotalus adamanteus), adamalysin II [TaxId: 8729] [55521] (4)
                  2. Western diamonback rattlesnake (Crotalus atrox), atrolysin C [TaxId: 8730] [55522] (3)
                  3. Taiwan habu (Trimeresurus mucrosquamatus), atrolysin E [TaxId: 103944] [75495] (4)
                  4. Five-pace snake (Agkistrodon acutus), acutolysin A [TaxId: 36307] [55523] (2)
                  5. Chinese five-pace snake (Agkistrodon acutus), acutolysin C [TaxId: 36307] [55524] (1)
                  6. Terciopelo (Bothrops asper), bap1 [TaxId: 8722] [103127] (1)
                  7. Habu (Trimeresurus flavoviridis), Trimerelysin II [TaxId: 88087] [111083] (1)
                     SQ P20165
               2. ADAM33 [118046]
                  1. Human (Homo sapiens) [TaxId: 9606] [118047] (2)
                     SQ Q9BZ11 204-409
           13. TNF-alpha converting enzyme, TACE, catalytic domain [55525] (1)
               1. TNF-alpha converting enzyme, TACE, catalytic domain [55526]
                  1. Human (Homo sapiens) [TaxId: 9606] [55527] (12)
           14. Matrix metalloproteases, catalytic domain [55528] (15)
               1. Fibroblast collagenase (MMP-1) [55529]
                  1. Human (Homo sapiens) [TaxId: 9606] [55530] (14)
                     SQ P03956 32-466
                  2. Pig (Sus scrofa) [TaxId: 9823] [55531] (3)
               2. MMP-2 [69778]
                  1. Human (Homo sapiens) [TaxId: 9606] [69779] (1)
               3. Neutrophil collagenase (MMP-8) [55532]
                  1. Human (Homo sapiens) [TaxId: 9606] [55533] (21)
               4. Gelatinase A [55534]
                  1. Human (Homo sapiens) [TaxId: 9606] [55535] (4)
               5. Stromelysin-1 (MMP-3) [55536]
                  1. Human (Homo sapiens), fibroblast [TaxId: 9606] [55537] (36)
               6. Matrilysin (MMP-7) [55538]
                  1. Human (Homo sapiens) [TaxId: 9606] [55539] (4)
               7. Gelatinase B (MMP-9) [75496]
                  1. Human (Homo sapiens) [TaxId: 9606] [75497] (13)
               8. Stromelysin-2 (MMP-10) [103128]
                  1. Human (Homo sapiens) [TaxId: 9606] [103129] (1)
               9. Stromelysin-3 (MMP-11) [64341]
                  1. Mouse (Mus musculus) [TaxId: 10090] [64342] (1)
               10. Macrophage elastase (MMP-12) [69780]
                   1. Human (Homo sapiens) [TaxId: 9606] [69781] (18)
                      SQ P39900 106-263 ! SQ P39900 106-264
               11. Collagenase-3 (MMP-13) [55540]
                   1. Human (Homo sapiens) [TaxId: 9606] [55541] (34)
                   2. Mouse (Mus musculus) [TaxId: 10090] [55542] (1)
               12. Membrane-type matrix metalloproteinase (CDMT1-MMP) [55543]
                   1. Human (Homo sapiens) [TaxId: 9606] [55544] (2)
               13. Matrix metalloproteinase-16 (MMP-16) [103130]
                   1. Human (Homo sapiens) [TaxId: 9606] [103131] (1)
           15. Predicted metal-dependent hydrolase [103132] (3)
               Pfam 02130; UPF0054; COG0319; MMP-like fold with a different sequence motif in the putative active site
               1. Hypothetical protein Aq_1354 [103133]
                  1. Aquifex aeolicus [TaxId: 63363] [103134] (1)
               2. Hypothetical protein YbeY [118048]
                  1. Escherichia coli [TaxId: 562] [118049] (1)
                     SQ P77385
               3. Hypothetical protein TM1509 [118050]
                  1. Thermotoga maritima [TaxId: 2336] [118051] (1)
                     SQ Q9X1J7
           16. Caur0242-like [160552] (1)
               Pfam 10103; DUF2342; there is a characteristic HExxH motif but no metal ion bound to it in the first structure.
               1. Uncharacterized protein Caur0242 [160553]
                  1. Chloroflexus aurantiacus [TaxId: 1108] [160554] (1)
                     SQ A9WCA2 43-391
           17. TTHA0227-like [160555] (2)
               PF06262; DUF1025; minimal zincin fold that retains 3-stranded mixed beta-sheet and contains HExxH motif in the C-terminal helix; no metal ion bound to this motif is observed in the first determined structures
               1. Uncharacterized protein TTHA0227 [160556]
                  1. Thermus thermophilus [TaxId: 274] [160557] (2)
                     SQ Q5SLR6 2-108
               2. Uncharacterized protein Acel_2062 [160558]
                  1. Acidothermus cellulolyticus [TaxId: 28049] [160559] (2)
                     SQ A0LWM4 1-113
        2. beta-N-acetylhexosaminidase-like domain [55545] (3)
           contains similar fold but lacks its catalytic centre
           uperfamily
           1. beta-N-acetylhexosaminidase domain [55546] (4)
              family GH20
              1. Bacterial chitobiase, Domain 2 [55547]
                 1. Serratia marcescens [TaxId: 615] [55548] (4)
              2. beta-N-acetylhexosaminidase, N-terminal domain [64343]
                 1. Streptomyces plicatus [TaxId: 1922] [64344] (6)
              3. beta-hexosaminidase B, N-terminal domain [89992]
                 1. Human (Homo sapiens) [TaxId: 9606] [89993] (12)
              4. beta-hexosaminidase A [160560]
                 1. Human (Homo sapiens) [TaxId: 9606] [160561] (8)
                    SQ P06865 23-166
           2. alpha-D-glucuronidase, N-terminal domain [82737] (2)
              family GH67
              1. alpha-D-glucuronidase, N-terminal domain [82738]
                 inverting reaction mechanism
                 1. Pseudomonas cellulosa [TaxId: 155077] [82739] (5)
                 2. Bacillus stearothermophilus [TaxId: 1422] [82740] (7)
           3. Hyaluronidase N-terminal domain-like [143618] (2)
              1. Hyaluronidase N-terminal domain [143619]
                 1. Clostridium perfringens [TaxId: 1502] [143620] (6)
                    SQ Q8XL08 41-178
              2. Glucosaminidase GH84, N-terminal domain [143621]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [143622] (12)
                    SQ Q89ZI2 25-147
   213. SH2-like [55549] (1)
        3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
        1. SH2 domain [55550] (1)
           uperfamily
           1. SH2 domain [55551] (39)
              Pfam 00017
              1. p56-lck tyrosine kinase [55552]
                 1. Human (Homo sapiens) [TaxId: 9606] [55553] (16)
              2. Carboxyl-terminal src kinase (csk) [75498]
                 1. Human (Homo sapiens) [TaxId: 9606] [75499] (1)
              3. c-src tyrosine kinase [55556]
                 1. Human (Homo sapiens) [TaxId: 9606] [55557] (42)
                 2. Chicken (Gallus gallus) [TaxId: 9031] [55558] (3)
                 3. Rous sarcoma virus [TaxId: 11886] [69782] (13)
              4. Tyrosine kinase Fyn [55559]
                 1. Human (Homo sapiens) [TaxId: 9606] [55560] (3)
              5. Tyrosine phosphatase Syp [55561]
                 1. Mouse (Mus musculus) [TaxId: 10090] [55562] (4)
              6. Growth factor receptor-bound protein 2 (GRB2) [55563]
                 1. Human (Homo sapiens) [TaxId: 9606] [55564] (25)
              7. Hemopoetic cell kinase Hck [55565]
                 1. Human (Homo sapiens) [TaxId: 9606] [55566] (4)
              8. Crk proto-oncogen [82741]
                 1. Human (Homo sapiens) [TaxId: 9606] [82742] (3)
              9. Shc adaptor protein [55567]
                 1. Human (Homo sapiens) [TaxId: 9606] [55568] (2)
              10. Phosphatidylinositol 3-kinase, p85-alpha subunit [55569]
                  1. Cow (Bos taurus) [TaxId: 9913] [55570] (7)
                  2. Human (Homo sapiens) [TaxId: 9606] [55571] (2)
                  3. Rat (Rattus norvegicus) [TaxId: 10116] [55572] (2)
              11. Proto-oncogen tyrosine kinase [55573]
                  1. Human (Homo sapiens) [TaxId: 9606] [55574] (2)
              12. Syk tyrosine kinase [55575]
                  1. Human (Homo sapiens) [TaxId: 9606] [55576] (3)
              13. Growth factor receptor-bound protein 10, GRB10 [89994]
                  1. Human (Homo sapiens) [TaxId: 9606] [89995] (1)
              14. Growth factor receptor-bound protein 7 [103135]
                  1. Human (Homo sapiens) [TaxId: 9606] [103136] (5)
              15. Tyrosine-protein kinase zap-70 [89996]
                  1. Human (Homo sapiens) [TaxId: 9606] [89997] (3)
              16. Phospholipase C-gamma-1 [55577]
                  1. Cow (Bos taurus) [TaxId: 9913] [55578] (3)
              17. P55 Blk protein tyrosine kinase [55579]
                  1. Mouse (Mus musculus) [TaxId: 10090] [55580] (2)
              18. Itk/tsk protein tyrosine kinase [82743]
                  1. Mouse (Mus musculus) [TaxId: 10090] [82744] (6)
              19. Abl tyrosine kinase [55581]
                  1. Human (Homo sapiens) [TaxId: 9606] [55582] (1)
                  2. Mouse (Mus musculus) [TaxId: 10090] [89998] (2)
              20. Csk homologous kinase Chk [64345]
                  1. Human (Homo sapiens) [TaxId: 9606] [64346] (1)
              21. STAT-1 [55583]
                  1. Human (Homo sapiens) [TaxId: 9606] [55584] (1)
              22. STAT3b [55585]
                  1. Mouse (Mus musculus) [TaxId: 10090] [55586] (1)
              23. STAT homologue [103137]
                  1. Dictyostelium discoideum [TaxId: 44689] [103138] (2)
              24. Cbl [55587]
                  1. Human (Homo sapiens) [TaxId: 9606] [55588] (12)
              25. Tyrosine phoshatase shp-2 [55589]
                  1. Human (Homo sapiens) [TaxId: 9606] [55590] (1)
              26. The Xlp protein Sap [55591]
                  1. Human (Homo sapiens) [TaxId: 9606] [55592] (6)
              27. Ews/fli1 activated transcript 2, Eat2 [89999]
                  1. Mouse (Mus musculus) [TaxId: 10090] [90000] (1)
              28. Adaptor protein Aps [103139]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [103140] (2)
              29. Tyrosine-protein kinase 6 (Breast tumor kinase, Brk) [111084]
                  1. Human (Homo sapiens) [TaxId: 9606] [111085] (1)
                     SQ Q13882 75-174
              30. GRB2-related adaptor protein 2 (MONA, GRID) [111086]
                  1. Mouse (Mus musculus) [TaxId: 10090] [111087] (3)
                     SQ O89100 53-147
              31. Beta-chimaerin, N-terminal domain [118052]
                  includes N-terminal tail and the linker to the next domain
                  1. Human (Homo sapiens) [TaxId: 9606] [118053] (1)
                     SQ P52757 23-468
              32. Hematopoietic SH2 domain containing protein HSH2D [143623]
                  1. Human (Homo sapiens) [TaxId: 9606] [143624] (1)
                     SQ Q96JZ2 24-129
              33. Suppressor of cytokine signaling 2, SOCS-2 [160562]
                  1. Human (Homo sapiens) [TaxId: 9606] [160563] (1)
                     SQ O14508 32-134
              34. Suppressor of cytokine signaling 4, SOCS-4 [160564]
                  1. Human (Homo sapiens) [TaxId: 9606] [160565] (1)
                     SQ Q8WXH5 274-385
   214. HPr-like [55593] (2)
        beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
        1. HPr-like [55594] (1)
           uperfamily
           1. HPr-like [55595] (8)
              1. Histidine-containing phosphocarrier protein (HPr) [55596]
                 1. Bacillus subtilis [TaxId: 1423] [55597] (6)
                 2. Enterococcus faecalis [TaxId: 1351] [55598] (3)
                 3. Escherichia coli [TaxId: 562] [55599] (14)
                 4. Mycoplasma capricolum [TaxId: 2095] [55600] (1)
                 5. Staphylococcus aureus [TaxId: 1280] [55601] (1)
                 6. Staphylococcus carnosus [TaxId: 1281] [55602] (1)
                 7. Bacillus megaterium [TaxId: 1404] [118054] (4)
                    SQ O69250
              2. Crh, catabolite repression HPr-like protein [69783]
                 1. Bacillus subtilis [TaxId: 1423] [69784] (10)
        2. Putative transcriptional regulator TM1602, C-terminal domain [75500] (1)
           uperfamily
           1. Putative transcriptional regulator TM1602, C-terminal domain [75501] (1)
              1. Putative transcriptional regulator TM1602, C-terminal domain [75502]
                 1. Thermotoga maritima [TaxId: 2336] [75503] (1)
   215. TrkA C-terminal domain-like [116725] (1)
        beta-X-beta(2)-X-beta-alpha; pseudo barrel capped by helix at one end; topological similarity to the HPr-like fold
        1. TrkA C-terminal domain-like [116726] (1)
           uperfamily
           1. TrkA C-terminal domain-like [116727] (2)
              Pfam 02080
              1. Potassium channel-related protein MthK, C-terminal domain [116728]
                 1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [116729] (9)
              2. Hypothetical protein PH0236, C-terminal domain [143625]
                 1. Pyrococcus horikoshii [TaxId: 53953] [143626] (4)
                    SQ O57975 108-201
   216. Hypothetical protein YjiA, C-terminal domain [90001] (1)
        beta-alpha-beta(4)-alpha; 2 layers: a/b; antiparallel sheet 15234; topological similarity to the HPr-like fold
        1. Hypothetical protein YjiA, C-terminal domain [90002] (1)
           uperfamily
           1. Hypothetical protein YjiA, C-terminal domain [90003] (1)
              1. Hypothetical protein YjiA, C-terminal domain [90004]
                 homologue of the cobalamin biosynthesis protein CobW
                 1. Escherichia coli [TaxId: 562] [90005] (1)
   217. YggU-like [69785] (1)
        beta(2)-loop-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243; some similarity to the Homing endonuclease-like fold
        1. YggU-like [69786] (1)
           uperfamily
           1. YggU-like [69787] (2)
              1. Hypothetical protein YggU [82745]
                 1. Escherichia coli, o157 [TaxId: 562] [82746] (2)
              2. Hypothetical protein MTH637 [69788]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69789] (1)
   218. Homing endonuclease-like [55603] (2)
        alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
        1. Glucose permease domain IIB [55604] (1)
           uperfamily
           1. Glucose permease domain IIB [55605] (1)
              1. Glucose permease domain IIB [55606]
                 1. Escherichia coli [TaxId: 562] [55607] (4)
                    there are differences in secondary structure packing between the two NMR-determined structures
        2. Homing endonucleases [55608] (2)
           uperfamily
           1. Group I mobile intron endonuclease [55609] (5)
              contains two extra helices in the C-terminal extension
              1. DNA endonuclease I-CreI [55610]
                 1. Chlamydomonas reinhardtii [TaxId: 3055] [55611] (13)
                    SQ P05725 2-154 ! SQ P05725
              2. DNA endonuclease I-dmoI [55612]
                 duplication: contains tandem repeat of this fold
                 1. Archaeon Desulfurococcus mobilis [TaxId: 2274] [55613] (2)
              3. DNA endonuclease I-MsoI [90006]
                 1. Monomastix sp. cl-1997 [TaxId: 141716] [90007] (1)
              4. DNA endonuclease I-AniI [103141]
                 duplication: contains tandem repeat of this fold
                 1. Aspergillus nidulans [TaxId: 162425] [103142] (1)
                    synonym: Emericella nidulans
              5. DNA endonuclease I-SceI [118055]
                 duplication: contains tandem repeat of this fold
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118056] (1)
                    SQ P03882
           2. Intein endonuclease [55614] (2)
              duplication: contains tandem repeat of this fold
              1. VMA1-derived endonuclease (VDE) PI-SceI [55615]
                 homing endonuclease with protein splicing activity
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55616] (7)
                    SQ P17255 284-737
              2. PI-Pfui intein [55617]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [55618] (1)
   219. T-fold [55619] (2)
        beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
        tunnel-shaped: its known members form wide oligomeric barrels different sizes
        1. Tetrahydrobiopterin biosynthesis enzymes-like [55620] (4)
           bind purine or pterin in topologically similar sites between subunits
           uperfamily
           1. GTP cyclohydrolase I [55621] (4)
              1. GTP cyclohydrolase I [55622]
                 beta-sheets of five subunits form a barrel, closed: n=20, S=20
                 1. Escherichia coli [TaxId: 562] [55623] (7)
                 2. Human (Homo sapiens) [TaxId: 9606] [55624] (1)
                 3. Rat (Rattus norvegicus) [TaxId: 10116] [69790] (3)
                    SQ P22288
                 4. Thermus thermophilus [TaxId: 274] [143627] (15)
                    SQ Q5SH52 32-216
           2. 6-pyruvoyl tetrahydropterin synthase [55625] (4)
              1. 6-pyruvoyl tetrahydropterin synthase [55626]
                 beta-sheets of three subunits form a barrel, closed: n=12, S=12
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [55627] (3)
                 2. Plasmodium falciparum [TaxId: 5833] [118057] (1)
                    SQ Q6LEZ4
                 3. Caenorhabditis elegans [TaxId: 6239] [143628] (1)
                    SQ O02058 1-139
                 4. Plasmodium vivax [TaxId: 5855] [143629] (2)
                    73% similarity to the Plasmodium falciparum enzyme
           3. DHN aldolase/epimerase [55628] (4)
              beta-sheets of four subunits form a barrel, closed: n=16, S=16
              1. 7,8-dihydroneopterin aldolase [55629]
                 1. Staphylococcus aureus [TaxId: 1280] [55630] (15)
                    SQ P56740
                 2. Bacteria (Mycobacterium tuberculosis) [TaxId: 1773] [103143] (2)
                    SQ O06275 2-115
                 3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111088] (1)
                    SQ Q9SF23
              2. 7,8-dihydroneopterin triphosphate epimerase [55631]
                 1. Escherichia coli [TaxId: 562] [55632] (1)
           4. Urate oxidase (uricase) [55633] (3)
              1. Urate oxidase (uricase) [55634]
                 duplication: one subunit consists of two domains of this fold; beta-sheets of two subunits form a barrel, closed: n=16, S=16
                 1. Aspergillus flavus [TaxId: 5059] [55635] (72)
                 2. Bacillus sp., strain TB-90 [TaxId: 1409] [111089] (1)
                    SQ Q45697 177-482
                 3. Arthrobacter globiformis [TaxId: 1665] [143630] (96)
        2. ApbE-like [143631] (2)
           duplication: contains two differently decorated beta(2)-alpha(2)-beta(2) subdomains, similar to other T-fold domains; probably does not form the tunnel-shaped oligomers
           uperfamily
           1. ApbE-like [143632] (1)
              Pfam 02424
              1. Hypothetical protein TM1553 [143633]
                 1. Thermotoga maritima [TaxId: 2336] [143634] (1)
                    SQ Q9X1N9 44-352
           2. DVU1097-like [160566] (1)
              Pfam 04040; DUF375
              1. Hypothetical protein DVU1097 [160567]
                 1. Desulfovibrio vulgaris [TaxId: 881] [160568] (1)
                    SQ Q72D34 1-248
   220. Cell cycle regulatory proteins [55636] (1)
        beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
        can form strand-exchange dimers
        1. Cell cycle regulatory proteins [55637] (1)
           uperfamily
           1. Cell cycle regulatory proteins [55638] (4)
              1. suc1 [55639]
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [55640] (2)
                    in hexamer, the beta-sheets of three dimers form a barrel, closed: n=12, S=12
              2. cks1 [55641]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55642] (1)
              3. CksHs2 [55643]
                 1. Human (Homo sapiens) [TaxId: 9606] [55644] (1)
              4. CksHs1 [55645]
                 1. Human (Homo sapiens) [TaxId: 9606] [55646] (5)
   221. YonK-like [160569] (1)
        intertwined dimer of beta(3)-alpha-beta subunits; assembles further in octamer with formation of a wide 16-stranded beta-barrel
        1. YonK-like [160570] (1)
           (Pro)phage and phage-related proteins
           1. Yonk-like [160571] (1)
              Pfam 09642
              1. Uncharacterized protein YonK [160572]
                 1. Bacillus subtilis [TaxId: 1423] [160573] (4)
                    SQ O31947 2-63
   222. BLIP-like [55647] (2)
        alpha(2)-beta(4); 2 layers: alpha/beta
        1. beta-lactamase-inhibitor protein, BLIP [55648] (1)
           uperfamily
           1. beta-lactamase-inhibitor protein, BLIP [55649] (1)
              duplication: consists of two clear structural repeats each having this fold
              1. beta-lactamase-inhibitor protein, BLIP [55650]
                 1. Streptomyces clavuligerus [TaxId: 1901] [55651] (6)
        2. BT0923-like [160574] (1)
           Duplication: tandem repeat of two similar structural subdomains, which associate like the BLIP repeats but differ from them by transposition of the helices
           1. BT0923-like [160575] (2)
              after putative calcium-regulated periplasmic protein BT0923 (PDB ID 3DUE; new)
              1. Putative periplasmic protein BVU2443 [160576]
                 1. Bacteroides vulgatus [TaxId: 821] [160577] (2)
                    SQ A6L337 20-146
              2. Putative periplasmic protein BVU2987 [160578]
                 1. Bacteroides vulgatus [TaxId: 821] [160579] (1)
                    SQ A6L4L1 20-145
   223. Ribosomal protein L9 C-domain [55652] (1)
        alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
        1. Ribosomal protein L9 C-domain [55653] (1)
           uperfamily
           1. Ribosomal protein L9 C-domain [55654] (3)
              1. Ribosomal protein L9 C-domain [55655]
                 1. Bacillus stearothermophilus [TaxId: 1422] [55656] (5)
                 2. Thermus thermophilus [TaxId: 274] [143635] (5)
                    SQ Q5SLQ1 55-146
                 3. Escherichia coli [TaxId: 562] [160580] (29)
                    SQ P0A7R1 59-149
   224. MbtH/L9 domain-like [55657] (2)
        beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
        1. L9 N-domain-like [55658] (2)
           uperfamily
           1. Ribosomal protein L9 N-domain [55659] (3)
              1. Ribosomal protein L9 N-domain [55660]
                 1. Bacillus stearothermophilus [TaxId: 1422] [55661] (10)
                 2. Thermus thermophilus [TaxId: 274] [143636] (5)
                    SQ Q5SLQ1 1-55
                 3. Escherichia coli [TaxId: 562] [160581] (29)
                    SQ P0A7R1 1-58
           2. N-terminal domain of RNase HI [55662] (1)
              1. N-terminal domain of RNase HI [55663]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55664] (1)
        2. MbtH-like [160582] (1)
           the first helix is replaced with an extended loop; contains extra C-terminal helix of variable position
           1. MbtH-like [160583] (1)
              Pfam 03621
              1. Uncharacterized protein PA2412 [160584]
                 1. Pseudomonas aeruginosa [TaxId: 287] [160585] (2)
                    SQ Q9I169 1-72
   225. Tombusvirus P19 core protein, VP19 [103144] (1)
        beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel sheet: order 2134
        1. Tombusvirus P19 core protein, VP19 [103145] (1)
           uperfamily
           1. Tombusvirus P19 core protein, VP19 [103146] (2)
              1. Tombusvirus P19 core protein, VP19 [103147]
                 an RNA silencing suppressor
                 1. Tomato bushy stunt virus, TBSV [TaxId: 12145] [103148] (1)
                 2. Carnation italian ringspot virus, CIRV [TaxId: 39443] [103149] (1)
   226. Ribonuclease PH domain 2-like [55665] (1)
        beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
        1. Ribonuclease PH domain 2-like [55666] (1)
           uperfamily
           1. Ribonuclease PH domain 2-like [55667] (14)
              1. Ribonuclease PH, domain 2 [103150]
                 1. Aquifex aeolicus [TaxId: 63363] [103151] (4)
                 2. Pseudomonas aeruginosa [TaxId: 287] [103152] (2)
                 3. Bacillus subtilis [TaxId: 1423] [103153] (3)
              2. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 [55668]
                 duplication of two-domain units formed by domains 1-2 and 4-5
                 1. Streptomyces antibioticus [TaxId: 1890] [55669] (2)
              3. Exosome complex exonuclease RRP45 [160586]
                 1. Human (Homo sapiens) [TaxId: 9606] [160587] (1)
                    SQ Q86Y41 185-302
              4. Exosome complex exonuclease RRP42 [160588]
                 1. Human (Homo sapiens) [TaxId: 9606] [160589] (1)
                    SQ Q15024 192-285
              5. Exosome complex exonuclease 1, ECX1 [160590]
                 1. Sulfolobus solfataricus [TaxId: 2287] [160591] (50)
                    SQ Q9UXC2 156-241! SQ Q9UXC2 156-248
                 2. Archaeoglobus fulgidus [TaxId: 2234] [160592] (6)
                    SQ O29757 154-252
              6. Exosome complex exonuclease RRP41 [160593]
                 1. Human (Homo sapiens) [TaxId: 9606] [160594] (1)
                    SQ Q9NPD3 152-241
              7. Exosome complex exonuclease RRP46 [160595]
                 1. Human (Homo sapiens) [TaxId: 9606] [160596] (1)
                    SQ Q9NQT4 147-235
              8. Exosome complex exonuclease 2, ECX2 [160597]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [160598] (6)
                    SQ O29756 179-257
                 2. Sulfolobus solfataricus [TaxId: 2287] [160599] (51)
                    SQ Q9UXC0 192-275
              9. Exosome complex exonuclease MTR3 [160600]
                 1. Human (Homo sapiens) [TaxId: 9606] [160601] (1)
                    SQ Q5RKV6 176-270
              10. Exosome complex exonuclease RRP43 [160602]
                  1. Human (Homo sapiens) [TaxId: 9606] [160603] (1)
                     SQ Q96B26 188-276
   227. Regulatory factor Nef [55670] (1)
        alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
        1. Regulatory factor Nef [55671] (1)
           uperfamily
           1. Regulatory factor Nef [55672] (1)
              1. Regulatory factor Nef [55673]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [55674] (4)
   228. CytB endotoxin-like [55675] (1)
        core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
        1. CytB endotoxin-like [55676] (1)
           uperfamily
           1. CytB endotoxin-like [55677] (2)
              Pfam 01338
              1. Mosquitocidal delta-endotoxin CytB [55678]
                 1. Bacillus thuringiensis, strain Kyushuensis [TaxId: 1428] [55679] (1)
              2. Volvatoxin A2 [111090]
                 1. Volvariella volvacea, different isoforms [TaxId: 36659] [111091] (4)
                    SQ Q6USC4
   229. Class II aaRS and biotin synthetases [55680] (1)
        contains large mixed beta-sheet
        1. Class II aaRS and biotin synthetases [55681] (4)
           uperfamily
           1. Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain [55682] (28)
              1. Seryl-tRNA synthetase (SerRS) [55683]
                 1. Thermus thermophilus, strain hb27 [TaxId: 274] [55684] (4)
              2. Lysyl-tRNA synthetase (LysRS) [55685]
                 contains an insertion of LEM/SAP-like HeH motif, residues 337-379
                 1. Escherichia coli, gene lysU [TaxId: 562] [55686] (5)
                 2. Escherichia coli, gene lysS [TaxId: 562] [55687] (2)
              3. Histidyl-tRNA synthetase (HisRS) [55688]
                 1. Escherichia coli [TaxId: 562] [55689] (7)
                 2. Staphylococcus aureus [TaxId: 1280] [55690] (1)
                 3. Thermus thermophilus [TaxId: 274] [55691] (3)
                 4. Archaeon Thermoplasma acidophilum [TaxId: 2303] [143637] (2)
                    SQ Q9HLX5 3-329
              4. Glycyl-tRNA synthetase (GlyRS) [55692]
                 1. Thermus thermophilus [TaxId: 274] [55693] (3)
              5. Threonyl-tRNA synthetase (ThrRS) [55694]
                 1. Escherichia coli [TaxId: 562] [55695] (5)
                 2. Staphylococcus aureus [TaxId: 1280] [103154] (2)
              6. Aspartyl-tRNA synthetase (AspRS) [55696]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55697] (3)
                 2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [55698] (1)
                 3. Thermus thermophilus, AspRS-2 [TaxId: 274] [90008] (1)
                    non-discriminating and archaeal-type enzyme
                 4. Escherichia coli [TaxId: 562] [55699] (3)
                 5. Thermus thermophilus, AspRS-1 [TaxId: 274] [55700] (3)
              7. Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS [55701]
                 1. Thermus thermophilus [TaxId: 274] [55702] (9)
                    identical sequence to Thermus aquaticus, TaxId: 271
              8. Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain [55703]
                 this domain is non-catalytic
                 1. Thermus thermophilus [TaxId: 274] [55704] (9)
                    identical sequence to Thermus aquaticus, TaxId: 271
              9. Glycyl-tRNA synthetase (GlyRS) alpha chain [75504]
                 1. Thermotoga maritima [TaxId: 2336] [75505] (1)
                    TM0216
              10. Alanyl-tRNA synthetase (AlaRS) [103155]
                  1. Aquifex aeolicus [TaxId: 63363] [103156] (7)
              11. Prolyl-tRNA synthetase (ProRS) [64347]
                  1. Thermus thermophilus [TaxId: 274] [64348] (4)
                  2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [90009] (4)
                  3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [90010] (1)
              12. The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-terminal domain [64349]
                  1. Mouse (Mus musculus) [TaxId: 10090] [64350] (2)
                  2. Human (Homo sapiens) [TaxId: 9606] [143638] (4)
                     SQ Q9UHN1 66-355
              13. Asparagine synthetase [55705]
                  1. Escherichia coli [TaxId: 562] [55706] (2)
              14. Hypothetical protein PF1951 [103157]
                  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [103158] (1)
                     AspRS-related protein
              15. ATP phosphoribosyltransferase regulatory subunit HisZ [118058]
                  shares histidine-binding site with the HisRS catalytic domain
                  1. Thermotoga maritima [TaxId: 2336] [118059] (1)
                     SQ Q9X0D3
                  2. Lactococcus lactis [TaxId: 1358] [143639] (8)
                     SQ Q02147 6-323
           2. Biotin holoenzyme synthetase [55707] (2)
              1. Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain [55708]
                 this structure contains an SH2-like fold
                 1. Escherichia coli [TaxId: 562] [55709] (5)
              2. Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain [143640]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143641] (28)
                    SQ O57883 1-188
           3. LplA-like [143642] (6)
              part of Pfam 03099
              1. Lipoyltransferase LipB [143643]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143644] (1)
                    SQ Q10404 1-216
              2. LplA-like protein SP1160, N-terminal domain [143645]
                 1. Streptococcus pneumoniae [TaxId: 1313] [143646] (1)
                    SQ Q97QP1 1-241
              3. Lipoate-protein ligase A [160604]
                 1. Streptococcus agalactiae [TaxId: 1311] [160605] (1)
                    SQ Q3D8N4 2-270
                 2. Thermoplasma acidophilum [TaxId: 2303] [160606] (11)
                    SQ Q9HKT1 1-257
              4. Two-domain LplA, N-terminal domain [160607]
                 1. Escherichia coli [TaxId: 562] [160608] (6)
                    SQ P32099 1-246
              5. Hypothetical protein BH3822 [160609]
                 1. Bacillus halodurans [TaxId: 86665] [160610] (1)
                    SQ Q9K6A7 12-276
           4. PH0223-like [160611] (1)
              Pfam 04017; DUF366
              1. Uncharacterized protein PH0223 [160612]
                 1. Pyrococcus horikoshii [TaxId: 53953] [160613] (6)
                    SQ O57962 3-190
   230. Subdomain of clathrin and coatomer appendage domain [55710] (1)
        beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
        1. Subdomain of clathrin and coatomer appendage domain [55711] (2)
           uperfamily
           1. Clathrin adaptor appendage, alpha and beta chain-specific domain [55712] (2)
              1. Alpa-adaptin AP2, C-terminal subdomain [55713]
                 1. Mouse (Mus musculus) [TaxId: 10090] [55714] (10)
                    SQ P17427 694-938 # 98% sequence identity
              2. Beta2-adaptin AP2, C-terminal subdomain [55715]
                 1. Human (Homo sapiens) [TaxId: 9606] [55716] (5)
           2. Coatomer appendage domain [103159] (2)
              1. Coatomer gamma subunit, C-terminal subdomain [103160]
                 1. Human (Homo sapiens) [TaxId: 9606] [103161] (1)
                 2. Cow (Bos taurus) [TaxId: 9913] [103162] (1)
   231. SCP-like [55717] (1)
        alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
        1. SCP-like [55718] (4)
           uperfamily
           1. Sterol carrier protein, SCP [55719] (5)
              Pfam 02036
              1. Sterol carrier protein 2 (SCP2) [55720]
                 1. Human (Homo sapiens) [TaxId: 9606] [55721] (2)
                 2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55722] (1)
                 3. Yellow fever mosquito (Aedes aegypti) [TaxId: 7159] [103163] (1)
              2. SCP2-like domain of MFE-2 [69791]
                 1. Human (Homo sapiens) [TaxId: 9606] [69792] (1)
              3. Hypothetical protein TT1886 (TTHA0401) [118060]
                 1. Thermus thermophilus [TaxId: 274] [118061] (1)
                    SQ Q5SL92
           2. Micothiol-dependent maleylpyruvate isomerase C-terminal domain-like [160614] (1)
              lacking the short edge strand 3
              1. Micothiol-dependent maleylpyruvate isomerase [160615]
                 1. Corynebacterium glutamicum [TaxId: 1718] [160616] (2)
                    SQ Q8NLC1 161-240
                    Cgl3021
           3. Alkylsulfatase C-terminal domain-like [160617] (1)
              1. Alkylsulfatase SdsA1 [160618]
                 1. Pseudomonas aeruginosa [TaxId: 287] [160619] (4)
                    SQ Q9I5I9 530-655
           4. EF1021 C-terminal domain-like [160620] (3)
              1. Hypothetical protein EF1021 [160621]
                 1. Enterococcus faecalis [TaxId: 1351] [160622] (6)
                    SQ Q836T6 287-397
              2. Putative acetyltransferase EF2353 [160623]
                 1. Enterococcus faecalis [TaxId: 1351] [160624] (6)
                    SQ Q831Y9 301-406
              3. Putative acetyltransferase Ava4977 [160625]
                 1. Anabaena variabilis [TaxId: 1172] [160626] (1)
                    SQ Q3M362 291-395
   232. Ta1353-like [103164] (1)
        core: beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 51423;
        1. Ta1353-like [103165] (1)
           uperfamily
           1. Ta1353-like [103166] (2)
              Pfam 04008
              1. Hypothetical protein Ta1353 [103167]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [103168] (1)
              2. Hypothetical protein TT1634 (TTHA1091) [118062]
                 1. Thermus thermophilus [TaxId: 274] [118063] (1)
                    SQ Q5SJC3
   233. Mog1p/PsbP-like [55723] (1)
        (beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
        1. Mog1p/PsbP-like [55724] (4)
           uperfamily
           1. Ran-binding protein mog1p [55725] (1)
              1. Ran-binding protein mog1p [55726]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55727] (2)
           2. PsbP-like [111092] (1)
              Pfam 01789
              1. Oxygen-evolving enhancer protein PsbP [111093]
                 1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [111094] (1)
                    SQ P18212
           3. PA0094-like [111095] (1)
              segment-swapped dimer; some sequence similarity to the PsbP-like family
              1. Hypothetical protein PA0094 [111096]
                 1. Pseudomonas aeruginosa [TaxId: 287] [111097] (1)
                    SQ Q9I738
           4. DIP2269-like [160627] (1)
              Pfam 09449; DUF2020
              1. Hypothetical protein DIP2269 [160628]
                 1. Corynebacterium diphtheriae [TaxId: 1717] [160629] (2)
                    SQ Q6NEK4 2-148
   234. SMI1/KNR4-like [160630] (1)
        alpha(4)-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet, order 1234(meander)
        1. SMI1/KNR4-like [160631] (1)
           1. SMI1/KNR4-like [160632] (3)
              Pfam 09346
              1. Uncharacterized protein Lin2918 [160633]
                 1. Listeria innocua [TaxId: 1642] [160634] (1)
                    SQ Q926X2 1-158
              2. Hypothetical protein PSPTO5518 [160635]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [160636] (1)
                    SQ Q87TZ9 1-135
              3. Uncharacterized protein YobK [160637]
                 1. Bacillus subtilis [TaxId: 1423] [160638] (2)
                    SQ O34596 1-152
   235. Acyl-CoA N-acyltransferases (Nat) [55728] (1)
        3 layers: a/b/a; contains mixed beta-sheet
        1. Acyl-CoA N-acyltransferases (Nat) [55729] (10)
           uperfamily
           1. N-acetyl transferase, NAT [55730] (60)
              1. Aminoglycoside 6'-N-acetyltransferase [55731]
                 1. Enterococcus faecium [TaxId: 1352] [55732] (4)
              2. Aminoglycoside 3-N-acetyltransferase [55733]
                 1. Serratia marcescens [TaxId: 615] [55734] (1)
              3. Aminoglycoside 2'-N-acetyltransferase [75506]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [75507] (4)
              4. Tabtoxin resistance protein [82747]
                 possesses HAT activity
                 1. Pseudomonas syringae [TaxId: 317] [82748] (2)
              5. Histone acetyltransferase domain of P300/CBP associating factor, PCAF [55735]
                 1. Human (Homo sapiens) [TaxId: 9606] [55736] (1)
              6. Catalytic domain of GCN5 histone acetyltransferase [55737]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55738] (1)
                 2. Tetrahymena thermophila [TaxId: 5911] [55739] (9)
                    SQ Q27198 49-209
                 3. Human (Homo sapiens) [TaxId: 9606] [143647] (1)
                    SQ Q92830 497-658
              7. Histone acetyltransferase HPA2 [55740]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55741] (2)
              8. Histone acetyltransferase HAT1 [55742]
                 contains additional N- and C-terminal (sub)domains
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55743] (1)
              9. Histone acetyltransferase ESA1 [55744]
                 most similar to HAT1 including the N- and C-terminal (sub)domains; the N-terminal domain contains a rudiment CCHC zinc-finger (res. 191-220); the C-terminal domain (res. 351-434) has "winged helix" DNA-binding fold
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55745] (4)
              10. Serotonin N-acetyltranferase [55746]
                  1. Sheep (Ovis aries) [TaxId: 9940] [55747] (7)
              11. Glucosamine-phosphate N-acetyltransferase GNA1 [64351]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64352] (3)
              12. Putative acetyltransferase YycN [90011]
                  1. Bacillus subtilis [TaxId: 1423] [90012] (2)
              13. Hypothetical protein YqiY [90013]
                  1. Bacillus subtilis [TaxId: 1423] [90014] (1)
              14. Probable acetyltransferase YdaF [90015]
                  1. Bacillus subtilis [TaxId: 1423] [90016] (1)
              15. Probable acetyltransferase YjcF [103169]
                  1. Bacillus subtilis [TaxId: 1423] [103170] (1)
              16. Putative phosphinothricin acetyltransferase YwnH [103171]
                  1. Bacillus subtilis [TaxId: 1423] [103172] (1)
              17. Hypothetical protein SA2309 [103173]
                  1. Staphylococcus aureus [TaxId: 1280] [103174] (2)
              18. Mycothiol synthase MshD [103175]
                  duplication: consists of two NAT domains swapped with the C-terminal strands with both domains binding acetyl-CoA; structural link with the other families
                  1. Mycobacterium tuberculosis [TaxId: 1773] [103176] (3)
                     Rv0819
              19. Aminoglycoside N-acetyltransferase AAC(6')-IY [111098]
                  1. Salmonella enteritidis [TaxId: 149539] [111099] (3)
                     SQ Q9R381
                  2. Salmonella choleraesuis [TaxId: 28901] [160639] (2)
              20. Protease synthase and sporulation negative regulatory protein PaiA [111100]
                  1. Bacillus subtilis [TaxId: 1423] [111101] (1)
                     SQ P21340
              21. Hypothetical protein AT1g77540 [118064]
                  1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118065] (3)
                     SQ Q8LEN2
              22. Hypothetical protein PA0115 [118066]
                  1. Pseudomonas aeruginosa [TaxId: 287] [118067] (1)
                     SQ Q9I717
              23. Probable acetyltransferase TTHA1209 [118068]
                  1. Thermus thermophilus [TaxId: 274] [118069] (2)
                     SQ Q5SJ05
              24. Putative acetyltransferase EF0945 [118070]
                  1. Enterococcus faecalis [TaxId: 1351] [118071] (1)
                     SQ Q836Z8
              25. Putative acetyltransferase PF0028 [118072]
                  1. Pyrococcus furiosus [TaxId: 2261] [118073] (1)
                     SQ Q8U4Q2
              26. Hypothetical protein PH1933 [143648]
                  1. Pyrococcus horikoshii [TaxId: 53953] [143649] (2)
                     SQ O59596 1-157
              27. Probable acetyltransferase BC2806 [143650]
                  1. Bacillus cereus [TaxId: 1396] [143651] (2)
                     SQ Q81CG1 1-140
              28. Diamine acetyltransferase 1 [143652]
                  1. Human (Homo sapiens) [TaxId: 9606] [143653] (18)
                     SQ P21673 2-170! SQ P21673 3-169
              29. Hypothetical protein YsnE [143654]
                  1. Bacillus subtilis [TaxId: 1423] [143655] (1)
                     SQ P94562 1-151
              30. Probable acetyltransferase Atu2258 [143656]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143657] (1)
                     SQ Q7CXI0 1-137
              31. Transcriptional regulator BH1968 [143658]
                  1. Bacillus halodurans [TaxId: 86665] [143659] (2)
                     SQ Q9KBG0 4-153
              32. Probable acetyltransferase Atu2290 [143660]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143661] (4)
                     SQ Q8UD38 6-169
              33. Probable acetyltransferase EF1919 [143662]
                  1. Enterococcus faecalis [TaxId: 1351] [143663] (2)
                     SQ Q833M5 1-157
              34. Putative acetyltransferase EF0244 [143664]
                  1. Enterococcus faecalis [TaxId: 1351] [143665] (4)
                     SQ Q839D1 1-161
              35. Hypothetical protein PH0736 [143666]
                  1. Pyrococcus horikoshii [TaxId: 53953] [143667] (2)
                     SQ O58467 1-182
              36. Hypothetical protein Rv1347c/MT1389 [143668]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [143669] (8)
                     SQ P64819 10-207
              37. Probable acetyltransferase YitI [143670]
                  1. Bacillus licheniformis [TaxId: 1402] [143671] (3)
                     SQ Q65LG7 2-146
              38. Probable histone acetyltransferase MYST1 [143672]
                  ESA1 orthologue
                  1. Human (Homo sapiens) [TaxId: 9606] [143673] (1)
                     SQ Q9H7Z6 178-448
              39. Hypothetical protein SA2161 [143674]
                  1. Staphylococcus aureus [TaxId: 1280] [143675] (2)
                     SQ Q7A3W2 1-133
              40. Probable N-acetyltransferase PA0478 [143676]
                  1. Pseudomonas aeruginosa [TaxId: 287] [143677] (2)
                     SQ Q9I640 3-158
              41. L7/L12-Ribosomal-protein-serine acetyltransferase RimL [143678]
                  1. Salmonella typhimurium [TaxId: 90371] [143679] (9)
                     SQ Q8ZPC0 1-176
              42. Probable acetyltransferase SP0256 [143680]
                  probable SA2161 ortholog
                  1. Streptococcus pneumoniae [TaxId: 1313] [143681] (1)
                     SQ Q97SR8 1-137
              43. Probable spermine/spermidine acetyltransferase EF1086 [143682]
                  1. Enterococcus faecalis [TaxId: 1351] [143683] (1)
                     SQ Q836M4 1-146
              44. Putative ribosomal-protein-serine acetyltransferase VC1889 [143684]
                  similar to RimL and RimJ
                  1. Vibrio cholerae [TaxId: 666] [143685] (1)
                     SQ Q9KQV9 1-178
              45. Hypothetical protein PA3270 [143686]
                  1. Pseudomonas aeruginosa [TaxId: 287] [143687] (4)
                     SQ Q9HYX1 11-193
              46. Diamine acetyltransferase 2 [143688]
                  1. Human (Homo sapiens) [TaxId: 9606] [143689] (4)
                     SQ Q96F10 3-169
              47. Hypothetical protein MW0638 [143690]
                  SA0631 ortholog
                  1. Staphylococcus aureus [TaxId: 1280] [143691] (1)
                     SQ Q8NXQ8 1-118
              48. Probable acetyltransferase PA4026 [143692]
                  1. Pseudomonas aeruginosa [TaxId: 287] [143693] (4)
                     SQ Q9HX01 1-153
              49. Hypothetical protein PA4866 [143694]
                  Putative phosphinothricin acetyltransferase
                  1. Pseudomonas aeruginosa [TaxId: 287] [143695] (3)
                     SQ Q9HUU7 3-172! SQ Q9HUU7 4-172
              50. IAA acetyltransferase [143696]
                  YvbK ortholojg
                  1. Bacillus cereus [TaxId: 1396] [143697] (4)
                     SQ Q81FK8 1-152
              51. Phosphinothricin acetyltransferase [143698]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143699] (4)
                     SQ Q8UGX8 2-164
              52. Putative acetyltransferase PA4794 [143700]
                  1. Pseudomonas aeruginosa [TaxId: 287] [143701] (1)
                     SQ Q9HV14 1-160
              53. Histone acetyltransferase MYST3 [143702]
                  ESA1 orthologue
                  1. Human (Homo sapiens) [TaxId: 9606] [143703] (2)
                     SQ Q92794 507-776
                     solution structure of the zinc-binding motif have been determined in isolation (PDB 1m36, scop_sp 103600)
              54. Probable acetyltranferase Atu2435 [143704]
                  1. Agrobacterium tumefaciens [TaxId: 358] [143705] (1)
                     SQ Q8UCP8 4-167
              55. Hypothetical protein YvbK (BSu33890) [143706]
                  1. Bacillus subtilis [TaxId: 1423] [143707] (4)
                     SQ O32248 5-156
              56. Probable N-acetyltransferase RPA1999 [143708]
                  1. Rhodopseudomonas palustris [TaxId: 1076] [143709] (1)
                     SQ Q6N8A5 2-157
              57. Hypothetical protein TTHA1254 [160640]
                  1. Thermus thermophilus [TaxId: 274] [160641] (2)
                     SQ Q5SIW0 1-130
           2. N-myristoyl transferase, NMT [55748] (3)
              duplication: consists of two NAT-like domains swapped with the C-terminal strands
              1. N-myristoyl transferase, NMT [55749]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55750] (3)
                 2. Yeast (Candida albicans) [TaxId: 5476] [55751] (3)
                 3. Human (Homo sapiens) [TaxId: 9606] [143710] (8)
                    SQ P30419 155-294! SQ P30419 295-496
           3. Autoinducer synthetase [75508] (2)
              Pfam 00765
              1. Acyl-homoserinelactone synthase EsaI [75509]
                 1. Pantoea stewartii subsp. stewartii [TaxId: 66271] [75510] (2)
              2. Autoinducer synthesis protein LasI [111102]
                 1. Pseudomonas aeruginosa [TaxId: 287] [111103] (1)
                    SQ P33883
           4. FemXAB nonribosomal peptidyltransferases [82749] (3)
              duplication: consists of two NAT-like domains swapped with the C-terminal strands
              1. Methicillin resistance protein FemA [82750]
                 transfer glycyl residue from tRNA-Gly
                 1. Staphylococcus aureus [TaxId: 1280] [82751] (1)
              2. Peptidyltransferase FemX [103177]
                 1. Weissella viridescens [TaxId: 1629] [103178] (8)
              3. Hypothetical protein BT3689 [160642]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [160643] (4)
                    SQ Q8A1H2 1-134! SQ Q8A1H2 135-298
           5. Hypothetical protein cg14615-pa [103179] (1)
              duplication: consists of two NAT-like domains swapped with the C-terminal strands
              1. Hypothetical protein cg14615-pa [103180]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103181] (1)
           6. LFTR-like [143711] (1)
              Pfam 03588; closer relative to the nonribosomal peptidyltransferases (scop_fa 82749); deletion of the N-terminal half of the N-terminal NAT-like domain after the domain duplication/swapping events
              1. Leucyl/phenylalanyl-tRNA-protein transferase, LFTR (Aat) [143712]
                 1. Escherichia coli [TaxId: 562] [143713] (1)
                    SQ P0A8P1 1-232
           7. Ornithine decarboxylase antizyme-like [143714] (1)
              Pfam 02100; may have evolved different function; putative active site maps to the same location in the common fold
              1. Ornithine decarboxylase antizyme [143715]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [143716] (1)
                    SQ P54370 93-218
           8. AstA-like [143717] (1)
              Pfam 04958; contains extra C-terminal domain, similar to the double psi beta-barrel fold (scop_cf 50684) with missing one strand and untangled psi-loops
              1. Arginine N-succinyltransferase, alpha chain, AstA [143718]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143719] (1)
                    SQ P80357 1-338
           9. Aq_1966-like [143720] (1)
              Pfam 06557; DUF1122; probable biological unit is homotrimeric; may have evolved different function; putative active site maps to the same location in the common fold
              1. Hypothetical protein Aq_1966 [143721]
                 1. Aquifex aeolicus [TaxId: 63363] [143722] (3)
                    SQ O67778 1-196
           10. EF1021-like [160644] (3)
               duplication: consists of two NAT domains swapped with the C-terminal strands; overall structural similarity to Mycothiol synthase and N-myristoyl transferase (NMT); the similarity to NMT extends to the participation of the protein C-terminus (after the SCP2-like C-terminal domain) in the active site
               1. Putative acetyltransferase EF2353 [160645]
                  1. Enterococcus faecalis [TaxId: 1351] [160646] (6)
                     SQ Q831Y9 10-300
               2. Putative acetyltransferase Ava4977 [160647]
                  1. Anabaena variabilis [TaxId: 1172] [160648] (1)
                     SQ Q3M362 8-290
               3. Hypothetical protein EF1021 [160649]
                  1. Enterococcus faecalis [TaxId: 1351] [160650] (6)
                     SQ Q836T6 2-286
   236. Gelsolin-like [55752] (3)
        3 layers: a/b/a; contains mixed beta-sheet
        1. Actin depolymerizing proteins [55753] (2)
           uperfamily
           1. Gelsolin-like [55754] (5)
              1. Villin, domain 1 (res. 1-126) [55755]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [55756] (2)
              2. Severin, domain 2 [55757]
                 1. Dictyostelium discoideum [TaxId: 44689] [55758] (3)
              3. Gelsolin [55759]
                 consists of six similar domains
                 1. Horse (Equus caballus) [TaxId: 9796] [55760] (2)
                    SQ Q28372 1-346
                 2. Human (Homo sapiens) [TaxId: 9606] [55761] (60)
                    SQ P20065 55-179
              4. Macrophage capping protein Cap G [75511]
                 1. Human (Homo sapiens) [TaxId: 9606] [75512] (2)
           2. Cofilin-like [55762] (11)
              1. Cofilin (actin depolymerizing factor, ADF) [55763]
                 1. Plant (Arabidopsis thaliana), ADF1 [TaxId: 3702] [55764] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55765] (3)
                 3. Acanthamoeba castellanii, actophorin [TaxId: 5755] [55766] (2)
                 4. Human (Homo sapiens), non-muscle isoform [TaxId: 9606] [111104] (2)
                    SQ P23528
              2. Cofilin-like domain of actin-binding protein abp1p [69793]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69794] (1)
              3. Destrin [55767]
                 1. Human and pig (Homo sapiens) and (Sus scrofa) [TaxId: 9606] [55768] (2)
                    identical sequence in both species
              4. Adf-H domain of twinfilin isoform-1 [82752]
                 interacts only with G-actin
                 1. Mouse (Mus musculus) [TaxId: 10090] [82753] (1)
              5. Coactosin-like protein Cotl1 (Clp) [111105]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111106] (2)
                    SQ Q9CQI6
                 2. Human (Homo sapiens) [TaxId: 9606] [111107] (5)
                    SQ Q14019
              6. Glia maturation factor beta, GMF-beta [111108]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111109] (1)
                    SQ Q9CQI3
              7. Glia maturation factor gamma, GMF-gamma [111110]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111111] (2)
                    SQ Q9ERL7
        2. C-terminal, gelsolin-like domain of Sec23/24 [82754] (1)
           uperfamily
           1. C-terminal, gelsolin-like domain of Sec23/24 [82755] (2)
              1. Sec23 [82756]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82757] (3)
              2. Sec24 [82758]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82759] (4)
        3. FLJ32549 C-terminal domain-like [160651] (1)
           alpha-beta(2)-alpha-beta(3)-alpha; similar to the Roadblock/LC7 domain
           1. FLJ32549 C-terminal domain-like [160652] (1)
              C-terminal part of Pfam 09404; DUF2003
              1. Hypothetical protein BC048403 [160653]
                 FLJ32549 ortholog
                 1. Mouse (Mus musculus) [TaxId: 10090] [160654] (1)
                    SQ Q6P1I3 295-440
   237. PHP14-like [143723] (1)
        beta(3)-alpha-beta(2)-alpha-beta; 3 layers, a/b/a; mixed beta-sheet, half-barrel, order: 132456; strands 2 and 5 are antiparallel to the rest
        1. PHP14-like [143724] (2)
           uperfamily
           1. Janus/Ocnus [143725] (1)
              Pfam 05005
              1. Phosphohistidine phosphatase 1, PHP14 [143726]
                 Janus-A homolog
                 1. Human (Homo sapiens) [TaxId: 9606] [143727] (7)
                    SQ Q9NRX4 1-125! SQ Q9NRX4 2-121! SQ Q9NRX4 5-122
           2. PPK middle domain-like [143728] (2)
              central part of Pfam 02503
              1. Polyphosphate kinase, PPK [143729]
                 1. Porphyromonas gingivalis [TaxId: 837] [143730] (2)
                    SQ Q7MTR1 113-317
                 2. Escherichia coli [TaxId: 562] [143731] (4)
                    SQ P0A7B1 107-314
   238. Profilin-like [55769] (10)
        core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
        1. Profilin (actin-binding protein) [55770] (1)
           alpha-beta(2)-alpha-beta(5)-alpha
           uperfamily
           1. Profilin (actin-binding protein) [55771] (8)
              1. Profilin (actin-binding protein) [55772]
                 1. Cow (Bos taurus) [TaxId: 9913] [55773] (3)
                 2. Human (Homo sapiens), isoform I [TaxId: 9606] [55774] (9)
                 3. Human (Homo sapiens), isoform II [TaxId: 9606] [55775] (1)
                 4. Acanthamoeba castellanii [TaxId: 5755] [55776] (5)
                 5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55777] (2)
                 6. Birch (Betula verrucosa) [TaxId: 3505] [55778] (1)
                 7. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [55779] (2)
                 8. Para rubber tree (Hevea brasiliensis), hevb8 [TaxId: 3981] [55780] (1)
        2. GAF domain-like [55781] (4)
           alpha(2)-beta(3)-alpha-beta(3)-alpha; antiparallel beta-sheet: order 321654
           uperfamily
           1. GAF domain [55782] (8)
              1. Hypothetical protein ykl069wp [55783]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55784] (1)
              2. 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains [82760]
                 GAF B is the nucleotide binding domain; the two domains are connected with a long helix;
                 1. Mouse (Mus musculus) [TaxId: 10090] [82761] (1)
              3. Hypothetical protein YebR [103182]
                 1. Escherichia coli [TaxId: 562] [103183] (1)
              4. Sensor protein PhyB2 [160655]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [160656] (2)
                    SQ Q6N5G2 140-333
              5. Phytochrome-like protein Cph1 [160657]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160658] (1)
                    SQ Q55168 131-326
              6. Sensor protein CYB2465 [160659]
                 1. Synechococcus sp. [TaxId: 1131] [160660] (1)
                    SQ Q2JIZ5 31-200
              7. Bacteriophytochrome BphP [160661]
                 1. Pseudomonas aeruginosa [TaxId: 287] [160662] (8)
                    SQ Q9HWR3 118-309
                 2. Deinococcus radiodurans [TaxId: 1299] [160663] (3)
                    SQ Q9RZA4 135-321! SQ Q9RZA4 137-325
           2. IclR ligand-binding domain-like [75513] (3)
              Pfam 01614
              1. Transcriptional regulator IclR, C-terminal domain [75514]
                 1. Thermotoga maritima [TaxId: 2336] [75515] (1)
                 2. Escherichia coli [TaxId: 562] [111112] (9)
                    SQ P16528 98-272
              2. Transcriptional regulator AllR, C-terminal domain [111113]
                 1. Escherichia coli [TaxId: 562] [111114] (1)
                    SQ P77734 97-269
           3. HrcA C-terminal domain-like [111115] (1)
              Pfam 01628; contains insert domain (140-229) of the Enolase N-terminal domain-like fold (scop_cf 54825)
              1. Heat-inducible transcription repressor HrcA, C-terminal domain [111116]
                 1. Thermotoga maritima [TaxId: 2336] [111117] (1)
                    SQ Q9WZV5
           4. Phytochrome-specific domain [160664] (2)
              Pfam 00360
              1. Bacteriophytochrome BphP [160665]
                 1. Pseudomonas aeruginosa [TaxId: 287] [160666] (8)
                    SQ Q9HWR3 310-494
              2. Phytochrome-like protein Cph1 [160667]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160668] (1)
                    SQ Q55168 327-514
        3. PYP-like sensor domain (PAS domain) [55785] (7)
           alpha-beta(2)-alpha(2)-beta(3)
           uperfamily
           1. PYP-like [55786] (2)
              1. Photoactive yellow protein, PYP [55787]
                 1. Ectothiorhodospira halophila [TaxId: 1053] [55788] (43)
                    SQ P16113
              2. PYP domain of sensor histidine kinase Ppr [82762]
                 1. Rhodospirillum centenum [TaxId: 34018] [82763] (1)
           2. Heme-binding PAS domain [55789] (3)
              1. Histidine kinase FixL heme domain [55790]
                 1. Rhizobium meliloti [TaxId: 382] [55791] (2)
                 2. Bradyrhizobium japonicum [TaxId: 375] [55792] (17)
                    SQ P23222 152-270
              2. Direct oxygen sensor protein, DOS [111118]
                 Heme-regulated cyclic AMP phosphodiesterase; formerly hypothetical protein YddU
                 1. Escherichia coli [TaxId: 562] [111119] (6)
                    SQ P76129 8-126 ! SQ P76129 12-124
           3. Flavin-binding PAS domain [88853] (3)
              contains PAC motif
              1. Photoreceptor phy3 flavin-binding domain, lov2 [64354]
                 1. Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818] [64355] (2)
              2. Putative blue light receptor, phot-lov1 domain [90017]
                 1. Green algae (Chlamydomonas reinhardtii) [TaxId: 3055] [90018] (3)
              3. Erg potassium channel, N-terminal domain [55794]
                 1. Human (Homo sapiens) [TaxId: 9606] [55795] (1)
           4. N-terminal PAS domain of Pas kinase [82764] (1)
              1. N-terminal PAS domain of Pas kinase [82765]
                 1. Human (Homo sapiens) [TaxId: 9606] [82766] (1)
           5. Hypoxia-inducible factor Hif2a, C-terminal domain [103184] (1)
              contains PAC motif
              1. Hypoxia-inducible factor Hif2a, C-terminal domain [103185]
                 endothelial pas domain protein 1, EPAS-1
                 1. Human (Homo sapiens) [TaxId: 9606] [103186] (1)
           6. PAS domain of steroid receptor coactivator 1A, NCo-A1 [103187] (1)
              1. PAS domain of steroid receptor coactivator 1A, NCo-A1 [103188]
                 1. Mouse (Mus musculus) [TaxId: 10090] [103189] (1)
           7. BphP N-terminal domain-like [160669] (4)
              Pfam 08446; PAS_2
              1. Sensor protein PhyB2 [160670]
                 1. Rhodopseudomonas palustris [TaxId: 1076] [160671] (2)
                    SQ Q6N5G2 26-139
              2. Bacteriophytochrome BphP [160672]
                 1. Deinococcus radiodurans [TaxId: 1299] [160673] (3)
                    SQ Q9RZA4 4-130! SQ Q9RZA4 5-130
                 2. Pseudomonas aeruginosa [TaxId: 287] [160674] (8)
                    SQ Q9HWR3 5-117
              3. Phytochrome-like protein Cph1 [160675]
                 1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160676] (1)
                    SQ Q55168 4-130
        4. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75516] (1)
           alpha(2)-beta(2)-alpha(2)-beta(3)-alpha; possibly related to the PAS domain
           uperfamily
           1. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75517] (1)
              1. Transcription factor TraR, N-terminal domain [75518]
                 1. Agrobacterium tumefaciens [TaxId: 358] [75519] (2)
        5. Sensory domain-like [103190] (3)
           alpha(2)-beta(2)-alpha(2)-beta(3); possibly related to the PAS domain
           uperfamily
           1. Sensory domain of two-component sensor kinase [103191] (2)
              1. Sensor kinase CitA [103192]
                 citrate-binding domain
                 1. Klebsiella pneumoniae [TaxId: 573] [103193] (5)
              2. Fumarate sensor DcuS [103194]
                 1. Escherichia coli [TaxId: 562] [103195] (2)
           2. YkuI C-terminal domain-like [143732] (2)
              PfamB 021678
              1. Hypothetical protein YkuI, C-terminal domain [143733]
                 1. Bacillus subtilis [TaxId: 1423] [143734] (2)
                    SQ O35014 263-407
              2. GGDEF family protein VP0354 [160677]
                 N-terminal region, consist of two sensory domain-like domains; there is a canonical sensory (PAS) domain in the middle region
                 1. Vibrio parahaemolyticus [TaxId: 670] [160678] (4)
                    SQ Q87SR8 207-299! SQ Q87SR8 35-206
           3. LuxQ-periplasmic domain-like [160679] (1)
              Pfam 09308; two-domain arrangement similar to the YkuI C-terminal domain-like
              1. Autoinducer 2 sensor kinase/phosphatase LuxQ [160680]
                 1. Vibrio harveyi [TaxId: 669] [160681] (4)
                    SQ P54302 51-271! SQ P54302 52-270
        6. SNARE-like [64356] (4)
           beta(2)-alpha-beta(3)-alpha(2)
           uperfamily
           1. Synatpobrevin N-terminal domain [64357] (2)
              1. Sec22b [64358]
                 1. Mouse (Mus musculus) [TaxId: 10090] [64359] (1)
              2. Synaptobrevin homolog 1 ykt6 [64360]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64361] (2)
           2. Sedlin (SEDL) [82767] (1)
              1. Sedlin (SEDL) [82768]
                 1. Mouse (Mus musculus) [TaxId: 10090] [82769] (3)
           3. Clathrin coat assembly domain [75521] (2)
              1. Mu2 adaptin (clathrin coat assembly protein AP50) [75522]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [75523] (1)
              2. Sigma2 adaptin (clathrin coat assembly protein AP17) [75524]
                 1. Mouse (Mus musculus) [TaxId: 10090] [75525] (1)
           4. SRP alpha N-terminal domain-like [90019] (2)
              1. Srx domain of the signal recognition particle receptor alpha-subunit [90020]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90021] (1)
              2. Signal recognition particle receptor alpha subunit, N-terminal domain [143735]
                 1. Human (Homo sapiens) [TaxId: 9606] [143736] (2)
                    SQ P08240 1-129
        7. Roadblock/LC7 domain [103196] (1)
           alpha-beta(2)-alpha-beta(3)-alpha; structurally most similar to the SNARE-like superfamily with a circular permutation of the terminal helices
           uperfamily
           1. Roadblock/LC7 domain [103197] (6)
              Pfam 03259
              1. Giding protein MglB [103198]
                 1. Thermus thermophilus [TaxId: 274] [103199] (1)
              2. MEK binding partner 1, MP1 [111120]
                 remote homolog that forms the characteristic complex structures with other members
                 1. Human (Homo sapiens) [TaxId: 9606] [111121] (2)
                    SQ Q9UHA4
                 2. Mouse (Mus musculus) [TaxId: 10090] [111122] (2)
                    SQ O88653
              3. Late endosomal/lysosomal Mp1 interacting protein p14 [111123]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111124] (5)
                    SQ Q9JHS3
              4. Dynein light chain 2A, cytoplasmic [118074]
                 1. Human (Homo sapiens) [TaxId: 9606] [118075] (8)
                    SQ Q9NP97
                 2. Mouse (Mus musculus) [TaxId: 10090] [160682] (2)
                    SQ P62627 1-95
        8. YeeU-like [143737] (1)
           beta(2)-alpha-beta(3); 2 layers, a/b; there is an oligomerization interface instead of the 'missing' helical layer
           uperfamily
           1. YagB/YeeU/YfjZ-like [143738] (3)
              Pfam 06154
              1. Hypothetical protein YfjZ [143739]
                 1. Escherichia coli [TaxId: 562] [143740] (2)
                    SQ P52141 1-105
              2. Hypothetical protein YeeU [143741]
                 1. Escherichia coli [TaxId: 562] [143742] (2)
                    SQ P76364 16-122
                 2. Shigella flexneri [TaxId: 623] [143743] (2)
                    SQ Q83JN9 4-120
        9. GlcG-like [143744] (1)
           alpha-beta(2)-alpha(3)-beta(2)-alpha; similar to the Roadblock/LC7 domain
           uperfamily
           1. GlcG-like [143745] (1)
              Pfam 03928; DUF336
              1. DhaI homolog [143746]
                 1. Klebsiella pneumoniae [TaxId: 573] [143747] (4)
                    SQ Q48422 2-143
        10. YNR034W-A-like [160683] (1)
            1. YNR034W-A-like [160684] (1)
               1. Uncharacterized protein YNR034W-A [160685]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [160686] (1)
                     SQ Q3E841 1-98
   239. Ligand-binding domain in the NO signalling and Golgi transport [111125] (1)
        an N-terminal helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomain enclose a ligand-binding cavity
        1. Ligand-binding domain in the NO signalling and Golgi transport [111126] (3)
           uperfamily
           1. H-NOX domain [111127] (1)
              binds heme between the N-terminal 4-helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomains
              1. Methyl-accepting chemotaxis protein [111128]
                 1. Thermoanaerobacter tengcongensis [TaxId: 119072] [111129] (4)
                    SQ Q8RBX6 1-191
           2. TRAPP components [118076] (2)
              Pfam 04051; form homo- and hetero-dimers with the first two helices of one subunit complementing the fold of the other subunit to the H-NOX domain fold
              1. Trafficking protein particle complex subunit 3, Bet3 homolog [118077]
                 covalently linked long fatty acid occupies the ligand-binding cavity
                 1. Mouse (Mus musculus) [TaxId: 10090] [118078] (3)
                    SQ O55013 9-173
              2. TRAPPC5, similar to trafficking protein particle complex 5 [160687]
                 1. Zebrafish (Brachydanio rerio) [TaxId: 7955] [160688] (2)
                    SQ Q6DGL5 21-188
           3. MJ1460-like [160689] (1)
              C-terminal part corresponds to Pfam 02830; V4R (vinyl 4 reductase) domain
              1. Hypothetical protein MJ1460 [160690]
                 1. Methanococcus jannaschii [TaxId: 2190] [160691] (2)
                    SQ Q58855 5-156
   240. Phage tail protein-like [143748] (1)
        alpha-beta-X-beta(2)-alpha-beta(2); 2 layers: a/b; mixed beta-sheet: order 12354, strands 1 and 2 are parallel
        1. Phage tail protein-like [143749] (2)
           Can form ring, tube-like oligomers, where the subunit beta-sheets are joined in a single beta-sheet (or barrel)
           uperfamily
           1. Lambda phage gpU-like [143750] (1)
              Pfam 06141
              1. Minor tail protein gpU [143751]
                 1. Bacteriophage lambda [TaxId: 10710] [143752] (1)
                    SQ P03732 2-130
           2. STM4215-like [143753] (1)
              1. Putative cytoplasmic protein STM4215 [143754]
                 forms a ring-like hexamer; possible prophage protein
                 1. Salmonella typhimurium [TaxId: 90371] [143755] (6)
                    SQ Q8ZKJ0 1-134
   241. PR-1-like [55796] (1)
        alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
        1. PR-1-like [55797] (1)
           uperfamily
           1. PR-1-like [55798] (4)
              Pfam 00188; groups mammalian SCP/TPX1; insects AG3/AG5; fungi SC7/SC14 and plant PR-1
              1. Pathogenesis-related protein 1 (PR1) [55799]
                 1. Tomato (Lycopersicon esculentum), P14a [TaxId: 4081] [55800] (1)
              2. Insect allergen 5 (AG5) [55801]
                 1. Yellow jacket (Vespula vulgaris), Ves v 5 [TaxId: 7454] [55802] (1)
              3. Golgi-associated PR-1 protein [111130]
                 1. Human (Homo sapiens) [TaxId: 9606] [111131] (1)
                    SQ Q9H4G4
              4. Cysteine-rich secretory protein (SteCRISP) [118079]
                 1. Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] [118080] (1)
                    SQ P60623 13-233
   242. Phoshotransferase/anion transport protein [55803] (1)
        beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342; loop crossing
        1. Phoshotransferase/anion transport protein [55804] (2)
           uperfamily
           1. IIA domain of mannitol-specific and ntr phosphotransferase EII [55805] (3)
              1. Nitrogen regulatory bacterial protein IIa-ntr [55806]
                 1. Escherichia coli [TaxId: 562] [55807] (1)
              2. Phosphotransferase IIa-mannitol [55808]
                 1. Escherichia coli [TaxId: 562] [55809] (2)
              3. Putative PTS protein STM3784 [118081]
                 1. Salmonella typhimurium [TaxId: 90371] [118082] (1)
                    SQ Q8ZL18
           2. Anion transport protein, cytoplasmic domain [64362] (1)
              elaborated with additional secondary structures
              1. Erythrocite membrane Band 3 [64363]
                 1. Human (Homo sapiens) [TaxId: 9606] [64364] (1)
   243. Nudix [55810] (1)
        beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
        contains beta-grasp motif
        1. Nudix [55811] (7)
           uperfamily
           1. MutT-like [55812] (20)
              1. Nucleoside triphosphate pyrophosphorylase (MutT) [55813]
                 1. Escherichia coli [TaxId: 562] [55814] (6)
              2. Coenzyme A pyrophosphatase [90022]
                 1. Deinococcus radiodurans [TaxId: 1299] [90023] (2)
              3. ADP-ribose pyrophosphatase [64365]
                 1. Escherichia coli [TaxId: 562] [64366] (5)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [103200] (5)
                    gene Rv1700
                 3. Thermus thermophilus [TaxId: 274] [118083] (11)
                    SQ Q84CU3
              4. ADP-ribose pyrophosphatase homologue YffH [103201]
                 1. Escherichia coli [TaxId: 562] [103202] (1)
              5. ADP compounds hydrolase NudE [103203]
                 1. Escherichia coli [TaxId: 562] [103204] (2)
              6. NUDT9 (mitochondrial ADP-ribose pyrophosphatase) [103205]
                 1. Human (Homo sapiens) [TaxId: 9606] [103206] (2)
              7. 7,8-dihydro-8-oxoguanine triphosphatase Hmth1 [103207]
                 1. Human (Homo sapiens) [TaxId: 9606] [103208] (1)
              8. Hypothetical protein DR1025 [103209]
                 1. Deinococcus radiodurans [TaxId: 1299] [103210] (4)
              9. Diadenosine tetraphosphate hydrolase (Ap4A hydrolase) [64367]
                 1. Narrow-leaved blue lupine (Lupinus angustifolius) [TaxId: 3871] [64368] (2)
                 2. Caenorhabditis elegans [TaxId: 6239] [75526] (2)
                 3. Human (Homo sapiens) [TaxId: 9606] [118084] (3)
                    SQ P50583
              10. Hypothetical protein PAE3301 [75527]
                  1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [75528] (3)
              11. Hypothetical protein EF1141 [143756]
                  1. Enterococcus faecalis [TaxId: 1351] [143757] (1)
                     SQ Q836H1 2-148
              12. AP6A hydrolase Ndx1 [143758]
                  1. Thermus thermophilus [TaxId: 274] [143759] (6)
                     SQ Q75UV1 1-126
              13. Hypothetical protein NE0184 [143760]
                  1. Nitrosomonas europaea [TaxId: 915] [143761] (1)
                     SQ Q82XR9 4-149
              14. Hypothetical protein SP1235 (spr1115) [143762]
                  1. Streptococcus pneumoniae [TaxId: 1313] [143763] (1)
                     SQ Q97QH6 1-155
              15. U8 snorna-binding protein x29 [143764]
                  nuclear decapping enzyme
                  1. African clawed frog (Xenopus laevis) [TaxId: 8355] [143765] (12)
                     SQ Q6TEC1 14-209
              16. Diphosphoinositol polyphosphate phosphohydrolase [143766]
                  1. Human (Homo sapiens) [TaxId: 9606] [143767] (2)
                     SQ O95989 8-142
           2. MutY C-terminal domain-like [103211] (2)
              1. Adenine glycosylase MutY, C-terminal domain [103212]
                 1. Bacillus stearothermophilus [TaxId: 1422] [103213] (3)
              2. A/G-specific adenine DNA glycosylase [143768]
                 MutY homolog
                 1. Human (Homo sapiens) [TaxId: 9606] [143769] (1)
                    SQ Q9UIF7 356-497
           3. NADH pyrophosphatase [103214] (1)
              duplication: consists of two structurally similar domains separated by a rubredoxin-like zinc finger; the N-terminal domain has a rudiment Nudix fold, the C-terminal, probably catalytic, domain has the canonical fold
              1. NADH pyrophosphatase [103215]
                 1. Escherichia coli [TaxId: 562] [103216] (1)
           4. IPP isomerase-like [64369] (4)
              1. Isopentenyl diphosphate isomerase [64370]
                 1. Escherichia coli [TaxId: 562] [64371] (25)
                    SQ Q46822
              2. Hypothetical protein DR0079 [103217]
                 1. Deinococcus radiodurans [TaxId: 1299] [103218] (1)
                 2. Deinococcus radiodurans str. R1 (Deinococcus radiodurans R1) [TaxId: 243230] [160692] (2)
              3. Hypothetical protein YfcD [143770]
                 1. Escherichia coli [TaxId: 562] [143771] (3)
                    SQ P65556 8-168
           5. GDP-mannose mannosyl hydrolase NudD [111132] (1)
              1. GDP-mannose mannosyl hydrolase NudD [111133]
                 1. Escherichia coli [TaxId: 562] [111134] (5)
                    SQ P32056
           6. BT0354 N-terminal domain-like [143772] (2)
              accosiated with the C-terminal "winged helix" domain (scop_sf 46785)
              1. Hypothetical protein EF2700, N-terminal domain [143773]
                 includes extra N-terminal alpha-hairpin, separated by a linker peptide
                 1. Enterococcus faecalis [TaxId: 1351] [143774] (2)
                    SQ Q830S2 3-204
              2. Hypothetical protein BT0354, N-terminal domain [143775]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [143776] (4)
                    SQ Q8AAV8 3-149
           7. mRNA decapping enzyme-like [143777] (1)
              part of Pfam 00293
              1. mRNA decapping enzyme Dcp2p catalytic domain [143778]
                 1. Schizosaccharomyces pombe [TaxId: 4896] [143779] (1)
                    SQ O13828 95-245
   244. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55815] (1)
        core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
        1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55816] (1)
           uperfamily
           1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55817] (3)
              1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55818]
                 1. Escherichia coli [TaxId: 562] [55819] (8)
                    SQ P07024 26-550
                 2. Candida albicans [TaxId: 5476] [160693] (2)
                    SQ Q5A5Q7 338-561
                 3. Thermus thermophilus [TaxId: 274] [160694] (1)
                    SQ Q5SIP1 330-534
   245. YrdC/RibB [55820] (1)
        core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta; 3 layers; mixed twisted sheet of 7 strands; order 7126354; strands 7 and 1 are parallel to each other
        1. YrdC/RibB [55821] (2)
           uperfamily
           1. YrdC-like [55822] (3)
              contains two additional strands in the C-terminal extension
              1. Hypothetical protein YrdC [55823]
                 1. Escherichia coli [TaxId: 562] [55824] (1)
              2. Hypothetical protein YciO [75529]
                 1. Escherichia coli [TaxId: 562] [75530] (2)
              3. Hypothetical protein MTH1692 [75531]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75532] (1)
           2. 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [64372] (4)
              contains one additional helix in the C-terminal extension
              1. 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [64373]
                 1. Escherichia coli [TaxId: 562] [64374] (3)
                 2. Magnaporthe grisea [TaxId: 148305] [75533] (5)
                 3. Archaeon Methanocaldococcus jannaschii [TaxId: 2190] [103219] (3)
                    SQ Q60364
                 4. Candida albicans [TaxId: 5476] [111135] (4)
                    SQ Q5A3V6
   246. GIY-YIG endonuclease [82770] (1)
        beta(2)-alpha(2)-beta-alpha-(beta); strand 4 is very short; 3 layers; antiparallel (mixed) beta-sheet; order 312(4)
        1. GIY-YIG endonuclease [82771] (1)
           uperfamily
           1. GIY-YIG endonuclease [82772] (1)
              1. Homing endonuclease I-TevI [82773]
                 intron-associated endonuclease 1
                 1. Bacteriophage T4 [TaxId: 10665] [82774] (2)
   247. YbaK/ProRS associated domain [55825] (1)
        core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
        1. YbaK/ProRS associated domain [55826] (1)
           uperfamily
           1. YbaK/ProRS associated domain [55827] (4)
              Pfam 04073
              1. Hypothetical protein HI1434 (YbaK homologue) [55828]
                 1. Haemophilus influenzae [TaxId: 727] [55829] (2)
              2. Hypothetical protein CC0111 [103220]
                 annotated as putative DNA-binding protein
                 1. Caulobacter crescentus [TaxId: 155892] [103221] (1)
              3. Hypothetical protein Atu3699 [111136]
                 1. Agrobacterium tumefaciens, strain C58 [TaxId: 358] [111137] (1)
                    SQ Q8U9M7
              4. Hypothetical protein APE2540 [118085]
                 1. Aeropyrum pernix [TaxId: 56636] [118086] (1)
                    SQ Q9Y8U3
   248. Thymidylate synthase/dCMP hydroxymethylase [55830] (1)
        contains large mixed beta-sheet
        1. Thymidylate synthase/dCMP hydroxymethylase [55831] (1)
           uperfamily
           1. Thymidylate synthase/dCMP hydroxymethylase [55832] (10)
              1. Thymidylate synthase [55833]
                 1. Escherichia coli [TaxId: 562] [55834] (56)
                 2. Lactobacillus casei [TaxId: 1582] [55835] (39)
                 3. Bacillus subtilis [TaxId: 1423] [55836] (5)
                 4. Bacteriophage T4 [TaxId: 10665] [55837] (1)
                 5. Pneumocystis carinii [TaxId: 4754] [55838] (2)
                 6. Rat (Rattus norvegicus) [TaxId: 10116] [55839] (2)
                 7. Human (Homo sapiens) [TaxId: 9606] [55840] (5)
              2. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, TS domain [55841]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [88964] (2)
                 2. Cryptosporidium hominis [TaxId: 237895] [100887] (8)
              3. dCMP hydroxymethylase [55843]
                 1. Bacteriophage T4 [TaxId: 10665] [55844] (3)
   249. Thymidylate synthase-complementing protein Thy1 [69795] (1)
        complex alpha+beta fold; contains antiparallel 5-stranded beta-sheet: order 12354
        1. Thymidylate synthase-complementing protein Thy1 [69796] (1)
           uperfamily
           1. Thymidylate synthase-complementing protein Thy1 [69797] (1)
              1. Thy1 homologue [69798]
                 1. Thermotoga maritima [TaxId: 2336] [69799] (9)
                    TM0449
   250. N-acetylmuramoyl-L-alanine amidase-like [55845] (1)
        contains mixed beta-sheet
        1. N-acetylmuramoyl-L-alanine amidase-like [55846] (1)
           uperfamily
           1. N-acetylmuramoyl-L-alanine amidase-like [55847] (10)
              Family 2 zinc amidase;
              1. AmpD protein [82775]
                 1. Citrobacter freundii [TaxId: 546] [82776] (1)
              2. Bacteriophage T7 lysozyme (Zn amidase) [55848]
                 1. Bacteriophage T7 [TaxId: 10760] [55849] (2)
              3. Peptidoglycan recognition protein-lb (Cg14704) [90024]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [90025] (1)
              4. Peptidoglycan-recognition protein-SA (Cg11709) [111139]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [111140] (2)
                    SQ Q9VYX7 37-203 ! SQ Q9VYX7
              5. Peptidoglycan recognition protein I-alpha [111141]
                 1. Human (Homo sapiens) [TaxId: 9606] [111142] (5)
                    SQ Q96LB9 177-341
              6. N-acetylmuramoyl-L-alanine amidase PlyG [143780]
                 1. Bacillus anthracis [TaxId: 1392] [143781] (6)
                    SQ Q81WA9 1-157
                    Prophage LambdaBa02
              7. Probable N-acetylmuramoyl-L-alanine amidase YbjR, N-terminal domain [143782]
                 1. Escherichia coli [TaxId: 562] [143783] (2)
                    SQ P75820 22-194
              8. Peptidoglycan-recognition protein-LC [143784]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143785] (3)
                    SQ Q9GNK5 335-499! SQ Q9GNK5 355-520
                    Cg4432; different splicing isoforms
              9. Peptidoglycan recognition protein, PGRP-S [143786]
                 1. Human (Homo sapiens) [TaxId: 9606] [143787] (1)
                    SQ O75594 30-196
              10. Peptidoglycan-recognition protein-LE [143788]
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143789] (4)
                     SQ Q9VXN9 174-344
   251. Cytochrome b5-like heme/steroid binding domain [55855] (1)
        beta-alpha-beta(2)-alpha(1,2)-(beta)-alpha(2)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 1532(4)
        1. Cytochrome b5-like heme/steroid binding domain [55856] (2)
           uperfamily
           1. Cytochrome b5 [55857] (7)
              1. Cytochrome b5 [55858]
                 1. Cow (Bos taurus) [TaxId: 9913] [55859] (16)
                    SQ P00171 7-88 ! SQ P00171 8-89
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [55860] (20)
                 3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55861] (1)
              2. Cytochrome b558 [55862]
                 a prokaryotic homologue of cytochrome b5
                 1. Ectothiorhodospira vacuolata [TaxId: 1054] [55863] (1)
              3. Flavocytochrome b2, N-terminal domain [55864]
                 C-terminal domain is beta/alpha barrel
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55865] (6)
              4. Sulfite oxidase, N-terminal domain [55866]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [55867] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [82777] (1)
           2. Steroid-binding domain [103222] (1)
              1. Putative steroid binding protein AT2G24940 [103223]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103224] (2)
   252. BTG domain-like [160695] (1)
        alpha(2)-beta-alpha(2)-beta(3); four-helical bundle, capped at one end by an antiparallel beta-sheet, order:1234
        1. BTG domain-like [160696] (1)
           1. BTG domain-like [160697] (2)
              Pfam 07742
              1. TOB1, N-terminal domain [160698]
                 1. Human (Homo sapiens) [TaxId: 9606] [160699] (5)
                    SQ P50616 1-115! SQ P50616 1-117
              2. NGF-inducible anti-proliferative protein PC3 (BTG2) [160700]
                 1. Human (Homo sapiens) [TaxId: 9606] [160701] (1)
                    SQ P78543 8-127
   253. DUSP-like [143790] (1)
        alpha-beta-alpha-X-beta-alpha-beta; three-helical bundle capped at one end by antiparallel beta-sheet, order: 213
        1. DUSP-like [143791] (1)
           uperfamily
           1. DUSP, domain in ubiquitin-specific proteases [143792] (1)
              Pfam 06337 (DUF1055); SMART 00695
              1. Ubiquitin carboxyl-terminal hydrolase 15 [143793]
                 1. Human (Homo sapiens) [TaxId: 9606] [143794] (1)
                    SQ Q9Y4E8 1-120
   254. DNA topoisomerase I domain [55868] (1)
        beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
        1. DNA topoisomerase I domain [55869] (1)
           uperfamily
           1. Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment [55870] (1)
              1. Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment [55871]
                 1. Vaccinia virus, strain WR [TaxId: 10245] [55872] (1)
   255. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55873] (1)
        8-stranded mixed beta-sheet; 2 layers: alpha/beta
        1. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55874] (4)
           uperfamily
           1. Heat shock protein 90, HSP90, N-terminal domain [55875] (3)
              1. HSP90 [55876]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55877] (21)
                 2. Human (Homo sapiens) [TaxId: 9606] [55878] (53)
                    SQ P08238 10-220 # HSP 90-beta isoform ! SQ P07900 16-223
                 3. Dog (Canis familiaris) [TaxId: 9615] [103225] (29)
                    SQ P41148 76-285; Endoplasmin, GRP94
           2. DNA gyrase/MutL, N-terminal domain [55879] (7)
              1. DNA gyrase B [55880]
                 1. Escherichia coli [TaxId: 562] [55881] (3)
                 2. Thermus thermophilus [TaxId: 274] [75534] (1)
              2. DNA topoisomerase II [103226]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103227] (2)
              3. Topoisomerase IV subunit B [103228]
                 1. Escherichia coli [TaxId: 562] [103229] (2)
              4. DNA mismatch repair protein MutL [55882]
                 1. Escherichia coli [TaxId: 562] [55883] (6)
              5. DNA mismatch repair protein PMS2 [69800]
                 1. Human (Homo sapiens) [TaxId: 9606] [69801] (3)
              6. Topoisomerase VI-B subunit [82778]
                 contains an H2TH domain inserted after this domain and before the second family-specific domain
                 1. Archaeon Sulfolobus shibatae [TaxId: 2286] [82779] (10)
           3. Histidine kinase [55884] (7)
              1. Histidine kinase domain of the osmosensor EnvZ [55885]
                 1. Escherichia coli [TaxId: 562] [55886] (1)
              2. Histidine kinase CheA [55887]
                 1. Thermotoga maritima [TaxId: 2336] [55888] (9)
              3. Histidine kinase PhoQ domain [69802]
                 1. Escherichia coli [TaxId: 562] [69803] (1)
              4. Anti-sigma factor spoIIab [75535]
                 1. Bacillus stearothermophilus [TaxId: 1422] [75536] (5)
                    SQ O32727
              5. Nitrogen regulation protein NtrB, C-terminal domain [111143]
                 1. Escherichia coli [TaxId: 562] [111144] (1)
                    SQ P06712 194-349
              6. Sensor histidine kinase TM0853 [143795]
                 1. Thermotoga maritima [TaxId: 2336] [143796] (1)
                    SQ Q9WZV7 321-481
              7. Sensor-type histidine kinase PrrB [143797]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143798] (6)
                    SQ P0A5Z8 299-446
           4. alpha-ketoacid dehydrogenase kinase, C-terminal domain [69804] (3)
              1. Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) [69805]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [69806] (3)
              2. Pyruvate dehydrogenase kinase [69807]
                 1. Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116] [69808] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [160702] (8)
                    SQ Q15120 177-301
   256. YehR-like [160703] (1)
        beta(3)-alpha-beta(2)-alpha(3)-beta; 2 layers, a/b; antiparallel beta-sheet, order: 612354
        1. YehR-like [160704] (1)
           1. YehR-like [160705] (1)
              Pfam 06998; DUF1307
              1. Hypothetical lipoprotein YehR [160706]
                 1. Escherichia coli [TaxId: 562] [160707] (1)
                    SQ P33354 24-153
   257. Sporulation response regulatory protein Spo0B [55889] (1)
        core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
        1. Sporulation response regulatory protein Spo0B [55890] (1)
           Histidine kinase-like fold lacking the kinase ATP-binding site
           uperfamily
           1. Sporulation response regulatory protein Spo0B [55891] (1)
              1. Sporulation response regulatory protein Spo0B [55892]
                 1. Bacillus subtilis [TaxId: 1423] [55893] (6)
   258. Ribonuclease Rh-like [55894] (1)
        alpha+beta fold
        1. Ribonuclease Rh-like [55895] (1)
           uperfamily
           1. Ribonuclease Rh-like [55896] (8)
              1. Ribonuclease Rh [55897]
                 1. Rhizopus niveus [TaxId: 4844] [55898] (1)
              2. Ribonuclease MC1 [55899]
                 1. Bitter gourd (Momordica charantia) [TaxId: 3673] [55900] (8)
                    SQ P23540
              3. RNase LE [55901]
                 1. Tomatoes (Lycopersicon esculentum) [TaxId: 4081] [55902] (1)
              4. RNase NW [103230]
                 1. Nicotiana glutinosa [TaxId: 35889] [103231] (1)
              5. S3-RNase [69809]
                 1. Japanese pear (Pyrus pyrifolia) [TaxId: 3767] [69810] (1)
              6. Gemetophytic self-incompatibility associated SF11-RNase [75537]
                 1. Winged tobacco (Nicotiana alata) [TaxId: 4087] [75538] (1)
              7. RNase-related protein [75539]
                 1. Hedge bindweed (Calystegia sepium) [TaxId: 47519] [75540] (1)
              8. Trichomaglin [111145]
                 1. Gourd (Trichosanthes lepiniana) [TaxId: 282652] [111146] (1)
                    SQ P84146
   259. YlxR-like [64375] (1)
        alpha+beta fold; could have evolved from a glucocorticoid receptor-like zinc finger domain
        1. YlxR-like [64376] (1)
           uperfamily
           1. YlxR-like [64377] (1)
              some family sequences retain zinc-binding residues
              1. Hypothetical cytosolic protein SP0554 [64378]
                 1. Streptococcus pneumoniae [TaxId: 1313] [64379] (1)
   260. YggX-like [111147] (1)
        beta(2)-alpha(3); contains zinc-less 'zinc finger'-like fold (scop_cf 57715; see also scop_cf 64375)
        1. YggX-like [111148] (1)
           uperfamily
           1. YggX-like [111149] (2)
              Pfam 04362
              1. Hypothetical protein PA5148 [111150]
                 1. Pseudomonas aeruginosa [TaxId: 287] [111151] (1)
                    SQ Q9HU36
              2. Hypothetical protein YggX [118087]
                 1. Salmonella typhimurium [TaxId: 90371] [118088] (1)
                    SQ P67617
   261. L28p-like [143799] (1)
        unusual fold consisting of three beta-hairpins, that form a paper clip-like structure, and two helices; could have evolved from a glucocorticoid receptor-like zinc finger domain (scop_cf 57715)
        1. L28p-like [143800] (2)
           In early ribosomal structures, L28p has been misinterpreted as L31p. in the Ribosomal protein L28p family, there are sequences containing two CxxC pairs. Threading these sequences into this fold brings the four cysteines in a similar site to the zinc-binding site of glucocorticoid receptor-like zinc fingers. In the Ribosomal protein L31p, there are also members with two CxxC pairs. However, these won't form a putative zinc-binding site in this fold. The L31p family are classified here temporarily, until its true fold is known
           uperfamily
           1. Ribosomal protein L28 [143801] (4)
              1. Ribosomal protein L28 (L28p) [143802]
                 1. Thermus thermophilus [TaxId: 274] [143803] (2)
                    SQ P60494 7-95
                 2. Deinococcus radiodurans [TaxId: 1299] [160708] (5)
                    SQ Q9RRG8 8-79
                 3. Escherichia coli [TaxId: 562] [160709] (18)
                    SQ P0A7M2 1-77
                 4. Thermotoga maritima [TaxId: 2336] [160710] (1)
                    SQ Q9WY96 1-70
           2. Ribosomal protein L31p [143804] (2)
              Pfam 01197
              1. Ribosomal protein L31p [143805]
                 1. Escherichia coli [TaxId: 562] [143806] (9)
                    SQ P0A7M9 1-70
                 2. Thermus thermophilus [TaxId: 274] [160711] (7)
                    SQ Q5SJE1 1-50
   262. YqaI-like [160712] (1)
        dimeric zinc-less 'zinc finger'-like fold; similar to the C-terminal strand-swapped B-box domain (scop_cf 57844)
        1. YqaI-like [160713] (1)
           1. YqaI-like [160714] (1)
              Pfam 09466
              1. Hypothetical protein YqaI [160715]
                 1. Bacillus subtilis [TaxId: 1423] [160716] (2)
                    SQ P45906 1-64
   263. Ornithine decarboxylase C-terminal domain [55903] (1)
        complex alpha+beta motif
        1. Ornithine decarboxylase C-terminal domain [55904] (1)
           uperfamily
           1. Ornithine decarboxylase C-terminal domain [55905] (1)
              1. Ornithine decarboxylase C-terminal domain [55906]
                 1. Lactobacillus sp., strain 30a [TaxId: 1591] [55907] (2)
   264. Pentein, beta/alpha-propeller [55908] (1)
        duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
        1. Pentein [55909] (7)
           uperfamily
           1. Ribosome anti-association factor eIF6 (aIF6) [55910] (2)
              1. Ribosome anti-association factor eIF6 (aIF6) [55911]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55912] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55913] (1)
           2. Amidinotransferase [55914] (2)
              common fold is elaborated with many active site-forming insertions
              1. L-arginine: glycine amidinotransferase [55915]
                 1. Human (Homo sapiens) [TaxId: 9606] [55916] (11)
              2. L-arginine: inosamine-phosphate amidinotransferase [55917]
                 1. Streptomyces griseus [TaxId: 1911] [55918] (1)
           3. Dimethylarginine dimethylaminohydrolase DDAH [64380] (1)
              functionally related to the amidinotransferase, similar active sites
              1. Dimethylarginine dimethylaminohydrolase DDAH [64381]
                 1. Pseudomonas aeruginosa [TaxId: 287] [64382] (1)
           4. Arginine deiminase [103232] (2)
              functionally related to the amidinotransferase, similar active sites
              1. Arginine deiminase [103233]
                 1. Pseudomonas aeruginosa [TaxId: 287] [103234] (17)
                 2. Mycoplasma arginini [TaxId: 2094] [103235] (2)
           5. Peptidylarginine deiminase Pad4, catalytic C-terminal domain [111152] (1)
              # functionally related to the amidinotransferase, similar active sites
              1. Peptidylarginine deiminase Pad4, catalytic C-terminal domain [111153]
                 1. Human (Homo sapiens) [TaxId: 9606] [111154] (7)
                    SQ Q9UM07
           6. Porphyromonas-type peptidylarginine deiminase [111155] (6)
              Pfam 04371; functionally related to the amidinotransferase, similar active site
              1. Agmatine iminohydrolase [111156]
                 1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [111157] (3)
                    SQ Q8GWW7
                 2. Streptococcus mutans [TaxId: 1309] [143807] (12)
                    SQ Q8DW17 2-370
                 3. Enterococcus faecalis [TaxId: 1351] [160717] (6)
                    SQ Q837U5 2-365
              2. Putative peptidyl-arginine deiminase [111158]
                 1. Helicobacter pylori J99 [TaxId: 85963] [111159] (1)
                    SQ Q9ZN18
                 2. Chlorobium tepidum [TaxId: 1097] [118089] (1)
                    SQ Q8KCB6
                 3. Porphyromonas gingivalis [TaxId: 837] [143808] (2)
                    SQ Q7MXM8 3-341
           7. Succinylarginine dihydrolase-like [143809] (1)
              Pfam 04996
              1. Succinylarginine dihydrolase [143810]
                 1. Escherichia coli [TaxId: 562] [143811] (14)
                    SQ P76216 2-441
   265. Creatinase/aminopeptidase [55919] (1)
        duplication: composed of two very similar alpha+beta folds
        1. Creatinase/aminopeptidase [55920] (1)
           uperfamily
           1. Creatinase/aminopeptidase [55921] (9)
              1. Creatinase, catalytic (C-terminal) domain [55922]
                 1. Pseudomonas putida [TaxId: 303] [55923] (1)
                 2. Actinobacillus sp. [TaxId: 41114] [75541] (1)
              2. Methionine aminopeptidase [55924]
                 1. Escherichia coli [TaxId: 562] [55925] (44)
                    SQ P07906
                 2. Thermotoga maritima [TaxId: 2336] [82780] (1)
                 3. Staphylococcus aureus [TaxId: 1280] [103236] (3)
                 4. Archaeon Pyrococcus furiosus [TaxId: 2261] [55926] (4)
                    contains insert domain with a circularly permuted "winged helix" fold
                 5. Human (Homo sapiens) [TaxId: 9606] [55927] (18)
                    SQ P50579 110-478
                    methionine aminopeptidase 2 contains insert domain with a circularly permuted "winged helix" fold
              3. Aminopeptidase P, C-terminal domain [55928]
                 1. Escherichia coli [TaxId: 562] [55929] (37)
                 2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103237] (1)
   266. gpW/gp25-like [160718] (1)
        alpha(2)-beta(3); similar to one structural repeat of the Creatinase/aminopeptidase family and the C-terminal subdomain of PanC
        1. gpW/gp25-like [160719] (1)
           Contains phage tail lysozyme
           1. gpW/gp25-like [160720] (1)
              Pfam 04965; T4 gene 25-like lysozyme
              1. Uncharacterized protein GSU0986 [160721]
                 1. Geobacter sulfurreducens [TaxId: 35554] [160722] (1)
                    SQ Q74EH6 23-133
   267. Glutamine synthetase/guanido kinase [55930] (1)
        duplication: common core consists of two beta-alpha-beta2-alpha repeats
        1. Glutamine synthetase/guanido kinase [55931] (5)
           uperfamily
           1. Glutamine synthetase catalytic domain [55932] (2)
              1. Glutamine synthetase, C-terminal domain [55933]
                 1. Salmonella typhimurium [TaxId: 90371] [55934] (18)
                 2. Mycobacterium tuberculosis [TaxId: 1773] [75542] (8)
           2. Guanido kinase catalytic domain [55935] (8)
              1. Creatine kinase, C-terminal domain [55936]
                 1. Chicken (Gallus gallus), mitochondria [TaxId: 9031] [55937] (1)
                 2. Chicken (Gallus gallus), brain-type [TaxId: 9031] [55938] (1)
                 3. Human (Homo sapiens), muscle isoform [TaxId: 9606] [90026] (1)
                 4. Human (Homo sapiens), mitochondria [TaxId: 9606] [55939] (1)
                 5. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55940] (3)
                 6. Cow (Bos taurus), retinal isoform [TaxId: 9913] [55941] (1)
                 7. Pacific electric ray (Torpedo californica) [TaxId: 7787] [82781] (2)
              2. Arginine kinase, C-terminal domain [55942]
                 1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [55943] (7)
                    SQ P51541
           3. Glutamate-cysteine ligase family 2 (GCS2) [111160] (2)
              Pfam 04107; structural and functional relationships to Glutamine synthetase
              1. Carboxylate-amine ligase YbdK [111161]
                 1. Escherichia coli [TaxId: 562] [111162] (1)
                    SQ P77213
                 2. Salmonella typhimurium [TaxId: 90371] [111163] (1)
                    SQ Q8ZR41
           4. Glutamate-cysteine ligase [118090] (1)
              Pfam 04262
              1. Gamma-glutamylcysteine synthetase GshA [118091]
                 1. Escherichia coli [TaxId: 562] [118092] (10)
                    SQ P0A6W9
           5. GatB/GatE catalytic domain-like [143812] (3)
              N-terminal and C-terminal parts correspond to Pfam 02934 (GatB_N) and Pfam 01162 (GatB), respectively
              1. Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, GatB, N-terminal domain [143813]
                 1. Staphylococcus aureus [TaxId: 1280] [143814] (5)
                    SQ P64201 2-293
              2. Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE [143815]
                 1. Methanobacterium thermoautotrophicum [TaxId: 145262] [143816] (2)
                    SQ O26803 1-270,396-444
                 2. Pyrococcus abyssi [TaxId: 29292] [143817] (2)
                    SQ Q9V0U0 5-276,408-456
   268. TBP-like [55944] (11)
        beta-alpha-beta(4)-alpha
        1. TATA-box binding protein-like [55945] (2)
           uperfamily
           1. TATA-box binding protein (TBP), C-terminal domain [55946] (5)
              duplication: consists of two clear structural repeats
              1. TATA-box binding protein (TBP), C-terminal domain [55947]
                 structure of the N-terminal domain is not known yet
                 1. Human (Homo sapiens) [TaxId: 9606] [55948] (5)
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [55949] (13)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55950] (8)
                 4. Archaeon Pyrococcus woesei [TaxId: 2262] [55951] (3)
                 5. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [103238] (1)
           2. DNA repair glycosylase, N-terminal domain [55952] (2)
              contains a single copy of this fold
              1. 3-Methyladenine DNA glycosylase II (gene alkA or aidA) [55953]
                 1. Escherichia coli [TaxId: 562] [55954] (35)
                    SQ P04395
              2. 8-oxoguanine glycosylase [55955]
                 1. Human (Homo sapiens) [TaxId: 9606] [55956] (23)
        2. MoaD-related protein, C-terminal domain [103239] (1)
           contains a single copy of this fold
           uperfamily
           1. MoaD-related protein, C-terminal domain [103240] (1)
              1. MoaD-related protein, C-terminal domain [103241]
                 1. Thermus thermophilus [TaxId: 274] [103242] (1)
        3. KA1-like [103243] (2)
           contains a single copy of this fold
           uperfamily
           1. Kinase associated domain 1, KA1 [103244] (1)
              Pfam 02149
              1. Map/microtubule affinity-regulating kinase 3 [103245]
                 1. Mouse (Mus musculus) [TaxId: 10090] [103246] (2)
                    SQ Q8C6G9 373-452
           2. Ssp2 C-terminal domain-like [160723] (3)
              PfamB 166430
              1. Carbon catabolite-derepressing protein kinase SNF1 [160724]
                 1. Saccharomyces cerevisiae [TaxId: 4932] [160725] (2)
                    SQ P06782 460-630
              2. Snf1-like protein kinase ssp2 [160726]
                 1. Schizosaccharomyces pombe [TaxId: 4896] [160727] (12)
                    SQ O74536 449-576
              3. 5'-AMP-activated protein kinase catalytic subunit alpha-1, AMPK1 [160728]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [160729] (3)
                    SQ P54645 396-548
        4. TT1751-like [103247] (1)
           contains a single copy of this fold decorated with additional structures; forms dimer
           uperfamily
           1. TT1751-like [103248] (2)
              Pfam 03625; DUF302
              1. Unnamed hypothetical protein [103249]
                 1. Bacillus stearothermophilus [TaxId: 1422] [103250] (1)
              2. Hypothetical protein TT1751 (TTHA1732) [111164]
                 1. Thermus thermophilus HB8 [TaxId: 300852] [111165] (1)
                    SQ Q84BQ8
        5. Cell-division protein ZipA, C-terminal domain [64383] (1)
           contains a single copy of this fold
           uperfamily
           1. Cell-division protein ZipA, C-terminal domain [64384] (1)
              1. Cell-division protein ZipA, C-terminal domain [64385]
                 1. Escherichia coli [TaxId: 562] [64386] (10)
        6. Phosphoglucomutase, C-terminal domain [55957] (1)
           contains a single copy of this fold and an extra beta-strand at the C-terminus
           uperfamily
           1. Phosphoglucomutase, C-terminal domain [55958] (4)
              Pfam 00408
              1. Phosphoglucomutase [55959]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55960] (6)
              2. Exocytosis-sensitive phosphoprotein, pp63/parafusin [69811]
                 1. Paramecium tetraurelia [TaxId: 5888] [69812] (2)
              3. Phosphomannomutase/phosphoglucomutase [81375]
                 1. Pseudomonas aeruginosa [TaxId: 287] [81374] (12)
              4. Phosphoacetylglucosamine mutase [118093]
                 1. Mouse (Mus musculus) [TaxId: 10090] [118094] (1)
                    SQ Q9CYR6 442-540
        7. Bet v1-like [55961] (10)
           contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix
           uperfamily
           1. Pathogenesis-related protein 10 (PR10)-like [55962] (8)
              1. Major tree pollen allergen [55963]
                 1. White birch (Betula verrucosa), Bet v 1 [TaxId: 3505] [55964] (5)
                 2. European white birch (Betula pendula), Bet v I-a [TaxId: 3505] [55965] (1)
                 3. European white birch (Betula pendula), Bet v 1-l [TaxId: 3505] [82782] (1)
                 4. Sweet cherry (Prunus avium), pru av 1 [TaxId: 42229] [64387] (2)
              2. Plant pathogenesis-related protein PR10 [75543]
                 1. Yellow lupine (Lupinus luteus) [TaxId: 3873] [75544] (4)
                 2. Jicama (Pachyrhizus erosus), SPE-16 [TaxId: 109171] [143818] (4)
                    SQ Q6T6J0 2-148
              3. Hypothetical protein At1G24000 [103251]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103252] (3)
              4. Major allergen api g 1 [143819]
                 1. Celery (Apium graveolens) [TaxId: 4045] [143820] (2)
                    SQ P49372 2-154
           2. STAR domain [55966] (4)
              1. Lipid transport domain of Mln64 [55967]
                 1. Human (Homo sapiens) [TaxId: 9606] [55968] (1)
              2. Cholesterol-regulated Start protein 4 (Stard4). [75545]
                 1. Mouse (Mus musculus) [TaxId: 10090] [75546] (1)
              3. Phosphatidylcholine transfer protein [75547]
                 1. Human (Homo sapiens) [TaxId: 9606] [75548] (3)
              4. Star-related lipid transfer protein 13 [160730]
                 1. Human (Homo sapiens) [TaxId: 9606] [160731] (3)
                    SQ Q9Y3M8 908-1104
           3. Phoshatidylinositol transfer protein, PITP [64388] (4)
              1. Phoshatidylinositol transfer protein, PITP [64389]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [64390] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [75549] (1)
                 3. Human (Homo sapiens) [TaxId: 9606] [103253] (1)
                 4. Rat (Rattus norvegicus), beta isoform [TaxId: 10116] [143821] (1)
                    SQ P53812 1-270
           4. Ring hydroxylating alpha subunit catalytic domain [55969] (7)
              Pfam 00848; contains a few insertion and C-terminal extension compared with Bet v1
              1. Naphthalene 1,2-dioxygenase alpha subunit, C-domain [55970]
                 1. Pseudomonas putida [TaxId: 303] [55971] (16)
                 2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [143822] (6)
                    SQ Q9X3R9 163-441
              2. Biphenyl dioxygenase large subunit BphA1, C-terminal domain [111166]
                 1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [111167] (2)
                    SQ Q53122 17-451
              3. 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO [143823]
                 1. Pseudomonas putida [TaxId: 303] [143824] (1)
                    SQ O05935 164-442
              4. Large subunit of cumene dioxygenase cumA1 [143825]
                 1. Pseudomonas fluorescens [TaxId: 294] [143826] (1)
                    SQ Q51743 181-459
              5. Terminal oxygenase component of carbazole CarAa [143827]
                 1. Janthinobacterium sp. j3 [TaxId: 213804] [143828] (10)
                    SQ Q84II6 143-384
              6. Nitrobenzene dioxygenase alpha subunit, NBDO-alpha [143829]
                 1. Comamonas sp. JS765 [TaxId: 58226] [143830] (3)
                    SQ Q8RTL4 153-439
           5. AHSA1 domain [111168] (11)
              Pfam 05146
              1. Hypothetical protein NE0264 [111169]
                 1. Nitrosomonas europaea [TaxId: 915] [111170] (1)
                    SQ Q82XK1
              2. Hypothetical protein MM0500 [118095]
                 1. Methanosarcina mazei [TaxId: 2209] [118096] (1)
                    SQ Q8PZJ2
              3. Hypothetical protein BH1534 [118097]
                 1. Bacillus halodurans [TaxId: 86665] [118098] (1)
                    SQ Q9KCN5
              4. Hypothetical protein BC4709 [118099]
                 1. Bacillus cereus [TaxId: 1396] [118100] (1)
                    SQ Q816V6
              5. Calicheamicin gene cluster protein CalC [143831]
                 possible link between the AHSA1 (Pfam 08327) and oligoketide cyclase/dehydrase-like (new Pfam 03364) families
                 1. Micromonospora echinospora [TaxId: 1877] [143832] (3)
                    SQ Q8KNF0 27-181
              6. Activator of 90 kda heat shock protein ATPase homolog 1, AHSA1 [143833]
                 1. Human (Homo sapiens) [TaxId: 9606] [143834] (1)
                    SQ O95433 204-335
              7. Hypothetical protein CV1439 [143835]
                 1. Chromobacterium violaceum [TaxId: 536] [143836] (6)
                    SQ Q7NY36 2-144
              8. Hypothetical protein EF2215 [160732]
                 1. Enterococcus faecalis [TaxId: 1351] [160733] (1)
                    SQ Q832L1 1-160
              9. Uncharacterized protein SPO3351 [160734]
                 1. Silicibacter pomeroyi [TaxId: 89184] [160735] (1)
                    SQ Q5LN61 2-144
              10. Hypothetical protein SA2116 [160736]
                  1. Staphylococcus aureus [TaxId: 1280] [160737] (1)
                     SQ Q2FEH1 5-168
              11. Uncharacterized protein BPP1335 [160738]
                  1. Bordetella parapertussis [TaxId: 519] [160739] (1)
                     SQ Q7WAN9 1-183
           6. oligoketide cyclase/dehydrase-like [118101] (3)
              Pfam 03654
              1. Hypothetical protein CC1736 [118102]
                 1. Caulobacter crescentus [TaxId: 155892] [118103] (1)
                    SQ Q9A7I7
              2. Hypothetical protein TTHA0849 [143837]
                 1. Thermus thermophilus [TaxId: 274] [143838] (4)
                    SQ Q5SK03 2-147
              3. Multifunctional enzyme TcmN, cyclase/aromatase domain [160740]
                 1. Streptomyces glaucescens [TaxId: 1907] [160741] (3)
                    SQ P16559 1-152! SQ P16559 1-155
           7. PA1206-like [143839] (1)
              1. Hypothetical protein PA1206 [143840]
                 1. Pseudomonas aeruginosa [TaxId: 287] [143841] (2)
                    SQ Q9I4D2 1-151
           8. Atu1531-like [160742] (2)
              Pfam 10604; Polyketide cyclase/dehydrase and lipid transport
              1. Uncharacterized protein XoxI [160743]
                 1. Bacillus cereus [TaxId: 1396] [160744] (2)
                    SQ Q81AY6 3-140
              2. Uncharacterized protein Atu1531 [160745]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160746] (2)
                    SQ Q7CZ16 1-133
           9. Smu440-like [160747] (1)
              PfamB 094079
              1. Hypothetical protein SMU440 [160748]
                 1. Streptococcus mutans [TaxId: 1309] [160749] (2)
                    SQ Q8DVN6 1-137
           10. CoxG-like [160750] (2)
               Pfam 06240
               1. Hypothetical protein APE2225 [160751]
                  1. Aeropyrum pernix [TaxId: 56636] [160752] (2)
                     SQ Q9Y9R3 1-147
               2. Hypothetical protein GKP20 [160753]
                  1. Geobacillus kaustophilus [TaxId: 1462] [160754] (1)
                     SQ Q5QL47 1-147
        8. Rbstp2229 protein [111171] (1)
           forms segment-swapped dimers further organized in hexamers
           uperfamily
           1. Rbstp2229 protein [111172] (1)
              1. Rbstp2229 protein [111173]
                 1. Bacillus stearothermophilus [TaxId: 1422] [111174] (1)
                    SQ P84137
        9. RalF, C-terminal domain [118104] (1)
           contains a single copy of this fold decorated with additional structures
           uperfamily
           1. RalF, C-terminal domain [118105] (1)
              1. RalF, C-terminal domain [118106]
                 1. Legionella pneumophila [TaxId: 446] [118107] (1)
                    SQ Q8RT31 2-353
        10. YwmB-like [143842] (1)
            duplication: tandem repeat of two circularly permuted motifs, alpha-beta-alpha-beta(4), assembled as in the TATA-box binding domain; forms a swapped dimer by exchanging the equivalent parts of the C-terminal motifs
            uperfamily
            1. YwmB-like [143843] (1)
               1. Hypothetical protein YwmB [143844]
                  1. Bacillus subtilis [TaxId: 1423] [143845] (1)
                     SQ O32277 31-244
        11. YugN-like [160755] (1)
            1. YugN-like [160756] (1)
               Pfam 08868
               1. Uncharacterized protein ABC2387 [160757]
                  YugN homologue
                  1. Bacillus clausii [TaxId: 79880] [160758] (1)
                     SQ Q5WFD8 1-114
   269. XisI-like [143846] (1)
        alpha-beta(4)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order 1234, meander; the open side of beta-sheet provides dimerization interface
        1. XisI-like [143847] (1)
           uperfamily
           1. XisI-like [143848] (3)
              Pfam 08869
              1. Hypothetical protein Ava3825 [143849]
                 1. Anabaena variabilis [TaxId: 1172] [143850] (2)
                    SQ Q3M6F6 1-111
              2. XisI [143851]
                 the fdxN element excision controlling factor
                 1. Anabaena variabilis [TaxId: 1172] [143852] (2)
                    SQ Q3MD55 2-118
                    Ava1458
              3. Hypothetical protein Ava3320 [143853]
                 1. Anabaena variabilis [TaxId: 1172] [143854] (1)
                    SQ Q3M7V9 2-113
   270. S-adenosylmethionine synthetase [55972] (1)
        duplication: consists of 3 similar intertwined domains
        structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
        1. S-adenosylmethionine synthetase [55973] (1)
           uperfamily
           1. S-adenosylmethionine synthetase [55974] (3)
              1. S-adenosylmethionine synthetase [55975]
                 synonym: methionine adenosyltransferase, MAT
                 1. Escherichia coli [TaxId: 562] [55976] (9)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [55977] (5)
                 3. Human (Homo sapiens), isoform type-2 [TaxId: 9606] [160759] (3)
                    SQ P31153 126-251! SQ P31153 16-125! SQ P31153 252-395
                    MAT2A
   271. DNA clamp [55978] (1)
        contains two helices and two beta sheets
        duplication: fold has internal pseudo two-fold symmetry
        1. DNA clamp [55979] (2)
           uperfamily
           1. DNA polymerase III, beta subunit [55980] (2)
              duplication: consists of three domains of this fold
              1. DNA polymerase III, beta subunit [55981]
                 1. Escherichia coli [TaxId: 562] [55982] (30)
                    SQ P00583
                 2. Thermotoga maritima [TaxId: 2336] [118108] (1)
                    SQ Q9WYA0
           2. DNA polymerase processivity factor [55983] (9)
              duplication: consists of two domains of this fold
              1. gp45 sliding clamp [55984]
                 1. Bacteriophage RB69 [TaxId: 12353] [55985] (2)
                 2. Bacteriophage T4 [TaxId: 10665] [55986] (1)
              2. UL42 [55987]
                 1. Human herpesvirus type 1 [TaxId: 10298] [55988] (1)
              3. Proliferating cell nuclear antigen (PCNA) [55989]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55990] (5)
                    SQ P15873
                 2. Human (Homo sapiens) [TaxId: 9606] [55991] (31)
                    SQ P12004
                 3. Archaeon Pyrococcus furiosus [TaxId: 2261] [55992] (4)
                 4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103254] (3)
                 5. Archaeon Sulfolobus tokodaii [TaxId: 111955] [111175] (1)
                    SQ Q975N2
              4. UL44 [111176]
                 1. Human cytomegalovirus, HHV-5 [TaxId: 10359] [111177] (3)
                    SQ P16790 1-290
   272. Hypothetical protein TM0160 [103255] (1)
        duplication: consists of two beta(3)-alpha(2) structural repeats; single barrel-like beta-sheet
        1. Hypothetical protein TM0160 [103256] (1)
           uperfamily
           1. Hypothetical protein TM0160 [103257] (1)
              1. Hypothetical protein TM0160 [103258]
                 1. Thermotoga maritima [TaxId: 2336] [103259] (1)
   273. TTHC002-like [160760] (1)
        alpha-beta-alpha-beta(3); forms dimer with a single beta-sheet, folded in a barrel-like shape
        1. TTHC002-like [160761] (1)
           1. TTHC002-like [160762] (1)
              1. Hypothetical protein TTHC002 [160763]
                 1. Thermus thermophilus [TaxId: 274] [160764] (2)
                    SQ Q5SGN2 7-86
   274. Molybdenum cofactor-binding domain [56002] (1)
        beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
        1. Molybdenum cofactor-binding domain [56003] (1)
           duplication: consists of 4 structural repeats arranged in 2 lobes
           contains one left-hand beta-alpha-beta unit per lobe
           uperfamily
           1. Molybdenum cofactor-binding domain [56004] (8)
              1. Aldehyde oxidoreductase [56005]
                 1. Desulfovibrio gigas [TaxId: 879] [56006] (3)
                    SQ Q46509
                 2. Desulfovibrio desulfuricans [TaxId: 876] [56007] (1)
              2. Xanthine oxidase, C-terminal domain [56008]
                 1. Cow (Bos taurus) [TaxId: 9913] [56009] (6)
                    SQ P80457
              3. Xanthine dehydrogenase chain B, C-terminal domain [69813]
                 1. Rhodobacter capsulatus [TaxId: 1061] [69814] (2)
              4. Carbon monoxide (CO) dehydrogenase molybdoprotein [56010]
                 1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [56011] (6)
                 2. Hydrogenophaga pseudoflava [TaxId: 47421] [56012] (2)
              5. Quinoline 2-oxidoreductase large subunit QorL [111178]
                 1. Pseudomonas putida [TaxId: 303] [111179] (1)
                    SQ P72224
              6. 4-hydroxybenzoyl-CoA reductase alpha subunit HrcA, C-terminal domain [118109]
                 1. Thauera aromatica [TaxId: 59405] [118110] (2)
                    SQ O33819
   275. NE1680-like [160765] (1)
        beta(2)-alpha-beta-alpha-beta; 2 layers, a/b; antiparallel sheet, order 3124
        1. NE1680-like [160766] (1)
           1. NE1680-like [160767] (1)
              Pfam 09630; DUF2024
              1. Hypothetical protein NE1680 [160768]
                 1. Nitrosomonas europaea [TaxId: 915] [160769] (1)
                    SQ Q82U33 1-85
   276. Nitrite and sulphite reductase 4Fe-4S domain-like [56013] (1)
        beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection between strands 1 and 2
        1. Nitrite and sulphite reductase 4Fe-4S domain-like [56014] (1)
           duplication: contains two domains of this fold
           uperfamily
           1. Nitrite and sulphite reductase 4Fe-4S domain-like [56015] (7)
              1. Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 [56016]
                 1. Escherichia coli [TaxId: 562] [56017] (12)
              2. Sulfite reductase NirA [160770]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [160771] (8)
                    SQ P71753 162-326! SQ P71753 407-555
              3. Dissimilatory sulfite reductase subunit beta, DsrB [160772]
                 1. Desulfovibrio vulgaris [TaxId: 881] [160773] (2)
                    SQ P45575 136-208,278-381
                 2. Archaeoglobus fulgidus [TaxId: 2234] [160774] (2)
                    SQ Q59110 123-196,262-366
              4. Ferredoxin--nitrite reductase, NIR [160775]
                 1. Spinach (Spinacia oleracea) [TaxId: 3562] [160776] (2)
                    SQ P05314 207-377! SQ P05314 463-588
                    chloroplastic
              5. Dissimilatory sulfite reductase subunit alpha, DsrA [160777]
                 1. Desulfovibrio vulgaris [TaxId: 881] [160778] (2)
                    SQ P45574 168-241,323-437
                 2. Archaeoglobus fulgidus [TaxId: 2234] [160779] (2)
                    SQ Q59109 168-239,306-418
   277. DeoB insert domain-like [143855] (1)
        alpha-beta-X-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 2 and 5 are antiparallel to the rest
        1. DeoB insert domain-like [143856] (1)
           uperfamily
           1. DeoB insert domain-like [143857] (1)
              1. Phosphopentomutase DeoB [143858]
                 1. Streptococcus mutans [TaxId: 1309] [143859] (2)
                    SQ Q8DTU0 108-226
   278. The spindle assembly checkpoint protein mad2 [56018] (1)
        core: alpha(2)-beta(2)-alpha-beta; mixed sheet: order 213
        1. The spindle assembly checkpoint protein mad2 [56019] (1)
           N- and C-termini undergo large conformational rearrangement upon ligand binding
           uperfamily
           1. The spindle assembly checkpoint protein mad2 [56020] (1)
              1. The spindle assembly checkpoint protein mad2 [56021]
                 1. Human (Homo sapiens) [TaxId: 9606] [56022] (7)
   279. Phospholipase D/nuclease [56023] (1)
        beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
        1. Phospholipase D/nuclease [56024] (5)
           uperfamily
           1. Nuclease [56025] (1)
              1. Nuclease Nuc [56026]
                 1. Salmonella typhimurium [TaxId: 90371] [56027] (2)
           2. Phospholipase D [64391] (1)
              duplication: contains two domains of this fold arranged as in the Nuc dimer
              1. Phospholipase D [64392]
                 1. Streptomyces sp. [TaxId: 1931] [64393] (8)
                    SQ P84147
           3. Tyrosyl-DNA phosphodiesterase TDP1 [69815] (2)
              1. Tyrosyl-DNA phosphodiesterase TDP1 [69816]
                 1. Human (Homo sapiens) [TaxId: 9606] [69817] (12)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111180] (1)
                    SQ P38319 79-538
           4. Polyphosphate kinase C-terminal domain [143860] (2)
              C-terminal part of Pfam 02503; similar to PLD; contains two domains of this fold arranged as in the Nuc dimer
              1. Polyphosphate kinase, PPK [143861]
                 1. Porphyromonas gingivalis [TaxId: 837] [143862] (4)
                    SQ Q7MTR1 318-505! SQ Q7MTR1 506-691
                 2. Escherichia coli [TaxId: 562] [143863] (8)
                    SQ P0A7B1 315-501! SQ P0A7B1 502-688
           5. TrmB middle domain-like [160780] (1)
              N-terminal part of PfamB 004822
              1. Transcriptional regulator TrmB [160781]
                 1. Thermococcus litoralis [TaxId: 2265] [160782] (1)
                    SQ Q7LYW4 110-246
   280. CorA soluble domain-like [143864] (1)
        beta(2)-alpha-beta-alpha(2)-beta(4)-alpha(3); 3 layers: a/b/a; mixed beta-sheet, order 2137654; strands 3 and 7 are parallel
        1. CorA soluble domain-like [143865] (1)
           uperfamily
           1. CorA soluble domain-like [143866] (1)
              N-terminal part of Pfam 01544
              1. Magnesium transport protein CorA, soluble domain [143867]
                 1. Thermotoga maritima [TaxId: 2336] [143868] (21)
                    SQ Q9WZ31 13-244! SQ Q9WZ31 9-285
   281. Monooxygenase (hydroxylase) regulatory protein [56028] (1)
        corner-like structure formed by two sheets and filled in with 2-3 helices
        1. Monooxygenase (hydroxylase) regulatory protein [56029] (1)
           duplication: consists of two beta-alpha-(beta)-beta(2) motifs; some topological similarity to the ferredoxin-like fold
           uperfamily
           1. Monooxygenase (hydroxylase) regulatory protein [56030] (4)
              note: the solution structure determinations disagree in the relative orientations of two motifs
              1. Soluble methane monooxygenase regulatory protein B [56031]
                 1. Escherichia coli [TaxId: 562] [56032] (1)
                 2. Methylosinus trichosporium [TaxId: 426] [56033] (1)
              2. Toluene-4-monooxygenase catalytic effector protein [64394]
                 1. Pseudomonas mendocina [TaxId: 300] [64395] (6)
              3. Phenol hydroxylase P2 protein [56034]
                 1. Pseudomonas sp., CF600 [TaxId: 306] [56035] (1)
   282. PurM C-terminal domain-like [56041] (1)
        3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
        1. PurM C-terminal domain-like [56042] (1)
           uperfamily
           1. PurM C-terminal domain-like [56043] (6)
              1. Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain [56044]
                 1. Escherichia coli [TaxId: 562] [56045] (1)
              2. Phosphoribosylformylglycinamidine synthase II, domains 2 and 4 [103260]
                 duplication: tandem repeats of two PurM-like units arranged like the PurM subunits in the dimer
                 1. Thermotoga maritima [TaxId: 2336] [103261] (17)
                    TM1246
              3. FGAM synthase PurL, PurM-like module, C1 and C2 domains [111181]
                 1. Salmonella typhimurium [TaxId: 90371] [111182] (1)
                    SQ P74881
              4. Thiamine monophosphate kinase (ThiL) C-terminal domain [118111]
                 1. Aquifex aeolicus [TaxId: 63363] [118112] (9)
                    SQ O67883
              5. Hydrogenase expression/formation protein HypE [160783]
                 1. Thermococcus kodakaraensis [TaxId: 311400] [160784] (2)
                    SQ Q5JII7 156-334
              6. Selenide, water dikinase SelD [160785]
                 1. Aquifex aeolicus [TaxId: 63363] [160786] (7)
                    SQ O67139 155-336
   283. PF0523-like [143869] (1)
        beta-alpha-beta-alpha(3)-beta-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order 4132; some similarity to the PurM C-terminal domain-like fold (scop_cf 56041)
        1. PF0523-like [143870] (1)
           uperfamily
           1. PF0523-like [143871] (1)
              Pfam 04416; DUF509
              1. Hypothetical protein PF0523 [143872]
                 1. Pyrococcus furiosus [TaxId: 2261] [143873] (1)
                    SQ Q8U3E5 2-137
   284. Chorismate synthase, AroC [103262] (1)
        duplication: consists of two DCoH-like beta(2)-alpha-beta(2)-alpha structural repeats; 3 layers, beta/alpha/beta
        1. Chorismate synthase, AroC [103263] (1)
           uperfamily
           1. Chorismate synthase, AroC [103264] (5)
              1. Chorismate synthase, AroC [103265]
                 1. Streptococcus pneumoniae [TaxId: 1313] [103266] (1)
                 2. Aquifex aeolicus [TaxId: 63363] [103267] (1)
                 3. Campylobacter jejuni [TaxId: 197] [103268] (1)
                 4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103269] (2)
                 5. Helicobacter pylori [TaxId: 210] [111183] (2)
                    SQ P56122
   285. Hsp33 domain [64396] (1)
        3 layers: beta/alpha/beta; buried helix
        1. Hsp33 domain [64397] (1)
           uperfamily
           1. Hsp33 domain [64398] (3)
              forms strand-swapped dimer
              1. Heat shock protein 33, Hsp33 [64399]
                 1. Escherichia coli [TaxId: 562] [64400] (2)
                 2. Bacillus subtilis [TaxId: 1423] [118113] (1)
                    SQ P37565
                 3. Thermotoga maritima [TaxId: 2336] [118114] (1)
                    SQ Q9X1B4
   286. MTH1598-like [69818] (1)
        beta(2)-alpha-beta-alpha-beta(4); 3 layers: beta/alpha/beta; some similarity to the Hsp33 fold
        1. MTH1598-like [69819] (1)
           uperfamily
           1. MTH1598-like [69820] (2)
              1. Hypothetical protein MTH1598 [69821]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69822] (1)
              2. Hypothetical protein TM1083 [75550]
                 1. Thermotoga maritima [TaxId: 2336] [75551] (1)
   287. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68929] (1)
        beta-alpha-beta(4)-alpha-beta(2); 3 layers: beta/alpha/beta; buried helix
        1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68930] (1)
           uperfamily
           1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68931] (1)
              1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68932]
                 1. Thermotoga maritima [TaxId: 2336] [53356] (1)
   288. OsmC-like [82783] (1)
        swapped dimer of beta(3)-alpha-beta(2)-alpha(2)-beta subunits; mixed beta-sheet; order: 321[4][5][6]; buried helix
        1. OsmC-like [82784] (2)
           uperfamily
           1. Ohr/OsmC resistance proteins [82785] (9)
              1. Organic hydroperoxide resistance protein Ohr [82786]
                 1. Pseudomonas aeruginosa, pa01 [TaxId: 287] [82787] (1)
                 2. Deinococcus radiodurans [TaxId: 1299] [103270] (1)
              2. Osmotically inducible protein OsmC [103271]
                 1. Escherichia coli [TaxId: 562] [103272] (2)
              3. Hypothetical protein MPN625 [103273]
                 1. Mycoplasma pneumoniae [TaxId: 2104] [103274] (1)
                 2. Thermus thermophilus [TaxId: 274] [103275] (1)
              4. Hypothetical protein VCA0330 [160787]
                 1. Vibrio cholerae [TaxId: 666] [160788] (2)
                    SQ Q9KMK9 7-161
              5. Hypothetical protein GSU2788 [160789]
                 1. Geobacter sulfurreducens [TaxId: 35554] [160790] (2)
                    SQ Q749F5 4-185! SQ Q749F5 5-186
              6. Uncharacterized protein Psyc0566 [160791]
                 1. Psychrobacter arcticus 273-4 [TaxId: 259536] [160792] (1)
                    SQ Q4FU81 1-132
              7. Hypothetical protein Ta0195 [160793]
                 1. Thermoplasma acidophilum [TaxId: 2303] [160794] (2)
                    SQ Q9HLN2 1-139
           2. YhfA-like [90027] (2)
              1. Hypothetical protein in CRP region [90028]
                 probably the same as YhfA
                 1. Escherichia coli [TaxId: 562] [90029] (1)
              2. Hypothetical protein TM0919 [111184]
                 1. Thermotoga maritima [TaxId: 2336] [111185] (1)
                    SQ Q9X021
   289. Hypothetical protein HI1480 [103276] (1)
        beta-alpha(4)-beta-alpha-beta; segregated alpha-helical and beta-sheet subdomains; dimeric beta-sheet barrel: n=6, S=10
        1. Hypothetical protein HI1480 [103277] (1)
           uperfamily
           1. Hypothetical protein HI1480 [103278] (1)
              1. Hypothetical protein HI1480 [103279]
                 1. Haemophilus influenzae [TaxId: 727] [103280] (1)
                    structural genomics
   290. ERH-like [143874] (1)
        beta(2)-alpha(2)-beta(2)-alpha; antiparallel beta-sheet, order:2134; helices are arranged in a bundle rather than packed agains beta-sheet; dimerises via with the formation of a flattened beta-barel: closed n=8, S=10
        1. ERH-like [143875] (1)
           uperfamily
           1. ERH-like [143876] (1)
              Pfam 01133
              1. Enhancer of rudimentary homolog, ERH [143877]
                 1. Mouse (Mus musculus) [TaxId: 10090] [143878] (7)
                    SQ P84089 1-104! SQ P84090 2-101
                    also includes 100% identical human protein P84090 (1W9G)
   291. Ribosomal protein S8 [56046] (1)
        consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
        1. Ribosomal protein S8 [56047] (1)
           uperfamily
           1. Ribosomal protein S8 [56048] (4)
              1. Ribosomal protein S8 [56049]
                 1. Bacillus stearothermophilus [TaxId: 1422] [56050] (1)
                 2. Thermus thermophilus [TaxId: 274] [56051] (46)
                    SQ P24319
                 3. Archaeon Methanococcus jannaschii [TaxId: 2190] [64401] (1)
                 4. Escherichia coli [TaxId: 562] [111186] (9)
                    SQ P02361
   292. Ribosomal protein L6 [56052] (1)
        consists of two beta-sheets and one alpha-helix packed around single core
        1. Ribosomal protein L6 [56053] (1)
           uperfamily
           1. Ribosomal protein L6 [56054] (6)
              1. Ribosomal protein L6 [56055]
                 duplication: consists of two domains of this fold
                 1. Bacillus stearothermophilus [TaxId: 1422] [56056] (9)
                 2. Archaeon Haloarcula marismortui [TaxId: 2238] [56057] (61)
                    SQ P14135
                 3. Human (Homo sapiens) [TaxId: 9606] [160795] (1)
                    SQ P32969 1-87
                 4. Escherichia coli [TaxId: 562] [160796] (54)
                    SQ P02390 1-81! SQ P02390 82-176
                 5. Thermus thermophilus [TaxId: 274] [160797] (22)
                    SQ Q72I19 11-81! SQ Q72I19 82-170
                 6. Deinococcus radiodurans [TaxId: 1299] [160798] (12)
                    SQ Q9RSL3 8-82! SQ Q9RSL3 83-172
   293. NE0471 N-terminal domain-like [143879] (1)
        beta(3)-alpha(n)-beta(3)-alpha; the two meander beta-sheets and helices are packed against the same core
        1. NE0471 N-terminal domain-like [143880] (1)
           uperfamily
           1. NE0471 N-terminal domain-like [143881] (1)
              1. Hypothetical protein NE0471 N-terminal domain [143882]
                 1. Nitrosomonas europaea [TaxId: 915] [143883] (2)
                    SQ Q82X29 4-87
   294. Lp2179-like [160799] (1)
        beta(2)-alpha-beta(4)-alpha-beta; contains two antiparallel beta-sheets (orders: 127 and 3456) packed against the longer C-terminal helix
        1. Lp2179-like [160800] (1)
           1. Lp2179-like [160801] (1)
              Pfam 08866, DUF1831
              1. Hypothetical protein Lp2179 [160802]
                 1. Lactobacillus plantarum [TaxId: 1590] [160803] (1)
                    SQ Q88V95 1-113
   295. RGC domain-like [143884] (1)
        consists of two beta-sheets and four helices eclosing a cental cavity
        1. RGC domain-like [143885] (1)
           uperfamily
           1. RGC domain [143886] (1)
              Pfam 03836; RasGAP C-terminus
              1. Ras GTPase-activating-like protein IQGAP1 [143887]
                 1. Human (Homo sapiens) [TaxId: 9606] [143888] (1)
                    SQ P46940 1559-1657
   296. Smc hinge domain [75552] (1)
        consists of 2 different alpha+beta subdomains; forms subdomain-swapped dimers
        1. Smc hinge domain [75553] (1)
           uperfamily
           1. Smc hinge domain [75554] (1)
              1. Smc hinge domain [75555]
                 1. Thermotoga maritima [TaxId: 2336] [75556] (3)
   297. DNA mismatch repair protein MutL [118115] (1)
        consists of two different alpha+beta (sub)domains; d1: [beta(3)-alpha-(insert of d2)-alpha(2)-beta; 2 layers, a/b; antiparallel sheet, order: 1234]; d2: [beta-alpha-beta(2)-alpha(2); 2 layers, a/b; antiparallel sheet, order: 132]
        1. DNA mismatch repair protein MutL [118116] (1)
           uperfamily
           1. DNA mismatch repair protein MutL [118117] (1)
              1. DNA mismatch repair protein MutL [118118]
                 1. Escherichia coli [TaxId: 562] [118119] (1)
                    SQ P23367 433-614 # structure of the N-terminal domains (1-349) is also known, scop_sp 55883 and 54226
   298. ATP-grasp [56058] (2)
        Consists of two subdomains with different alpha+beta folds
        shares functional and structural similarities with the PIPK and protein kinase superfamilies
        1. Glutathione synthetase ATP-binding domain-like [56059] (9)
           uperfamily
           1. ATP-binding domain of peptide synthetases [56060] (4)
              1. Prokaryotic glutathione synthetase, C-domain [56061]
                 1. Escherichia coli [TaxId: 562] [56062] (4)
              2. D-ala-D-ala ligase, C-domain [56063]
                 1. Escherichia coli, gene ddlB [TaxId: 562] [56064] (3)
              3. D-alanine:D-lactate ligase VanA, C-domain [56065]
                 1. Leuconostoc mesenteroides, Ddl2 [TaxId: 1245] [56066] (1)
                 2. Enterococcus faecium [TaxId: 1352] [64402] (1)
           2. Lysine biosynthesis enzyme LysX ATP-binding domain [103281] (1)
              1. Lysine biosynthesis enzyme LysX ATP-binding domain [103282]
                 1. Thermus thermophilus [TaxId: 274] [103283] (2)
           3. BC ATP-binding domain-like [56067] (8)
              1. Biotin carboxylase (BC), domain 2 [56068]
                 subunit of acetyl-CoA and pyruvate carboxylases
                 1. Escherichia coli [TaxId: 562] [56069] (13)
                 2. Aquifex aeolicus [TaxId: 63363] [103284] (1)
              2. Glycinamide ribonucleotide synthetase (GAR-syn), domain 2 [56070]
                 1. Escherichia coli [TaxId: 562] [56071] (1)
                 2. Thermotoga maritima [TaxId: 2336] [111187] (1)
                    SQ Q9X0X7
              3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), domain 2 [56072]
                 1. Escherichia coli [TaxId: 562] [56073] (6)
              4. Glycinamide ribonucleotide transformylase PurT, domain 2 [56074]
                 1. Escherichia coli [TaxId: 562] [56075] (7)
              5. Carbamoyl phosphate synthetase (CPS), large subunit ATP-binding domains [56076]
                 duplication: CPS large subunit contains two full BC-like lobes: carboxyphosphate and carbamoyl phosphate domains
                 1. Escherichia coli [TaxId: 562] [56077] (10)
                    SQ P00968
              6. Acetyl-CoA carboxylase, BC-M subdomain [118120]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118121] (2)
                    SQ Q00955 13-566
           4. Synapsin C-terminal domain [56078] (3)
              1. Synapsin [56079]
                 1. Cow (Bos taurus) [TaxId: 9913] [56080] (2)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [103285] (2)
              2. Synapsin II [90030]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [90031] (2)
           5. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56081] (2)
              1. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56082]
                 1. Escherichia coli [TaxId: 562] [56083] (18)
                 2. Pig (Sus scrofa) [TaxId: 9823] [56084] (6)
                    GTP-specific enzyme
           6. Pyruvate phosphate dikinase, N-terminal domain [56085] (3)
              1. Pyruvate phosphate dikinase, N-terminal domain [56086]
                 the common fold is interrupted by a 4-helical subdomain (residues 112-198)
                 1. Clostridium symbiosum [TaxId: 1512] [56087] (7)
                 2. Trypanosoma brucei [TaxId: 5691] [75557] (1)
                 3. Maize (Zea mays) [TaxId: 4577] [143889] (2)
                    SQ P11155 74-453
           7. Eukaryotic glutathione synthetase ATP-binding domain [56088] (2)
              circularly permuted version of prokaryotic enzyme
              1. Eukaryotic glutathione synthetase ATP-binding domain [56089]
                 1. Human (Homo sapiens) [TaxId: 9606] [56090] (1)
                 2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82788] (2)
           8. Glutathionylspermidine synthase ATP-binding domain-like [143890] (1)
              both terminal parts of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
              1. Glutathionylspermidine synthase, synthetase domain [143891]
                 1. Escherichia coli [TaxId: 562] [143892] (10)
                    SQ P0AES0 201-378,497-615
           9. PurP ATP-binding domain-like [160804] (3)
              Pfam 06973; DUF1297
              1. 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP [160805]
                 1. Thermococcus kodakaraensis [TaxId: 311400] [160806] (3)
                    SQ Q5JD28 98-310
                 2. Methanocaldococcus jannaschii [TaxId: 2190] [160807] (4)
                    SQ Q57600 124-361
                 3. Pyrococcus furiosus [TaxId: 2261] [160808] (12)
                    SQ Q8U0R7 100-334
        2. DNA ligase/mRNA capping enzyme, catalytic domain [56091] (4)
           has a circularly permuted topology
           uperfamily
           1. ATP-dependent DNA ligase catalytic domain [56092] (3)
              1. ATP-dependent DNA ligase, N-terminal domain [56093]
                 1. Bacteriophage T7 [TaxId: 10760] [56094] (1)
                 2. Chlorella virus PBCV-1 [TaxId: 10506] [56095] (7)
              2. DNA ligase I (LIG1) [118122]
                 1. Human (Homo sapiens) [TaxId: 9606] [118123] (1)
                    SQ P18858 262-901
           2. Adenylation domain of NAD+-dependent DNA ligase [56096] (3)
              1. Adenylation domain of NAD+-dependent DNA ligase [56097]
                 contains additional, N-terminal all-alpha subdomain
                 1. Bacillus stearothermophilus [TaxId: 1422] [56098] (1)
                 2. Thermus filiformis [TaxId: 276] [56099] (2)
                 3. Enterococcus faecalis [TaxId: 1351] [118124] (2)
                    SQ Q837V6 5-317
           3. mRNA capping enzyme [56100] (2)
              1. RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain [56101]
                 1. Chlorella virus PBCV-1 [TaxId: 10506] [56102] (3)
              2. mRNA capping enzyme alpha subunit [90032]
                 1. Yeast (Candida albicans) [TaxId: 5476] [90033] (1)
           4. RNA ligase [103286] (2)
              1. RNA ligase 2, N-terminal domain [103287]
                 1. Bacteriophage T4 [TaxId: 10665] [103288] (1)
              2. RNA editing ligase MP52 [118125]
                 1. Trypanosoma brucei [TaxId: 5691] [118126] (1)
                    SQ P82863 52-316
   299. SAICAR synthase-like [56103] (1)
        consists of two alpha+beta subdomains
        1. SAICAR synthase-like [56104] (3)
           shares functional and structural similarities with the ATP-grasp fold and protein kinase superfamilies
           uperfamily
           1. SAICAR synthase [56105] (2)
              1. SAICAR synthase [56106]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56107] (6)
                 2. Thermotoga maritima [TaxId: 2336] [75558] (1)
                    TM1243
           2. Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta [56108] (1)
              1. Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta [56109]
                 1. Human (Homo sapiens) [TaxId: 9606] [56110] (1)
           3. Inositol polyphosphate kinase (IPK) [111188] (2)
              Pfam 03770
              1. Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A [111189]
                 1. Human (Homo sapiens) [TaxId: 9606] [111190] (3)
                    SQ P23677 187-461
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [111191] (1)
                    SQ P17105 203-458
   300. Protein kinase-like (PK-like) [56111] (1)
        consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
        1. Protein kinase-like (PK-like) [56112] (7)
           shares functional and structural similarities with the ATP-grasp fold and PIPK
           uperfamily
           1. Protein kinases, catalytic subunit [88854] (74)
              members organized in the groups and subfamiles specified by the comments
              1. Cyclin-dependent PK, CDK2 [88855]
                 CMGC group; CDKs subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [88856] (146)
                    SQ P24941
                 2. (Plasmodium falciparum) [TaxId: 5833] [103289] (4)
                    CDK2 homologue Pfpk5
              2. Cyclin-dependent PK, CDK5 [88857]
                 CMGC group; CDKs subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [88858] (4)
                    SQ Q00535
              3. Cyclin-dependent PK, CDK6 [88859]
                 CMGC group; CDKs subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [88860] (8)
              4. MAP kinase p38 [56129]
                 CMGC group; ERK/MAPK subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [56130] (65)
                 2. Mouse (Mus musculus) [TaxId: 10090] [56131] (3)
              5. MAP kinase p38-gamma [56132]
                 CMGC group; ERK/MAPK subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [56133] (1)
              6. MAP kinase Erk2 [56134]
                 CMGC group; ERK/MAPK subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [56135] (1)
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [56136] (10)
              7. c-jun N-terminal kinase (jnk3s) [56137]
                 CMGC group; ERK/MAPK subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [56138] (17)
              8. Glycogen synthase kinase-3 beta (Gsk3b) [69823]
                 CMGC group; GSK3 subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [69824] (17)
                    SQ P49841 35-383 ! SQ P49841 35-384
              9. Protein kinase CK2, alpha subunit [56142]
                 CMGC group; CK2 subfamily; serine/threonine kinase
                 1. Human (Homo sapiens) [TaxId: 9606] [75559] (4)
                 2. Maize (Zea mays) [TaxId: 4577] [56143] (21)
                 3. Rattus norvegicus [TaxId: 10116] [160809] (8)
              10. Sky1p [56148]
                  CMGC group; Clk subfamily; serine/threonine kinase
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56149] (5)
              11. cAMP-dependent PK, catalytic subunit [56116]
                  AGC group; PKA subfamily; serine/threonine kinase
                  1. Pig (Sus scrofa) [TaxId: 9823] [56117] (3)
                  2. Cow (Bos taurus) [TaxId: 9913] [56118] (32)
                     SQ P00517
                  3. Mouse (Mus musculus) [TaxId: 10090] [56119] (17)
                  4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64403] (1)
              12. Pkb kinase (Akt-2) [82791]
                  AGC group; RAC/Akt subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [82792] (18)
              13. G-protein coupled receptor kinase 2 [90034]
                  AGC group; GRKs subfamily; serine/threonine kinase
                  1. Cow (Bos taurus) [TaxId: 9913] [90035] (6)
              14. 3-phosphoinositide dependent protein kinase-1 Pdk1 [90036]
                  AGC group; PBK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [90037] (13)
                     SQ O15530 75-363
              15. Calmodulin-dependent protein kinase [56120]
                  CaMK group; CAMKI subfamily; serine/threonine kinase
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [56121] (1)
              16. Titin, kinase domain [56124]
                  CaMK group; CAMKI subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56125] (1)
              17. Twitchin, kinase domain [56126]
                  CaMK group; CAMKI subfamily; serine/threonine kinase
                  1. California sea hare (Aplysia californica), twk43 [TaxId: 6500] [56127] (1)
                  2. Caenorhabditis elegans, pjk4 [TaxId: 6239] [56128] (1)
              18. Death-associated protein kinase, Dap [75560]
                  CaMK group; CAMKI subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [75561] (6)
                     SQ P53355 2-285
              19. gamma-subunit of glycogen phosphorylase kinase (Phk) [56122]
                  CaMK group; CAMKI subfamily; serine/threonine kinase
                  1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [56123] (3)
              20. MAP kinase activated protein kinase 2, mapkap2 [82789]
                  CaMK group; MAPKAPK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [82790] (6)
              21. Cell cycle checkpoint kinase chk1 [64404]
                  CaMK group; CAMKL subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [64405] (36)
              22. pak1 [56146]
                  OPK group; PAK/STE20 subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56147] (2)
              23. Mycobacterial protein kinase PknB, catalytic domain [82793]
                  OPK group; PKN subfamily; serine/threonine kinase
                  1. Mycobacterium tuberculosis [TaxId: 1773] [82794] (6)
              24. Casein kinase-1, CK1 [56139]
                  OPK group; CKI subfamily; serine/threonine kinase
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [56140] (2)
                  2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [56141] (3)
              25. Aurora-related kinase 1 (aurora-2) [90038]
                  OPK group; AIRK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [90039] (10)
              26. B-Raf kinase [103290]
                  OPK group; RAF subfamily; serine/threonine kinase; possible evolutionary link to tyrosine kinases
                  1. Human (Homo sapiens) [TaxId: 9606] [103291] (2)
              27. Type I TGF-beta receptor R4 [56144]
                  TKL group; STKR subfamily; serine/threonine kinase; possible evolutionary link to tyrosine kinases
                  1. Human (Homo sapiens) [TaxId: 9606] [56145] (4)
                     SQ P36897 200-500 ! SQ P36897 201-503
              28. c-src tyrosine kinase [56155]
                  PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56156] (10)
                  2. Chicken (Gallus gallus) [TaxId: 9031] [56157] (1)
              29. Haemopoetic cell kinase Hck [56151]
                  PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56152] (4)
              30. Lymphocyte kinase (lck) [56153]
                  PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56154] (19)
              31. Bruton's tyrosine kinase (Btk) [75564]
                  PTK group; Tec/Atk subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [75565] (1)
              32. Carboxyl-terminal src kinase (csk) [56164]
                  PTK group; CSK subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56165] (4)
              33. Abelsone tyrosine kinase (abl) [56166]
                  PTK group; Abl subfamily; non-membrane spanning protein tyrosine kinase
                  1. Mouse (Mus musculus) [TaxId: 10090] [56167] (10)
              34. Musk tyrosine kinase [82797]
                  PTK group; MUSK subfamily; non-membrane spanning protein tyrosine kinase
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [82798] (1)
              35. Focal adhesion kinase 1 (fak) [103292]
                  PTK group; FAK subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [103293] (6)
              36. EGF receptor tyrosine kinase, Erbb-1 [82795]
                  PTK group; EGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [82796] (10)
                     SQ P00533 702-1018
              37. ephb2 receptor tyrosine kinase [69827]
                  PTK group; Eph/Elk/Eck subfamily; membrane spanning protein tyrosine kinase
                  1. Mouse (Mus musculus) [TaxId: 10090] [69828] (1)
              38. epha2 receptor tyrosine kinase [103294]
                  PTK group; Eph/Elk/Eck subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [103295] (1)
              39. Tie2 kinase [64406]
                  PTK group; Tie/Tck subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [64407] (1)
              40. Fibroblast growth factor receptor 1 [56158]
                  PTK group; FGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56159] (4)
              41. Fibroblast growth factor receptor 2 [75562]
                  PTK group; FGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [75563] (4)
                     SQ P21802 467-765
              42. Vascular endothelial growth factor receptor 2 (kdr) [56160]
                  PTK group; PDGFR/VEGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56161] (4)
              43. c-KIT receptor [103296]
                  PTK group; PDGFR/VEGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [103297] (3)
                     SQ P10721 547-935
              44. Fl cytokine receptor [103298]
                  PTK group; CSF-1/PDGF receptor subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [103299] (1)
              45. Insulin receptor [56162]
                  PTK group; InsR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [56163] (13)
              46. Insulin-like growth factor 1 receptor [69825]
                  PTK group; InsR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [69826] (9)
              47. Hepatocyte growth factor receptor, c-MET [103300]
                  PTK group; HGFR subfamily; membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [103301] (6)
              48. Ribosomal protein S6 kinase alpha 5, Msk1 [111192]
                  AGC group (?); S6 kinase subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111193] (1)
                     SQ O75582 24-345
              49. Tyrosine-protein kinase Itk/Tsk [111194]
                  PTK group; Tec/Atk subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111195] (3)
                     SQ Q08881 357-619
              50. Protein kinase wnk1 [111196]
                  OPK group; WNK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111197] (1)
                     SQ Q9JIH7 211-480
              51. Tyrosine-protein kinase ZAP-70 [111198]
                  PTK group; SYK/ZAP-70 subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111199] (1)
                     SQ P43403 328-606 # structure of the N-terminal SH2 domains (1-132;133-256) is also known: 1m61 (scop_sp 89997)
              52. Activated CDC42 kinase 1, ACK1 [111200]
                  PTK group; Tck subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111201] (3)
                     SQ Q07912 117-389
              53. Mitogen-activated protein kinase 8 (jnk1) [111202]
                  CMGC group; ERK/MAPK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [111203] (2)
                     SQ P45983 9-363
              54. Serine/threonine protein kinase TAO2 [118127]
                  OPK group; serine/threonine kinase
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [118128] (4)
                     SQ Q9JLS3 12-320
              55. Protein kinase C, theta type [118129]
                  AGC group; PKC subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118130] (1)
                     SQ Q04759 377-696
              56. Tyrosine-protein kinase SYK [118131]
                  PTK group; SYK/ZAP-70 subfamily; non-membrane spanning protein tyrosine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118132] (3)
                     SQ P43405 363-635 # structure of the SH2 domain tandem region (9-265) is also known (scop_sp 55576)
              57. Proto-oncogene serine/threonine-protein kinase Pim-1 [118133]
                  OPK group(?); PIM subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118134] (8)
                     SQ P11309 33-305 ! SQ P11309 32-308
              58. Dual specificity mitogen-activated protein kinase kinase 2, Mek2 [118135]
                  OPK group (?); MAPKK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118136] (1)
                     SQ P36507 60-393
              59. Dual specificity mitogen-activated protein kinase kinase 1, Mek1 [118137]
                  OPK group (?); MAPKK subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118138] (2)
                     SQ Q02750 61-381
              60. Cell division protein kinase 7, CDK7 [118139]
                  CMGC group; CDKs subfamily; serine/threonine kinase
                  1. Human (Homo sapiens) [TaxId: 9606] [118140] (1)
                     SQ P50613 13-311
              61. Serine/threonine-protein kinase Nek2 [143893]
                  NIMA subfamily (NimA-related protein kinase 2)
                  1. Human (Homo sapiens) [TaxId: 9606] [143894] (1)
                     SQ P51955 3-271
              62. Cell division protein kinase 9, CDK9 [160810]
                  1. Human (Homo sapiens) [TaxId: 9606] [160811] (3)
                     SQ P50750 8-325
              63. STE20-like serine/threonine-protein kinase, SLK [160812]
                  1. Human (Homo sapiens) [TaxId: 9606] [160813] (3)
                     SQ Q9H2G2 21-308
           2. Actin-fragmin kinase, catalytic domain [56168] (1)
              Atypical protein kinases
              1. Actin-fragmin kinase, catalytic domain [56169]
                 1. Physarum polycephalum [TaxId: 5791] [56170] (1)
           3. MHCK/EF2 kinase [64408] (1)
              Atypical protein kinases
              1. Trp Ca-channel kinase domain [64409]
                 contains closed beta-barrel (n=6; S=10) in the N-terminal subdomain
                 1. Mouse (Mus musculus) [TaxId: 10090] [64410] (3)
           4. Phoshoinositide 3-kinase (PI3K), catalytic domain [56171] (2)
              1. Phoshoinositide 3-kinase (PI3K), catalytic domain [56172]
                 1. Pig (Sus scrofa) [TaxId: 9823] [56173] (5)
                 2. Human (Homo sapiens) [TaxId: 9606] [56174] (3)
           5. Choline kinase [90040] (1)
              1. Choline kinase [90041]
                 1. Caenorhabditis elegans [TaxId: 6239] [90042] (1)
           6. APH phosphotransferases [64411] (5)
              1. Type IIIa 3',5"-aminoglycoside phosphotransferase [64412]
                 1. Enterococcus faecalis [TaxId: 1351] [64413] (5)
              2. Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase) [103302]
                 1. Bacteria (Klebsiella pneumoniae) [TaxId: 573] [103303] (1)
              3. Methylthioribose kinase MtnK [160814]
                 1. Bacillus subtilis [TaxId: 1423] [160815] (12)
                    SQ O31663 5-396
              4. Homoserine kinase ThrB [160816]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160817] (1)
                    SQ Q8UHA8 5-320
              5. RdoA [160818]
                 Hypothetical protein YihE
                 1. Escherichia coli [TaxId: 562] [160819] (1)
                    SQ P0C0K3 4-328
           7. RIO1-like kinases [111204] (1)
              Pfam 01163
              1. Rio2 serine protein kinase C-terminal domain [111205]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [111206] (5)
                    SQ O30245 # AF2426
   301. FAD-binding/transporter-associated domain-like [56175] (1)
        consists of two alpha+beta subdomains
        1. FAD-binding/transporter-associated domain-like [56176] (4)
           uperfamily
           1. FAD-linked oxidases, N-terminal domain [56177] (5)
              1. Vanillyl-alcohol oxidase [56178]
                 1. Fungus (Penicillium simplicissimum) [TaxId: 69488] [56179] (16)
                    SQ P56216
              2. Flavoprotein subunit of p-cresol methylhydroxylase [56180]
                 the other subunit is a short-chain cytochrome c
                 1. Pseudomonas putida [TaxId: 303] [56181] (5)
              3. D-lactate dehydrogenase [56182]
                 1. Escherichia coli [TaxId: 562] [56183] (1)
              4. Cholesterol oxidase [64414]
                 1. Brevibacterium sterolicum [TaxId: 1702] [64415] (2)
              5. Cytokinin dehydrogenase 1 [111207]
                 1. Maize (Zea mays) [TaxId: 4577] [111208] (4)
                    SQ Q9T0N8
           2. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain [56184] (2)
              1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain [56185]
                 1. Escherichia coli [TaxId: 562] [56186] (5)
                 2. Staphylococcus aureus [TaxId: 1280] [64416] (1)
           3. CO dehydrogenase flavoprotein N-terminal domain-like [56187] (6)
              1. Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain [56188]
                 1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [56189] (7)
                 2. Hydrogenophaga pseudoflava [TaxId: 47421] [56190] (2)
              2. Xanthine oxidase, domain 3 (?) [56191]
                 1. Cow (Bos taurus) [TaxId: 9913] [56192] (7)
                    SQ P80457
              3. Xanthine dehydrogenase chain A, domain 3 [69829]
                 1. Rhodobacter capsulatus [TaxId: 1061] [69830] (2)
              4. Quinoline 2-oxidoreductase medium subunit QorM [111209]
                 1. Pseudomonas putida [TaxId: 303] [111210] (1)
                    SQ P72222
              5. 4-hydroxybenzoyl-CoA reductase beta subunit HrcB, N-terminal domain [118141]
                 1. Thauera aromatica [TaxId: 59405] [118142] (2)
                    SQ O33820
           4. CorC/HlyC domain-like [160820] (12)
              Pfam 03471; similar to the C-terminal subdomain of FAD-binding domain with transposition of strands 3 and 4; possible adenosine cofactor-binding domain
              1. Putative hemolysin SMU1693 [160821]
                 HlyX
                 1. Streptococcus mutans [TaxId: 1309] [160822] (1)
                    SQ O68574 352-435
              2. Hypothetical protein CT0541 [160823]
                 1. Chlorobium tepidum [TaxId: 1097] [160824] (12)
                    SQ Q8KEZ1 345-428
              3. Uncharacterized protein NE2227 [160825]
                 1. Nitrosomonas europaea [TaxId: 915] [160826] (2)
                    SQ Q82SS8 431-515
              4. Hypothetical protein HI0107 [160827]
                 1. Haemophilus influenzae [TaxId: 727] [160828] (1)
                    SQ Q57017 343-420
              5. Putative protein NMB1485 [160829]
                 1. Neisseria meningitidis [TaxId: 487] [160830] (1)
                    SQ Q9JYP7 441-516
              6. Putative hemolysin EF0700 [160831]
                 1. Enterococcus faecalis [TaxId: 1351] [160832] (1)
                    SQ Q837X5 350-433
              7. Hypothetical protein PG0272 [160833]
                 1. Porphyromonas gingivalis [TaxId: 837] [160834] (1)
                    SQ Q7MXD1 327-413
              8. Uncharacterized protein NMB0537 [160835]
                 1. Neisseria meningitidis [TaxId: 487] [160836] (4)
                    SQ Q9K0P8 191-274
              9. Hypothetical protein HD1797 [160837]
                 1. Haemophilus ducreyi [TaxId: 730] [160838] (2)
                    SQ Q7VKS4 347-428
              10. Hemolysin TlyC [160839]
                  1. Xylella fastidiosa [TaxId: 2371] [160840] (2)
                     SQ Q87DZ3 353-439! SQ Q87DZ3 355-439
              11. Probable hemolysin CV0231 [160841]
                  1. Chromobacterium violaceum [TaxId: 536] [160842] (6)
                     SQ Q7P1I2 341-427
              12. Uncharacterized protein Cgl1194/Cg1349 [160843]
                  1. Corynebacterium glutamicum [TaxId: 1718] [160844] (1)
                     SQ Q8NR63 356-453
   302. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56193] (1)
        consists of two alpha+beta subdomains
        1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56194] (1)
           uperfamily
           1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56195] (2)
              1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56196]
                 N-terminal domain is a FAD-binding domain
                 1. Escherichia coli [TaxId: 562] [56197] (5)
                 2. Staphylococcus aureus [TaxId: 1280] [64417] (1)
   303. Methenyltetrahydromethanopterin cyclohydrolase [56198] (1)
        consists of two alpha+beta subdomains
        1. Methenyltetrahydromethanopterin cyclohydrolase [56199] (1)
           uperfamily
           1. Methenyltetrahydromethanopterin cyclohydrolase [56200] (1)
              1. Methenyltetrahydromethanopterin cyclohydrolase [56201]
                 1. Archaeon Methanopyrus kandleri [TaxId: 2320] [56202] (1)
   304. Prim-pol domain [56746] (1)
        consists of two alpha+beta domains
        1. Prim-pol domain [56747] (3)
           uperfamily
           1. PriA-like [56748] (3)
              contains additional insert all-alpha subdomain
              1. DNA primase [56749]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56750] (1)
                 2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103304] (2)
              2. DNA primase small subunit PriA [143895]
                 includes insert zinc-finger domain and extra C-terminal alpha+beta subdomain
                 1. Sulfolobus solfataricus [TaxId: 2287] [143896] (1)
                    SQ Q97Z83 3-329
           2. Bifunctional DNA primase/polymerase N-terminal domain [103305] (1)
              1. Bifunctional DNA primase/polymerase N-terminal domain [103306]
                 1. Archaeon Sulfolobus islandicus [TaxId: 43080] [103307] (3)
           3. HP0184-like [143897] (1)
              stand-alone domain with the least decorated Prim-pol fold
              1. Hypothetical protein HP0184 [143898]
                 1. Helicobacter pylori [TaxId: 210] [143899] (1)
                    SQ O24984 3-178
   305. Hect, E3 ligase catalytic domain [56203] (1)
        consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit; conformational flexibility of domain orientation
        1. Hect, E3 ligase catalytic domain [56204] (1)
           uperfamily
           1. Hect, E3 ligase catalytic domain [56205] (2)
              1. Ubiquitin-protein ligase E3a (E6ap) [56206]
                 1. Human (Homo sapiens) [TaxId: 9606] [56207] (2)
              2. WW domain-containing protein 1, WWP1 [103308]
                 1. Human (Homo sapiens) [TaxId: 9606] [103309] (1)
   306. Nitrile hydratase alpha chain [56208] (1)
        4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
        1. Nitrile hydratase alpha chain [56209] (1)
           duplication: contains two structural repeats
           uperfamily
           1. Nitrile hydratase alpha chain [56210] (3)
              1. Iron-containing nitrile hydratase [56211]
                 1. Rhodococcus erythropolis [TaxId: 1833] [56212] (9)
                    also Rhodococcus sp. R312
              2. Cobalt-containing nitrile hydratase [82799]
                 1. Pseudonocardia thermophila [TaxId: 1848] [82800] (5)
                    SQ Q7SID2
                 2. Bacillus smithii [TaxId: 1479] [118143] (1)
                    SQ Q84FS5 # 93% sequence identity; Bacillus sp. RAPc8 TaxID: 218609
   307. 4'-phosphopantetheinyl transferase [56213] (1)
        beta-alpha(3)-beta(2) motif
        1. 4'-phosphopantetheinyl transferase [56214] (2)
           possibly related to the IspF (d.79.5) and YjgF-like superfamilies (d.79.1)
           uperfamily
           1. Holo-(acyl carrier protein) synthase ACPS [64418] (2)
              forms trimers with three closely packed beta-sheets similar to the IspF trimers
              1. Holo-(acyl carrier protein) synthase ACPS [64419]
                 1. Bacillus subtilis [TaxId: 1423] [64420] (3)
                 2. Streptococcus pneumoniae [TaxId: 1313] [64421] (3)
           2. 4'-Phosphopantetheinyl transferase SFP [56215] (1)
              monomeric; tandem duplication of beta-alpha(3)-beta(2) motif
              1. 4'-Phosphopantetheinyl transferase SFP [63407]
                 1. Bacillus subtilis [TaxId: 1423] [56217] (1)
   308. DNase I-like [56218] (1)
        contains beta-sandwich; duplication of alpha+beta motif
        1. DNase I-like [56219] (3)
           uperfamily
           1. DNase I-like [56220] (8)
              1. DNA-repair enzyme exonuclease III [56221]
                 1. Escherichia coli [TaxId: 562] [56222] (1)
              2. DNA repair endonuclease Hap1 [56223]
                 Major apurinic/apyrimidinic endonuclease APE1
                 1. Human (Homo sapiens) [TaxId: 9606] [56224] (9)
              3. Deoxyribonuclease I [56225]
                 1. Cow (Bos taurus) [TaxId: 9913] [56226] (11)
              4. Endonuclease domain of LINE-1 reverse transcriptase homolog [111211]
                 1. Human (Homo sapiens) [TaxId: 9606] [111212] (1)
                    SQ P08547 2-237
              5. Cytolethal distending toxin subunit B [111213]
                 1. Haemophilus ducreyi [TaxId: 730] [111214] (1)
                    SQ O06523 23-283
                 2. Actinobacillus actinomycetemcomitans [TaxId: 714] [143900] (2)
                    SQ Q7DK12 23-283
                 3. Escherichia coli [TaxId: 562] [143901] (1)
                    SQ Q46669 19-269
              6. Endonuclease domain of TRAS1 retrotransposon (ORF2) [111215]
                 1. Silkworm (Bombyx mori) [TaxId: 7091] [111216] (1)
                    SQ Q93139 1-184
           2. Inositol polyphosphate 5-phosphatase (IPP5) [64422] (2)
              1. Synaptojanin, IPP5C domain [64423]
                 1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64424] (2)
              2. Salivary nitrophorin [103310]
                 heme-binding homologue of IPP5
                 1. Bedbug (Cimex lectularius) [TaxId: 79782] [103311] (5)
                    SQ O7674 23-302
           3. Sphingomyelin phosphodiesterase-like [143902] (2)
              part of Pfam 03372
              1. Sphingomyelin phosphodiesterase C [143903]
                 1. Bacillus cereus [TaxId: 1396] [143904] (10)
                    SQ P11889 34-332
                 2. Listeria ivanovii [TaxId: 1638] [143905] (1)
                    SQ Q9RLV9 41-333
   309. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56227] (1)
        contains sandwich; duplication of alpha+beta motif with single mixed sheet
        motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
        1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56228] (1)
           uperfamily
           1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56229] (2)
              1. Aldehyde ferredoxin oxidoreductase [56230]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56231] (1)
              2. Formaldehyde ferredoxin oxidoreductase [56232]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56233] (2)
   310. Ntn hydrolase-like [56234] (2)
        4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
        1. N-terminal nucleophile aminohydrolases (Ntn hydrolases) [56235] (7)
           N-terminal residue provides two catalytic groups, nucleophile and proton donor
           uperfamily
           1. Class II glutamine amidotransferases [56236] (9)
              has slightly different topology than other families do
              1. Glucosamine 6-phosphate synthase, N-terminal domain [56237]
                 1. Escherichia coli [TaxId: 562] [56238] (8)
                    SQ P17169 1-238
              2. Glutamine PRPP amidotransferase, N-terminal domain [56239]
                 1. Bacillus subtilis [TaxId: 1423] [56240] (2)
                 2. Escherichia coli [TaxId: 562] [56241] (5)
              3. Asparagine synthetase B, N-terminal domain [56242]
                 1. Escherichia coli [TaxId: 562] [56243] (1)
              4. beta-Lactam synthetase [69831]
                 Asparagine synthetase B homologue
                 1. Streptomyces clavuligerus [TaxId: 1901] [69832] (5)
                 2. Pectobacterium carotovorum [TaxId: 554] [103312] (2)
                    carbapenam synthetase CarA
              5. Alpha subunit of glutamate synthase, N-terminal domain [69833]
                 1. Azospirillum brasilense [TaxId: 192] [69834] (7)
                 2. Synechocystis sp. [TaxId: 1143] [75566] (5)
              6. Hypothetical protein YafJ (PA1307) [111217]
                 1. Pseudomonas aeruginosa [TaxId: 287] [111218] (1)
                    SQ Q9I437
           2. Penicillin acylase, catalytic domain [56244] (4)
              1. Penicillin acylase [56245]
                 also contains 2 all-alpha and a beta-barrel domains
                 will be divided into domains in future release
                 1. Escherichia coli [TaxId: 562] [56246] (24)
                 2. Providencia rettgeri [TaxId: 587] [56247] (1)
              2. Cephalosporin acylase [64425]
                 1. Brevundimonas diminuta [TaxId: 293] [64426] (4)
                 2. Pseudomonas sp., glutarylamidase [TaxId: 306] [69835] (5)
           3. Penicillin V acylase [56248] (1)
              1. Penicillin V acylase [56249]
                 1. Bacillus sphaericus [TaxId: 1421] [56250] (2)
           4. Proteasome subunits [56251] (14)
              1. Proteasome beta subunit (catalytic) [56252]
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56253] (50)
                 2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90043] (1)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56254] (112)
                    The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
                 4. Cow (Bos taurus) [TaxId: 9913] [75567] (1)
                 5. Rhodococcus erythropolis [TaxId: 1833] [103313] (9)
              2. Proteasome alpha subunit (non-catalytic) [56255]
                 contains an extension to the common fold at the N-terminus
                 1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56256] (50)
                 2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90044] (2)
                 3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56257] (108)
                    The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
                 4. Cow (Bos taurus) [TaxId: 9913] [75568] (1)
                 5. Rhodococcus erythropolis [TaxId: 1833] [103314] (9)
              3. HslV (ClpQ) protease [56258]
                 dodecameric prokaryotic homologue of proteasome
                 1. Escherichia coli [TaxId: 562] [56259] (7)
                 2. Haemophilus influenzae [TaxId: 727] [56260] (6)
                 3. Thermotoga maritima [TaxId: 2336] [90045] (1)
                 4. Bacillus subtilis [TaxId: 1423] [160845] (26)
                    SQ P39070 2-181
           5. (Glycosyl)asparaginase [56261] (3)
              1. Glycosylasparaginase (aspartylglucosaminidase, AGA) [56262]
                 the precursor chain is cleaved onto 2 fragments by autoproteolysis
                 1. Human (Homo sapiens) [TaxId: 9606] [56263] (2)
                 2. Flavobacterium meningosepticum [TaxId: 238] [56264] (8)
                 3. Escherichia coli [TaxId: 562] [103315] (3)
                    SQ P37595
                    isoaspartyl peptidase with L-asparaginase activity
                    putative L-asparaginase YbiK
           6. Gamma-glutamyltranspeptidase-like [143906] (4)
              Pfam 01019
              1. Hypothetical protein Ta0994 [143907]
                 1. Thermoplasma acidophilum [TaxId: 2303] [143908] (4)
                    SQ Q9HJH4 1-516
              2. Cephalosporin acylase [143909]
                 1. Bacillus halodurans [TaxId: 86665] [143910] (4)
                    SQ Q9KEI5 3-539
              3. Gamma-glutamyltranspeptidase, GGT [143911]
                 1. Helicobacter pylori [TaxId: 210] [143912] (1)
                    SQ O25743 29-375,380-565
                 2. Escherichia coli [TaxId: 562] [143913] (14)
                    SQ P18956 29-387,391-580! SQ P18956 29-580
           7. SPO2555-like [160846] (1)
              Pfam 06267; DUF1028
              1. Hypothetical protein SPO2555 [160847]
                 1. Silicibacter pomeroyi [TaxId: 89184] [160848] (1)
                    SQ Q5LQD5 1-229
        2. Archaeal IMP cyclohydrolase PurO [75569] (1)
           has a putative active site in the same topological location as the Ntn hydrolase but lacks the N-terminal nucleophile
           uperfamily
           1. Archaeal IMP cyclohydrolase PurO [75570] (1)
              Pfam 07826
              1. Hypothetical protein MTH1020 [75571]
                 1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75572] (13)
   311. DmpA/ArgJ-like [56265] (1)
        duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
        1. DmpA/ArgJ-like [56266] (2)
           convergent similarity to the Ntn amidohydrolases
           uperfamily
           1. DmpA-like [56267] (1)
              Pfam 03576
              1. L-aminopeptidase D-Ala-esterase/amidase DmpA [56268]
                 1. Ochrobactrum anthropi [TaxId: 529] [56269] (1)
           2. ArgJ-like [111219] (1)
              Pfam 01960; contains extra C-terminal alpha+beta domain [beta-alpha(2)-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet, order: 51423, strands 1 and 4 are parallel to each other]
              1. Glutamate N-acetyltransferase 2 (ornithine acetyltransferase) [111220]
                 1. Streptomyces clavuligerus [TaxId: 1901] [111221] (3)
                    SQ Q53940
                    d1: 8-260; d2: 261-390
   312. Pyruvoyl-dependent histidine and arginine decarboxylases [56270] (1)
        duplication of beta-alpha-beta(2) motif; 4 layers: alpha/beta/beta/alpha; contains "silk" beta-sandwich
        1. Pyruvoyl-dependent histidine and arginine decarboxylases [56271] (2)
           two chains result from self-processing single-chain precursor; form heterohexamer
           uperfamily
           1. Arginine decarboxylase [90046] (1)
              1. Arginine decarboxylase [90047]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [90048] (3)
           2. Histidine decarboxylase [56272] (1)
              1. Histidine decarboxylase [56273]
                 1. Lactobacillus sp., strain 30a [TaxId: 1591] [56274] (6)
   313. S-adenosylmethionine decarboxylase [56275] (1)
        duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
        1. S-adenosylmethionine decarboxylase [56276] (2)
           uperfamily
           1. S-adenosylmethionine decarboxylase [56277] (2)
              1. S-adenosylmethionine decarboxylase [56278]
                 1. Human (Homo sapiens) [TaxId: 9606] [56279] (8)
                 2. Potato (Solanum tuberosum) [TaxId: 4113] [82801] (1)
           2. Bacterial S-adenosylmethionine decarboxylase [111222] (1)
              Pfam 02675;homodimer; the subunit fold and assembly are similar to those of the structural repeats of the eukaryotic enzyme
              1. S-adenosylmethionine decarboxylase (SamDC, SpeH) [111223]
                 1. Thermotoga maritima [TaxId: 2336] [111224] (4)
                    SQ Q9WZC3
   314. Metallo-hydrolase/oxidoreductase [56280] (1)
        duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
        1. Metallo-hydrolase/oxidoreductase [56281] (14)
           uperfamily
           1. Zn metallo-beta-lactamase [56282] (10)
              1. Zn metallo-beta-lactamase [56283]
                 1. Bacillus cereus [TaxId: 1396] [56284] (7)
                    SQ P04190 31-257
                 2. Bacteroides fragilis [TaxId: 817] [56285] (9)
                 3. Xanthomonas maltophilia [TaxId: 40324] [56286] (20)
                 4. Pseudomonas aeruginosa, IMP-1 [TaxId: 287] [56287] (8)
                 5. Pseudomonas aeruginosa, VIM-2 [TaxId: 287] [103316] (2)
                 6. Fluoribacter gormanii, (Legionella gormanii) FEZ-1 [TaxId: 464] [82802] (3)
                 7. Chryseobacterium meningosepticum, carbapenemase BLAB-1 [TaxId: 238] [90049] (1)
                 8. Aeromonas hydrophila, CphA [TaxId: 644] [118144] (5)
                    SQ P26918 28-252
                 9. Bradyrhizobium japonicum [TaxId: 375] [160849] (2)
                    SQ Q89GW5 29-292
                 10. Pseudomonas putida [TaxId: 303] [160850] (2)
           2. Hypothetical protein TM0207 [103317] (1)
              1. Hypothetical protein TM0207 [103318]
                 1. Thermotoga maritima [TaxId: 2336] [103319] (1)
           3. Glyoxalase II (hydroxyacylglutathione hydrolase) [56288] (3)
              1. Glyoxalase II (hydroxyacylglutathione hydrolase) [56289]
                 1. Human (Homo sapiens) [TaxId: 9606] [56290] (2)
                 2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118145] (3)
                    SQ Q9SID3
                 3. Salmonella typhimurium [TaxId: 90371] [160851] (1)
                    SQ Q8ZRM2 1-251
           4. ROO N-terminal domain-like [56291] (3)
              1. Rubredoxin oxygen:oxidoreductase (ROO), N-terminal domain [56292]
                 1. Desulfovibrio gigas [TaxId: 879] [56293] (1)
              2. ROO-like flavoprotein TM0755, N-terminal domain [111225]
                 1. Thermotoga maritima [TaxId: 2336] [111226] (1)
                    SQ Q9WZL4 #
              3. Nitric oxide reductase N-terminal domain [143914]
                 1. Moorella thermoacetica [TaxId: 1525] [143915] (12)
                    SQ Q9FDN7 2-250
           5. Methyl parathion hydrolase [111227] (1)
              1. Methyl parathion hydrolase [111228]
                 1. Pseudomonas sp. WBC-3 [TaxId: 165468] [111229] (1)
                    SQ Q841S6 Q693X1 Q93SP1
           6. Coenzyme PQQ synthesis protein B, PqqB [118146] (1)
              1. Coenzyme PQQ synthesis protein B, PqqB [118147]
                 1. Pseudomonas putida [TaxId: 303] [118148] (1)
                    SQ Q88QV5
           7. RNase Z-like [143916] (3)
              part of Pfam 00753; tRNA 3'-endonuclease; elaborated with additional structures and insert alpha(2)-beta(2) subdomain
              1. Ribonuclease Z (RNase Z) [143917]
                 1. Bacillus subtilis [TaxId: 1423] [143918] (3)
                    SQ P54548 1-307
                 2. Escherichia coli [TaxId: 562] [143919] (1)
                    SQ P0A8V0 1-305
                 3. Thermotoga maritima [TaxId: 2336] [143920] (4)
                    SQ Q9WZW8 1-280
           8. Pce catalytic domain-like [143921] (1)
              part of Pfam 00753
              1. Teichoic acid phosphorylcholine esterase Pce (LytD), N-terminal domain [143922]
                 1. Streptococcus pneumoniae [TaxId: 1313] [143923] (3)
                    SQ Q8DQ62 26-334! SQ Q8DQ62 30-334
           9. YhfI-like [143924] (1)
              part of Pfam 00753
              1. Hypothetical protein BA1088 (BAS1016) [143925]
                 B. subtilis YhfI ortholog
                 1. Bacillus anthracis [TaxId: 1392] [143926] (4)
                    SQ Q81U06 1-244
           10. beta-CASP RNA-metabolising hydrolases [143927] (4)
               contains insertion of a single helicase-like alpha/beta domain (from scop_sf 52540) but without the P-loop motif
               1. Hypothetical protein EF2904 [143928]
                  1. Enterococcus faecalis [TaxId: 1351] [143929] (2)
                     SQ Q82ZZ3 5-429
               2. Cleavage factor two protein 2, CFT2 [160852]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [160853] (1)
                     SQ Q12102 1-422,627-717
               3. Putative RNA-degradation protein TTHA0252 [160854]
                  1. Thermus thermophilus [TaxId: 274] [160855] (1)
                     SQ Q5SLP1 1-431
               4. Cleavage and polyadenylation specificity factor subunit 3 [160856]
                  1. Human (Homo sapiens) [TaxId: 9606] [160857] (1)
                     SQ Q9UKF6 9-459
           11. TM0894-like [143930] (1)
               part of Pfam 00753
               1. Hypothetical protein TM0894 [143931]
                  1. Thermotoga maritima [TaxId: 2336] [143932] (4)
                     SQ Q9WZZ6 1-207
           12. Ava3068-like [160858] (1)
               1. Hypothetical protein Ava3068 [160859]
                  1. Anabaena variabilis [TaxId: 1172] [160860] (2)
                     SQ Q3M8K9 1-200
           13. Alkylsulfatase-like [160861] (1)
               subfamily of Pfam 00753; includes all-alpha linker subdomain
               1. Alkylsulfatase SdsA1 [160862]
                  1. Pseudomonas aeruginosa [TaxId: 287] [160863] (4)
                     SQ Q9I5I9 20-524
           14. PqsE-like [160864] (1)
               part of Pfam 00753; extended C-terminal region with extra helices
               1. Quinolone signal response protein PqsE [160865]
                  1. Pseudomonas aeruginosa [TaxId: 287] [160866] (3)
                     SQ Q02IG5 1-301
   315. PP2C-like [81607] (1)
        4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
        1. PP2C-like [81606] (1)
           contain binuclear metal (Mn) centre
           uperfamily
           1. PP2C-like [81605] (2)
              Pfam 00481
              1. Protein serine/threonine phosphatase 2C, catalytic domain [81604]
                 1. Human (Homo sapiens) [TaxId: 9606] [81603] (1)
              2. putative serine/threonine phosphatase pstp/ppp [118149]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [118150] (1)
                    SQ P71588
   316. Metallo-dependent phosphatases [56299] (1)
        4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
        1. Metallo-dependent phosphatases [56300] (12)
           different families of this superfamily are groupped in a single Pfam family, Pfam 00149
           uperfamily
           1. Purple acid phosphatase-like [56301] (4)
              1. Plant purple acid phosphatase, catalytic domain [56302]
                 also contain an Ig-like domain
                 1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [56303] (9)
                 2. Sweet potato (Ipomoea batatas) [TaxId: 4120] [118151] (1)
                    SQ Q9SE00 39-462
              2. Mammalian purple acid phosphatase [56304]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [56305] (2)
                 2. Pig (Sus scrofa) [TaxId: 9823] [56306] (1)
           2. DNA double-strand break repair nuclease [64427] (1)
              contains C-terminal alpha/beta subdomain
              1. Mre11 [64428]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64429] (3)
                    SQ Q8U1N9
           3. 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [56307] (3)
              1. 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [56308]
                 1. Escherichia coli [TaxId: 562] [56309] (8)
                    SQ P07024 26-550
                 2. Thermus thermophilus [TaxId: 274] [160867] (1)
                    SQ Q5SIP1 28-534
                 3. Candida albicans [TaxId: 5476] [160868] (2)
                    SQ Q5A5Q7 16-337
           4. Protein serine/threonine phosphatase [56310] (9)
              1. Protein phosphatase-1 (PP-1) [56311]
                 1. Rabbit (Oryctolagus cuniculus), alpha isoform [TaxId: 9986] [56312] (1)
                 2. Human (Homo sapiens), beta isoform [TaxId: 9606] [64430] (5)
                    SQ P36873
                 3. Human (Homo sapiens), gamma isoform [TaxId: 9606] [111230] (1)
                    SQ P37140 1-308
                 4. Rattus norvegicus [TaxId: 10116] [160869] (4)
              2. Protein phosphatase-2B (PP-2B, calcineurin A subunit) [56313]
                 1. Cow (Bos taurus) [TaxId: 9913] [56314] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [56315] (5)
              3. lambda ser/thr protein phosphatase [64431]
                 1. Bacteriophage lambda [TaxId: 10710] [64432] (1)
              4. Serine/threonine protein phosphatase 5, PP5 [111231]
                 1. Human (Homo sapiens) [TaxId: 9606] [111232] (5)
                    SQ P53041 176-499
              5. Protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha [143933]
                 1. Human (Homo sapiens) [TaxId: 9606] [143934] (11)
                    SQ P67775 2-294
           5. Phosphoesterase-related [82803] (1)
              1. Hypothetical protein PF1291 [82804]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82805] (1)
           6. TT1561-like [103320] (2)
              similar to purple acid and protein phosphatases
              1. Hypothetical protein TT1561 [103321]
                 1. Thermus thermophilus [TaxId: 274] [103322] (1)
              2. Uncharacterized protein Aq_1956 [160870]
                 1. Aquifex aeolicus [TaxId: 63363] [160871] (1)
                    SQ O67769 4-260
           7. YfcE-like [111233] (6)
              1. Putative phosphodiesterase MJ0936 [111234]
                 1. Methanococcus jannaschii [TaxId: 2190] [111235] (7)
                    SQ Q58346
              2. Phosphodiesterase yfcE [111236]
                 1. Escherichia coli [TaxId: 562] [111237] (1)
                    SQ P76495
              3. Vacuolar protein sorting 29, VPS29 [143935]
                 1. Mouse (Mus musculus) [TaxId: 10090] [143936] (5)
                    SQ Q9QZ88 1-182
                 2. Cryptosporidium parvum [TaxId: 5807] [143937] (2)
                    SQ Q5CYJ7 5-197
                 3. Homo sapiens [TaxId: 9606] [160872] (2)
              4. Uncharacterized protein SP1879 [160873]
                 1. Streptococcus pneumoniae [TaxId: 1313] [160874] (1)
                    SQ Q97NX4 1-173
           8. Hypothetical protein aq_1666 [118152] (1)
              1. Hypothetical protein aq_1666 [118153]
                 1. Aquifex aeolicus [TaxId: 63363] [118154] (1)
                    SQ O67582
           9. DR1281-like [118155] (2)
              1. Putative phosphatase DR1281 [118156]
                 1. Deinococcus radiodurans [TaxId: 1299] [118157] (1)
                    SQ Q9RUV0
              2. Hypothetical protein MPN349 [118158]
                 1. Mycoplasma pneumoniae [TaxId: 2104] [118159] (1)
                    SQ P75429
           10. TTHA0625-like [143938] (1)
               part of Pfam 00149
               1. Hypothetical protein TTHA0625 [143939]
                  1. Thermus thermophilus [TaxId: 274] [143940] (8)
                     SQ Q5SKL8 1-252
           11. GpdQ-like [160875] (2)
               part of Pfam 00149
               1. Rv0805 cyclic nucleotide phosphodiesterase [160876]
                  1. Mycobacterium tuberculosis [TaxId: 1773] [160877] (3)
                     SQ O06629 10-265
               2. Glycerophosphodiesterase GpdQ [160878]
                  1. Enterobacter aerogenes [TaxId: 548] [160879] (14)
                     SQ Q6XBH1 1-271
           12. ADPRibase-Mn-like [160880] (1)
               contains Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase (ADPRibase-Mn); part of Pfam 00149
               1. Uncharacterized C17orf48 homolog zgc:64213 [160881]
                  1. Zebrafish (Danio rerio) [TaxId: 7955] [160882] (1)
                     SQ Q7T291 3-322
   317. Carbon-nitrogen hydrolase [56316] (1)
        4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
        1. Carbon-nitrogen hydrolase [56317] (2)
           Pfam 00795; some topological similarities to the metallo-dependent phosphatases and DNase I-like nucleases
           uperfamily
           1. Nitrilase [56318] (2)
              1. NIT-FHIT fusion protein, N-terminal domain [56319]
                 1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [56320] (1)
              2. hypothetical protein yl85 [69836]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69837] (1)
           2. Carbamilase [64433] (3)
              1. N-carbamoyl-D-aminoacid amidohydrolase [64434]
                 1. Agrobacterium sp. [TaxId: 361] [64435] (5)
                    SQ P60327
                 2. Agrobacterium radiobacter [TaxId: 358] [64436] (9)
              2. Hypothetical protein PH0642 [103323]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103324] (1)
   318. CNF1/YfiH-like putative cysteine hydrolases [64437] (1)
        4 layers: alpha/beta/beta/alpha; mixed beta sheets
        1. CNF1/YfiH-like putative cysteine hydrolases [64438] (3)
           uperfamily
           1. Type 1 cytotoxic necrotizing factor, catalytic domain [64439] (1)
              1. Type 1 cytotoxic necrotizing factor, catalytic domain [64440]
                 1. Escherichia coli [TaxId: 562] [64441] (2)
           2. YfiH-like [111238] (5)
              Pfam 02578; COG1496
              1. Hypothetical protein YlmD [111239]
                 1. Bacillus stearothermophilus [TaxId: 1422] [111240] (1)
                    SQ P84138
              2. Hypothetical protein NMB0706 [111241]
                 1. Neisseria meningitidis, serogroup B [TaxId: 487] [111242] (1)
                    SQ Q9K0A8
              3. Hypothetical protein yfiH [111243]
                 1. Salmonella typhi [TaxId: 90370] [111244] (1)
                    SQ Q8Z4J1
                 2. Shigella flexneri [TaxId: 623] [111245] (2)
                    SQ Q83K13
              4. Hypothetical protein CC0490 [111246]
                 1. Caulobacter crescentus [TaxId: 155892] [111247] (1)
                    SQ Q9AAV3
           3. CheD-like [160883] (1)
              Pfam 03975
              1. Chemoreceptor glutamine deamidase CheD [160884]
                 1. Thermotoga maritima [TaxId: 2336] [160885] (2)
                    SQ Q9X005 1-157
   319. ADC synthase [56321] (1)
        duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
        1. ADC synthase [56322] (1)
           the active site is formed by additional structures inserted into the core structure
           uperfamily
           1. ADC synthase [56323] (7)
              1. Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit, TrpE [56324]
                 1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [56325] (1)
                 2. Salmonella typhimurium [TaxId: 90371] [64442] (1)
                 3. Serratia marcescens [TaxId: 615] [64443] (2)
              2. P-aminobenzoate synthase component I [69838]
                 Aminodeoxychorismate synthase
                 1. Escherichia coli [TaxId: 562] [69839] (2)
              3. Menaquinone-specific isochorismate synthase MenF [143941]
                 1. Escherichia coli [TaxId: 562] [143942] (4)
                    SQ P38051 2-429
              4. Salicylate synthetase Irp9 [143943]
                 1. Yersinia enterocolitica [TaxId: 630] [143944] (4)
                    SQ Q9X9I8 2-434
              5. Salicylate synthase MbtI [143945]
                 Mycobactin synthetase protein I
                 1. Mycobacterium tuberculosis [TaxId: 1773] [143946] (5)
                    SQ Q7D785 15-449
   320. Sulfolobus fructose-1,6-bisphosphatase-like [111248] (1)
        4 layers: a/b/b/a; antiparallel beta sheets; similarities to ferredoxin-like fold (scop_cf 54861) in the N-terminal part (1-120) and to the Bacterial S-adenosylmethionine decarboxylase subunit (scop_fa 997656) in the C-terminal part (121-340)
        1. Sulfolobus fructose-1,6-bisphosphatase-like [111249] (1)
           uperfamily
           1. Sulfolobus fructose-1,6-bisphosphatase-like [111250] (1)
              Pfam 01950
              1. ST0318 [111251]
                 1. Archaeon Sulfolobus tokodaii [TaxId: 111955] [111252] (1)
                    SQ Q975V5
   321. LDH C-terminal domain-like [56326] (1)
        unusual fold, defines family
        1. LDH C-terminal domain-like [56327] (2)
           uperfamily
           1. Lactate & malate dehydrogenases, C-terminal domain [56328] (28)
              N-terminal domain is NAD-binding module (alpha/beta Rossmann-fold domain)
              1. Malate dehydrogenase [56329]
                 1. Pig (Sus scrofa) [TaxId: 9823] [56330] (3)
                 2. Sorghum (Sorghum vulgare), chloroplast [TaxId: 4558] [56331] (1)
                 3. Flaveria bidentis, chloroplast [TaxId: 4224] [56332] (1)
                 4. Escherichia coli [TaxId: 562] [56333] (8)
                 5. Thermus flavus [TaxId: 274] [56334] (2)
                 6. Thermus thermophilus [TaxId: 274] [82806] (9)
                    identical sequence to that from the Thermus flavus enzyme
                 7. Archaeon Haloarcula marismortui [TaxId: 2238] [56335] (17)
                 8. Aquaspirillum arcticum [TaxId: 87645] [56336] (3)
                 9. Chloroflexus aurantiacus [TaxId: 1108] [69840] (7)
                    SQ P80040
                 10. Chlorobium tepidum [TaxId: 1097] [69841] (1)
                 11. Chlorobium vibrioforme [TaxId: 1098] [69842] (2)
              2. L-2-hydroxyisocapronate dehydrogenase, L-HICDH [56337]
                 1. Lactobacillus confusus [TaxId: 1583] [56338] (1)
              3. Lactate dehydrogenase [56339]
                 1. Pig (Sus scrofa) [TaxId: 9823] [56340] (3)
                 2. Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606] [64444] (2)
                 3. Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606] [64445] (1)
                 4. Mouse (Mus musculus) [TaxId: 10090] [56341] (4)
                 5. Dogfish (Squalus acanthias) [TaxId: 7797] [56342] (3)
                 6. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [56343] (9)
                 7. Plasmodium berghei [TaxId: 5821] [103325] (7)
                 8. Toxoplasma gondii [TaxId: 5811] [103326] (4)
                 9. Bacillus stearothermophilus [TaxId: 1422] [56344] (9)
                 10. Lactobacillus casei [TaxId: 1582] [56345] (1)
                 11. Lactobacillus pentosus [TaxId: 1589] [69843] (1)
                 12. Bifidobacterium longum, strain am101-2 [TaxId: 216816] [56346] (2)
                 13. Thermotoga maritima [TaxId: 2336] [56347] (1)
                 14. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111253] (2)
                     SQ O08349
                 15. Clostridium thermocellum [TaxId: 1515] [118160] (1)
                     SQ Q4CDK5
              4. MJ0490, lactate/malate dehydrogenase [64446]
                 1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64447] (2)
           2. AglA-like glucosidase [90050] (5)
              family 4 glycosyl hydrolase
              1. Alpha-glucosidase AglA [90051]
                 1. Thermotoga maritima [TaxId: 2336] [90052] (1)
                    TM1834
              2. Putative alpha-glucosidase TM0752 [103327]
                 1. Thermotoga maritima [TaxId: 2336] [103328] (1)
              3. Maltose-6'-phosphate glucosidase GlvA [103329]
                 1. Bacillus subtilis [TaxId: 1423] [103330] (1)
                    SQ P54716
              4. 6-phospho-beta-glucosidase [111254]
                 1. Bacillus stearothermophilus [TaxId: 1422] [111255] (1)
                    SQ P84135
                 2. Thermotoga maritima [TaxId: 2336] [111256] (3)
                    SQ Q9X108
   322. DNA breaking-rejoining enzymes [56348] (1)
        core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
        1. DNA breaking-rejoining enzymes [56349] (2)
           uperfamily
           1. Lambda integrase-like, catalytic core [56350] (5)
              1. Integrase [56351]
                 1. Bacteriophage HP1 [TaxId: 10690] [56352] (1)
              2. Integrase (Int) [56353]
                 1. Bacteriophage lambda [TaxId: 10710] [56354] (8)
              3. Cre recombinase [56355]
                 1. Bacteriophage P1 [TaxId: 10678] [56356] (24)
                    SQ P06956 20-341
              4. Recombinase XerD [56357]
                 1. Escherichia coli [TaxId: 562] [56358] (1)
              5. Flp recombinase [56359]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56360] (3)
           2. Eukaryotic DNA topoisomerase I, catalytic core [56361] (2)
              1. Eukaryotic DNA topoisomerase I, catalytic core [56362]
                 1. Human (Homo sapiens) [TaxId: 9606] [56363] (15)
                    SQ P11387 203-765 ! SQ P11387 203-767
                 2. Vaccinia virus [TaxId: 10245] [56364] (1)
   323. Replication modulator SeqA, C-terminal DNA-binding domain [82807] (1)
        consists of seven alpha-helices and three-stranded beta-sheet
        1. Replication modulator SeqA, C-terminal DNA-binding domain [82808] (1)
           uperfamily
           1. Replication modulator SeqA, C-terminal DNA-binding domain [82809] (1)
              1. Replication modulator SeqA, C-terminal DNA-binding domain [82810]
                 binds to fully methylated and hemimethylated GATC sequences at oriC
                 1. Escherichia coli [TaxId: 562] [82811] (3)
                    SQ P36658 71-181
   324. SMAD MH1 domain [56365] (1)
        consists of four alpha-helices and three beta-ribbons
        1. SMAD MH1 domain [56366] (1)
           uperfamily
           1. SMAD MH1 domain [56367] (1)
              1. SMAD MH1 domain [56368]
                 1. Human (Homo sapiens) [TaxId: 9606] [56369] (2)
   325. YopH tyrosine phosphatase N-terminal domain [64448] (1)
        consists of four alpha-helices and two beta-hairpins
        1. YopH tyrosine phosphatase N-terminal domain [64449] (1)
           uperfamily
           1. YopH tyrosine phosphatase N-terminal domain [64450] (2)
              1. YopH tyrosine phosphatase N-terminal domain [64451]
                 1. Yersinia pestis [TaxId: 632] [64452] (1)
                 2. Yersinia pseudotuberculosis [TaxId: 633] [69844] (2)
   326. Rotavirus NSP2 fragment, N-terminal domain [75573] (1)
        consists of six alpha-helices and two beta-hairpins
        1. Rotavirus NSP2 fragment, N-terminal domain [75574] (1)
           uperfamily
           1. Rotavirus NSP2 fragment, N-terminal domain [75575] (1)
              1. Rotavirus NSP2 fragment, N-terminal domain [75576]
                 1. Simian 11 rotavirus [TaxId: 10923] [75577] (5)
   327. Rv2827c C-terminal domain-like [160886] (1)
        multihelical array flanked by two three-stranded mixed beta-sheets
        1. Rv2827c C-terminal domain-like [160887] (1)
           1. Rv2827c C-terminal domain-like [160888] (1)
              the C-terminal part (~210 residues) of Pfam 09407; DUF2005
              1. Hypothetical protein Rv2827c [160889]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [160890] (2)
                    SQ P71625 83-294
   328. Phosphoprotein oligomerization domain-like [160891] (1)
        intertwinned homodimer of beta(2)-alpha-beta(2) motifs; 3 layers: b/a/b; each antiparallel beta-sheet is formed by the N-terminal beta-hairpin of one subunit and the C-terminal beta-hairpin of the other subunit; order 1243
        1. Phosphoprotein oligomerization domain-like [160892] (1)
           1. Phosphoprotein oligomerization domain-like [160893] (1)
              middle part of Pfam 00922
              1. Phosphoprotein P (M1) [160894]
                 1. Vesicular stomatitis indiana virus [TaxId: 11277] [160895] (6)
                    SQ P04880 107-171
   329. Taf5 N-terminal domain-like [160896] (1)
        multihelical cluster with a C-terminal beta-alpha(2)-beta motif; one central buried helix; parallel beta-ribbon
        1. Taf5 N-terminal domain-like [160897] (1)
           1. Taf5 N-terminal domain-like [160898] (3)
              Pfam 04494
              1. TAF5 subunit of TFIID [160899]
                 1. Human (Homo sapiens) [TaxId: 9606] [160900] (8)
                    SQ Q15542 195-343
                 2. Saccharomyces cerevisiae [TaxId: 4932] [160901] (1)
                    SQ P38129 149-282
                 3. Encephalitozoon cuniculi [TaxId: 6035] [160902] (5)
                    SQ Q8SQS4 18-148
   330. Jann2411-like [160903] (1)
        unusual fold; consists of seven alpha-helices and three beta-hairpins
        1. Jann2411-like [160904] (1)
           1. Jann2411-like [160905] (1)
              Pfam 07336; DUF1470
              1. Uncharacterized protein Jann2411 [160906]
                 1. Jannaschia sp. ccs1 [TaxId: 290400] [160907] (1)
                    SQ Q28PN4 1-184
   331. ATP12-like [160908] (1)
        contains an N-terminal beta-sheet that forms a beta-triangle structure; the remainder is a multihelical array of long and short helices
        1. ATP12-like [160909] (1)
           1. ATP12-like [160910] (2)
              Pfam 07542; F1-ATPase chaperone
              1. Uncharacterized protein Atu1473 [160911]
                 1. Agrobacterium tumefaciens [TaxId: 358] [160912] (2)
                    SQ A9CJ14 1-261
              2. ATP12 ATPase [160913]
                 1. Paracoccus denitrificans [TaxId: 266] [160914] (5)
                    SQ A1B060 2-235! SQ A1B060 3-235
   332. Ribosome inactivating proteins (RIP) [56370] (1)
        contains mixed beta-sheet
        1. Ribosome inactivating proteins (RIP) [56371] (2)
           uperfamily
           1. Plant cytotoxins [56372] (17)
              1. alpha-Trichosanthin [56373]
                 1. Mongolian snake gourd (Trichosanthes kirilowii Maxim.) [TaxId: 3677] [56374] (10)
              2. Bryodin [56375]
                 1. Red briony (Bryonia dioica) [TaxId: 3652] [56376] (1)
              3. Beta-luffin [103331]
                 1. Smooth loofah (Luffa cylindrica) [TaxId: 3670] [103332] (1)
              4. alpha-Momorcharin (momordin) [56377]
                 1. Bitter gourd (Momordica charantia) [TaxId: 3673] [56378] (8)
              5. Beta-momorcharin [56379]
                 (almost) identical with the anti-tumor and anti-HIV-1 protein MAP30
                 1. Bitter gourd (Momordica charantia) [TaxId: 3673] [56380] (2)
              6. Mistletoe lectin I A-chain [56381]
                 1. European mistletoe (Viscum album) [TaxId: 3972] [56382] (12)
                    different sequence variants
                    SQ P81446 1-249
                    SQ Q6ITZ3 1-240
              7. Abrin A-chain [56383]
                 1. Abrus precatorius [TaxId: 3816] [56384] (1)
              8. Lectin 1 A-chain [90053]
                 1. Mongolian snake-gourd (Trichosanthes kirilowii) [TaxId: 3677] [90054] (1)
              9. Pokeweed antiviral protein alpha [56385]
                 1. Pokeweed (Phytolacca americana) [TaxId: 3527] [56386] (7)
              10. Antiviral protein 3 [90055]
                  1. Pokeweed (Phytolacca americana) [TaxId: 3527] [90056] (1)
              11. Antiviral protein S [103333]
                  seed isoform
                  1. Pokeweed (Phytolacca americana) [TaxId: 3527] [103334] (4)
              12. Dianthin 30 [103335]
                  1. Clove pink (Dianthus caryophyllus) [TaxId: 3570] [103336] (4)
                     SQ P24476 24-278
              13. Saporin So6 [56387]
                  1. Common soapwort (Saponaria officinalis) [TaxId: 3572] [56388] (1)
              14. Ricin A-chain [56389]
                  1. Castor bean (Ricinus communis) [TaxId: 3988] [56390] (24)
                     SQ P06750 28-286
              15. Ebulin A-chain [56391]
                  1. Sambucus ebulus [TaxId: 28503] [56392] (4)
              16. Bouganin [160915]
                  1. Bougainvillea (Bougainvillea spectabilis) [TaxId: 146096] [160916] (1)
                     SQ Q8W4U4 27-272
              17. Agglutinin-1 chain A [160917]
                  1. Abrus precatorius [TaxId: 3816] [160918] (1)
                     SQ Q9M6E9 22-268
           2. Shiga toxin, A-chain [56395] (2)
              1. Shiga toxin, A-chain [56396]
                 1. Shigella dysenteriae, toxin I [TaxId: 622] [56397] (2)
                 2. Shigella dysenteriae, toxin II [TaxId: 622] [103337] (2)
   333. ADP-ribosylation [56398] (1)
        unusual fold
        1. ADP-ribosylation [56399] (7)
           uperfamily
           1. ADP-ribosylating toxins [56400] (12)
              1. Heat-labile toxin, A-chain [56401]
                 1. Escherichia coli, type IB [TaxId: 562] [56402] (9)
                 2. Escherichia coli, type IIB [TaxId: 562] [56403] (1)
              2. Diphtheria toxin, N-terminal domain [56404]
                 1. Corynebacterium diphtheriae [TaxId: 1717] [56405] (7)
              3. Exotoxin A, C-terminal domain [56406]
                 1. Pseudomonas aeruginosa [TaxId: 287] [56407] (21)
              4. Pertussis toxin, S1 subunit [56408]
                 1. Bordetella pertussis [TaxId: 520] [56409] (3)
              5. Cholera toxin [56410]
                 1. Vibrio cholerae [TaxId: 666] [56411] (9)
              6. Vegetative insecticidal protein 2 (VIP2) [56412]
                 duplication: consists of two domains of this fold, the second of which is catalytic
                 1. Bacillus cereus [TaxId: 1396] [56413] (2)
              7. Enzymatic component (Ia) of iota-toxin [82812]
                 mammalian-targeted relative of VIP2; C-terminal domain is catalytic, N-terminal domain interacts with Ib (binding component)
                 1. Clostridium perfringens [TaxId: 1502] [82813] (4)
              8. Exoenzyme c3 [56414]
                 1. Clostridium botulinum [TaxId: 1491] [56415] (14)
                    SQ P15879 41-251
                 2. Staphylococcus aureus [TaxId: 1280] [103338] (2)
                 3. Clostridium botulinum C bacteriophage [TaxId: 12336] [118161] (2)
                    SQ Q00901 44-244
              9. Anthrax toxin lethal factor, middle domain [69845]
                 includes an all-alpha insert subdomain
                 1. Bacillus anthracis [TaxId: 1392] [69846] (10)
           2. Ecto-ART [82814] (1)
              the two disulfide bridges and N-terminal alpha helices are characteristic for all ecto-ARTs
              1. Eukaryotic mono-ADP-ribosyltransferase ART2.2 [82815]
                 NAD glycohydrolase and auto-ADP-ribosylation activity
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [82816] (6)
           3. Poly(ADP-ribose) polymerase, C-terminal domain [56416] (3)
              1. Poly(ADP-ribose) polymerase, C-terminal domain [56417]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [56418] (7)
                 2. Mouse (Mus musculus) [TaxId: 10090] [82817] (1)
                 3. Human (Homo sapiens) [TaxId: 9606] [103339] (8)
                    SQ P09874 661-1010
           4. AvrPphF ORF2, a type III effector [111257] (1)
              shares the common structural core with other families; unknown function
              1. AvrPphF ORF2, a type III effector [111258]
                 1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [111259] (1)
                    SQ Q9K2L5 29-204
           5. Tpt1/KptA [118162] (1)
              Pfam 01885; contains extra N-terminal domain similar to the "winged helix" DNA-binding domain (scop_sf 46785)
              1. Probable RNA 2'-phosphotransferase KptA [118163]
                 1. Aeropyrum pernix [TaxId: 56636] [118164] (1)
                    SQ Q9YFP5 37-216; d1: (1-76); d2: (88-182)
           6. BC2332-like [143947] (1)
              minimized common structural core with two large, mainly helical insertions on one side forming dimerization "domain"
              1. Hypothetical protein BC2332 [143948]
                 1. Bacillus cereus [TaxId: 1396] [143949] (2)
                    SQ Q81DM5 2-195
           7. CC0527-like [143950] (1)
              Pfam 06108; DUF952
              1. Hypothetical protein CC0527 [143951]
                 1. Caulobacter crescentus [TaxId: 155892] [143952] (3)
                    SQ Q9AAR9 2-114
   334. Peptide deformylase [56419] (1)
        alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
        1. Peptide deformylase [56420] (1)
           nickel-dependent enzyme
           uperfamily
           1. Peptide deformylase [56421] (9)
              1. Peptide deformylase [56422]
                 1. Escherichia coli [TaxId: 562] [56423] (21)
                 2. Pseudomonas aeruginosa [TaxId: 287] [75578] (4)
                 3. Leptospira interrogans [TaxId: 173] [103340] (1)
                    SQ Q72S74
                 4. Staphylococcus aureus [TaxId: 1280] [75579] (6)
                    SQ Q9F4L4
                 5. Streptococcus pneumoniae [TaxId: 1313] [90057] (1)
                 6. Thermotoga maritima [TaxId: 2336] [90058] (1)
                 7. Bacillus stearothermophilus [TaxId: 1422] [75580] (1)
                 8. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [75581] (3)
                 9. Thermus thermophilus [TaxId: 274] [118165] (1)
                    SQ P43522
   335. LCCL domain [69847] (1)
        unusual fold
        1. LCCL domain [69848] (1)
           uperfamily
           1. LCCL domain [69849] (1)
              1. Cochlin [69850]
                 1. Human (Homo sapiens) [TaxId: 9606] [69851] (1)
   336. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56424] (1)
        unusual fold
        1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56425] (1)
           uperfamily
           1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56426] (7)
              1. L-aspartate oxidase [56427]
                 1. Escherichia coli [TaxId: 562] [56428] (3)
              2. Succinate dehydogenase [82818]
                 1. Escherichia coli [TaxId: 562] [82819] (2)
              3. Fumarate reductase [56429]
                 1. Escherichia coli [TaxId: 562] [56430] (7)
                 2. Wolinella succinogenes [TaxId: 844] [56431] (8)
              4. Flavocytochrome c3 (respiratory fumarate reductase) [56432]
                 contains additional N-terminal multiheme domain
                 1. Shewanella frigidimarina [TaxId: 56812] [56433] (16)
                 2. Shewanella putrefaciens [TaxId: 24] [56434] (3)
              5. Adenylylsulfate reductase A subunit [69852]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69853] (2)
   337. C-type lectin-like [56435] (1)
        unusual fold
        1. C-type lectin-like [56436] (8)
           uperfamily
           1. C-type lectin domain [56437] (51)
              Pfam 00059
              1. Lithostathine, inhibitor of stone formation [56438]
                 1. Human (Homo sapiens) [TaxId: 9606] [56439] (2)
              2. Pancreatitis-associated protein 1 [103341]
                 1. Human (Homo sapiens) [TaxId: 9606] [103342] (2)
              3. CD94 [56440]
                 1. Human (Homo sapiens) [TaxId: 9606] [56441] (7)
              4. CD69 [56442]
                 1. Human (Homo sapiens) [TaxId: 9606] [56443] (3)
              5. NK cell-activating receptor nkg2d [64453]
                 1. Mouse (Mus musculus) [TaxId: 10090] [64454] (2)
                 2. Human (Homo sapiens) [TaxId: 9606] [64455] (3)
              6. Macrophage mannose receptor, CRD4 [56444]
                 1. Human (Homo sapiens) [TaxId: 9606] [56445] (2)
              7. Ovocleidin-17 [90059]
                 major protein of the eggshell calcified layer
                 1. Chicken (Gallus gallus) [TaxId: 9031] [90060] (1)
              8. Galactose-specific C-type lectin [90061]
                 1. Western diamondback rattlesnake (Crotalus atrox) [TaxId: 8730] [90062] (2)
              9. Snake coagglutinin alpha chain [88861]
                 heterodimeric coagulation factors IX/X-binding protein (IX/X-BP)
                 1. Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] [88862] (7)
                 2. Habu snake (Trimeresurus flavoviridis), flavocetin-A [TaxId: 88087] [88863] (1)
                 3. Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] [88864] (4)
                 4. Hundred-pace snake (Deinagkistrodon acutus), different isoforms [TaxId: 36307] [88865] (3)
                 5. Puff adder (Bitis arietans), bitiscetin [TaxId: 8692] [88866] (2)
                 6. Snake (Echis multisquamatus), Ems16 [TaxId: 93050] [103343] (2)
                    SQ Q7T2Q1 24-157
                 7. South american rattlesnake (Crotalus durissus terrificus), convulxin [TaxId: 8732] [103344] (1)
                 8. Taiwan habu (Trimeresurus mucrosquamatus), mucrocetin [TaxId: 103944] [103345] (1)
                 9. Saw-scaled viper (Echis carinatus), echicetin [TaxId: 40353] [103346] (1)
                 10. Malayan pit viper (Calloselasma rhodostoma), rhodocetin [TaxId: 8717] [143953] (1)
                     SQ P81397 1-132
              10. Snake coagglutinin beta chain [88867]
                  heterodimeric coagulation factors IX/X-binding protein (IX/X-BP)
                  1. Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] [88868] (7)
                  2. Habu snake (Trimeresurus flavoviridis), flavocetin-A [TaxId: 88087] [88869] (1)
                  3. Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] [88870] (4)
                  4. Sharp-nosed viper (Deinagkistrodon acutus) [TaxId: 36307] [88871] (3)
                  5. Puff adder (Bitis arietans), bitiscetin [TaxId: 8692] [88872] (2)
                  6. Snake (Echis multisquamatus), Ems16 [TaxId: 93050] [103347] (2)
                     SQ Q7T2Q0 27-153
                  7. South american rattlesnake (Crotalus durissus terrificus), convulxin [TaxId: 8732] [103348] (1)
                  8. Taiwan habu (Trimeresurus mucrosquamatus), mucrocetin [TaxId: 103944] [103349] (1)
                  9. Saw-scaled viper (Echis carinatus), echicetin [TaxId: 40353] [103350] (1)
                  10. Malayan pit viper (Calloselasma rhodostoma), rhodocetin [TaxId: 8717] [143954] (1)
                      SQ P81398 2-128
              11. Type II antifreeze protein [56450]
                  1. Sea raven (Hemitripterus americanus) [TaxId: 8094] [56451] (1)
              12. Eosinophil major basic protein [64457]
                  1. Human (Homo sapiens) [TaxId: 9606] [64458] (3)
              13. NK cell receptor [56452]
                  1. Mouse (Mus musculus), ly49-a [TaxId: 10090] [56453] (1)
                  2. Mouse (Mus musculus), ly49-c [TaxId: 10090] [103351] (7)
                  3. Mouse (Mus musculus), ly49-i [TaxId: 10090] [75582] (1)
              14. H1 subunit of the asialoglycoprotein receptor [56454]
                  1. Human (Homo sapiens) [TaxId: 9606] [56455] (1)
              15. DC-SIGN (dendritic cell-specific ICAM-3 grabbing nonintegrin) [69855]
                  1. Human (Homo sapiens) [TaxId: 9606] [69856] (6)
                     SQ Q9NNX6 253-384
              16. DC-SIGNR (DC-SIGN related receptor) [69857]
                  1. Human (Homo sapiens) [TaxId: 9606] [69858] (4)
                     SQ Q9NNX6 219-397
              17. EBV gp42 [75583]
                  1. Epstein-Barr virus [TaxId: 10376] [75584] (1)
              18. E-selectin, C-lectin domain [56456]
                  folowed by EGF-like module
                  1. Human (Homo sapiens) [TaxId: 9606] [56457] (2)
              19. P-selectin, C-lectin domain [116731]
                  followed by EGF-like module
                  1. Human (Homo sapiens) [TaxId: 9606] [116732] (3)
              20. Mannose-binding protein A, C-lectin domain [56458]
                  1. Human (Homo sapiens) [TaxId: 9606] [56459] (1)
                  2. Rat (Rattus norvegicus) [TaxId: 10116] [56460] (38)
              21. Surfactant protein, lectin domain [56461]
                  1. Human (Homo sapiens), SP-D [TaxId: 9606] [56462] (36)
                  2. Rat (Rattus norvegicus), SP-A [TaxId: 10116] [103352] (2)
              22. Lectin TC14 [56463]
                  1. Tunicate (Polyandrocarpa misakiensis) [TaxId: 7723] [56464] (2)
              23. Tetranectin [56465]
                  trimeric plasminogen binding protein with an alpha-helical coiled coil
                  1. Human (Homo sapiens) [TaxId: 9606] [56466] (3)
                     SQ P05452 85-202
              24. Aggrecan core protein [111260]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [111261] (1)
                     SQ P07897 1912-2037
              25. Lectin CEL-I [111262]
                  1. Cucumaria echinata [TaxId: 40245] [111263] (2)
                     SQ Q7M462
              26. Hypothetical protein F28B4.3 [118166]
                  1. Caenorhabditis elegans [TaxId: 6239] [118167] (1)
                     SQ Q19853 1193-1329
              27. Oxidised low density lipoprotein [143955]
                  1. Human (Homo sapiens) [TaxId: 9606] [143956] (16)
                     SQ P78380 140-270
              28. Low affinity immunoglobulin epsilon Fc receptor [143957]
                  1. Human (Homo sapiens) [TaxId: 9606] [143958] (2)
                     SQ P06734 156-298
           2. Aerolysin/Pertussis toxin (APT) domain [56467] (2)
              1. Pertussis toxin, S2/S3 subunits, N-terminal domain [56468]
                 1. Bordetella pertussis [TaxId: 520] [56469] (3)
              2. Proaerolysin, N-terminal domain [56470]
                 1. Aeromonas hydrophila [TaxId: 644] [56471] (9)
           3. Invasin/intimin cell-adhesion fragment, C-terminal domain [56472] (2)
              1. Intimin [56473]
                 1. Escherichia coli [TaxId: 562] [56474] (3)
                    an enteropathogenic serotype
              2. Invasin [56475]
                 1. Yersinia pseudotuberculosis [TaxId: 633] [56476] (1)
           4. Link domain [56477] (2)
              1. TSG-6, Link module [56478]
                 1. Human (Homo sapiens) [TaxId: 9606] [56479] (7)
              2. CD44, hyaluronan binding domain [103353]
                 contains extra N-terminal beta-strand and C-terminal beta-hairpin
                 1. Human (Homo sapiens) [TaxId: 9606] [103354] (3)
           5. Endostatin [56480] (3)
              decorated with many insertions in the common fold
              1. Endostatin [56481]
                 1. Human (Homo sapiens) [TaxId: 9606] [56482] (1)
                 2. Mouse (Mus musculus) [TaxId: 10090] [56483] (3)
              2. Endostatin domain of collagen alpha1(xv) [56484]
                 1. Mouse (Mus musculus) [TaxId: 10090] [56485] (1)
           6. Noncollagenous (NC1) domain of collagen IV [75585] (2)
              duplication: consists of two subdomains of this fold; segment swapping within and between individual domains
              1. Noncollagenous (NC1) domain of collagen IV [75586]
                 1. Human (Homo sapiens) [TaxId: 9606] [75587] (1)
                 2. Cow (Bos taurus) [TaxId: 9913] [82820] (3)
                    SQ P02462 1445-1667
           7. Sulfatase-modifying factor-like [143959] (2)
              Pfam 03781 (DUF323); fold decorated with many additional structures; C-alpha-formyglycine-generating enzyme
              1. Sulfatase modifying factor 1 [143960]
                 1. Human (Homo sapiens) [TaxId: 9606] [143961] (14)
                    SQ Q8NBK3 86-371
              2. Sulfatase modifying factor 2 [143962]
                 1. Human (Homo sapiens) [TaxId: 9606] [143963] (2)
                    SQ Q8NBJ7 28-294
           8. Mtd variable domain [143964] (1)
              fold decorated with many additional structures; overall similarity to the Sulfatase modifying factor family; lacks the characteristic disulfide
              1. Major tropism determinant (Mtd), C-terminal domain [143965]
                 1. Bordetella phage bpp-1 [TaxId: 194699] [143966] (13)
                    SQ Q775D6 171-380
                    includes related Bordetella phage proteins
   338. Hemolytic lectin CEL-III, C-terminal domain [111264] (1)
        unusual fold
        1. Hemolytic lectin CEL-III, C-terminal domain [111265] (1)
           uperfamily
           1. Hemolytic lectin CEL-III, C-terminal domain [111266] (1)
              1. Hemolytic lectin CEL-III, C-terminal domain [111267]
                 1. Cucumaria echinata [TaxId: 40245] [111268] (5)
                    SQ Q868M7 11-442
   339. SRCR-like [56486] (2)
        unusual fold; disulfide-rich; core: beta-x-alpha-beta-loop-beta
        1. SRCR-like [56487] (2)
           uperfamily
           1. Scavenger receptor cysteine-rich (SRCR) domain [56488] (1)
              has some structural similarity to the long-chain scorpion toxins
              1. M2BP [56489]
                 1. Human (Homo sapiens) [TaxId: 9606] [56490] (1)
           2. Hepsin, N-terminal domain [103355] (1)
              1. Hepsin, N-terminal domain [103356]
                 1. Human (Homo sapiens) [TaxId: 9606] [103357] (4)
                    SQ P05981 50-159
        2. A heparin-binding domain [56491] (1)
           uperfamily
           1. A heparin-binding domain [56492] (1)
              1. N-terminal domain of the amyloid precursor protein [56493]
                 1. Human (Homo sapiens) [TaxId: 9606] [56494] (1)
   340. Fibrinogen C-terminal domain-like [56495] (1)
        unusual fold
        1. Fibrinogen C-terminal domain-like [56496] (1)
           uperfamily
           1. Fibrinogen C-terminal domain-like [56497] (8)
              1. Fibrinogen C-terminal domains [56498]
                 1. Human (Homo sapiens), gamma [TaxId: 9606] [68904] (21)
                    SQ P02679
                 2. Human (Homo sapiens), beta [TaxId: 9606] [68903] (14)
                    SQ P02675
                 3. Human (Homo sapiens), fibrinogen-420, alpha-E [TaxId: 9606] [56500] (1)
                 4. Chicken (Gallus gallus), gamma [TaxId: 9031] [69859] (1)
                 5. Chicken (Gallus gallus), beta [TaxId: 9031] [69860] (1)
                 6. Sea lamprey (Petromyzon marinus), beta [TaxId: 7757] [75588] (2)
                 7. Sea lamprey (Petromyzon marinus), gamma [TaxId: 7757] [75589] (2)
              2. Tachylectin 5a [69861]
                 1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [69862] (1)
   341. gp120 core [56501] (1)
        unusual fold
        1. gp120 core [56502] (1)
           uperfamily
           1. gp120 core [56503] (1)
              1. gp120 core [56504]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [56505] (24)
   342. Methionine synthase activation domain-like [56506] (1)
        unusual fold; core: beta-alpha(2)-beta(2)-alpha(2)-beta-alpha-beta; antiparallel beta-sheet: order 12354
        1. Methionine synthase activation domain-like [56507] (2)
           uperfamily
           1. Methionine synthase SAM-binding domain [56508] (1)
              1. Methionine synthase SAM-binding domain [56509]
                 1. Escherichia coli [TaxId: 562] [56510] (4)
           2. Hypothetical protein TM0269 [75590] (1)
              1. Hypothetical protein TM0269 [75591]
                 1. Thermotoga maritima [TaxId: 2336] [75592] (1)
   343. UbiD C-terminal domain-like [143967] (1)
        alpha-beta(2)-alpha-beta-alpha-beta(2); 3 layers, a/b/a; mixed beta-sheet, order: 12354, strands 2,3 and 5 are parallel to each other
        1. UbiD C-terminal domain-like [143968] (1)
           uperfamily
           1. UbiD C-terminal domain-like [143969] (1)
              C-terminal part of Pfam 01977; hexamerisation domain
              1. 3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD [143970]
                 1. Escherichia coli [TaxId: 562] [143971] (3)
                    SQ P0AAB4 326-491
   344. Hypothetical protein TM0875 [90063] (1)
        unusual fold; core: beta(2)-loop-beta(2)-alpha-beta; mixed beta-sheet: order 51243; parallel strands 2 and 4
        1. Hypothetical protein TM0875 [90064] (1)
           uperfamily
           1. Hypothetical protein TM0875 [90065] (1)
              1. Hypothetical protein TM0875 [90066]
                 1. Thermotoga maritima [TaxId: 2336] [90067] (1)
   345. Metal cation-transporting ATPase, ATP-binding domain N [81661] (1)
        unusual fold; core: beta-alpha(2)-beta(3)-alpha(2)-beta(2); 6-stranded antiparallel beta-sheet, order: 165432
        1. Metal cation-transporting ATPase, ATP-binding domain N [81660] (1)
           uperfamily
           1. Metal cation-transporting ATPase, ATP-binding domain N [81659] (5)
              1. Calcium ATPase [81658]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81657] (17)
                    SQ P04191
              2. Sodium/potassium-transporting ATPase alpha chain [90068]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [90069] (2)
                 2. Pig (Sus scrofa) [TaxId: 9823] [111269] (1)
                    SQ Q6PIE5 384-590
              3. Potassium-transporting ATPase B chain, KdpB [111270]
                 minimal fold of this domain:
                 1. Escherichia coli [TaxId: 562] [111271] (4)
                    SQ P03960 316-451
              4. Cation-transporting ATPase [143972]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143973] (3)
                    SQ O29777 435-547
   346. Suppressor of Fused, N-terminal domain [103358] (1)
        unusual fold; bifurcated beta-sheet; left-handed beta-alpha-beta unit
        1. Suppressor of Fused, N-terminal domain [103359] (1)
           uperfamily
           1. Suppressor of Fused, N-terminal domain [103360] (1)
              1. Suppressor of Fused, N-terminal domain [103361]
                 1. Human (Homo sapiens) [TaxId: 9606] [103362] (1)
   347. Nitric oxide (NO) synthase oxygenase domain [56511] (1)
        unusual fold
        1. Nitric oxide (NO) synthase oxygenase domain [56512] (1)
           uperfamily
           1. Nitric oxide (NO) synthase oxygenase domain [56513] (6)
              1. Nitric oxide (NO) synthase oxygenase domain [56514]
                 1. Mouse (Mus musculus) [TaxId: 10090] [56515] (51)
                    SQ P29477 77-496 ! SQ P29477 77-495
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [82821] (45)
                    SQ P29476 298-716
                 3. Human (Homo sapiens) [TaxId: 9606] [56516] (15)
                 4. Cow (Bos taurus) [TaxId: 9913] [56517] (43)
                    SQ P29473 67-482
                 5. Bacillus subtilis [TaxId: 1423] [82822] (4)
                 6. Staphylococcus aureus [TaxId: 1280] [82823] (1)
   348. Penicillin binding protein dimerisation domain [56518] (1)
        unusual fold
        1. Penicillin binding protein dimerisation domain [56519] (1)
           uperfamily
           1. Penicillin binding protein dimerisation domain [56520] (2)
              contains an insert subdomain of ClpS-like fold
              1. Penicillin-binding protein 2x (pbp-2x), N-terminal domain [56521]
                 the insert subdomain (residues 93-183) is usually disordered in the structures
                 1. Streptococcus pneumoniae [TaxId: 1313] [56522] (6)
              2. Penicillin binding protein 2a (PBP2A), middle domain [82824]
                 the insert subdomain (residues 168-239) is fully ordered
                 1. Staphylococcus aureus [TaxId: 1280] [82825] (5)
                    SQ O54286 27-668
   349. Oxidoreductase molybdopterin-binding domain [56523] (1)
        unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
        1. Oxidoreductase molybdopterin-binding domain [56524] (1)
           uperfamily
           1. Oxidoreductase molybdopterin-binding domain [56525] (3)
              Pfam 00174
              1. Sulfite oxidase, middle catalytic domain [56526]
                 1. Chicken (Gallus gallus) [TaxId: 9031] [56527] (5)
                 2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [103363] (1)
              2. Bacterial sulfite oxidase YedY [118168]
                 1. Escherichia coli [TaxId: 562] [118169] (2)
                    SQ P76342 63-329
   350. FAH [56528] (1)
        unusual fold; contains 3 layers of beta-sheet structure
        1. FAH [56529] (1)
           uperfamily
           1. FAH [56530] (6)
              1. Fumarylacetoacetate hydrolase, FAH, C-terminal domain [63432]
                 1. Mouse (Mus musculus) [TaxId: 10090] [56532] (6)
              2. Putative isomerase YcgM [90070]
                 1. Escherichia coli [TaxId: 562] [90071] (1)
              3. 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase HpcE [64459]
                 duplication: tandem repeat of two FAH domains
                 1. Escherichia coli [TaxId: 562] [64460] (2)
              4. Hypothetical protein Ynl168c [111272]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111273] (1)
                    SQ P53889
              5. 2-keto-4-pentenoate hydratase MhpD [111274]
                 1. Escherichia coli [TaxId: 562] [111275] (1)
                    SQ P77608
              6. FAHD1 (Flj36880, YISKL) [118170]
                 1. Human (Homo sapiens) [TaxId: 9606] [118171] (1)
                    SQ Q6P587
   351. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56533] (1)
        unusual fold
        1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56534] (1)
           uperfamily
           1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56535] (5)
              1. Tyrosine hydroxylase [56536]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [56537] (2)
              2. Phenylalanine hydroxylase, PAH [56538]
                 1. Human (Homo sapiens) [TaxId: 9606] [56539] (15)
                    SQ P00439 117-424
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [56540] (2)
                 3. Chromobacterium violaceum [TaxId: 536] [75593] (3)
              3. Tryptophan hydroxylase [82826]
                 1. Human (Homo sapiens) [TaxId: 9606] [82827] (1)
   352. Substrate-binding domain of HMG-CoA reductase [56541] (1)
        unusual fold
        1. Substrate-binding domain of HMG-CoA reductase [56542] (1)
           uperfamily
           1. Substrate-binding domain of HMG-CoA reductase [56543] (2)
              1. Substrate-binding domain of HMG-CoA reductase [56544]
                 1. Human (Homo sapiens) [TaxId: 9606] [56545] (9)
                 2. Pseudomonas mevalonii [TaxId: 32044] [56546] (5)
                    SQ P13702 4-377
   353. Argininosuccinate synthetase, C-terminal domain [69863] (1)
        unusual fold
        1. Argininosuccinate synthetase, C-terminal domain [69864] (1)
           uperfamily
           1. Argininosuccinate synthetase, C-terminal domain [69865] (3)
              1. Argininosuccinate synthetase, C-terminal domain [69866]
                 1. Escherichia coli [TaxId: 562] [69867] (4)
                 2. Thermus thermophilus [TaxId: 274] [75594] (7)
                 3. Thermotoga maritima [TaxId: 2336] [111276] (1)
                    SQ Q9X2A1
   354. Hypothetical protein PH1602 [103364] (1)
        complex alpha+beta fold; contains a region of similarity to the ferredoxin-like fold
        1. Hypothetical protein PH1602 [103365] (1)
           uperfamily
           1. Hypothetical protein PH1602 [103366] (1)
              1. Hypothetical protein PH1602 [103367]
                 1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103368] (1)
   355. IlvD/EDD N-terminal domain-like [143974] (1)
        contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
        1. IlvD/EDD N-terminal domain-like [143975] (1)
           uperfamily
           1. lvD/EDD N-terminal domain-like [143976] (1)
              N-terminal part of Pfam 00920
              1. 6-phosphogluconate dehydratase EDD [143977]
                 1. Shewanella oneidensis [TaxId: 70863] [143978] (2)
                    SQ Q8EEA0 1-418
   356. DNA methylase specificity domain [116733] (1)
        comprises the N-terminal, double beta-helix like structure and C-terminal alpha-hairpin
        1. DNA methylase specificity domain [116734] (2)
           uperfamily
           1. TaqI C-terminal domain-like [116735] (1)
              1. DNA methylase TaqI, C-terminal domain [116736]
                 1. Thermus aquaticus [TaxId: 271] [116737] (18)
           2. Type I restriction modification DNA specificity domain [143979] (2)
              Pfam 01420
              1. Bipartite methylase S protein MG438 [143980]
                 duplication; contains two structural repeats made of this domain and extra C-terminal coiled coil each; overall structure is similar to MJ0130
                 1. Mycoplasma genitalium [TaxId: 2097] [143981] (2)
                    SQ Q49434 1-193! SQ Q49434 194-374
              2. Bipartite methylase S protein MJ0130 [143982]
                 duplication: comprises two repeats of this domain, separated by a coiled coil made by additional long helices at the C-end of each repeat
                 1. Methanocaldococcus jannaschii [TaxId: 2190] [143983] (4)
                    SQ Q57594 1-220! SQ Q57594 221-425
   357. GCM domain [90072] (1)
        consists of two different alpha+beta subdomains; 2 zinc-binding sites
        1. GCM domain [90073] (1)
           DNA-binding domain
           uperfamily
           1. GCM domain [90074] (1)
              1. Mgcm1 [90075]
                 1. Mouse (Mus musculus) [TaxId: 10090] [90076] (1)
   358. Conserved core of transcriptional regulatory protein vp16 [56547] (1)
        unusual fold
        1. Conserved core of transcriptional regulatory protein vp16 [56548] (1)
           uperfamily
           1. Conserved core of transcriptional regulatory protein vp16 [56549] (1)
              1. Conserved core of transcriptional regulatory protein vp16 [56550]
                 1. Herpes simplex virus type 1 [TaxId: 10298] [56551] (1)
   359. Insert subdomain of RNA polymerase alpha subunit [56552] (1)
        unusual fold; contains a left-handed beta-alpha-beta unit
        1. Insert subdomain of RNA polymerase alpha subunit [56553] (1)
           uperfamily
           1. Insert subdomain of RNA polymerase alpha subunit [56554] (4)
              1. RNA polymerase alpha subunit [56555]
                 1. Escherichia coli [TaxId: 562] [56556] (1)
                 2. Thermus aquaticus [TaxId: 271] [64461] (7)
                 3. Thermus thermophilus [TaxId: 274] [75595] (30)
                    SQ Q9Z9H6; part of multichain biological unit
              2. RPB3 [64462]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64463] (25)
                    SQ P16370; part of multichain biological unit
   360. Baseplate structural protein gp11 [56557] (1)
        unusual fold; trimer
        1. Baseplate structural protein gp11 [56558] (1)
           uperfamily
           1. Baseplate structural protein gp11 [56559] (1)
              1. Baseplate structural protein gp11 [56560]
                 1. Bacteriophage T4 [TaxId: 10665] [56561] (1)
   361. Receptor-binding domain of short tail fibre protein gp12 [88873] (1)
        unusual fold; trimer
        1. Receptor-binding domain of short tail fibre protein gp12 [88874] (1)
           uperfamily
           1. Receptor-binding domain of short tail fibre protein gp12 [88875] (1)
              1. Receptor-binding domain of short tail fibre protein gp12 [88876]
                 intertwinned homotrimer; subdivided into the neck, collar, head and bonnet regions
                 1. Bacteriophage T4 [TaxId: 10665] [88877] (2)
   362. Outer capsid protein sigma 3 [64464] (1)
        unusual fold
        1. Outer capsid protein sigma 3 [64465] (1)
           uperfamily
           1. Outer capsid protein sigma 3 [64466] (1)
              1. Outer capsid protein sigma 3 [64467]
                 1. Reovirus [TaxId: 10891] [64468] (12)
   363. Phosphoprotein M1, C-terminal domain [118172] (1)
        consists of 6 helices and one beta-hairpin
        1. Phosphoprotein M1, C-terminal domain [118173] (1)
           uperfamily
           1. Phosphoprotein M1, C-terminal domain [118174] (1)
              C-terminal part of Pfam 03012
              1. Phosphoprotein M1, C-terminal domain [118175]
                 1. Rabies virus, strain CVS-11 [TaxId: 11292] [118176] (1)
                    SQ P22363 186-296
   364. L,D-transpeptidase pre-catalytic domain-like [143984] (1)
        unusual fold, made of four helices and four 2-3 stranded beta-sheets
        1. L,D-transpeptidase pre-catalytic domain-like [143985] (1)
           uperfamily
           1. L,D-transpeptidase pre-catalytic domain-like [143986] (1)
              1. L,D-transpeptidase, pre-catalytic domain [143987]
                 1. Enterococcus faecium [TaxId: 1352] [143988] (1)
                    SQ Q3Y185 217-338
   365. YbiA-like [143989] (1)
        consists of six alpha-helices and two two-stranded beta-sheets
        1. YbiA-like [143990] (1)
           uperfamily
           1. YbiA-like [143991] (1)
              1. Hypothetical protein YbiA [143992]
                 1. Escherichia coli [TaxId: 562] [143993] (1)
                    SQ P30176 1-160
   366. NinB [103369] (1)
        unusual fold; intertwined dimer; consists of two different structural domains
        1. NinB [103370] (1)
           uperfamily
           1. NinB [103371] (1)
              1. NinB [103372]
                 1. Bacteriophage lambda [TaxId: 10710] [103373] (1)
   367. AF2331-like [143994] (1)
        interlocked dimer of beta-alpha-beta(2)-alpha-beta-(alpha) subunits; 3 layers: b/b/a
        1. AF2331-like [143995] (1)
           uperfamily
           1. AF2331-like [143996] (1)
              1. Hypothetical protein AF2331 [143997]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [143998] (2)
                    SQ O27953 1-92
   368. SSo0622-like [111277] (1)
        alpha(2)-beta(2)-alpha-beta-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel beta-sheet: order 21354; strands 1,3 and 5 and the C-terminal helix are longer than other secondary structures
        1. SSo0622-like [111278] (1)
           the dimer, formed in the crystals, is a probable biological unit
           uperfamily
           1. SSo0622-like [111279] (1)
              Pfam 02676
              1. Hypothetical protein SSo0622 [111280]
                 1. Sulfolobus solfataricus [TaxId: 2287] [111281] (1)
                    SQ Q9UX16
   369. Putative modulator of DNA gyrase, PmbA/TldD [111282] (1)
        consists of two different alpha+beta domains; d1: [duplication of alpha-beta(3)-alpha motif; 2 layers: a/b; antiparallel beta-sheet, order: 321456; strands 1, 2, 4 and 5 are twice longer than other secondary structures]; d2 [ complex fold; contains beta-barrel (n=5, S=10)]
        1. Putative modulator of DNA gyrase, PmbA/TldD [111283] (1)
           uperfamily
           1. Putative modulator of DNA gyrase, PmbA/TldD [111284] (2)
              Pfam 01523
              1. PmbA-related protein TM0727 [111285]
                 1. Thermotoga maritima [TaxId: 2336] [111286] (1)
                    SQ Q9WZI6; d1: 1-214; d2: 215-433
              2. Putative modulator of DNA gyrase BT3649 [118177]
                 1. Bacteroides thetaiotaomicron [TaxId: 818] [118178] (1)
                    SQ Q8A1L2
   370. PSTPO5379-like [160919] (1)
        complex fold; consists of two alpha+beta subdomains, one is inserted in the other
        1. PSTPO5379-like [160920] (1)
           1. PSTPO5379-like [160921] (1)
              Pfam 07286; DUF1445
              1. Uncharacterized protein PSTPO5379 [160922]
                 1. Pseudomonas syringae pv. tomato [TaxId: 323] [160923] (2)
                    SQ Q87UC6 7-262
   371. PG1388-like [160924] (1)
        consists of 2 alpha+beta subdomains, each having a meander beta-sheet; d1: alpha(2)-beta(7); d2: alpha(2)-beta(2)-alpha(2)-beta(2)
        1. PG1388-like [160925] (1)
           1. PG1388-like [160926] (1)
              PfamB 104512
              1. Hypothetical protein PG1388 [160927]
                 1. Porphyromonas gingivalis [TaxId: 837] [160928] (2)
                    SQ Q7MUU3 66-262
   372. Oxysterol-binding protein-like [143999] (1)
        core: large meander beta-sheet of 12 strands wrapped around the N-terminal (distorted) alpha-hairpin; some similarity to transmembrane beta-barrel proteins
        1. Oxysterol-binding protein-like [144000] (1)
           uperfamily
           1. Oxysterol-binding protein [144001] (1)
              Pfam 01237
              1. Oxysterol-binding protein homolog 4, KES1 [144002]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144003] (8)
                    SQ P35844 2-434! SQ P35844 30-434
   373. ORC1-binding domain [144004] (1)
        complex fold, composed of an alpha hairpin, meander beta-sheet and a five-stranded barrel of unusual topology
        1. ORC1-binding domain [144005] (1)
           uperfamily
           1. ORC1-binding domain [144006] (1)
              1. Regulatory protein SIR1 [144007]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144008] (4)
                    SQ P21691 484-611! SQ P21691 485-613! SQ P21691 487-611
   374. CofE-like [144009] (1)
        consists of two different domains; d1: beta-alpha-beta-alpha-beta(2)-alpha-beta, mixed sheet of 5 strands, order:15234, strands 2 and 3 are parralel; d2 is inserted in d1 after strand 2 and comprises a helix-turn-helix motif and two 3-stranded sheets
        1. CofE-like [144010] (1)
           uperfamily
           1. CofE-like [144011] (1)
              Pfam 01996; DUF129; contains known activity
              1. F420-0:gamma-glutamyl ligase CofE [144012]
                 1. Archaeoglobus fulgidus [TaxId: 2234] [144013] (4)
                    SQ O28028 1-249
   375. Peptidoglycan deacetylase N-terminal noncatalytic region [144014] (1)
        consists of two different domains, d1: [alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; mixed beta-sheet, order 12345, strands 2 and 3 are parallel to each other with a left-handed crossover connection], d2: alpha-beta(3)-alpha; 2 layers; antiparallel beta-sheet, order 123]
        1. Peptidoglycan deacetylase N-terminal noncatalytic region [144015] (1)
           uperfamily
           1. Peptidoglycan deacetylase N-terminal noncatalytic region [144016] (1)
              1. Peptidoglycan GlcNAc deacetylase [144017]
                 1. Streptococcus pneumoniae [TaxId: 1313] [144018] (2)
                    SQ Q8DP63 46-267
   376. Non-globular alpha+beta subunits of globular proteins [56567] (1)
        not a true fold
        1. Non-globular alpha+beta subunits of globular proteins [56568] (3)
           not a true superfamily
           uperfamily
           1. Phycoerythrin 545 alpha-subunits [56569] (1)
              consists of a long beta-hairpin and a single alpha-helix
              1. Phycoerythrin 545 alpha-subunits [56570]
                 1. Cryptophyte (Rhodomonas sp. CS24) [TaxId: 79257] [56571] (5)
                    SQ P30943 38-104 ! SQ Q00433 53-128
           2. Virulence effector SptP domain [69868] (1)
              1. Virulence effector SptP domain [69869]
                 1. Salmonella typhimurium [TaxId: 90371] [69870] (1)
           3. Ubiquinol-cytochrome c reductase 8 kDa protein [90077] (1)
              beta-hairpin and a short alpha-helix bound to the core subunits
              1. Ubiquinol-cytochrome c reductase 8 kDa protein [90078]
                 1. Cow (Bos taurus) [TaxId: 9913] [90079] (14)
                    SQ P13272 1-57 ! SQ P13272
                    there are other PDB entries with lower resolution structures of the Ubiquinol-cytochrome c reductase complex, in which this subunit has incomplete and probably mistraced structure that is not classified in scop
5. Multi-domain proteins (alpha and beta) [56572] (66)
   Folds consisting of two or more domains belonging to different classes
   1. Serpins [56573] (1)
      contains a cluster of helices and a beta-sandwich
      1. Serpins [56574] (1)
         uperfamily
         1. Serpins [56575] (17)
            1. Elastase inhibitor [56576]
               1. Horse (Equus caballus) [TaxId: 9796] [56577] (1)
            2. Ovalbumin [56578]
               1. Hen (Gallus gallus) [TaxId: 9031] [56579] (3)
            3. Antichymotrypsin, alpha-1 [56580]
               1. Human (Homo sapiens) [TaxId: 9606] [56581] (5)
            4. Antitrypsin, alpha-1 [56582]
               1. Human (Homo sapiens) [TaxId: 9606] [56583] (15)
            5. Antithrombin [56584]
               1. Cow (Bos taurus) [TaxId: 9913] [56585] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [56586] (33)
                  SQ P01008
            6. Plasminogen activator inhibitor-1 [56587]
               1. Human (Homo sapiens) [TaxId: 9606] [56588] (9)
            7. Plasminogen activator inhibitor-2 [56589]
               1. Human (Homo sapiens) [TaxId: 9606] [56590] (2)
            8. Heparin cofactor II (Hc-II, leuserpin 2) [82833]
               1. Human (Homo sapiens) [TaxId: 9606] [82834] (2)
            9. Protein C inhibitor [82835]
               1. Human (Homo sapiens) [TaxId: 9606] [82836] (1)
            10. Neuroserpin [69871]
                1. Mouse (Mus musculus) [TaxId: 10090] [69872] (1)
            11. Serpin K [56591]
                1. Tobacco hawkmoth (Manduca sexta) [TaxId: 7130] [56592] (1)
            12. Alaserpin (serpin 1) [64469]
                1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [64470] (1)
                   Michaelis serpin-trypsin complex
            13. Viral serpin crmA (cytokine response modifier protein) [56593]
                1. Cowpox virus [TaxId: 10243] [56594] (3)
            14. Pigment epithelium-derived factor, PEDF [64471]
                1. Human (Homo sapiens) [TaxId: 9606] [64472] (1)
            15. Thermopin [90080]
                Serpin from a thermophilic prokaryote
                1. Thermobifida fusca [TaxId: 2021] [90081] (2)
                   SQ Q47NK3
            16. Maspin [118179]
                1. Human (Homo sapiens) [TaxId: 9606] [118180] (2)
                   SQ P36952
   2. FdhE-like [144019] (1)
      consists on the N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and the C-terminal helix packed together
      1. FdhE-like [144020] (1)
         uperfamily
         1. FdhE-like [144021] (1)
            Pfam 04216
            1. FdhE homolog PA4809 [144022]
               1. Pseudomonas aeruginosa [TaxId: 287] [144023] (1)
                  SQ Q9HV00 19-308
   3. FlhC-like [160929] (1)
      3 domains; d1 & d2 are similar three-helical bundles, with d1 containing an HTH motif; d3: zinc finger of a rubredoxin-like fold
      1. FlhC-like [160930] (1)
         1. FlhC-like [160931] (1)
            Pfam 05280
            1. Flagellar transcriptional activator FlhC [160932]
               1. Escherichia coli [TaxId: 562] [160933] (2)
                  SQ P0ABY7 5-160
   4. Replication terminator protein (Tus) [56595] (1)
      contains a cluster of helices and a beta-sandwich
      1. Replication terminator protein (Tus) [56596] (1)
         uperfamily
         1. Replication terminator protein (Tus) [56597] (1)
            1. Replication terminator protein (Tus) [56598]
               1. Escherichia coli [TaxId: 562] [56599] (4)
   5. VPA0735-like [160934] (1)
      consists of a cluster of helices and two beta-sandwich domains of similar topology; probable duplication
      1. VPA0735-like [160935] (1)
         1. VPA0735-like [160936] (1)
            the N-terminal beta-sandwich domain corresponds to Pfam 06863 (DUF1254); the C-terminal beta-sandwich domains corresponds to Pfam 06742 (DUF1214); the two Pfam families are structurally related
            1. Hypothetical protein VPA0735 [160937]
               1. Vibrio parahaemolyticus [TaxId: 670] [160938] (2)
                  SQ Q87I71 22-482
   6. 2-methylcitrate dehydratase PrpD [103377] (1)
      consists of an all-alpha and alpha+beta domains
      1. 2-methylcitrate dehydratase PrpD [103378] (1)
         uperfamily
         1. 2-methylcitrate dehydratase PrpD [103379] (1)
            1. 2-methylcitrate dehydratase PrpD [103380]
               1. Escherichia coli [TaxId: 562] [103381] (1)
   7. Antivirulence factor [103382] (1)
      contains a helical bundle with a buried helix and an alpha+beta insert domain
      1. Antivirulence factor [103383] (1)
         uperfamily
         1. Antivirulence factor [103384] (1)
            1. Type III effector AvrB [103385]
               1. Pseudomonas syringae [TaxId: 317] [103386] (4)
   8. Api92-like [160939] (1)
      2 domains; d1: [alpha+beta with similarity to ferredoxin-like fold]; d2: [6 helices, bundle, one buried central helix], inserted into d1
      1. Api92-like [160940] (1)
         1. Api92-like [160941] (1)
            Pfam 06924; DUF1281
            1. Hypothetical protein api92 [160942]
               1. Yersinia pseudotuberculosis [TaxId: 633] [160943] (1)
                  SQ Q6EVP2 3-282
   9. PH0156-like [160944] (1)
      2 (sub)domains; d1: [alpha/beta with central mixed beta-sheet, order: 23415876, similarity to the G protein but no P-loop]; d2: [all-alpha, 5 helices, provides dimerization interface]
      1. PH0156-like [160945] (1)
         1. PH0156-like [160946] (1)
            PfamB 117416
            1. Hypothetical protein PH0156 [160947]
               1. Pyrococcus horikoshii [TaxId: 53953] [160948] (2)
                  SQ O57895 1-241
   10. YacF-like [160949] (1)
       2 domains; d1: kinked four-helical bundle, inserted in d2: beta-sandwich of 7 strands in two sheets
       1. YacF-like [160950] (1)
          probable biological unit is a dimer
          1. YacF-like [160951] (1)
             Pfam 07072; DUF1342
             1. Uncharacterized protein VP2528 [160952]
                1. Vibrio parahaemolyticus [TaxId: 670] [160953] (2)
                   SQ Q87LT3 1-245
   11. Virulence-associated V antigen [103387] (1)
       consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
       1. Virulence-associated V antigen [103388] (1)
          uperfamily
          1. Virulence-associated V antigen [103389] (1)
             1. Low calcium response locus protein V, LcrV [103390]
                1. Yersinia pestis [TaxId: 632] [103391] (1)
   12. Heme-dependent catalase-like [56633] (1)
       contains an (8,10) beta-barrel and an all-alpha domain
       1. Heme-dependent catalase-like [56634] (2)
          uperfamily
          1. Heme-dependent catalases [56635] (9)
             1. Catalase I [56636]
                1. Cow (Bos taurus) [TaxId: 9913] [56637] (20)
                2. Human (Homo sapiens) [TaxId: 9606] [56638] (6)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56639] (1)
                4. Proteus mirabilis [TaxId: 584] [56640] (8)
                5. Helicobacter pylori [TaxId: 210] [103392] (6)
                6. Enterococcus faecalis [TaxId: 1351] [103393] (1)
                7. Micrococcus lysodeikticus [TaxId: 1270] [56641] (4)
                8. Pseudomonas syringae [TaxId: 317] [75599] (1)
             2. Catalase II [56642]
                contains additional flavodoxin-like domain at C-terminus
                1. Escherichia coli, HPII [TaxId: 562] [56643] (14)
          2. Allene oxide synthase [118183] (1)
             1. Allene oxide synthase-lipoxygenase protein, N-terminal domain [118184]
                1. Black sea rod (Plexaura homomalla) [TaxId: 47982] [118185] (1)
                   SQ O16025 1-374
   13. Acyl-CoA dehydrogenase NM domain-like [56644] (1)
       2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
       1. Acyl-CoA dehydrogenase NM domain-like [56645] (2)
          flavoprotein: binds FAD; constituent families differ in the numbers of C-terminal domains (four-helical bundles)
          uperfamily
          1. Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains [56646] (12)
             1. Butyryl-CoA dehydrogenase, NM domains [56647]
                1. Megasphaera elsdenii [TaxId: 907] [56648] (1)
                2. Rat (Rattus norvegicus) [TaxId: 10116] [69877] (1)
             2. Medium chain acyl-CoA dehydrogenase, NM domains [56649]
                1. Pig (Sus scrofa) [TaxId: 9823] [56650] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [56651] (8)
                   SQ P11310 34-421
                3. Thermus thermophilus [TaxId: 274] [118186] (1)
                   SQ Q5SJ70 32-409
             3. Isovaleryl-coa dehydrogenase, NM domains [56652]
                1. Human (Homo sapiens) [TaxId: 9606] [56653] (1)
             4. Isobutyryl-CoA dehydrogenase [103394]
                1. Human (Homo sapiens) [TaxId: 9606] [103395] (1)
             5. Protein FkbI [103396]
                involved in biosynthesis of methoxymalonyl extender unit of fk520 polyketide immunosuppressant
                1. Streptomyces hygroscopicus [TaxId: 1912] [103397] (1)
             6. Glutaryl-CoA dehydrogenase GCDH [111293]
                1. Human (Homo sapiens) [TaxId: 9606] [111294] (4)
                   SQ Q92947
             7. 4-hydroxybutyryl-CoA dehydratase AbfD, NM domains [118187]
                1. Clostridium aminobutyricum [TaxId: 33953] [118188] (1)
                   SQ P55792
             8. Acyl-CoA dehydrogenase [144024]
                1. Thermus thermophilus [TaxId: 274] [144025] (8)
                   SQ Q5SGZ2 2-234
             9. Nitroalkane oxidase [144026]
                1. Fusarium oxysporum [TaxId: 5507] [144027] (18)
                   SQ Q8X1D8 2-260
          2. acyl-CoA oxidase N-terminal domains [75600] (2)
             1. Peroxisomal acyl-CoA oxidase-II, domains 1 and 2 [75601]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [75602] (2)
             2. Acyl-coenzyme A oxidase 1, domains 1 and 2 [118189]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118190] (1)
                   SQ O65202
   14. Carbohydrate phosphatase [56654] (1)
       N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
       1. Carbohydrate phosphatase [56655] (2)
          uperfamily
          1. Inositol monophosphatase/fructose-1,6-bisphosphatase-like [56656] (14)
             1. Fructose-1,6-bisphosphatase [56657]
                1. Pig (Sus scrofa) [TaxId: 9823] [56658] (54)
                2. Human (Homo sapiens) [TaxId: 9606] [56659] (1)
                3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [56660] (1)
                4. Spinach (Spinacia oleracea) [TaxId: 3562] [56661] (1)
                5. Garden pea (Pisum sativum) [TaxId: 3888] [56662] (3)
             2. Inositol monophosphatase [56663]
                1. Human (Homo sapiens) [TaxId: 9606] [56664] (8)
             3. Archaeal inositol monophosphatase/fructose-1,6-bisphosphatase [56665]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [56666] (3)
                   MJ0109
                   structural genomics
                2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75608] (5)
                3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103398] (1)
                   PH1897
                4. Pyrococcus furiosus [TaxId: 2261] [118191] (1)
                   SQ Q8TZH9
             4. Inositol polyphosphate 1-phosphatase [56667]
                1. Cow (Bos taurus), brain [TaxId: 9913] [56668] (1)
             5. 3';5'-adenosine bisphosphatase, PAP phosphatase [56669]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69878] (4)
                2. Yeast (Candida albicans) [TaxId: 5476] [56670] (1)
                   sequence identical to that of Saccharomyces cerevisiae
             6. PIPase [64475]
                enzyme displaying both inositol-polyphosphate 1-phosphatase and 3'-phosphoadenosine-5'-phosphate phosphatase activities
                1. Rat (Rattus norvegicus) [TaxId: 10116] [64476] (1)
          2. GlpX-like bacterial fructose-1,6-bisphosphatase [90087] (1)
             similar to the other family in overall domain architecture but each domain has a permuted topology
             1. Glycerol metabolism protein GlpX [90088]
                1. Escherichia coli [TaxId: 562] [90089] (1)
   15. DNA/RNA polymerases [56671] (1)
       divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
       1. DNA/RNA polymerases [56672] (6)
          "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain
          uperfamily
          1. DNA polymerase I [56673] (12)
             1. DNA polymerase I (Klenow fragment) [56674]
                1. Escherichia coli [TaxId: 562] [56675] (14)
                2. Thermus aquaticus [TaxId: 271] [56676] (13)
                3. Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] [56677] (45)
                   SQ Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
                   SQ Q45458 298-876 # 88% sequence identity
             2. T7 phage DNA polymerase [56678]
                1. Bacteriophage T7 [TaxId: 10760] [56679] (16)
                   SQ P00581
             3. Family B DNA polymerase [56680]
                1. Escherichia coli [TaxId: 562] [103399] (1)
                2. Bacteriophage RB69 [TaxId: 12353] [56681] (27)
                3. Archaeon Thermococcus gorgonarius [TaxId: 71997] [56682] (3)
                4. Archaeon Thermococcus sp., 9on-7 [TaxId: 35749] [56683] (1)
                5. Archaeon Desulfurococcus tok [TaxId: 108142] [56684] (2)
                6. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [56685] (2)
                   SQ P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
                7. Sulfolobus solfataricus [TaxId: 2287] [118192] (1)
                   SQ P26811 40-864
             4. phi29 DNA polymerase [118193]
                1. Bacteriophage phi-29 [TaxId: 10756] [118194] (18)
                   SQ P03680
          2. Lesion bypass DNA polymerase (Y-family), catalytic domain [100888] (6)
             contains a distinct 'fingers' domain possibly related to the C-terminal subdomain of hypothetical protein Ta1206 (1qw2)
             1. DinB homolog (DBH) [100889]
                1. Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287] [100890] (62)
                2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [100891] (3)
                3. Sulfolobus acidocaldarius Brock et al. 1972 (Sulfolobus acidocaldarius) [TaxId: 2285] [160954] (3)
             2. DNA polymerase eta [100892]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [100893] (5)
             3. DNA polymerase iota [111295]
                1. Human (Homo sapiens) [TaxId: 9606] [111296] (8)
                   SQ Q9UNA4
             4. DNA polymerase kappa [111297]
                1. Human (Homo sapiens) [TaxId: 9606] [111298] (1)
                   SQ Q9UBT6 71-517
          3. Reverse transcriptase [56686] (3)
             1. MMLV reverse transcriptase [56687]
                1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [56688] (22)
                   SQ P03355 RE 144-594
             2. HIV-1 reverse transcriptase [56689]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [56690] (191)
                   SQ P04585 159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ P03366 186-725 # chain A coverage; chain B coverage: 156-584 ! SQ P04585 158-698 # chain A coverage; chain B is shorter: 159-595
                2. Human immunodeficiency virus type 2 [TaxId: 11709] [82840] (2)
          4. T7 RNA polymerase [56691] (1)
             1. T7 RNA polymerase [56692]
                multidomain; mostly alpha
                1. Bacteriophage T7 [TaxId: 10760] [56693] (11)
          5. RNA-dependent RNA-polymerase [56694] (11)
             1. Viral RNA polymerase [56695]
                1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [56696] (13)
                   SQ P03300 1748-2208
                2. Hepatitis C virus [TaxId: 11103] [56697] (30)
                3. Rabbit hemorrhagic disease virus [TaxId: 11976] [69882] (2)
                4. Norwalk virus [TaxId: 11983] [103400] (3)
                5. Bovine viral diarrhea virus [TaxId: 11099] [103401] (3)
                6. Human rhinovirus 1B, HRV-1B [TaxId: 12129] [111299] (1)
                   SQ P12916 1698-2157
                7. Human rhinovirus 16, HRV-16 [TaxId: 31708] [111300] (1)
                   SQ Q82122 1694-2153
                8. Human rhinovirus 14, HRV-14 [TaxId: 12131] [111301] (1)
                   SQ P03303 1720-2179
                9. Foot-and-mouth disease virus [TaxId: 12110] [111302] (10)
                   SQ Q9QCE4 1858-2327
                10. Avian infectious bursal disease virus [TaxId: 10995] [160955] (1)
                    SQ Q9Q6Q5 31-804
             2. Reovirus polymerase lambda3 [82841]
                contains additional N-terminal domain (res. 1-380) and C-terminal "bracelet" domain (res. 891-1267)
                1. Reovirus [TaxId: 10891] [82842] (5)
          6. dsRNA phage RNA-dependent RNA-polymerase [64480] (1)
             1. dsRNA phage RNA-dependent RNA-polymerase [64481]
                1. Bacteriophage PHI-6 [TaxId: 10879] [64482] (11)
   16. beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1)
       Multidomain subunits of complex domain organization
       1. beta and beta-prime subunits of DNA dependent RNA-polymerase [64484] (2)
          The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit
          uperfamily
          1. RNA-polymerase beta [64485] (3)
             1. RBP2 [64491]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64492] (30)
                   SQ P08518; part of multichain biological unit
             2. RNA-polymerase beta [64488]
                1. Thermus aquaticus [TaxId: 271] [64489] (4)
                2. Thermus thermophilus [TaxId: 274] [75609] (24)
                   SQ Q8RQE9; part of multichain biological unit
          2. RNA-polymerase beta-prime [64490] (3)
             1. RBP1 [64486]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64487] (25)
                   SQ P04050; part of multichain biological unit
             2. RNA-polymerase beta-prime [64493]
                1. Thermus aquaticus [TaxId: 271] [64494] (4)
                2. Thermus thermophilus [TaxId: 274] [75610] (24)
                   SQ Q8RQE8; part of multichain biological unit
   17. Poly(A) polymerase catalytic subunit-like [160956] (1)
       3 domains; d1: all-alpha, contains HhH motif; d2: alpha+beta of nucleotidyltransferase fold (scop_cf 81302); d3: [alpha+beta; beta(3)-alpha-beta(3)-alpha(2); 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 123654, strands 2 and 5 are antiparallel to the rest
       1. Poly(A) polymerase catalytic subunit-like [160957] (1)
          Central domain d2 is distantly related to the nucleotidyltransferase superfamily (scop_sf 81301)
          1. Poxvirus poly(A) polymerase catalytic subunit-like [160958] (1)
             Pfam 03296
             1. Poly(A) polymerase catalytic subunit, PAPL [160959]
                1. Vaccinia virus [TaxId: 10245] [160960] (2)
                   SQ P23371 12-479
   18. Adenylylcyclase toxin (the edema factor) [81299] (1)
       3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
       1. Adenylylcyclase toxin (the edema factor) [81298] (1)
          Domain 1 has topological and active site similarity to the Nucleotidyltransferases (eg. 1kny N-domain); domain 3 binds calmodulin
          uperfamily
          1. Adenylylcyclase toxin (the edema factor) [69887] (1)
             decorated with many insertions and the C-terminal domain
             1. Adenylylcyclase toxin (the edema factor) [69888]
                1. Bacillus anthracis [TaxId: 1392] [69889] (7)
                   SQ P40136
   19. Prokaryotic type I DNA topoisomerase [56711] (1)
       4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
       1. Prokaryotic type I DNA topoisomerase [56712] (1)
          duplication: the protein chain passing through the domains 2-4 makes two structural repeats
          The active site is formed by the toprim and "winged helix" domains (domains 1 and 4); these two domains are also found in the type II topoisomerase (DNA gyrase A) and in the alpha subunit of topoisomerase IV
          uperfamily
          1. Prokaryotic type I DNA topoisomerase [56713] (3)
             domain 4 contains the catalytic tyrosine residue
             1. DNA topoisomerase I, 67K N-terminal domain [56714]
                1. Escherichia coli [TaxId: 562] [56715] (12)
             2. DNA topoisomerase III [56716]
                1. Escherichia coli [TaxId: 562] [56717] (2)
             3. Topoisomerase "domain" of reverse gyrase [69890]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69891] (2)
   20. Type II DNA topoisomerase [56718] (1)
       4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
       1. Type II DNA topoisomerase [56719] (1)
          uperfamily
          1. Type II DNA topoisomerase [56720] (2)
             domain 2 contains the catalytic tyrosine residue
             1. DNA topoisomerase II, C-terminal fragment (residues 410-1202) [56721]
                the N-terminal fragment is homologous to known structure of DNA gyrase B
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56722] (3)
             2. DNA Gyrase A [56723]
                1. Escherichia coli [TaxId: 562] [56724] (3)
   21. DNA topoisomerase IV, alpha subunit [56725] (1)
       2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
       1. DNA topoisomerase IV, alpha subunit [56726] (1)
          uperfamily
          1. DNA topoisomerase IV, alpha subunit [56727] (1)
             domain 2 contains the catalytic tyrosine residue
             1. DNA topoisomerase IV, alpha subunit [56728]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [56729] (1)
   22. DNA primase core [56730] (1)
       2 domains: (1) alpha+beta; (2) toprim alpha/beta
       1. DNA primase core [56731] (2)
          uperfamily
          1. DNA primase DnaG catalytic core [56732] (1)
             1. DNA primase DnaG catalytic core [56733]
                1. Escherichia coli [TaxId: 562] [56734] (3)
          2. Primase fragment of primase-helicase protein [90090] (1)
             1. Primase fragment of primase-helicase protein [90091]
                1. Bacteriophage T7 [TaxId: 10760] [90092] (2)
   23. Recombination protein RecR [111303] (1)
       consists of three domains: alpha-helical dimerisation domain (res. 1-53) with HhH motif; 'treble cleft' C4 zinc-finger domain (54-76); and Toprim domain (76-199; segment-swapped dimer)
       1. Recombination protein RecR [111304] (1)
          uperfamily
          1. Recombination protein RecR [111305] (1)
             three sequential domains correspond to Pfam 00633, Pfam 02132 and Pfam 01751, respectively
             1. Recombination protein RecR [111306]
                1. Deinococcus radiodurans [TaxId: 1299] [111307] (3)
                   SQ Q9ZNA2
   24. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1)
       2 domains: alpha+beta and all-beta
       1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56741] (1)
          uperfamily
          1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56742] (2)
             1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56743]
                1. Human (Homo sapiens) [TaxId: 9606] [56744] (15)
                   SQ P11387 203-765 ! SQ P11387 203-767
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56745] (1)
   25. D-aminoacid aminotransferase-like PLP-dependent enzymes [56751] (1)
       2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
       1. D-aminoacid aminotransferase-like PLP-dependent enzymes [56752] (1)
          uperfamily
          1. D-aminoacid aminotransferase-like PLP-dependent enzymes [56753] (5)
             1. D-aminoacid aminotransferase [56754]
                1. Bacillus sp., strain YM-1 [TaxId: 1409] [56755] (7)
                   domain 1: 1-120; domain 2: 121-277
                2. Bacillus stearothermophilus [TaxId: 1422] [56756] (1)
             2. Branched-chain aminoacid aminotransferase [56757]
                1. Escherichia coli [TaxId: 562] [56758] (6)
                   domain 1: 4-126; domain 2: 137-308
                2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [64508] (9)
             3. Aminodeoxychorismate lyase [56759]
                1. Escherichia coli [TaxId: 562] [56760] (3)
   26. HydB/Nqo4-like [56761] (1)
       3 domains: (1) all-alpha; (2&3) alpha+beta
       1. HydB/Nqo4-like [56762] (2)
          uperfamily
          1. Nickel-iron hydrogenase, large subunit [56763] (5)
             1. Nickel-iron hydrogenase, large subunit [56764]
                1. Desulfovibrio gigas [TaxId: 879] [56765] (4)
                2. Desulfovibrio vulgaris [TaxId: 881] [56766] (16)
                3. Desulfovibrio fructosovorans [TaxId: 878] [56767] (1)
                4. Desulfomicrobium baculatum [TaxId: 899] [56768] (1)
                5. Desulfovibrio desulfuricans [TaxId: 876] [64509] (1)
          2. Nqo4-like [144028] (1)
             Pfam 00346; Respiratory-chain NADH dehydrogenase, 49 Kd subunit
             1. NADH-quinone oxidoreductase chain 4, Nqo4 [144029]
                1. Thermus thermophilus [TaxId: 274] [144030] (4)
                   SQ Q56220 35-409
   27. HydA/Nqo6-like [56769] (1)
       2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
       1. HydA/Nqo6-like [56770] (2)
          uperfamily
          1. Nickel-iron hydrogenase, small subunit [56771] (5)
             1. Nickel-iron hydrogenase, small subunit [56772]
                1. Desulfovibrio gigas [TaxId: 879] [56773] (4)
                2. Desulfovibrio vulgaris [TaxId: 881] [56774] (16)
                3. Desulfovibrio fructosovorans [TaxId: 878] [56775] (1)
                4. Desulfomicrobium baculatum [TaxId: 899] [56776] (1)
                5. Desulfovibrio desulfuricans [TaxId: 876] [64510] (1)
          2. Nq06-like [144031] (1)
             Pfam 01058
             1. NAD-quinone oxidoreductase chain 6, Nqo6 [144032]
                1. Thermus thermophilus [TaxId: 274] [144033] (4)
                   SQ Q56218 14-174
   28. Dehydroquinate synthase-like [56795] (1)
       2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
       1. Dehydroquinate synthase-like [56796] (2)
          uperfamily
          1. Dehydroquinate synthase, DHQS [56797] (2)
             1. Dehydroquinate synthase, DHQS [56798]
                1. Aspergillus nidulans [TaxId: 162425] [56799] (10)
                   SQ P07547
                2. Thermus thermophilus [TaxId: 274] [103402] (1)
          2. Iron-containing alcohol dehydrogenase [69892] (6)
             Pfam 00465
             1. Glycerol dehydrogenase [69893]
                1. Bacillus stearothermophilus [TaxId: 1422] [69894] (3)
                2. Thermotoga maritima [TaxId: 2336] [69895] (1)
                   TM0423
             2. Alcohol dehydrogenase TM0920 [75612]
                1. Thermotoga maritima [TaxId: 2336] [75613] (2)
             3. Hypothetical oxidoreductase yqhD [111308]
                1. Escherichia coli [TaxId: 562] [111309] (1)
                   SQ Q46856
             4. Lactaldehyde reductase FucO [111310]
                1. Escherichia coli [TaxId: 562] [111311] (5)
                   SQ P11549
             5. NADH-dependent butanol dehydrogenase A (TM0820) [111312]
                1. Thermotoga maritima [TaxId: 2336] [111313] (1)
                   SQ Q9WZS7
   29. Siroheme synthase middle domains-like [75614] (1)
       2 domains: (1) alpha+beta, 2 layers; (2) 3/4-helical bundle, right-handed twist, left-handed superhelix
       1. Siroheme synthase middle domains-like [75615] (1)
          uperfamily
          1. Siroheme synthase middle domains-like [75616] (2)
             1. Siroheme synthase CysG, domains 2 and 3 [103403]
                1. Salmonella typhimurium [TaxId: 90371] [103404] (3)
             2. Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains [75617]
                involved in siroheme synthesis
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75618] (1)
   30. Acetyl-CoA synthetase-like [56800] (1)
       4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
       1. Acetyl-CoA synthetase-like [56801] (1)
          uperfamily
          1. Acetyl-CoA synthetase-like [56802] (8)
             1. Luciferase [56803]
                1. Firefly (Photinus pyralis) [TaxId: 7054] [56804] (2)
             2. Dihydroxybenzoate-AMP ligase DhbE [82843]
                1. Bacillus subtilis [TaxId: 1423] [82844] (3)
             3. Phenylalanine activating domain of gramicidin synthetase 1 [56805]
                1. Bacillus brevis [TaxId: 1393] [56806] (1)
             4. Acetyl-CoA synthetase [90093]
                1. Salmonella enterica [TaxId: 28901] [90094] (2)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103405] (1)
             5. Long chain fatty acid-CoA ligase TT0168 [111314]
                1. Thermus thermophilus [TaxId: 274] [111315] (3)
                   SQ Q6L8F0
             6. 4-chlorobenzoyl CoA ligase [111316]
                1. Alcaligenes sp. AL3007 [TaxId: 206162] [111317] (2)
                   SQ Q8GN86
                2. Alcaligenes sp. [TaxId: 512] [160961] (2)
   31. Ribosomal protein L1 [56807] (1)
       2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
       1. Ribosomal protein L1 [56808] (1)
          uperfamily
          1. Ribosomal protein L1 [56809] (4)
             1. Ribosomal protein L1 [56810]
                1. Thermus thermophilus [TaxId: 274] [56811] (16)
                2. Archaeon Methanococcus jannaschii [TaxId: 2190] [56812] (4)
                3. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [56813] (1)
                4. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82845] (1)
   32. Release factor [75619] (1)
       4 domains: (1) 3-helical bundle; (2) alpha+beta of ferredoxin-like fold (3 and 4) alpha+beta of dsRDB-like fold
       1. Release factor [75620] (1)
          uperfamily
          1. Release factor [75621] (3)
             Pfam 00472
             1. Polypeptide chain release factor 2 (RF2) [75622]
                1. Escherichia coli [TaxId: 562] [75623] (1)
             2. Peptide chain release factor 1, RF1 [111318]
                1. Thermotoga maritima [TaxId: 2336] [111319] (2)
                   SQ Q9X183
                2. Escherichia coli [TaxId: 562] [160962] (1)
                   SQ P0A7I0 7-354
   33. YaeB-like [118195] (1)
       2 domains; d1: [beta-barrel (n=6, S=10), similar to the Reductase/isomerase/elongation factor common domain fold (scop_cf 50412), provides homodimerisation interface]; d2: [alpha+beta (disordered)]
       1. YaeB-like [118196] (1)
          uperfamily
          1. YaeB-like [118197] (1)
             Pfam 01980
             1. Hypothetical protein HI0510 [118198]
                1. Haemophilus influenzae [TaxId: 727] [118199] (1)
                   SQ P44740
   34. MalF N-terminal region-like [160963] (1)
       consists of 3 N-terminal transmembrane helices, an alpha+beta linker domain and a beta-barrel (n=7; S=8) with one overside loop
       1. MalF N-terminal region-like [160964] (1)
          1. MalF N-terminal region-like [160965] (1)
             PfamB 001917
             1. Maltose transport system permease protein MalF [160966]
                1. Escherichia coli [TaxId: 562] [160967] (1)
                   SQ P02916 13-260
   35. YebC-like [75624] (1)
       3 domains: (1) 3-helical bundle; (2 and 3 ) alpha+beta of different folds: domain 3 has a ferredoxin-like fold and is inserted in domain 2
       1. YebC-like [75625] (1)
          uperfamily
          1. YebC-like [75626] (3)
             1. Hypothetical protein YebC [75627]
                1. Escherichia coli [TaxId: 562] [75628] (1)
             2. Hypothetical protein aq1575 [75629]
                1. Aquifex aeolicus [TaxId: 63363] [75630] (1)
             3. Hypothetical protein HP0162 [82846]
                1. Helicobacter pylori [TaxId: 210] [82847] (1)
   36. Cullin homology domain [75631] (1)
       3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
       1. Cullin homology domain [75632] (1)
          uperfamily
          1. Cullin homology domain [75633] (2)
             1. Cullin homolog 1, cul-1 [75634]
                1. Human (Homo sapiens) [TaxId: 9606] [75635] (3)
                   SQ Q13616 17-776
             2. Cullin-4A [160968]
                1. Human (Homo sapiens) [TaxId: 9606] [160969] (1)
                   SQ Q13619 402-675
   37. Sec1/munc18-like (SM) proteins [56814] (1)
       3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
       1. Sec1/munc18-like (SM) proteins [56815] (1)
          uperfamily
          1. Sec1/munc18-like (SM) proteins [56816] (3)
             1. Neuronal Sec1, NSec1 [56817]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [56818] (1)
                2. Longfin inshore squid (Loligo pealei) [TaxId: 6621] [56819] (3)
             2. Sly1P protein [82848]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82849] (1)
   38. Prismane protein-like [56820] (1)
       3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology
       1. Prismane protein-like [56821] (3)
          uperfamily
          1. Carbon monoxide dehydrogenase [64514] (3)
             1. Ni-containing carbon monoxide dehydrogenase [64515]
                1. Carboxydothermus hydrogenoformans [TaxId: 129958] [64516] (7)
                2. Rhodospirillum rubrum [TaxId: 1085] [69896] (1)
             2. Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) beta (CODH) subunit [82850]
                1. Moorella thermoacetica [TaxId: 1525] [82851] (6)
          2. Hybrid cluster protein (prismane protein) [56822] (2)
             contains extra N-terminal 3-helical bundle domain
             1. Hybrid cluster protein (prismane protein) [56823]
                1. Desulfovibrio vulgaris [TaxId: 881] [56824] (6)
                2. Desulfovibrio desulfuricans [TaxId: 876] [75636] (4)
          3. Acetyl-CoA synthase [82852] (2)
             4 domains: structures and assembly of domains 1 and 2 are similar to those of domains 1 and 3 of the CODH subunit; (3 and 4) alpha+beta
             1. Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) alpha (ACS) subunit [82853]
                1. Moorella thermoacetica [TaxId: 1525] [82854] (6)
             2. Monomeric acetyl-CoA synthase [103406]
                1. Carboxydothermus hydrogenoformans [TaxId: 129958] [103407] (1)
   39. Subunits of heterodimeric actin filament capping protein Capz [90095] (1)
       3 domains: (1) protozoan pheromone-like alpha-helical bundle; (2) rubredoxin-like domain lacking metal-binding site; (3) alpha+beta heterodimerisation domain: alpha-beta(5)-alpha
       1. Subunits of heterodimeric actin filament capping protein Capz [90096] (2)
          uperfamily
          1. Capz alpha-1 subunit [90097] (1)
             1. Capz alpha-1 subunit [90098]
                1. Chicken (Gallus gallus) [TaxId: 9031] [90099] (1)
          2. Capz beta-1 subunit [90100] (1)
             1. Capz beta-1 subunit [90101]
                1. Chicken (Gallus gallus) [TaxId: 9031] [90102] (1)
   40. beta-lactamase/transpeptidase-like [56600] (1)
       contains a cluster of helices and an alpha+beta sandwich
       1. beta-lactamase/transpeptidase-like [56601] (3)
          uperfamily
          1. beta-Lactamase/D-ala carboxypeptidase [56602] (38)
             1. D-ala carboxypeptidase/transpeptidase [56603]
                1. Streptomyces sp., K15 [TaxId: 1931] [56604] (7)
                2. Streptomyces sp., R61 [TaxId: 1931] [56605] (15)
                   SQ P15555 34-378 ! SQ P15555
             2. Esterase EstB [69873]
                1. Burkholderia gladioli [TaxId: 28095] [69874] (2)
             3. beta-Lactamase, class A [56606]
                1. Escherichia coli, TEM-1 [TaxId: 562] [56607] (35)
                2. Klebsiella pneumoniae, TEM52 [TaxId: 573] [64473] (1)
                3. Escherichia coli, TOHO-1 [TaxId: 562] [56608] (5)
                4. Proteus vulgaris [TaxId: 585] [75596] (1)
                5. Klebsiella pneumoniae, SHV-1 [TaxId: 573] [56609] (15)
                   SQ Q5PSW7 ! SQ P14557 22-286
                   inhibited by tazobactam
                6. Klebsiella pneumoniae, SHV-2 [TaxId: 573] [90082] (1)
                   almost identical sequence to SHV-1
                7. Pseudomonas aeruginosa, PSE-4 carbenicillinase [TaxId: 287] [56610] (2)
                8. Staphylococcus aureus [TaxId: 1280] [56611] (16)
                9. Bacillus licheniformis [TaxId: 1402] [56612] (5)
                10. Enterobacter cloacae, NMC-A carbapenemase [TaxId: 550] [56613] (2)
                11. Streptomyces albus G [TaxId: 1962] [56614] (1)
                12. Mycobacterium fortuitum [TaxId: 1766] [56615] (1)
                13. Pseudomonas aeruginosa, PER-1 [TaxId: 287] [56616] (1)
                14. Serratia marcescens, Sme-1 [TaxId: 615] [56617] (1)
                    imipenem-hydrolyzing
                15. Stenotrophomonas maltophilia, L2 [TaxId: 40324] [103374] (2)
             4. AMPC beta-Lactamase, class C [56618]
                contains small alpha+beta subdomain inserted in the common fold
                1. Citrobacter freundii [TaxId: 546] [56619] (3)
                2. Enterobacter cloacae, P99, cephalosporinase [TaxId: 550] [56620] (10)
                   SQ P05364 22-380 ! SQ P05364 22-381
                3. Escherichia coli, cephalosporinase [TaxId: 562] [56621] (60)
             5. Class D beta-lactamase [56622]
                1. Escherichia coli, OXA-1 [TaxId: 562] [82837] (1)
                2. Salmonella typhimurium, OXA-2 [TaxId: 90371] [90083] (1)
                3. Pseudomonas aeruginosa, OXA-10 [TaxId: 287] [56623] (12)
                4. Pseudomonas aeruginosa, OXA-13 [TaxId: 287] [64474] (3)
             6. Penicillin receptor BlaR, C-terminal domain [103375]
                closely related to class D beta-lactamase
                1. Bacillus licheniformis [TaxId: 1402] [103376] (1)
             7. Penicillin-binding protein 2x (pbp-2x), transpeptidase domain [56624]
                1. Streptococcus pneumoniae [TaxId: 1313] [56625] (14)
             8. Penicillin binding protein 2a (PBP2A), C-terminal domain [82838]
                1. Staphylococcus aureus [TaxId: 1280] [82839] (5)
                   SQ O54286 27-668
             9. Penicillin-binding protein 5, N-terminal domain [69875]
                1. Escherichia coli [TaxId: 562] [69876] (8)
             10. D-aminopeptidase, N-terminal domain [56626]
                 1. Ochrobactrum anthropi [TaxId: 529] [56627] (1)
             11. Pencillin binding protein 4 (PbpD), N-terminal domain [111287]
                 1. Staphylococcus aureus [TaxId: 1280] [111288] (1)
                    SQ Q53613 21-383
             12. Regulatory protein BlaR1 [111289]
                 1. Staphylococcus aureus [TaxId: 1280] [111290] (3)
                    SQ P18357 338-582 ! SQ P18357 334-581 ! SQ P18357 338-583
             13. D,D-carboxypeptidase DacA, N-terminal domain [118181]
                 1. Streptococcus pneumoniae [TaxId: 1313] [118182] (1)
                    SQ P72518 25-393
             14. Penicillin-binding protein 1a, transpeptidase domain [144034]
                 1. Streptococcus pneumoniae [TaxId: 1313] [144035] (2)
                    SQ Q8DR59 266-650! SQ Q8DR59 267-650
             15. Penicillin-binding protein 1b, transpeptidase domain [144036]
                 1. Streptococcus pneumoniae [TaxId: 1313] [144037] (3)
                    SQ O70038 337-789! SQ O70038 337-791
             16. D-Amino acid amidase DaaA [144038]
                 1. Ochrobactrum anthropi [TaxId: 529] [144039] (24)
                    SQ Q9LCC8 2-363
             17. Penicillin-binding protein 2, PBP2 [160970]
                 1. Staphylococcus aureus [TaxId: 1280] [160971] (7)
                    SQ Q2YY56 293-692
             18. 6-aminohexanoate-dimer hydrolase NylC [160972]
                 NylB'
                 1. Flavobacterium sp. [TaxId: 239] [160973] (3)
                    SQ P07062 5-392
          2. Glutaminase [90084] (2)
             Pfam 04960
             1. Probable glutaminase YbgJ [90085]
                1. Bacillus subtilis [TaxId: 1423] [90086] (5)
             2. Probable glutaminase YbaS [111291]
                1. Escherichia coli [TaxId: 562] [111292] (1)
                   SQ P77454
          3. Dac-like [144040] (3)
             Pfam 02113; D-Ala-D-Ala carboxypeptidase 3 (S13) family; contains a large insertion comprising two subdomains: (d1) aplha+beta with topological similarity to one subunit of the DTD-like family (scop_fa 69501) and (d2) six-stranded beta-sandwich with a crossed-loop topology
             1. Penicillin-binding protein DacC [144041]
                1. Bacillus subtilis [TaxId: 1423] [144042] (3)
                   SQ P39844 34-491
             2. D-alanyl-D-alanine carboxypeptidase Dac [144043]
                1. Actinomadura sp. [TaxId: 1989] [144044] (12)
                   SQ P39045 50-516
             3. DD-carboxypeptidase DacB [144045]
                Penicillin-binding protein 4
                1. Escherichia coli [TaxId: 562] [144046] (6)
                   SQ P24228 22-477
   41. Upper collar protein gp10 (connector protein) [56825] (1)
       2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
       1. Upper collar protein gp10 (connector protein) [56826] (1)
          uperfamily
          1. Upper collar protein gp10 (connector protein) [56827] (1)
             1. Upper collar protein gp10 (connector protein) [56828]
                1. Bacteriophage phi-29 [TaxId: 10756] [56829] (4)
   42. AF1531-like [160974] (1)
       2 domains; d1: incomplete barrel similar to the OB-fold domain of ribosomal L2 protein, d2: six helices, array
       1. AF1531-like [160975] (1)
          1. AF1531-like [160976] (1)
             Pfam 04919; DUF655
             1. Hypothetical protein AF1531 [160977]
                1. Archaeoglobus fulgidus [TaxId: 2234] [160978] (1)
                   SQ O28741 16-195
   43. Phase 1 flagellin [64517] (1)
       3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
       1. Phase 1 flagellin [64518] (1)
          uperfamily
          1. Phase 1 flagellin [64519] (1)
             1. Phase 1 flagellin [64520]
                1. Salmonella typhimurium [TaxId: 90371] [64521] (2)
   44. 39 kda initiator binding protein, IBP39, C-terminal domains [103408] (1)
       2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha+beta, Frataxin-like
       1. 39 kda initiator binding protein, IBP39, C-terminal domains [103409] (1)
          uperfamily
          1. 39 kda initiator binding protein, IBP39, C-terminal domains [103410] (1)
             1. 39 kda initiator binding protein, IBP39, C-terminal domains [103411]
                1. Trichomonas vaginalis [TaxId: 5722] [103412] (3)
   45. AF1104-like [111320] (1)
       2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
       1. AF1104-like [111321] (1)
          uperfamily
          1. AF1104-like [111322] (3)
             Pfam 01937
             1. Hypothetical protein At2g17340 [111323]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111324] (2)
                   SQ Q949P3; d1: 36-117; d2: 118-365
             2. Hypothetical protein AF1104 [144047]
                1. Archaeoglobus fulgidus [TaxId: 2234] [144048] (2)
                   SQ O29161 7-288
             3. Hypothetical protein PH1575 [144049]
                1. Pyrococcus horikoshii [TaxId: 53953] [144050] (2)
                   SQ O59272 1-284
   46. SSO1389-like [160979] (1)
       2 domains; d1: [alpha/beta, central parallel beta-sheet of 6 strands, order 321456, Rossmann-like]; d2: [alpha+beta, cluster of helices and a small 4-stranded beta-sheet]
       1. SSO1389-like [160980] (1)
          1. Cas_DxTHG [160981] (1)
             Pfam 09455; CRISPR-associated DxTHG family
             1. Hypothetical protein SSO1389 [160982]
                1. Sulfolobus solfataricus [TaxId: 2287] [160983] (2)
                   SQ Q97YD5 1-377
   47. Urocanase [111325] (1)
       3 domains; d1: alpha+beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta of the NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar to scop_fa 51883 and scop_fa 51736); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheet
       1. Urocanase [111326] (1)
          uperfamily
          1. Urocanase [111327] (2)
             Pfam 01175
             1. Urocanate hydratase HutU [111328]
                1. Pseudomonas putida [TaxId: 303] [111329] (3)
                   SQ P25080; d1:4-138; d2:135-350; d3: 351-557
                2. Bacillus stearothermophilus [TaxId: 1422] [118200] (1)
                   SQ Q5L084 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
   48. NAD kinase/diacylglycerol kinase-like [111330] (1)
       2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (scop_sf 53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats of beta(3) unit]
       1. NAD kinase/diacylglycerol kinase-like [111331] (2)
          uperfamily
          1. NAD kinase-like [111332] (2)
             Pfam 01513
             1. Inorganic polyphosphate/ATP-NAD kinase PpnK [111333]
                1. Archaeoglobus fulgidus [TaxId: 2234] [111334] (11)
                   SQ O30297; d1:1-96; d2:101-227
                2. Mycobacterium tuberculosis [TaxId: 1773] [111335] (4)
                   SQ O33196; d1:5-132; d2:140-275
          2. Diacylglycerol kinase-like [160984] (3)
             N-terminal, catalytic domain is covered by Pfam 00781
             1. Lipid kinase YegS [160985]
                1. Salmonella typhimurium [TaxId: 90371] [160986] (4)
                   SQ Q8ZNP1 1-299
                2. Escherichia coli [TaxId: 562] [160987] (3)
                   SQ P76407 4-299! SQ P76407 5-299
             2. Diacylglycerol kinase DgkB [160988]
                1. Staphylococcus aureus [TaxId: 1280] [160989] (2)
                   SQ Q6GFF9 1-312
   49. QueA-like [111336] (1)
       2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474)
       1. QueA-like [111337] (1)
          uperfamily
          1. QueA-like [111338] (2)
             Pfam 02547
             1. Queuosine biosynthesis protein queA [111339]
                1. Thermotoga maritima [TaxId: 2336] [111340] (1)
                   SQ Q9WZ44
                2. Thermus thermophilus [TaxId: 274] [118201] (1)
                   SQ Q5SMH0
   50. CbiD-like [111341] (1)
       2 domains; (1) alpha+beta (res 1-192), a circularly permuted rS5 domain 2-like fold (scop_cf 54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order 2134
       1. CbiD-like [111342] (1)
          uperfamily
          1. CbiD-like [111343] (1)
             Pfam 01888
             1. Cobalamin biosynthesis protein CbiD [111344]
                1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111345] (1)
                   SQ O29535
   51. Rap/Ran-GAP [111346] (1)
       consists of two domains; d1: alpha+beta (78-190; alpha-beta(4)-alpha-beta-alpha; 3 layers; antiparallel beta-sheet of 5 strands; order 51234); d2: alpha/beta similar to the G-domain fold (191-381; scop_fa 52592)
       1. Rap/Ran-GAP [111347] (1)
          uperfamily
          1. Rap/Ran-GAP [111348] (1)
             Pfam 02145
             1. Rap1 GTPase-activating protein 1, Rap1GAP [111349]
                1. Human (Homo sapiens) [TaxId: 9606] [111350] (1)
                   SQ P47736
   52. Vacuolar ATP synthase subunit C [118202] (1)
       2 alpha+beta (sub)domains [each has a ferredoxin-like fold; scop_cf 54861], connected with 3-helical bundle; duplication: two repeats of beta-alpha-beta-[alpha coiled-coil]-beta-alpha-beta motif
       1. Vacuolar ATP synthase subunit C [118203] (1)
          uperfamily
          1. Vacuolar ATP synthase subunit C [118204] (1)
             Pfam 03223
             1. Vacuolar ATP synthase subunit C [118205]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118206] (1)
                   SQ P31412
   53. Thermophilic metalloprotease-like [144051] (1)
       consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices
       1. Thermophilic metalloprotease-like [144052] (1)
          uperfamily
          1. Thermophilic metalloprotease (M29) [144053] (2)
             Pfam 02073
             1. Aminopeptidase T [144054]
                1. Thermus thermophilus [TaxId: 274] [144055] (5)
                   SQ P42778 3-408
             2. Aminopeptidase S, AMPS [144056]
                1. Staphylococcus aureus [TaxId: 1280] [144057] (1)
                   SQ Q8NVU1 3-415
   54. ImpE-like [144058] (1)
       consists of two domains; d1: right-handed superhelix of five helices; d2: pseudo beta-barrel containing structurally similar part to the "Histone-like" proteins from archaea (scop_fa 54161)
       1. ImpE-like [144059] (1)
          uperfamily
          1. ImpE-like [144060] (1)
             Pfam 07024
             1. Hypothetical protein VPA1032 [144061]
                1. Vibrio parahaemolyticus [TaxId: 670] [144062] (1)
                   SQ Q87HD3 2-265
   55. CV3147-like [160990] (1)
       2 domains; d1: [alpha/beta; 3 layers, a/b/a, mixed beta-sheet of 8 strands, order 12543876, strands 1, 7 and 8 are antiparallel to the rest]; d2: [pseudo beta-barrel of 6 strands, meander]
       1. CV3147-like [160991] (1)
          1. CV3147-like [160992] (1)
             Pfam 06032; DUF917
             1. Hypothetical protein CV3147 [160993]
                1. Chromobacterium violaceum [TaxId: 536] [160994] (2)
                   SQ Q7NTB2 2-390
   56. Heme iron utilization protein-like [144063] (1)
       2 domains; d1 - 3-helical bundle similar to the homeodomain-like fold; d2 - 6-stranded beta-barrel capped by two helices at one end, similar topology to the PH-like fold
       1. Heme iron utilization protein-like [144064] (2)
          uperfamily
          1. HemS/ChuS-like [144065] (2)
             Pfam 05171; Haemin-degrading proteins; duplication: consists of thandem repeat of this fold joined at the 'free' ends of their PH-like barrels
             1. Hemin transport protein HemS [144066]
                1. Yersinia enterocolitica [TaxId: 630] [144067] (2)
                   SQ P31517 3-341! SQ P31517 4-341
             2. Heme oxygenase ChuS [144068]
                1. Escherichia coli O157:H7 [TaxId: 83334] [144069] (2)
                   SQ Q8X5N8 1-337
          2. ChuX-like [144070] (1)
             Pfam 06228; DUF1008; single-domain subunits form a dimer similar to the HemS/ChuS subunits
             1. Hypothetical protein AGR_C_4470p [144071]
                1. Agrobacterium tumefaciens [TaxId: 358] [144072] (1)
                   SQ Q7CX01 11-186
   57. HI0933 insert domain-like [160995] (1)
       2 domains; d1: barrel, closed, n=6, S=12, greek-key; d2: four-helical bundle, inserted in d1
       1. HI0933 insert domain-like [160996] (1)
          1. HI0933 insert domain-like [160997] (2)
             C-terminal part of Pfam 03486
             1. Hypothetical protein HI0933 [160998]
                1. Haemophilus influenzae [TaxId: 727] [160999] (1)
                   SQ P44941 195-342
             2. Flavoprotein BC4706 [161000]
                1. Bacillus cereus [TaxId: 1396] [161001] (1)
                   SQ Q816V9 193-361
   58. NSP3 homodimer [69902] (1)
       2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
       1. NSP3 homodimer [69903] (1)
          uperfamily
          1. NSP3 homodimer [69904] (1)
             1. NSP3 homodimer [69905]
                non-structural RNA-binding protein
                1. Simian 11 rotavirus [TaxId: 10923] [69906] (1)
   59. E2F-DP heterodimerization region [144073] (1)
       heterodimeric fold with the N-terminal long helices of both chains forming a parallel coiled coil and their C-terminal folded beta-hairpins interlocking together in a beta-sandwich
       1. E2F-DP heterodimerization region [144074] (2)
          uperfamily
          1. DP dimerization segment [144075] (1)
             Pfam 08781
             1. Transcription factor DP-1 [144076]
                1. Human (Homo sapiens) [TaxId: 9606] [144077] (1)
                   SQ Q14186 199-346
          2. E2F dimerization segment [144078] (1)
             PfamB 001971
             1. Transcription factor E2F1 [144079]
                1. Human (Homo sapiens) [TaxId: 9606] [144080] (1)
                   SQ Q01094 201-301
   60. Membrane penetration protein mu1 [69907] (1)
       4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
       1. Membrane penetration protein mu1 [69908] (1)
          uperfamily
          1. Membrane penetration protein mu1 [69909] (1)
             1. Membrane penetration protein mu1 [69910]
                1. Reovirus [TaxId: 10891] [69911] (1)
   61. Flu NP-like [161002] (1)
       consists of alpha+beta and all-alpha domains; biological unit is a trimer
       1. flu NP-like [161003] (1)
          1. Flu NP-like [161004] (1)
             Pfam 00506; Influenza virus nucleoprotein
             1. Nucleocapsid protein [161005]
                1. Influenza A virus [TaxId: 11320] [161006] (3)
                   SQ Q1I2B5 21-489
   62. Viral glycoprotein ectodomain-like [161007] (1)
       complex fold; contains three rigid, mostly-beta domains and an alpha-helical region, acting as a conformatiomal switch ("fusion stalk")
       1. Viral glycoprotein ectodomain-like [161008] (2)
          1. Glycoprotein B-like [161009] (1)
             Pfam 00606; Herpesvirus Glycoprotein B
             1. Glycoprotein B [161010]
                1. Human herpesvirus 1 [TaxId: 10298] [161011] (3)
                   SQ P06437 111-725
          2. Spike glycoprotein-like [161012] (1)
             Pfam 00974; Rhabdovirus spike glycoprotein
             1. Spike glycoprotein [161013]
                1. Vesicular stomatitis indiana virus [TaxId: 11277] [161014] (4)
                   SQ P04883 17-425
                   representative prefusion form 2CMZ; representative acidic conformation 2J6J
   63. Reovirus inner layer core protein p3 [56830] (1)
       large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
       1. Reovirus inner layer core protein p3 [56831] (2)
          uperfamily
          1. Orbivirus core [56832] (1)
             1. BTV vp3 [56833]
                1. Bluetongue virus, strain 1 [TaxId: 40051] [56834] (1)
          2. Phytoreovirus core [103413] (1)
             1. RDV p3 [103414]
                1. Rice dwarf virus [TaxId: 10991] [103415] (1)
   64. L-A virus major coat protein [82855] (1)
       large protein without apparent domain division
       1. L-A virus major coat protein [82856] (1)
          uperfamily
          1. L-A virus major coat protein [82857] (1)
             1. L-A virus major coat protein [82858]
                1. Saccharomyces cerevisiae virus L-A [TaxId: 11008] [82859] (1)
   65. Major capsid protein VP5 [103416] (1)
       large protein without apparent domain division
       1. Major capsid protein VP5 [103417] (1)
          uperfamily
          1. Major capsid protein VP5 [103418] (1)
             1. Major capsid protein VP5 [103419]
                1. Herpes simplex virus 1 [TaxId: 10298] [103420] (1)
   66. Viral ssDNA binding protein [118207] (1)
       2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array]
       1. Viral ssDNA binding protein [118208] (1)
          uperfamily
          1. Viral ssDNA binding protein [118209] (1)
             Pfam 00747
             1. Infected cell protein 8, ICP8 [118210]
                1. Herpes simplex virus 1 [TaxId: 10298] [118211] (1)
                   SQ P04296 9-1130 # d1: 9-1038; d2: 1048-1130
6. Membrane and cell surface proteins and peptides [56835] (58)
   Does not include proteins in the immune system
   1. Toxins' membrane translocation domains [56836] (5)
      multi-helical domains of various folds which is thought to unfold in the membrane
      1. Colicin [56837] (1)
         uperfamily
         1. Colicin [56838] (4)
            contains "globin-like fold" with additional N-terminal and C-terminal helices
            1. Colicin A [56839]
               1. Escherichia coli [TaxId: 562] [56840] (1)
            2. Colicin B C-terminal domain [103421]
               1. Escherichia coli [TaxId: 562] [103422] (1)
            3. Colicin N [56841]
               contains an additional N-terminal a+b domain with six-stranded meander b-sheet
               1. Escherichia coli [TaxId: 562] [56842] (1)
            4. Colicin Ia [56843]
               the first ~450 residues are organized in coiled-coil structures
               1. Escherichia coli [TaxId: 562] [56844] (1)
      2. Diphtheria toxin, middle domain [56845] (1)
         uperfamily
         1. Diphtheria toxin, middle domain [56846] (1)
            1. Diphtheria toxin, middle domain [56847]
               contains globin-like fold with two additional helices at N-termini but has no counterpart to the first globin helix (A)
               1. Corynebacterium diphtheriae [TaxId: 1717] [56848] (6)
      3. delta-Endotoxin (insectocide), N-terminal domain [56849] (1)
         uperfamily
         1. delta-Endotoxin (insectocide), N-terminal domain [56850] (4)
            seven-helical bundle with central helix surrounded by six others
            1. delta-Endotoxin (insectocide), N-terminal domain [56851]
               1. Bacillus thuringiensis tenebrionis, CRYIIIA (BT13) [TaxId: 1444] [56852] (1)
               2. Bacillus thuringiensis, CRY3bb1 [TaxId: 1428] [64522] (1)
               3. Bacillus thuringiensis, CRYIA (A) [TaxId: 1428] [56853] (1)
               4. Bacillus thuringiensis subsp. kurstaki, CRY2AA [TaxId: 29339] [64523] (1)
      4. Bcl-2 inhibitors of programmed cell death [56854] (1)
         PROVISIONAL CLASSIFICATION, based on structural similarity to the diphtheria toxin domain
         uperfamily
         1. Bcl-2 inhibitors of programmed cell death [56855] (13)
            Pfam 00452
            1. Bcl-2 [64524]
               1. Human (Homo sapiens) [TaxId: 9606] [64525] (5)
            2. Apoptosis regulator Bcl-xL [56856]
               1. Human (Homo sapiens) [TaxId: 9606] [56857] (15)
               2. Mouse (Mus musculus) [TaxId: 10090] [103423] (3)
               3. Rat (Rattus norvegicus) [TaxId: 10116] [56858] (1)
            3. Apoptosis regulator Bcl-w [90103]
               1. Human (Homo sapiens) [TaxId: 9606] [90104] (3)
            4. Proapoptotic molecule Bid [56859]
               1. Human (Homo sapiens) [TaxId: 9606] [56860] (1)
               2. Mouse (Mus musculus) [TaxId: 10090] [56861] (1)
            5. Proapoptotic molecule Bax [56862]
               1. Human (Homo sapiens) [TaxId: 9606] [56863] (2)
            6. Bcl-2 homolog [75637]
               1. Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] [75638] (1)
            7. Apoptosis regulator ced-9 [103424]
               1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [103425] (3)
                  SQ P41958 74-237
            8. Early antigen protein R [103426]
               1. Epstein-Barr virus [TaxId: 10376] [103427] (1)
            9. EAT/MCL-1 (Myeloid cell leukemia sequence 1) [118212]
               1. Mouse (Mus musculus) [TaxId: 10090] [118213] (4)
                  SQ P97287 152-308
            10. Bcl-2 homolog V-bcl-2 [144081]
                1. Murid herpesvirus 4 [TaxId: 33708] [144082] (5)
                   SQ P89884 6-136
      5. Exotoxin A, middle domain [56864] (1)
         uperfamily
         1. Exotoxin A, middle domain [56865] (1)
            1. Exotoxin A, middle domain [56866]
               six-helical domain
               1. Pseudomonas aeruginosa [TaxId: 287] [56867] (2)
   2. Family A G protein-coupled receptor-like [81322] (1)
      core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane
      1. Family A G protein-coupled receptor-like [81321] (2)
         uperfamily
         1. Bacteriorhodopsin-like [81319] (6)
            1. Bacteriorhodopsin [56871]
               a light-driven proton pump
               1. Archaeon Halobacterium halobium [TaxId: 2242] [56872] (3)
               2. Archaeon Halobacterium salinarum [TaxId: 2242] [56873] (60)
                  SQ P02945 17-245
            2. Archaerhodopsin-1 [90105]
               1. Archaeon Halobacterium sp. [TaxId: 2243] [90106] (1)
            3. Halorhodopsin [56874]
               a light-driven chloride pump
               1. Archaeon Halobacterium salinarum [TaxId: 2242] [56875] (1)
            4. Sensory rhodopsin II [64526]
               1. Archaeon Natronobacterium pharaonis [TaxId: 2257] [64527] (7)
            5. Sensory rhodopsin [118224]
               1. Anabaena sp. PCC 7120 [TaxId: 103690] [118225] (1)
                  SQ Q8YSC4 # alr3165
         2. Rhodopsin-like [81320] (1)
            Individual TM segments have a number of kinks and distortions
            1. Rhodopsin [56876]
               1. Cow (Bos taurus) [TaxId: 9913] [56877] (12)
                  SQ P02699
   3. Single transmembrane helix [81407] (38)
      not a true fold
      1. Photosystem II reaction centre subunit H, transmembrane region [81490] (1)
         uperfamily
         1. Photosystem II reaction centre subunit H, transmembrane region [81489] (3)
            1. Photosystem II reaction centre subunit H, transmembrane region [81488]
               1. Rhodopseudomonas viridis [TaxId: 1079] [81485] (11)
                  synonym: blastochloris viridis
               2. Rhodobacter sphaeroides [TaxId: 1063] [81486] (39)
                  SQ P11846
               3. Thermochromatium tepidum [TaxId: 1050] [81487] (1)
      2. Mitochondrial cytochrome c oxidase subunit IV [81406] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit IV [81405] (1)
            1. Mitochondrial cytochrome c oxidase subunit IV [81404]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81403] (21)
      3. Mitochondrial cytochrome c oxidase subunit VIa [81411] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIa [81410] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIa [81409]
               probably responsible for the dimerization of the mitochondrial cytochrome c oxidase
               1. Cow (Bos taurus) [TaxId: 9913] [81408] (21)
      4. Mitochondrial cytochrome c oxidase subunit VIc [81415] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIc [81414] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIc [81413]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81412] (21)
      5. Mitochondrial cytochrome c oxidase subunit VIIa [81419] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIIa [81418] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIIa [81417]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81416] (21)
      6. Mitochondrial cytochrome c oxidase subunit VIIb [81423] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIIb [81422] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIIb [81421]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81420] (21)
      7. Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) [81427] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) [81426] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) [81425]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81424] (21)
      8. Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) [81431] (1)
         uperfamily
         1. Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) [81430] (1)
            1. Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) [81429]
               function unknown, probably acts as a regulator or is required for the assembly
               1. Cow (Bos taurus) [TaxId: 9913] [81428] (21)
      9. Bacterial aa3 type cytochrome c oxidase subunit IV [81469] (1)
         uperfamily
         1. Bacterial aa3 type cytochrome c oxidase subunit IV [81468] (2)
            1. Bacterial aa3 type cytochrome c oxidase subunit IV [81467]
               interacts with subunit I and III, function unknown, non-essential for the enzymatic activity
               1. Paracoccus denitrificans [TaxId: 266] [81465] (1)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81466] (2)
      10. Bacterial ba3 type cytochrome c oxidase subunit IIa [81473] (1)
          uperfamily
          1. Bacterial ba3 type cytochrome c oxidase subunit IIa [81472] (1)
             1. Bacterial ba3 type cytochrome c oxidase subunit IIa [81471]
                functionally important, corresponds to the first helix of the aa3 type subunit II absent in the ba3 type subunit II
                1. Thermus thermophilus [TaxId: 274] [81470] (5)
      11. F1F0 ATP synthase subunit B, membrane domain [81573] (1)
          uperfamily
          1. F1F0 ATP synthase subunit B, membrane domain [81572] (1)
             1. F1F0 ATP synthase subunit B, membrane domain [81571]
                1. Escherichia coli [TaxId: 562] [81570] (1)
      12. Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81496] (1)
          uperfamily
          1. Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81495] (3)
             1. Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81494]
                1. Cow (Bos taurus) [TaxId: 9913] [81491] (19)
                   SQ P00125
                2. Chicken (Gallus gallus) [TaxId: 9031] [81492] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81493] (9)
      13. ISP transmembrane anchor [81502] (1)
          uperfamily
          1. ISP transmembrane anchor [81501] (5)
             1. Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region [81500]
                1. Cow (Bos taurus) [TaxId: 9913] [81497] (13)
                   SQ P13272; precursor of chains I,E and V,R
                2. Chicken (Gallus gallus) [TaxId: 9031] [81498] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81499] (9)
             2. ISP subunit from the cytochrome b6f complex, transmembrane anchor [103428]
                1. Mastigocladus laminosus [TaxId: 83541] [103429] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103430] (1)
      14. Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81508] (1)
          uperfamily
          1. Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81507] (3)
             1. Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81506]
                together with cytochrome b binds to ubiquinone
                1. Cow (Bos taurus) [TaxId: 9913] [81503] (19)
                   SQ P13271 #SP ! SQ P13271
                2. Chicken (Gallus gallus) [TaxId: 9031] [81504] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81505] (9)
      15. Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81514] (1)
          uperfamily
          1. Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81513] (3)
             1. Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81512]
                interacts with cytochrome c1 and ISP
                1. Cow (Bos taurus) [TaxId: 9913] [81509] (18)
                   SQ P00130
                2. Chicken (Gallus gallus) [TaxId: 9031] [81510] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81511] (9)
      16. Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81518] (1)
          uperfamily
          1. Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81517] (1)
             1. Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81516]
                the smallest subunit of the complex, interacts with subunit 10 and ISP, peripherally located
                1. Cow (Bos taurus) [TaxId: 9913] [81515] (15)
                   SQ P07552
      17. Subunit III of photosystem I reaction centre, PsaF [81536] (1)
          uperfamily
          1. Subunit III of photosystem I reaction centre, PsaF [81535] (1)
             1. Subunit III of photosystem I reaction centre, PsaF [81534]
                1. Synechococcus elongatus [TaxId: 32046] [81533] (1)
      18. Subunit VIII of photosystem I reaction centre, PsaI [81540] (1)
          uperfamily
          1. Subunit VIII of photosystem I reaction centre, PsaI [81539] (1)
             1. Subunit VIII of photosystem I reaction centre, PsaI [81538]
                1. Synechococcus elongatus [TaxId: 32046] [81537] (1)
      19. Subunit IX of photosystem I reaction centre, PsaJ [81544] (1)
          uperfamily
          1. Subunit IX of photosystem I reaction centre, PsaJ [81543] (1)
             1. Subunit IX of photosystem I reaction centre, PsaJ [81542]
                1. Synechococcus elongatus [TaxId: 32046] [81541] (1)
      20. Subunit XII of photosystem I reaction centre, PsaM [81548] (1)
          uperfamily
          1. Subunit XII of photosystem I reaction centre, PsaM [81547] (1)
             1. Subunit XII of photosystem I reaction centre, PsaM [81546]
                1. Synechococcus elongatus [TaxId: 32046] [81545] (1)
      21. Subunit PsaX of photosystem I reaction centre [81552] (1)
          uperfamily
          1. Subunit PsaX of photosystem I reaction centre [81551] (1)
             1. Subunit PsaX of photosystem I reaction centre [81550]
                1. Synechococcus elongatus [TaxId: 32046] [81549] (1)
      22. Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor [81597] (1)
          uperfamily
          1. Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor [81596] (1)
             1. Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor [81595]
                1. Escherichia coli [TaxId: 562] [81594] (2)
      23. Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103431] (1)
          uperfamily
          1. Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103432] (2)
             1. Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103433]
                1. Mastigocladus laminosus [TaxId: 83541] [103434] (1)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103435] (1)
      24. PetL subunit of the cytochrome b6f complex [103436] (1)
          uperfamily
          1. PetL subunit of the cytochrome b6f complex [103437] (2)
             1. PetL subunit of the cytochrome b6f complex [103438]
                1. Mastigocladus laminosus [TaxId: 83541] [103439] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103440] (1)
      25. PetM subunit of the cytochrome b6f complex [103441] (1)
          uperfamily
          1. PetM subunit of the cytochrome b6f complex [103442] (2)
             1. PetM subunit of the cytochrome b6f complex [103443]
                1. Mastigocladus laminosus [TaxId: 83541] [103444] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103445] (1)
      26. PetG subunit of the cytochrome b6f complex [103446] (1)
          uperfamily
          1. PetG subunit of the cytochrome b6f complex [103447] (2)
             1. PetG subunit of the cytochrome b6f complex [103448]
                1. Mastigocladus laminosus [TaxId: 83541] [103449] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103450] (1)
      27. PetN subunit of the cytochrome b6f complex [103451] (1)
          uperfamily
          1. PetN subunit of the cytochrome b6f complex [103452] (2)
             1. PetN subunit of the cytochrome b6f complex [103453]
                1. Mastigocladus laminosus [TaxId: 83541] [103454] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103455] (1)
      28. Preprotein translocase SecE subunit [103456] (1)
          uperfamily
          1. Preprotein translocase SecE subunit [103457] (2)
             1. Preprotein translocase SecE subunit [103458]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [103459] (4)
                2. Canis lupus familiaris [TaxId: 9615] [161015] (1)
      29. Sec-beta subunit [103460] (1)
          uperfamily
          1. Sec-beta subunit [103461] (2)
             1. Sec-beta subunit [103462]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [103463] (4)
                2. Canis lupus familiaris [TaxId: 9615] [161016] (1)
      30. Oligosaccharyltransferase subunit ost4p [103464] (1)
          uperfamily
          1. Oligosaccharyltransferase subunit ost4p [103465] (1)
             1. Oligosaccharyltransferase subunit ost4p [103466]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103467] (1)
      31. Photosystem II reaction center protein L, PsbL [161017] (1)
          1. PsbL-like [161018] (1)
             Pfam 02419
             1. Photosystem II reaction center protein L, PsbL [161019]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161020] (1)
                   SQ Q8DIN8 1-37
      32. Photosystem II reaction center protein J, PsbJ [161021] (1)
          1. PsbJ-like [161022] (1)
             Pfam 01788
             1. Photosystem II reaction center protein J, PsbJ [161023]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161024] (1)
                   SQ P59087 7-40
      33. Photosystem II 10 kDa phosphoprotein PsbH [161025] (1)
          1. PsbH-like [161026] (1)
             Pfam 00737
             1. Photosystem II reaction center protein H, PsbH [161027]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161028] (1)
                   SQ Q8DJ43 2-65
      34. Photosystem II reaction center protein T, PsbT [161029] (1)
          1. PsbT-like [161030] (1)
             Pfam 01405
             1. Photosystem II reaction center protein T, PsbT [161031]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161032] (1)
                   SQ Q8DIQ0 1-30
      35. Photosystem II reaction center protein M, PsbM [161033] (1)
          1. PsbM-like [161034] (1)
             Pfam 05151
             1. Photosystem II reaction center protein M, PsbM [161035]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161036] (1)
                   SQ Q8DHA7 1-36
      36. Photosystem II reaction center protein K, PsbK [161037] (1)
          1. PsbK-like [161038] (1)
             Pfam 02533
             1. Photosystem II reaction center protein K, PsbK [161039]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161040] (1)
                   SQ Q9F1K9 10-46
      37. Photosystem II reaction center protein I, PsbI [161041] (1)
          1. PsbI-like [161042] (1)
             Pfam 02532
             1. Photosystem II reaction center protein I, PsbI [161043]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161044] (1)
                   SQ Q8DJZ6 1-35
      38. Cytochrome b559 subunits [161045] (1)
          1. Cytochrome b559 subunits [161046] (2)
             Pfam 00283 comprises PsbF beta subunit (PsbF) and the transmembrane helix of alpha subunit (PsbE) that bind one heme group between them; the lumenal region of the alpha subunit is covered by Pfam 00284
             1. Cytochrome b559 subunit alpha, PsbE [161047]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161048] (1)
                   SQ Q8DIP0 3-84
             2. Cytochrome b559 subunit beta, PsbF [161049]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161050] (1)
                   SQ Q8DIN9 11-45
   4. Bacterial photosystem II reaction centre, L and M subunits [81484] (1)
      five transmembrane helices forming a sheet-like structure
      1. Bacterial photosystem II reaction centre, L and M subunits [81483] (1)
         uperfamily
         1. Bacterial photosystem II reaction centre, L and M subunits [81482] (8)
            L and M are probably related to each other
            1. L (light) subunit [81477]
               1. Rhodopseudomonas viridis [TaxId: 1079] [81474] (11)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81475] (67)
                  SQ P02954
               3. Thermochromatium tepidum [TaxId: 1050] [81476] (1)
            2. M (medium) subunit [81481]
               1. Rhodopseudomonas viridis [TaxId: 1079] [81478] (11)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81479] (65)
                  SQ P02953
               3. Thermochromatium tepidum [TaxId: 1050] [81480] (1)
            3. Photosystem II reaction center d2 protein PsbD2 [161051]
               1. Thermosynechococcus elongatus [TaxId: 146786] [161052] (1)
                  SQ Q8CM25 13-352
            4. Photosystem Q(B) protein 1, PsbA1 [161053]
               1. Thermosynechococcus elongatus [TaxId: 146786] [161054] (1)
                  SQ P0A445 10-344
   5. Cytochrome c oxidase subunit I-like [81443] (1)
      12 transmembrane helices in an approximate threefold rotational symmetric arrangement
      1. Cytochrome c oxidase subunit I-like [81442] (1)
         uperfamily
         1. Cytochrome c oxidase subunit I-like [81441] (5)
            the largest and best conserved subunit, contains two heme groups, low spin heme a and high spin heme a3
            1. Mitochondrial cytochrome c oxidase, subunit I [81433]
               1. Cow (Bos taurus) [TaxId: 9913] [81432] (21)
            2. Bacterial aa3 type cytochrome c oxidase subunit I [81436]
               1. Paracoccus denitrificans [TaxId: 266] [81434] (2)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81435] (6)
            3. Bacterial ba3 type cytochrome c oxidase subunit I [81438]
               1. Thermus thermophilus [TaxId: 274] [81437] (2)
            4. Cytochrome O ubiquinol oxidase, subunit I [81440]
               1. Escherichia coli [TaxId: 562] [81439] (1)
   6. Cytochrome c oxidase subunit III-like [81453] (1)
      core: 7 transmembrane helices organized into two bundles, one formed by the first two helices and the other by the rest
      1. Cytochrome c oxidase subunit III-like [81452] (1)
         uperfamily
         1. Cytochrome c oxidase subunit III-like [81451] (4)
            function unknown, possibly involved in the assembly or form the entrance to "oxygen" channel
            1. Mitochondrial cytochrome c oxidase, subunit III [81445]
               1. Cow (Bos taurus) [TaxId: 9913] [81444] (21)
            2. Bacterial aa3 type cytochrome c oxidase subunit III [81448]
               1. Paracoccus denitrificans [TaxId: 266] [81446] (1)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81447] (2)
            3. Cytochrome O ubiquinol oxidase, subunit III [81450]
               1. Escherichia coli [TaxId: 562] [81449] (1)
   7. Transmembrane helix hairpin [81334] (5)
      two antiparallel transmembrane helices
      1. Cytochrome c oxidase subunit II-like, transmembrane region [81464] (1)
         uperfamily
         1. Cytochrome c oxidase subunit II-like, transmembrane region [81463] (5)
            1. Mitochondrial cytochrome c oxidase, subunit II [81455]
               1. Cow (Bos taurus) [TaxId: 9913] [81454] (21)
            2. Bacterial aa3 type cytochrome c oxidase subunit II [81458]
               1. Paracoccus denitrificans [TaxId: 266] [81456] (3)
               2. Rhodobacter sphaeroides [TaxId: 1063] [81457] (6)
            3. Bacterial ba3 type cytochrome c oxidase subunit II [81460]
               1. Thermus thermophilus [TaxId: 274] [81459] (5)
                  the "missing" first helix is complemented by the ba3 subunit IIa
            4. Cytochrome O ubiquinol oxidase, subunit II [81462]
               1. Escherichia coli [TaxId: 562] [81461] (1)
      2. F1F0 ATP synthase subunit C [81333] (1)
         uperfamily
         1. F1F0 ATP synthase subunit C [81332] (1)
            1. F1F0 ATP synthase subunit C [56891]
               1. Escherichia coli [TaxId: 562] [56892] (6)
      3. Magnesium transport protein CorA, transmembrane region [144083] (1)
         forms homopentameric channel
         uperfamily
         1. Magnesium transport protein CorA, transmembrane region [144084] (1)
            C-terminal part of Pfam 01544
            1. Magnesium transport protein CorA [144085]
               1. Thermotoga maritima [TaxId: 2336] [144086] (20)
                  SQ Q9WZ31 286-349
      4. Htr2 transmembrane domain-like [158212] (1)
         1. Htr2 transmembrane domain-like [158213] (1)
            1. Sensory rhodopsin II transducer, Htr2 [158214]
               1. Natronomonas pharaonis [TaxId: 2257] [158215] (3)
                  SQ P42259 27-79! SQ P42259 29-79
      5. PsbZ-like [161055] (1)
         1. PsbZ-like [161056] (1)
            Pfam 01737; Ycf9
            1. Photosystem II reaction center protein Z, PsbZ [161057]
               1. Thermosynechococcus elongatus [TaxId: 146786] [161058] (1)
                  SQ Q8DHJ2 1-62
   8. F1F0 ATP synthase subunit A [81337] (1)
      core: up-and-down bundle of four transmembrane helices
      1. F1F0 ATP synthase subunit A [81336] (1)
         uperfamily
         1. F1F0 ATP synthase subunit A [81335] (1)
            1. F1F0 ATP synthase subunit A [56893]
               1. Escherichia coli [TaxId: 562] [56894] (1)
   9. ATP synthase B chain-like [161059] (1)
      long single helix, part of the stator subcomplex
      1. ATP synthase B chain-like [161060] (1)
         1. ATP synthase B chain-like [161061] (1)
            Pfam 05405
            1. ATP synthase subunit b, mitochondrial [161062]
               1. Cow (Bos taurus) [TaxId: 9913] [161063] (2)
                  SQ P13619 121-225
   10. ATP synthase D chain-like [161064] (1)
       non-globular, mostly helical component of the stator subcomplex
       1. ATP synthase D chain-like [161065] (1)
          1. ATP synthase D chain-like [161066] (1)
             Pfam 05873
             1. ATP synthase subunit d, mitochondrial [161067]
                1. Cow (Bos taurus) [TaxId: 9913] [161068] (2)
                   SQ P13620 4-123
   11. Aquaporin-like [81339] (1)
       core: 8 helices, 2 short helices are surrounded by 6 long transmembrane helices
       1. Aquaporin-like [81338] (1)
          uperfamily
          1. Aquaporin-like [56895] (6)
             duplication: consist of two similar structural parts
             1. Aquaporin-1 [56896]
                1. Human (Homo sapiens) [TaxId: 9606] [56897] (3)
                2. Cow (Bos taurus) [TaxId: 9913] [75642] (1)
             2. Aquaporin-0 [103468]
                1. Sheep (Ovis aries) [TaxId: 9940] [103469] (2)
                2. Cow (Bos taurus) [TaxId: 9913] [118226] (3)
                   SQ P06624
             3. Aquaporin Z [103470]
                1. Escherichia coli [TaxId: 562] [103471] (9)
             4. Glycerol uptake facilitator protein GlpF [56898]
                glycerol conducting channel, related to aquaporin
                1. Escherichia coli [TaxId: 562] [56899] (4)
   12. Ammonium transporter [111351] (1)
       11 transmembrane helices; duplication: consist of 2 structural repeats of five helices each plus extra C-terminal helix
       1. Ammonium transporter [111352] (1)
          uperfamily
          1. Ammonium transporter [111353] (1)
             Pfam 00909
             1. Ammonium transporter AmtB [111354]
                1. Escherichia coli [TaxId: 562] [111355] (15)
                   SQ P37905 2-407
   13. MFS general substrate transporter [103472] (1)
       12 transmembrane helices; duplication: the N- and C-terminal halves are structurally similar
       1. MFS general substrate transporter [103473] (2)
          uperfamily
          1. Glycerol-3-phosphate transporter [103474] (1)
             1. Glycerol-3-phosphate transporter [103475]
                1. Escherichia coli [TaxId: 562] [103476] (1)
          2. LacY-like proton/sugar symporter [103477] (1)
             1. Lactose permease [103478]
                1. Escherichia coli [TaxId: 562] [103479] (4)
   14. SNF-like [161069] (1)
       12 transmembrane helices; duplication: consists of two structurally similar halves
       1. SNF-like [161070] (1)
          1. SNF-like [161071] (1)
             Pfam 00209; Sodium:neurotransmitter symporter
             1. Na(+):neurotransmitter symporter homologue LeuT [161072]
                1. Aquifex aeolicus [TaxId: 63363] [161073] (5)
                   SQ O67854 5-513
   15. Proton glutamate symport protein [118214] (1)
       multihelical membrane protein; partial structural duplication in the C-terminal region; oligomeric state: trimer
       1. Proton glutamate symport protein [118215] (1)
          uperfamily
          1. Proton glutamate symport protein [118216] (1)
             1. Proton glutamate symport protein [118217]
                1. Pyrococcus horikoshii [TaxId: 53953] [118218] (7)
                   SQ O59010 # PH1295
   16. Clc chloride channel [81341] (1)
       core: 18 transmembrane helices
       1. Clc chloride channel [81340] (1)
          uperfamily
          1. Clc chloride channel [69912] (2)
             duplication: consist of two similar structural parts
             1. Clc chloride channel [69913]
                1. Escherichia coli [TaxId: 562] [69914] (32)
                2. Salmonella typhimurium [TaxId: 90371] [69915] (1)
   17. Voltage-gated potassium channels [81325] (1)
       oligomeric transmembrane alpha-helical proteins
       1. Voltage-gated potassium channels [81324] (1)
          uperfamily
          1. Voltage-gated potassium channels [81323] (6)
             1. Potassium channel protein [56901]
                1. Streptomyces coelicolor [TaxId: 1902] [56902] (34)
                   identical sequence to Streptomyces lividans, TaxId: 1916
                   SQ Q54397 22-124
                2. Streptomyces lividans [TaxId: 1916] [161074] (5)
             2. Potassium channel-related protein MthK [75643]
                calcium gated potassium channel
                1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75644] (1)
             3. Potassium channel KVAP [90107]
                1. Archaeon Aeropyrum pernix [TaxId: 56636] [90108] (4)
             4. Inward rectifier potassium channel Kirbac1.1 [90109]
                1. Burkholderia pseudomallei [TaxId: 28450] [90110] (1)
             5. Inward rectifier potassium channel kirbac3.1 [118227]
                1. Magnetospirillum magnetotacticum [TaxId: 188] [118228] (2)
                   SQ Q8YY97 # 46% sequence identity; Anabaena sp. PCC 7120 TaxID: 103690
   18. Small-conductance potassium channel [81328] (1)
       oligomeric transmembrane alpha-helical protein
       1. Small-conductance potassium channel [81327] (1)
          uperfamily
          1. Small-conductance potassium channel [81326] (1)
             1. Small-conductance potassium channel [64528]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [64529] (2)
   19. Gated mechanosensitive channel [81331] (1)
       oligomeric transmembrane alpha-helical protein
       1. Gated mechanosensitive channel [81330] (1)
          uperfamily
          1. Gated mechanosensitive channel [81329] (1)
             1. Gated mechanosensitive channel [56904]
                Large-conductance ion channel
                1. Mycobacterium tuberculosis [TaxId: 1773] [56905] (5)
   20. Neurotransmitter-gated ion-channel transmembrane pore [90111] (1)
       heteropentameric transmembrane alpha-helical protein; 4 transmembrane helices per subunit
       1. Neurotransmitter-gated ion-channel transmembrane pore [90112] (1)
          uperfamily
          1. Neurotransmitter-gated ion-channel transmembrane pore [90113] (4)
             1. Acetylcholine receptor protein, alpha chain [90114]
                1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [90115] (1)
             2. Acetylcholine receptor protein, beta chain [90116]
                1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [90117] (1)
             3. Acetylcholine receptor protein, delta chain [90118]
                1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [90119] (1)
             4. Acetylcholine receptor protein, gamma chain [90120]
                1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [90121] (1)
   21. Mechanosensitive channel protein MscS (YggB), transmembrane region [82860] (1)
       oligomeric fold; 3 transmembrane helices per subunit
       1. Mechanosensitive channel protein MscS (YggB), transmembrane region [82861] (1)
          uperfamily
          1. Mechanosensitive channel protein MscS (YggB), transmembrane region [82862] (1)
             1. Mechanosensitive channel protein MscS (YggB), transmembrane region [82863]
                homoheptameric protein
                1. Escherichia coli [TaxId: 562] [82864] (14)
   22. Multidrug resistance efflux transporter EmrE [103480] (1)
       oligomeric fold; 3 transmembrane helices per subunit
       1. Multidrug resistance efflux transporter EmrE [103481] (1)
          uperfamily
          1. Multidrug resistance efflux transporter EmrE [103482] (1)
             1. Multidrug resistance efflux transporter EmrE [103483]
                1. Escherichia coli [TaxId: 562] [103484] (1)
   23. V-type ATP synthase subunit C [103485] (1)
       9 transmembrane helices
       1. V-type ATP synthase subunit C [103486] (1)
          duplication: consists of three similar structural parts
          uperfamily
          1. V-type ATP synthase subunit C [103487] (1)
             1. V-type ATP synthase subunit C [103488]
                1. Thermus thermophilus [TaxId: 274] [103489] (2)
   24. Preprotein translocase SecY subunit [103490] (1)
       10 transmembrane helices forming of a gated channel
       1. Preprotein translocase SecY subunit [103491] (1)
          duplication: consists of two similar structural parts
          uperfamily
          1. Preprotein translocase SecY subunit [103492] (1)
             1. Preprotein translocase SecY subunit [103493]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [103494] (2)
   25. Photosystem I subunits PsaA/PsaB [81559] (1)
       core:11 transmembrane helices
       1. Photosystem I subunits PsaA/PsaB [81558] (1)
          uperfamily
          1. Photosystem I subunits PsaA/PsaB [81557] (2)
             Photosystem I p700 chlorophyll a apoprotein a1/a2
             1. Apoprotein a1, PsaA [81554]
                1. Synechococcus elongatus [TaxId: 32046] [81553] (1)
             2. Apoprotein a2, PsaB [81556]
                1. Synechococcus elongatus [TaxId: 32046] [81555] (1)
   26. Photosystem I reaction center subunit X, PsaK [81564] (1)
       core: hairpin of two transmembrane helices
       1. Photosystem I reaction center subunit X, PsaK [81563] (1)
          uperfamily
          1. Photosystem I reaction center subunit X, PsaK [81562] (1)
             1. Photosystem I reaction center subunit X, PsaK [81561]
                1. Synechococcus elongatus [TaxId: 32046] [81560] (1)
   27. Photosystem I reaction center subunit XI, PsaL [81569] (1)
       core: three transmembrane helices, bundle
       1. Photosystem I reaction center subunit XI, PsaL [81568] (1)
          uperfamily
          1. Photosystem I reaction center subunit XI, PsaL [81567] (1)
             1. Photosystem I reaction center subunit XI, PsaL [81566]
                1. Synechococcus elongatus [TaxId: 32046] [81565] (1)
   28. ABC transporter involved in vitamin B12 uptake, BtuC [81346] (1)
       multihelical; complex architecture with several transmembrane helices
       1. ABC transporter involved in vitamin B12 uptake, BtuC [81345] (1)
          uperfamily
          1. ABC transporter involved in vitamin B12 uptake, BtuC [75648] (1)
             1. ABC transporter involved in vitamin B12 uptake, BtuC [75649]
                1. Escherichia coli [TaxId: 562] [75650] (1)
   29. ABC transporter transmembrane region [90122] (1)
       multihelical; complex architecture with several transmembrane helices
       1. ABC transporter transmembrane region [90123] (1)
          uperfamily
          1. ABC transporter transmembrane region [90124] (3)
             1. Multidrug resistance ABC transporter MsbA, N-terminal domain [90125]
                a low-resolution structure of the E.coli MsbA in an open conformation is also available (f.35.1.1)
                1. Vibrio cholerae [TaxId: 666] [90126] (1)
                2. Salmonella typhimurium [TaxId: 90371] [161075] (12)
                   SQ P63359 10-328
             2. Putative multidrug export ATP-binding/permease protein SAV1866 [144087]
                1. Staphylococcus aureus [TaxId: 1280] [144088] (4)
                   SQ Q99T13 1-323
   30. Multidrug efflux transporter AcrB transmembrane domain [82865] (1)
       12 transmembrane helices; duplication: the N- and C-terminal halves of the whole proteins are structurally similar
       1. Multidrug efflux transporter AcrB transmembrane domain [82866] (1)
          uperfamily
          1. Multidrug efflux transporter AcrB transmembrane domain [82867] (1)
             1. Multidrug efflux transporter AcrB transmembrane domain [82868]
                1. Escherichia coli [TaxId: 562] [82869] (6)
   31. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81649] (1)
       core: three transmembrane helices, up-and-down bundle
       1. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81648] (1)
          uperfamily
          1. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81647] (5)
             a part (domain) of mitochondrial cytochrome b subunit, separate subunit in plants and cyanobacteria
             1. Mitochondrial cytochrome b subunit, C-terminal domain [81646]
                1. Cow (Bos taurus) [TaxId: 9913] [81643] (17)
                   SQ P00157
                2. Chicken (Gallus gallus) [TaxId: 9031] [81644] (5)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81645] (9)
             2. Subunit IV of the cytochrome b6f complex [103495]
                1. Mastigocladus laminosus [TaxId: 83541] [103496] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103497] (1)
   32. Heme-binding four-helical bundle [81344] (3)
       core: four transmembrane helices, up-and-down bundle, binds one or two heme groups in between the helices
       1. Transmembrane di-heme cytochromes [81342] (2)
          Three of the four heme-ligands are conserved between the two families; both heme groups bind similarly but not identically
          uperfamily
          1. Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81642] (5)
             a part (domain) of a larger mitochondrial cytochrome b subunit, separate subunit in plants and cyanobacteria
             1. Mitochondrial cytochrome b subunit, N-terminal domain [81641]
                also includes extra transmembrane (linker) helix absent in plants and cyanobacteria subunits
                1. Cow (Bos taurus) [TaxId: 9913] [81638] (17)
                   SQ P00157
                2. Chicken (Gallus gallus) [TaxId: 9031] [81639] (5)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81640] (9)
             2. Cytochrome b6 subunit of the cytochrome b6f complex [103498]
                1. Mastigocladus laminosus [TaxId: 83541] [103499] (6)
                2. Chlamydomonas reinhardtii [TaxId: 3055] [103500] (1)
          2. Formate dehydrogenase N, cytochrome (gamma) subunit [75645] (1)
             1. Formate dehydrogenase N, cytochrome (gamma) subunit [75646]
                1. Escherichia coli [TaxId: 562] [75647] (2)
       2. Respiratory nitrate reductase 1 gamma chain [103501] (1)
          possible link between the two other superfamilies: this subunit corresponds to the gamma subunit of a functionally related Formate dehydrogenase N complex but is structurally closer to the Fumarate reductase subunit FrdC
          uperfamily
          1. Respiratory nitrate reductase 1 gamma chain [103502] (1)
             1. Respiratory nitrate reductase 1 gamma chain [103503]
                1. Escherichia coli [TaxId: 562] [103504] (6)
                   SQ P11350
       3. Fumarate reductase respiratory complex transmembrane subunits [81343] (2)
          two distinct families: in one family the common fold is contained in a single-chain subunit, in the other it is formed by two chains
          uperfamily
          1. Fumarate reductase respiratory complex cytochrome b subunit, FrdC [56910] (1)
             duplication: consists of two structural repeats; the heme-binding sites are related by pseudo two fold symmetry
             1. Fumarate reductase respiratory complex cytochrome b subunit, FrdC [56911]
                1. Wolinella succinogenes [TaxId: 844] [56913] (8)
          2. Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) [81373] (4)
             consists of two homologous non-identical subunits that form a heterodimer; may or may not contain heme groups
             1. Succinate dehydrogenase subunit SdhC [82870]
                Cytochrome b556 subunit
                1. Escherichia coli [TaxId: 562] [82871] (3)
             2. Succinate dehydrogenase subunit SdhD [82872]
                membrane anchor protein
                1. Escherichia coli [TaxId: 562] [82873] (3)
             3. Fumarate reductase subunit FrdC [81370]
                1. Escherichia coli [TaxId: 562] [81369] (7)
                   is not known to bind heme
             4. Fumarate reductase subunit FrdD [81372]
                1. Escherichia coli [TaxId: 562] [81371] (7)
                   is not known to bind heme
   33. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81525] (1)
       membrane-associated alpha-helical protein; no transmembrane helices
       1. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81524] (1)
          location - matrix side of the bc1 complex
          uperfamily
          1. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81523] (3)
             probably important for the complex assembly, caps the matrix face of cytochrome b
             1. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81522]
                1. Cow (Bos taurus) [TaxId: 9913] [81519] (19)
                   SQ P00129
                2. Chicken (Gallus gallus) [TaxId: 9031] [81520] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81521] (9)
   34. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81532] (1)
       membrane-associated alpha-helical protein; no transmembrane helices
       1. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81531] (1)
          location - intermembrane side of the bc1 complex
          uperfamily
          1. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81530] (3)
             "acidic/hinge protein", essential for the complex formation, interacts with the functional domain of cytochrome c1
             1. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81529]
                1. Cow (Bos taurus) [TaxId: 9913] [81526] (19)
                   SQ P00126
                2. Chicken (Gallus gallus) [TaxId: 9031] [81527] (3)
                3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81528] (9)
   35. Mitochondrial ATP synthase coupling factor 6 [111356] (1)
       2 helices, hairpin
       1. Mitochondrial ATP synthase coupling factor 6 [111357] (1)
          uperfamily
          1. Mitochondrial ATP synthase coupling factor 6 [111358] (1)
             Pfam 05511
             1. ATPase subunit F6 [111359]
                1. Cow (Bos taurus) [TaxId: 9913] [111360] (3)
                   SQ P02721 33-108
   36. Calcium ATPase, transmembrane domain M [81666] (1)
       core: multihelical; consists of three transmembrane regions of 2, 2 and 6 helices, separated by cytoplasmic domains
       1. Calcium ATPase, transmembrane domain M [81665] (1)
          uperfamily
          1. Calcium ATPase, transmembrane domain M [81664] (1)
             1. Calcium ATPase, transmembrane domain M [81663]
                the N-terminal 40 residues interact with /form a part of transduction domain A
                1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81662] (17)
                   SQ P04191
   37. Light-harvesting complex subunits [56917] (1)
       membrane all-alpha fold
       1. Light-harvesting complex subunits [56918] (1)
          uperfamily
          1. Light-harvesting complex subunits [56919] (5)
             1. Light-harvesting complex subunits [56920]
                1. Purple bacterium (Rhodoblastus acidophilus) [TaxId: 1074] [56921] (20)
                2. Rhodospirillum molischianum [TaxId: 1083] [56922] (1)
                3. Rhodobacter sphaeroides [TaxId: 1063] [56923] (2)
                4. Rhodoblastus acidophilus [TaxId: 1074] [69916] (1)
                5. Rhodospirillum rubrum [TaxId: 1085] [144089] (1)
                   SQ P02947 1-52
   38. Photosystem II antenna protein-like [161076] (1)
       6 transmembrane helices arranged in three antiparallel pairs (hairpins), segregated by cofactors; there can be insertions of different small subdomains in different exposed loops
       1. Photosystem II antenna protein-like [161077] (1)
          1. Photosystem II antenna protein-like [161078] (2)
             Pfam 00421
             1. Photosystem II core light harvesting protein PsbB [161079]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161080] (1)
                   SQ Q8DIQ1 2-489
             2. Photosystem II CP43 protein PsbC [161081]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161082] (1)
                   SQ Q8DIF8 15-461
   39. Mitochondrial carrier [103505] (1)
       membrane all-alpha fold; 6-helical "barrel" with internal binding cavity
       1. Mitochondrial carrier [103506] (1)
          duplication: consists of three alpha-hairpin repeats
          uperfamily
          1. Mitochondrial carrier [103507] (1)
             1. ADP,ATP carrier protein [103508]
                1. Cow (Bos taurus), heart isoform t1 [TaxId: 9913] [103509] (1)
   40. Chlorophyll a-b binding protein [103510] (1)
       membrane all-alpha fold; three transmembrane helices
       1. Chlorophyll a-b binding protein [103511] (1)
          duplication: contains two structural repeats
          uperfamily
          1. Chlorophyll a-b binding protein [103512] (1)
             1. Chlorophyll a-b binding protein [103513]
                part of chloroplast major light-harvesting complex; see also low-resolution structure of pea protein, PDB entry 1VCR
                1. Spinach (Spinacia oleracea) [TaxId: 3562] [103514] (1)
   41. MAPEG domain-like [161083] (1)
       4 helices, bundle; left-handed superhelix
       1. MAPEG domain-like [161084] (1)
          1. MAPEG domain [161085] (3)
             Pfam 01124
             1. Arachidonate 5-lipoxygenase-activating protein, FLAP [161086]
                1. Human (Homo sapiens) [TaxId: 9606] [161087] (12)
                   SQ P20292 1-139
             2. Microsomal glutathione S-transferase 1 [161088]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [161089] (1)
                   SQ P08011 10-148
             3. Leukotriene C4 synthase [161090]
                1. Human (Homo sapiens) [TaxId: 9606] [161091] (14)
                   SQ Q16873 2-147
   42. MgtE membrane domain-like [161092] (1)
       5 transmembrane helices; bundle, right-handed twist
       1. MgtE membrane domain-like [161093] (1)
          homodimer, swapped with the N-terminal helices
          1. MgtE membrane domain-like [161094] (1)
             Pfam 01769; Divalent cation transporter
             1. Mg2+ transporter MgtE [161095]
                1. Thermus thermophilus [TaxId: 274] [161096] (4)
                   SQ Q5SMG8 276-448
   43. MetI-like [161097] (1)
       core: 5 transmembrane helices; flattened bundle
       1. MetI-like [161098] (1)
          1. MetI-like [161099] (5)
             Pfam 00528; Binding-protein-dependent transport system inner membrane component
             1. Sulfate/molybdate ABC transporter, permease protein [161100]
                1. Methanosarcina acetivorans [TaxId: 2214] [161101] (2)
                   SQ Q8TTZ4 13-260
             2. Molybdate/tungstate transport system permease protein WtpB (ModB) [161102]
                1. Archaeoglobus fulgidus [TaxId: 2234] [161103] (4)
                   SQ O30143 1-252
             3. Maltose transport system permease protein MalG [161104]
                1. Escherichia coli [TaxId: 562] [161105] (1)
                   SQ P68183 7-296
             4. Maltose transport system permease protein MalF [161106]
                1. Escherichia coli [TaxId: 562] [161107] (1)
                   SQ P02916 261-504
             5. D-methionine transport system permease protein MetI [161108]
                Synonym: YaeE
                1. Escherichia coli [TaxId: 562] [161109] (4)
                   SQ P31547 6-208
   44. Rhomboid-like [144090] (1)
       6 transmembrane helices
       1. Rhomboid-like [144091] (1)
          uperfamily
          1. Rhomboid-like [144092] (2)
             Pfam 01694; transmembrane serine protease
             1. GlpG homolog HI0618 [144093]
                1. Haemophilus influenzae [TaxId: 727] [144094] (1)
                   SQ P44783 4-192
             2. GlpG [144095]
                1. Escherichia coli [TaxId: 562] [144096] (7)
                   SQ P09391 91-272
   45. Cation efflux protein transmembrane domain-like [161110] (1)
       6 transmembrane helices, bundle
       1. Cation efflux protein transmembrane domain-like [161111] (1)
          1. Cation efflux protein transmembrane domain-like [161112] (1)
             N-terminal part of Pfam 01545
             1. Ferrous-iron efflux pump FieF [161113]
                1. Escherichia coli [TaxId: 562] [161114] (2)
                   SQ P69380 5-208
   46. Connexin43 [118219] (1)
       mostly unstructured; 2 helices, hairpin
       1. Connexin43 [118220] (1)
          uperfamily
          1. Connexin43 [118221] (1)
             Pfam 03508
             1. Gap junction alpha-1 protein, C-terminal domain [118222]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [118223] (1)
                   SQ P08050 251-381
   47. Transmembrane beta-barrels [56924] (6)
       not a true fold, gathers together transmembrane barrels of different (n,S)
       1. OMPA-like [56925] (4)
          forms (8,10) barrel
          uperfamily
          1. Outer membrane protein [56926] (3)
             1. Outer membrane protein A (OMPA) transmembrane domain [56927]
                1. Escherichia coli [TaxId: 562] [56928] (4)
             2. Outer membrane protein X (OMPX) [56929]
                1. Escherichia coli [TaxId: 562] [56930] (5)
                   SQ P36546
             3. Outer membrane protein NspA [90127]
                1. Neisseria meningitidis [TaxId: 487] [90128] (1)
          2. Outer membrane enzyme PagP [82874] (1)
             1. Outer membrane enzyme PagP [82875]
                1. Escherichia coli [TaxId: 562] [82876] (3)
                   SQ Q7C2L2
          3. GNA1870 immunodominant domain-like [144097] (1)
             related to Pfam 01298; GNA1870 is a bacterial cell surface-exposed lipoprotein
             1. Lipoprotein GNA1870 immunodominant domain [144098]
                1. Neisseria meningitidis [TaxId: 487] [144099] (1)
                   SQ Q6QCC2 120-274
          4. PsbO-like [161115] (1)
             Pfam 01716; MSP
             1. Manganese-stabilising protein, PsbO [161116]
                1. Thermosynechococcus elongatus [TaxId: 146786] [161117] (1)
                   SQ P0A431 30-271
       2. OMPT-like [69917] (2)
          forms (10,12) barrel
          uperfamily
          1. Outer membrane protease OMPT [69918] (1)
             1. Outer membrane protease OMPT [69919]
                1. Escherichia coli [TaxId: 562] [69920] (1)
          2. Outer membrane adhesin/invasin OpcA [75651] (1)
             1. Outer membrane adhesin/invasin OpcA [75652]
                1. Neisseria meningitidis [TaxId: 487] [75653] (2)
       3. Autotransporter [103515] (1)
          forms (12,14) barrel; contains a long alpha-helix running along the barrel axis
          uperfamily
          1. Autotransporter [103516] (1)
             1. Translocator domain of NalP [103517]
                1. Neisseria meningitidis [TaxId: 487] [103518] (2)
       4. Outer membrane phospholipase A (OMPLA) [56931] (1)
          forms (12,16) barrel
          uperfamily
          1. Outer membrane phospholipase A (OMPLA) [56932] (1)
             1. Outer membrane phospholipase A (OMPLA) [56933]
                1. Escherichia coli [TaxId: 562] [56934] (7)
       5. Porins [56935] (4)
          uperfamily
          1. Porin [56936] (5)
             trimer, one subunit folds into (16,20) barrel
             1. Porin [56937]
                1. Escherichia coli, different sequences [TaxId: 562] [56938] (21)
                2. Rhodobacter capsulatus [TaxId: 1061] [56939] (2)
                3. Rhodopseudomonas blastica, strain DSM2131 [TaxId: 1075] [56940] (9)
                4. Klebsiella pneumoniae [TaxId: 573] [56941] (1)
                5. Comamonas acidovorans [TaxId: 80866] [64534] (3)
                   Anion-selective porin OMP32
          2. Maltoporin-like [56942] (3)
             trimer, one subunit folds into (18,22) barrel
             1. Maltoporin (also LamB protein) [56943]
                1. Escherichia coli [TaxId: 562] [56944] (8)
                2. Salmonella typhimurium [TaxId: 90371] [56945] (2)
             2. Sucrose-specific porin [56946]
                1. Enterobacterium (Salmonella typhimurium) [TaxId: 90371] [56947] (3)
          3. Ligand-gated protein channel [56948] (4)
             monomeric (22,24) barrel; ~150 N-terminal residues form a "plug" or "cork" subdomain
             1. Ferric hydroxamate uptake receptor FhuA [56949]
                1. Escherichia coli [TaxId: 562] [56950] (11)
             2. Ferric enterobactin receptor FepA [56951]
                1. Escherichia coli [TaxId: 562] [56952] (1)
             3. Outer membrane transporter FecA [75654]
                1. Escherichia coli [TaxId: 562] [75655] (5)
             4. Outer membrane cobalamin transporter BtuB [90129]
                vitamin B12 receptor
                1. Escherichia coli [TaxId: 562] [90130] (8)
          4. Outer membrane protein transport protein [111361] (1)
             Pfam 03349; monomeric (14,16) barrel; plugged by an N-terminal all-alpha subdomain (1-40)
             1. Long-chain fatty acid transport protein FadL [111362]
                1. Escherichia coli [TaxId: 562] [111363] (2)
                   SQ P10384
       6. Tsx-like channel [111364] (1)
          forms (12,16) barrel
          uperfamily
          1. Tsx-like channel [111365] (1)
             Pfam 03502
             1. Nucleoside-specific channel-forming protein tsx (NupA) [111366]
                1. Escherichia coli [TaxId: 562] [111367] (3)
                   SQ P22786
   48. Outer membrane efflux proteins (OEP) [56953] (1)
       subunit fold contains tandem repeat of alpha-beta hairpin-alpha(2) motif
       trimeric fold contains barrel (n=12, S=18) formed by beta-hairpins, two from each subunit, and a bundle of helices with a channel running through it
       1. Outer membrane efflux proteins (OEP) [56954] (1)
          uperfamily
          1. Outer membrane efflux proteins (OEP) [56955] (2)
             Pfam 02321
             1. Integral outer membrane protein TolC, efflux pump component [56956]
                1. Escherichia coli [TaxId: 562] [56957] (2)
                   SQ P02930
             2. Outer membrane protein OprM [118229]
                1. Pseudomonas aeruginosa [TaxId: 287] [118230] (1)
                   SQ Q51487 18-485
   49. HlyD-like secretion proteins [111368] (1)
       consists of three domains: beta-barrel (res. 29-38,170-259; scop_cf 50412); barrel-sandwich hybrid (39-72,135-169; scop_sf 51230) and long alpha-hairpin (73-134; scop_cf 46556)
       1. HlyD-like secretion proteins [111369] (1)
          uperfamily
          1. HlyD-like secretion proteins [111370] (1)
             Pfam 00529
             1. Multidrug resistance protein MexA domain [111371]
                periplasmic component of efflux pump; channel-forming oligomer, interacts with TolC
                1. Pseudomonas aeruginosa [TaxId: 287] [111372] (2)
                   SQ P52477
   50. Leukocidin-like [56958] (1)
       subunit fold contains beta-sandwich of Ig-like (grerk-key) topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel
       1. Leukocidin-like [56959] (2)
          uperfamily
          1. Leukocidin (pore-forming toxin) [56960] (4)
             heptameric fold contains barrel (n=14, S=14) formed by beta-ribbon arms, one from each subunit
             1. Alpha-hemolysin [56961]
                1. Staphylococcus aureus [TaxId: 1280] [56962] (1)
             2. Leucocidin K component LukF-PV [56963]
                1. Staphylococcus aureus [TaxId: 1280] [56964] (1)
             3. Leukocidin F (HlgB) [56965]
                1. Staphylococcus aureus [TaxId: 1280] [56966] (3)
             4. Leucocidin S component LukS-PV [111373]
                1. Staphylococcus aureus bacteriophage PVL [TaxId: 71366] [111374] (1)
                   SQ O80066
          2. Porin MspA [103519] (1)
             octameric fold contains barrel (n=16, S=16) formed by beta-ribbon arms, one from each subunit
             1. Porin MspA [103520]
                1. Mycobacterium smegmatis [TaxId: 1772] [103521] (1)
   51. Lipovitellin-phosvitin complex; beta-sheet shell regions [56967] (1)
       contains several large open beta-sheets
       1. Lipovitellin-phosvitin complex; beta-sheet shell regions [56968] (1)
          uperfamily
          1. Lipovitellin-phosvitin complex; beta-sheet shell regions [56969] (1)
             1. Lipovitellin-phosvitin complex; beta-sheet shell regions [56970]
                1. Lamprey (Ichthyomyzon unicuspis) [TaxId: 30308] [56971] (2)
   52. Aerolisin/ETX pore-forming domain [56972] (1)
       3 domains: (1) alpha+beta; (2&3) all-beta
       1. Aerolisin/ETX pore-forming domain [56973] (2)
          uperfamily
          1. (Pro)aerolysin, pore-forming lobe [56974] (1)
             1. (Pro)aerolysin, pore-forming lobe [56975]
                contains the APT module at the N-terminus
                1. Aeromonas hydrophila [TaxId: 644] [56976] (9)
          2. ETX/MTX2 [111375] (1)
             Pfam 03318
             1. Epsilon-toxin, ETX [111376]
                1. Clostridium perfringens [TaxId: 1502] [111377] (1)
                   SQ Q57398
   53. Perfringolysin [56977] (1)
       2 domains: (1) alpha+beta; (2) all-beta, similar to the CalB domain fold but the two last strands are transposed
       1. Perfringolysin [56978] (1)
          uperfamily
          1. Perfringolysin [56979] (1)
             1. Perfringolysin [56980]
                1. Clostridium perfringens [TaxId: 1502] [56981] (3)
   54. Viral glycoprotein, central and dimerisation domains [56982] (1)
       2 intertwined domains; all-beta and alpha+beta
       1. Viral glycoprotein, central and dimerisation domains [56983] (1)
          uperfamily
          1. Viral glycoprotein, central and dimerisation domains [56984] (3)
             1. Envelope glycoprotein [56985]
                1. Tick-borne encephalitis virus [TaxId: 11084] [56986] (2)
                2. Dengue virus type 2 [TaxId: 11060] [90131] (9)
                   SQ P12823 281-675
             2. Fusion glycoprotein E1 [75656]
                1. Semliki forest virus [TaxId: 11033] [75657] (3)
   55. VP4 membrane interaction domain [111378] (1)
       2 domains; d1: complexed all-beta fold; d2: coiled-coil (trimeric) helical region
       1. VP4 membrane interaction domain [111379] (1)
          uperfamily
          1. VP4 membrane interaction domain [111380] (1)
             1. VP4 membrane interaction domain [111381]
                1. Rhesus rotavirus [TaxId: 10969] [111382] (1)
                   SQ Q91HI9 253-522
   56. Head and neck region of the ectodomain of NDV fusion glycoprotein [69921] (1)
       3 intertwined all-beta domains
       1. Head and neck region of the ectodomain of NDV fusion glycoprotein [69922] (1)
          uperfamily
          1. Head and neck region of the ectodomain of NDV fusion glycoprotein [69923] (1)
             1. Head and neck region of the ectodomain of NDV fusion glycoprotein [69924]
                1. Newcastle disease virus [TaxId: 11176] [69925] (1)
   57. OmpH-like [111383] (1)
       trimer; one subunit consists of an alpha/beta oligomerization subdomain [3-stranded parallel beta-sheet, order 213], and an antiparallel coiled coil
       1. OmpH-like [111384] (1)
          uperfamily
          1. OmpH-like [111385] (1)
             Pfam 03938
             1. Periplasmic chaperon skp (HlpA) [111386]
                1. Escherichia coli [TaxId: 562] [111387] (2)
                   SQ P11457
   58. Anthrax protective antigen [56987] (1)
       4 domains; I (res. 14-225) and II (226-487) are beta-sandwiches of similar gamma-crystallin like topologies; III (488-594) has a beta-grasp like fold; IV (595-735) has an Ig-like fold
       1. Anthrax protective antigen [56988] (1)
          uperfamily
          1. Anthrax protective antigen [56989] (1)
             1. Anthrax protective antigen [56990]
                1. Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] [56991] (3)
                   SQ P13423
7. Small proteins [56992] (90)
   Usually dominated by metal ligand, heme, and/or disulfide bridges
   1. Insulin-like [56993] (1)
      nearly all-alpha
      can be classified as disulfide-rich
      1. Insulin-like [56994] (1)
         uperfamily
         1. Insulin-like [56995] (6)
            1. Insulin [56996]
               1. Cow (Bos taurus) [TaxId: 9913] [56997] (6)
               2. Human (Homo sapiens) [TaxId: 9606] [56998] (60)
                  SQ P01308
               3. Pig (Sus scrofa) [TaxId: 9823] [56999] (26)
            2. Relaxin [57000]
               1. Human (Homo sapiens) [TaxId: 9606] [57001] (1)
            3. Insulin-like growth factor [57002]
               1. Human (Homo sapiens) [TaxId: 9606] [57003] (21)
                  SQ P05019 49-110
            4. Bombyxin-II [57004]
               1. Silkworm (Bombyx mori) [TaxId: 7091] [57005] (2)
   2. Knottins (small inhibitors, toxins, lectins) [57015] (19)
      disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
      1. Plant lectins/antimicrobial peptides [57016] (2)
         uperfamily
         1. Hevein-like agglutinin (lectin) domain [57017] (6)
            1. Wheat germ agglutinin (WGA) [57018]
               one subunit consists of four homologous domains
               1. Wheat (Triticum aestivum), also known as Triticum vulgare [TaxId: 4565] [57019] (9)
            2. Isolectin VI [57020]
               consists of two homologous domains
               1. Stinging nettle (Urtica dioica), UDA [TaxId: 3501] [57021] (6)
            3. Hevein [57022]
               single domain
               1. Hevea brasiliensis [TaxId: 3981] [57023] (3)
                  SQ P02877 18-49
            4. Lectin-C [103522]
               consists of three homologous domains
               1. American pokeweed (Phytolacca americana) [TaxId: 3527] [103523] (1)
            5. Lectin-D [103524]
               consists of two homologous domains
               1. American pokeweed (Phytolacca americana) [TaxId: 3527] [103525] (3)
            6. Antifungal peptide 2 [111392]
               1. Hardy rubber tree (Eucommia ulmoides) [TaxId: 4392] [111393] (2)
                  SQ P83597
         2. Antimicrobial peptide 2, AC-AMP2 [57024] (1)
            1. Antimicrobial peptide 2, AC-AMP2 [57025]
               1. Tassel (Amaranthus caudatus) [TaxId: 3567] [57026] (1)
      2. Plant inhibitors of proteinases and amylases [57027] (1)
         uperfamily
         1. Plant inhibitors of proteinases and amylases [57028] (7)
            1. Trypsin inhibitor [57029]
               1. Bitter gourd (Momordica charantia), linn. Cucurbitaceae, seed [TaxId: 3673] [57030] (2)
               2. Squash (Cucurbita maxima) [TaxId: 3661] [57031] (7)
               3. Spiny bitter cucumber (Momordica cochinchinensis), MCOTI-II [TaxId: 3674] [64535] (4)
               4. Vegetable marrow (Cucurbita pepo) [TaxId: 3663] [57032] (2)
               5. Jumping cucumber (Ecballium elaterium) [TaxId: 3679] [57033] (16)
                  SQ P12071
            2. Carboxypeptidase A inhibitor [57034]
               1. Potato [TaxId: 4113] [57035] (3)
            3. alpha-amylase inhibitor (AAI) [57036]
               1. Prince's feather (Amaranthus hypochondriacus) [TaxId: 28502] [57037] (3)
      3. Cyclotides [57038] (4)
         macrocyclic plant knottins closed with the formation of an Asn-Gly peptide
         uperfamily
         1. Kalata B1 [57039] (1)
            1. Kalata B1 [57040]
               cyclic 29-residue polypeptide
               1. African plant (Oldenlandia affinis) [TaxId: 60225] [57041] (8)
                  SQ P58454 71-97
         2. Cycloviolacin [57042] (2)
            1. Cycloviolacin O1 [57043]
               cyclic 30-residue polypeptide
               1. Plant (Viola odorata) [TaxId: 97441] [57044] (2)
            2. Root cyclotide 1 [118231]
               1. Australian violet (Viola hederacea) [TaxId: 180952] [118232] (1)
                  SQ P83937
         3. Circulin A [57045] (1)
            1. Circulin A [57046]
               cyclic 30-residue polypeptide
               1. Chassalia parviflora [TaxId: 58431] [57047] (1)
         4. Palicourein [103526] (1)
            1. Palicourein [103527]
               1. Palicourea condensata [TaxId: 272141] [103528] (1)
      4. Gurmarin-like [57048] (2)
         uperfamily
         1. Gurmarin, a sweet taste-suppressing polypeptide [57049] (1)
            1. Gurmarin, a sweet taste-suppressing polypeptide [57050]
               1. Gymnema sylvestre [TaxId: 4068] [57051] (2)
         2. Antifungal peptide [57052] (2)
            1. Antifungal peptide PAFP-S [57053]
               1. Pokeweed (Phytolacca americana) [TaxId: 3527] [57054] (1)
            2. Antifungal peptide Alo3 [103529]
               1. Insect (Acrocinus longimanus) [TaxId: 227548] [103530] (1)
      5. Agouti-related protein [57055] (1)
         uperfamily
         1. Agouti-related protein [57056] (1)
            1. Agouti-related protein [57057]
               1. Synthetic, based on Homo sapiens sequence [57058] (2)
      6. omega toxin-like [57059] (5)
         uperfamily
         1. Conotoxin [57060] (13)
            1. Conotoxin [57061]
               1. Sea snail (Conus geographus), G IVa [TaxId: 6491] [57062] (4)
                  SQ P01522 46-72
               2. Synthetic, based on Conus geographus, GS [57063] (1)
               3. Sea snail (Conus magus), M VIIc [TaxId: 6492] [57064] (2)
               4. Sea snail (Conus magus), M VIIa [TaxId: 6492] [57065] (7)
                  SQ P05484 46-70
               5. Conus striatus, S VIb [TaxId: 6493] [57066] (1)
               6. Conus striatus, SO3 [TaxId: 6493] [57067] (1)
               7. Conus purpurascens, kappa-pVIIa [TaxId: 41690] [57068] (2)
               8. Conus tulipa, T VIIa [TaxId: 6495] [57069] (1)
               9. Conus ermineus, E VIa [TaxId: 55423] [57070] (2)
               10. Conus textile, Tx VII [TaxId: 6494] [57071] (1)
               11. Conus textile, Tx VIa [TaxId: 6494] [82877] (1)
               12. Conus gloriamaris, Tx IXa [TaxId: 37336] [82878] (1)
                   Spasmodic conotoxin
               13. Marble cone (Conus marmoreus), mrVIb [TaxId: 42752] [111394] (1)
                   SQ Q26443
         2. Spider toxins [57072] (25)
            1. omega-Agatoxin IV, IVa, IVb [57073]
               1. Funnel web spider (Agelenopsis aperta) [TaxId: 6908] [57074] (6)
            2. mu-Agatoxin-I [57075]
               1. Funnel web spider (Agelenopsis aperta) [TaxId: 6908] [57076] (1)
            3. ACTX-HI:OB4219 [69926]
               1. Funnel-web spider (Hadronyche infensa) [TaxId: 153481] [69927] (2)
            4. Atracotoxin-hvI (versutoxin) [57077]
               1. Australian funnel-web spider (Hadronyche versuta) [TaxId: 6904] [57078] (3)
            5. J-atracotoxin-hv1c [57079]
               1. Australian funnel-web spider (Hadronyche versuta) [TaxId: 6904] [57080] (1)
            6. Atracotoxin-hv2a [69928]
               1. Funnel-web spider (Hadronyche versuta) [TaxId: 6904] [69929] (2)
            7. Robustoxin [57081]
               1. Funnel-web spider (Atrax robustus) [TaxId: 6903] [57082] (1)
            8. Huwentoxin-I [57083]
               1. Chinese bird spider (Selenocosmia huwena) [TaxId: 29017] [57084] (1)
            9. Hainantoxin-I [82879]
               1. Spider (Selenocosmia hainana) [TaxId: 209901] [82880] (1)
            10. Huwentoxin-II [57085]
                1. Chinese bird spider (Selenocosmia huwena) [TaxId: 29017] [57086] (1)
            11. Huwentoxin-IV [75658]
                1. Chinese bird spider (Selenocosmia huwena) [TaxId: 29017] [75659] (1)
            12. Hainantoxin-IV [82881]
                1. Spider (Selenocosmia hainana) [TaxId: 209901] [82882] (3)
            13. Lectin SHL-I [57087]
                1. Chinese bird spider (Selenocosmia huwena) [TaxId: 29017] [57088] (1)
            14. SGtx1 [103531]
                1. Spider (Scodra griseipes) [TaxId: 118974] [103532] (1)
            15. Hanatoxin 1 [57089]
                1. Tarantula (Grammostola spatulata) [TaxId: 432528] [57090] (1)
            16. Grammotoxin SIA, GrTx [75660]
                1. Tarantula (Grammostola spatulata) [TaxId: 432528] [75661] (1)
            17. Heteropdatoxin 2, hptx2 [57091]
                1. Giant crab spider (Heteropoda venatoria) [TaxId: 152925] [57092] (1)
            18. GSmtx2 [75662]
                1. Chilean rose tarantula (Grammostola spatulata) [TaxId: 432528] [75663] (1)
            19. GSmtx4 [75664]
                1. Chilean rose tarantula (Grammostola spatulata) [TaxId: 432528] [75665] (2)
                   SQ Q7YT39 47-80
            20. Psalmotoxin 1 [103533]
                1. Spider (Psalmopoeus cambridgei) [TaxId: 179874] [103534] (1)
            21. Maurocalcin [57093]
                scorpion toxin with a spider toxin-like fold
                1. Scorpio maurus [TaxId: 53956] [57094] (1)
            22. Imperatoxin A [90132]
                scorpion toxin with a spider toxin-like fold
                1. Emperor scorpion (Pandinus imperator) [TaxId: 55084] [90133] (1)
            23. Tachystatin [75666]
                1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [75667] (1)
            24. Phrixotoxin 1 (PaTX1) [118233]
                1. Chilean copper tarantula (Phrixotrichus auratus) [TaxId: 269635] [118234] (1)
                   SQ P61230
            25. Huwentoxin-X [118235]
                1. Spider (Selenocosmia hainana) [TaxId: 209901] [118236] (1)
                   SQ P68424
         3. Insect toxins [69930] (2)
            1. PTU-1 [69931]
               1. Assassin bug (Peirates turpis) [TaxId: 181095] [69932] (1)
            2. ADO1 [103535]
               1. Assassin bug (Agriosphodrus dohrni) [TaxId: 184613] [103536] (1)
         4. Albumin 1 [90134] (2)
            1. Leginsulin [90135]
               a plant hormone
               1. Soybean (Glycine max) [TaxId: 3847] [90136] (1)
            2. Pab1, subunit b [103537]
               insecticidal protein
               1. Garden pea (Pisum sativum) [TaxId: 3888] [103538] (1)
         5. Vhv1.1, polydnaviral gene product [118237] (1)
            1. Vhv1.1, polydnaviral gene product [118238]
               1. Campoletis sonorensis virus, CsIV [TaxId: 10484] [118239] (2)
                  SQ Q89632 162-208
      7. Scorpion toxin-like [57095] (5)
         uperfamily
         1. Long-chain scorpion toxins [57096] (22)
            1. Scorpion toxin [57097]
               1. Centruroides sculpturatus, variant 2 [TaxId: 218467] [69933] (2)
               2. Centruroides sculpturatus, variant 3 [TaxId: 218467] [57098] (1)
               3. Centruroides sculpturatus, beta [TaxId: 218467] [57099] (2)
               4. Centruroides sculpturatus, variant 1 [TaxId: 218467] [57100] (2)
               5. Centruroides sculpturatus, variant V [TaxId: 218467] [57101] (2)
               6. Scorpion (Androctonus australis hector), Toxin II [TaxId: 70175] [57102] (3)
                  SQ P01484
               7. Mexican scorpion (Centruroides noxius), toxin II [TaxId: 6878] [57103] (1)
               8. Scorpion (Buthotus judaicus), BJXTR-IT [TaxId: 6863] [57104] (1)
               9. Scorpion (Buthus martensii), toxin m8 [TaxId: 34649] [57105] (1)
               10. Chinese scorpion (Buthus martensii), toxin m1 [TaxId: 34649] [57106] (5)
                   SQ P45697
               11. Chinese scorpion (Buthus martensii), toxin m2 [TaxId: 34649] [57107] (1)
               12. Chinese scorpion (Buthus martensii), toxin m4 [TaxId: 34649] [57108] (1)
               13. Indian red scorpion (Buthus tamulus), neurotoxin [TaxId: 34647] [57109] (3)
               14. Brazilian scorpion (Tityus serrulatus) [TaxId: 6887] [57110] (2)
               15. Bark scorpion (Centruroides sculpturatus), cse-v5 [TaxId: 218467] [64536] (3)
               16. Mexican scorpion (Centruroides noxius) [TaxId: 6878] [111395] (1)
                   SQ P63019
               17. Scorpion (Buthus martensii), BmK IT-AP [TaxId: 34649] [118240] (1)
                   SQ O77091 19-90
            2. alpha toxin [57111]
               Anti-mammal and anti-insect scorpion toxin
               1. Leiurus quinquestriatus quinquestriatus, LQQIII [TaxId: 6885] [57112] (1)
               2. Scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57113] (3)
               3. Chinese scorpion (Buthus martensii karsch) [TaxId: 34649] [103539] (2)
            3. Tx10 alpha-like toxin [103540]
               1. Chinese scorpion (Buthus martensii) [TaxId: 34649] [103541] (1)
            4. LQH III alpha-like toxin, LQH [57114]
               1. Hebraei scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57115] (2)
         2. Short-chain scorpion toxins [57116] (38)
            1. Bmtx1 [57117]
               1. Buthus martensii [TaxId: 34649] [57118] (1)
            2. Bmktx [57119]
               1. Buthus martensii [TaxId: 34649] [57120] (1)
            3. Bmtx2 [57121]
               1. Buthus martensii [TaxId: 34649] [57122] (1)
            4. Bmtx3 [103542]
               1. Buthus martensii karsch [TaxId: 34649] [103543] (1)
            5. Bmp02 neurotoxin [57123]
               1. Chinese scorpion (Buthus martensii) [TaxId: 34649] [57124] (1)
            6. Bekm-1 [82883]
               1. Lesser asian scorpion (Buthus eupeus) [TaxId: 34648] [82884] (2)
            7. alpha-KTX, K+-channel blocker [64537]
               1. Brazilian scorpion (Tityus serrulatus), Tstx-k alpha [TaxId: 6887] [64538] (1)
               2. Scorpion (Tityus cambridgei) [TaxId: 184226] [69934] (1)
            8. Neurotoxin bmk37 [103544]
               1. Chinese scorpion (Buthus martensi karsch) [TaxId: 34649] [103545] (2)
            9. Bmkx [103546]
               1. Chinese scorpion (Buthus martensi karsch) [TaxId: 34649] [103547] (2)
            10. Hongotoxin 1 [103548]
                1. Scorpion (Centruroides margaritatus) [TaxId: 29018] [103549] (1)
            11. Margatoxin [57125]
                1. Scorpion (Centruroides margaritatus) [TaxId: 29018] [57126] (1)
            12. Noxiustoxin [57127]
                1. Mexican scorpion (Centruroides noxius) [TaxId: 6878] [57128] (1)
            13. Maurotoxin [57129]
                1. Scorpion (Scorpio maurus) [TaxId: 53956] [57130] (3)
                   SQ P80719
                2. Scorpio maurus palmatus [TaxId: 53957] [161118] (1)
            14. Charybdotoxin [57131]
                1. Scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57132] (4)
            15. Scyllatoxin [57133]
                1. Scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57134] (1)
            16. Agitoxin [57135]
                1. Scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57136] (1)
            17. Chlorootoxin [57137]
                1. Scorpion (Leiurus quinquestriatus), venom [TaxId: 6883] [57138] (1)
            18. Butantoxin [57139]
                1. Brazilian scorpion (Tityus serrulatus) [TaxId: 6887] [57140] (2)
            19. Toxin ts kappa [57141]
                1. Scorpion (Tityus serrulatus) [TaxId: 6887] [57142] (1)
            20. Toxin I5a [57143]
                1. Scorpion (Buthus eupeus) [TaxId: 34648] [57144] (1)
            21. Toxin analog [57145]
                1. Scorpion (Androctonus mauretanicus mauretanicus) [TaxId: 6860] [57146] (1)
            22. Toxin analog P01 [57147]
                1. Scorpion (Androctonus mauretanicus mauretanicus) [TaxId: 6860] [57148] (1)
            23. OSK1 TOXIN [57149]
                1. Central asian scorpion (Orthochirus scrobiculosus) [TaxId: 6892] [57150] (1)
            24. Kaliotoxin (KTX) [57151]
                1. Scorpion (Androctonus mauretanicus mauretanicus) [TaxId: 6860] [57152] (3)
                2. Androctonus mauretanicus [TaxId: 6859] [161119] (1)
            25. LQ2 toxin [57153]
                1. Scorpion (Leiurus quinquestriatus hebraeus) [TaxId: 6884] [57154] (1)
            26. Pandinus toxin [57155]
                1. Emperor scorpion (Pandinus imperator), PITX-Ka [TaxId: 55084] [57156] (1)
                2. Emperor scorpion (Pandinus imperator), PITX-Kb [TaxId: 55084] [57157] (1)
            27. PI4, potassium channel blocking toxin 4 [103550]
                1. Scorpion (Pandinus imperator) [TaxId: 55084] [103551] (1)
            28. Cobatoxin 1 [103552]
                1. Scorpion (Centruroides noxius) [TaxId: 6878] [103553] (1)
            29. PI7 [57158]
                nontoxic peptide?
                1. Scorpion (Pandinus imperator) [TaxId: 55084] [57159] (1)
            30. Ergtoxin (HERG specific toxin CnErg1) [90137]
                1. Scorpion (Centruroides noxius) [TaxId: 6878] [90138] (2)
                   SQ Q86QT3 21-62
            31. K+ toxin-like peptide Bmp07 (BmKK2) [111396]
                1. Chinese scorpion (Buthus martensi karsch) [TaxId: 34649] [111397] (1)
                   SQ Q95NK7
            32. Neurotoxin bmp01 [111398]
                1. Chinese scorpion (Buthus martensii karsch) [TaxId: 34649] [111399] (1)
                   SQ Q9U8D2
            33. Neurotoxin bmp03 [111400]
                1. Chinese scorpion (Buthus martensii karsch) [TaxId: 34649] [111401] (1)
                   SQ Q9U8D1
            34. Istx [118241]
                1. Scorpion (Opisthacanthus madagascariensis) [TaxId: 167108] [118242] (1)
                   SQ Q10726 2-33 # 53% sequence identity
         3. Defensin MGD-1 [57160] (1)
            1. Defensin MGD-1 [57161]
               1. Mediterranean mussel (Mytilus galloprovincialis) [TaxId: 29158] [57162] (1)
         4. Insect defensins [57163] (6)
            1. Heliomicin [69935]
               1. Tobacco budworm (Heliothis virescens) [TaxId: 7102] [69936] (2)
            2. Defensin ARD1 [103554]
               1. Archaeoprepona demophon [TaxId: 191427] [103555] (3)
            3. Drosomycin [57164]
               inducible antifungal protein
               1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [57165] (1)
            4. Defensin A [57166]
               1. Flesh fly (Phormia terranovae) [TaxId: 34676] [57167] (1)
               2. Flesh fly (Sarcophaga peregrina), sapesin [TaxId: 7386] [74659] (1)
            5. Antimicrobial peptide termicin [90139]
               1. Termite (Pseudacanthotermes spiniger) [TaxId: 115113] [90140] (1)
         5. Plant defensins [57170] (10)
            1. gamma-Thionin [57171]
               1. Barley (Hordeum vulgare) [TaxId: 4513] [57172] (1)
               2. English wheat (Triticum turgidum) [TaxId: 4571] [57173] (1)
            2. Floral defensin 1 [103556]
               flower-specific gamma-thionin
               1. Common tobacco (Nicotiana tabacum), NAD1 [TaxId: 4097] [103557] (1)
               2. Garden petunia (Petunia x hybrida), PHD1 [TaxId: 4102] [103558] (1)
            3. Antifungal protein 1 (RS-AFP1) [57174]
               1. Radish (Raphanus sativus) [TaxId: 3726] [57175] (1)
            4. Antimicrobial protein 1 (AH-AMP1) [57176]
               1. Horse chestnut (Aesculus hippocastanum) [TaxId: 43364] [57177] (1)
            5. Defensin 1 (PSD1) [69937]
               1. Pea (Pisum sativum) [TaxId: 3888] [69938] (1)
            6. Brazzein [57178]
               sweet protein
               1. J'oublie (Pentadiplandra brazzeana) [TaxId: 43545] [57179] (2)
            7. Trypsin/chymotrypsin inhibitor ATT [82885]
               1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [82886] (1)
            8. S-locus pollen protein [103559]
               1. Brassica rapa [TaxId: 3711] [103560] (1)
      8. Cellulose-binding domain [57180] (1)
         uperfamily
         1. Cellulose-binding domain [57181] (1)
            1. Cellobiohydrolase I [57182]
               1. Trichoderma reesei, ct-cbh I [TaxId: 51453] [57183] (6)
      9. Growth factor receptor domain [57184] (1)
         uperfamily
         1. Growth factor receptor domain [57185] (9)
            1. Insulin-like growth factor-binding protein-5 (IGFBP-5) [57186]
               1. Human (Homo sapiens) [TaxId: 9606] [57187] (2)
            2. Type 1 insulin-like growth factor receptor Cys-rich domain [57188]
               contains 3 cystine-knot subdomains and 4 single-disulfide cystine knot-like subdomains
               1. Human (Homo sapiens) [TaxId: 9606] [57189] (1)
            3. Receptor protein-tyrosine kinase Erbb-3 Cys-rich domains [75668]
               1. Human (Homo sapiens) [TaxId: 9606] [75669] (1)
            4. EGF receptor Cys-rich domains [82887]
               1. Human (Homo sapiens) [TaxId: 9606] [82888] (15)
            5. Protooncoprotein Her2 extracellular domain [82889]
               1. Human (Homo sapiens) [TaxId: 9606] [82890] (2)
               2. Rat (Rattus norvegicus) [TaxId: 10116] [82891] (1)
            6. Insulin-like growth factor-binding protein 4 [161120]
               1. Human (Homo sapiens) [TaxId: 9606] [161121] (2)
                  SQ P22692 24-103
            7. Insulin receptor [161122]
               1. Human (Homo sapiens) [TaxId: 9606] [161123] (1)
                  SQ P06213 184-338
            8. Insulin-like growth factor-binding protein 4, IGFBP4 [161124]
               1. Human (Homo sapiens) [TaxId: 9606] [161125] (3)
                  SQ P22692 22-113
      10. Colipase-like [57190] (1)
          uperfamily
          1. Colipase-like [57191] (2)
             1. (Pro)colipase [57192]
                duplication: consists of two (sub)domains of this common fold
                1. Pig (Sus scrofa) [TaxId: 9823] [57193] (6)
             2. Intestinal toxin 1 [57194]
                1. Black mamba (Dendroaspis polylepis polylepis) [TaxId: 8620] [57195] (1)
      11. EGF/Laminin [57196] (7)
          uperfamily
          1. EGF-type module [57197] (27)
             1. Factor IX (IXa) [57198]
                1. Human (Homo sapiens) [TaxId: 9606] [57199] (7)
                2. Pig (Sus scrofa) [TaxId: 9823] [57200] (31)
             2. Coagulation factor VIIa [57201]
                1. Human (Homo sapiens) [TaxId: 9606] [57202] (19)
                   SQ P08709 108-202 ! SQ P08709 107-202
             3. E-selectin, EGF-domain [57203]
                1. Human (Homo sapiens) [TaxId: 9606] [57204] (5)
             4. Factor X, N-terminal module [57205]
                1. Human (Homo sapiens) [TaxId: 9606] [57206] (75)
                   SQ P00742 127-178
                2. Cow (Bos taurus) [TaxId: 9913] [57207] (5)
             5. Activated protein c (autoprothrombin IIa) [57208]
                1. Human (Homo sapiens) [TaxId: 9606] [57209] (1)
             6. Prostaglandin H2 synthase-1, EGF-like module [57210]
                the rest of protein is heme-linked peroxidase, all-alpha fold
                1. Sheep (Ovis aries) [TaxId: 9940] [57211] (22)
                   SQ P05979 32-584
                2. Mouse (Mus musculus) [TaxId: 10090] [57212] (8)
             7. P-selectin, EGF-domain [57213]
                1. Human (Homo sapiens) [TaxId: 9606] [57214] (1)
             8. Epidermal growth factor, EGF [57215]
                1. Mouse (Mus musculus) [TaxId: 10090] [57216] (8)
                2. Human (Homo sapiens) [TaxId: 9606] [69939] (4)
             9. Transforming growth factor alpha [57217]
                1. Human (Homo sapiens) [TaxId: 9606] [57218] (6)
             10. Epiregulin, EGF-domain [103561]
                 1. Human (Homo sapiens) [TaxId: 9606] [103562] (2)
             11. Betacellulin-2 [75670]
                 1. Human (Homo sapiens) [TaxId: 9606] [75671] (2)
             12. Heparin-binding epidermal growth factor, HBEGF [57219]
                 extracellular domain
                 1. Human (Homo sapiens) [TaxId: 9606] [57220] (1)
             13. Plasminogen activator (urokinase-type) [57221]
                 1. Human (Homo sapiens) [TaxId: 9606] [57222] (12)
             14. Heregulin-alpha, EGF-like domain [57223]
                 1. Human (Homo sapiens) [TaxId: 9606] [57224] (4)
             15. Thrombomodulin, different EGF-like domains [57225]
                 1. Human (Homo sapiens) [TaxId: 9606] [57226] (6)
             16. Fibrillin-1 [57227]
                 duplication: contains 47 EFG-like domains
                 1. Human (Homo sapiens) [TaxId: 9606] [57228] (8)
             17. Mannose-binding protein associated serine protease 2, MASP2 [90141]
                 EGF-like domain separates two CUB domains
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [90142] (1)
                 2. Human (Homo sapiens) [TaxId: 9606] [111402] (1)
                    SQ O00187 17-181
             18. Complement C1S component [90143]
                 1. Human (Homo sapiens) [TaxId: 9606] [90144] (1)
             19. Complement protease C1R [57229]
                 1. Human (Homo sapiens) [TaxId: 9606] [57230] (1)
             20. Plasminogen activator (tissue-type), t-PA [57231]
                 1. Human (Homo sapiens) [TaxId: 9606] [57232] (1)
             21. Low density lipoprotein (LDL) receptor, different EGF domains [64539]
                 1. Human (Homo sapiens) [TaxId: 9606] [64540] (7)
                    SQ P01130 272-353
             22. Neurogenic locus notch homolog protein 1, Notch1 [118243]
                 1. Human (Homo sapiens) [TaxId: 9606] [118244] (4)
                    SQ P46531 411-526
          2. Integrin beta EGF-like domains [69940] (1)
             1. Integrin beta EGF-like domains [69941]
                1. Human (Homo sapiens) [TaxId: 9606] [69942] (5)
                   SQ P05106 27-716
          3. EGF-like domain of nidogen-1 [64541] (1)
             1. EGF-like domain of nidogen-1 [64542]
                1. Mouse (Mus musculus) [TaxId: 10090] [64543] (2)
          4. Laminin-type module [57233] (1)
             1. Laminin gamma1 chain [57234]
                1. Mouse (Mus musculus) [TaxId: 10090] [57235] (3)
          5. Follistatin (FS) module N-terminal domain, FS-N [57236] (2)
             1. Domain of BM-40/SPARC/osteonectin [57237]
                the N-terminal part of FS module
                1. Human (Homo sapiens) [TaxId: 9606] [57238] (2)
             2. Domain of follistatin [90145]
                the N-terminal part of the heparin-binding module, FS1
                1. Rat (Rattus norvegicus) [TaxId: 10116] [90146] (3)
          6. Merozoite surface protein 1 (MSP-1) [57239] (3)
             1. Merozoite surface protein 1 (MSP-1) [57240]
                1. Malaria parasite (Plasmodium cynomolgi) [TaxId: 5827] [57241] (1)
                2. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [57242] (3)
                3. Malaria parasite (Plasmodium knowlesi) [TaxId: 5850] [82892] (1)
          7. Cripto EGF-like domain-like [144100] (1)
             1. Cripto growth factor [144101]
                Teratocarcinoma-derived growth factor
                1. Mouse (Mus musculus) [TaxId: 10090] [144102] (1)
                   SQ P51865 96-134
      12. Bromelain inhibitor VI (cysteine protease inhibitor) [57243] (1)
          uperfamily
          1. Bromelain inhibitor VI (cysteine protease inhibitor) [57244] (1)
             1. Bromelain inhibitor VI (cysteine protease inhibitor) [57245]
                duplication: consists of two subdomains of this fold
                1. Pineapple (Ananas comosus) [TaxId: 4615] [57246] (2)
      13. Bowman-Birk inhibitor, BBI [57247] (1)
          uperfamily
          1. Bowman-Birk inhibitor, BBI [57248] (10)
             1. Bowman-Birk inhibitor, BBI [57249]
                duplication: consists of two sequence repeats each having this fold
                1. Soybean (Glycine max), PI-II [TaxId: 3847] [57250] (1)
                2. Soybean (Glycine max) [TaxId: 3847] [57251] (4)
                3. Winter pea (Pisum sativum) [TaxId: 3888] [57252] (1)
                4. Mung bean (Vigna radiata) [TaxId: 157791] [57253] (1)
                5. Barley (Hordeum vulgare) [TaxId: 4513] [57254] (4)
                   further duplication: consist of two BBI domains
                6. Adzuki bean (Phaseolus angularis) [TaxId: 3914] [57255] (1)
                7. Lima bean (Phaseolus lunatus) [TaxId: 3884] [82893] (1)
                8. Snail medic (Medicago scutellata) [TaxId: 36901] [90147] (2)
                9. Cowpea (Vigna unguiculata) [TaxId: 3917] [161126] (3)
                   SQ P17734 17-72! SQ Q84X88 44-100
                10. Vigna radiata var. radiata [TaxId: 3916] [161127] (1)
      14. Elafin-like [57256] (1)
          uperfamily
          1. Elafin-like [57257] (2)
             1. Elafin, elastase-specific inhibitor [57258]
                1. Human (Homo sapiens) [TaxId: 9606] [57259] (2)
             2. Nawaprin [103563]
                1. Spitting cobra (Naja nigricollis) [TaxId: 8654] [103564] (1)
      15. Leech antihemostatic proteins [57262] (2)
          uperfamily
          1. Huristasin-like [57263] (3)
             1. Hirustasin [57264]
                1. Medicinal leech (Hirudo medicinalis) [TaxId: 6421] [57265] (3)
             2. Bdellastasin [57266]
                1. Medicinal leech (Hirudo medicinalis) [TaxId: 6421] [57267] (3)
             3. Factor Xa inhibitor antistasin [57268]
                duplication: consists of two similar domain
                1. Mexican leech (Haementeria officinalis) [TaxId: 6410] [57269] (1)
          2. Hirudin-like [57270] (3)
             1. Hirudin [57271]
                1. Leech (Hirudo medicinalis) [TaxId: 6421] [57272] (8)
             2. Decorsin [57273]
                1. North american leech (Macrobdella decora) [TaxId: 6405] [57274] (1)
             3. Haemadin [57275]
                1. Indian leech (Haemadipsa sylvestris) [TaxId: 13555] [57276] (1)
      16. Granulin repeat [57277] (1)
          uperfamily
          1. Granulin repeat [57278] (3)
             1. N-terminal domain of granulin-1 [57279]
                1. Carp (Cyprinus carpio) [TaxId: 7962] [57280] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [57281] (1)
             2. Oryzain beta chain [64544]
                1. Rice (Oryza sativa) [TaxId: 4530] [64545] (1)
      17. Satiety factor CART (cocaine and amphetamine regulated transcript) [64546] (1)
          uperfamily
          1. Satiety factor CART (cocaine and amphetamine regulated transcript) [64547] (1)
             1. Satiety factor CART (cocaine and amphetamine regulated transcript) [64548]
                1. Human (Homo sapiens) [TaxId: 9606] [64549] (1)
      18. DPY module [90148] (1)
          uperfamily
          1. DPY module [90149] (1)
             1. Dumpy [90150]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [90151] (1)
      19. Bubble protein [103565] (1)
          uperfamily
          1. Bubble protein [103566] (1)
             1. Bubble protein [103567]
                1. Penicillium brevicompactum [TaxId: 5074] [103568] (1)
   3. PMP inhibitors [57282] (1)
      disulfide-rich fold; all-beta: 3 antiparallel strands
      1. PMP inhibitors [57283] (1)
         uperfamily
         1. PMP inhibitors [57284] (4)
            1. Protease inhibitor PMP-C [57285]
               1. Migratory locust (Locusta migratoria) [TaxId: 7004] [57286] (2)
            2. Protease inhibitor PMP-D2V [69943]
               1. Migratory locust (Locusta migratoria) [TaxId: 7004] [69944] (1)
            3. Protease inhibitor SGCI [69945]
               1. Desert locust (Schistocerca gregaria) [TaxId: 7010] [69946] (2)
            4. Protease inhibitor SGTI [69947]
               1. Desert locust (Schistocerca gregaria) [TaxId: 7010] [69948] (2)
                  SQ Q8WQ22 23-57 # Locusta migratoria migratorioides
   4. Midkine [57287] (1)
      disulfide-rich fold; all-beta: 3 antiparallel strands
      1. Midkine [57288] (2)
         uperfamily
         1. Midkine, a heparin-binding growth factor, N-terminal domain [57289] (1)
            1. Midkine, a heparin-binding growth factor, N-terminal domain [57290]
               1. Synthetic [57291] (1)
         2. Midkine, a heparin-binding growth factor, C-terminal domain [57292] (1)
            1. Midkine, a heparin-binding growth factor, C-terminal domain [57293]
               1. Synthetic [57294] (1)
   5. TSP-1 type 1 repeat [82894] (1)
      disulfide-rich fold; all-beta: 3 antiparallel strands
      1. TSP-1 type 1 repeat [82895] (1)
         uperfamily
         1. TSP-1 type 1 repeat [82896] (1)
            1. Thrombospondin-1 (TSP-1) [82897]
               1. Human (Homo sapiens) [TaxId: 9606] [82898] (1)
   6. Amb V allergen [57295] (1)
      disulfide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
      1. Amb V allergen [57296] (1)
         uperfamily
         1. Amb V allergen [57297] (1)
            1. Amb V allergen [57298]
               1. Giant ragweed (Ambrosia trifida), pollen [TaxId: 4214] [57299] (3)
   7. Snake toxin-like [57301] (1)
      disulfide-rich fold: nearly all-beta
      1. Snake toxin-like [57302] (3)
         uperfamily
         1. Snake venom toxins [57303] (36)
            1. Erabutoxin B (also neurotoxin B) [57304]
               1. Sea snake (Laticauda semifasciata) [TaxId: 8631] [57305] (7)
            2. gamma-Cardiotoxin [57306]
               1. Snake (Naja nigricollis) [TaxId: 8654] [57307] (3)
            3. Fasciculin [57308]
               different isoforms
               1. Green mamba (Dendroaspis angusticeps) [TaxId: 8618] [57309] (8)
            4. Muscarinic toxin [90152]
               acetylcholine receptor binding protein
               1. Green mamba (Dendroaspis angusticeps) [TaxId: 8618] [90153] (1)
            5. Erabutoxin A [57310]
               1. Broad-banded blue sea snake (Laticauda semifasciata) [TaxId: 8631] [57311] (3)
            6. Neurotoxin I [57312]
               1. Snake (Naja naja oxiana) [TaxId: 8657] [57313] (2)
                  SQ P01382
            7. Cardiotoxin V4II (Toxin III) [57314]
               1. Naja mossambica mossambica [TaxId: 196380] [57315] (1)
            8. Cardiotoxin V [57316]
               1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57317] (2)
            9. alpha-Cobratoxin [57318]
               1. Cobra (Naja siamensis) [TaxId: 84476] [57319] (7)
               2. Monocled cobra (Naja naja kaouthia) [TaxId: 8649] [82899] (2)
                  identical sequence to the Naja naja siamensis toxin
            10. Long neurotoxin 1 (component LSIII) [57320]
                1. Sea snake (Laticauda semifasciata) [TaxId: 8631] [57321] (1)
            11. FS2 toxin [57322]
                1. Black mamba (Dendroaspis polylepis polylepis) [TaxId: 8620] [57323] (1)
            12. Bungarotoxin [57324]
                1. Many-banded krait (Bungarus multicinctus), Alpha-bungarotoxin [TaxId: 8616] [57325] (22)
                2. Many-banded krait (Bungarus multicinctus), kappa-bungarotoxin [TaxId: 8616] [57326] (1)
                3. Many-banded krait (Bungarus multicinctus), neuronal bungarotoxin [TaxId: 8616] [57327] (1)
                4. Many-banded krait (Bungarus multicinctus), gamma-bungarotoxin [TaxId: 8616] [111403] (1)
                   SQ Q9YGJ0 22-89
            13. Bucandin [57328]
                1. Malayan krait (Bungarus candidus) [TaxId: 92438] [57329] (2)
            14. Cardiotoxin CTXI [57330]
                1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57331] (1)
            15. Cardiotoxin CTX IIB [57332]
                1. Naja mossambica mossambica [TaxId: 196380] [57333] (1)
            16. Cardiotoxin II [57334]
                1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57335] (3)
                2. Central asian cobra (Naja naja oxiana) [TaxId: 8657] [57336] (3)
            17. Cardiotoxin III [57337]
                1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57338] (7)
                   SQ P60301 22-81
            18. Cardiotoxin IV [57339]
                1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57340] (2)
            19. Cobrotoxin II (ct2) [57341]
                1. Taiwan cobra (Naja naja atra) [TaxId: 8656] [57342] (3)
                   SQ P60770 22-83
                2. Monocled cobra (Naja kaouthia) [TaxId: 8649] [57343] (1)
            20. alpha-Toxin [57344]
                1. Spitting cobra (Naja nigricollis) [TaxId: 8654] [57345] (2)
                2. Black mamba (Dendroaspis polylepis polylepis) [TaxId: 8620] [57346] (1)
            21. Neurotoxin II (Nt2, cobrotoxin B) [57347]
                1. Central asian cobra (Naja naja oxiana) [TaxId: 8657] [57348] (1)
                2. Monocled cobra (Naja kaouthia) [TaxId: 8649] [64550] (1)
                3. Chinese cobra (Naja atra) [TaxId: 8656] [103569] (2)
                   SQ P80958 22-82
            22. Toxin B (long neurotoxin) [57349]
                1. King cobra (Ophiophagus hannah) [TaxId: 8665] [57350] (2)
            23. Candoxin [69949]
                1. Malayan krait (Bungarus candidus) [TaxId: 92438] [69950] (1)
            24. Bucain [111404]
                1. Malaysian krait (Bungarus candidus) [TaxId: 92438] [111405] (3)
                   SQ P83346
            25. Irditoxin subunit A [144103]
                1. Brown tree snake (Boiga irregularis) [TaxId: 92519] [144104] (1)
                   SQ A0S864 35-109
            26. Irditoxin subunit B [144105]
                1. Brown tree snake (Boiga irregularis) [TaxId: 92519] [144106] (1)
                   SQ A0S865 35-111
            27. Denmotoxin [144107]
                1. Mangrove snake (Boiga dendrophila) [TaxId: 46286] [144108] (2)
                   SQ Q06ZW0 33-111
         2. Dendroaspin [57351] (1)
            1. Dendroaspin [57352]
               lacks neurotoxicity; acts as the disintegrins: contains RGD-motif
               1. Dendroaspis jamesoni kaimosae [TaxId: 8619] [57353] (1)
         3. Extracellular domain of cell surface receptors [57354] (9)
            1. CD59 [57355]
               1. Human (Homo sapiens) [TaxId: 9606] [57356] (10)
            2. Type II activin receptor [57357]
               1. Mouse (Mus musculus) [TaxId: 10090] [57358] (4)
               2. Rat (Rattus norvegicus) [TaxId: 10116] [90154] (2)
               3. Mouse (Mus musculus), isoform IIB [TaxId: 10090] [111406] (3)
                  SQ P27040 23-120; 100% sequence identity to the rat domain of the same type IIb (scop_sp 90154)
            3. BMP receptor Ia ectodomain [57359]
               1. Human (Homo sapiens) [TaxId: 9606] [57360] (6)
            4. TGF-beta type II receptor extracellular domain [69951]
               elaborated with additional structures resulting in a beta-sandwich fold
               1. Human (Homo sapiens) [TaxId: 9606] [69952] (4)
               2. Chicken (Gallus gallus) [TaxId: 9031] [82900] (1)
            5. Urokinase plasminogen activator surface receptor uPAR [161128]
               duplication: tandem repeat of three similar domains; the N-terminal and C-terminal domains belong to Pfam 00021; uPAR/Ly6
               1. Human (Homo sapiens) [TaxId: 9606] [161129] (12)
                  SQ Q03405 109-209! SQ Q03405 210-299! SQ Q03405 23-108
            6. Urokinase plasminogen activator surface receptor, UPAR [161130]
               duplication; comprises three domains of this fold
               1. Human (Homo sapiens) [TaxId: 9606] [161131] (33)
                  SQ Q03405 111-210! SQ Q03405 114-210! SQ Q03405 211-297! SQ Q03405 211-301! SQ Q03405 23-102! SQ Q03405 23-104
   8. BPTI-like [57361] (1)
      disulfide-rich alpha+beta fold
      1. BPTI-like [57362] (3)
         uperfamily
         1. Small Kunitz-type inhibitors & BPTI-like toxins [57363] (12)
            1. Pancreatic trypsin inhibitor, BPTI [57364]
               1. Cow (Bos taurus) [TaxId: 9913] [57365] (90)
            2. Collagen type VI (domain C5 from alpha 3 chain) [57366]
               1. Human (Homo sapiens) [TaxId: 9606] [57367] (6)
            3. Tissue factor pathway inhibitor [57368]
               1. Human (Homo sapiens) [TaxId: 9606] [57369] (5)
            4. Alzheimer's amyloid B-protein precursor, APPI [57370]
               1. Human (Homo sapiens) [TaxId: 9606] [57371] (5)
            5. Bikunin from inter-alpha-inhibitor complex [57372]
               1. Human (Homo sapiens) [TaxId: 9606] [57373] (1)
            6. alpha-Dendrotoxin [57374]
               1. Green mamba (Dendroaspis angusticeps) [TaxId: 8618] [57375] (1)
            7. Venom basic protease inhibitor IX (VIIIb) [90155]
               1. Banded krait (Bungarus fasciatus) [TaxId: 8613] [90156] (1)
            8. beta2-bungarotoxin, neurotoxin chain [57376]
               1. Many-banded krait (Bungarus multicinctus) [TaxId: 8616] [57377] (1)
            9. Trypsin inhibitor [57378]
               1. Sea anemone (Stichodactyla helianthus) [TaxId: 6123] [57379] (1)
            10. Dendrotoxin K [57380]
                1. Black mamba (Dendroaspis polylepis polylepis) [TaxId: 8620] [57381] (1)
            11. Dendrotoxin I [57382]
                1. African elapid snake (Dendroaspis polylepis polylepis) [TaxId: 8620] [57383] (2)
            12. Calcicludine (cac) [57384]
                1. Green mamba (Dendroaspis angusticeps) [TaxId: 8618] [57385] (1)
         2. Soft tick anticoagulant proteins [57386] (2)
            1. Ornithodorin [57387]
               duplication: consists of two BPTI-like domains
               1. Soft tick (Ornithodoros moubata) [TaxId: 6938] [57388] (1)
            2. Anticoagulant protein, factor Xa inhibitor [57389]
               1. Soft tick (Ornithodoros moubata) [TaxId: 6938] [57390] (4)
         3. Tick tryptase inhibitor-like [161132] (1)
            1. Tryptase inhibitor [161133]
               1. Brown ear tick (Rhipicephalus appendiculatus) [TaxId: 34631] [161134] (1)
                  SQ Q1EG59 45-95
   9. Defensin-like [57391] (1)
      Disulfide-rich fold, nearly all-beta
      1. Defensin-like [57392] (3)
         uperfamily
         1. Defensin [57393] (17)
            1. Defensin HNP-3 [57394]
               1. Human (Homo sapiens) [TaxId: 9606] [57395] (1)
            2. Beta-defensin, BD [63384]
               1. Human (Homo sapiens), HBD1 [TaxId: 9606] [64551] (4)
               2. Human (Homo sapiens), HBD2 [TaxId: 9606] [63385] (4)
               3. Human (Homo sapiens), HBD3 [TaxId: 9606] [75672] (1)
               4. Mouse (Mus musculus), MBD5 [TaxId: 10090] [64552] (1)
               5. Mouse (Mus musculus), MBD6 [TaxId: 10090] [64553] (1)
               6. Cow (Bos taurus), BD12 [TaxId: 9913] [63386] (1)
               7. King penguin (Aptenodytes patagonicus), spheniscin-2 [TaxId: 9234] [103570] (1)
            3. Alpha-defensin rk-1 [64554]
               1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [64555] (1)
            4. Defensin-like peptide, DLP [57400]
               1. Duckbilled platypus (Ornithorhynchus anatinus), DLP-1 [TaxId: 9258] [57401] (1)
               2. Duckbilled platypus (Ornithorhynchus anatinus), DLP-2 [TaxId: 9258] [57402] (3)
            5. BDs-I defensin [57403]
               1. Sea anemone (Anemonia sulcata) [TaxId: 6108] [57404] (2)
            6. Sea anemone neurotoxin-1 [57405]
               1. Sea anemone (Stichodactyla helianthus) [TaxId: 6123] [57406] (3)
            7. Sea anemone toxin IA [57407]
               1. Sea anemone (Anemonia sulcata) [TaxId: 6108] [57408] (1)
            8. Anthopleurin-A [57409]
               1. Giant green sea anemone (Anthopleura xanthogrammica) [TaxId: 6112] [57410] (1)
            9. Anthopleurin-B [57411]
               1. Giant green sea anemone (Anthopleura xanthogrammica) [TaxId: 6112] [57412] (1)
            10. Defensin-related cryptdin 4 [118245]
                1. Mouse (Mus musculus) [TaxId: 10090] [118246] (2)
                   SQ P28311 61-92
         2. Myotoxin [90157] (1)
            structurally similar to beta-defensin
            1. Crotamine [90158]
               1. South american rattlesnake (Crotalus durissus terrificus) [TaxId: 8732] [90159] (2)
         3. Tick carboxypeptidase inhibitor-like [161135] (1)
            1. Carboxypeptidase inhibitor [161136]
               consists of two structurally similar to beta-defensin domains
               1. Tick (Rhipicephalus bursa) [TaxId: 67831] [161137] (8)
                  SQ Q5EPH2 23-59! SQ Q5EPH2 60-96
   10. Hairpin loop containing domain-like [57413] (1)
       alpha+beta fold with two crossing loops
       1. Hairpin loop containing domain-like [57414] (3)
          the middle part is structurally similar to some knottins and defensins but differs in the disulfide pattern
          uperfamily
          1. Hairpin loop containing domain [57415] (1)
             1. Hepatocyte growth factor [57416]
                heparin-binding domain
                1. Human (Homo sapiens) [TaxId: 9606] [57417] (8)
          2. Anti-platelet protein [64556] (1)
             1. Anti-platelet protein [64557]
                1. Leech (Haementeria officinalis) [TaxId: 6410] [64558] (1)
          3. Pan module (APPLE domain) [82901] (1)
             probable carbohydrate-binding function
             1. Pan module from microneme protein 5 (MIC-5) [82902]
                1. Eimeria tenella [TaxId: 5802] [82903] (1)
   11. Neurotoxin III (ATX III) [57418] (1)
       disulfide-rich fold
       1. Neurotoxin III (ATX III) [57419] (1)
          uperfamily
          1. Neurotoxin III (ATX III) [57420] (1)
             1. Neurotoxin III (ATX III) [57421]
                1. Sea anemone (Anemonia sulcata) [TaxId: 6108] [57422] (1)
   12. LDL receptor-like module [57423] (1)
       disulfide-rich calcium-binding fold
       1. LDL receptor-like module [57424] (1)
          uperfamily
          1. LDL receptor-like module [57425] (6)
             1. Ligand-binding domain of low-density lipoprotein receptor [57426]
                1. Human (Homo sapiens) [TaxId: 9606] [57427] (13)
                   SQ P01130 272-353
             2. soluble Tva ectodomain, sTva47 [69953]
                the viral-binding domain of Tva
                1. Quail (Coturnix coturnix) [TaxId: 9091] [69954] (2)
             3. Very low-density lipoprotein receptor [103571]
                1. Human (Homo sapiens) [TaxId: 9606] [103572] (1)
             4. Hemoglobin linker chain l1 [144109]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144110] (1)
                   SQ Q9GV76 85-126
             5. Extracellular hemoglobin linker l2 subunit [144111]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144112] (1)
                   SQ Q2I743 98-138
             6. Extracellular hemoglobin linker l3 subunit [144113]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144114] (1)
                   SQ Q2I742 78-118
   13. Crambin-like [57428] (1)
       disulfide-rich alpha+beta fold
       1. Crambin-like [57429] (1)
          uperfamily
          1. Crambin-like [57430] (9)
             1. Crambin [57431]
                1. Abyssinian cabbage (Crambe abyssinica) [TaxId: 3721] [57432] (21)
             2. beta-Purothionin [57433]
                1. Wheat (Triticum aestivum) [TaxId: 4565] [57434] (1)
             3. alpha-1-Purothionin [57435]
                1. Wheat (Triticum aestivum) [TaxId: 4565] [57436] (1)
             4. Viscotoxin a3 [57437]
                1. European mistletoe (Viscum album) [TaxId: 3972] [57438] (2)
             5. Viscotoxin a2 [90160]
                1. European mistletoe (Viscum album) [TaxId: 3972] [90161] (1)
             6. Viscotoxin b [103573]
                1. European mistletoe (Viscum album) [TaxId: 3972] [103574] (1)
             7. Viscotoxin c1 [90162]
                1. European mistletoe (Viscum album) [TaxId: 3972] [90163] (1)
             8. Hellethionin D [90164]
                1. Helleborus purpurascens [TaxId: 171899] [90165] (1)
             9. Hordothionin [118247]
                1. Barley (Hordeum vulgare) [TaxId: 4513] [118248] (1)
                   SQ P21742 28-72
   14. Kringle-like [57439] (1)
       disulfide-rich fold; nearly all-beta
       1. Kringle-like [57440] (2)
          uperfamily
          1. Kringle modules [57441] (9)
             1. Plasminogen [63400]
                1. Human (Homo sapiens) [TaxId: 9606] [63401] (22)
             2. Prothrombin [57448]
                1. Cow (Bos taurus) [TaxId: 9913] [57449] (5)
             3. Meizothrombin [57450]
                1. Cow (Bos taurus) [TaxId: 9913] [57451] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [57452] (1)
             4. Urokinase-type plasminogen activator [57453]
                1. Human (Homo sapiens) [TaxId: 9606] [57454] (13)
             5. Apolipoprotein A [57455]
                1. Human (Homo sapiens), IV-10/M66 variant [TaxId: 9606] [57456] (3)
                2. Human (Homo sapiens), IV-6 variant [TaxId: 9606] [75673] (1)
                3. Human (Homo sapiens), IV-7 variant [TaxId: 9606] [64559] (1)
             6. NK1 fragment of hepatocyte growth factor [57457]
                1. Human (Homo sapiens) [TaxId: 9606] [57458] (7)
          2. Fibronectin type II module [57459] (4)
             shorter two-disulfide version of a kringle module
             1. PDC-109, collagen-binding type II domain [57460]
                1. Cow (Bos taurus) [TaxId: 9913] [57461] (2)
             2. Fibronectin [57462]
                1. Human (Homo sapiens) [TaxId: 9606] [57463] (4)
             3. Gelatinase A (MMP-2) type II modules [57464]
                duplication: tandem repeat of three modules inserted in the catalytic domain
                1. Human (Homo sapiens) [TaxId: 9606] [57465] (6)
             4. Gelatinase B (MMP-9) type II modules [75674]
                duplication: tandem repeat of three modules inserted in the catalytic domain
                1. Human (Homo sapiens) [TaxId: 9606] [75675] (1)
   15. Kazal-type serine protease inhibitors [100894] (1)
       1. Kazal-type serine protease inhibitors [100895] (2)
          conserved core consists of a helix and a loop crosslinked with two disulfides
          uperfamily
          1. Ovomucoid domain III-like [57468] (14)
             1. Ovomucoid domains [57469]
                unless specified in the comment, the listed structures are of domain III
                1. Turkey (Meleagris gallopavo) [TaxId: 9103] [57470] (39)
                2. Japanese quail (Coturnix coturnix japonica) [TaxId: 93934] [57471] (2)
                3. Silver pheasant (Lophura nycthemera) [TaxId: 9046] [57472] (4)
             2. Secretory trypsin inhibitor [57473]
                1. Human (Homo sapiens) [TaxId: 9606] [57474] (3)
                2. Pig (Sus scrofa) [TaxId: 9823] [57475] (1)
             3. Blood-sucking insect-derived tryptase inhibitor [57476]
                duplication: contains two domains of this fold
                1. Bug (Rhodnius prolixus), rhodniin [TaxId: 13249] [57477] (2)
                2. Triatoma infestans [TaxId: 30076] [161138] (2)
                   SQ Q95P16 170-222! SQ Q95P16 5-50
                   infestin
             4. Dipetalin [75676]
                1. Dipetalogaster maximus, dipetalin [TaxId: 72496] [75677] (1)
             5. Domain of BM-40/SPARC/osteonectin [57478]
                the C-terminal part of FS module
                1. Human (Homo sapiens) [TaxId: 9606] [57479] (2)
             6. Domain of follistatin [90166]
                the C-terminal part of the heparin-binding module, FS1
                1. Rat (Rattus norvegicus) [TaxId: 10116] [90167] (3)
             7. Seminal plasma inhibitor IIa [57480]
                1. Cow (Bos taurus) [TaxId: 9913] [57481] (2)
             8. PEC-60 peptide [57482]
                1. Pig (Sus scrofa) [TaxId: 9823] [57483] (1)
             9. Leech derived tryptase inhibitor (LDTI-C) [57484]
                1. Medicinal leech (Hirudo medicinalis) [TaxId: 6421] [57485] (2)
             10. Ascidian trypsin inhibitor [75678]
                 1. Sea squirt (Halocynthia roretzi) [TaxId: 7729] [75679] (1)
          2. Serine proteinase inhibitor lekti [69960] (1)
             1. Serine proteinase inhibitor lekti [69961]
                kazal-type 5 serine protease inhibitor; consists of several similar domains
                1. Human (Homo sapiens) [TaxId: 9606] [69962] (3)
                   SQ Q9NQ38 28-77
   16. Plant proteinase inhibitors [100896] (1)
       disulfide-rich small alpha+beta fold; topological similarity to the Ovomucoid domain III
       1. Plant proteinase inhibitors [100897] (1)
          uperfamily
          1. Plant proteinase inhibitors [57486] (3)
             1. Plant chymotrypsin inhibitor [57487]
                1. Potato tuber (Solanum tuberosum) [TaxId: 4113] [57488] (1)
             2. Multidomain proteinase inhibitor [57489]
                1. Winged tobacco (Nicotiana alata) [TaxId: 4087] [57490] (4)
             3. Wound-induced proteinase inhibitor-II [90168]
                two-domain inhibitor; consists of one continuous domain of canonical fold and one discontinuous, circularly-permutated domain
                1. Tomato (Lycopersicon esculentum) [TaxId: 4081] [90169] (2)
   17. Trefoil/Plexin domain-like [57491] (3)
       disulfide-rich fold; common core is alpha+beta with two conserved disulfides
       1. Trefoil [57492] (1)
          uperfamily
          1. Trefoil [57493] (3)
             1. Pancreatic spasmolytic polypeptide [57494]
                duplication: consists of two homologous domains
                1. Pig (Sus scrofa) [TaxId: 9823] [57495] (4)
             2. PNR-2/PS2, TFF1 [57496]
                single trefoil motif protein
                1. Human (Homo sapiens) [TaxId: 9606] [57497] (2)
             3. Intestinal trefoil factor [57498]
                1. Human (Homo sapiens) [TaxId: 9606] [57499] (2)
       2. Plexin repeat [103575] (1)
          uperfamily
          1. Plexin repeat [103576] (3)
             Pfam 01437
             1. Semaphorin 4d [103577]
                1. Human (Homo sapiens) [TaxId: 9606] [103578] (1)
             2. Hepatocyte growth factor receptor [111407]
                1. Human (Homo sapiens) [TaxId: 9606] [111408] (2)
                   SQ P08581 40-564
             3. Integrin beta-3 [118249]
                1. Human (Homo sapiens) [TaxId: 9606] [118250] (2)
                   SQ P05106 27-716 ! SQ P05106 27-466
       3. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118251] (1)
          alpha-beta(2)-alpha; fragment of a larger dimeric protein
          uperfamily
          1. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118252] (1)
             1. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118253]
                1. Trypanosoma brucei brucei [TaxId: 5702] [118254] (1)
                   SQ P26332 385-459 # structure of the N-terminal domain (27-390) is also known (scop_sp 58090)
   18. Necrosis inducing protein 1, NIP1 [103579] (1)
       disulfide-rich fold; all-beta; duplication: contains two structural repeats
       1. Necrosis inducing protein 1, NIP1 [103580] (1)
          uperfamily
          1. Necrosis inducing protein 1, NIP1 [103581] (1)
             1. Necrosis inducing protein 1, NIP1 [103582]
                1. Leaf blotch of barley (Rhynchosporium secalis) [TaxId: 38038] [103583] (1)
   19. Cystine-knot cytokines [57500] (1)
       disulfide-rich fold; common core is all-beta
       1. Cystine-knot cytokines [57501] (7)
          uperfamily
          1. Platelet-derived growth factor-like [57502] (5)
             1. Platelet-derived growth factor BB [57503]
                1. Human (Homo sapiens) [TaxId: 9606] [57504] (1)
             2. Vascular endothelial growth factor, VEGF [57505]
                1. Human (Homo sapiens) [TaxId: 9606] [57506] (25)
                   SQ P15692 40-133
                2. Aspic viper (Vipera aspis aspis) [TaxId: 8706] [118255] (1)
                   SQ P67863 1-100 # svVEGF (toxin); vammin
                3. Russell's viper (Daboia russelli russelli) [TaxId: 8707] [118256] (1)
                   SQ P67861 2-95 # svVEGF (toxin); VR-1
             3. Placenta growth factor-1, PLGF-1 [64560]
                1. Human (Homo sapiens) [TaxId: 9606] [64561] (2)
          2. Transforming growth factor (TGF)-beta [57507] (7)
             1. TGF-beta3 [57508]
                1. Human (Homo sapiens) [TaxId: 9606] [57509] (4)
             2. TGF-beta2 [57510]
                1. Human (Homo sapiens) [TaxId: 9606] [57511] (2)
             3. TGF-beta1 [57512]
                1. Human (Homo sapiens) [TaxId: 9606] [57513] (3)
             4. Bone morphogenetic protein-7 (BMP-7) [57514]
                1. Human (Homo sapiens) [TaxId: 9606] [57515] (4)
             5. Bone morphogenetic protein-2 (BMP-2) [57516]
                1. Human (Homo sapiens) [TaxId: 9606] [57517] (15)
             6. Activin A (Inhibin beta A) [90170]
                1. Human (Homo sapiens) [TaxId: 9606] [90171] (14)
                   SQ P08476 311-426
             7. Glial cell-derived neurotrophic factor, GDNF [57518]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [57519] (1)
          3. Noggin [82904] (1)
             1. Noggin [82905]
                BMP-7 antagonist
                1. Human (Homo sapiens) [TaxId: 9606] [82906] (1)
          4. Neurotrophin [57520] (5)
             1. Brain-derived neurotrophic factor, BDNF [88882]
                1. Human (Homo sapiens) [TaxId: 9606] [88883] (2)
             2. Neurotrophin 3, NT3 [88884]
                1. Human (Homo sapiens) [TaxId: 9606] [88885] (5)
             3. Neurotrophin 4, NT4 [57523]
                1. Human (Homo sapiens) [TaxId: 9606] [57524] (3)
             4. beta-Nerve growth factor [57525]
                1. Mouse (Mus musculus) [TaxId: 10090] [57526] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [57527] (4)
                   SQ P01138
          5. Gonadodropin/Follitropin [57528] (3)
             1. Glycoprotein hormones alpha chain (Gonadotropin A, Follitropin alpha) [63395]
                1. Human (Homo sapiens) [TaxId: 9606] [63397] (9)
             2. Gonadotropin B chain [63396]
                1. Human (Homo sapiens) [TaxId: 9606] [63398] (3)
             3. Follicle stimulating hormone, follitropin, beta chain [64562]
                1. Human (Homo sapiens) [TaxId: 9606] [64563] (3)
          6. Interleukin 17F, IL-17F [69955] (1)
             1. Interleukin 17F, IL-17F [69956]
                1. Human (Homo sapiens) [TaxId: 9606] [69957] (1)
          7. Coagulogen [57531] (1)
             1. Coagulogen [57532]
                1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [57533] (1)
   20. Complement control module/SCR domain [57534] (1)
       disulfide-rich all-beta fold
       1. Complement control module/SCR domain [57535] (1)
          uperfamily
          1. Complement control module/SCR domain [57536] (15)
             Pfam 00084
             1. Factor H, 15th and 16th modules [57537]
                1. Human (Homo sapiens) [TaxId: 9606] [57538] (3)
             2. Complement control protein [57539]
                1. Vaccinia virus [TaxId: 10245] [57540] (15)
                   SQ P10998
                   a complement protein that regulates both pathways of complement activation and binds heparan sulfate proteoglycans
             3. CD46 (membrane cofactor protein, MCP) [57541]
                1. Human (Homo sapiens) [TaxId: 9606] [57542] (5)
             4. beta2-glycoprotein I [57543]
                consists of five modules with the C-terminal module fold being altered
                1. Human (Homo sapiens) [TaxId: 9606] [57544] (4)
             5. Complement decay-accelerating factor (Daf, CD55) [90172]
                1. Human (Homo sapiens) [TaxId: 9606] [90173] (21)
             6. Complement receptor 1, cr1 [75680]
                1. Human (Homo sapiens) [TaxId: 9606] [75681] (3)
             7. Complement receptor 2, cr2 [64564]
                1. Human (Homo sapiens) [TaxId: 9606] [64565] (6)
             8. Complement C1S protease domain [64566]
                1. Human (Homo sapiens) [TaxId: 9606] [64567] (1)
             9. Complement C1R protease domains [75682]
                1. Human (Homo sapiens) [TaxId: 9606] [75683] (4)
             10. Mannan-binding lectin serine protease 2 (MASP-2) domains [111409]
                 1. Human (Homo sapiens) [TaxId: 9606] [111410] (2)
                    SQ O00187 366-686
             11. GABA-B receptor 1 [118257]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [118258] (2)
                    SQ Q9Z0U4 96-159
             12. Complement factor B [144115]
                 contains tandemrepeat of three SCR (Sushi) domains
                 1. Human (Homo sapiens) [TaxId: 9606] [144116] (3)
                    SQ P00751 102-162! SQ P00751 163-224! SQ P00751 34-101
             13. Interleukin-2 receptor alpha chain [144117]
                 consists of two segment-swapped SCR domains
                 1. Human (Homo sapiens) [TaxId: 9606] [144118] (8)
                    SQ P01589 121-186! SQ P01589 124-186! SQ P01589 125-186! SQ P01589 22-85
             14. Interleukin-15 receptor subunit alpha [161139]
                 1. Mouse (Mus musculus) [TaxId: 10090] [161140] (2)
                    SQ Q60819 35-103
                 2. Human (Homo sapiens) [TaxId: 9606] [161141] (11)
                    SQ Q13261 31-108! SQ Q13261 31-96
   21. Crisp domain-like [57545] (1)
       disulfide-rich all-alpha fold
       1. Crisp domain-like [57546] (2)
          uperfamily
          1. Sea anemone toxin k [57547] (2)
             1. Sea anemone toxin k [57548]
                1. Sea anemone (Bunodosoma granulifera), BGK [TaxId: 31164] [57549] (1)
                2. Sun anemone (Stichodactyla helianthus), SHK [TaxId: 6123] [57550] (3)
          2. Crisp domain [118259] (1)
             Pfam 08562; contains extra N-terminal knottin-like subdomain
             1. Cysteine-rich secretory protein (SteCRISP) [118260]
                1. Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] [118261] (1)
                   SQ P60623 13-233
   22. Blood coagulation inhibitor (disintegrin) [57551] (1)
       small disulfide-rich
       1. Blood coagulation inhibitor (disintegrin) [57552] (1)
          uperfamily
          1. Blood coagulation inhibitor (disintegrin) [57553] (6)
             1. Echistatin [57554]
                1. Saw-scaled viper (Echis carinatus) [TaxId: 40353] [57555] (2)
             2. Flavoridin (triflavin) [57556]
                1. Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] [57557] (2)
             3. Kistrin (rhodostomin) [57558]
                1. Agkistrodon rhodostoma [TaxId: 8717] [57559] (6)
                   SQ P30403 408-475
             4. Obtustatin [82907]
                1. Blunt-nosed viper (Vipera lebetina obtusa) [TaxId: 209528] [82908] (1)
                   non-RGD disintegrin; conserved cysteines form different disulfides (?)
             5. Salmosin [103584]
                1. Halys viper (Agkistrodon halys) [TaxId: 8714] [103585] (1)
             6. Schistatin [111411]
                1. Saw-scaled viper (Echis carinatus), different isoforms [TaxId: 40353] [111412] (2)
                   SQ P83658
   23. Methylamine dehydrogenase, L chain [57560] (1)
       disulfide-rich; nearly all-beta
       1. Methylamine dehydrogenase, L chain [57561] (1)
          uperfamily
          1. Methylamine dehydrogenase, L chain [57562] (2)
             1. Methylamine dehydrogenase [57563]
                1. Paracoccus denitrificans [TaxId: 266] [57564] (21)
                2. Gram negative methylotrophic bacteria (Thiobacillus versutus) [TaxId: 34007] [57565] (3)
   24. Serine protease inhibitors [57566] (1)
       disulfide-rich; nearly all-beta
       1. Serine protease inhibitors [57567] (2)
          uperfamily
          1. ATI-like [57568] (4)
             1. Ascaris trypsin inhibitor, ATI [57569]
                1. Pig roundworm (Ascaris suum) [TaxId: 6253] [57570] (4)
             2. Ascaris elastase inhibitor [57571]
                1. Pig roundworm (Ascaris suum) [TaxId: 6253] [57572] (1)
             3. Anticoagulant protein [57573]
                1. Dog hookworm (Ancylostoma caninum) [TaxId: 29170] [57574] (2)
             4. Chymotrypsin inhibitor AMCI [57575]
                1. Honeybee (Apis mellifera) [TaxId: 7460] [57576] (1)
          2. BSTI [57577] (1)
             1. BSTI [57578]
                1. Fire-bellied toad (Bombina bombina) [TaxId: 8345] [57579] (1)
   25. TB module/8-cys domain [57580] (1)
       disulfide-rich; alpha+beta
       1. TB module/8-cys domain [57581] (1)
          uperfamily
          1. TB module/8-cys domain [57582] (2)
             transforming growth factor beta binding protein-like domain
             1. Fibrillin [57583]
                1. Human (Homo sapiens) [TaxId: 9606] [57584] (5)
             2. Transforming growth factor-beta binding protein-1 [103586]
                1. Human (Homo sapiens) [TaxId: 9606] [103587] (1)
   26. TNF receptor-like [57585] (1)
       duplication: consists of three similar disulfide-rich domains
       1. TNF receptor-like [57586] (2)
          uperfamily
          1. TNF receptor-like [57587] (5)
             Pfam 00020; TNFR/NGFR cysteine-rich region
             1. Tumor necrosis factor (TNF) receptor [57588]
                1. Human (Homo sapiens) [TaxId: 9606] [57589] (4)
             2. Death receptor-5 (dr5) fragment [57590]
                1. Human (Homo sapiens) [TaxId: 9606] [57591] (12)
             3. Cellular receptor HveA [64568]
                1. Human (Homo sapiens) [TaxId: 9606] [64569] (5)
             4. Low affinity neurotrophin receptor p75NTR [111413]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [111414] (9)
                   SQ P07174 31-190 # fragment contains 3 complete and 1 partial (C-terminal) 'domains'
             5. Tumor necrosis factor receptor superfamily member 4, OX40L receptor [144119]
                1. Human (Homo sapiens) [TaxId: 9606] [144120] (9)
                   SQ P43489 143-168! SQ P43489 29-82! SQ P43489 83-142
          2. BAFF receptor-like [90174] (3)
             only fragments of the receptor structures are available; no domain division is provided here
             1. Tumor necrosis factor receptor superfamily member 13c, BAFF-R, Br3 [90175]
                1. Human (Homo sapiens) [TaxId: 9606] [90176] (2)
                   also includes the PDB entry (1p0t) that together with the entry (1otz) provides the multimeric structure of the complex of BAFF receptor with BAFF. In these entries protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
             2. Tumor necrosis factor receptor superfamily member 17, BCMA [90177]
                1. Human (Homo sapiens) [TaxId: 9606] [90178] (2)
                   SQ Q02223 8-43
             3. Tumor necrosis factor receptor superfamily member 13B, TACI [118262]
                1. Human (Homo sapiens) [TaxId: 9606] [118263] (2)
                   SQ O14836 68-109
   27. Heparin-binding domain from vascular endothelial growth factor [57592] (1)
       duplication: consists of two similar disulfide-rich domains, alpha+beta
       1. Heparin-binding domain from vascular endothelial growth factor [57593] (1)
          uperfamily
          1. Heparin-binding domain from vascular endothelial growth factor [57594] (1)
             1. Heparin-binding domain from vascular endothelial growth factor [57595]
                1. Human (Homo sapiens) [TaxId: 9606] [57596] (3)
   28. Antifungal protein (AGAFP) [57597] (1)
       disulfide-rich; all-beta: open barrel, 5 strands; OB-fold-like
       1. Antifungal protein (AGAFP) [57598] (1)
          uperfamily
          1. Antifungal protein (AGAFP) [57599] (1)
             1. Antifungal protein (AGAFP) [57600]
                1. Mold (Aspergillus giganteus) [TaxId: 5060] [57601] (1)
   29. FnI-like domain [57602] (1)
       disulfide-rich, all-beta
       1. FnI-like domain [57603] (2)
          uperfamily
          1. Fibronectin type I module [57604] (2)
             1. Fibronectin [57605]
                1. Human (Homo sapiens) [TaxId: 9606] [57606] (44)
             2. Tissue-type plasminogen activator, t-PA [57607]
                1. Human (Homo sapiens) [TaxId: 9606] [57608] (3)
          2. VWC domain [118264] (1)
             Pfam 00093; similar to FnI domain in the N-terminal part, contains extra C-terminal subdomain
             1. Collagen alpha 1(II) chain precursor [118265]
                1. Human (Homo sapiens) [TaxId: 9606] [118266] (1)
                   SQ P02458 29-97
   30. Thyroglobulin type-1 domain [57609] (1)
       disulfide-rich, alpha+beta
       1. Thyroglobulin type-1 domain [57610] (1)
          uperfamily
          1. Thyroglobulin type-1 domain [57611] (4)
             Pfam 00086
             1. Class II MHC associated p41 invariant chain fragment [57612]
                1. Human (Homo sapiens) [TaxId: 9606] [57613] (2)
             2. Insulin-like growth factor binding protein 6 [111415]
                1. Human (Homo sapiens) [TaxId: 9606] [111416] (1)
                   SQ P24592 161-240
             3. Insulin-like growth factor-binding protein 1, IGFBP1 [161142]
                1. Human (Homo sapiens) [TaxId: 9606] [161143] (2)
                   SQ P08833 174-256
             4. Insulin-like growth factor-binding protein 4, IGFBP4 [161144]
                1. Human (Homo sapiens) [TaxId: 9606] [161145] (1)
                   SQ P22692 172-250
   31. Type X cellulose binding domain, CBDX [57614] (1)
       disulfide-rich, alpha+beta
       1. Type X cellulose binding domain, CBDX [57615] (1)
          uperfamily
          1. Type X cellulose binding domain, CBDX [57616] (1)
             1. Endo-1;4-beta-xylanase A CBDX [57617]
                1. Pseudomonas fluorescens, subsp. cellulosa [TaxId: 294] [57618] (2)
   32. Cellulose docking domain, dockering [64570] (1)
       disulfide-rich, alpha+beta
       1. Cellulose docking domain, dockering [64571] (1)
          uperfamily
          1. Cellulose docking domain, dockering [64572] (1)
             1. Cellulose docking domain, dockering [64573]
                1. Piromyces equi [TaxId: 99929] [64574] (2)
   33. Carboxypeptidase inhibitor [57619] (1)
       disulfide-rich, alpha+beta
       1. Carboxypeptidase inhibitor [57620] (1)
          uperfamily
          1. Carboxypeptidase inhibitor [57621] (1)
             1. Carboxypeptidase inhibitor [57622]
                1. Medicinal leech (Hirudo medicinalis) [TaxId: 6421] [57623] (8)
   34. Invertebrate chitin-binding proteins [57624] (1)
       disulfide-rich
       1. Invertebrate chitin-binding proteins [57625] (2)
          shares a putative chitin-binding motif with the plant lectins/antimicrobial peptides superfamily but lacks one of the conserved disulfides of the knottin fold
          uperfamily
          1. Tachycitin [57626] (1)
             1. Tachycitin [57627]
                an antimicrobial protein with chitin-binding function
                1. Horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [57628] (1)
          2. Antifungal peptide scarabaecin [90179] (1)
             1. Antifungal peptide scarabaecin [90180]
                1. Beetle (Oryctes rhinoceros) [TaxId: 72550] [90181] (1)
   35. Pheromone ER-23 [69963] (1)
       disulfide-rich, all-alpha
       1. Pheromone ER-23 [69964] (1)
          uperfamily
          1. Pheromone ER-23 [69965] (1)
             1. Pheromone ER-23 [69966]
                1. Euplotes raikovi [TaxId: 5938] [69967] (1)
   36. Mollusk pheromone [90182] (1)
       disulfide-rich; all-alpha
       1. Mollusk pheromone [90183] (1)
          uperfamily
          1. Mollusk pheromone [90184] (1)
             1. Attractin [90185]
                1. California sea hare (Aplysia californica) [TaxId: 6500] [90186] (1)
   37. Apical membrane antigen 1 [82909] (1)
       disulfide-rich, alpha+beta
       1. Apical membrane antigen 1 [82910] (1)
          uperfamily
          1. Apical membrane antigen 1 [82911] (1)
             1. Apical membrane antigen 1 [82912]
                1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [82913] (3)
   38. Somatomedin B domain [90187] (1)
       disulfide-rich
       1. Somatomedin B domain [90188] (1)
          uperfamily
          1. Somatomedin B domain [90189] (1)
             1. Vitronectin [90190]
                1. Human (Homo sapiens) [TaxId: 9606] [90191] (6)
                   SQ P04004 20-70
   39. Notch domain [90192] (1)
       disulfide-rich; all-alpha; calcium-binding
       1. Notch domain [90193] (1)
          uperfamily
          1. Notch domain [90194] (1)
             also called DSL domain or LNR repeat
             1. Neurogenic locus notch homolog protein 1 [90195]
                1. Human (Homo sapiens) [TaxId: 9606] [90196] (1)
   40. Mini-collagen I, C-terminal domain [103588] (1)
       disulfide-rich
       1. Mini-collagen I, C-terminal domain [103589] (1)
          uperfamily
          1. Mini-collagen I, C-terminal domain [103590] (1)
             1. Mini-collagen I, C-terminal domain [103591]
                1. Hydra sp. [TaxId: 6086] [103592] (2)
                   SQ Q00484 126-149
   41. Hormone receptor domain [111417] (1)
       disulfide-rich all-beta fold; contains beta sandwich of 5 strands
       1. Hormone receptor domain [111418] (1)
          uperfamily
          1. Hormone receptor domain [111419] (2)
             Pfam 02793; HRM
             1. Corticotropin releasing factor receptor 2, CRFR-2beta [111420]
                1. Mouse (Mus musculus) [TaxId: 10090] [111421] (1)
                   SQ Q60748 39-133
             2. Pituitary adenylate cyclase-activating polypeptide type I receptor [161146]
                1. Human (Homo sapiens) [TaxId: 9606] [161147] (1)
                   SQ P41586 17-143
   42. Resistin [111422] (1)
       disulfide-rich six-stranded beta-sandwich; jelly-roll
       1. Resistin [111423] (1)
          uperfamily
          1. Resistin [111424] (2)
             Pfam 06954
             1. Resistin (ADSF, FIZZ3) [111425]
                1. Mouse (Mus musculus) [TaxId: 10090] [111426] (2)
                   SQ Q99P87 26-114
             2. Resistin-like beta (FIZZ2) [111427]
                1. Mouse (Mus musculus) [TaxId: 10090] [111428] (1)
                   SQ Q99P86 25-105
   43. YAP1 redox domain [111429] (1)
       bipartite cysteine-rich all-alpha domain; a single helix in the N-terminal part (chain A) is linked by disulfides to the C-terminal part (chain B) [3-helical bundle of the RuvA C-terminal domain-like fold (scop_cf 46928)
       1. YAP1 redox domain [111430] (1)
          uperfamily
          1. YAP1 redox domain [111431] (1)
             1. YAP1 redox domain [111432]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111433] (1)
                   SQ P19880 279-313,565-650
   44. Toxic hairpin [57006] (4)
       disulfide crosslinked alpha-helical hairpin
       1. Heat-stable enterotoxin B [57007] (1)
          uperfamily
          1. Heat-stable enterotoxin B [57008] (1)
             contains 2 disulfides
             1. Heat-stable enterotoxin B [57009]
                1. Escherichia coli [TaxId: 562] [57010] (1)
       2. Neurotoxin B-IV [57011] (1)
          uperfamily
          1. Neurotoxin B-IV [57012] (1)
             contains 4 disulfides
             1. Neurotoxin B-IV [57013]
                1. Milky ribbon worm (Cerebratulus lacteus) [TaxId: 6221] [57014] (1)
       3. Pollen allergen ole e 6 [111388] (1)
          contains 3 disulfides
          uperfamily
          1. Pollen allergen ole e 6 [111389] (1)
             1. Pollen allergen ole e 6 [111390]
                1. Common olive (Olea europaea) [TaxId: 4146] [111391] (1)
                   SQ O24172
       4. VhTI-like [161148] (1)
          1. VhTI-like [161149] (1)
             1. Trypsin inhibitor VhTI [161150]
                1. Veronica hederifolia [TaxId: 202477] [161151] (1)
                   SQ P85981 7-29
   45. Tim10-like [144121] (1)
       alpha-hairpin crosslinked by two disulfides; assembles into a heterohexameric ring-like structure
       1. Tim10-like [144122] (1)
          uperfamily
          1. Tim10/DDP [144123] (2)
             Pfam 02953; note: not a zinc finger
             1. Mitochondrial import inner membrane translocase subunit Tim9 [144124]
                1. Human (Homo sapiens) [TaxId: 9606] [144125] (2)
                   SQ Q9Y5J7 13-85
             2. Mitochondrial import inner membrane translocase subunit Tim10 [144126]
                1. Human (Homo sapiens) [TaxId: 9606] [144127] (3)
                   SQ P62072 13-77
   46. Cysteine zipper [144128] (1)
       string of helices that contain cysteines at almost every turn; folds upon itself and is crosslnked by multiple disulfides
       1. Vanabin-like [144129] (1)
          uperfamily
          1. Vanabin-like [144130] (1)
             1. Vanadium-binding protein 2, vanabin 2 [144131]
                1. Vanadium-rich ascidian (Ascidia sydneiensis samea) [TaxId: 79730] [144132] (1)
                   SQ Q86BW2 29-120
   47. GLA-domain [57629] (1)
       Calcium ion-bound
       1. GLA-domain [57630] (1)
          gamma-carboxy-glutamic acid-rich domain
          uperfamily
          1. GLA-domain [57631] (9)
             1. Coagulation factor VIIa [57632]
                1. Human (Homo sapiens) [TaxId: 9606] [57633] (2)
             2. Prothrombin [57634]
                1. Cow (Bos taurus) [TaxId: 9913] [57635] (5)
             3. Coagulation factor IX (IXa) [57636]
                1. Human (Homo sapiens) [TaxId: 9606] [57637] (8)
                2. Pig (Sus scrofa) [TaxId: 9823] [57638] (15)
             4. Coagulation factor X [57639]
                1. Cow (Bos taurus) [TaxId: 9913] [57640] (3)
                2. Human (Homo sapiens) [TaxId: 9606] [103593] (1)
             5. Coagulation factor XIV (Protein C) [75684]
                1. Human (Homo sapiens) [TaxId: 9606] [75685] (1)
             6. Osteocalcin [103594]
                1. Cow (Bos taurus) [TaxId: 9913] [103595] (1)
                2. Pig (Sus scrofa) [TaxId: 9823] [103596] (1)
   48. Cholecystokinin A receptor, N-domain [57641] (1)
       a few helical turns and a disulfide-crosslinked loop
       1. Cholecystokinin A receptor, N-domain [57642] (1)
          uperfamily
          1. Cholecystokinin A receptor, N-domain [57643] (1)
             1. Cholecystokinin A receptor, N-domain [57644]
                1. Human (Homo sapiens) [TaxId: 9606] [57645] (1)
   49. HIV-1 VPU cytoplasmic domain [57646] (1)
       a few helical turns assembled without a hydrophobic core?
       1. HIV-1 VPU cytoplasmic domain [57647] (1)
          uperfamily
          1. HIV-1 VPU cytoplasmic domain [57648] (1)
             1. HIV-1 VPU cytoplasmic domain [57649]
                1. Human immunodeficiency virus type 1 [TaxId: 11676] [57650] (1)
   50. HIPIP (high potential iron protein) [57651] (1)
       folds around 4Fe-4S cluster
       1. HIPIP (high potential iron protein) [57652] (1)
          uperfamily
          1. HIPIP (high potential iron protein) [57653] (7)
             1. HIPIP (high potential iron protein) [57654]
                1. Rhodocyclus tenuis [TaxId: 1066] [57655] (1)
                2. Allochromatium vinosum, (formerly Chromatium vinosum) [TaxId: 1049] [57656] (8)
                3. Chromatium purpuratum [TaxId: 37487] [57657] (1)
                4. Ectothiorhodospira halophila [TaxId: 1053] [57658] (3)
                5. Ectothiorhodospira vacuolata [TaxId: 1054] [57659] (1)
                6. Thermochromatium tepidum [TaxId: 1050] [57660] (4)
                7. Rhodoferax fermentans, a phototrophic bacterium [TaxId: 28066] [90197] (1)
   51. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57661] (1)
       folds around 4Fe-4S cluster
       1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57662] (1)
          uperfamily
          1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57663] (1)
             1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57664]
                1. Synechocystis sp. [TaxId: 1143] [57665] (6)
   52. beta-beta-alpha zinc fingers [57666] (1)
       simple fold, consisting of the N-terminal beta-hairpin and C-terminal alpha-helical region; each part provides two zinc-coordinating residues with the observed sequences including C2H2, C2HC and CHHC
       1. beta-beta-alpha zinc fingers [57667] (7)
          uperfamily
          1. Classic zinc finger, C2H2 [57668] (30)
             1. ZIF268 [57669]
                duplication: consists of 3 fingers
                1. Mouse (Mus musculus) [TaxId: 10090] [57670] (14)
             2. V(D)J recombination activating protein 1 (RAG1), dimerization domain [57671]
                1. Mouse (Mus musculus) [TaxId: 10090] [57672] (1)
             3. Tramtrack protein (two zinc-finger peptide) [57673]
                1. Drosophila melanogaster [TaxId: 7227] [57674] (1)
             4. ADR1 [57675]
                1. Synthetic, based on Saccharomyces cerevisiae sequence [57676] (5)
             5. XFIN, third domain [57677]
                1. Xenopus laevis [TaxId: 8355] [57678] (1)
             6. ZFY [57679]
                1. Human (Homo sapiens) [TaxId: 9606] [57680] (5)
                   SQ P08048 570-598
             7. SWI5 zinc-finger domains [57681]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57682] (2)
             8. Five-finger GLI1 [57683]
                1. Human (Homo sapiens) [TaxId: 9606] [57684] (1)
             9. Enhancer binding protein [57685]
                duplication: consists of two Zn fingers
                1. Human (Homo sapiens) [TaxId: 9606] [57686] (3)
             10. Transcription factor sp1 [57687]
                 1. Human (Homo sapiens) [TaxId: 9606] [57688] (4)
             11. Transactivation domain of cre-bp1/atf-2 [57689]
                 1. Human (Homo sapiens) [TaxId: 9606] [57690] (1)
             12. Ying-yang 1 (yy1, zinc finger domain) [57691]
                 duplication: consists of 4 fingers
                 1. Human (Homo sapiens) [TaxId: 9606] [57692] (1)
             13. Transcription factor IIIA, TFIIIA [57693]
                 duplication: consists of 6 fingers
                 1. Xenopus laevis [TaxId: 8355] [57694] (9)
             14. GAGA factor [57695]
                 1. Drosophila melanogaster [TaxId: 7227] [57696] (2)
             15. Kruppel-like factor 3, Bklf [103597]
                 1. Mouse (Mus musculus) [TaxId: 10090] [103598] (3)
             16. Zinc finger protein ZFPM1 (FOG-1) [111434]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111435] (1)
                    SQ O35615 328-360
             17. Zinc finger protein 295, ZNF295 [118267]
                 1. Human (Homo sapiens) [TaxId: 9606] [118268] (1)
                    SQ Q9ULJ3 713-806
             18. Wilms' tumor protein, WT1 [118269]
                 1. Human (Homo sapiens) [TaxId: 9606] [118270] (1)
                    SQ P19544 381-408
             19. Zinc finger protein 292, ZNF292 [144133]
                 1. Human (Homo sapiens) [TaxId: 9606] [144134] (1)
                    SQ O60281 1340-1400
             20. Zinc finger protein 512, ZNF512 [144135]
                 1. Human (Homo sapiens) [TaxId: 9606] [144136] (2)
                    SQ Q96ME7 142-194! SQ Q96ME7 195-224
             21. Zinc finger protein 462, ZNF462 [144137]
                 1. Human (Homo sapiens) [TaxId: 9606] [144138] (1)
                    SQ Q96JM2 719-793
             22. Zinc finger protein 692, ZNF692 [144139]
                 1. Human (Homo sapiens) [TaxId: 9606] [144140] (2)
                    SQ Q9BU19 328-357! SQ Q9BU19 358-393
             23. Zinc fingers and homeoboxes protein 1, ZHX1 [144141]
                 1. Human (Homo sapiens) [TaxId: 9606] [144142] (2)
                    SQ Q9UKY1 60-95! SQ Q9UKY1 96-153
             24. Zinc finger protein 24 [144143]
                 1. Human (Homo sapiens) [TaxId: 9606] [144144] (2)
                    SQ P17028 272-304! SQ P17028 305-330
             25. Zinc finger protein 297b [144145]
                 1. Human (Homo sapiens) [TaxId: 9606] [144146] (2)
                    SQ O43298 370-422! SQ O43298 423-486
             26. GLI-Krueppel family member HKR3 [144147]
                 ZBTB48
                 1. Mouse (Mus musculus) [TaxId: 10090] [144148] (4)
                    SQ Q1H9T6 284-310! SQ Q1H9T6 311-338! SQ Q1H9T6 339-368! SQ Q1H9T6 369-394
             27. Zinc finger protein 64, ZFP68 [144149]
                 1. Human (Homo sapiens) [TaxId: 9606] [144150] (5)
                    SQ Q9NPA5 174-199! SQ Q9NPA5 200-227! SQ Q9NPA5 228-256! SQ Q9NPA5 341-368! SQ Q9NPA5 369-397
             28. Transcriptional repressor CTCF [144153]
                 1. Human (Homo sapiens) [TaxId: 9606] [144154] (4)
                    SQ P49711 399-434! SQ P49711 435-462! SQ P49711 515-550! SQ P49711 551-587
             29. Zinc finger and SCAN domain-containing protein 16, ZSCAN16 [144155]
                 Zinc finger protein 435
                 1. Human (Homo sapiens) [TaxId: 9606] [144156] (2)
                    SQ Q9H4T2 224-261! SQ Q9H4T2 262-288
             30. PATZ1 [161152]
                 Zinc finger protein 278
                 1. Human (Homo sapiens) [TaxId: 9606] [161153] (7)
                    SQ Q9HBE1 286-338! SQ Q9HBE1 350-384! SQ Q9HBE1 355-379! SQ Q9HBE1 380-409! SQ Q9HBE1 380-411! SQ Q9HBE1 407-445! SQ Q9HBE1 410-436
          2. Plant C2H2 finger (QALGGH zinc finger) [90198] (1)
             1. SUPERMAN zinc finger domain [90199]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [90200] (1)
          3. C2HC finger [57697] (3)
             1. U-shaped transcription factor, different fingers [57698]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [57699] (4)
             2. Monocytic leukemia zinc finger protein Moz [103599]
                1. Human (Homo sapiens) [TaxId: 9606] [103600] (1)
                   this zinc finger is only a fragment of a bigger subdomain in the structure of functional HAT domain (scop_sp 143703)
             3. Cell growth regulating nucleolar protein LyaR [118271]
                1. Mouse (Mus musculus) [TaxId: 10090] [118272] (1)
                   SQ Q08288 1-66
          4. HkH motif-containing C2H2 finger [111436] (4)
             putative dsRNA-specific zinc finger with a helix-kink-helix (HkH) motif; the kink results from the incompatibility of the cation-coordinating H-x5-H motif with a regular alpha-helix and contributes to RNA recognition
             1. Spliceosomal protein U1C [111437]
                1. Human (Homo sapiens) [TaxId: 9606] [111438] (1)
                   SQ P09234 1-61
             2. Zinc finger protein 593, ZNF593 [144151]
                1. Human (Homo sapiens) [TaxId: 9606] [144152] (1)
                   SQ O00488 28-94
             3. dsRNA-binding protein ZFa (ZNF346, JAZ) [161154]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [161155] (2)
                   SQ Q8AVN9 2-73!SQ Q8AVN9 74-128
             4. Zinc finger homeobox protein 4, ZFHX4 [161156]
                1. Human (Homo sapiens) [TaxId: 9606] [161157] (1)
                   SQ Q9JJN9 2937-2984
          5. CHHC finger [161158] (1)
             1. U11/U12 small nuclear ribonucleoprotein 48 kDa protein, U11-48K [161159]
                1. Human (Homo sapiens) [TaxId: 9606] [161160] (2)
                   SQ Q6IEG0 53-87
          6. variant C2H2 finger [118273] (1)
             contains extra C-terminal, alpha-helical subdomain
             1. Protein arginine N-methyltransferase 3 [118274]
                1. Mouse (Mus musculus) [TaxId: 10090] [118275] (1)
                   SQ Q922H1 38-145
          7. BED zinc finger [144157] (1)
             Pfam 02892; contains extra N-terminal and C-terminal helices bundled together with the core helix
             1. Zinc finger BED domain-containing protein 1 [144158]
                dREF homolog
                1. Human (Homo sapiens) [TaxId: 9606] [144159] (1)
                   SQ O96006 23-82
   53. Zn2/Cys6 DNA-binding domain [57700] (1)
       all-alpha dimetal(zinc)-bound fold
       1. Zn2/Cys6 DNA-binding domain [57701] (1)
          duplication: two structural repeats are related by the pseudo dyad
          uperfamily
          1. Zn2/Cys6 DNA-binding domain [57702] (6)
             1. Gal4 [57703]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57704] (4)
             2. PPR1 [57705]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57706] (1)
             3. PUT3 [57707]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57708] (2)
             4. Hap1 (Cyp1) [57709]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57710] (4)
             5. CD2-Lac9 [57711]
                1. Milk yeast (Kluyveromyces lactis) [TaxId: 28985] [57712] (1)
             6. Ethanol regulon transcriptional activator ALCR DNA-binding domain [57713]
                1. Emericella nidulans, also known as Aspergillus nidulans [TaxId: 162425] [57714] (4)
   54. Glucocorticoid receptor-like (DNA-binding domain) [57715] (1)
       alpha+beta metal(zinc)-bound fold
       1. Glucocorticoid receptor-like (DNA-binding domain) [57716] (18)
          uperfamily
          1. Erythroid transcription factor GATA-1 [57717] (3)
             single zinc-binding motif
             1. Erythroid transcription factor GATA-1 [57718]
                1. Chicken (Gallus gallus) [TaxId: 9031] [57719] (8)
                2. Mouse (Mus musculus) [TaxId: 10090] [57720] (2)
                3. Emericella nidulans [TaxId: 162425] [161161] (24)
          2. Nuclear receptor [57721] (12)
             duplication: two zinc-binding motifs
             1. Retinoid X receptor (RXR-alpha) DNA-binding domain [57722]
                1. Human (Homo sapiens) [TaxId: 9606] [57723] (7)
             2. Thyroid hormone receptor (TR-beta) DNA-binding domain [57724]
                1. Human (Homo sapiens) [TaxId: 9606] [57725] (1)
             3. Orphan nuclear receptor NGFI-B DNA-binding domain [57726]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [57727] (1)
             4. Estrogen receptor DNA-binding domain [57728]
                1. Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606] [57729] (2)
                   identical sequences
             5. Steroid hormone receptor Err2 DNA-binding domain [90201]
                1. Human (Homo sapiens) [TaxId: 9606] [90202] (1)
             6. Ecdysone receptor DNA-binding domain [103601]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103602] (3)
             7. Ultraspiracle protein [103603]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103604] (1)
             8. Glucocorticoid receptor DNA-binding domain [57730]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [57731] (7)
             9. Retinoic acid receptor DNA-binding domain [57732]
                1. Human (Homo sapiens) [TaxId: 9606] [57733] (2)
             10. Orphan nuclear receptor reverb DNA-binding domain [57734]
                 1. Human (Homo sapiens) [TaxId: 9606] [57735] (3)
             11. Vitamin D3 receptor, VDR, DNA-binding domain [75686]
                 1. Human (Homo sapiens) [TaxId: 9606] [75687] (4)
             12. Androgen receptor [111439]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [111440] (1)
                    SQ P15207 538-611
          3. Transcription factor grauzone Cg33133-Pa, zinc finger associated domain [103605] (1)
             1. Transcription factor grauzone Cg33133-Pa, zinc finger associated domain [103606]
                protein-protein interaction module
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103607] (1)
          4. LIM domain [57736] (21)
             duplication: contains two (sub)domains of this fold
             1. Cysteine-rich (intestinal) protein, CRP, CRIP [57737]
                1. Chicken (Gallus gallus) [TaxId: 9031] [57738] (2)
                2. Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934] [57739] (4)
                3. Rat (Rattus rattus) [TaxId: 10117] [57740] (1)
                4. Human (Homo sapiens) [TaxId: 9606] [144160] (2)
                   SQ P52943 1-30! SQ P52943 31-63
                   CRP2
             2. Pinch (particularly interesting new Cys-His) protein [57741]
                1. Human (Homo sapiens) [TaxId: 9606] [57742] (8)
             3. Rhombotin-2 (Lmo2) [90203]
                1. Mouse (Mus musculus) [TaxId: 10090] [90204] (1)
             4. LIM only 4 (Lmo4) [90205]
                1. Mouse (Mus musculus) [TaxId: 10090] [90206] (2)
                   SQ P61969 19-152
             5. Actin-binding LIM protein 2, abLIM2 [111441]
                1. Human (Homo sapiens) [TaxId: 9606] [111442] (2)
                   SQ Q6H8Q1 73-140, 212-271
             6. Four and a half LIM domains protein 2, FHL2 [144161]
                Skeletal muscle lim-protein 3
                1. Human (Homo sapiens) [TaxId: 9606] [144162] (6)
                   SQ Q14192 128-159! SQ Q14192 162-186! SQ Q14192 187-218! SQ Q14192 221-249! SQ Q14192 250-279! SQ Q14192 98-127
             7. Four and a half LIM domains protein 1, FHL-1 [144163]
                Skeletal muscle lim-protein 1
                1. Human (Homo sapiens) [TaxId: 9606] [144164] (7)
                   SQ Q13642 128-159! SQ Q13642 161-185! SQ Q13642 186-216! SQ Q13642 39-66! SQ Q13642 67-97! SQ Q13642 90-127! SQ Q13642 98-127
             8. Eplin, LIMA1 [144165]
                Epithelial protein lost in neoplasm
                1. Human (Homo sapiens) [TaxId: 9606] [144166] (2)
                   SQ Q9UHB6 381-417! SQ Q9UHB6 416-457
             9. Four and a half LIM domains 3, FHL3 [144167]
                Skeletal muscle lim-protein 2
                1. Human (Homo sapiens) [TaxId: 9606] [144168] (4)
                   SQ Q13643 127-159! SQ Q13643 152-186! SQ Q13643 187-218! SQ Q13643 98-126
             10. PDZ and LIM domain protein 5, Enigma [144169]
                 1. Human (Homo sapiens) [TaxId: 9606] [144170] (2)
                    SQ Q96HC4 400-444! SQ Q96HC4 445-476
             11. PDZ and LIM domain protein 1 Elfin [144171]
                 C-terminal LIM domain protein 1
                 1. Human (Homo sapiens) [TaxId: 9606] [144172] (2)
                    SQ O00151 249-279! SQ O00151 280-314
             12. Nedd9 interacting protein with calponin homology, NICAL (MICAL1) [144173]
                 1. Human (Homo sapiens) [TaxId: 9606] [144174] (2)
                    SQ Q8TDZ2 687-722! SQ Q8TDZ2 723-755
             13. Leupaxin [144175]
                 1. Human (Homo sapiens) [TaxId: 9606] [144176] (2)
                    SQ O60711 260-295! SQ O60711 296-327
             14. Thyroid receptor interacting protein 6, TRIP6 [144177]
                 1. Human (Homo sapiens) [TaxId: 9606] [144178] (4)
                    SQ Q15654 279-305! SQ Q15654 306-337! SQ Q15654 363-396! SQ Q15654 364-396
             15. Actin-binding LIM protein 3, abLIM-3 [144179]
                 1. Human (Homo sapiens) [TaxId: 9606] [144180] (2)
                    SQ O94929 141-176! SQ O94929 177-207
             16. Four and a half LIM domains protein 5, FHL-5 [144181]
                 1. Human (Homo sapiens) [TaxId: 9606] [144182] (2)
                    SQ Q5TD97 222-250! SQ Q5TD97 251-284
             17. Lim domain kinase 2 [144183]
                 1. Human (Homo sapiens) [TaxId: 9606] [144184] (2)
                    SQ P53671 62-95! SQ P53671 96-129
             18. PDZ and LIM domain protein 3, PDLIM3 [144185]
                 Alpha-actinin-2-associated LIM protein
                 1. Mouse (Mus musculus) [TaxId: 10090] [144186] (2)
                    SQ O70209 270-301! SQ O70209 271-301
          5. LASP-1 [57743] (1)
             1. LASP-1 [57744]
                1. Pig (Sus scrofa) [TaxId: 9823] [57745] (1)
          6. DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain [57746] (1)
             1. DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain [57747]
                1. Human (Homo sapiens) [TaxId: 9606] [57748] (2)
          7. Ribosomal protein L24e [57749] (1)
             1. Ribosomal protein L24e [57750]
                1. Archaeon Haloarcula marismortui [TaxId: 2238] [57751] (44)
                   SQ P14116
          8. Hypothetical zinc finger protein YacG [82914] (1)
             Zn-binding site is particularly similar to that of ribosomal protein L24e
             1. Hypothetical zinc finger protein YacG [82915]
                1. Escherichia coli [TaxId: 562] [82916] (1)
          9. Ribosomal protein S14 [57752] (2)
             1. Ribosomal protein S14 [57753]
                1. Thermus thermophilus [TaxId: 274] [57754] (45)
                   SQ P24320
                2. Escherichia coli [TaxId: 562] [161162] (24)
                   SQ P02370 1-100
          10. C-terminal, Zn-finger domain of MutM-like DNA repair proteins [81627] (6)
              1. DNA repair protein MutM (Fpg) [81622]
                 1. Thermus thermophilus [TaxId: 274] [81610] (1)
                 2. Bacillus stearothermophilus [TaxId: 1422] [81613] (9)
                 3. Escherichia coli [TaxId: 562] [81618] (1)
                 4. Lactococcus lactis [TaxId: 1358] [81619] (7)
                    SQ P42371
              2. Endonuclease VIII [82917]
                 1. Escherichia coli [TaxId: 562] [82918] (9)
                    SQ P50465
              3. Endonuclease VIII-like 1 (NEIL1) [111443]
                 1. Human (Homo sapiens) [TaxId: 9606] [111444] (1)
                    SQ Q96FI4 1-333
          11. ClpX chaperone zinc binding domain [103608] (1)
              1. ClpX chaperone zinc binding domain [103609]
                 1. Escherichia coli [TaxId: 562] [103610] (7)
          12. PARP-type zinc finger [111445] (1)
              Pfam 00645
              1. DNA ligase III [111446]
                 1. Human (Homo sapiens) [TaxId: 9606] [111447] (1)
                    SQ P49916 1-117
          13. Prokaryotic DksA/TraR C4-type zinc finger [111448] (1)
              Pfam 01258; Pfam coverage extends to the second helix of the upstream alpha-hairpin domain
              1. DnaK suppressor protein DksA, zinc finger domain [111449]
                 1. Escherichia coli [TaxId: 562] [111450] (1)
                    SQ P18274 7-151
          14. Type II thymidine kinase zinc finger [118276] (3)
              C-terminal part of Pfam 00265
              1. Thymidine kinase, TK1, C-terminal domain [118277]
                 1. Human (Homo sapiens) [TaxId: 9606] [118278] (3)
                    SQ P04183 18-191
                 2. Ureaplasma urealyticum [TaxId: 2130] [118279] (8)
                    SQ Q9PPP5 11-211
                 3. Clostridium acetobutylicum [TaxId: 1488] [118280] (1)
                    SQ Q97F65
          15. A20-like zinc finger [144187] (2)
              Pfam 01754
              1. RabGEF1 (Rabex-5), ubiquitin-binding domain [144188]
                 binds to ubiquitin with the extended C-terminal helix
                 1. Cow (Bos taurus) [TaxId: 9913] [144189] (4)
                    SQ O18973 14-73
                 2. Human (Homo sapiens) [TaxId: 9606] [144190] (5)
                    SQ Q9UJ41 17-74
          16. THAP domain [161163] (1)
              Pfam 05485
              1. THAP domain-containing protein 2 [161164]
                 1. Human (Homo sapiens) [TaxId: 9606] [161165] (1)
                    SQ Q9H0W7 1-86
          17. TRASH domain [161166] (1)
              SMART 00746
              1. Zinc finger MYM-type protein 5 [161167]
                 1. Human (Homo sapiens) [TaxId: 9606] [161168] (1)
                    SQ Q9UJ78 229-277
          18. FwdE C-terminal domain-like [161169] (1)
              the C-terminus of PF02663; FwdE
              1. Uncharacterized protein Ta1109 [161170]
                 1. Thermoplasma acidophilum [TaxId: 2303] [161171] (1)
                    SQ Q9HJ63 169-201
   55. SBT domain [103611] (1)
       consist of two different zn-binding subdomains, each subdomain resembles a distorted glucocorticoid receptor-like fold
       1. SBT domain [103612] (1)
          uperfamily
          1. SBT domain [103613] (3)
             Pfam 03110
             1. Squamosa promoter binding protein-like 4, DNA-binding domain [103614]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103615] (1)
             2. Squamosa promoter binding protein-like 7, DNA-binding domain [103616]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103617] (1)
             3. Squamosa-promoter binding-like protein 12, DNA-binding domain [118281]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118282] (1)
                   SQ Q9S7P5 124-181
   56. Retrovirus zinc finger-like domains [57755] (1)
       metal(zinc)-bound fold
       1. Retrovirus zinc finger-like domains [57756] (1)
          uperfamily
          1. Retrovirus zinc finger-like domains [57757] (6)
             1. GAG protein p55 [57758]
                1. Synthetic, based on Human immunodeficiency virus [57759] (1)
             2. HIV nucleocapsid [57760]
                duplication: two similar zinc-binding motifs
                1. Human immunodeficiency virus type 1, different isolates [TaxId: 11676] [57761] (12)
                   SQ P03350 389-429
                2. Human immunodeficiency virus type 2 [TaxId: 11709] [57762] (2)
             3. Nucleocapsid protein from mason-pfizer monkey virus (MPMV) [57763]
                1. Mason-pfizer monkey virus [TaxId: 11855] [57764] (1)
             4. Zinc finger protein ncp10 [57765]
                1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [57766] (6)
                   SQ P03332 479-534
             5. Nucleic acid binding protein p14 [57767]
                1. Mouse mammary tumor virus [TaxId: 11757] [57768] (2)
   57. Rubredoxin-like [57769] (17)
       metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
       1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57770] (1)
          uperfamily
          1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57771] (2)
             in the Pyrococcus abyssi MetRS structure there is a tandem repeat of two such domains swapped with their zinc-binding 'knuckles', this duplicated finger occupies a larger region (124-183) than defined below; there is a structurally equivalent region in the E. coli enzyme lacking the second zinc-binding site
             1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57772]
                1. Escherichia coli [TaxId: 562] [57773] (9)
                2. Pyrococcus abyssi [TaxId: 29292] [111451] (1)
                   SQ Q9V011 1-606; C-domain 616-722 is solved separately: 1MKH
       2. Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
          uperfamily
          1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57775] (8)
             1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57776]
                1. Bacillus stearothermophilus [TaxId: 1422] [57777] (3)
                2. Bacillus subtilis [TaxId: 1423] [103618] (1)
                3. Bacillus globisporus [TaxId: 1459] [103619] (1)
                4. Escherichia coli [TaxId: 562] [57778] (6)
                   contains a rudiment form of the domain that lacks zn-binding site
                5. Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913] [57779] (1)
                   contains a rudiment "zinc-finger" subdomain
                6. Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913] [57780] (2)
                   contains a rudiment "zinc-finger" subdomain
                7. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57781] (4)
                   contains a rudiment "zinc-finger" subdomain
                8. Maize (Zea mays) [TaxId: 4577] [57782] (1)
       3. NADH pyrophosphatase intervening domain [116738] (1)
          uperfamily
          1. NADH pyrophosphatase intervening domain [116739] (1)
             1. NADH pyrophosphatase intervening domain [116740]
                1. Escherichia coli [TaxId: 562] [116741] (1)
       4. Zinc beta-ribbon [57783] (5)
          uperfamily
          1. Transcriptional factor domain [57784] (6)
             1. Transcriptional factor SII, C-terminal domain [57785]
                1. Human (Homo sapiens) [TaxId: 9606] [57786] (1)
             2. Transcription initiation factor TFIIB, N-terminal domain [57789]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [57790] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [57791] (3)
                   SQ Q00403 2-59
             3. RBP9 subunit of RNA polymerase II [57787]
                contains two differently decorated domains of this fold
                1. Archaeon Thermococcus celer [TaxId: 2264] [57788] (1)
                2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64575] (41)
                   SQ P27999; part of multichain biological unit
             4. Transcription initiation factor TFIIE-alpha [118283]
                1. Human (Homo sapiens) [TaxId: 9606] [118284] (1)
                   SQ P29083 113-174
          2. DNA primase zinc finger [57792] (2)
             contains alpha-helices in the N- and C-terminal extensions (linkers?)
             1. Zinc-binding domain of DNA primase [57793]
                1. Bacillus stearothermophilus [TaxId: 1422] [57794] (1)
             2. Zinc-binding domain of primase-helicase [90207]
                1. Bacteriophage T7 [TaxId: 10760] [90208] (1)
          3. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57795] (1)
             Duplication: contains tandem repeats of several domains with zinc-binding sites being lost in some of them
             1. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57796]
                1. Escherichia coli [TaxId: 562] [57797] (1)
          4. Putative zinc binding domain [118285] (1)
             Pfam 05129; DUF701
             1. Hypothetical UPF0222 protein MGC4549 [118286]
                1. Mouse (Mus musculus) [TaxId: 10090] [118287] (1)
                   SQ P60003
          5. PhnA zinc-binding domain [144191] (1)
             Pfam 08274
             1. Hypothetical protein PA0128, N-terminal domain [144192]
                1. Pseudomonas aeruginosa [TaxId: 287] [144193] (1)
                   SQ Q9I704 2-39
       5. Casein kinase II beta subunit [57798] (1)
          uperfamily
          1. Casein kinase II beta subunit [57799] (3)
             contains alpha-helices in the N- and C-terminal extensions (linkers?)
             1. Casein kinase II beta subunit [57800]
                1. Human (Homo sapiens) [TaxId: 9606] [57801] (4)
                2. African clawed frog (Xenopus laevis) [TaxId: 8355] [118288] (1)
                   SQ P28021 7-178 # 100% identical to the human enzyme (SQ P13862 7-178)
                3. Rattus norvegicus [TaxId: 10116] [161172] (2)
       6. Rubredoxin-like [57802] (3)
          uperfamily
          1. Rubredoxin [57803] (10)
             1. Rubredoxin [57804]
                1. Desulfovibrio vulgaris [TaxId: 881] [57805] (7)
                2. Desulfovibrio gigas [TaxId: 879] [57806] (3)
                3. Desulfovibrio desulfuricans, strain 27774 [TaxId: 876] [57807] (1)
                4. Clostridium pasteurianum [TaxId: 1501] [57808] (23)
                   SQ P00268
                5. Archaeon Pyrococcus furiosus [TaxId: 2261] [57809] (11)
                   SQ P24297
                6. Guillardia theta [TaxId: 55529] [57810] (2)
             2. Two-iron rubredoxin [103620]
                1. Pseudomonas oleovorans [TaxId: 301] [103621] (1)
             3. Rubrerythrin, C-terminal domain [57811]
                1. Desulfovibrio vulgaris [TaxId: 881] [57812] (10)
                   SQ P24931
                2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103622] (3)
             4. Nigerythrin, C-terminal domain [144194]
                1. Desulfovibrio vulgaris [TaxId: 881] [144195] (6)
                   SQ P30820 167-202
          2. Desulforedoxin [57813] (3)
             1. Desulforedoxin [57814]
                dimeric mono-domain protein with two rubredoxin-type metal centres
                1. Desulfovibrio gigas [TaxId: 879] [57815] (4)
             2. Desulfoferrodoxin N-terminal domain [57816]
                1. Desulfovibrio desulfuricans [TaxId: 876] [57817] (13)
                2. Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887] [111452] (3)
                   SQ Q46495
          3. Cytochrome c oxidase Subunit F [57818] (1)
             membrane-anchored rubredoxin-like domain
             1. Cytochrome c oxidase Subunit F [57819]
                1. Cow (Bos taurus) [TaxId: 9913] [57820] (21)
       7. Zn-finger domain of Sec23/24 [82919] (1)
          uperfamily
          1. Zn-finger domain of Sec23/24 [82920] (2)
             1. Sec23 [82921]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82922] (3)
             2. Sec24 [82923]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82924] (4)
       8. Ran binding protein zinc finger-like [90209] (1)
          contains CxxxxC-x(n)-CxxC zinc-binding site; similar to the Sec23/24 zinc finger domain
          uperfamily
          1. Ran binding protein zinc finger-like [90210] (6)
             1. Znf265, first zinc-finger domain [90211]
                1. Human (Homo sapiens) [TaxId: 9606] [90212] (1)
             2. Npl4 [90215]
                a ubiquitin-interacting domain
                1. Rat (Rattus norvegicus) [TaxId: 10116] [90216] (2)
             3. MDM4 [144196]
                1. Human (Homo sapiens) [TaxId: 9606] [144197] (1)
                   SQ O15151 300-340
             4. MDM2 [144198]
                1. Human (Homo sapiens) [TaxId: 9606] [144199] (2)
                   SQ Q00987 290-335
             5. Vacuolar protein-sorting-associated protein 36, VPS36 [161173]
                1. Saccharomyces cerevisiae [TaxId: 4932] [161174] (2)
                   SQ Q06696 115-161
             6. Nuclear pore complex protein nup153 [161175]
                1. Human (Homo sapiens) [TaxId: 9606] [161176] (1)
                   SQ P49790 722-750
       9. Hypothetical protein Ta0289 C-terminal domain [103623] (1)
          contains CxxC-x(n)-CxxxxC zinc-binding site; sequence similarity to NAD-dependent DNA ligase zinc-finger subdomain
          uperfamily
          1. Hypothetical protein Ta0289 C-terminal domain [103624] (1)
             1. Hypothetical protein Ta0289 C-terminal domain [103625]
                1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [103626] (1)
       10. Hypothetical protein MTH1184 [57821] (1)
           contains two CXC motifs
           uperfamily
           1. Hypothetical protein MTH1184 [57822] (1)
              possible metal-binding fold
              1. Hypothetical protein MTH1184 [57823]
                 1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [57824] (1)
       11. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
           uperfamily
           1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57826] (2)
              1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57827]
                 1. Escherichia coli [TaxId: 562] [57828] (59)
                    SQ P00478
                 2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [111453] (2)
       12. Zn-binding ribosomal proteins [57829] (8)
           uperfamily
           1. Ribosomal protein L37ae [57830] (1)
              1. Ribosomal protein L37ae [57831]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [57832] (58)
                    SQ P60619
           2. Ribosomal protein L37e [57833] (1)
              1. Ribosomal protein L37e [57834]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [57835] (40)
                    SQ P32410
           3. Ribosomal protein L44e [57836] (1)
              1. Ribosomal protein L44e [57837]
                 1. Archaeon Haloarcula marismortui [TaxId: 2238] [57838] (40)
                    SQ P32411
           4. Ribosomal protein S27e [90217] (1)
              1. Ribosomal protein S27e [90218]
                 1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90219] (1)
           5. Ribosomal protein L32p [144200] (3)
              Pfam 01783; metal ion-binding site is lost in some members; includes the N-terminal, mainly helical tail
              1. Ribosomal protein L32p [144201]
                 1. Escherichia coli [TaxId: 562] [144202] (27)
                    SQ P0A7N4 1-56
                 2. Thermus thermophilus [TaxId: 274] [161177] (7)
                    SQ P80339 1-59
                 3. Deinococcus radiodurans [TaxId: 1299] [161178] (10)
                    SQ P49228 2-59
           6. Ribosomal protein L33p [144203] (3)
              Pfam 00471; corresponds structurally and functionally to the ribosomal L44e from eukaryota and archaea; metal ion-binding site is lost in most members
              1. Ribosomal protein L33p [144204]
                 1. Escherichia coli [TaxId: 562] [144205] (9)
                    SQ P0A7N9 1-54
                 2. Deinococcus radiodurans [TaxId: 1299] [161179] (6)
                    SQ Q9RSS4 2-54
                 3. Thermus thermophilus [TaxId: 274] [161180] (9)
                    SQ P35871 8-52
           7. Ribosomal protein L40e [161181] (1)
              Pfam 01020
              1. Ribosomal protein L40e [161182]
                 1. Sulfolobus solfataricus [TaxId: 2287] [161183] (1)
                    SQ Q980V5 1-56
           8. Ribosomal protein S27a [161184] (1)
              Pfam 01599
              1. Ribosomal protein S27ae [161185]
                 1. Thermoplasma acidophilum [TaxId: 2303] [161186] (1)
                    SQ Q9HJ78 1-55
       13. RNA polymerase subunits [63393] (2)
           uperfamily
           1. RBP12 subunit of RNA polymerase II [64576] (1)
              1. RBP12 subunit of RNA polymerase II [64577]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64578] (30)
                    SQ P40422; part of multichain biological unit
           2. RpoE2-like [111454] (1)
              Pfam 04035
              1. putative DNA-directed RNA polymerase subunit E'' (RpoE2) [111455]
                 1. Pyrococcus furiosus [TaxId: 2261] [111456] (1)
                    SQ Q8U440
       14. NOB1 zinc finger-like [144206] (1)
           uperfamily
           1. NOB1 zinc finger-like [144207] (1)
              1. RNA-binding protein NOB1 (Nin one binding) [144208]
                 1. Mouse (Mus musculus) [TaxId: 10090] [144209] (1)
                    SQ Q8BW10 251-316
       15. Nop10-like SnoRNP [144210] (1)
           uperfamily
           1. Nucleolar RNA-binding protein Nop10-like [144211] (3)
              Pfam 04135; contains N-terminal zinc-finger domain similar to the insert finger of the Initiation factor eIF2 gamma subunit (scop_pr 75204)
              1. H/aca ribonucleoprotein complex subunit 3 [144212]
                 lacks the zinc-binding site, mostly unstructured
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144213] (2)
                    SQ Q6Q547 2-58
              2. Ribosome biogenesis protein Nop10 [144214]
                 1. Archaeon Pyrococcus furiosus [TaxId: 2261] [144215] (4)
                    SQ Q8U1R4 4-55
                 2. Archaeon Methanococcus jannaschii [TaxId: 2190] [144216] (2)
                    SQ P81303 1-60
       16. CSL zinc finger [144217] (1)
           uperfamily
           1. CSL zinc finger [144218] (2)
              Pfam 05207
              1. DelGEF-interacting protein 1, DelGIP1 [144219]
                 1. Mouse (Mus musculus) [TaxId: 10090] [144220] (1)
                    SQ Q8K0W9 1-69
              2. Diphthamide biosynthesis protein 3, DPH3 [144221]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144222] (2)
                    SQ Q3E840 1-82! SQ Q3E840 2-82
       17. YfgJ-like [161187] (1)
           duplication: consists of two rubredoxin-like (sub)domains, interlocked together
           1. YfgJ-like [161188] (1)
              Pfam 07191, DUF1407
              1. Hypothetical protein YfgJ [161189]
                 1. Escherichia coli [TaxId: 562] [161190] (1)
                    SQ P76575 13-83
   58. Ribosomal protein L36 [57839] (1)
       zinc-bound beta-ribbon motif
       1. Ribosomal protein L36 [57840] (1)
          uperfamily
          1. Ribosomal protein L36 [57841] (3)
             1. Ribosomal protein L36 [57842]
                1. Thermus thermophilus [TaxId: 274] [57843] (6)
                2. Escherichia coli [TaxId: 562] [144223] (27)
                   SQ P0A7Q6 1-38
                3. Deinococcus radiodurans [TaxId: 1299] [161191] (10)
                   SQ Q9RSK0 1-36
   59. Zinc-binding domain of translation initiation factor 2 beta [75688] (1)
       zinc-bound beta-ribbon motif
       1. Zinc-binding domain of translation initiation factor 2 beta [75689] (1)
          uperfamily
          1. Zinc-binding domain of translation initiation factor 2 beta [75690] (2)
             1. Zinc-binding domain of translation initiation factor 2 beta [75691]
                1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75692] (1)
                2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [103627] (1)
   60. WRKY DNA-binding domain [118289] (1)
       zinc-bound 4-stranded meander beta-sheet, distinct from the beta-ribbon motifs
       1. WRKY DNA-binding domain [118290] (1)
          uperfamily
          1. WRKY DNA-binding domain [118291] (1)
             Pfam 03106
             1. WRKY DNA-binding protein 4 [118292]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118293] (1)
                   SQ Q9XI90 399-468
   61. B-box zinc-binding domain [57844] (1)
       zinc-bound alpha+beta motif
       1. B-box zinc-binding domain [57845] (1)
          uperfamily
          1. B-box zinc-binding domain [57846] (7)
             1. Nuclear factor XNF7 [57847]
                1. African clawed frog (Xenopus laevis) [TaxId: 8355] [57848] (1)
             2. Midline-2 [161192]
                1. Human (Homo sapiens) [TaxId: 9606] [161193] (1)
                   SQ Q9UJV3 162-232
             3. Tripartite motif-containing protein 29 [161194]
                1. Human (Homo sapiens) [TaxId: 9606] [161195] (1)
                   SQ Q14134 212-270
             4. Tripartite motif-containing protein 39 [161196]
                1. Human (Homo sapiens) [TaxId: 9606] [161197] (2)
                   SQ Q9HCM9 104-143
             5. Midline-1 [161198]
                1. Human (Homo sapiens) [TaxId: 9606] [161199] (1)
                   SQ O15344 168-214
             6. Zinc finger FYVE domain-containing protein 19 [161200]
                1. Mouse (Mus musculus) [TaxId: 10090] [161201] (1)
                   SQ Q9DAZ9 336-389
             7. Ubiquitin ligase trim63 [161202]
                1. Human (Homo sapiens) [TaxId: 9606] [161203] (1)
                   SQ Q969Q1 119-169
   62. RING/U-box [57849] (1)
       dimetal(zinc)-bound alpha+beta motif; structurally diverse
       1. RING/U-box [57850] (6)
          uperfamily
          1. RING finger domain, C3HC4 [57851] (14)
             1. CBL [57852]
                1. Human (Homo sapiens) [TaxId: 9606] [57853] (1)
             2. V(D)J recombination activating protein 1 (RAG1), dimerization domain [57854]
                1. Mouse (Mus musculus) [TaxId: 10090] [57855] (1)
             3. Immediate early protein, IEEHV [57856]
                1. Equine herpesvirus 1 [TaxId: 10326] [57857] (1)
             4. Acute promyelocytic leukaemia proto-oncoprotein PML [57858]
                1. Human (Homo sapiens) [TaxId: 9606] [57859] (1)
             5. TFIIH Mat1 subunit [57860]
                1. Human (Homo sapiens) [TaxId: 9606] [57861] (1)
             6. Not-4 N-terminal RING finger domain [64579]
                1. Human (Homo sapiens) [TaxId: 9606] [64580] (2)
             7. brca1 RING domain [69968]
                1. Human (Homo sapiens) [TaxId: 9606] [69969] (1)
             8. bard1 RING domain [69970]
                1. Human (Homo sapiens) [TaxId: 9606] [69971] (1)
             9. RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex [75693]
                1. Human (Homo sapiens) [TaxId: 9606] [75694] (7)
                   SQ P62877 19-106
             10. EL5 RING-H2 domain [90220]
                 binding domain for E2 ubiquitin ligase
                 1. Rice (Oryza sativa) [TaxId: 4530] [90221] (1)
             11. Deltex protein 2 RING-H2 domain [111457]
                 1. Mouse (Mus musculus) [TaxId: 10090] [111458] (1)
                    SQ Q8R3P2 389-489
             12. Ariadne-1 protein homolog [111459]
                 1. Human (Homo sapiens) [TaxId: 9606] [111460] (1)
                    SQ Q9Y4X5 336-394
             13. Cellulose synthase A catalytic subunit 7, IRX3 [118294]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118295] (1)
                    SQ Q9SWW6 26-95
             14. UbcM4-interacting protein 4 (KIAA0161) [118296]
                 1. Human (Homo sapiens) [TaxId: 9606] [118297] (1)
          2. U-box [90222] (4)
             Associated with multi-ubiquitination; lacks the RING-domain metal ion-binding residues
             1. Pre-mRNA splicing factor Prp19 [90223]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90224] (7)
             2. E3 ubiquitin ligase PUB14 [111461]
                Armadillo repeat containing protein
                1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [111462] (1)
                   SQ Q8VZ40 249-321
             3. Ubiquitin conjugation factor E4A [118298]
                1. Human (Homo sapiens) [TaxId: 9606] [118299] (1)
                   SQ Q14139 977-1061
             4. STIP1 homology and U box-containing protein 1, STUB1 [144224]
                1. Mouse (Mus musculus) [TaxId: 10090] [144225] (8)
                   SQ Q9WUD1 225-304! SQ Q9WUD1 227-301
          3. Variant RING domain [118300] (2)
             1. IE1B protein (ORF K3), N-terminal domain [118301]
                1. Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296] [118302] (1)
                   SQ P90495 1-60
             2. Protein c14orf4 (KIAA1865) [144226]
                1. Human (Homo sapiens) [TaxId: 9606] [144227] (1)
                   SQ Q9H1B7 705-786
          4. IBR domain [144228] (1)
             Smart 00647; RING-associated domain
             1. Ring finger protein 31 [144229]
                1. Human (Homo sapiens) [TaxId: 9606] [144230] (1)
                   SQ Q96EP0 779-851
          5. Zf-UBP [161204] (3)
             Pfam 02148
             1. Hypothetical protein RPA1320 [161205]
                1. Rhodopseudomonas palustris [TaxId: 1076] [161206] (1)
                   SQ Q6NA67 1-102
             2. Ubiquitin carboxyl-terminal hydrolase 5, UBP5 [161207]
                1. Human (Homo sapiens) [TaxId: 9606] [161208] (4)
                   SQ P45974 169-285
             3. Ubiquitin carboxyl-terminal hydrolase 33, UBP33 [161209]
                1. Human (Homo sapiens) [TaxId: 9606] [161210] (1)
                   SQ Q8TEY7 36-130
          6. ZZ domain [161211] (3)
             Pfam 00569
             1. CREB-binding protein, CBP [161212]
                1. Mouse (Mus musculus) [TaxId: 10090] [161213] (1)
                   SQ P45481 1700-1751
             2. Zinc finger ZZ-type-containing protein 2 [161214]
                1. Human (Homo sapiens) [TaxId: 9606] [161215] (1)
                   SQ Q8NEG5 208-292
             3. Zinc finger ZZ-type-containing protein 3, ZZZ3 [161216]
                1. Human (Homo sapiens) [TaxId: 9606] [161217] (1)
                   SQ Q8IYR1 313-381
   63. ArfGap/RecO-like zinc finger [57862] (1)
       zinc-bound alpha+beta motif
       1. ArfGap/RecO-like zinc finger [57863] (2)
          uperfamily
          1. Pyk2-associated protein beta ARF-GAP domain [57864] (1)
             1. Pyk2-associated protein beta ARF-GAP domain [57865]
                core is similar to that of the RING finger but lacks one zinc-binding site
                1. Mouse (Mus musculus) [TaxId: 10090] [57866] (1)
          2. RecO C-terminal domain-like [118303] (1)
             C-terminal part of Pfam 02565
             1. Recombinational repair protein RecO, C-terminal domain [118304]
                1. Deinococcus radiodurans [TaxId: 1299] [118305] (1)
                   SQ Q9RW50 # DR0819
   64. Metallothionein [57867] (1)
       metal(iron)-bound fold
       duplication: consists of clear structural/sequence repeats
       1. Metallothionein [57868] (1)
          uperfamily
          1. Metallothionein [57869] (11)
             1. Metallothionein [57870]
                1. Human (Homo sapiens) [TaxId: 9606] [57871] (2)
                2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [57872] (2)
                3. Rat (Rattus rattus) [TaxId: 10117] [57873] (3)
                4. Mouse (Mus musculus) [TaxId: 10090] [57874] (3)
                5. Black rockcod (Notothenia coriiceps) [TaxId: 8208] [90225] (2)
                6. Crab (Callinectes sapidus), alpha and beta domains [TaxId: 6763] [57875] (4)
                7. American lobster (Homarus americanus) [TaxId: 6706] [75695] (2)
                8. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57876] (6)
                   SQ P07215 13-48
                9. Purple sea urchin (Strongylocentrotus purpuratus) [TaxId: 7668] [57877] (2)
                10. Neurospora crassa [TaxId: 5141] [118306] (1)
                    SQ P02807
             2. Cyanobacterial metallothionein SmtA [64581]
                1. Synechococcus sp., PCC 7942 [TaxId: 1131] [64582] (1)
   65. Zinc domain conserved in yeast copper-regulated transcription factors [57878] (1)
       metal(zinc)-bound alpha+beta fold
       1. Zinc domain conserved in yeast copper-regulated transcription factors [57879] (1)
          uperfamily
          1. Zinc domain conserved in yeast copper-regulated transcription factors [57880] (1)
             1. Zinc domain conserved in yeast copper-regulated transcription factors [57881]
                1. Synthetic [57882] (1)
   66. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57883] (1)
       metal(zinc)-bound alpha+beta fold
       1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57884] (1)
          uperfamily
          1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57885] (1)
             1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57886]
                (crystal structure of the rest of protein is also published)
                1. Escherichia coli [TaxId: 562] [57887] (2)
   67. Cysteine-rich domain [57888] (1)
       dimetal(zinc)-bound alpha+beta fold
       1. Cysteine-rich domain [57889] (3)
          uperfamily
          1. Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) [57890] (6)
             Pfam 00130
             1. Protein kinase C-delta (PKCdelta) [57891]
                1. Mouse (Mus musculus) [TaxId: 10090] [57892] (2)
             2. RAF-1 [57893]
                1. Human (Homo sapiens) [TaxId: 9606] [57894] (2)
             3. Protein kinase c-gamma [57895]
                1. Rat (Rattus rattus) [TaxId: 10117] [57896] (2)
             4. Kinase suppressor of Ras, Ksr [69972]
                1. Mouse (Mus musculus) [TaxId: 10090] [69973] (2)
             5. Diacylglycerol kinase delta [103628]
                1. Human (Homo sapiens) [TaxId: 9606] [103629] (1)
             6. Beta-chimaerin, middle domain [118307]
                1. Human (Homo sapiens) [TaxId: 9606] [118308] (1)
                   SQ P52757 23-468
          2. TFIIH p44 subunit cysteine-rich domain [57899] (1)
             1. TFIIH p44 subunit cysteine-rich domain [57900]
                1. Human (Homo sapiens) [TaxId: 9606] [57901] (1)
          3. C1-like domain [111463] (1)
             contains Pfam 03107 (C1_2) and Pfam 07649 (C1_3)
             1. Pdi-like hypothetical protein At1g60420 [111464]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111465] (1)
                   SQ O80763 Q8LB68 476-553
   68. AN1-like Zinc finger [118309] (1)
       dimetal(zinc)-bound alpha+beta fold; partial similarity to the Cysteine-rich domain fold (scop_cf 57888)
       1. AN1-like Zinc finger [118310] (1)
          uperfamily
          1. AN1-like Zinc finger [118311] (6)
             Pfam 01428
             1. AN1-type zinc finger protein 1 [118312]
                1. Mouse (Mus musculus) [TaxId: 10090] [118313] (1)
                   SQ Q8BFR6 43-116
             2. ANUBL1 (AN1, ubiquitin-like, homolog) [118314]
                1. Mouse (Mus musculus) [TaxId: 10090] [118315] (1)
                   SQ Q86XD8 732-802
             3. Zinc finger A20 and AN1 domains containing protein At2g36320 [118316]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118317] (1)
                   SQ Q9SJM6 92-142
             4. Zinc finger A20 domain containing protein 2 [118318]
                1. Mouse (Mus musculus) [TaxId: 10090] [118319] (1)
                   SQ O88878 134-194
             5. Zinc finger A20 and AN1 domains containing protein At1g12440 [118320]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118321] (1)
                   SQ Q6NNI8 89-149
             6. Zinc finger A20 and AN1 domains containing protein At1g12040 [118322]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118323] (1)
                   SQ Q9SZ69 106-156
   69. HIT/MYND zinc finger-like [144231] (1)
       dimetal(zinc)-bound alpha+beta fold; structural similarity to members of the Cysteine-rich domain fold (scop_cf 57888)
       1. HIT/MYND zinc finger-like [144232] (2)
          uperfamily
          1. MYND zinc finger [144233] (3)
             Pfam 01753
             1. Deformed epidermal autoregulatory factor 1, DEAF-1 [144234]
                Zinc finger MYND domain-containing protein 5
                1. Human (Homo sapiens) [TaxId: 9606] [144235] (1)
                   SQ O75398 503-544
             2. Zinc finger MYND domain-containing protein 10, ZMYND10 [144236]
                BLu protein
                1. Human (Homo sapiens) [TaxId: 9606] [144237] (2)
                   SQ O75800 354-430! SQ O75800 384-440
             3. Zinc finger MYND domain-containing protein 2, MTG8 [144238]
                Protein CBFA2T1
                1. Human (Homo sapiens) [TaxId: 9606] [144239] (2)
                   SQ Q06455 505-551
                   1499
          2. HIT zinc finger [144240] (1)
             Pfam 04438
             1. Zinc finger HIT domain containing protein 2, ZNHIT2 [144241]
                aka FON protein
                1. Human (Homo sapiens) [TaxId: 9606] [144242] (1)
                   SQ Q9UHR6 1-46
   70. CHY zinc finger-like [161218] (1)
       trimetal-bound fold; integration of HIT/MYND-like and rubredoxin-like fingers
       1. CHY zinc finger-like [161219] (1)
          1. CHY zinc finger [161220] (1)
             Pfam 05495
             1. RING finger and CHY zinc finger domain-containing protein 1 [161221]
                1. Mouse (Mus musculus) [TaxId: 10090] [161222] (1)
                   SQ Q9CR50 9-82
   71. FYVE/PHD zinc finger [57902] (1)
       dimetal(zinc)-bound alpha+beta fold
       1. FYVE/PHD zinc finger [57903] (3)
          uperfamily
          1. FYVE, a phosphatidylinositol-3-phosphate binding domain [57904] (6)
             1. vps27p protein [57905]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57906] (1)
             2. Eea1 [64583]
                1. Human (Homo sapiens) [TaxId: 9606] [64584] (3)
             3. Hrs [57907]
                protein involved in membrane trafficking and signal transduction
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [57908] (1)
             4. Effector domain of rabphilin-3a [57909]
                contains additional N-terminal long alpha-helix
                1. Rat (Rattus norvegicus) [TaxId: 10116] [57910] (1)
             5. Zinc finger FYVE domain containing protein 19 [118324]
                1. Mouse (Mus musculus) [TaxId: 10090] [118325] (1)
                   SQ Q9DAZ9 1-75
             6. Rififylin (FYVE-RING finger protein Sakura) [118326]
                1. Human (Homo sapiens) [TaxId: 9606] [118327] (1)
                   SQ Q8WZ73 45-139
          2. PHD domain [57911] (14)
             1. Williams-Beuren syndrome transcription factor, WSTF [57912]
                1. Human (Homo sapiens) [TaxId: 9606] [57913] (1)
             2. Nuclear corepressor KAP-1 (TIF-1beta) [57914]
                1. Human (Homo sapiens) [TaxId: 9606] [57915] (1)
             3. Mi2-beta (CHD4) [90226]
                chromodomain-helicase-DNA-binding protein 4
                1. Human (Homo sapiens) [TaxId: 9606] [90227] (2)
             4. PHD finger protein At5g26210 [118328]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118329] (1)
                   SQ O81488 201-251
             5. PHD finger protein At1g33420 [118330]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118331] (1)
                   SQ Q9C810 595-653
             6. Death associated transcription factor 1, Datf1 (DIO-1) [118332]
                1. Mouse (Mus musculus) [TaxId: 10090] [118333] (1)
                   SQ Q8C9B9 257-319
             7. Inhibitor of growth protein 4, Ing4 [118334]
                1. Mouse (Mus musculus) [TaxId: 10090] [118335] (2)
                   SQ Q8C0D7 188-245
                2. Homo sapiens [TaxId: 9606] [161223] (5)
             8. PHD finger protein 8 [118336]
                1. Mouse (Mus musculus) [TaxId: 10090] [118337] (1)
                   SQ Q80TJ7 1-66
             9. PHD finger protein 7 (NYD-SP6) [118338]
                1. Mouse (Mus musculus) [TaxId: 10090] [118339] (1)
                   SQ Q9DAG9 232-304
             10. PHD Inhibitor of growth protein 2, Ing2 [118340]
                 1. Mouse (Mus musculus) [TaxId: 10090] [118341] (1)
                    SQ Q9ESK4 205-262
             11. PHD finger protein 22 [118342]
                 1. Mouse (Mus musculus) [TaxId: 10090] [118343] (1)
                    SQ Q9D168 150-224
             12. Sumoylation ligase E3, SIZ1 [118344]
                 1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118345] (1)
                    SQ Q680Q4 104-168
             13. V(D)J recombination-activating protein 2, Rag2 [161224]
                 1. Mouse (Mus musculus) [TaxId: 10090] [161225] (14)
                    SQ P21784 414-487
          3. variant PHD-like domain [118346] (1)
             1. Hypothetical protein KIAA1045 [118347]
                1. Human (Homo sapiens) [TaxId: 9606] [118348] (1)
                   SQ Q9UPV7 123-198
   72. Zn-binding domains of ADDBP [57916] (1)
       metal(zinc)-bound alpha+beta fold
       1. Zn-binding domains of ADDBP [57917] (1)
          duplication: contains two Zn-binding domains of similar fold
          uperfamily
          1. Zn-binding domains of ADDBP [57918] (2)
             1. First Zn-domain of early E2A DNA-binding protein, ADDBP [57919]
                Single-stranded DNA-binding protein
                1. Human adenovirus type 5 [TaxId: 28285] [57920] (4)
             2. Second Zn-domain of early E2A DNA-binding protein, ADDBP [57921]
                Single-stranded DNA-binding protein
                1. Human adenovirus type 5 [TaxId: 28285] [57922] (4)
   73. Inhibitor of apoptosis (IAP) repeat [57923] (1)
       metal(zinc)-bound alpha+beta fold
       1. Inhibitor of apoptosis (IAP) repeat [57924] (1)
          uperfamily
          1. Inhibitor of apoptosis (IAP) repeat [57925] (7)
             1. 2MIHB/C-IAP-1 [57926]
                baculoviral inhibitor of apoptosis
                1. Human (Homo sapiens) [TaxId: 9606] [57927] (4)
             2. BIR domains of XIAP [57928]
                1. Human (Homo sapiens) [TaxId: 9606] [57929] (14)
                   SQ P98170 241-356
             3. BIR domains of DIAP1 [69974]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [69975] (6)
             4. Anti-apoptotic protein survivin [57930]
                contains a long alpha-helix after the common fold
                1. Human (Homo sapiens) [TaxId: 9606] [57931] (7)
                2. Mouse (Mus musculus) [TaxId: 10090] [82925] (3)
             5. BIR-containing protein 7 (ML-IAP, livin) [103630]
                1. Human (Homo sapiens) [TaxId: 9606] [103631] (8)
                   SQ Q96CA5 78-159
             6. BIR-containing protein 8 [118349]
                1. Human (Homo sapiens) [TaxId: 9606] [118350] (2)
                   SQ Q96P09 1-84
   74. CCCH zinc finger [90228] (1)
       metal(zinc)-bound alpha+beta fold
       1. CCCH zinc finger [90229] (1)
          uperfamily
          1. CCCH zinc finger [90230] (4)
             C-x8-C-x5-C-x3-H type and similar
             1. Tristetraproline (ttp, tis11, nup475) [90231]
                1. Mouse (Mus musculus) [TaxId: 10090] [90232] (1)
             2. Butyrate response factor 2 (Tis11D) [103632]
                1. Human (Homo sapiens) [TaxId: 9606] [103633] (1)
             3. Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) [144243]
                1. Human (Homo sapiens) [TaxId: 9606] [144244] (2)
                   SQ Q9UPT8 417-445! SQ Q9UPT8 446-501
             4. Target of EGR1 protein 1, TOE1 [161226]
                1. Human (Homo sapiens) [TaxId: 9606] [161227] (1)
                   SQ Q96GM8 285-321
   75. E6 C-terminal domain-like [161228] (1)
       alpha+beta zinc-binding fold with topological similarity to the fold of lambda cro protein
       1. E6 C-terminal domain-like [161229] (1)
          1. E6 C-terminal domain-like [161230] (1)
             C-terminal part of Pfam 00518
             1. E6 oncoprotein [161231]
                1. Human papillomavirus type 16 [TaxId: 333760] [161232] (1)
                   SQ P03126 88-151
   76. E7 C-terminal domain-like [161233] (1)
       alpha+beta zinc-binding domain; beta(2)-alpha(2)
       1. E7 C-terminal domain-like [161234] (1)
          1. E7 C-terminal domain-like [161235] (2)
             C-terminal part of Pfam 00527
             1. E7 oncoprotein [161236]
                1. Human papillomavirus type 45 [TaxId: 10593] [161237] (3)
                   SQ P21736 55-106
                2. Human papillomavirus type 1a [TaxId: 10583] [161238] (2)
                   SQ P06465 42-93
   77. Zinc finger domain of DNA polymerase-alpha [90233] (1)
       Zn-binding, all-alpha fold
       1. Zinc finger domain of DNA polymerase-alpha [90234] (1)
          some sequence similarity to the TAZ domain Zn-binding sites
          uperfamily
          1. Zinc finger domain of DNA polymerase-alpha [90235] (1)
             1. Zinc finger domain of DNA polymerase-alpha [90236]
                1. Human (Homo sapiens) [TaxId: 9606] [90237] (3)
   78. TAZ domain [57932] (1)
       all-alpha fold; Zn-binding sites are in the loops connecting helices
       1. TAZ domain [57933] (1)
          uperfamily
          1. TAZ domain [57934] (2)
             1. CREB-binding transcriptional adaptor protein CBP (p300) [57935]
                1. Mouse (Mus musculus) [TaxId: 10090] [57936] (2)
                2. Human (Homo sapiens) [TaxId: 9606] [75696] (3)
   79. T-antigen specific domain-like [161239] (1)
       all-alpha zinc-binding domain; there are two zinc ion-binding sites with a common CxCxxC motif but different fourth ligands
       1. T-antigen specific domain-like [161240] (1)
          1. T-antigen specific domain-like [161241] (1)
             Pfam 02380
             1. Small t antigen, ST-AG [161242]
                1. Simian virus 40 [TaxId: 10633] [161243] (2)
                   SQ P03081 91-170
   80. Cysteine-rich DNA binding domain, (DM domain) [82926] (1)
       alpha-helical fold with two Zn-binding sites
       1. Cysteine-rich DNA binding domain, (DM domain) [82927] (1)
          uperfamily
          1. Cysteine-rich DNA binding domain, (DM domain) [82928] (1)
             1. DM domain of Doublesex (dsx) [82929]
                1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [82930] (1)
   81. Coronavirus NSP10-like [144245] (1)
       binds two zinc ion per subunit; forms a dodecameric shell
       1. Coronavirus NSP10-like [144246] (1)
          uperfamily
          1. Coronavirus NSP10-like [144247] (1)
             partly covered by PfamB 001266
             1. Nonstructural protein 10, NSP10 [144248]
                1. SARS coronavirus [TaxId: 227859] [144249] (49)
                   SQ P59641 4239-4359! SQ P59641 4240-4362
   82. Zinc hairpin stack [161244] (1)
       stack of beta-hairpins; in the middle hairpins, there is HCxxCxxC motif, the first and the last residues of which contribute to the zinc-binding site on one side of hairpin, whereas the middle residues contribute to the zinc-binding site on the other side
       1. Zinc hairpin stack [161245] (1)
          1. Zinc hairpin stack [161246] (1)
             PfamB 004087
             1. RING finger and CHY zinc finger domain-containing protein 1 [161247]
                1. Mouse (Mus musculus) [TaxId: 10090] [161248] (1)
                   SQ Q9CR50 83-138
   83. DnaJ/Hsp40 cysteine-rich domain [57937] (1)
       metal(zinc)-bound extended beta-hairpin fold
       1. DnaJ/Hsp40 cysteine-rich domain [57938] (1)
          uperfamily
          1. DnaJ/Hsp40 cysteine-rich domain [57939] (2)
             1. Cysteine-rich domain of the chaperone protein DnaJ [57940]
                1. Escherichia coli [TaxId: 562] [57941] (1)
             2. Mitochondrial protein import protein mas5 (Hsp40, Ydj1), insert domain [103634]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103635] (1)
   84. HSP33 redox switch-like [118351] (1)
       alpha+beta zinc-binding domain; alpha(2)-beta(2)-alpha
       1. HSP33 redox switch-like [118352] (1)
          uperfamily
          1. HSP33 redox switch-like [118353] (3)
             1. HSP33, C-terminal domain [118354]
                1. Escherichia coli [TaxId: 562] [118355] (1)
                   SQ P45803 225-285
                2. Bacillus subtilis [TaxId: 1423] [118356] (1)
                   SQ P37565
                3. Thermotoga maritima [TaxId: 2336] [118357] (1)
                   SQ Q9X1B4
   85. CCHHC domain [103636] (1)
       metal(zinc)-bound fold
       1. CCHHC domain [103637] (1)
          uperfamily
          1. CCHHC domain [103638] (1)
             1. Neural zinc finger transcription factor 1 [103639]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [103640] (1)
   86. Sec-C motif [103641] (1)
       metal(zinc)-bound fold
       1. Sec-C motif [103642] (1)
          uperfamily
          1. Sec-C motif [103643] (3)
             1. Preprotein translocase SecA C-terminal domain [103644]
                1. Haemophilus influenzae [TaxId: 727] [103645] (1)
                2. Escherichia coli [TaxId: 562] [111466] (3)
                   SQ P10408 878-901
             2. Hypothetical protein Psyc2064 [161249]
                1. Psychrobacter arcticus [TaxId: 334543] [161250] (2)
                   SQ Q4FPZ7 1-39! SQ Q4FPZ7 159-183
   87. Viral leader polypeptide zinc finger [144250] (1)
       consists of small beta-hairpin with CxH motif and short helix with CxxC motif
       1. Viral leader polypeptide zinc finger [144251] (1)
          uperfamily
          1. Viral leader polypeptide zinc finger [144252] (1)
             1. Polyprotein leader polypeptide [144253]
                1. Mengo encephalomyocarditis virus [TaxId: 12107] [144254] (1)
                   SQ P32540 1-32
   88. TSP type-3 repeat [103646] (1)
       metal(calcium)-bound fold
       1. TSP type-3 repeat [103647] (1)
          uperfamily
          1. TSP type-3 repeat [103648] (1)
             1. Thrombospondin-1 [103649]
                1. Human (Homo sapiens) [TaxId: 9606] [103650] (1)
   89. Expressed protein At2g23090/F21P24.15 [118358] (1)
       not assigned; partly disordered
       1. Expressed protein At2g23090/F21P24.15 [118359] (1)
          putative zinc-finger protein
          uperfamily
          1. Expressed protein At2g23090/F21P24.15 [118360] (1)
             1. Expressed protein At2g23090/F21P24.15 [118361]
                1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118362] (1)
                   SQ O64818 2-78
   90. Intrinsically disordered proteins [144255] (1)
       not a true fold
       1. TSP9-like [144256] (1)
          uperfamily
          1. TSP9-like [144257] (1)
             1. Thylakoid soluble phosphoprotein TSP9 [144258]
                1. Spinach (Spinacia oleracea) [TaxId: 3562] [144259] (1)
                   SQ Q8GT36 21-103
8. Coiled coil proteins [57942] (7)
   Not a true class
   1. Parallel coiled-coil [57943] (34)
      this is not a true fold; includes oligomers of shorter identical helices
      1. Triple coiled coil domain of C-type lectins [57944] (1)
         uperfamily
         1. Triple coiled coil domain of C-type lectins [57945] (5)
            1. Mannose-binding protein A [57946]
               1. Rat (Rattus norvegicus) [TaxId: 10116] [57947] (22)
               2. Human (Homo sapiens) [TaxId: 9606] [57948] (1)
            2. Surfactant protein [57949]
               1. Human (Homo sapiens), SP-D [TaxId: 9606] [57950] (37)
               2. Rat (Rattus norvegicus), SP-A [TaxId: 10116] [103651] (2)
            3. Tetranectin [57951]
               1. Human (Homo sapiens) [TaxId: 9606] [57952] (1)
      2. Trimerization domain of TRAF [57953] (1)
         uperfamily
         1. Trimerization domain of TRAF [57954] (2)
            1. TRAF2 [57955]
               1. Human (Homo sapiens) [TaxId: 9606] [57956] (10)
            2. TRAF3 [57957]
               1. Human (Homo sapiens) [TaxId: 9606] [57958] (5)
                  SQ Q13114 377-568
      3. Leucine zipper domain [57959] (1)
         uperfamily
         1. Leucine zipper domain [57960] (18)
            1. GCN4 [57961]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57962] (79)
                  SQ P03069 249-279 ! SQ P03069 249-281
               2. synthetic construct [161251] (4)
            2. CD2-Gal4 [57963]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57964] (4)
            3. PPR1 [57965]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57966] (1)
            4. PUT3 [57967]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57968] (2)
            5. HAP1 [57969]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [57970] (3)
            6. PAP1 [57971]
               1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [57972] (1)
            7. C-fos [57973]
               1. Human (Homo sapiens) [TaxId: 9606] [57974] (3)
            8. C-jun [57975]
               1. Human (Homo sapiens) [TaxId: 9606] [57976] (8)
                  SQ P05412 253-314
            9. C-myc [57977]
               1. Human (Homo sapiens) [TaxId: 9606] [57978] (2)
            10. Max [57979]
                1. Human (Homo sapiens) [TaxId: 9606] [57980] (2)
            11. Transcription factor Creb [57981]
                1. Mouse (Mus musculus) [TaxId: 10090] [57982] (1)
            12. Atf4 [57983]
                1. Human (Homo sapiens) [TaxId: 9606] [57984] (1)
            13. C/ebp beta [57985]
                1. Mouse (Mus musculus) [TaxId: 10090] [57986] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [64590] (10)
            14. C/ebp alpha [90238]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [90239] (1)
            15. Cyclic-AMP-dependent transcription factor ATF-2 [118363]
                1. Human (Homo sapiens) [TaxId: 9606] [118364] (1)
                   SQ P15336 336-396
            16. Trans-activator protein BZLF1 [144260]
                1. Human herpesvirus 4 [TaxId: 10376] [144261] (4)
                   SQ P03206 175-236! SQ P03206 178-236
      4. Inovirus (filamentous phage) major coat protein [57987] (1)
         uperfamily
         1. Inovirus (filamentous phage) major coat protein [57988] (8)
            1. Inovirus (filamentous phage) major coat protein [57989]
               1. Bacteriophage fd [TaxId: 10864] [57990] (7)
               2. Bacteriophage pf1 [TaxId: 10871] [57991] (10)
                  SQ P03621
               3. Bacteriophage if1 [TaxId: 10868] [57992] (1)
               4. Bacteriophage ike [TaxId: 10867] [57993] (1)
               5. Bacteriophage xf [TaxId: 356629] [57994] (1)
               6. Bacteriophage M13 [TaxId: 10870] [57995] (2)
               7. Bacteriophage pf3 [TaxId: 10872] [57996] (1)
               8. Bacteriophage ph75, Inovirus ph75 [TaxId: 144736] [64591] (3)
      5. Tropomyosin [57997] (1)
         uperfamily
         1. Tropomyosin [57998] (5)
            1. Tropomyosin [57999]
               1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [58000] (5)
               2. Pig (Sus scrofa) [TaxId: 9823] [58001] (1)
               3. Chicken (Gallus gallus) [TaxId: 9031] [64592] (1)
               4. Rat (Rattus norvegicus) [TaxId: 10116] [75697] (6)
               5. Saccharomyces cerevisiae [TaxId: 4932] [161252] (1)
      6. Chicken cartilage matrix protein [58002] (1)
         uperfamily
         1. Chicken cartilage matrix protein [58003] (1)
            1. Chicken cartilage matrix protein [58004]
               trimeric coiled-coil domain
               1. Chicken (Gallus gallus) [TaxId: 9031] [58005] (1)
      7. Assembly domain of cartilage oligomeric matrix protein [58006] (1)
         uperfamily
         1. Assembly domain of cartilage oligomeric matrix protein [58007] (1)
            1. Assembly domain of cartilage oligomeric matrix protein [58008]
               pentameric coiled-coil
               1. Rat (Rattus norvegicus) [TaxId: 10116] [58009] (3)
      8. Fibrinogen coiled-coil and central regions [58010] (1)
         uperfamily
         1. Fibrinogen coiled-coil and central regions [58011] (12)
            in the central region two triple coiled-coils are stacked end-to-end and interlock with N-terminal tails
            1. Fibrinogen alpha chain [88887]
               1. Chicken (Gallus gallus) [TaxId: 9031] [88888] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [88889] (32)
                  SQ P02671 150-209
               3. Cow (Bos taurus) [TaxId: 9913] [88890] (2)
               4. Sea lamprey (Petromyzon marinus) [TaxId: 7757] [88891] (2)
            2. Fibrinogen beta chain [88892]
               1. Chicken (Gallus gallus) [TaxId: 9031] [88894] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [88895] (15)
                  SQ P02675
               3. Cow (Bos taurus) [TaxId: 9913] [88896] (2)
               4. Sea lamprey (Petromyzon marinus) [TaxId: 7757] [88897] (2)
            3. Fibrinogen gamma chain [88898]
               1. Chicken (Gallus gallus) [TaxId: 9031] [88899] (1)
               2. Human (Homo sapiens) [TaxId: 9606] [88900] (18)
                  SQ P02679
               3. Cow (Bos taurus) [TaxId: 9913] [88901] (2)
               4. Sea lamprey (Petromyzon marinus) [TaxId: 7757] [88902] (2)
      9. Coiled-coil domain of nucleotide exchange factor GrpE [58014] (1)
         uperfamily
         1. Coiled-coil domain of nucleotide exchange factor GrpE [58015] (1)
            1. Coiled-coil domain of nucleotide exchange factor GrpE [58016]
               1. Escherichia coli [TaxId: 562] [58017] (1)
      10. Coiled-coil dimerization domain from cortexillin I [58018] (1)
          uperfamily
          1. Coiled-coil dimerization domain from cortexillin I [58019] (1)
             1. Coiled-coil dimerization domain from cortexillin I [58020]
                1. Dictyostelium discoideum [TaxId: 44689] [58021] (2)
      11. XRCC4, C-terminal oligomerization domain [58022] (1)
          uperfamily
          1. XRCC4, C-terminal oligomerization domain [58023] (1)
             1. XRCC4, C-terminal oligomerization domain [58024]
                1. Human (Homo sapiens) [TaxId: 9606] [58025] (2)
      12. Intermediate filament protein, coiled coil region [64593] (1)
          uperfamily
          1. Intermediate filament protein, coiled coil region [64594] (2)
             C-terminal part of Pfam 00038
             1. Vimentin coil [64595]
                1. Human (Homo sapiens) [TaxId: 9606] [64596] (3)
             2. Lamin A/C [118365]
                1. Human (Homo sapiens) [TaxId: 9606] [118366] (1)
                   SQ P02545 313-386 # structure of the C-terminal tail domain (435-552) is also known (scop_sp 74856)
      13. Delta-sleep-inducing peptide immunoreactive peptide [58026] (1)
          uperfamily
          1. Delta-sleep-inducing peptide immunoreactive peptide [58027] (1)
             1. Delta-sleep-inducing peptide immunoreactive peptide [58028]
                1. Pig (Sus scrofa) [TaxId: 9823] [58029] (1)
      14. Rotavirus nonstructural proteins [58030] (2)
          not a true superfamily
          uperfamily
          1. NSP4 oligomerization domain [58031] (1)
             1. NSP4 oligomerization domain [58032]
                1. Simian rotavirus, SA11 [TaxId: 10922] [58033] (2)
          2. NSP3 C-terminal domain, NS34 [75699] (1)
             1. NSP3 C-terminal domain, NS34 [75700]
                1. Simian rotavirus, SA11 [TaxId: 10922] [75701] (1)
      15. Multimerization domain of the phosphoprotein from sendai virus [58034] (1)
          uperfamily
          1. Multimerization domain of the phosphoprotein from sendai virus [58035] (1)
             1. Multimerization domain of the phosphoprotein from sendai virus [58036]
                1. Sendai virus [TaxId: 11191] [58037] (1)
      16. SNARE fusion complex [58038] (1)
          tetrameric parallel coiled coil
          uperfamily
          1. SNARE fusion complex [58039] (18)
             1. Synaptobrevin [88903]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88904] (3)
                2. Longfin squid (Loligo pealei) [TaxId: 6621] [88905] (1)
                3. Saccharomyces cerevisiae [TaxId: 4932] [161253] (1)
             2. Endobrevin [88906]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88907] (1)
             3. Syntaxin 1A [88908]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88909] (6)
                   SQ P32851 196-259
                   a globular structure of a larger fragment containing this region is available; (1dn1), chain B
                2. Longfin squid (Loligo pealei) [TaxId: 6621] [88910] (1)
                3. Saccharomyces cerevisiae [TaxId: 4932] [161254] (3)
             4. Syntaxin 7 [88911]
                complex with endobrevin, VTI1B and syntaxin 8
                1. Mouse (Mus musculus) [TaxId: 10090] [88912] (1)
             5. Syntaxin 8 [88913]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88914] (1)
             6. Synaptosomal-associated protein SNAP-23 [90240]
                1. Human (Homo sapiens) [TaxId: 9606] [90241] (1)
                2. Saccharomyces cerevisiae [TaxId: 4932] [161255] (1)
             7. Synaptosomal-associated protein SNAP-25 [88915]
                provides up to two different helical regions to synaptic fusion complexes
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88916] (4)
                   SQ P13795 7-83; 142-204 # identical sequences to human species
                2. Human (Homo sapiens) [TaxId: 9606] [88917] (2)
                   SQ P60880 146-204 # identical sequence to rat species
                3. Longfin squid (Loligo pealei) [TaxId: 6621] [88918] (1)
             8. Vesicle transport v-SNARE protein VTI1b [88919]
                1. Mouse (Mus musculus) [TaxId: 10090] [88920] (1)
             9. Complexin [88921]
                1. Rat (Rattus norvegicus) [TaxId: 10116] [88922] (1)
             10. Synaphin [88923]
                 1. Longfin squid (Loligo pealei) [TaxId: 6621] [88924] (1)
             11. M-tomosyn [111467]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [111468] (1)
                    SQ Q9Z152
      17. Outer membrane lipoprotein [58042] (1)
          uperfamily
          1. Outer membrane lipoprotein [58043] (1)
             1. Outer membrane lipoprotein [58044]
                forms trimer
                1. Escherichia coli [TaxId: 562] [58045] (12)
                   SQ P69776 25-74
      18. Fibritin [58046] (1)
          uperfamily
          1. Fibritin [58047] (1)
             1. Fibritin [58048]
                biological unit: trimer; fragmented coiled coil capped with beta-hairpin triplet
                1. Bacteriophage T4 [TaxId: 10665] [58049] (7)
                   SQ P10104
      19. N-terminal coiled coil domain from apc [58050] (1)
          uperfamily
          1. N-terminal coiled coil domain from apc [58051] (1)
             1. N-terminal coiled coil domain from apc [58052]
                1. Human (Homo sapiens) [TaxId: 9606] [58053] (1)
      20. Tetrabrachion [58054] (1)
          uperfamily
          1. Tetrabrachion [58055] (1)
             1. Tetrabrachion [58056]
                a naturally occurring parallel right-handed coiled-coil tetramer
                1. Archaeon Staphylothermus marinus [TaxId: 2280] [58057] (1)
      21. Eea1 homodimerisation domain [69979] (1)
          uperfamily
          1. Eea1 homodimerisation domain [69980] (1)
             1. Eea1 homodimerisation domain [69981]
                1. Human (Homo sapiens) [TaxId: 9606] [69982] (1)
      22. Mitotic arrest deficient-like 1, Mad1 [75704] (1)
          uperfamily
          1. Mitotic arrest deficient-like 1, Mad1 [75705] (1)
             1. Mitotic arrest deficient-like 1, Mad1 [75706]
                1. Human (Homo sapiens) [TaxId: 9606] [75707] (1)
      23. Dimerization motif of sir4 [90242] (1)
          uperfamily
          1. Dimerization motif of sir4 [90243] (1)
             1. Dimerization motif of sir4 [90244]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90245] (2)
                   SQ P11978 1272-1346
      24. Head morphogenesis protein gp7 [90246] (1)
          uperfamily
          1. Head morphogenesis protein gp7 [90247] (1)
             1. Head morphogenesis protein gp7 [90248]
                1. Bacteriophage phi-29 [TaxId: 10756] [90249] (2)
      25. Troponin coil-coiled subunits [90250] (2)
          form heterodimeric coiled coil
          uperfamily
          1. Troponin T [90251] (2)
             1. Troponin T [90252]
                1. Human (Homo sapiens) [TaxId: 9606] [90253] (2)
                2. Chicken (Gallus gallus) [TaxId: 9031] [144262] (2)
                   SQ P12620 159-248
          2. Troponin I [90254] (2)
             1. Troponin I [90255]
                1. Human (Homo sapiens) [TaxId: 9606] [90256] (2)
                2. Chicken (Gallus gallus) [TaxId: 9031] [144263] (2)
                   SQ P68246 3-118! SQ P68246 3-143
      26. Myosin rod fragments [90257] (1)
          uperfamily
          1. Myosin rod fragments [90258] (2)
             1. Myosin S2N51 [90259]
                1. Bay scallop (Argopecten irradians) [TaxId: 31199] [90260] (2)
             2. Myosin heavy chain, cardiac muscle beta isoform [144264]
                1. Human (Homo sapiens) [TaxId: 9606] [144265] (5)
                   SQ P12883 838-963
      27. G protein-binding domain [103652] (2)
          uperfamily
          1. RhoA-binding domain [103653] (2)
             1. Rho-associated, coiled-coil containing protein kinase [103654]
                1. Cow (Bos taurus) [TaxId: 9913] [103655] (1)
                2. Human (Homo sapiens) [TaxId: 9606] [103656] (1)
          2. Rabaptin-5 [118367] (1)
             1. Rabaptin-5 [118368]
                1. Human (Homo sapiens) [TaxId: 9606] [118369] (2)
                   SQ Q15276 552-641, 804-849
      28. Geminin coiled-coil domain [111469] (1)
          uperfamily
          1. Geminin coiled-coil domain [111470] (2)
             1. Geminin coiled-coil domain [111471]
                1. Human (Homo sapiens) [TaxId: 9606] [111472] (2)
                   SQ O75496 70-152
                2. Mouse (Mus musculus) [TaxId: 10090] [111473] (1)
                   SQ O88513 79-156
      29. Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain [118370] (1)
          tetrameric parallel coiled coil with a right-handed twist
          uperfamily
          1. Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain [118371] (1)
             1. Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain [118372]
                1. Human (Homo sapiens) [TaxId: 9606] [118373] (2)
                   SQ P50552 337-378 # structure of the N-terminal, EVH1 domain (1-114) is also known (scop_sp 50773)
      30. MPN010-like [144266] (1)
          segmented trimeric coiled coil
          uperfamily
          1. MPN010-like [144267] (1)
             Pfam 01519; DUF16
             1. Hypothetical protein MPN010 [144268]
                1. Mycoplasma pneumoniae [TaxId: 2104] [144269] (3)
                   SQ P75103 50-130
      31. Eferin C-derminal domain-like [144270] (1)
          uperfamily
          1. Eferin C-derminal domain-like [144271] (2)
             contains PfamB 042332, PfamB 026102
             1. Rab11 family-interacting protein 2 [144272]
                1. Human (Homo sapiens) [TaxId: 9606] [144273] (3)
                   SQ Q7L804 468-502
             2. Rab11 family-interacting protein 3 (Rab11-FIP3, Eferin) [144274]
                1. Human (Homo sapiens) [TaxId: 9606] [144275] (4)
                   SQ O75154 703-756! SQ O75154 715-756
      32. Heterotrimerisation domain of extracellular hemoglobin linker subunits [144276] (1)
          uperfamily
          1. Heterotrimerisation domain of extracellular hemoglobin linker subunits [144277] (3)
             1. Extracellular hemoglobin linker l2 subunit [144278]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144279] (1)
                   SQ Q2I743 47-97
             2. Extracellular hemoglobin linker l3 [144280]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144281] (1)
                   SQ Q2I742 26-77
             3. Hemoglobin linker chain l1 [144282]
                1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [144283] (1)
                   SQ Q9GV76 24-84
      33. Sec2 N-terminal region [144284] (1)
          dimeric coiled coil
          uperfamily
          1. Sec2 N-terminal region [144285] (1)
             1. Rab guanine nucleotide exchange factor Sec2 [144286]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144287] (24)
                   SQ P17065 16-162! SQ P17065 31-144
      34. RILP dimerisation region [161256] (1)
          1. RILP dimerisation region [161257] (1)
             1. Rab-interacting lysosomal protein RLIP [161258]
                1. Human (Homo sapiens) [TaxId: 9606] [161259] (1)
                   SQ Q96NA2 244-308
   2. Tetramerization domain of the Mnt repressor [58058] (1)
      1. Tetramerization domain of the Mnt repressor [58059] (1)
         tetrameric antiparallel bundle with a right-handed twist
         uperfamily
         1. Tetramerization domain of the Mnt repressor [58060] (1)
            1. Tetramerization domain of the Mnt repressor [58061]
               1. Salmonella bacteriophage P22 [TaxId: 10754] [58062] (1)
   3. Stalk segment of viral fusion proteins [58063] (3)
      core: trimeric coiled coil
      1. Influenza hemagglutinin (stalk) [58064] (1)
         uperfamily
         1. Influenza hemagglutinin (stalk) [58065] (2)
            1. Influenza hemagglutinin (stalk) [58066]
               trimer
               1. Influenza A virus, different strains [TaxId: 11320] [58067] (48)
               2. Influenza C virus [TaxId: 11552] [58068] (1)
      2. Virus ectodomain [58069] (1)
         uperfamily
         1. Virus ectodomain [58070] (12)
            1. Retrovius gp41 protease-resistant core [58071]
               coiled coil; biological unit: trimer
               1. Human immunodeficiency virus type 1 [TaxId: 11676] [58072] (22)
               2. Simian immunodeficiency virus [TaxId: 11723] [58073] (10)
               3. Visna virus [TaxId: 11741] [64597] (1)
               4. synthetic construct [161260] (1)
            2. HTLV-1 gp21 [58074]
               1. Human T-cell leukemia virus type 1 [TaxId: 11908] [58075] (1)
            3. Core structure of Ebo gp2 [58076]
               1. Ebola virus [TaxId: 205488] [58077] (2)
            4. MoMLV p15 core fragment [58627]
               1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [58628] (1)
            5. Paramyxovirus sv5 fusion protein core [58078]
               trimer of heterodimers
               1. Simian virus 5, strain w3 [TaxId: 11207] [58079] (1)
            6. Stalk of the ectodomain of NDV fusion glycoprotein [69983]
               1. Newcastle disease virus [TaxId: 11176] [69984] (1)
            7. HRSV fusion protein core [58080]
               1. Human respiratory syncytial virus [TaxId: 11250] [58081] (1)
            8. HERV-FRD_6p24.1 provirus ancestral Env polyprotein [144288]
               1. Human (Homo sapiens) [TaxId: 9606] [144289] (3)
                  SQ P60508 391-443
            9. Fusion glycoprotein f0 [161261]
               1. Mumps virus [TaxId: 11161] [161262] (1)
                  SQ P11236 123-179,448-479
      3. Coronavirus S2 glycoprotein [111474] (1)
         uperfamily
         1. Coronavirus S2 glycoprotein [111475] (2)
            Pfam 01601
            1. E2 spike glycoprotein [111476]
               1. Murine hepatitis virus, MHV [TaxId: 11138] [111477] (2)
                  SQ P11224 969-1024,1224-1254
               2. Human coronavirus (strain SARS) [TaxId: 227859] [111478] (20)
                  SQ P59594 896-972,1142-1183
                  SQ Q6UZF0 914-949,1148-1193
   4. Antiparallel coiled-coil [58086] (17)
      this is not a true fold; contains at least two very long antiparallel helices
      1. Variant surface glycoprotein (N-terminal domain) [58087] (1)
         uperfamily
         1. Variant surface glycoprotein (N-terminal domain) [58088] (1)
            1. Variant surface glycoprotein (N-terminal domain) [58089]
               1. Trypanosoma brucei [TaxId: 5691] [58090] (2)
      2. Clostridium neurotoxins, "coiled-coil" domain [58091] (1)
         uperfamily
         1. Clostridium neurotoxins, "coiled-coil" domain [58092] (2)
            1. Botulinum neurotoxin [58093]
               1. Clostridium botulinum, serotype A [TaxId: 1491] [58094] (1)
               2. Clostridium botulinum, serotype B [TaxId: 1491] [58095] (14)
      3. Colicin Ia, N-terminal domain [58096] (1)
         uperfamily
         1. Colicin Ia, N-terminal domain [58097] (1)
            1. Colicin Ia, N-terminal domain [58098]
               1. Escherichia coli [TaxId: 562] [58099] (1)
      4. Colicin E3 receptor domain [69985] (1)
         uperfamily
         1. Colicin E3 receptor domain [69986] (1)
            1. Colicin E3 receptor domain [69987]
               1. Escherichia coli [TaxId: 562] [69988] (5)
      5. Bacterial hemolysins [58100] (2)
         uperfamily
         1. Hemolysin E (HlyE, ClyA, SheA) [58101] (1)
            1. Hemolysin E (HlyE, ClyA, SheA) [58102]
               1. Escherichia coli [TaxId: 562] [58103] (1)
         2. HBL-like [161263] (1)
            Pfam 05791; Bacillus haemolytic enterotoxin
            1. Hemolysin BL (HBL) binding component B [161264]
               1. Bacillus cereus [TaxId: 1396] [161265] (1)
                  SQ Q9REG6 2-341
      6. Methyl-accepting chemotaxis protein (MCP) signaling domain [58104] (1)
         uperfamily
         1. Methyl-accepting chemotaxis protein (MCP) signaling domain [58105] (2)
            1. Cytoplasmic domain of a serine chemotaxis receptor [58106]
               long antiparallel four helical-bundle structure
               1. Escherichia coli [TaxId: 562] [58107] (1)
            2. Methyl-accepting chemotaxis protein 2, MCP2 [144290]
               1. Thermotoga maritima [TaxId: 2336] [144291] (2)
                  SQ Q9X0M7 225-529
      7. Oligomerization domain of hepatitis delta antigen [58108] (1)
         uperfamily
         1. Oligomerization domain of hepatitis delta antigen [58109] (1)
            1. Oligomerization domain of hepatitis delta antigen [58110]
               1. Hepatitis D virus [TaxId: 12475] [58111] (2)
      8. F1 ATPase inhibitor, IF1, C-terminal domain [64602] (1)
         uperfamily
         1. F1 ATPase inhibitor, IF1, C-terminal domain [64603] (1)
            1. F1 ATPase inhibitor, IF1, C-terminal domain [64604]
               antiparallel right-handed coiled-coil
               1. Cow (Bos taurus) [TaxId: 9913] [64605] (4)
      9. Chemotaxis phosphatase CheZ [75708] (1)
         dimerizes with the formation of a 4-helical bundle
         uperfamily
         1. Chemotaxis phosphatase CheZ [75709] (1)
            1. Chemotaxis phosphatase CheZ [75710]
               1. Escherichia coli [TaxId: 562] [75711] (1)
      10. Rad50 coiled-coil Zn hook [75712] (1)
          dimerizes via a CxxC motif in the loop, zinc-hook
          uperfamily
          1. Rad50 coiled-coil Zn hook [75713] (1)
             1. Rad50 coiled-coil Zn hook [75714]
                1. Archaeon Pyrococcus furiosus [TaxId: 2261] [75715] (1)
      11. C-terminal domain of PLC-beta [69989] (1)
          left-handed antiparallel coiled-coil; dimerizes with the formation of a 4-helical bundle
          uperfamily
          1. C-terminal domain of PLC-beta [69990] (1)
             1. C-terminal domain of PLC-beta [69991]
                1. Turkey (Meleagris gallopavo) [TaxId: 9103] [69992] (1)
      12. Tumor suppressor gene product Apc [82931] (1)
          uperfamily
          1. Tumor suppressor gene product Apc [82932] (1)
             1. Tumor suppressor gene product Apc [82933]
                1. Human (Homo sapiens) [TaxId: 9606] [82934] (1)
      13. Proline/betaine transporter ProP, C-terminal cytoplasmic domain [103661] (1)
          uperfamily
          1. Proline/betaine transporter ProP, C-terminal cytoplasmic domain [103662] (1)
             1. Proline/betaine transporter ProP, C-terminal cytoplasmic domain [103663]
                1. Escherichia coli [TaxId: 562] [103664] (1)
      14. Fzo-like conserved region [111479] (1)
          antiparallel coiled-coil in the crystals
          uperfamily
          1. Fzo-like conserved region [111480] (1)
             Pfam 04799
             1. Transmembrane GTPase MFN1 (Mitofusin 1) [111481]
                1. Mouse (Mus musculus) [TaxId: 10090] [111482] (1)
                   SQ Q811U4 660-735
      15. occludin/ELL-like [144292] (1)
          antiparallel hairpin with a kinked second helix; similar to the N-terminal structure of the thermostable carboxypeptidase 1 (scop_pr 82731)
          uperfamily
          1. Occludin/ELL domain [144293] (1)
             Pfam 07303
             1. Occludin [144294]
                1. Human (Homo sapiens) [TaxId: 9606] [144295] (2)
                   SQ Q16625 416-522
      16. Gam-like [161266] (1)
          homodimeric fold with a ring-like structure formed by kinked coiled-coil and a beta-ribboon, interrupted by small helical insertions
          1. Gam-like [161267] (1)
             Pfam 07352; Bacteriophage Mu Gam-like protein
             1. Host-nuclease inhibitor protein Gam, putative [161268]
                1. Desulfovibrio vulgaris [TaxId: 881] [161269] (2)
                   SQ Q72CZ5 9-161
      17. PspA lactotransferrin-binding region [161270] (1)
          3 helices, the middle one is longer than the two others
          1. PspA lactotransferrin-binding region [161271] (1)
             1. Pneumococcal surface protein A, PspA [161272]
                1. Streptococcus pneumoniae [TaxId: 1313] [161273] (2)
                   SQ Q8DRI0 198-319
   5. Apolipoprotein A-I [58112] (1)
      tetrameric antiparallel coiled coil, closed in a circuit
      1. Apolipoprotein A-I [58113] (1)
         uperfamily
         1. Apolipoprotein A-I [58114] (1)
            1. Apolipoprotein A-I [58115]
               individual chains can form an up-and-down bundles
               1. Human (Homo sapiens) [TaxId: 9606] [58116] (1)
   6. Apolipoprotein A-II [82935] (1)
      segmented tetrameric parallel coiled coil
      1. Apolipoprotein A-II [82936] (1)
         uperfamily
         1. Apolipoprotein A-II [82937] (1)
            1. Apolipoprotein A-II [82938]
               1. Human (Homo sapiens) [TaxId: 9606] [82939] (2)
   7. Synuclein [118374] (1)
      1. Synuclein [118375] (1)
         uperfamily
         1. Synuclein [118376] (1)
            Pfam 01387
            1. Alpha-synuclein [118377]
               1. Human (Homo sapiens) [TaxId: 9606] [118378] (1)
                  SQ P37840 1-140
9. Low resolution protein structures [58117] (26)
   Not a true class
   1. Ribosome and ribosomal fragments [58118] (1)
      1. Ribosome and ribosomal fragments [58119] (3)
         uperfamily
         1. Ribosome complexes [58120] (9)
            1. 70S ribosome functional complex [58121]
               1. Thermus thermophilus [TaxId: 274] [58122] (48)
               2. Escherichia coli [TaxId: 562] [58123] (92)
               3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111483] (2)
               4. Thermotoga maritima Huber et al. 1986 (Thermotoga maritima) [TaxId: 2336] [161274] (2)
               5. Canis lupus familiaris [TaxId: 9615] [161275] (25)
               6. Spinacia oleracea [TaxId: 3562] [161276] (2)
               7. Mesembryanthemum crystallinum [TaxId: 3544] [161277] (2)
               8. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [161278] (11)
               9. Haloarcula marismortui [TaxId: 2238] [161279] (1)
         2. Large subunit [58124] (6)
            1. 50S subunit [58125]
               1. Archaeon Haloarcula marismortui [TaxId: 2238] [58126] (254)
               2. Deinococcus radiodurans [TaxId: 1299] [69993] (12)
               3. Escherichia coli [TaxId: 562] [58127] (1)
               4. Canis lupus familiaris [TaxId: 9615] [161280] (1)
               5. Spinacia oleracea [TaxId: 3562] [161281] (2)
               6. Nicotiana tabacum [TaxId: 4097] [161282] (1)
         3. Small subunit [58132] (1)
            1. 30S subunit [58133]
               1. Thermus thermophilus [TaxId: 274] [58134] (13)
   2. Collagen fibre [144296] (1)
      1. Collagen fibre [144297] (1)
         uperfamily
         1. Collagen fibre [144298] (1)
            1. Collagen I alpha [144299]
               hetero oligomer of isoforms 1 and 2
               1. Rat (Rattus norvegicus) [TaxId: 10116] [144300] (6)
   3. Fatty acid synthase [144301] (1)
      1. Fatty acid synthase [144302] (1)
         uperfamily
         1. Fatty acid syntase [144303] (2)
            1. mammalian fatty acid synthase [144304]
               1. Pig (Sus scrofa) [TaxId: 9823] [144305] (2)
            2. Fungal fatty acid syntase [144306]
               1. Thermomyces lanuginosus [TaxId: 5541] [144307] (1)
   4. Helicase [58135] (1)
      1. Helicase [58136] (1)
         uperfamily
         1. Helicase [58137] (1)
            1. RecA [58138]
               1. Escherichia coli [TaxId: 562] [58139] (2)
   5. ATP synthase [58140] (1)
      1. ATP synthase [58141] (1)
         uperfamily
         1. ATP synthase [58142] (3)
            1. ATP synthase [58143]
               1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [58144] (1)
               2. Escherichia coli [TaxId: 562] [58145] (2)
               3. Cow (Bos taurus) [TaxId: 9913] [161283] (7)
   6. Membrane ion ATPase [82940] (1)
      1. Membrane ion ATPase [82941] (1)
         uperfamily
         1. Membrane ion ATPase [82942] (1)
            1. Proton ATPase [82943]
               1. Fungi (Neurospora crassa) [TaxId: 5141] [82944] (1)
   7. Multidrug resistance ABC transporter [64606] (1)
      1. Multidrug resistance ABC transporter [64607] (1)
         uperfamily
         1. Multidrug resistance ABC transporter [64608] (1)
            1. MsbA [64609]
               1. Escherichia coli [TaxId: 562] [64610] (1)
   8. Electron transport chains [58146] (1)
      1. Electron transport chains [58147] (1)
         uperfamily
         1. Electron transport chains [58148] (4)
            not a true family
            1. Cytochrome f-plastocyanin complex [58149]
               1. Plant (Spinacia oleracea) and (Brassica rapa) [TaxId: 3562] [58150] (1)
               2. Prochlorothrix hollandica Burger-Wiersma et al. 1989 (Prochlorothrix hollandica) [TaxId: 1223] [161284] (1)
            2. Ferredoxin-cytochrome complex [58151]
               1. interspecies complex: Desulfomicrobium norvegicum and Desulfovibrio vulgaris [58152] (1)
            3. [Fe]-hydrogenase/cytochrome c553 complex [58153]
               1. interspecies complex: Desulfovibrio desulfuricans and Desulfovibrio vulgaris [58154] (1)
   9. Photosystems [58155] (1)
      1. Photosystems [58156] (1)
         uperfamily
         1. Photosystems [58157] (6)
            not a true family
            1. Photosynthetic reaction center and core antenna system (trimeric) [58158]
               1. Synechococcus elongatus [TaxId: 32046] [58159] (1)
            2. Photosystem II [58160]
               there is a higher resolution structure of Thermosynechococcus elongatus photosystem II (1s5l); however, PDB entry 1S5L designates protein chains by both upper case and lower case letters creating problems with its processing and presentation; there are two copies of the photosystem II complex: one with the upper case chains and the other with lower case chains
               1. Thermosynechococcus elongatus, bp-1 (formerly Synechococcus elongatus) [TaxId: 146786] [58161] (2)
               2. Thermosynechococcus vulcanus [TaxId: 32053] [82945] (2)
            3. RC-LH1 core complex [103665]
               1. Rhodopseudomonas palustris [TaxId: 1076] [103666] (1)
            4. Plant photosystem I [103667]
               1. Pea (Pisum sativum) [TaxId: 3888] [103668] (1)
            5. Chlorophyll a-b binding protein [103669]
               light-harvesting chlorophyll a/b protein complex with an icosahedral assembly
               1. Garden pea (Pisum sativum) [TaxId: 3888] [103670] (1)
                  a higher resolution structure of a homologous protein is also available, PDB entry 1RWT
   10. Viruses and virus-receptor complexes [58162] (1)
       1. Viruses and virus-receptor complexes [58163] (1)
          uperfamily
          1. Viruses and virus-receptor complexes [58164] (12)
             1. HRV16 complexed with d1d2-ICAM-1 [58165]
                1. Human rhinovirus 16 [TaxId: 31708] [58166] (1)
             2. HRV14 complexed with d1d2-ICAM-1 [58167]
                1. Human rhinovirus 14 [TaxId: 12131] [58168] (1)
             3. Poliovirus complexed with three domain CD155 [58169]
                1. Human poliovirus type 1 [TaxId: 12080] [58170] (2)
             4. FMDV complexed with a neutralizing Fab fragment [58171]
                1. Foot-and-mouth disease virus [TaxId: 12110] [58172] (1)
             5. SFV capsid [58173]
                1. Semliki forest virus [TaxId: 11033] [58174] (1)
             6. Coxsackievirus b3 (m strain) with its cellular receptor car [69994]
                1. Human (Homo sapiens) [TaxId: 9606] [69995] (1)
             7. p3 shell [69996]
                1. Bacteriophage prd1 [TaxId: 10658] [69997] (5)
             8. Decay-accelerating factor bound to echovirus 7 [75716]
                1. Human (Homo sapiens) and human echovirus 7 [TaxId: 9606] [75717] (1)
             9. Structural proteins [82946]
                1. Sindbis virus [TaxId: 11034] [82947] (1)
             10. PBCV-1 virus capsid, quasi-atomic model [82948]
                 1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82949] (1)
             11. Bacteriophage alpha3 assembly [82950]
                 1. Bacteriophage alpha3 [TaxId: 10849] [82951] (1)
             12. PRD1 capsid assembly [118379]
                 1. Bacteriophage PRD1 [TaxId: 10658] [118380] (1)
   11. Reovirus components [58175] (1)
       1. Reovirus components [58176] (1)
          uperfamily
          1. Reovirus components [58177] (3)
             1. Reovirus core [58178]
                1. Reovirus sp. [TaxId: 10891] [58179] (1)
             2. Minor core protein lambda 3 [103671]
                RNA-dependent RNA-polymerase
                1. Reovirus [TaxId: 10891] [103672] (1)
             3. outer-capsid protein mu1 and reovirus core [144308]
                1. Mammalian orthoreovirus 3 [TaxId: 538123] [144309] (1)
   12. Virus envelope proteins [75718] (1)
       1. Virus envelope proteins [75719] (1)
          uperfamily
          1. Virus envelope proteins [75720] (2)
             1. Virus envelope proteins [75721]
                1. Dengue virus [TaxId: 12637] [75722] (3)
                2. Yellow fever virus [TaxId: 11089] [103673] (1)
   13. Bacteriophage HK97 procapsid (prohead II) [64611] (1)
       1. Bacteriophage HK97 procapsid (prohead II) [64612] (1)
          uperfamily
          1. Bacteriophage HK97 procapsid (prohead II) [64613] (1)
             1. Bacteriophage HK97 procapsid (prohead II) [64614]
                1. Bacteriophage HK97 [TaxId: 37554] [64615] (1)
   14. Bacteriophage T4 3D cryo-EM reconstruction [103674] (1)
       1. Bacteriophage T4 3D cryo-EM reconstruction [103675] (1)
          uperfamily
          1. Bacteriophage T4 3D cryo-EM reconstruction [103676] (1)
             1. Bacteriophage T4 3D cryo-EM reconstruction [103677]
                1. Bacteriophage T4 [TaxId: 10665] [103678] (7)
   15. RNA polymerase [58180] (1)
       1. RNA polymerase [58181] (1)
          uperfamily
          1. RNA polymerase [58182] (3)
             1. DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits [58183]
                1. Thermus aquaticus [TaxId: 271] [58184] (3)
                2. Thermus thermophilus [TaxId: 274] [161285] (1)
             2. Complete 12-subunit RNA polymerase II complex [90261]
                1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90262] (38)
   16. Blood clotting [58187] (1)
       1. Blood clotting [58188] (1)
          uperfamily
          1. Blood clotting [58189] (2)
             1. Fibrinogen [58190]
                1. Cow (Bos taurus) [TaxId: 9913] [58191] (1)
                2. Chicken (Gallus gallus) [TaxId: 9031] [58192] (1)
   17. Microtubule complexes [58193] (1)
       1. Microtubule complexes [58194] (1)
          uperfamily
          1. Microtubule complexes [58195] (3)
             1. Tubulin:stathmin-like domain complex [58196]
                1. interspecies complex: Rattus norvegicus and Bos taurus [58197] (1)
                2. Cow (Bos taurus) [TaxId: 9913] [161286] (4)
             2. Kif1a head-microtubule complex [75723]
                1. interspecies complex: Mus musculus and Sus scrofa [75724] (1)
   18. Muscle protein complexes [64616] (1)
       1. Muscle protein complexes [64617] (1)
          uperfamily
          1. Muscle protein complexes [64618] (3)
             1. Heavy meromyosin subfragment [64619]
                1. Chicken (Gallus gallus) [TaxId: 9031] [64620] (1)
             2. Averaged rigor crossbridges from tomograms of insect flight muscle [82952]
                1. Chicken (Gallus gallus) and Rabbit (Oryctolagus cuniculus) [TaxId: 9031] [82953] (11)
             3. Actinin [103679]
                1. Chicken (Gallus gallus) [TaxId: 9031] [103680] (1)
   19. Ep-cadherin [103681] (1)
       1. Ep-cadherin [103682] (1)
          uperfamily
          1. Ep-cadherin [103683] (1)
             1. Ep-cadherin [103684]
                1. Mouse (Mus musculus) [TaxId: 10090] [103685] (4)
   20. Transferrin receptor-transferrin complex [103686] (1)
       1. Transferrin receptor-transferrin complex [103687] (1)
          uperfamily
          1. Transferrin receptor-transferrin complex [103688] (1)
             1. Transferrin receptor-transferrin complex [103689]
                1. Human (Homo sapiens) [TaxId: 9606] [103690] (1)
   21. Signal recognition particle (SRP) complex [103691] (1)
       1. Signal recognition particle (SRP) complex [103692] (1)
          uperfamily
          1. Signal recognition particle (SRP) complex [103693] (1)
             1. Signal recognition particle (SRP) complex [103694]
                1. interspecies complex [103695] (1)
   22. GroE chaperon [69998] (1)
       1. GroE chaperon [69999] (1)
          uperfamily
          1. GroE chaperon [70000] (1)
             1. GroE chaperon [70001]
                1. Escherichia coli [TaxId: 562] [70002] (3)
   23. clathrin assemblies [111484] (1)
       1. clathrin assemblies [111485] (1)
          uperfamily
          1. clathrin assemblies [111486] (3)
             1. AP1 clathrin adaptor core [111487]
                1. Mouse (Mus musculus) [TaxId: 10090] [111488] (2)
                2. Homo sapiens [TaxId: 9606] [161287] (1)
             2. Clathrin D6 coat [118381]
                1. Cow (Bos taurus) [TaxId: 9913] [118382] (3)
   24. anthrax toxin protective antigen-receptor complex [111489] (1)
       1. anthrax toxin protective antigen-receptor complex [111490] (1)
          uperfamily
          1. anthrax toxin protective antigen-receptor complex [111491] (1)
             1. anthrax toxin protective antigen-receptor complex [111492]
                1. interspecies complex: Bacillus anthracis and Homo sapiens [111493] (1)
   25. Computational models partly based on experimental data [58198] (1)
       1. Computational models partly based on experimental data [58199] (1)
          uperfamily
          1. Computational models partly based on experimental data [58200] (6)
             this is not a true family
             1. Cytochrome c' [58201]
                1. Rhodobacter capsulatus [TaxId: 1061] [58202] (1)
             2. Tumor suppressor p15(ink4b) [58203]
                1. Mouse (Mus musculus) [TaxId: 10090] [58204] (1)
             3. Nodulation protein NodF [58205]
                1. Rhizobium leguminosarum [TaxId: 384] [58206] (1)
             4. Ribosomal L11 protein in complex with thiostrepton and a 23S rRNA fragment [103696]
                1. Thermotoga maritima [TaxId: 2336] [103697] (1)
             5. Ternary complex formed between MarA, the alpha-CTD of RNA polymerase and DNA [118383]
                1. Escherichia coli [TaxId: 562] [118384] (1)
             6. Hypothetical protein PF1455 [144310]
                1. Pyrococcus furiosus [TaxId: 2261] [144311] (1)
                   SQ Q8U0X6 2-74
   26. Proteins of incorrect, partial and unknown sequence [58207] (1)
       1. Proteins of incorrect, partial and unknown sequence [58208] (1)
          uperfamily
          1. Proteins of incorrect, partial and unknown sequence [58209] (12)
             1. Lactate dehydrogenase [58210]
                1. Dogfish (Squalus acanthias) [TaxId: 7797] [58211] (1)
             2. Glutathione reductase [58212]
                1. Human (Homo sapiens) [TaxId: 9606] [58213] (1)
             3. Hemerythrin [58214]
                1. Siphonosoma [TaxId: 6443] [58215] (1)
             4. KDPG aldolase [58216]
                1. Pseudomonas putida [TaxId: 303] [58217] (1)
             5. Pyruvate kinase [58218]
                1. Cat (Felis catus) [TaxId: 9685] [58219] (1)
             6. Phosphoglycerate kinase [58220]
                1. Horse (Equus caballus) [TaxId: 9796] [58221] (1)
             7. Catalase [58222]
                1. Penicillium vitale [TaxId: 5079] [58223] (2)
             8. Hexokinase [58224]
                1. Baker's yeast (Saccharomyces cerevisiae), BIII [TaxId: 4932] [58225] (1)
                2. Baker's yeast (Saccharomyces cerevisiae), A [TaxId: 4932] [58226] (1)
             9. Serum amyloid P component, SAP [58227]
                1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [58228] (1)
             10. TNV coat protein [58229]
                 1. Tobacco necrosis virus [TaxId: 12054] [58230] (1)
             11. Dihydrolipoamide dehydrogenase [90263]
                 1. Pig (Sus scrofa) [TaxId: 9823] [90264] (1)
10. Peptides [58231] (121)
    Peptides and fragments. Not a true class
    1. Membrane ion channel-forming peptide antibiotics containing D-aminoacids [58232] (1)
       1. Membrane ion channel-forming peptide antibiotics containing D-aminoacids [58233] (2)
          uperfamily
          1. Gramicidin [58234] (1)
             1. Gramicidin [58235]
                different conformations
                1. Bacillus brevis [TaxId: 1393] [58236] (21)
          2. Peptaibol [58237] (8)
             1. Chrysospermin C [58238]
                1. Hypomyces chrysospermus, congruent with Apiocrea chrysosperma [TaxId: 5131] [58239] (1)
             2. Zervamicin IIb [70003]
                1. Emericellopsis salmosynnemata [TaxId: 118885] [70004] (2)
             3. Antiamoebin I [82954]
                1. Emericellopsis [TaxId: 45244] [82955] (1)
             4. Alamecitin [58241]
                1. Trichoderma viride [TaxId: 5547] [58242] (1)
             5. Trichotoxin_a50e [82956]
                1. Trichoderma viride [TaxId: 5547] [82957] (1)
             6. Cephaibol A [103698]
                1. Acremonium tubakii [TaxId: 146077] [103699] (1)
             7. Cephaibol B [103700]
                1. Acremonium tubakii [TaxId: 146077] [103701] (1)
             8. Cephaibol C [103702]
                1. Acremonium tubakii [TaxId: 146077] [103703] (1)
    2. Lantibiotic peptides [58243] (1)
       peptide antibiotic
       1. Lantibiotic peptides [58244] (3)
          uperfamily
          1. Actagardine [58245] (1)
             1. Actagardine [58246]
                1. Actinoplanes liguriae [TaxId: 69484] [58247] (1)
          2. Mersacidin [58248] (1)
             1. Mersacidin [58249]
                1. Bacillus sp., Hil Y-85 [TaxId: 1409] [58250] (4)
          3. Nisin [111494] (1)
             1. Nisin [111495]
                1. Lactococcus lactis [TaxId: 1358] [111496] (1)
    3. Leucocin-like bacteriocin [100898] (1)
       consists of a conserved, disulfide-containing N-terminal region (forming a beta-sheet) and a C-terminal helix
       1. Leucocin-like bacteriocin [100899] (1)
          uperfamily
          1. Leucocin-like bacteriocin [100900] (3)
             1. Leucocin [58254]
                antibacterial peptide, bacteriocin
                1. Leuconostoc gelidum [TaxId: 1244] [58255] (3)
             2. Sakacin P [103704]
                1. Lactobacillus sake [TaxId: 1599] [103705] (3)
             3. Carnobacteriocin B2 [58276]
                1. Carnobacterium piscicola [TaxId: 2751] [58277] (2)
    4. Antimicrobial beta-hairpin [58251] (1)
       contains beta-hairpin crosslinked by disulfide bridge(s)
       1. Antimicrobial beta-hairpin [58252] (8)
          not a true superfamily
          uperfamily
          1. Insect defense peptide thanatin [58256] (1)
             1. Insect defense peptide thanatin [58257]
                1. Podisus maculiventris [TaxId: 29025] [58258] (1)
          2. Androctonin [58259] (1)
             1. Androctonin [58260]
                1. Scorpion (Androctonus australis) [TaxId: 6858] [58261] (1)
          3. Gomesin [75725] (1)
             1. Gomesin [75726]
                1. Mygalomorphae spider (Acanthoscurria gomesiana) [TaxId: 115339] [75727] (1)
          4. Tachyplesin I [82958] (2)
             1. Tachyplesin I [82959]
                horseshoe crab antimicrobial peptide
                1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [82960] (4)
                2. synthetic, polyphemusin I [111497] (1)
          5. theta defensin-like [58262] (2)
             1. Protegrin 1 (PG1) [58263]
                1. Pig (Sus scrofa) [TaxId: 9823] [58264] (1)
             2. RTD-1 [64621]
                a cyclic antimicrobial defensin from rhesus macaque leukocytes
                1. Synthetic, based on Rhesus macaque sequence [64622] (1)
          6. Lactoferricin B (lfcinb) [58265] (1)
             1. Lactoferricin B (lfcinb) [58266]
                Antimicrobial peptide derived from bovine lactoferrin
                1. Synthetic, based on Bos taurus sequence [58267] (1)
          7. Hepcidin [82961] (2)
             1. Hepcidin [82962]
                1. Synthetic, based on human sequence [82963] (2)
                2. synthetic, based on the hybrid white striped bass sequence [118385] (1)
                   SQ P82951 65-85
          8. Cyclic trypsin inhibitor STFI-1 [90265] (1)
             1. Cyclic trypsin inhibitor STFI-1 [90266]
                1. Sunflower (Helianthus annuus l.) [TaxId: 4232] [90267] (2)
    5. Antimicrobial helix [58268] (1)
       antibiotic peptide
       1. Antimicrobial helix [58269] (5)
          not a true superfamily
          uperfamily
          1. Magainin [58270] (2)
             1. Magainin 2 [58271]
                1. Xenopus laevis [TaxId: 8355] [58272] (2)
             2. Cecropin A-Magainin 2 hybrid peptide [58273]
                1. synthetic, hybrid of Hyalophora cecropia and Xenopus laevis sequences [58274] (10)
          2. Moricin [75728] (2)
             1. Moricin [75729]
                1. Silkworm (Bombyx mori) [TaxId: 7091] [75730] (1)
                2. Manduca sexta [TaxId: 7130] [161288] (1)
          3. Tachykinin peptides [82964] (3)
             1. Kassinin [82965]
                1. Frog (Kassina senegalensis) [TaxId: 8415] [82966] (1)
             2. Eledoisin [82967]
                1. Octopod (Eledone moschata) [TaxId: 6641] [82968] (1)
             3. Neurokinin A [103706]
                1. Synthetic, mammalian sequence [103707] (1)
          4. Cytotoxic linear peptide IsCT [118386] (1)
             1. Cytotoxic linear peptide IsCT [118387]
                1. Scorpion (Opisthacanthus madagascariensis) [TaxId: 167108] [118388] (4)
                   SQ Q8MMJ7 24-36
          5. Distinctin [144312] (2)
             1. Distinctin chain B [144313]
                1. synthetic [144314] (2)
             2. Distinctin chain A [144315]
                1. synthetic [144316] (2)
    6. Macrocyclic bacteriocins [58278] (1)
       macrocyclic antimicrobial peptide; bacteriocin
       1. Macrocyclic bacteriocins [58279] (2)
          uperfamily
          1. Microcin J25 [58280] (1)
             1. Microcin J25 [58281]
                1. Escherichia coli [TaxId: 562] [58282] (3)
                   SQ Q9X2V7 38-58
          2. Subtilosin A [111498] (1)
             unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons
             1. Subtilosin A [111499]
                1. Bacillus subtilis [TaxId: 1423] [111500] (1)
                   SQ O07623 9-43
    7. Peptide hormones [58283] (1)
       contains one alpha-helix
       1. Peptide hormones [58284] (1)
          this is not a true superfamily
          uperfamily
          1. Peptide hormones [58285] (27)
             1. Pancreatic polypeptide [58286]
                1. Cow (Bos taurus) [TaxId: 9913] [58287] (3)
                2. Turkey (Meleagris gallopavo) [TaxId: 9103] [58288] (2)
                   SQ P68249
             2. Neuropeptide Y [58289]
                1. Human (Homo sapiens) [TaxId: 9606] [58290] (2)
                2. Pig (Sus scrofa) [TaxId: 9823] [58291] (2)
             3. Peptide YY, PYY [58292]
                1. Pig (Sus scrofa) [TaxId: 9823] [58293] (6)
                   SQ P68005
                2. Human (Homo sapiens) [TaxId: 9606] [144317] (2)
                   SQ P10082 29-64! SQ P10082 31-64
             4. Neuropeptide Y analogues [58294]
                1. Synthetic [58295] (6)
             5. Neuropeptide F [75731]
                1. Sheep tapeworm (Moniezia expansa) [TaxId: 28841] [75732] (1)
             6. Deaminooxytocin [58296]
                ten-residue peptide with one disulfide
                1. Synthetic [58297] (2)
             7. Glucagon [58298]
                1. Pig (Sus scrofa) [TaxId: 9823] [58299] (3)
                2. Synthetic, Homo sapiens analog [58300] (1)
             8. Glucagon-like peptide-1-(7-36)-amide [82969]
                1. Human (Homo sapiens) [TaxId: 9606] [82970] (1)
             9. Exendin-4 [70005]
                glucagone-like hormone
                1. Synthetic [70006] (1)
                2. synthetic construct [161289] (1)
                3. Homo sapiens [TaxId: 9606] [161290] (1)
             10. Calcitonin [58301]
                 1. Eel (Anguilla japonica) [TaxId: 7937] [58302] (3)
                 2. Pink salmon (Oncorhynchus gorbuscha) [TaxId: 8017] [90268] (1)
                 3. Chum salmon (Oncorhynchus keta) [TaxId: 8018] [144318] (2)
                    SQ P01263 83-114
             11. Neuromedin B [58303]
                 1. Synthetic [58304] (2)
             12. Hypocretin-2/orexin- b' [58305]
                 1. Human (Homo sapiens) [TaxId: 9606] [58306] (1)
             13. Motilin [82971]
                 1. Synthetic, based on human sequence [82972] (1)
             14. Transportan (galanin-like peptide) [103708]
                 1. Synthetic [103709] (1)
             15. Neurokinin B [111501]
                 1. Synthetic [111502] (1)
                    SQ Q9UHF0 81-90 # human TaxID: 9606
             16. Orexin [111503]
                 1. Human (Homo sapiens) [TaxId: 9606] [111504] (2)
                    SQ O43612 35-66 ! SQ O43612 34-66
             17. Pardaxin P-4 [111505]
                 1. Red sea moses sole (Pardachirus marmoratus) [TaxId: 31087] [111506] (1)
                    SQ P81861
             18. Gastric inhibitory polypeptide, GIP [118389]
                 1. Human (Homo sapiens) [TaxId: 9606] [118390] (1)
                    SQ P09681 52-81
             19. Pituitary adenylate cyclase-activating polypeptide, PACAP [161291]
                 1. Human (Homo sapiens) [TaxId: 9606] [161292] (1)
                    SQ P18509 137-169
    8. Angiotensin [90269] (1)
       1. Angiotensin [90270] (1)
          uperfamily
          1. Angiotensin [90271] (2)
             1. Angiotensin I [90272]
                1. Synthetic, based on human sequence [90273] (1)
             2. Angiotensin II [90274]
                1. Synthetic, based on human sequence [90275] (1)
    9. delta toxin-like [58307] (3)
       single alpha helix
       1. delta-Toxin [58308] (1)
          uperfamily
          1. delta-Toxin [58309] (1)
             1. delta-Toxin [58310]
                1. Synthetic [58311] (2)
       2. Antimicrobial peptide HP(2-20) [90276] (1)
          uperfamily
          1. Antimicrobial peptide HP(2-20) [90277] (1)
             1. Antimicrobial peptide HP(2-20) [90278]
                1. Synthetic, derived from the Helicobacter pylori ribosomal protein L1 [90279] (7)
                   SQ P56029 2-20
       3. Anticancer peptides [118391] (1)
          uperfamily
          1. Anticancer peptides [118392] (1)
             1. Anticancer peptides [118393]
                derived from Escherichia coli EIIA-Glc peptide (SQ P69783 1-13) and Litoria raniformis aurein 1.2 (SQ P82387)
                1. synthetic [118394] (4)
    10. PSP1-like [58312] (1)
        1. PSP1-like [58313] (1)
           uperfamily
           1. PSP1-like [58314] (8)
              1. Plasmatocyte-spreading peptide PSP1 [58315]
                 1. Pseudoplusia includens [TaxId: 76492] [58316] (2)
              2. Growth-blocking peptide GBP [58317]
                 1. Braconid wasp (Apanteles kariyai) [TaxId: 7404] [58318] (1)
                    parasite of armyworm (Pseudaletia separata?)
                 2. Cabbage moth (Mamestra brassicae) [TaxId: 55057] [161293] (1)
                    SQ O96060 130-152
                 3. Tobacco cutworm (Spodoptera litura) [TaxId: 69820] [161294] (1)
                    SQ O96061 122-144
                 4. synthetic construct [161295] (2)
              3. Paralytic peptide [58319]
                 1. Insect (Manduca sexta) [TaxId: 7130] [58320] (1)
                 2. Silkworm (Bombyx mori) [TaxId: 7091] [82973] (1)
                 3. Silkmoth (Antheraea yamamai) [TaxId: 7121] [118395] (1)
                    SQ Q9UA40 108-130 # 95% sequence identity
    11. Arg-rich RNA binding peptides [58321] (7)
        1. 30S ribosomal protein THX [58322] (1)
           uperfamily
           1. 30S ribosomal protein THX [58323] (1)
              1. 30S ribosomal protein THX [58324]
                 1. Thermus thermophilus [TaxId: 274] [58325] (44)
                    SQ P62612
        2. HIV-1 REV fragments [58326] (1)
           uperfamily
           1. HIV-1 REV fragments [58327] (1)
              1. HIV-1 REV fragments [58328]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [58329] (6)
        3. RSG-1.2 peptide [58330] (1)
           uperfamily
           1. RSG-1.2 peptide [58331] (1)
              1. RSG-1.2 peptide [58332]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [58333] (1)
        4. TAT peptides [58334] (1)
           uperfamily
           1. TAT peptides [58335] (2)
              1. TAT peptides [58336]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [58337] (1)
                 2. Bovine immunodeficiency virus [TaxId: 11657] [58338] (2)
        5. Box B RNA-binding N peptide [58339] (1)
           uperfamily
           1. Box B RNA-binding N peptide [58340] (4)
              1. Box B RNA-binding N peptide [58341]
                 1. Salmonella bacteriophage P22 [TaxId: 10754] [58342] (1)
                 2. Bacteriophage lambda [TaxId: 10710] [58343] (1)
                 3. Bacteriophage HK022 [TaxId: 10742] [70007] (1)
                 4. Bacteriophage phi-21 [TaxId: 10737] [90280] (1)
        6. HTLV-1 peptide [58344] (1)
           uperfamily
           1. HTLV-1 peptide [58345] (1)
              1. HTLV-1 peptide [58346]
                 bound to its RNA aptamer target
                 1. Synthetic [58347] (1)
        7. Ilarvirus coat protein N-terminal fragment [118396] (1)
           uperfamily
           1. Ilarvirus coat protein N-terminal fragment [118397] (1)
              N-terminal part of Pfam 01787; RNA-binding helix
              1. Ilarvirus coat protein N-terminal fragment [118398]
                 1. Alfalfa mosaic virus (strain YSMV) [TaxId: 12325] [118399] (1)
                    SQ P24264 1-26
    12. DNA-binding domains of HMG-I(Y) [58348] (1)
        1. DNA-binding domains of HMG-I(Y) [58349] (1)
           uperfamily
           1. DNA-binding domains of HMG-I(Y) [58350] (1)
              1. DNA-binding domains of HMG-I(Y) [58351]
                 1. Human (Homo sapiens) [TaxId: 9606] [58352] (4)
    13. VPR protein fragments [58353] (1)
        1. VPR protein fragments [58354] (1)
           uperfamily
           1. VPR protein fragments [58355] (1)
              1. VPR protein fragments [58356]
                 1. Human immunodeficiency virus type 1 [TaxId: 11676] [58357] (13)
    14. Inactivation gate of potassium and sodium channels [58358] (1)
        1. Inactivation gate of potassium and sodium channels [58359] (1)
           uperfamily
           1. Inactivation gate of potassium and sodium channels [58360] (5)
              it is not a true family
              1. Potassium channel RAW3 [58361]
                 1. Synthetic, based on mammalian sequence [58362] (1)
                 2. Synthetic, expressed in Escherichia coli [58363] (2)
              2. Potassium channel RCK4 [58364]
                 1. Synthetic, based on mammalian sequence [58365] (2)
              3. Sodium channel IIA [58366]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [58367] (1)
              4. Potassium voltage-gated channel subfamily H (HERG) extracellular linker [103710]
                 1. Synthetic, based on human sequence [103711] (1)
    15. Coagulation factor VIII, membrane-binding peptide [58368] (1)
        1. Coagulation factor VIII, membrane-binding peptide [58369] (1)
           uperfamily
           1. Coagulation factor VIII, membrane-binding peptide [58370] (1)
              1. Coagulation factor VIII, membrane-binding peptide [58371]
                 1. Human (Homo sapiens) [TaxId: 9606] [58372] (2)
    16. Phosphocholine cytidylyltransferase membrane-binding peptides [58373] (1)
        1. Phosphocholine cytidylyltransferase membrane-binding peptides [58374] (1)
           uperfamily
           1. Phosphocholine cytidylyltransferase membrane-binding peptides [58375] (1)
              1. Phosphocholine cytidylyltransferase membrane-binding peptides [58376]
                 alpha-helix
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [58377] (2)
    17. Parathyroid hormone fragments (residues between 1 and 39) [58378] (1)
        1. Parathyroid hormone fragments (residues between 1 and 39) [58379] (1)
           uperfamily
           1. Parathyroid hormone fragments (residues between 1 and 39) [58380] (3)
              1. Parathyroid hormone fragments (residues between 1 and 39) [58381]
                 1. Human (Homo sapiens) [TaxId: 9606] [58382] (14)
                 2. Cow (Bos taurus) [TaxId: 9913] [58383] (1)
                 3. synthetic construct [161296] (2)
    18. Corticotropin releasing hormone [58384] (1)
        1. Corticotropin releasing hormone [58385] (1)
           uperfamily
           1. Corticotropin releasing hormone [58386] (3)
              1. Corticotropin releasing hormone [58387]
                 1. Human (Homo sapiens) [TaxId: 9606] [58388] (2)
                 2. synthetic construct [161297] (2)
                 3. Ovis aries [TaxId: 9940] [161298] (2)
    19. Liposaccharide-binding protein CAP18 (residues 106-137) [58389] (1)
        1. Liposaccharide-binding protein CAP18 (residues 106-137) [58390] (1)
           uperfamily
           1. Liposaccharide-binding protein CAP18 (residues 106-137) [58391] (1)
              1. Liposaccharide-binding protein CAP18 (residues 106-137) [58392]
                 1. Synthetic, based on rabbit sequence [58393] (1)
    20. Polymorphic antigen SPAM-H1 (residues 90-127) [58394] (1)
        1. Polymorphic antigen SPAM-H1 (residues 90-127) [58395] (1)
           uperfamily
           1. Polymorphic antigen SPAM-H1 (residues 90-127) [58396] (1)
              1. Polymorphic antigen SPAM-H1 (residues 90-127) [58397]
                 1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [58398] (1)
    21. Insect toxins [58399] (1)
        1. Insect toxins [58400] (2)
           uperfamily
           1. Mellitin-like toxins [58401] (2)
              1. Mellitin [58402]
                 1. Honeybee (Apis mellifera) [TaxId: 7460] [58403] (2)
              2. Mastoparan [64623]
                 1. Wasp (Vespula lewisii) [TaxId: 7452] [64624] (1)
           2. Poneratoxin (Pac-Tx) [103712] (1)
              1. Poneratoxin (Pac-Tx) [103713]
                 1. Ant (Paraponera clavata) [TaxId: 55425] [103714] (1)
    22. Tertiapin [58404] (1)
        small disulfide-rich peptide
        1. Tertiapin [58405] (1)
           uperfamily
           1. Tertiapin [58406] (1)
              1. Tertiapin [58407]
                 1. Honeybee venom (Apis mellifera) [TaxId: 7460] [58408] (1)
    23. Antifreeze polypeptide HPLC-6 [58409] (1)
        1. Antifreeze polypeptide HPLC-6 [58410] (1)
           uperfamily
           1. Antifreeze polypeptide HPLC-6 [58411] (1)
              1. Antifreeze polypeptide HPLC-6 [58412]
                 1. Winter flounder (Pseudopleuronectes americanus) [TaxId: 8265] [58413] (3)
    24. Troponin I fragments [58414] (1)
        1. Troponin I fragments [58415] (1)
           uperfamily
           1. Troponin I fragments [58416] (3)
              1. Troponin I fragments [58417]
                 1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [58418] (1)
                 2. Human (Homo sapiens), cardiac isoform [TaxId: 9606] [58419] (2)
                 3. Chicken (Gallus gallus) [TaxId: 9031] [144319] (2)
                    SQ P68246 132-183
    25. Pilin fragments [58420] (1)
        1. Pilin fragments [58421] (1)
           uperfamily
           1. Pilin fragments [58422] (3)
              1. Pilin, fragment 128-144 [58423]
                 1. Pseudomonas aeruginosa, strain k pak pilin [TaxId: 287] [58424] (4)
                 2. Pseudomonas aeruginosa, strain o pao pilin [TaxId: 287] [58425] (2)
                 3. Pseudomonas aeruginosa, strain kb7 [TaxId: 287] [58426] (2)
    26. RP71935 [58427] (1)
        1. RP71935 [58428] (1)
           uperfamily
           1. RP71935 [58429] (1)
              1. RP71935 [58430]
                 21-residue disulfide-bound peptide
                 1. Actinomycete, strain sp9440 [TaxId: 100235] [58431] (2)
    27. Atrial natriuretic peptide [58432] (1)
        1. Atrial natriuretic peptide [58433] (1)
           uperfamily
           1. Atrial natriuretic peptide [58434] (1)
              1. Atrial natriuretic peptide [58435]
                 A-type receptor specific hypotensive hormone
                 1. Human (Homo sapiens) [TaxId: 9606] [58436] (1)
    28. Compstatin [58437] (1)
        1. Compstatin [58438] (1)
           uperfamily
           1. Compstatin [58439] (1)
              1. Compstatin [58440]
                 1. Synthetic chemical synthesis [58441] (1)
    29. Membrane-bound antimicrobial peptides [58442] (1)
        1. Membrane-bound antimicrobial peptides [58443] (1)
           uperfamily
           1. Membrane-bound antimicrobial peptides [58444] (2)
              no or little secondary structure
              1. Tritrpticin [58445]
                 1. Synthetic, based on Sus scrofa sequence [58446] (1)
              2. Indolicidin [58447]
                 1. Synthetic, based on Bos taurus sequence [58448] (5)
    30. Endothelin-like [58449] (1)
        small disulfide-rich
        1. Endothelin-like [58450] (1)
           uperfamily
           1. Endothelin-like [58451] (3)
              1. Endothelin-1 [58452]
                 1. Human (Homo sapiens) [TaxId: 9606] [58453] (4)
                    SQ P05305 51-68
                 2. Synthetic [58454] (2)
              2. Sarafotoxin S6B [58455]
                 1. Synthetic, based on sequence from asp Atractaspis engaddensis venom [58456] (1)
    31. Heat-stable enterotoxin (HSE) [58457] (1)
        1. Heat-stable enterotoxin (HSE) [58458] (1)
           uperfamily
           1. Heat-stable enterotoxin (HSE) [58459] (2)
              short disulfide-bound peptide
              1. Heat-stable enterotoxin [58460]
                 1. Escherichia coli [TaxId: 562] [58461] (3)
              2. Guanylin [58462]
                 endogenous ligand to the HSE receptor
                 1. Human (Homo sapiens) [TaxId: 9606] [58463] (4)
    32. Conotoxins [58464] (1)
        disulfide-rich fold
        1. Conotoxins [58465] (7)
           all apart omega class; it is not a true superfamily
           uperfamily
           1. mu-conotoxin [58466] (4)
              1. mu-Conotoxin GIIIa [58467]
                 1. Conus geographus [TaxId: 6491] [58468] (4)
              2. mu-Conotoxin GIIIb [58469]
                 1. Conus geographus [TaxId: 6491] [58470] (1)
              3. Mu-conotoxin pIIIa [103715]
                 1. Conus purpurascens [TaxId: 41690] [103716] (1)
              4. Mu-conotoxin smIIIa [103717]
                 1. Conus stercusmuscarum [TaxId: 89452] [103718] (1)
           2. alpha-conotoxin [58471] (11)
              13-16 residue peptide with 2 disulfides
              1. alpha-conotoxin PNI1 [58472]
                 1. Conus pennaceus [TaxId: 37335] [58473] (1)
              2. alpha-conotoxin PNIB [58474]
                 1. Conus pennaceus [TaxId: 37335] [58475] (1)
              3. alpha-conotoxin IM1 [58476]
                 1. Conus imperialis [TaxId: 35631] [58477] (5)
              4. alpha-conotoxin MII [58478]
                 1. Synthetic [58479] (1)
              5. G1 alpha-conotoxin [58480]
                 1. Conus geographus [TaxId: 6491] [58481] (5)
              6. alpha-conotoxin GID [82974]
                 1. Conus geographus [TaxId: 6491] [82975] (1)
              7. alpha-conotoxin CNIA [58482]
                 1. Conus consors [TaxId: 101297] [58483] (1)
              8. alpha-conotoxin auIB [58484]
                 1. Conus aulicus [TaxId: 89437] [58485] (3)
              9. alpha-conotoxin SI [58486]
                 1. Conus striatus [TaxId: 6493] [58487] (2)
              10. Alpha-conotoxin EI [103719]
                  1. Conus ermineus [TaxId: 55423] [103720] (1)
              11. Alpha-conotoxin GIC [111507]
                  1. Conus geographus [TaxId: 6491] [111508] (1)
                     SQ Q86RB2 21-36
           3. Alpha-a-conotoxin [58488] (2)
              1. AA-conotoxin pIVa [58489]
                 1. Conus purpurascens [TaxId: 41690] [58490] (1)
              2. Alpha-a-conotoxin eIVa [103721]
                 1. Conus ermineus [TaxId: 55423] [103722] (1)
           4. psi-conotoxin [58491] (2)
              1. psi-conotoxin pIIIe [58492]
                 1. Conus purpurascens [TaxId: 41690] [58493] (2)
              2. psi-conotoxin pIIIf [90281]
                 1. Conus purpurascens [TaxId: 41690] [90282] (1)
           5. Conotoxin tiA [75733] (1)
              1. Conotoxin tiA [75734]
                 1. Conus tulipa [TaxId: 6495] [75735] (1)
           6. Conotoxin mrIB [75736] (1)
              1. Conotoxin mrIB [75737]
                 1. Conus marmoreus [TaxId: 42752] [75738] (1)
           7. Delta-conotoxin [103723] (1)
              1. delta-conotoxin eVIa1 [103724]
                 1. Conus ermineus [TaxId: 55423] [103725] (1)
    33. Conantokin [58494] (1)
        1. Conantokin [58495] (2)
           gamma-carboxyglutamic acid (GLA)-rich peptide; active conformation may be stabilized by metal ions
           uperfamily
           1. Conantokin G (conatoxin G) [58496] (1)
              1. Conantokin G (conatoxin G) [58497]
                 1. Conus geographus [TaxId: 6491] [58498] (3)
           2. Conantokin-T [58499] (1)
              1. Conantokin-T [58500]
                 1. Conus tulipa [TaxId: 6495] [58501] (1)
    34. Contryphan-R [58502] (1)
        1. Contryphan-R [58503] (1)
           uperfamily
           1. Contryphan-R [58504] (1)
              1. Contryphan-R [58505]
                 contains D-tryptophan
                 1. Conus radiatus [TaxId: 61198] [58506] (6)
    35. Kappa-hefutoxin-like [58507] (2)
        hairpin of two short helices crosslinked with two disulfides
        1. Immunodominant region of protein G of BRSV [58508] (1)
           uperfamily
           1. Immunodominant region of protein G of BRSV [58509] (2)
              1. Immunodominant region of protein G of BRSV [58510]
                 1. Bovine respiratory syncytial virus [TaxId: 11246] [58511] (1)
                 2. Human respiratory syncytial virus [TaxId: 11250] [90283] (2)
        2. Potassium channel toxins [75739] (1)
           uperfamily
           1. Potassium channel toxins [75740] (1)
              1. Kappa-hefutoxin [75741]
                 1. Synthetic [75742] (1)
    36. Penaeidin-3a [103726] (1)
        1. Penaeidin-3a [103727] (1)
           uperfamily
           1. Penaeidin-3a [103728] (1)
              1. Penaeidin-3a [103729]
                 antimicrobial peptide; consists of N-terminal proline-rich tail and C-terminal cysteine-rich domain
                 1. Pacific white shrimp (Litopenaeus vannamei) [TaxId: 6689] [103730] (1)
    37. Bradykinin [58512] (1)
        1. Bradykinin [58513] (1)
           uperfamily
           1. Bradykinin [58514] (2)
              1. Bradykinin [64625]
                 1. SP Human (Homo sapiens) [TaxId: 9606] [64626] (1)
              2. Bradykinin antagonist B-9340 [58515]
                 1. Synthetic [58516] (1)
    38. Transmembrane helical fragments [58517] (1)
        1. Transmembrane helical fragments [58518] (1)
           uperfamily
           1. Transmembrane helical fragments [58519] (32)
              the member of this family may be not related
              1. Bacteriorhodopsin fragments [58520]
                 1. Archaeon Halobacterium halobium [TaxId: 2242] [58521] (3)
              2. Rhodopsin fragments [58522]
                 1. Synthetic, based on Bos taurus sequence [58523] (6)
              3. Band 3 [58524]
                 1. Synthetic peptides based on human band 3 sequence [58525] (9)
              4. Pulmonary surfactant-associated polypeptide C (SP-C) [58526]
                 1. Pig (Sus scrofa) [TaxId: 9823] [58527] (1)
              5. Surfactant Protein B (SP-B) miniprotein constructs [58528]
                 1. Synthetic, based on Homo sapiens sequence [58529] (7)
                    SQ P07988 208-225,263-278
              6. beta-Adrenoreceptor [58530]
                 1. Turkey (Meleagris gallopavo) [TaxId: 9103] [58531] (1)
              7. Dimeric transmembrane domain of glycophorin A [58532]
                 right-hand twisted coiled coil
                 1. Human (Homo sapiens) [TaxId: 9606] [58533] (1)
              8. F1F0 ATP synthase subunit C fragments [58534]
                 1. Escherichia coli [TaxId: 562] [58535] (1)
              9. Membrane domain of the subunit b of ATP synthase [58536]
                 1. Escherichia coli [TaxId: 562] [58537] (1)
              10. alpha-subunit of nicotinic acetylcholine receptor [58538]
                  M3 transmembrane segment
                  1. Synthetic, based on Torpedo californica sequence [58539] (1)
              11. Membrane spanning segment 2 (M2) of the acetylcholine receptor [58540]
                  1. Rat (Rattus norvegicus) [TaxId: 10116] [58541] (2)
                  2. Pacific electric ray (Torpedo californica) [TaxId: 7787] [58542] (2)
              12. Transmembrane segment 2 of NMDA receptor NR1 [58543]
                  1. Human (Homo sapiens) [TaxId: 9606] [58544] (1)
              13. Cystic fibrosis transmembrane conductance regulator [58545]
                  1. Synthetic [58546] (4)
              14. Second repeat (is2mic) from voltage-gated sodium channel [58547]
                  1. Synthetic, based on Rattus norvegicus sequence [58548] (1)
              15. Cytoplasmic domain of p23 [58549]
                  1. Synthetic, based on Oryctolagus cuniculus sequence [58550] (2)
              16. Active domain of protein icp47 [58551]
                  1. Herpes simplex virus type 1, strain 17 [TaxId: 10298] [58552] (1)
              17. fragment of hepatitis C envelope glycoprotein E (residues 350-370) [58553]
                  1. Synthetic [58554] (1)
              18. Neu/erbb-2 membrane spanning segment [64627]
                  1. Synthetic, based on Rattus norvegicus sequence [64628] (1)
              19. Membrane binding peptide of semliki forest virus mRNA capping enzyme nsp1 [64629]
                  1. Synthetic [64630] (1)
              20. Sarcolipin [70008]
                  1. Synthetic [70009] (1)
              21. Potassium channel fragment L45 [75743]
                  1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75744] (2)
              22. Amphipathic domain of YopD [75745]
                  1. Synthetic, Yersinia pestis-based [75746] (1)
              23. Matrix protein M2 transmembrane peptide [82976]
                  1. Synthetic, Inluenza A virus-based [82977] (2)
                  2. Influenza A virus [TaxId: 11320] [161299] (1)
                  3. synthetic construct [161300] (8)
              24. N-terminal membrane anchor of the glucose-specific IIa component [90284]
                  1. Escherichia coli [TaxId: 562] [90285] (1)
                     amphipathic helix; this region is partly disordered in the crystal structure of the whole protein (d1gl)a CH F
              25. Pheromone alpha factor receptor [103731]
                  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103732] (1)
              26. Glycine receptor alpha-1 chain [103733]
                  1. Human (Homo sapiens) [TaxId: 9606] [103734] (2)
                     SQ P23415 281-337
              27. Vpu protein [103735]
                  1. Human immunodeficiency virus type 1, HIV-1 [TaxId: 11676] [103736] (3)
              28. Membrane anchor domain of the nonstructural protein 5a (NS5a) [111509]
                  1. Hepatitis C virus, HCV [TaxId: 11103] [111510] (5)
                     SQ P27958 1972-2003
              29. ASLV fusion peptide [118400]
                  1. Rous sarcoma virus [TaxId: 11886] [118401] (1)
                     SQ P03397 418-445
    39. Topogenic peptides [58555] (4)
        1. Ferredoxin chloroplastic transit peptide [58556] (1)
           uperfamily
           1. Ferredoxin chloroplastic transit peptide [58557] (1)
              1. Ferredoxin chloroplastic transit peptide [58558]
                 1. Unicellular eukaryote green alga (Chlamydomonas reinhardtii) [TaxId: 3055] [58559] (1)
        2. Vacuolar targeting peptide from NA-PROPI (residues 29-54) [58560] (1)
           uperfamily
           1. Vacuolar targeting peptide from NA-PROPI (residues 29-54) [58561] (1)
              1. Vacuolar targeting peptide from NA-PROPI (residues 29-54) [58562]
                 1. Winged tobacco (Nicotiana alata) [TaxId: 4087] [58563] (1)
        3. Microcin leader peptide [58564] (1)
           uperfamily
           1. Microcin leader peptide [58565] (1)
              1. Microcin leader peptide [58566]
                 1. Escherichia coli [TaxId: 562] [58567] (1)
        4. ATP synthase beta chain, mitochondrial prepeptide [103737] (1)
           uperfamily
           1. ATP synthase beta chain, mitochondrial prepeptide [103738] (1)
              1. ATP synthase beta chain, mitochondrial prepeptide [103739]
                 1. Leadwort-leaved tobacco (Nicotiana plumbaginifolia) [TaxId: 4092] [103740] (1)
    40. Phospholamban fragments [58568] (1)
        1. Phospholamban fragments [58569] (1)
           uperfamily
           1. Phospholamban fragments [58570] (3)
              1. Phospholamban fragments [58571]
                 1. Human (Homo sapiens) [TaxId: 9606] [58572] (1)
                 2. Pig (Sus scrofa) [TaxId: 9823] [58573] (2)
                 3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [103741] (1)
    41. Influenza hemagglutinin fragments [64631] (1)
        1. Influenza hemagglutinin fragments [64632] (1)
           uperfamily
           1. Influenza hemagglutinin fragments [64633] (2)
              1. Influenza hemagglutinin fragments [64634]
                 1. Synthetic [64635] (5)
                 2. Influenza B virus [TaxId: 11520] [161301] (1)
    42. Fragments of bowman-birk inhibitor [58574] (1)
        1. Fragments of bowman-birk inhibitor [58575] (1)
           uperfamily
           1. Fragments of bowman-birk inhibitor [58576] (1)
              1. Fragments of bowman-birk inhibitor [58577]
                 1. Synthetic [58578] (3)
    43. Fragments of apolipoproteins [58579] (1)
        1. Fragments of apolipoproteins [58580] (1)
           uperfamily
           1. Fragments of apolipoproteins [58581] (10)
              1. Fragments of apolipoproteins [58582]
                 1. Human (Homo sapiens), synthetic, C-I residues 7-24 [58583] (1)
                 2. Human (Homo sapiens), synthetic, C-I residues 35-53 [58584] (1)
                 3. Human (Homo sapiens), synthetic, C-I residues 1-38 [58585] (1)
                 4. Human (Homo sapiens), synthetic, C-I 57 residues [58586] (1)
                 5. Human (Homo sapiens), synthetic, A-I residues 166-185 [58587] (3)
                 6. Human (Homo sapiens), synthetic, A-I residues 142-187 [58588] (2)
                 7. Human (Homo sapiens), synthetic, E residues 263-286 [58589] (1)
                 8. Human (Homo sapiens), synthetic, E residues 267-289 [58590] (1)
                 9. Human (Homo sapiens), synthetic, C-II [58591] (4)
                    SQ P02655 23-101
                 10. Baboons (Papio sp.), synthetic, APO-C1 [58592] (1)
    44. Transactivation protein TAT [58593] (1)
        1. Transactivation protein TAT [58594] (1)
           uperfamily
           1. Transactivation protein TAT [58595] (2)
              1. Transactivation protein TAT [58596]
                 1. Equine infectious anemia virus, EIAV [TaxId: 11665] [58597] (2)
                 2. Human immunodeficiency virus type 1 [TaxId: 11676] [58598] (4)
    45. Proline pipe [58599] (1)
        1. Proline pipe [58600] (1)
           uperfamily
           1. Proline pipe [58601] (1)
              1. Tus proline repeat domain (residues 223-244) [58602]
                 1. Escherichia coli [TaxId: 562] [58603] (1)
    46. Amyloid peptides [58604] (1)
        1. Amyloid peptides [58605] (1)
           uperfamily
           1. Amyloid peptides [58606] (5)
              1. Alzheimer's disease amyloid beta-peptide [58607]
                 1. Human (Homo sapiens) [TaxId: 9606] [58608] (14)
                    SQ P05067 696-706 # coverage from PDB
                 2. Rat (Rattus norvegicus) [TaxId: 10116] [82978] (1)
              2. Islet amyloid polypeptide [103742]
                 1. Human (Homo sapiens) [TaxId: 9606] [103743] (1)
              3. Transthyretin amyloid peptide [103744]
                 1. Human (Homo sapiens) [TaxId: 9606] [103745] (1)
              4. Fibril-forming peptide [118402]
                 1. Synthetic [118403] (1)
    47. Gelsolin fragment (residues 150-169) [58609] (1)
        1. Gelsolin fragment (residues 150-169) [58610] (1)
           uperfamily
           1. Gelsolin fragment (residues 150-169) [58611] (1)
              1. Gelsolin fragment (residues 150-169) [58612]
                 1. Synthetic [58613] (1)
    48. Acetylcholine receptor fragment (residues alpha 67-76) [58614] (1)
        1. Acetylcholine receptor fragment (residues alpha 67-76) [58615] (1)
           uperfamily
           1. Acetylcholine receptor fragment (residues alpha 67-76) [58616] (1)
              1. Acetylcholine receptor fragment (residues alpha 67-76) [58617]
                 has different conformations in free and antibody-bound forms
                 1. Pacific electric ray (Torpedo californica) [TaxId: 7787] [58618] (2)
    49. Thrombomodulin EGF domain fragment (residues 409-426) [58619] (1)
        1. Thrombomodulin EGF domain fragment (residues 409-426) [58620] (1)
           uperfamily
           1. Thrombomodulin EGF domain fragment (residues 409-426) [58621] (1)
              1. Thrombomodulin EGF domain fragment (residues 409-426) [58622]
                 1. Human (Homo sapiens) [TaxId: 9606] [58623] (3)
    50. C-terminal fragment of thermolysin [63387] (1)
        1. C-terminal fragment of thermolysin [63388] (1)
           uperfamily
           1. C-terminal fragment of thermolysin [63389] (1)
              1. C-terminal fragment of thermolysin [63390]
                 1. Bacillus thermoproteolyticus [TaxId: 1427] [63391] (1)
    51. Capsid protein major homology region peptide analog [58629] (1)
        1. Capsid protein major homology region peptide analog [58630] (1)
           uperfamily
           1. Capsid protein major homology region peptide analog [58631] (2)
              1. Capsid protein major homology region peptide analog [58632]
                 1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [58633] (1)
                 2. Human immunodeficiency virus type 1, HIV-1 [TaxId: 11676] [58634] (1)
    52. CD4 and CD8 receptor regions [58635] (1)
        1. CD4 and CD8 receptor regions [58636] (1)
           uperfamily
           1. CD4 and CD8 receptor regions [58637] (2)
              interact with proto-oncogene tyrosine-protein kinase lck
              1. T-cell surface glycoprotein CD4 [58638]
                 1. Human (Homo sapiens) [TaxId: 9606] [58639] (2)
              2. T-cell surface glycoprotein CD8 alpha chain [103746]
                 1. Human (Homo sapiens) [TaxId: 9606] [103747] (1)
    53. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103748] (1)
        1. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103749] (1)
           uperfamily
           1. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103750] (1)
              1. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103751]
                 zinc ion-mediated interaction
                 1. Human (Homo sapiens) [TaxId: 9606] [103752] (2)
    54. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58640] (1)
        1. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58641] (1)
           uperfamily
           1. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58642] (1)
              1. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58643]
                 1. Synthetic [58644] (2)
    55. GroES fragments [58645] (1)
        1. GroES fragments [58646] (1)
           uperfamily
           1. GroES fragments [58647] (2)
              1. GroES, fragment of mobile loop [58648]
                 1. Escherichia coli [TaxId: 562] [58649] (1)
              2. cpn10 (GroES) N-terminal fragment [90286]
                 1. Mycobacterium tuberculosis [TaxId: 1773] [90287] (2)
    56. cAMP and cGMP phosphodiesterase (PDE) fragments [58650] (1)
        1. cAMP and cGMP phosphodiesterase (PDE) fragments [58651] (1)
           uperfamily
           1. cAMP and cGMP phosphodiesterase (PDE) fragments [58652] (2)
              not a true family
              1. N-terminal splice region of cAMP phosphodiesterase [58653]
                 1. Rat (Rattus norvegicus) [TaxId: 10116] [58654] (1)
              2. cGMP-PDE gamma [58655]
                 1. Cow (Bos taurus) [TaxId: 9913] [58656] (1)
    57. HIV-1 Nef protein fragments [58657] (1)
        1. HIV-1 Nef protein fragments [58658] (1)
           uperfamily
           1. HIV-1 Nef protein fragments [58659] (1)
              1. HIV-1 Nef protein fragments [58660]
                 1. Synthetic [58661] (3)
    58. HIV-1 envelope gp120 protein fragments [58662] (1)
        1. HIV-1 envelope gp120 protein fragments [58663] (1)
           uperfamily
           1. HIV-1 envelope gp120 protein fragments [58664] (2)
              1. V3 loop fragments [58665]
                 1. Synthetic [58666] (4)
              2. C5 fragment [82979]
                 1. Synthetic [82980] (1)
    59. HIV-1 gp41 fragments [70010] (1)
        1. HIV-1 gp41 fragments [70011] (1)
           uperfamily
           1. HIV-1 gp41 fragments [70012] (4)
              1. HIV-1 gp41 TRP-rich peptide [70013]
                 1. Synthetic [70014] (2)
              2. Peptide mimicking the loop 600-612 [82981]
                 1. Synthetic [82982] (8)
              3. Fragment 659-671 13-mer peptide [82983]
                 2f5 mab epitope
                 1. Synthetic [82984] (3)
              4. N-Terminal fusion peptide [90288]
                 1. Synthetic [90289] (1)
    60. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58667] (1)
        1. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58668] (1)
           uperfamily
           1. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58669] (1)
              1. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58670]
                 1. Synthetic [58671] (1)
    61. P27(KIP1) fragment 22-106 [58672] (1)
        1. P27(KIP1) fragment 22-106 [58673] (1)
           uperfamily
           1. P27(KIP1) fragment 22-106 [58674] (1)
              1. P27(KIP1) fragment 22-106 [58675]
                 1. Human (Homo sapiens) [TaxId: 9606] [58676] (1)
    62. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58677] (1)
        1. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58678] (1)
           uperfamily
           1. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58679] (1)
              1. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58680]
                 1. Cow (Bos taurus) [TaxId: 9913] [58681] (2)
    63. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90290] (1)
        1. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90291] (1)
           uperfamily
           1. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90292] (1)
              1. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90293]
                 1. Cow (Bos taurus) [TaxId: 9913] [90294] (1)
    64. alpha-lactalbumin peptide model [58682] (1)
        1. alpha-lactalbumin peptide model [58683] (1)
           uperfamily
           1. alpha-lactalbumin peptide model [58684] (1)
              1. alpha-lactalbumin peptide model [58685]
                 1. Synthetic [58686] (1)
    65. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58687] (1)
        1. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58688] (1)
           uperfamily
           1. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58689] (1)
              1. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58690]
                 1. Salmonella bacteriophage P22 [TaxId: 10754] [58691] (2)
    66. Immunoreceptor tyrosine kinase activation motif, ITAM [58692] (1)
        1. Immunoreceptor tyrosine kinase activation motif, ITAM [58693] (1)
           uperfamily
           1. Immunoreceptor tyrosine kinase activation motif, ITAM [58694] (1)
              1. Ig-alpha [58695]
                 1. Synthetic [58696] (1)
    67. Integrin fragments [58697] (1)
        1. Integrin fragments [58698] (1)
           uperfamily
           1. Integrin fragments [58699] (3)
              1. Cytoplasmic domain of the integrin alpha-iib subunit [58700]
                 1. Synthetic [58701] (5)
              2. Cytoplasmic domain of the integrin beta-3 [75747]
                 1. Synthetic [75748] (4)
              3. Ion-selective ligand for platelet integrin alphaiib-beta3 [75749]
                 1. Synthetic [75750] (4)
    68. Human glutathione reductase (HGR) inhibitor [58702] (1)
        1. Human glutathione reductase (HGR) inhibitor [58703] (1)
           uperfamily
           1. Human glutathione reductase (HGR) inhibitor [58704] (1)
              1. Human glutathione reductase (HGR) inhibitor [58705]
                 protein-dimerization inhibitor based on a fragment from the enzyme sequence
                 1. Synthetic [58706] (1)
    69. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58707] (1)
        1. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58708] (1)
           uperfamily
           1. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58709] (1)
              1. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58710]
                 as bound to the large subunit
                 1. Mouse (Mus musculus) [TaxId: 10090] [58711] (1)
    70. Histone H3 C-terminal fragment 130-135 [58712] (1)
        1. Histone H3 C-terminal fragment 130-135 [58713] (1)
           uperfamily
           1. Histone H3 C-terminal fragment 130-135 [58714] (1)
              1. Histone H3 C-terminal fragment 130-135 [58715]
                 as bound to a monoclonal antibody
                 1. Synthetic, based on Homo sapiens sequence [58716] (5)
    71. Smad-binding domain of Sara [58717] (1)
        1. Smad-binding domain of Sara [58718] (1)
           uperfamily
           1. Smad-binding domain of Sara [58719] (1)
              1. Smad-binding domain of Sara [58720]
                 1. Human (Homo sapiens) [TaxId: 9606] [58721] (2)
    72. Transactivation domain [81275] (1)
        1. Transactivation domain [74800] (1)
           uperfamily
           1. Transactivation domain [74801] (2)
              1. C-terminal activation domain (CTAD) of HIF-1alpha [74802]
                 1. Human (Homo sapiens) [TaxId: 9606] [74803] (4)
              2. Cbp/p300-interacting transactivator 2, Cited2 [90295]
                 1. Human (Homo sapiens) [TaxId: 9606] [90296] (2)
    73. Nuclear receptor coactivator Src-1 [100901] (1)
        1. Nuclear receptor coactivator Src-1 [48682] (1)
           uperfamily
           1. Nuclear receptor coactivator Src-1 [48683] (1)
              1. Nuclear receptor coactivator Src-1 [48684]
                 1. Human (Homo sapiens) [TaxId: 9606] [48685] (3)
                    SQ O43792 687-697 ! SQ O43792 687-700
    74. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90297] (1)
        1. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90298] (1)
           uperfamily
           1. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90299] (1)
              1. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90300]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90301] (1)
    75. BRCA2 BRC4 repeat [82985] (1)
        1. BRCA2 BRC4 repeat [82986] (1)
           uperfamily
           1. BRCA2 BRC4 repeat [82987] (1)
              1. BRCA2 BRC4 repeat [82988]
                 1. Human (Homo sapiens) [TaxId: 9606] [82989] (1)
    76. Peptide derived from p-21 activated kinase [58722] (1)
        1. Peptide derived from p-21 activated kinase [58723] (1)
           uperfamily
           1. Peptide derived from p-21 activated kinase [58724] (2)
              1. Peptide derived from p-21 activated kinase [58725]
                 1. Mouse (Mus musculus) [TaxId: 10090] [58726] (1)
                 2. Norway rat (Rattus norvegicus) [TaxId: 10116] [58727] (1)
    77. pak1 autoregulatory domain [58728] (1)
        1. pak1 autoregulatory domain [58729] (1)
           uperfamily
           1. pak1 autoregulatory domain [58730] (1)
              1. pak1 autoregulatory domain [58731]
                 1. Human (Homo sapiens) [TaxId: 9606] [58732] (1)
    78. Translocated intimin receptor (tir) intimin-binding domain [58733] (1)
        1. Translocated intimin receptor (tir) intimin-binding domain [58734] (1)
           uperfamily
           1. Translocated intimin receptor (tir) intimin-binding domain [58735] (1)
              1. Translocated intimin receptor (tir) intimin-binding domain [58736]
                 1. Escherichia coli [TaxId: 562] [58737] (1)
    79. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58738] (1)
        1. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58739] (1)
           uperfamily
           1. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58740] (4)
              1. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58741]
                 1. Synthetic [58742] (2)
                 2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [111511] (1)
                    SQ P07293 358-374
                 3. Human (Homo sapiens) [TaxId: 9606] [111512] (1)
                    SQ Q13936 428-443
                 4. Rat (Rattus norvegicus) [TaxId: 10116] [111513] (1)
                    SQ P22002 452-476
    80. Tumor suppressor p53 fragments [58743] (1)
        1. Tumor suppressor p53 fragments [58744] (1)
           uperfamily
           1. Tumor suppressor p53 fragments [58745] (2)
              1. C-terminal negative regulatory domain [58746]
                 1. Synthetic [58747] (1)
              2. N-terminal, MDM-2 binding domain [103753]
                 selectively cytotoxic to cancer cells
                 1. Synthetic [103754] (2)
    81. FxFG nucleoporin repeats [58748] (1)
        1. FxFG nucleoporin repeats [58749] (1)
           uperfamily
           1. FxFG nucleoporin repeats [58750] (1)
              1. FxFG nucleoporin repeats [58751]
                 1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [58752] (1)
    82. beta-Catenine bound non-globular protein regions [58753] (1)
        1. beta-Catenine bound non-globular protein regions [58754] (1)
           uperfamily
           1. beta-Catenine bound non-globular protein regions [58755] (3)
              1. TCF3-CBD (catenin-binding domain) [58756]
                 1. Frog (Xenopus) [TaxId: 262014] [58757] (1)
              2. htcf-4 [70015]
                 1. Human (Homo sapiens) [TaxId: 9606] [70016] (2)
              3. Phosphorylated E-cadherin [64636]
                 1. Mouse (Mus musculus) [TaxId: 10090] [64637] (2)
    83. Synaptobrevin-II fragments [58758] (1)
        1. Synaptobrevin-II fragments [58759] (1)
           uperfamily
           1. Synaptobrevin-II fragments [58760] (1)
              1. Synaptobrevin-II fragments [58761]
                 1. Synthetic [58762] (1)
    84. VMIP-II fragment [58763] (1)
        1. VMIP-II fragment [58764] (1)
           uperfamily
           1. VMIP-II fragment [58765] (1)
              1. VMIP-II fragment [58766]
                 1. Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] [58767] (1)
    85. Papillomavirus e6-interacting peptide of e6ap [58768] (1)
        1. Papillomavirus e6-interacting peptide of e6ap [58769] (1)
           uperfamily
           1. Papillomavirus e6-interacting peptide of e6ap [58770] (1)
              1. Papillomavirus e6-interacting peptide of e6ap [58771]
                 1. Human (Homo sapiens) [TaxId: 9606] [58772] (1)
    86. Isolated insulin B-chain [58773] (1)
        1. Isolated insulin B-chain [58774] (1)
           uperfamily
           1. Isolated insulin B-chain [58775] (3)
              1. Isolated insulin B-chain [58776]
                 1. Synthetic, based on Bos taurus sequence [58777] (1)
                 2. synthetic construct [161302] (52)
                 3. Homo sapiens [TaxId: 9606] [161303] (4)
    87. N-terminal hairpin of ubiquitin (residues 1-17) [58778] (1)
        1. N-terminal hairpin of ubiquitin (residues 1-17) [58779] (1)
           uperfamily
           1. N-terminal hairpin of ubiquitin (residues 1-17) [58780] (1)
              1. N-terminal hairpin of ubiquitin (residues 1-17) [58781]
                 1. Synthetic, based on Bos taurus sequence [58782] (1)
    88. alpha-helical hairpin of p8mtcp1 [58783] (1)
        1. alpha-helical hairpin of p8mtcp1 [58784] (1)
           uperfamily
           1. alpha-helical hairpin of p8mtcp1 [58785] (1)
              1. alpha-helical hairpin of p8mtcp1 [58786]
                 1. Synthetic [58787] (1)
    89. Syndecan-4 cytoplasmic domain [64638] (1)
        1. Syndecan-4 cytoplasmic domain [64639] (1)
           uperfamily
           1. Syndecan-4 cytoplasmic domain [64640] (1)
              1. Syndecan-4 cytoplasmic domain [64641]
                 1. Synthetic [64642] (2)
    90. Actin-binding peptides [70017] (1)
        1. Actin-binding peptides [70018] (1)
           uperfamily
           1. Actin-binding peptides [70019] (2)
              1. Thymosin beta9 [70020]
                 actin-binding peptide
                 1. Cow (Bos taurus) [TaxId: 9913] [70021] (1)
              2. Ciboulot [111514]
                 1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [111515] (1)
                    SQ O97428 10-34
    91. Pituitary adenylate cyclase activating polypeptide, pacap21 [64643] (1)
        1. Pituitary adenylate cyclase activating polypeptide, pacap21 [64644] (1)
           uperfamily
           1. Pituitary adenylate cyclase activating polypeptide, pacap21 [64645] (1)
              1. Pituitary adenylate cyclase activating polypeptide, pacap21 [64646]
                 1. Synthetic [64647] (1)
    92. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70022] (1)
        1. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70023] (1)
           uperfamily
           1. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70024] (1)
              1. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70025]
                 1. Synthetic [70026] (1)
    93. Prepeptide of 5-ALAS [70027] (1)
        1. Prepeptide of 5-ALAS [70028] (1)
           uperfamily
           1. Prepeptide of 5-ALAS [70029] (1)
              1. Prepeptide of 5-ALAS [70030]
                 1. Synthetic, mouse-based [70031] (2)
    94. Cholecystokinin receptor fragments [64648] (1)
        1. Cholecystokinin receptor fragments [64649] (1)
           uperfamily
           1. Cholecystokinin receptor fragments [64650] (2)
              1. Cholecystokinin A (CCK-A) receptor [64651]
                 1. Synthetic [64652] (1)
              2. Gastrin/cholecystokinin B receptor [82990]
                 1. Synthetic [82991] (1)
    95. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70032] (1)
        1. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70033] (1)
           uperfamily
           1. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70034] (1)
              1. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70035]
                 1. Synthetic [70036] (1)
    96. Trypsin inhibitor SFTIf-1 [64653] (1)
        1. Trypsin inhibitor SFTIf-1 [64654] (1)
           uperfamily
           1. Trypsin inhibitor SFTIf-1 [64655] (1)
              1. Trypsin inhibitor SFTIf-1 [64656]
                 1. Sunflower (Helianthus annuus) [TaxId: 4232] [64657] (2)
    97. Prion protein fragments [70037] (1)
        1. Prion protein fragments [70038] (1)
           uperfamily
           1. Prion protein fragments [70039] (3)
              1. Prion protein fragments [70040]
                 1. Synthetic, sheep sequence-based [70041] (3)
                 2. Human (Homo sapiens) [TaxId: 9606] [103755] (2)
                 3. synthetic construct [161304] (2)
    98. Tumor suppressor protein p19-ARF fragment [70042] (1)
        1. Tumor suppressor protein p19-ARF fragment [70043] (1)
           uperfamily
           1. Tumor suppressor protein p19-ARF fragment [70044] (1)
              1. Tumor suppressor protein p19-ARF fragment [70045]
                 1. Mouse (Mus musculus) [TaxId: 10090] [70046] (1)
    99. Antennapedia homeodomain fragments [70047] (1)
        1. Antennapedia homeodomain fragments [70048] (1)
           uperfamily
           1. Antennapedia homeodomain fragments [70049] (1)
              1. Antennapedia homeodomain fragments [70050]
                 1. Synthetic [70051] (4)
    100. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75751] (1)
         1. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75752] (1)
            uperfamily
            1. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75753] (1)
               1. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75754]
                  1. Synthetic [75755] (4)
    101. alpha-2a adrenergic receptor pepride t3-i2 [75756] (1)
         1. alpha-2a adrenergic receptor pepride t3-i2 [75757] (1)
            uperfamily
            1. alpha-2a adrenergic receptor pepride t3-i2 [75758] (1)
               1. alpha-2a adrenergic receptor pepride t3-i2 [75759]
                  1. Synthetic [75760] (4)
    102. Catestatin fragment from chromogranin A [75761] (1)
         1. Catestatin fragment from chromogranin A [75762] (1)
            uperfamily
            1. Catestatin fragment from chromogranin A [75763] (1)
               1. Catestatin fragment from chromogranin A [75764]
                  1. Synthetic, human sequence-based [75765] (2)
    103. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82992] (1)
         1. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82993] (1)
            uperfamily
            1. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82994] (1)
               1. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82995]
                  1. Synthetic [82996] (1)
    104. N-terminal fragment of gastric H/K-ATPase [82997] (1)
         1. N-terminal fragment of gastric H/K-ATPase [82998] (1)
            uperfamily
            1. N-terminal fragment of gastric H/K-ATPase [82999] (1)
               1. N-terminal fragment of gastric H/K-ATPase [83000]
                  1. Synthetic, based on pig sequence [83001] (2)
    105. Barstar fragment [83002] (1)
         1. Barstar fragment [83003] (1)
            uperfamily
            1. Barstar fragment [83004] (1)
               1. Barstar fragment [83005]
                  1. Bacillus amyloliquefaciens [TaxId: 1390] [83006] (1)
    106. Cannabinoid receptor 1 (CB1) fragment [83007] (1)
         1. Cannabinoid receptor 1 (CB1) fragment [83008] (1)
            uperfamily
            1. Cannabinoid receptor 1 (CB1) fragment [83009] (1)
               1. Cannabinoid receptor 1 (CB1) fragment [83010]
                  1. Synthetic, based on human sequence [83011] (2)
    107. Ribosomal protein L10 [64658] (1)
         1. Ribosomal protein L10 [64659] (1)
            uperfamily
            1. Ribosomal protein L10 [64660] (1)
               1. Ribosomal protein L10 [64661]
                  two alpha-helical segments visible in the crystal structure
                  1. Archaeon Haloarcula marismortui [TaxId: 2238] [64662] (42)
                     SQ P15825
    108. Ubiquitin interacting motif (UIM) [90302] (1)
         1. Ubiquitin interacting motif (UIM) [90303] (1)
            uperfamily
            1. Ubiquitin interacting motif (UIM) [90304] (2)
               amphipathic helix
               1. Vacuolar protein sorting-associated protein vps27p [90305]
                  1. Synthetic, based on yeast sequence [90306] (3)
               2. 26s proteasome non-ATPase regulatory subunit 4 (s5a) [103756]
                  1. Human (Homo sapiens) [TaxId: 9606] [103757] (3)
    109. Metal-binding peptide from MerP [103758] (1)
         1. Metal-binding peptide from MerP [103759] (1)
            uperfamily
            1. Metal-binding peptide from MerP [103760] (1)
               1. Metal-binding peptide from MerP [103761]
                  1. Shigella flexneri [TaxId: 623] [103762] (1)
    110. Marinostatin, MstI [103763] (1)
         1. Marinostatin, MstI [103764] (1)
            uperfamily
            1. Marinostatin, MstI [103765] (1)
               1. Marinostatin, MstI [103766]
                  a protease inhibitor containing two ester linkages
                  1. Alteromonas sp. [TaxId: 232] [103767] (1)
    111. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103768] (1)
         1. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103769] (1)
            uperfamily
            1. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103770] (2)
               1. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103771]
                  1. Synthetic, based on L. braziliensis sequence [103772] (1)
                  2. Synthetic, based on human sequence [103773] (1)
    112. NTR, cyclotide processing element [111516] (1)
         1. NTR, cyclotide processing element [111517] (1)
            uperfamily
            1. NTR, cyclotide processing element [111518] (2)
               1. Cyclotide k1 [111519]
                  1. Sweet violet (Viola odorata) [TaxId: 97441] [111520] (1)
                     SQ Q5USN7 150-177
               2. Kalata B3/B6 [111521]
                  1. Oldenlandia affinis [TaxId: 60225] [111522] (1)
                     SQ P58455
    113. HMG-box transcription factor 1 fragments [111523] (1)
         1. HMG-box transcription factor 1 fragments [111524] (1)
            uperfamily
            1. HMG-box transcription factor 1 fragments [111525] (1)
               1. HMG-box transcription factor 1 fragments [111526]
                  1. Human (Homo sapiens) [TaxId: 9606] [111527] (1)
                     SQ Q8TBM1 358-380
    114. MAD protein fragments [111528] (1)
         1. MAD protein fragments [111529] (1)
            uperfamily
            1. MAD protein fragments [111530] (1)
               1. MAD protein fragments [111531]
                  1. Human (Homo sapiens) [TaxId: 9606] [111532] (1)
                     SQ Q05195 6-21 # structure of the B-HLH-Z region (57-136) is also known (1nlw chains A and D; scop_sp: 81753)
    115. Fragments of TNF receptors [111533] (1)
         1. Fragments of TNF receptors [111534] (1)
            uperfamily
            1. Fragments of TNF receptors [111535] (1)
               1. Lymphotoxin-beta receptor [111536]
                  1. Human (Homo sapiens) [TaxId: 9606] [111537] (1)
                     SQ P36941 384-408
    116. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111538] (1)
         1. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111539] (1)
            uperfamily
            1. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111540] (1)
               1. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111541]
                  1. Human (Homo sapiens) [TaxId: 9606] [111542] (1)
                     SQ O14745 321-358
    117. Ribosomal protein L34p [144320] (1)
         non-globular, mainly alpha-helical
         1. Ribosomal protein L34p [144321] (1)
            uperfamily
            1. Ribosomal protein L34p [144322] (3)
               Pfam 00468
               1. Ribosomal protein L34p [144323]
                  1. Escherichia coli [TaxId: 562] [144324] (8)
                     SQ P0A7P5 1-46
                  2. Deinococcus radiodurans [TaxId: 1299] [161305] (10)
                     SQ Q9RSH2 1-46
                  3. Thermus thermophilus [TaxId: 274] [161306] (11)
                     SQ P80340 1-49
    118. Ribosomal protein S21p [161307] (1)
         non-globular, mainly alpha-helical
         1. Ribosomal protein S21p [161308] (1)
            1. Ribosomal protein S21p [161309] (1)
               Pfam 01165
               1. Ribosomal protein S21, RpsU [161310]
                  1. Escherichia coli [TaxId: 562] [161311] (24)
                     SQ P68679 4-54
    119. Retinoblastoma-associated protein RB1 fragments [144325] (1)
         1. Retinoblastoma-associated protein RB1 fragments [144326] (1)
            uperfamily
            1. Retinoblastoma-associated protein RB1 fragments [144327] (1)
               1. Retinoblastoma-associated protein RB1 fragments [144328]
                  1. Human (Homo sapiens) [TaxId: 9606] [144329] (1)
                     SQ P06400 829-872
    120. Genome linked protein vpg [144330] (1)
         1. Genome linked protein vpg [144331] (1)
            uperfamily
            1. Genome linked protein vpg [144332] (1)
               PfamB 000297
               1. Genome linked protein vpg [144333]
                  1. synthetic [144334] (2)
    121. Programmed cell death protein 5 fragments [144335] (1)
         1. Programmed cell death protein 5 fragments [144336] (1)
            uperfamily
            1. Programmed cell death protein 5 fragments [144337] (1)
               1. Programmed cell death protein 5 fragments [144338]
                  1. Human (Homo sapiens) [TaxId: 9606] [144339] (1)
                     SQ O14737 1-26
11. Designed proteins [58788] (44)
    Experimental structures of proteins with essentially non-natural sequences. Not a true class
    1. New fold designs [103774] (1)
       1. New fold designs [103775] (1)
          uperfamily
          1. alpha+beta folds [103776] (2)
             1. Top7 [103777]
                beta(2)-alpha-beta-alpha-beta(2); 2 layers: a/b; antiparallel beta-sheet: order 21354
                1. Synthetic, computationally designed sequence [103778] (1)
                2. unidentified [TaxId: 32644] [161312] (1)
    2. In vitro evolution products [103779] (1)
       1. In vitro evolution products [103780] (1)
          uperfamily
          1. Function-directed selections [103781] (1)
             1. Artificial nucleotide binding protein (ANBP) [103782]
                binds ADP; contains zinc-binding site similar to that of the transcription factor GATA-1
                1. Synthetic [103783] (1)
    3. Hybrid and chimeric proteins [58789] (1)
       1. Hybrid and chimeric proteins [58790] (1)
          uperfamily
          1. Hybrid and chimeric proteins [58791] (3)
             1. Hybrid protein between chymotrypsin inhibitor CI-2 and helix E from subtilisin Carlsberg [58792]
                1. Barley (Hordeum vulgare), hiproly strain [TaxId: 4513] [58793] (1)
             2. Tmzip: a chimeric peptide model of the n-terminus of alpha tropomyosin [58794]
                dimeric coiled coil
                1. Synthetic, based on Rattus rattus sequence [58795] (1)
             3. Genetically engineered molecular motor [58796]
                myosin II heavy chain fused to alpha-actinin spectrin-like repeats 1 and 2
                1. Dictyostelium discoideum [TaxId: 44689] [58797] (1)
    4. Amphiphilic (amphipathic) alpha helix [58798] (1)
       1. Amphiphilic (amphipathic) alpha helix [58799] (1)
          uperfamily
          1. Amphiphilic (amphipathic) alpha helix [58800] (3)
             1. Designed sequence 'Alpha 1' [58801]
                1. Synthetic [58802] (3)
             2. Model helical basic peptides [58803]
                1. Synthetic, based on human platelet factor 4 [58804] (3)
             3. Octameric de novo designed peptide [83012]
                packing of helices in octamer is similar to that of the Uteroglobin-like dimer (see 2utg)
                1. Synthetic [83013] (1)
    5. Collagen-like peptides [58805] (1)
       1. Collagen-like peptides [58806] (1)
          uperfamily
          1. Collagen-like peptides [58807] (8)
             1. Collagen-like peptides [58808]
                1. Synthetic, (pro-pro-gly)9 [83014] (1)
                2. Synthetic (pro-pro-gly)n [58809] (4)
                3. Synthetic [(pro-hyp-gly)4-glu-lys-gly(pro-hyp-gly)5] [58810] (1)
                4. Synthetic [(pro-hyp-gly)4-pg-(pro-hyp-gly)5] [103784] (1)
                   contains a discontinuity in the repeating tripeptide sequence
                5. Synthetic (contains biological sequence) [100902] (1)
                6. Synthetic (contains integrin-binding sequence) [64663] (2)
                7. Synthetic, [(pro-pro-gly)10]3 triple helix model [70052] (2)
                8. Synthetic, (pro-hyp-gly)n [111543] (3)
    6. Coiled serine [58812] (1)
       1. Coiled serine [58813] (1)
          uperfamily
          1. Coiled serine [58814] (2)
             1. Coiled serine [58815]
                1. Synthetic [58816] (1)
                2. synthetic construct [161313] (1)
    7. Designed trimeric coiled-coil [100903] (1)
       1. Designed trimeric coiled-coil [100904] (1)
          uperfamily
          1. Designed trimeric coiled-coil [100905] (4)
             not a true family
             1. Amyloidogenic design-1 [103785]
                1. synthetic [103786] (1)
             2. VaLd trimeric coiled-coil [58820]
                1. Synthetic [58821] (1)
             3. Unnamed design-1 [100906]
                1. Synthetic [64668] (1)
             4. Unnamed design-2 [100907]
                1. Synthetic [75766] (1)
    8. Designed heterodimeric coiled-coil [58822] (1)
       1. Designed heterodimeric coiled-coil [58823] (1)
          uperfamily
          1. Designed heterodimeric coiled-coil [58824] (2)
             1. Designed heterodimeric leucine zipper [58825]
                1. Synthetic, GCN4-based [58826] (2)
             2. iaal-e3/k3 heterodimer [118404]
                1. synthetic [118405] (1)
    9. Thermostable heterotrimeric coiled coil [58827] (1)
       1. Thermostable heterotrimeric coiled coil [58828] (1)
          uperfamily
          1. Thermostable heterotrimeric coiled coil [58829] (1)
             1. Thermostable heterotrimeric coiled coil [58830]
                1. Synthetic [58831] (1)
    10. Designed four-helix bundle protein [58832] (1)
        1. Designed four-helix bundle protein [58833] (1)
           uperfamily
           1. Designed four-helix bundle protein [58834] (5)
              this is not a true family
              1. De novo designed protein s-824 [103787]
                 single-chain four-helical protein
                 1. Synthetic [103788] (1)
                 2. unidentified [TaxId: 32644] [161314] (1)
              2. DHP1 [58835]
                 1. Synthetic non-biological source [58836] (1)
              3. Artificial diiron protein [58837]
                 dimeric alpha-hairpin fold
                 1. Synthetic, different variants [58838] (15)
              4. Molecular maquette scaffold [83015]
                 1. Synthetic [83016] (1)
    11. Designed single chain three-helix bundle [58839] (1)
        not a true fold: both possible topologies are created
        1. Designed single chain three-helix bundle [58840] (1)
           uperfamily
           1. Designed single chain three-helix bundle [58841] (3)
              1. De novo bundle (a3d) [58842]
                 1. Synthetic [58843] (1)
              2. Domain swapped dimer [58844]
                 1. Synthetic [58845] (1)
              3. Alpha3W [75767]
                 de novo designed protein model of radical enzymes
                 1. Synthetic [75768] (1)
    12. Peptide f (amphiphilic octadecapeptide) [58846] (1)
        1. Peptide f (amphiphilic octadecapeptide) [58847] (1)
           uperfamily
           1. Peptide f (amphiphilic octadecapeptide) [58848] (1)
              1. Peptide f (amphiphilic octadecapeptide) [58849]
                 Designed sequence (EQLLKALEFLLKELLEKL),
                 1. Synthetic [58850] (1)
    13. Retro-GCN4 leucine zipper [58851] (1)
        1. Retro-GCN4 leucine zipper [58852] (1)
           uperfamily
           1. Retro-GCN4 leucine zipper [58853] (1)
              1. Retro-GCN4 leucine zipper [58854]
                 1. Synthetic [58855] (1)
    14. Glytm1bzip [70053] (1)
        1. Glytm1bzip [70054] (1)
           uperfamily
           1. Glytm1bzip [70055] (1)
              1. Glytm1bzip [70056]
                 a chimeric peptide model of tropomyosin and GCN4 coiled coils
                 1. Chimeric (Rattus norvegicus) and (saccharomyces cerevisiae) [70057] (1)
    15. Zinc finger design [58856] (1)
        1. Zinc finger design [58857] (1)
           uperfamily
           1. Zinc finger design [58858] (11)
              1. Designed zinc finger protein [58859]
                 1. Synthetic consensus sequence, non-biological source [58860] (1)
                 2. Mus musculus [TaxId: 10090] [161315] (1)
                 3. Homo sapiens [TaxId: 9606] [161316] (87)
              2. Zinc finger with an artificial beta-turn [58861]
                 original sequence taken from the third zinc finger domain of the human transcriptional repressor protein yy1
                 1. Synthetic, based on Homo sapiens sequence [58862] (1)
                 2. Homo sapiens [TaxId: 9606] [161317] (4)
              3. FSD-EY [64669]
                 1. Synthetic [64670] (1)
              4. TATA box-binding zinc finger, TATAZF [64671]
                 1. Mouse (Mus musculus), Zif268 based [TaxId: 10090] [64672] (2)
              5. E6-binding zinc finger, different constructs [111544]
                 1. Synthetic [111545] (2)
                 2. Homo sapiens [TaxId: 9606] [161318] (1)
              6. AART, designed six-finger protein [144340]
                 1. synthetic [144341] (2)
              7. HIV REV-targetting Znf29 [161319]
                 1. synthetic [161320] (2)
    16. Protein A Ig(Fc)-binding domain mimics [58863] (1)
        1. Protein A Ig(Fc)-binding domain mimics [58864] (1)
           uperfamily
           1. Protein A Ig(Fc)-binding domain mimics [58865] (1)
              1. Protein A Ig(Fc)-binding domain mimics [58866]
                 1. Synthetic [58867] (7)
    17. Zinc finger based beta-beta-alpha motif [58868] (1)
        1. Zinc finger based beta-beta-alpha motif [58869] (1)
           uperfamily
           1. Zinc finger based beta-beta-alpha motif [58870] (5)
              1. Full sequence design 1 (fsd-1) [58871]
                 1. Synthetic [58872] (2)
              2. Computationally designed peptide with a beta-beta-alpha fold selection [58873]
                 1. Synthetic [58874] (1)
              3. 23-residue designed metal-free peptide based on the zinc finger domains [58875]
                 1. Synthetic [58876] (1)
              4. BBA5 [111546]
                 1. Synthetic [111547] (1)
              5. Segment-swapped tetrameric beta-beta-alpha mini-protein [111548]
                 1. Synthetic [111549] (3)
    18. helix-turn-helix motif [58877] (1)
        1. helix-turn-helix motif [58878] (1)
           uperfamily
           1. helix-turn-helix motif [58879] (2)
              1. Alpha-t-alpha, a de novo designed peptide [58880]
                 1. Synthetic non-biological sequence [58881] (1)
              2. De novo designed 21 residue peptide [111550]
                 1. synthetic [111551] (1)
    19. alpha2d [58882] (1)
        1. alpha2d [58883] (1)
           uperfamily
           1. alpha2d [58884] (1)
              1. alpha2d [58885]
                 1. Synthetic [58886] (1)
    20. Right-handed coiled coil [58887] (1)
        1. Right-handed coiled coil [58888] (1)
           uperfamily
           1. Right-handed coiled coil [58889] (3)
              1. RH4 designed right-handed coiled coil tetramer [58890]
                 1. Synthetic non-biological sequence [58891] (1)
              2. RH3 designed right-handed coiled coil trimer [118406]
                 1. synthetic [118407] (1)
                 2. synthetic construct [161321] (1)
    21. TPR domain-based design [90307] (1)
        1. TPR domain-based design [90308] (1)
           uperfamily
           1. TPR domain-based design [90309] (6)
              alpha-helical arrays from an idealized TPR motif
              1. Designed protein cTPR3 [90310]
                 1. Synthetic [90311] (1)
                 2. Homo sapiens [TaxId: 9606] [161322] (1)
              2. Designed protein cTPR2 [90312]
                 1. Synthetic [90313] (1)
              3. An 8 repeat consensus TPR superhelix [144342]
                 1. synthetic [144343] (2)
                 2. Bacillus subtilis [TaxId: 1423] [161323] (1)
                 3. Yersinia enterocolitica [TaxId: 630] [161324] (1)
    22. Erythropoietin (EPO) mimetic peptides [58892] (1)
        1. Erythropoietin (EPO) mimetic peptides [58893] (1)
           uperfamily
           1. Erythropoietin (EPO) mimetic peptides [58894] (1)
              1. Erythropoietin (EPO) mimetic peptides [58895]
                 1. Synthetic [58896] (3)
    23. IL-1 receptor type 1 antagonist peptide AF10847 [58897] (1)
        1. IL-1 receptor type 1 antagonist peptide AF10847 [58898] (1)
           uperfamily
           1. IL-1 receptor type 1 antagonist peptide AF10847 [58899] (1)
              1. IL-1 receptor type 1 antagonist peptide AF10847 [58900]
                 1. Synthetic [58901] (1)
    24. Octreotide (Sandostatine), a somatostatine analogue [58902] (1)
        1. Octreotide (Sandostatine), a somatostatine analogue [58903] (1)
           uperfamily
           1. Octreotide (Sandostatine), a somatostatine analogue [58904] (1)
              1. Octreotide (Sandostatine), a somatostatine analogue [58905]
                 1. Synthetic [58906] (2)
    25. Calmodulin [58907] (1)
        1. Calmodulin [58908] (1)
           uperfamily
           1. Calmodulin [58909] (1)
              1. Calmodulin [58910]
                 1. Synthetic [58911] (3)
                    consensus sequence from a number of sources
    26. WW domain-based designs [58912] (1)
        1. WW domain-based designs [58913] (1)
           uperfamily
           1. WW domain-based designs [58914] (4)
              1. Prototype WW domain [58915]
                 1. Synthetic [58916] (1)
                 2. Homo sapiens [TaxId: 9606] [161325] (1)
                 3. Mus musculus [TaxId: 10090] [161326] (6)
              2. CC45 [161327]
                 An artificial WW domain designed using Statistical Coupling Analysis
                 1. Synthetic [161328] (1)
    27. Artificial ankyrin repeat proteins [83017] (1)
        1. Artificial ankyrin repeat proteins [83018] (1)
           uperfamily
           1. Artificial ankyrin repeat proteins [83019] (9)
              1. Sank e3_5 [83020]
                 1. Synthetic [83021] (1)
                 2. synthetic construct [161329] (1)
              2. 3ank [83022]
                 1. Synthetic [83023] (1)
                 2. synthetic construct [161330] (1)
                 3. Homo sapiens [TaxId: 9606] [161331] (2)
                 4. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [161332] (2)
              3. 4ank [83024]
                 1. Synthetic [83025] (1)
                 2. unidentified [TaxId: 32644] [161333] (1)
              4. Off7 [111552]
                 1. synthetic [111553] (1)
    28. Carboxypeptidase A prodomain-based design [103789] (1)
        1. Carboxypeptidase A prodomain-based design [103790] (1)
           uperfamily
           1. Carboxypeptidase A prodomain-based design [103791] (1)
              1. Carboxypeptidase A prodomain-based design [103792]
                 1. Synthetic, sequence chosen for maximal predicted stability [103793] (1)
    29. Ubiquitin [144344] (1)
        1. Ubiquitin [144345] (1)
           uperfamily
           1. Ubiquitin [144346] (4)
              1. Ubiquitin [144347]
                 1. synthetic [144348] (14)
                 2. Paramecium tetraurelia strain d4-2 [TaxId: 412030] [161334] (1)
                 3. Saccharomyces cerevisiae [TaxId: 4932] [161335] (1)
                 4. Homo sapiens [TaxId: 9606] [161336] (4)
    30. Cro lambda fold design [144349] (1)
        1. Cro lambda fold design [144350] (1)
           uperfamily
           1. Cro lambda fold design [144351] (1)
              1. Sn4m [144352]
                 1. synthetic [144353] (1)
    31. Scorpion toxin-based designs [58917] (1)
        1. Scorpion toxin-based designs [58918] (2)
           uperfamily
           1. Potassium channel toxin hstx1 [58919] (1)
              1. Potassium channel toxin hstx1 [58920]
                 1. Synthetic [58921] (1)
           2. Mini-protein reproducing the core of the CD4 surface [58922] (1)
              1. Mini-protein reproducing the core of the CD4 surface [58923]
                 interacting with the hiv-1 envelope glycoprotein
                 1. Synthetic [58924] (9)
    32. TH (toxin hand)-motif beta-sheet mini-protein designs [64673] (1)
        1. TH (toxin hand)-motif beta-sheet mini-protein designs [64674] (1)
           uperfamily
           1. TH (toxin hand)-motif beta-sheet mini-protein designs [64675] (3)
              1. TH 10A-ox [64676]
                 1. Synthetic [64677] (1)
              2. TH 1-ox [64678]
                 1. Synthetic [64679] (1)
              3. TH10B-ox [64680]
                 1. Synthetic [64681] (1)
    33. Inhibitor of mammalian ribonucleotide reductase [58925] (1)
        1. Inhibitor of mammalian ribonucleotide reductase [58926] (1)
           uperfamily
           1. Inhibitor of mammalian ribonucleotide reductase [58927] (1)
              1. Inhibitor of mammalian ribonucleotide reductase [58928]
                 1. Synthetic [58929] (1)
    34. Integrin-binding RGD peptide [64682] (1)
        1. Integrin-binding RGD peptide [64683] (1)
           uperfamily
           1. Integrin-binding RGD peptide [64684] (1)
              1. Integrin-binding RGD peptide [64685]
                 1. Synthetic [64686] (2)
    35. Peptide antagonists of IGF-1 [64687] (1)
        1. Peptide antagonists of IGF-1 [64688] (1)
           uperfamily
           1. Peptide antagonists of IGF-1 [64689] (1)
              1. Peptide antagonists of IGF-1 [64690]
                 1. Synthetic [64691] (7)
    36. beta-hairpin design [64692] (1)
        1. beta-hairpin design [64693] (1)
           uperfamily
           1. beta-hairpin design [64694] (9)
              1. Tryptophan zipper 1 [64695]
                 1. Synthetic [64696] (1)
              2. Tryptophan zipper 2 [64697]
                 1. Synthetic [64698] (1)
              3. Tryptophan zipper 4 [64699]
                 1. Synthetic [64700] (1)
              4. DP-TT2 [64701]
                 1. Synthetic [64702] (1)
              5. Peptide MBH12 (rg-kwty-ng-itye-gr) [70058]
                 1. Synthetic [70059] (2)
              6. A minimal peptide scaffold for beta-turn display [83026]
                 1. Synthetic [83027] (2)
              7. Bhpw_pdg, beta-hairpin peptide [103794]
                 1. Synthetic [103795] (1)
              8. Bhp_hwlv, disulfide cyclized beta-hairpin [103796]
                 1. Synthetic [103797] (1)
              9. Chignolin [103798]
                 1. Synthetic [103799] (1)
    37. Trp-cage miniprotein [75769] (1)
        1. Trp-cage miniprotein [75770] (1)
           uperfamily
           1. Trp-cage miniprotein [75771] (1)
              1. Trp-cage miniprotein, different constructs [75772]
                 1. Synthetic [75773] (2)
    38. Synthetic high affinity IgE receptor antagonists [64703] (1)
        1. Synthetic high affinity IgE receptor antagonists [64704] (2)
           not a true superfamily
           uperfamily
           1. Hairpin peptide [64705] (1)
              1. Hairpin peptide [64706]
                 1. Synthetic [64707] (1)
           2. Zeta peptides [75774] (2)
              1. E109 [75775]
                 1. Synthetic [75776] (1)
              2. E131 [75777]
                 1. Synthetic [75778] (1)
    39. IFN mimetic syr6 [75779] (1)
        1. IFN mimetic syr6 [75780] (1)
           uperfamily
           1. IFN mimetic syr6 [75781] (1)
              1. IFN mimetic syr6 [75782]
                 1. Synthetic [75783] (2)
    40. TAZ (CH) Zn-binding domain based design [75784] (1)
        1. TAZ (CH) Zn-binding domain based design [75785] (1)
           uperfamily
           1. TAZ (CH) Zn-binding domain based design [75786] (1)
              1. Fragment of the CH1 domain of cbp [75787]
                 1. Synthetic [75788] (1)
    41. Beta-sheet designs [75789] (1)
        1. Beta-sheet designs [75790] (1)
           uperfamily
           1. Beta-sheet designs [75791] (2)
              1. B4dimer [75792]
                 de novo designed eight-stranded beta-sheet assembled using a disulfide bond
                 1. Synthetic [75793] (2)
              2. Betacore [75794]
                 designed water soluble four-stranded antiparallel beta-sheet protein
                 1. Synthetic [75795] (1)
    42. PW2, a tryptophan-rich anticocidial peptide [75796] (1)
        1. PW2, a tryptophan-rich anticocidial peptide [75797] (1)
           uperfamily
           1. PW2, a tryptophan-rich anticocidial peptide [75798] (1)
              1. PW2, a tryptophan-rich anticocidial peptide [75799]
                 1. Synthetic [75800] (1)
    43. Designed EF-hand type cation-binding loop [111554] (1)
        1. Designed EF-hand type cation-binding loop [111555] (1)
           uperfamily
           1. Designed EF-hand type cation-binding loop [111556] (1)
              1. Lanthanide-binding peptide [111557]
                 1. Synthetic [111558] (1)
    44. Metalloporphyrin-binding designed peptides [90314] (1)
        1. Metalloporphyrin-binding designed peptides [90315] (1)
           uperfamily
           1. Metalloporphyrin-binding designed peptides [90316] (2)
              1. Mimochrome, heme-binding design [90317]
                 1. Synthetic [90318] (2)
              2. De novo designed cyclic peptide [103800]
                 1. Synthetic [103801] (1)