Structural Classification of Proteins

Class: All alpha proteins

Lineage:

Root: scop
Class: All alpha proteins [46456]

Folds:

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)
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
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
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
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
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
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
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)
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
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
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
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)
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)
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
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
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
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
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
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
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
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)
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)
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
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
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)
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)
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)
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)
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)
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)
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
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
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
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
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
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
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)
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
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)
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)
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
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
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
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
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
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)
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)
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)
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
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
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)
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)
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)
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
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)
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
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
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
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)
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
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
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
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
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
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
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)
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
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
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)
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)
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)
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)
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)
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)
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)
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
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
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)
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)
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)
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)
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)
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
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)
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
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)
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
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
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
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)
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
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)
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
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
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
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
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
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
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
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
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
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)
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)
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)
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
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
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
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
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
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)
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
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
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)
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
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
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
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)
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)
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)
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
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
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)
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
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
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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)
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
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)
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)
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)
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
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
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
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
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
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
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)
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
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
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
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
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)
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)
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
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
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)
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)
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
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)
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
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)
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)
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)
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
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
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
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
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
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)
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
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
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
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)
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)
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)
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
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
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)
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
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)
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
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
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
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
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
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
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
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)
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)
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
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)
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)
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)
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
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
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
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)
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
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)
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
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)
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
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
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)
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)
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)
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)
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)
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)
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)
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)
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
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)
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)
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)
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
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
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)
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)
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)
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
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)
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
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)
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
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
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
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)
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)
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
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)
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
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
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)
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
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
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
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
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)
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
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
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
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
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
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
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
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)
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
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)
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)
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)
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
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
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)
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)
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
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
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)
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)
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
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)
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
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
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
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
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
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
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)
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
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
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)
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)
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)
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
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
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
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
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)
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
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