Structural Classification of Proteins

Class: Alpha and beta proteins (a/b)

: Mainly parallel beta sheets (beta-alpha-beta units)

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)

Folds:

TIM beta/alpha-barrel [51350] (33)
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites
1. Triosephosphate isomerase (TIM) [51351] (1)
  uperfamily
  1. Triosephosphate isomerase (TIM) [51352] (18)
    1. Triosephosphate isomerase [51353]
      1. Chicken (Gallus gallus) [TaxId: 9031] [51354] (16)
        SQ P00940
      2. Human (Homo sapiens) [TaxId: 9606] [51355] (5)
      3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [102035] (3)
      4. Nematode (Caenorhabditis elegans) [TaxId: 6239] [82235] (1)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51356] (7)
      6. Trypanosoma brucei [TaxId: 5691] [51357] (19)
      7. Trypanosoma cruzi [TaxId: 5693] [51358] (5)
        SQ P52270
      8. Plasmodium falciparum [TaxId: 5833] [51359] (9)
        SQ Q07412
      9. Leishmania mexicana [TaxId: 5665] [51360] (4)
      10. Entamoeba histolytica [TaxId: 5759] [82236] (1)
      11. Escherichia coli [TaxId: 562] [51361] (1)
      12. Synthetic, hybrid between Escherichia coli and chicken TIM [51362] (1)
      13. Bacillus stearothermophilus [TaxId: 1422] [51363] (2)
      14. Vibrio marinus [TaxId: 90736] [51364] (2)
      15. Thermotoga maritima [TaxId: 2336] [51365] (1)
      16. Archaeon Pyrococcus woesei [TaxId: 2262] [63891] (1)
      17. Thermoproteus tenax [TaxId: 2271] [110342] (1)
        SQ Q8NKN9
      18. Trypanosoma (Trypanozoon) brucei brucei (Trypanosoma brucei brucei) [TaxId: 39700] [159375] (2)
2. Ribulose-phoshate binding barrel [51366] (6)
  uperfamily
  1. Histidine biosynthesis enzymes [51367] (6)
    structural evidence for the gene duplication within the barrel fold
    1. Phosphoribosylformimino-5-aminoimidazole carboxamide ribotite isomerase HisA [51368]
      1. Thermotoga maritima [TaxId: 2336] [51369] (1)
      2. Streptomyces coelicolor [TaxId: 1902] [141744] (2)
        SQ P16250 2-240
    2. Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF [51370]
      1. Thermotoga maritima [TaxId: 2336] [51371] (4)
      2. Thermus thermophilus [TaxId: 274] [82237] (1)
      3. Baker's yeast (Saccharomyces cerevisiae), His7 [TaxId: 4932] [69379] (4)
      4. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69380] (1)
  2. D-ribulose-5-phosphate 3-epimerase [51372] (5)
    1. D-ribulose-5-phosphate 3-epimerase [51373]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [51374] (1)
      2. Rice (Oryza sativa) [TaxId: 4530] [82238] (2)
      3. Synechocystis sp. PCC 6803 [TaxId: 1148] [110343] (1)
        SQ P74061
      4. Plasmodium falciparum [TaxId: 5833] [117359] (1)
        SQ Q8I5L3
      5. Streptococcus pyogenes [TaxId: 1314] [141745] (12)
        SQ Q9A1H8 3-219
  3. Decarboxylase [51375] (13)
    1. Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase) [51376]
      1. Bacillus subtilis [TaxId: 1423] [51377] (1)
      2. Escherichia coli [TaxId: 562] [51378] (3)
      3. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51379] (20)
      4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51380] (2)
      5. Thermotoga maritima [TaxId: 2336] [141746] (1)
        SQ Q9WYG7 1-198
      6. Plasmodium vivax [TaxId: 5855] [141747] (1)
      7. Pyrococcus horikoshii [TaxId: 53953] [141748] (8)
        SQ O58462 1-208
    2. 3-keto-L-gulonate 6-phosphate decarboxylase [75050]
      1. Escherichia coli [TaxId: 562] [75051] (18)
        SQ P39304
    3. Protozoan orotidine monophosphate decarboxylase [141749]
      1. Plasmodium vivax [TaxId: 5855] [141750] (1)
      2. Plasmodium falciparum [TaxId: 5833] [141751] (2)
        SQ Q8T6J6 1-323
      3. Plasmodium berghei [TaxId: 5821] [141752] (2)
        SQ Q4Z4C3 2-325
      4. Plasmodium yoelii [TaxId: 5861] [141753] (1)
        SQ Q7RPE4 2-322
      5. Plasmodium falciparum (isolate 3D7) (Plasmodium falciparum 3D7) [TaxId: 36329] [159376] (14)
  4. Tryptophan biosynthesis enzymes [51381] (12)
    1. N-(5'phosphoribosyl)antranilate isomerase, PRAI [51382]
      1. Escherichia coli [TaxId: 562] [51383] (1)
        merged in bifunctional enzyme with IPG synthase
      2. Thermotoga maritima [TaxId: 2336] [51384] (3)
      3. Thermus thermophilus [TaxId: 274] [102036] (1)
    2. Indole-3-glycerophosphate synthase, IPGS [51385]
      1. Escherichia coli [TaxId: 562] [51386] (2)
        merged in bifunctional enzyme with PRA isomerase
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51387] (6)
      3. Thermotoga maritima [TaxId: 2336] [75052] (2)
        TM0140
      4. Thermus thermophilus [TaxId: 274] [102037] (1)
    3. Trp synthase alpha-subunit [51388]
      1. Salmonella typhimurium [TaxId: 90371] [51389] (49)
      2. Thermus thermophilus [TaxId: 274] [102038] (2)
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [51390] (7)
      4. Escherichia coli [TaxId: 562] [117360] (6)
        SQ P00928
      5. Maize (Zea mays) [TaxId: 4577] [117361] (3)
        SQ P42390
  5. NanE-like [117362] (2)
    Pfam 04131
    1. Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE [117363]
      1. Staphylococcus aureus [TaxId: 1280] [117364] (1)
        SQ P65517
      2. Streptococcus pyogenes [TaxId: 1314] [141754] (2)
        SQ P65522 4-233
  6. PdxS-like [141755] (1)
    Pfam 01680; SOR/SNZ
    1. Pyridoxal biosynthesis lyase PdxS [141756]
      PLP synthase
      1. Bacillus stearothermophilus [TaxId: 1422] [141757] (6)
        SQ Q5L3Y2 18-271
3. Thiamin phosphate synthase [51391] (1)
  uperfamily
  1. Thiamin phosphate synthase [51392] (2)
    1. Thiamin phosphate synthase [51393]
      1. Bacillus subtilis [TaxId: 1423] [51394] (8)
      2. Archaeon (Pyrococcus furiosus) [TaxId: 2261] [110344] (1)
        SQ Q8U192
4. Pyridoxine 5'-phosphate synthase [63892] (1)
  uperfamily
  1. Pyridoxine 5'-phosphate synthase [63893] (1)
    1. Pyridoxine 5'-phosphate synthase [63894]
      1. Escherichia coli [TaxId: 562] [63895] (7)
5. FMN-linked oxidoreductases [51395] (1)
  uperfamily
  1. FMN-linked oxidoreductases [51396] (30)
    1. Dihydroorotate dehydrogenase [51397]
      1. Lactococcus lactis, isozyme A [TaxId: 1358] [51398] (13)
      2. Lactococcus lactis, isozyme B [TaxId: 1358] [51399] (3)
        PyrD subunit
      3. Escherichia coli [TaxId: 562] [82239] (1)
      4. Human (Homo sapiens) [TaxId: 9606] [51400] (11)
      5. Rat (Rattus norvegicus) [TaxId: 10116] [102039] (2)
      6. Trypanosoma brucei [TaxId: 5691] [141758] (4)
        SQ Q57U83 2-313
      7. Plasmodium falciparum [TaxId: 5833] [141759] (1)
        SQ Q08210 158-566
        homolog, mitochonrial
    2. Old yellow enzyme (OYE) [51401]
      1. Lager yeast (Saccharomyces pastorianus) [TaxId: 27292] [51402] (5)
      2. Yeast (Candida albicans) [TaxId: 5476] [51403] (2)
    3. 12-oxophytodienoate reductase (OPR, OYE homolog) [63896]
      1. Tomato (Lycopersicon esculentum), OPR1 [TaxId: 4081] [63897] (3)
      2. Thale cress (Arabidopsis thaliana), OPR1 [TaxId: 3702] [102040] (2)
        At1G76680
      3. Thale cress (Arabidopsis thaliana), OPR3 [TaxId: 3702] [102041] (5)
    4. Glycolate oxidase [51404]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [51405] (4)
    5. Membrane-associated (S)-mandelate dehydrogenase [63898]
      1. Pseudomonas putida [TaxId: 303] [63899] (3)
    6. Pentaerythritol tetranirate reductase [63900]
      1. Enterobacter cloacae [TaxId: 550] [63901] (15)
        SQ P71278
    7. Morphinone reductase [75053]
      1. Pseudomonas putida [TaxId: 303] [75054] (1)
    8. Trimethylamine dehydrogenase, N-terminal domain [51406]
      two other domains are alpha/beta Rossmann-like fold and beta/beta/alpha fold
      1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51407] (5)
    9. 2,4-dienoyl-CoA reductase, N-terminal domain [102042]
      1. Escherichia coli [TaxId: 562] [102043] (1)
    10. Flavocytochrome b2, C-terminal domain [51408]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51409] (16)
        SQ P00175
        N-terminal domain homologous to cytochrome b5
    11. Dihydropyrimidine dehydrogenase, domain 4 [51410]
      1. Pig (Sus scrofa) [TaxId: 9823] [51411] (5)
    12. Alpha subunit of glutamate synthase, central and FMN domains [69381]
      Central domain (residues 423-780) may be a rudiment form of the FMN domain
      1. Azospirillum brasilense [TaxId: 192] [69382] (7)
      2. Synechocystis sp. [TaxId: 1143] [75055] (5)
    13. Isopentenyl-diphosphate delta-isomerase [89454]
      1. Bacillus subtilis [TaxId: 1423] [89455] (2)
      2. Thermus thermophilus [TaxId: 274] [141760] (6)
        SQ Q53W52 23-332
      3. Thermus thermophilus HB8 [TaxId: 300852] [159377] (4)
    14. Putative flavin oxidoreducatase TM0096 [102044]
      Dihydrouridine synthase (Dus) homologue; contains extra C-terminal alpha-helical domain
      1. Thermotoga maritima [TaxId: 2336] [102045] (1)
    15. PcrB protein homolog YerE [102046]
      provisional classification; it is not known whether this protein binds FMN or not
      1. Bacillus subtilis [TaxId: 1423] [102047] (1)
    16. Hydroxyacid oxidase [141761]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141762] (8)
        SQ Q07523 1-349
    17. NADPH dehydrogenase NamA [141763]
      OYE homolog
      1. Bacillus subtilis [TaxId: 1423] [141764] (8)
        SQ P54550 1-337
        probable NADH-dependent flavin oxidoreductase YqjM
    18. (S)-3-O-geranylgeranylglyceryl phosphate synthase [141765]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141766] (4)
        SQ O29844 1-231
        PcrB homolog AF0403
6. Inosine monophosphate dehydrogenase (IMPDH) [51412] (1)
  The phosphate moiety of substrate binds in the 'common' phosphate-binding site
  uperfamily
  1. Inosine monophosphate dehydrogenase (IMPDH) [51413] (8)
    1. Inosine monophosphate dehydrogenase (IMPDH) [51414]
      1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [51415] (1)
      2. Streptococcus pyogenes [TaxId: 1314] [51416] (1)
      3. Tritrichomonas foetus [TaxId: 5724] [51417] (9)
      4. Human (Homo sapiens), type I [TaxId: 9606] [89456] (1)
      5. Human (Homo sapiens), type II [TaxId: 9606] [51418] (3)
      6. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [63902] (1)
      7. Thermotoga maritima [TaxId: 2336] [159378] (1)
        SQ Q9X168 1-85,213-457
      8. Pyrococcus horikoshii [TaxId: 53953] [159379] (1)
        SQ O58045 3-96,207-480
7. PLP-binding barrel [51419] (2)
  circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
  uperfamily
  1. Alanine racemase-like, N-terminal domain [51420] (9)
    1. Alanine racemase [51421]
      1. Bacillus stearothermophilus [TaxId: 1422] [51422] (8)
      2. Pseudomonas aeruginosa [TaxId: 287] [110345] (1)
        SQ Q9HTQ2
      3. Streptomyces lavendulae [TaxId: 1914] [110346] (3)
        SQ Q65YW7
    2. Eukaryotic ornithine decarboxylase [51423]
      1. Human (Homo sapiens) [TaxId: 9606] [51424] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [51425] (1)
      3. Trypanosoma brucei [TaxId: 5691] [51426] (5)
        SQ P07805
    3. Diaminopimelate decarboxylase LysA [89457]
      most similar to eukaryotic ODC
      1. Mycobacterium tuberculosis [TaxId: 1773] [89458] (2)
      2. Escherichia coli [TaxId: 562] [102048] (2)
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [110347] (2)
        SQ Q58497
  2. "Hypothetical" protein ybl036c [51427] (1)
    1. "Hypothetical" protein ybl036c [51428]
      structure from BNL's human proteome project
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51429] (2)
8. NAD(P)-linked oxidoreductase [51430] (1)
  uperfamily
  1. Aldo-keto reductases (NADP) [51431] (20)
    Common fold covers whole protein structure
    1. FR-1 (fibroblast growth factor-induced) protein [51432]
      1. Mouse (Mus musculus) [TaxId: 10090] [51433] (1)
    2. Voltage-dependent K+ channel beta subunit [51434]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51435] (6)
    3. Aflatoxin aldehyde reductase (akr7a1) [75056]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [75057] (1)
    4. Aldose reductase (aldehyde reductase) [51436]
      1. Human (Homo sapiens) [TaxId: 9606] [51437] (57)
        SQ P15121
      2. Pig (Sus scrofa) [TaxId: 9823] [51438] (8)
    5. 3-alpha-hydroxysteroid dehydrogenase [51439]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51440] (3)
      2. Human (Homo sapiens), type III [TaxId: 9606] [69383] (6)
        bile acid binding protein
    6. CHO reductase [51441]
      1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [51442] (1)
    7. Hypothetical protein C07D8.6 [102049]
      Aldo-keto reductase family 1 member c1
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102050] (1)
    8. Prostaglandin d2 11-ketoreductase (akr1c3) [102051]
      Aldo-keto reductase family 1 member c3
      1. Human (Homo sapiens) [TaxId: 9606] [102052] (10)
        SQ P42330
    9. 2,5-diketo-D-gluconic acid reductase A [51443]
      1. Corynebacterium sp. [TaxId: 1720] [51444] (3)
      2. Escherichia coli [TaxId: 562] [102053] (1)
      3. Thermotoga maritima [TaxId: 2336] [117365] (1)
        SQ Q9X0A2
    10. Hypothetical oxidoreductase YdhF [89459]
      1. Escherichia coli [TaxId: 562] [89460] (2)
    11. Putative oxidoreductase IolS [102054]
      vegetative protein 147, VEG147, AKR11A
      1. Bacillus subtilis [TaxId: 1423] [102055] (2)
    12. Putative oxidoreductase YhdN [102056]
      General stress protein 69, GSP69, AKR11B
      1. Bacillus subtilis [TaxId: 1423] [102057] (1)
    13. Tas protein [89461]
      1. Escherichia coli [TaxId: 562] [89462] (1)
    14. Xylose reductase [75058]
      1. Fungi (Candida tenuis) [TaxId: 45596] [75059] (5)
        SQ O74237
    15. 20alpha-hydroxysteroid dehydrogenase [109609]
      1. Human (Homo sapiens) [TaxId: 9606] [109610] (2)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110348] (2)
        SQ P80508
9. (Trans)glycosidases [51445] (14)
  uperfamily
  1. Amylase, catalytic domain [51446] (54)
    members of the family may contain various insert subdomains
    in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain
    1. Bacterial alpha-amylase [51447]
      1. Bacillus licheniformis [TaxId: 1402] [51448] (4)
      2. Chimera (Bacillus amyloliquefaciens) and (Bacillus licheniformis) [TaxId: 1390] [63903] (4)
        the N-terminal 300 residues are from B. amyloliquefaciens
      3. Pseudoalteromonas haloplanktis (Alteromonas haloplanktis) [TaxId: 228] [51449] (9)
      4. Bacillus subtilis [TaxId: 1423] [51450] (2)
        SQ P00691
      5. Bacillus stearothermophilus [TaxId: 1422] [51451] (1)
      6. Bacillus sp., ksm-k38 [TaxId: 1409] [89463] (6)
      7. Archaeon Pyrococcus woesei [TaxId: 2262] [89464] (3)
      8. Bacillus sp. 707 [TaxId: 1416] [117366] (4)
        SQ P19571 38-518
      9. Halothermothrix orenii [TaxId: 31909] [141767] (1)
        SQ Q8GPL8 28-436
      10. Bacillus halmapalus [TaxId: 79882] [141768] (3)
        SQ P19571 38-431
    2. Maltosyltransferase [63904]
      similar to bacterial alpha-amylase; contains larger insertion domain
      1. Thermotoga maritima [TaxId: 2336] [63905] (2)
    3. Cyclodextrin glycosyltransferase [51452]
      contains two more all-beta domains, one is Immunoglobulin-like and the other is trasthyretin-like
      1. Bacillus circulans, different strains [TaxId: 1397] [51453] (36)
      2. Bacillus stearothermophilus [TaxId: 1422] [51454] (1)
      3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [51455] (2)
      4. Bacillus sp. 1011, alkaliphilic [TaxId: 1410] [51456] (8)
        SQ P05618
      5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [51457] (2)
      6. Thermoanaerobacterium [TaxId: 28895] [159380] (2)
    4. Animal alpha-amylase [51458]
      contains Ca2+-binding subdomain, residues 100-170
      1. Pig (Sus scrofa) [TaxId: 9823] [51459] (14)
      2. Human (Homo sapiens) [TaxId: 9606] [51460] (43)
        SQ P04746 16-511 ! SQ 04746
      3. Yellow mealworm (Tenebrio molitor), larva [TaxId: 7067] [51461] (4)
    5. Fungal alpha-amylases [51462]
      1. Aspergillus niger, acid amylase [TaxId: 5061] [51463] (1)
      2. Aspergillus oryzae, Taka-amylase [TaxId: 5062] [51464] (8)
    6. Maltogenic amylase, central domain [51465]
      contains an additional N-terminal domain
      1. Thermus sp. [TaxId: 275] [51466] (2)
      2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [75060] (1)
      3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [75061] (9)
      4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [51467] (25)
    7. Neopullulanase, central domain [82240]
      homologous to Maltogenic amylase
      1. Bacillus stearothermophilus [TaxId: 1422] [82241] (4)
    8. Cyclomaltodextrinase, central domain [102058]
      protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
      1. Flavobacterium sp. 92 [TaxId: 197856] [102059] (1)
    9. Maltooligosyl trehalose synthase [82242]
      elaborated with several large insertions in the common fold
      1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82243] (1)
    10. Glycosyltrehalose trehalohydrolase, central domain [51468]
      contains an additional N-terminal domain
      1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [51469] (2)
      2. Deinococcus radiodurans [TaxId: 1299] [141769] (9)
        SQ Q9RX51 111-528
    11. 1,4-alpha-glucan branching enzyme, central domain [82244]
      1. Escherichia coli [TaxId: 562] [82245] (1)
    12. Isoamylase, central domain [51470]
      1. Pseudomonas amyloderamosa [TaxId: 32043] [51471] (1)
    13. G4-amylase (1,4-alpha-D-glucan maltotetrahydrolase) [51472]
      1. Pseudomonas stutzeri [TaxId: 316] [51473] (9)
    14. Plant alpha-amylase [51474]
      1. Barley (Hordeum vulgare), seeds, AMY2 isozyme [TaxId: 4513] [51475] (3)
      2. Barley (Hordeum vulgare), AMY1 isozyme [TaxId: 4513] [89465] (10)
    15. 4-alpha-glucanotransferase [75062]
      1. Thermotoga maritima [TaxId: 2336] [75063] (2)
    16. Oligo-1,6, glucosidase [51476]
      1. Bacillus cereus [TaxId: 1396] [51477] (1)
    17. Isomaltulose synthase PalI [89466]
      1. Klebsiella sp., lx3 [TaxId: 576] [89467] (1)
    18. Amylosucrase [69384]
      1. Neisseria polysaccharea [TaxId: 489] [69385] (10)
    19. Sucrose phosphorylase [102060]
      sequence and close structural relationship to amylosucrase; variations in the C-terminal domain fold
      1. Bifidobacterium adolescentis [TaxId: 1680] [102061] (5)
    20. Melibiase [75064]
      1. Chicken (Gallus gallus) [TaxId: 9031] [75065] (2)
        alpha-N-acetylgalactosaminidase
      2. Rice (Oryza sativa) [TaxId: 4530] [89468] (1)
        alpha-galactosidase
      3. Human (Homo sapiens) [TaxId: 9606] [102062] (2)
        alpha-galactosidase A
      4. Trichoderma reesei [TaxId: 51453] [110349] (2)
        Alpha-galactosidase agl1
        SQ Q92456
    21. Amylomaltase MalQ [51478]
      4-alpha-glucanotransferase; single-domain amylase with several insertions in the common fold
      1. Thermus aquaticus [TaxId: 271] [51479] (4)
        synonym: Thermus thermophilus
      2. Aquifex aeolicus [TaxId: 63363] [141770] (2)
        SQ O66937 1-485
      3. Potato (Solanum tuberosum) [TaxId: 4113] [141771] (1)
        SQ Q06801 54-576
    22. A4 beta-galactosidase [82246]
      the catalytic domain is very similar to that of the bacterial beta-amylase; but contains a typical alpha-amylase extra domain
      1. Thermus thermophilus [TaxId: 274] [82247] (2)
    23. Bacterial beta-amylase [51485]
      protein contains additional starch-binding domain
      1. Bacillus cereus [TaxId: 1396] [51486] (14)
    24. beta-Amylase [51481]
      Common fold covers whole protein structure
      1. Soybean (Glycine max) [TaxId: 3847] [51482] (19)
        SQ P10538
      2. Barley (Hordeum vulgare) [TaxId: 4513] [51483] (1)
      3. Sweet potato (Ipomoea batatas) [TaxId: 4120] [51484] (1)
    25. Pullulanase PulA [159381]
      1. Klebsiella pneumoniae [TaxId: 573] [159382] (3)
        SQ P07206 410-972
  2. beta-glycanases [51487] (54)
    consist of a number of sequence families
    1. Xylanase [51488]
      1. Clostridium thermocellum, XynZ [TaxId: 1515] [51489] (1)
        belongs to family F
      2. Bacillus stearothermophilus, Xt6 [TaxId: 1422] [69386] (4)
        SQ P40943
      3. Bacillus stearothermophilus, Ixt6 [TaxId: 1422] [102063] (1)
        intra-cellular xylanase
      4. Cellvibrio mixtus [TaxId: 39650] [102064] (4)
      5. Penicillium simplicissimum [TaxId: 69488] [51490] (1)
        belongs to family 10
      6. Thermotoga maritima [TaxId: 2336] [141772] (4)
        SQ Q9WXS5 23-346
    2. Endoglucanase CelA [51491]
      1. Clostridium cellulolyticum [TaxId: 1521] [51492] (1)
    3. Endoglucanase CelC [51493]
      1. Clostridium thermocellum [TaxId: 1515] [51494] (3)
    4. Exo-beta-(1,3)-glucanase [51495]
      1. Yeast (Candida albicans) [TaxId: 5476] [51496] (4)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102065] (1)
    5. Endoglucanase homologue TM1752 [102066]
      1. Thermotoga maritima [TaxId: 2336] [102067] (1)
    6. Endocellulase E1 [51497]
      1. Acidothermus cellulolyticus [TaxId: 28049] [51498] (3)
    7. Endocellulase EngI [75066]
      1. Thermoascus aurantiacus [TaxId: 5087] [75067] (2)
    8. Endoglucanase Cel5a [51499]
      1. Bacillus agaradhaerens [TaxId: 76935] [51500] (20)
        SQ O85465 30-329
      2. Erwinia chrysanthemi [TaxId: 556] [51501] (1)
      3. Bacillus subtilis [TaxId: 1423] [75068] (1)
      4. Pseudoalteromonas haloplanktis [TaxId: 228] [141773] (4)
        SQ O86099 33-325
    9. Alkaline cellulase K catalytic domain [63906]
      1. Bacillus sp. [TaxId: 1409] [63907] (2)
    10. Beta-mannanase [51502]
      1. Thermomonospora fusca [TaxId: 2021] [51503] (3)
      2. Trichoderma reesei [TaxId: 51453] [51504] (5)
      3. Tomato (Lycopersicon esculentum) [TaxId: 4081] [141774] (1)
        SQ Q93WT4 30-399
      4. Bacillus sp. JAMB-602 [TaxId: 244966] [141775] (1)
        SQ Q4W8M3 34-490
        contains additional C-terminal domain (CBM)
    11. Exomannosidase [102068]
      mannosyl-oligosaccharide glucosidase
      1. Cellvibrio mixtus [TaxId: 39650] [102069] (2)
        SQ Q6QT42 46-455
    12. Beta-1,4-galactanase [89469]
      1. Fungus (Aspergillus aculeatus) [TaxId: 5053] [89470] (2)
      2. Thielavia heterothallica, aka Myceliophthora thermophila [TaxId: 78579] [89471] (2)
        Myceliophthora thermophila is the anamorph name whilst Thielavia heterothallica is the teleomorph name
      3. Humicola insolens [TaxId: 34413] [89472] (1)
      4. Bacillus licheniformis [TaxId: 1402] [117367] (7)
        SQ Q65CX5 36-422 ! SQ Q65CX5 28-424
    13. Mannanase A, ManA [63908]
      1. Pseudomonas cellulosa (Cellvibrio japonicus) [TaxId: 155077] [63909] (5)
      2. Cellulomonas fimi [TaxId: 1708] [141776] (3)
        SQ Q9XCV5 55-420
    14. Plant beta-glucanases [51507]
      1. Barley (Hordeum vulgare), 1,3-beta-glucanase [TaxId: 4513] [51508] (1)
      2. Barley (Hordeum vulgare), 1,3-1,4-beta-glucanase [TaxId: 4513] [51509] (2)
      3. Banana (Musa acuminata), 1,3-beta-glucanase [TaxId: 4641] [141777] (1)
        SQ O22317 29-340
    15. beta-Galactosidase, domain 3 [51510]
      1. Escherichia coli [TaxId: 562] [51511] (25)
        SQ P00722
      2. Arthrobacter sp. c2-2 [TaxId: 192168] [141778] (6)
        SQ Q8KRF6 313-609
    16. beta-Glucuronidase, domain 3 [51512]
      1. Human (Homo sapiens) [TaxId: 9606] [51513] (1)
    17. Xylanase A, catalytic core [51514]
      1. Streptomyces lividans [TaxId: 1916] [51515] (9)
        SQ P26514 43-344
      2. Penicillium simplicissimum [TaxId: 69488] [51516] (7)
      3. Pseudomonas fluorescens [TaxId: 294] [51517] (8)
        SQ P14768 265-610
      4. Thermoascus aurantiacus [TaxId: 5087] [51518] (10)
      5. Streptomyces olivaceoviridis [TaxId: 1921] [51519] (12)
        SQ Q7SI98
        N-terminal domain; fused with a ricin A-like beta-trefoil domain
      6. Cellulomonas fimi [TaxId: 1708] [51520] (9)
        synonym: beta-1,4-glycanase Cex
      7. Streptomyces halstedii [TaxId: 1944] [102070] (1)
      8. Emericella nidulans (Aspergillus nidulans) [TaxId: 162425] [110350] (1)
        SQ Q00177
    18. Xylanase 10c [102071]
      Endo-beta-1,4-xylanase
      1. Cellvibrio japonicus [TaxId: 155077] [102072] (2)
    19. Glucosylceramidase, catalytic domain [89473]
      acid-beta-glucosidase; glycosyl hydrolase family 30; contains additional beta-domain similar to one found in alpha amylases
      1. Human (Homo sapiens) [TaxId: 9606] [89474] (27)
    20. Glycosyl hydrolase family 5 xylanase, catalytic domain [102073]
      overall domain organization is similar to the homologous glucosylceramidase
      1. Erwinia chrysanthemi [TaxId: 556] [102074] (1)
    21. Alpha-L-arabinofuranosidase, catalytic domain [102075]
      glycosyl hydrolase family 51
      1. Bacillus stearothermophilus [TaxId: 1422] [102076] (4)
      2. Clostridium thermocellum [TaxId: 1515] [141779] (12)
        SQ Q4CJG5 17-386
    22. Beta-D-xylosidase, catalytic domain [102077]
      glycosyl hydrolase family 39
      1. Thermoanaerobacterium saccharolyticum [TaxId: 28896] [102078] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [141780] (24)
        SQ Q9ZFM2 15-361
    23. endo-1,4-beta-mannosidase [141781]
      1. Blue mussel (Mytilus edulis) [TaxId: 6550] [141782] (1)
        SQ Q8WPJ2 18-367
    24. Endoglucanase H N-terminal domain [141783]
      1. Clostridium thermocellum [TaxId: 1515] [141784] (4)
        SQ P16218 29-304! SQ P16218 31-304
    25. Exochitosanase CsxA [159383]
      1. Amycolatopsis orientalis [TaxId: 31958] [159384] (2)
        SQ Q56F26 336-674
    26. Five-domain beta-mannosidase, domain 3 [159385]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [159386] (18)
        SQ Q8AAK6 330-678! SQ Q8AAK6 331-678
  3. Putative alpha-L-fucosidase, catalytic domain [102079] (1)
    glycosyl hydrolase family 29; contains additional beta-barrel with a topological similarity to the C-terminal domain of alpha amylases
    1. Putative alpha-L-fucosidase, catalytic domain [102080]
      1. Thermotoga maritima [TaxId: 2336] [102081] (3)
        TM0306
  4. Family 1 of glycosyl hydrolase [51521] (15)
    1. Plant beta-glucosidase (myrosinase) [51522]
      1. White mustard (Sinapis alba) [TaxId: 3728] [51523] (17)
      2. Creeping white clover (Trifolium repens) [TaxId: 3899] [51524] (1)
        Cyanogenic beta-glucosidase
      3. Maize (Zea mays), zmglu1 [TaxId: 4577] [51525] (9)
        SQ P49235
      4. Sorghum bicolor [TaxId: 4558] [110351] (2)
        SQ Q41290
    2. 6-phospho-beta-D-galactosidase, PGAL [51526]
      1. Lactococcus lactis [TaxId: 1358] [51527] (4)
    3. Beta-glucosidase A [51528]
      1. Bacillus polymyxa [TaxId: 1406] [51529] (5)
      2. Bacillus circulans, subsp. alkalophilus [TaxId: 1397] [51530] (1)
      3. Streptomyces sp. [TaxId: 1931] [82248] (2)
      4. Thermotoga maritima [TaxId: 2336] [89475] (40)
        SQ Q08638
      5. Thermus thermophilus [TaxId: 274] [89476] (1)
      6. Thermus nonproteolyticus [TaxId: 116039] [89477] (1)
      7. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141785] (1)
        SQ O58104 1-423
    4. beta-Glycosidase [51531]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51532] (14)
        SQ P22498
      2. Archaeon Thermosphaera aggregans [TaxId: 54254] [51533] (1)
    5. Thioglucosidase [141786]
      1. Cabbage aphid (Brevicoryne brassicae) [TaxId: 69196] [141787] (2)
        SQ Q95X01 3-464
  5. Type II chitinase [51534] (22)
    glycosylase family 18
    1. Hevamine A (chitinase/lysozyme) [51535]
      1. Para rubber tree (Hevea brasiliensis) [TaxId: 3981] [51536] (7)
    2. Xylanase inhibitor protein I, XIP-I [89478]
      1. Wheat (Triticum aestivum) [TaxId: 4565] [89479] (3)
        SQ Q8L5C6
    3. Seed storage protein [51537]
      close relation of hevamine, may bind chitin
      1. Vicia narbonensis, Narbonin [TaxId: 3912] [51538] (1)
      2. Jack bean (Canavalia ensiformis), Concanavalin B [TaxId: 3823] [51539] (1)
    4. Endo-beta-N-acetylglucosaminidase [51540]
      1. Flavobacterium meningosepticum, endoglycosidase F1 [TaxId: 238] [51541] (1)
      2. Flavobacterium meningosepticum, endoglycosidase F3 [TaxId: 238] [51542] (2)
      3. Streptomyces plicatus, endoglycosidase H [TaxId: 1922] [51543] (8)
    5. Chitinase A, catalytic domain [51544]
      1. Serratia marcescens [TaxId: 615] [51545] (11)
        SQ P07254 24-563
    6. Chitinase B, catalytic domain [51546]
      1. Serratia marcescens [TaxId: 615] [51547] (14)
    7. Psychrophilic chitinase B [82249]
      1. Arthrobacter sp., tad20 [TaxId: 1667] [82250] (1)
    8. Chitinase A1 [75069]
      1. Bacillus circulans [TaxId: 1397] [75070] (1)
    9. Chitinase 1 [51548]
      1. Fungus (Coccidioides immitis) [TaxId: 5501] [51549] (4)
      2. Aspergillus fumigatus [TaxId: 5085] [117368] (26)
        SQ Q873X9
    10. Chitotriosidase [82251]
      1. Human (Homo sapiens) [TaxId: 9606] [82252] (10)
    11. Signal processing protein (SPC-40, MGP-40) [89480]
      secreted during involution
      1. Goat (Capra hircus) [TaxId: 9925] [89481] (14)
      2. Cow (Bos taurus) [TaxId: 9913] [110352] (1)
        SQ P30922
      3. Sheep (Ovis aries) [TaxId: 9940] [109611] (12)
        SQ Q6TMG6
      4. Buffalo (Bubalus bubalis) [TaxId: 89462] [110353] (3)
        SQ Q7YS85
      5. Pig (Sus scrofa) [TaxId: 9823] [117369] (4)
        SQ Q5UC99
    12. Chitinase-3 like protein 1 (GP-39, YKL-40) [89482]
      1. Human (Homo sapiens) [TaxId: 9606] [89483] (7)
    13. Chitinase-like lectin ym1, saccharide binding domain [63910]
      1. Mouse (Mus musculus) [TaxId: 10090] [63911] (2)
    14. Imaginal disc growth factor-2 [75071]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75072] (2)
  6. 1,4-beta-N-acetylmuraminidase [63912] (3)
    Glycosyl hydrolase family 25; probably have evolved from a type II chitinase ancestor
    permutation of the common fold; strand 8 is antiparallel to the rest of the barrel
    1. Streptomyces lysozyme [63913]
      supersedes and corrects the old structure from S. erythraeus; 0LZ6
      1. Streptomyces coelicolor, "mueller" dsm3030 [TaxId: 1902] [63914] (1)
    2. N-terminal domain of endolysin [89484]
      1. Bacteriophage cp-1 [TaxId: 10747] [89485] (6)
    3. Unnamed hypothetical protein [102082]
      homologue of BH2215 from the complete Bacillus halodurans genome
      1. Bacillus stearothermophilus [TaxId: 1422] [102083] (1)
  7. beta-N-acetylhexosaminidase catalytic domain [51550] (5)
    Glycosyl hydrolase family 20, GH20
    1. Bacterial chitobiase (beta-N-acetylhexosaminidase) [51551]
      1. Serratia marcescens [TaxId: 615] [51552] (4)
    2. beta-N-acetylhexosaminidase [63915]
      1. Streptomyces plicatus [TaxId: 1922] [63916] (6)
    3. beta-hexosaminidase B [89486]
      1. Human (Homo sapiens) [TaxId: 9606] [89487] (12)
    4. Dispersin B, DspB [141788]
      N-acetyl-beta-hexosaminidase
      1. Actinobacillus actinomycetemcomitans [TaxId: 714] [141789] (1)
        SQ Q840G9 16-359
    5. beta-hexosaminidase A [159387]
      1. Human (Homo sapiens) [TaxId: 9606] [159388] (8)
        SQ P06865 167-528
  8. alpha-D-glucuronidase/Hyaluronidase catalytic domain [82253] (4)
    Glycosyl hydrolase family 67, GH67; structurally related to GH20; contains extra C-terminal alpha-helical subdomain
    1. alpha-D-glucuronidase catalytic domain [82254]
      inverting reaction mechanism
      1. Pseudomonas cellulosa [TaxId: 155077] [82255] (5)
      2. Bacillus stearothermophilus [TaxId: 1422] [82256] (7)
    2. Glucosaminidase GH84, catalytic domain [141790]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [141791] (12)
        SQ Q89ZI2 148-457
    3. Hyaluronidase catalytic domain [141792]
      1. Clostridium perfringens [TaxId: 1502] [141793] (6)
        SQ Q8XL08 179-495
  9. NagZ-like [51553] (2)
    Pfam 00933; Glycosyl hydrolase family 3 domain
    1. Beta-D-glucan exohydrolase, N-terminal domain [51554]
      interdomain linker forms an additional, N-terminal strand
      1. Barley (Hordeum vulgare) [TaxId: 4513] [51555] (9)
    2. Beta-hexosaminidase NagZ [117370]
      1. Vibrio cholerae [TaxId: 666] [117371] (2)
        SQ Q9KU37
  10. Bee venom hyaluronidase [69387] (1)
    distorted barrel lacks the second strand
    1. Bee venom hyaluronidase [69388]
      1. Honeybee (Apis mellifera) [TaxId: 7460] [69389] (4)
  11. Outer surface protein, N-terminal domain [110354] (1)
    corresponds to the N-terminal part of Pfam 05913
    1. Outer surface protein, N-terminal domain [110355]
      1. Bacillus cereus [TaxId: 1396] [110356] (1)
        SQ Q81HJ5
  12. YicI catalytic domain-like [117372] (2)
    1. Putative glucosidase YicI, domain 2 [117373]
      1. Escherichia coli [TaxId: 562] [117374] (15)
        SQ P31434
    2. Alpha-galactosidase GalA catalytic domain [141794]
      includes extra C-terminal all-beta subdomain, 4-stranded meander beta-sheet
      1. Thermotoga maritima [TaxId: 2336] [141795] (1)
        SQ O33835 178-525
  13. Glycosyl hydrolases family 35 catalytic domain [117375] (1)
    Pfam 01301
    1. Beta-galactosidase LacA, N-terminal domain [117376]
      1. Penicillium sp. [TaxId: 5081] [117377] (2)
        SQ Q700S9 41-1011
  14. TM1410-like [141796] (1)
    Pfam 03537
    1. Hypothetical protein TM1410 [141797]
      1. Thermotoga maritima [TaxId: 2336] [141798] (6)
        SQ Q9X1D0 28-312
10. Metallo-dependent hydrolases [51556] (18)
  the beta-sheet barrel is similarly distorted and capped by a C-terminal helix
  has transition metal ions bound inside the barrel
  uperfamily
  1. Adenosine/AMP deaminase [51557] (4)
    1. Adenosine deaminase (ADA) [51558]
      Common fold covers the whole protein structure
      1. Mouse (Mus musculus) [TaxId: 10090] [51559] (8)
      2. Cow (Bos taurus) [TaxId: 9913] [82257] (20)
        SQ P56658 3-350 ! SQ P56658
      3. Plasmodium yoelii [TaxId: 5861] [141799] (2)
        SQ Q7RMV2 8-364
    2. AMP deaminase (AMPD), catalytic domain [141800]
      elaborated fold with additional structures
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141801] (1)
        SQ O80452 212-839
  2. Dihydroorotase [63917] (1)
    1. Dihydroorotase [63918]
      1. Escherichia coli [TaxId: 562] [63919] (9)
  3. Cytosine deaminase catalytic domain [69390] (1)
    1. Cytosine deaminase catalytic domain [69391]
      1. Escherichia coli [TaxId: 562] [69392] (8)
        SQ P25524
  4. alpha-subunit of urease, catalytic domain [51560] (3)
    1. alpha-subunit of urease, catalytic domain [51561]
      1. Klebsiella aerogenes [TaxId: 28451] [51562] (27)
      2. Bacillus pasteurii [TaxId: 1474] [51563] (6)
      3. Helicobacter pylori [TaxId: 210] [69393] (2)
  5. Hydantoinase (dihydropyrimidinase), catalytic domain [75073] (9)
    1. D-hydantoinase [75074]
      1. Thermus sp. [TaxId: 275] [75075] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [75076] (1)
      3. Burkholderia pickettii [TaxId: 329] [89488] (1)
      4. Bacillus sp. AR9 [TaxId: 301298] [141802] (2)
        SQ Q5DLU2 2-460
    2. L-hydantoinase [75077]
      1. Arthrobacter aurescens [TaxId: 43663] [75078] (1)
    3. Dihydropyrimidinase related protein-1 [102084]
      1. Mouse (Mus musculus) [TaxId: 10090] [102085] (1)
    4. Two-domain dihydroorotase [141803]
      1. Aquifex aeolicus [TaxId: 63363] [141804] (3)
        SQ O66990 56-365
    5. Dihydropyrimidine amidohydrolase Pyd2 [141805]
      1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [141806] (12)
        SQ Q9P903 57-440
      2. Dictyostelium discoideum [TaxId: 44689] [141807] (1)
        SQ Q86LT2 60-393
  6. SAH/MTA deaminase-like [82258] (5)
    1. Hypothetical protein TM0936, probable catalytic domain [82259]
      1. Thermotoga maritima [TaxId: 2336] [82260] (3)
    2. Hypothetical protein GOS_1943094 [159389]
      1. Environmental samples [159390] (1)
    3. Guanine deaminase [159391]
      1. Clostridium acetobutylicum [TaxId: 1488] [159392] (2)
        SQ Q97MB6 64-373
        CAC0282
      2. Bradyrhizobium japonicum [TaxId: 375] [159393] (1)
        SQ Q89NG0 71-395
        Blr3880
      3. Human (Homo sapiens) [TaxId: 9606] [159394] (1)
        SQ Q9Y2T3 76-388
  7. Isoaspartyl dipeptidase, catalytic domain [89489] (1)
    1. Isoaspartyl dipeptidase, catalytic domain [89490]
      1. Escherichia coli [TaxId: 562] [89491] (5)
        SQ P39377
  8. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82261] (3)
    1. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82262]
      1. Bacillus subtilis [TaxId: 1423] [102086] (1)
      2. Thermotoga maritima [TaxId: 2336] [82263] (1)
        TM0814
      3. Escherichia coli [TaxId: 562] [141808] (10)
        SQ P0AF18 54-350
  9. D-aminoacylase, catalytic domain [82264] (1)
    1. N-acyl-D-aminoacid amidohydrolase, catalytic domain [82265]
      contains small a/b subdomain inserted after strand 7; unusual for the superfamily metal coordination by Cys
      1. Alcaligenes faecalis [TaxId: 511] [82266] (8)
  10. TatD Mg-dependent DNase-like [82267] (4)
    1. Hypothetical protein TM0667 [82268]
      1. Thermotoga maritima [TaxId: 2336] [82269] (1)
    2. Putative deoxyribonuclease YcfH [141809]
      1. Escherichia coli [TaxId: 562] [141810] (2)
        SQ P0AFQ7 1-265
    3. Deoxyribonuclease TatD (MttC) [141811]
      1. Escherichia coli [TaxId: 562] [141812] (1)
        SQ P27859 1-260
    4. Putative deoxyribonuclease YjjV [141813]
      1. Escherichia coli [TaxId: 562] [141814] (1)
        SQ P39408 1-259
  11. Phosphotriesterase-like [51564] (4)
    1. Phosphotriesterase (parathion hydrolase, PTE) [51565]
      1. Pseudomonas diminuta [TaxId: 293] [51566] (10)
        SQ P0A434 30-365
      2. Flavobacterium sp. atcc 27551 [TaxId: 74567] [102087] (2)
        identical sequence to the Pseudomonas diminuta PTE
      3. Agrobacterium tumefaciens [TaxId: 358] [141815] (3)
        SQ Q93LD7 32-360
    2. Phosphotriesterase homology protein [51567]
      1. Escherichia coli [TaxId: 562] [51568] (1)
  12. Renal dipeptidase [75079] (1)
    1. Renal dipeptidase [75080]
      1. Human (Homo sapiens) [TaxId: 9606] [75081] (2)
  13. Uronate isomerase-like [75082] (2)
    contains all-alpha subdomain inserted after the first strand
    1. Uronate isomerase TM0064 [75083]
      1. Thermotoga maritima [TaxId: 2336] [75084] (1)
    2. Uncharacterized protein BH0493 [159395]
      1. Bacillus halodurans [TaxId: 86665] [159396] (13)
        SQ Q9KFI6 1-423
  14. Adenine deaminase-like [141816] (1)
    1. Putative adenine deaminase EF0837 [141817]
      1. Enterococcus faecalis [TaxId: 1351] [141818] (1)
        SQ Q837K0 53-319
  15. PP1699/LP2961-like [141819] (5)
    Pfam 04909; Amidohydrolase; stand-alone domain
    1. Putative 2-pyrone-4,6-dicarboxylic acid hydrolase PP1699 [141820]
      1. Pseudomonas putida [TaxId: 303] [141821] (2)
        SQ Q88M75 10-280
    2. Thermophilic reversible gamma-resorcylate decarboxylase [141822]
      1. Rhizobium sp. MTP-10005 [TaxId: 267998] [141823] (12)
        SQ Q60GU1 1-325
    3. 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase NbaD [141824]
      1. Pseudomonas fluorescens [TaxId: 294] [141825] (4)
        SQ Q83V25 3-333
    4. 4-oxalomesaconate hydratase LigJ [141826]
      1. Rhodopseudomonas palustris [TaxId: 1076] [141827] (2)
        SQ Q6N0R4 1-342
    5. Putative amidohydrolase LP2961 [141828]
      1. Lactobacillus plantarum [TaxId: 1590] [141829] (2)
        SQ Q88TJ2 2-307
  16. DR0824-like [159397] (1)
    1. Hypothetical protein DR0824 [159398]
      predicted isoguanine deaminase/xanthine hydrolase
      1. Deinococcus radiodurans [TaxId: 1299] [159399] (1)
        SQ Q9RW45 91-398
  17. Imidazolonepropionase-like [159400] (4)
    1. Uncharacterized protein BL1453 [159401]
      Possible prolidase
      1. Bifidobacterium longum [TaxId: 216816] [159402] (1)
        SQ Q8G4D5 69-392
    2. Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421 [159403]
      1. Environmental samples [159404] (2)
        marine metagenome
    3. Imidazolonepropionase [159405]
      1. Bacillus subtilis [TaxId: 1423] [159406] (4)
        SQ P42084 74-373
      2. Agrobacterium tumefaciens [TaxId: 358] [159407] (4)
        SQ Q8U8Z6 78-378
  18. Zn-dependent arginine carboxypeptidase-like [159408] (3)
    1. Xaa-Pro dipeptidase [159409]
      1. Alteromonas macleodii [TaxId: 28108] [159410] (2)
    2. Zn-dependent arginine carboxypeptidase [159411]
      1. Unidentified organism [TaxId: 32644] [159412] (16)
    3. Uncharacterized protein EAJ56179 [159413]
      1. Unidentified organism [TaxId: 32644] [159414] (8)
        94% identity to the Burkholderia phytofirmans ortholog Bphyt_2089 (SQ B2T4I1)
11. Aldolase [51569] (8)
  Common fold covers whole protein structure
  uperfamily
  1. Class I aldolase [51570] (37)
    the catalytic lysine forms schiff-base intermediate with substrate
    possible link between the aldolase superfamily and the phosphate-binding beta/alpha barrels
    1. Deoxyribose-phosphate aldolase DeoC [69394]
      1. Escherichia coli [TaxId: 562] [69395] (4)
        SQ P00882
      2. Thermotoga maritima [TaxId: 2336] [82270] (1)
        TM1559
      3. Aquifex aeolicus [TaxId: 63363] [82271] (1)
      4. Thermus thermophilus [TaxId: 274] [89492] (2)
      5. Archaeon Aeropyrum pernix [TaxId: 56636] [89493] (1)
      6. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [141830] (2)
        SQ Q8ZXK7 1-226
    2. Archaeal fructose 1,6-bisphosphate aldolase [102088]
      1. Archaeon Thermoproteus tenax [TaxId: 2271] [102089] (23)
    3. N-acetylneuraminate lyase [51571]
      1. Escherichia coli [TaxId: 562] [51572] (4)
      2. Haemophilus influenzae [TaxId: 727] [51573] (6)
    4. Dihydrodipicolinate synthase [51574]
      1. Escherichia coli [TaxId: 562] [51575] (14)
      2. Thermotoga maritima [TaxId: 2336] [102090] (1)
      3. Mycobacterium tuberculosis [TaxId: 1773] [141831] (8)
        SQ P63945 5-300
      4. Bacillus anthracis [TaxId: 1392] [141832] (8)
        SQ Q81WN7 1-292
    5. Fructose-1,6-bisphosphate aldolase [51576]
      1. Human (Homo sapiens), muscle isozyme [TaxId: 9606] [51577] (3)
      2. Human (Homo sapiens), liver isozyme [TaxId: 9606] [51578] (17)
      3. Rabbit (Oryctolagus cuniculus), muscle isozyme [TaxId: 9986] [51580] (42)
      4. Rabbit (Oryctolagus cuniculus), liver isozyme [TaxId: 9986] [63920] (1)
      5. Drosophila melanogaster [TaxId: 7227] [51579] (1)
      6. Plasmodium falciparum [TaxId: 5833] [51581] (1)
      7. Trypanosome (Leishmania mexicana) [TaxId: 5665] [51582] (13)
      8. Trypanosome (Trypanosoma brucei) [TaxId: 5691] [51583] (1)
      9. Plasmodium yoelii yoelii [TaxId: 73239] [141833] (2)
        SQ Q7RMC9 3-258
      10. Human (Homo sapiens), brain isozyme [TaxId: 9606] [141834] (12)
        SQ P09972 2-343
    6. KDPG aldolase [51584]
      1. Escherichia coli [TaxId: 562] [51585] (11)
      2. Pseudomonas putida [TaxId: 303] [102091] (1)
      3. Thermotoga maritima [TaxId: 2336] [110357] (7)
        SQ Q9WXS1
    7. Hypothetical protein HI0047 [102092]
      putative KHG/KDPG aldolase
      1. Haemophilus influenzae [TaxId: 727] [102093] (1)
    8. Type I 3-dehydroquinate dehydratase [51586]
      1. Salmonella typhi [TaxId: 90370] [51587] (3)
      2. Staphylococcus aureus [TaxId: 1280] [117378] (2)
        SQ Q6GII7
    9. Transaldolase [51588]
      probably related to class I aldolases by a circular permutation
      1. Escherichia coli [TaxId: 562] [51589] (7)
      2. Human (Homo sapiens) [TaxId: 9606] [51590] (1)
      3. Mouse (Mus musculus) [TaxId: 10090] [141835] (4)
        SQ Q93092 13-331
    10. Decameric fructose-6-phosphate aldolase/transaldolase [75085]
      forms helix-swapped pentamers
      1. Escherichia coli [TaxId: 562] [75086] (1)
      2. Thermotoga maritima [TaxId: 2336] [117379] (1)
        SQ Q9WYD1
      3. Thermus thermophilus [TaxId: 274] [141836] (10)
        SQ Q5SJE8 1-211
        clear orthologue of the E.coli protein; annotated as transaldolase in UniProt
    11. Putative aldolase YihT [110358]
      1. Salmonella typhimurium [TaxId: 90371] [110359] (1)
        SQ Q9L7R9
    12. 2-keto-3-deoxy gluconate aldolase Eda [110360]
      1. Sulfolobus solfataricus [TaxId: 2287] [110361] (4)
        SQ Q97U28
  2. Class II FBP aldolase [51591] (3)
    metal-dependent
    1. Fructose-bisphosphate aldolase (FBP aldolase) [51592]
      1. Escherichia coli [TaxId: 562] [51593] (4)
      2. Thermus aquaticus [TaxId: 271] [102094] (2)
    2. Tagatose-1,6-bisphosphate aldolase [75087]
      1. Escherichia coli [TaxId: 562] [75088] (1)
  3. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51594] (5)
    hybrid of classes I and II aldolase
    1. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51595]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51596] (12)
      2. Human (Homo sapiens) [TaxId: 9606] [63921] (2)
      3. Pseudomonas aeruginosa [TaxId: 287] [51597] (2)
      4. Escherichia coli [TaxId: 562] [51598] (4)
      5. Prosthecochloris vibrioformis [TaxId: 1098] [110362] (3)
        SQ Q59334
  4. Class I DAHP synthetase [51599] (6)
    1. 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG) [51600]
      1. Escherichia coli, phenylalanine-regulated isozyme [TaxId: 562] [51601] (4)
      2. Baker's yeast (Saccharomyces cerevisiae), tyrosine-regulated isozyme [TaxId: 4932] [82272] (11)
      3. Thermotoga maritima [TaxId: 2336] [110363] (5)
        SQ Q9WYH8
    2. 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase) [51602]
      1. Escherichia coli [TaxId: 562] [51603] (10)
        SQ P17579
      2. Haemophilus influenzae [TaxId: 727] [102095] (1)
      3. Aquifex aeolicus [TaxId: 63363] [63922] (20)
  5. HMGL-like [89494] (3)
    Pfam 00682
    1. 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain [89495]
      1. Pseudomonas sp. [TaxId: 306] [89496] (1)
        gene product DmpG
    2. 2-isopropylmalate synthase LeuA, catalytic domain [110364]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110365] (1)
        SQ P96420
    3. Transcarboxylase 5S subunit, N-terminal domain [110366]
      1. Propionibacterium freudenreichii shermanii [TaxId: 1752] [110367] (6)
        SQ Q70AC7 3-474
  6. NeuB-like [110368] (2)
    Pfam 03102
    1. Spore coat polysaccharide biosynthesis protein SpsE, N-terminal domain [110369]
      1. Bacillus subtilis [TaxId: 1423] [110370] (1)
        SQ P39625
    2. Capsule biosynthesis protein SiaC, N-terminal domain [117380]
      1. Neisseria meningitidis [TaxId: 487] [117381] (4)
        SQ Q57265
  7. GatZ-like [141837] (1)
    Pfam 08013
    1. Putative tagatose 6-phosphate kinase 1 GatZ [141838]
      1. Escherichia coli [TaxId: 562] [141839] (4)
        SQ P37191 1-420
  8. Class-II DAHP synthetase [141840] (1)
    Pfam 01474
    1. Probable DAHP synthetase AroG, phenylalanine-repressible [141841]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141842] (2)
        SQ O53512 1-462
12. Enolase C-terminal domain-like [51604] (2)
  binds metal ion (magnesium or manganese) in conserved site inside barrel
  N-terminal alpha+beta domain is common to this superfamily
  uperfamily
  1. Enolase [51605] (8)
    1. Enolase [51606]
      Fold of this protein slightly differs from common fold in topology
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51607] (18)
      2. European lobster (Homarus vulgaris) [TaxId: 6707] [51608] (2)
      3. Trypanosoma brucei brucei [TaxId: 5702] [89497] (1)
      4. Enterococcus hirae [TaxId: 1354] [89498] (1)
      5. Escherichia coli [TaxId: 562] [69396] (5)
      6. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110371] (5)
        SQ P09104
      7. Streptococcus pneumoniae [TaxId: 1313] [141843] (2)
        SQ Q8DPS0 138-433
      8. Trypanosoma brucei [TaxId: 5691] [159415] (6)
  2. D-glucarate dehydratase-like [51609] (20)
    1. D-glucarate dehydratase [51610]
      1. Pseudomonas putida [TaxId: 303] [51611] (1)
      2. Escherichia coli [TaxId: 562] [51612] (6)
    2. O-succinylbenzoate synthase [51613]
      1. Escherichia coli [TaxId: 562] [51614] (7)
    3. Muconate-lactonizing enzyme [51615]
      1. Pseudomonas putida [TaxId: 303] [51616] (5)
    4. Mandelate racemase [51617]
      1. Pseudomonas putida [TaxId: 303] [51618] (6)
    5. Chlormuconate cycloisomerase [51619]
      1. Alcaligenes eutrophus [TaxId: 106590] [51620] (2)
      2. Pseudomonas sp. p51 [TaxId: 65067] [102096] (1)
    6. L-Ala-D/L-Glu epimerase [69397]
      1. Escherichia coli [TaxId: 562] [69398] (1)
      2. Bacillus subtilis [TaxId: 1423] [69399] (2)
        SQ O34508
    7. beta-Methylaspartase [69400]
      1. Clostridium tetanomorphum [TaxId: 1553] [69401] (2)
      2. Citrobacter amalonaticus [TaxId: 35703] [69402] (2)
    8. Hypothetical protein Atu3453 [102097]
      1. Agrobacterium tumefaciens [TaxId: 358] [102098] (1)
    9. N-acylamino acid racemase [110372]
      1. Amycolatopsis sp. [TaxId: 37632] [110373] (4)
        SQ Q44244 # similar activity to a remotely related O-succinylbenzoate synthase from E. coli
      2. Deinococcus radiodurans [TaxId: 1299] [110374] (4)
        SQ Q9RYA6
      3. Enterococcus faecalis [TaxId: 1351] [117382] (1)
        SQ Q838J7; EF0450; protein assignment by sequence similarity
      4. Listeria innocua [TaxId: 1642] [117383] (1)
        SQ Q927X3; Lin2664; protein assignment by sequence similarity
    10. Hypothetical protein Bll6730 [117384]
      1. Bradyrhizobium japonicum [TaxId: 375] [117385] (21)
        SQ Q89FH0
    11. RTS beta protein [117386]
      1. Xanthomonas campestris pv. campestris [TaxId: 340] [117387] (1)
        SQ Q8P3K2; extended, mainly helical linker between the domains
    12. Hypothetical protein YitF [141844]
      1. Bacillus subtilis [TaxId: 1423] [141845] (10)
        SQ O06741 115-371
    13. Putative dehydratase protein STM2273 [141846]
      1. Salmonella typhimurium [TaxId: 90371] [141847] (2)
        SQ Q8ZNH1 123-400
13. Phosphoenolpyruvate/pyruvate domain [51621] (7)
  uperfamily
  1. Pyruvate kinase [51622] (6)
    1. Pyruvate kinase, N-terminal domain [51623]
      this domain is interrupted by an all-beta domain
      C-terminal domain is alpha/beta
      1. Cat (Felis catus) [TaxId: 9685] [51624] (1)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [51625] (14)
      3. Human (Homo sapiens) [TaxId: 9606] [82273] (4)
      4. Leishmania mexicana [TaxId: 5665] [51626] (8)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51627] (2)
      6. Escherichia coli [TaxId: 562] [51628] (3)
  2. Pyruvate phosphate dikinase, C-terminal domain [51629] (3)
    1. Pyruvate phosphate dikinase, C-terminal domain [51630]
      1. Clostridium symbiosum [TaxId: 1512] [51631] (7)
      2. Trypanosoma brucei [TaxId: 5691] [75089] (1)
      3. Maize (Zea mays) [TaxId: 4577] [141848] (2)
        SQ P11155 592-947
  3. Phosphoenolpyruvate carboxylase [51632] (1)
    1. Phosphoenolpyruvate carboxylase [51633]
      the common fold is decorated with many additional helices
      1. Escherichia coli [TaxId: 562] [51634] (4)
  4. Phosphoenolpyruvate mutase/Isocitrate lyase-like [88704] (6)
    forms a swapped dimer
    1. Phosphoenolpyruvate mutase [51636]
      1. Blue mussel (Mytilus edulis) [TaxId: 6550] [51637] (6)
    2. 2-methylisocitrate lyase [89499]
      1. Escherichia coli [TaxId: 562] [89500] (2)
      2. Salmonella typhimurium [TaxId: 90371] [102099] (2)
    3. Isocitrate lyase [51642]
      elaborated with additional subdomains
      1. Aspergillus nidulans [TaxId: 162425] [51643] (1)
      2. Mycobacterium tuberculosis [TaxId: 1773] [51644] (3)
      3. Escherichia coli [TaxId: 562] [63923] (1)
  5. HpcH/HpaI aldolase [51638] (4)
    forms a swapped dimer; contains a PK-type metal-binding site
    1. 2-dehydro-3-deoxy-galactarate aldolase [51639]
      1. Escherichia coli [TaxId: 562] [51640] (2)
    2. Macrophomate synthase [89501]
      Intermolecular Diels-Alderase
      1. Macrophoma commelinae [TaxId: 108330] [89502] (1)
    3. Citrate lyase, beta subunit [110375]
      non-swapped trimer
      1. Deinococcus radiodurans [TaxId: 1299] [110376] (1)
        SQ Q9RUZ0 4-234
      2. Mycobacterium tuberculosis [TaxId: 1773] [117388] (2)
        SQ O06162
  6. Ketopantoate hydroxymethyltransferase PanB [89503] (3)
    1. Ketopantoate hydroxymethyltransferase PanB [89504]
      dodecameric enzyme; a C-terminal helix exchange is observed in the M. tuberculosis enzyme but not in the E. coli enzyme
      1. Mycobacterium tuberculosis [TaxId: 1773] [89505] (1)
      2. Escherichia coli [TaxId: 562] [89506] (1)
      3. Neisseria meningitidis [TaxId: 487] [102100] (2)
  7. Mll9387-like [159416] (1)
    Pfam 09370; TIM-barrel signal transduction protein; forms a swapped dimer similar to the Phosphoenolpyruvate mutase/Isocitrate lyase-like and HpcH/HpaI aldolase families
    1. Uncharacterized protein Mll9387 [159417]
      1. Mesorhizobium loti [TaxId: 381] [159418] (6)
        SQ Q981G2 8-284
14. Malate synthase G [51645] (1)
  uperfamily
  1. Malate synthase G [51646] (2)
    1. Malate synthase G [51647]
      contains the insert of all-beta (sub)domain and the C-terminal extension of all-alpha (sub)domain
      1. Escherichia coli [TaxId: 562] [51648] (4)
        SQ P37330 2-722 # NMR-derived model
      2. Mycobacterium tuberculosis [TaxId: 1773] [82274] (4)
15. RuBisCo, C-terminal domain [51649] (1)
  uperfamily
  1. RuBisCo, large subunit, C-terminal domain [51650] (12)
    N-terminal domain is alpha+beta
    1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [51651]
      1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [51652] (5)
      2. Spinach (Spinacia oleracea) [TaxId: 3562] [51653] (11)
      3. Galdieria partita [TaxId: 83374] [51654] (2)
      4. Chlamydomonas reinhardtii [TaxId: 3055] [69403] (74)
      5. Alcaligenes eutrophus [TaxId: 106590] [51655] (1)
      6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [51656] (16)
      7. Rhodospirillum rubrum [TaxId: 1085] [51657] (5)
      8. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [69404] (1)
      9. Chlorobium tepidum [TaxId: 1097] [117389] (3)
        SQ Q8KBL4 1-428
      10. Rice (Oryza sativa) [TaxId: 4530] [117390] (1)
        SQ P12089
      11. Archaeon Halothiobacillus neapolitanus [TaxId: 927] [141849] (1)
        SQ O85040 143-460
      12. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141850] (10)
        SQ O58677 134-424
16. Xylose isomerase-like [51658] (7)
  different families share similar but non-identical metal-binding sites
  uperfamily
  1. Endonuclease IV [51659] (2)
    1. Endonuclease IV [51660]
      DNA repair enzyme
      1. Escherichia coli [TaxId: 562] [51661] (2)
      2. Bacillus anthracis [TaxId: 1392] [141851] (1)
        SQ Q81LV1 2-298
  2. IolI-like [75090] (3)
    1. Hypothetical protein IolI [75091]
      1. Bacillus subtilis [TaxId: 1423] [75092] (2)
    2. Hypothetical protein Lmo2234 [141852]
      1. Listeria monocytogenes [TaxId: 1639] [141853] (2)
        SQ Q8Y542 10-284
    3. Putative cytoplasmic protein STM4435 [159419]
      1. Salmonella typhimurium [TaxId: 90371] [159420] (1)
        SQ Q8ZK48 1-271
  3. Hypothetical protein YgbM (EC1530) [75093] (1)
    1. Hypothetical protein YgbM (EC1530) [75094]
      1. Escherichia coli [TaxId: 562] [75095] (1)
  4. L-rhamnose isomerase [51662] (1)
    1. L-rhamnose isomerase [51663]
      1. Escherichia coli [TaxId: 562] [51664] (3)
  5. Xylose isomerase [51665] (12)
    1. D-xylose isomerase [51666]
      1. Streptomyces albus [TaxId: 1888] [51667] (1)
      2. Streptomyces murinus [TaxId: 33900] [51668] (1)
      3. Streptomyces olivochromogenes [TaxId: 1963] [51669] (9)
      4. Streptomyces rubiginosus [TaxId: 1929] [51670] (24)
      5. Streptomyces diastaticus, M1033 [TaxId: 1956] [51671] (2)
      6. Arthrobacter, strain b3728 [TaxId: 1663] [51672] (17)
      7. Actinoplanes missouriensis [TaxId: 1866] [51673] (14)
      8. Clostridium thermosulfurogenes, also known as Thermoanaerobacter thermosulfurigenes [TaxId: 33950] [51674] (1)
      9. Bacillus stearothermophilus [TaxId: 1422] [51675] (1)
      10. Thermotoga neapolitana [TaxId: 2337] [51676] (1)
      11. Thermus aquaticus, subsp. Caldophilus [TaxId: 271] [51677] (1)
      12. Thermus aquaticus, subsp. Thermophilus [TaxId: 271] [51678] (1)
  6. UxuA-like [110377] (1)
    Pfam 03786
    1. Mannonate dehydratase UxuA [110378]
      1. Enterococcus faecalis (Streptococcus faecalis) [TaxId: 1351] [110379] (1)
        SQ Q82ZC9
  7. KguE-like [141854] (1)
    part of Pfam 01261
    1. Hypothetical protein PA2260 [141855]
      2-ketogluconate utilization operon protein KguE
      1. Pseudomonas aeruginosa [TaxId: 287] [141856] (3)
        SQ Q9I1L3 3-252
17. Bacterial luciferase-like [51679] (4)
  consists of clearly related families of somewhat different folds
  uperfamily
  1. Bacterial luciferase (alkanal monooxygenase) [51680] (2)
    typical (beta/alpha)8-barrel fold
    heterodimer of two similar chains
    1. Bacterial luciferase alpha chain, LuxA [88705]
      1. Vibrio harveyi [TaxId: 669] [88706] (3)
    2. Bacterial luciferase beta chain, LuxB [88707]
      1. Vibrio harveyi [TaxId: 669] [88708] (5)
  2. Non-fluorescent flavoprotein (luxF, FP390) [51683] (2)
    incomplete beta/alpha barrel with mixed beta-sheet of 7 strands
    1. Non-fluorescent flavoprotein (luxF, FP390) [51684]
      1. Photobacterium leiognathi [TaxId: 553611] [51685] (1)
      2. Photobacterium phosphoreum [TaxId: 659] [51686] (1)
  3. F420 dependent oxidoreductases [51687] (3)
    1. Coenzyme F420 dependent tetrahydromethanopterin reductase [51688]
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [51689] (1)
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63924] (1)
    2. Coenzyme F420 dependent secondary alcohol dehydrogenase [102101]
      1. Archaeon Methanoculleus thermophilicus [TaxId: 2200] [102102] (1)
  4. Ssud-like monoxygenases [82275] (2)
    1. Alkanesulfonate monooxygenase SsuD [82276]
      1. Escherichia coli [TaxId: 562] [82277] (2)
    2. Putative monooxygenase YtnJ [110380]
      1. Bacillus subtilis [TaxId: 1423] [110381] (2)
        SQ O34974
18. Nicotinate/Quinolinate PRTase C-terminal domain-like [51690] (2)
  incomplete beta/alpha barrel with parallel beta-sheet of 7 strands
  uperfamily
  1. NadC C-terminal domain-like [51691] (6)
    1. Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain [51692]
      1. Salmonella typhimurium [TaxId: 90371] [51693] (1)
      2. Mycobacterium tuberculosis [TaxId: 1773] [51694] (4)
      3. Thermotoga maritima [TaxId: 2336] [89507] (1)
        TM1645
    2. Nicotinate-nucleotide pyrophosphorylase PF1904 [141857]
      1. Pyrococcus furiosus [TaxId: 2261] [141858] (6)
        SQ Q8TZS9 111-389
    3. Putative nicotinate phosphoribosyltransferase EF2626 [141859]
      includes extra C-terminal region that wraps around the N-terminal domain and contains an all-beta domain, this domain is distinct from but probably related to the Ta1145 extra domain
      1. Enterococcus faecalis [TaxId: 1351] [141860] (1)
        SQ Q830Y8 141-485
    4. Nicotinate phosphoribosyltransferase Ta1145 [141861]
      includes extra C-terminal region that wraps around the N-terminal domain and contains a rubredoxin-like subdomain
      1. Thermoplasma acidophilum [TaxId: 2303] [141862] (1)
        SQ Q9HJ28 120-389
  2. Monomeric nicotinate phosphoribosyltransferase C-terminal domain [110910] (3)
    1. Nicotinate phosphoribosyltransferase, C-terminal domain [110911]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110912] (1)
        SQ P39683
      2. Agrobacterium tumefaciens [TaxId: 358] [117391] (1)
        SQ Q8UIS9
      3. Pseudomonas aeruginosa [TaxId: 287] [141863] (4)
        SQ Q9HW26 143-397
        NAPRTase 2
19. PLC-like phosphodiesterases [51695] (3)
  uperfamily
  1. Mammalian PLC [51696] (2)
    1. Phospholipase C isozyme D1 (PLC-D1) [51697]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51698] (10)
    2. Phospholipase C-beta-2 [159421]
      1. Human (Homo sapiens) [TaxId: 9606] [159422] (2)
        SQ Q00722 312-660
  2. Bacterial PLC [51699] (2)
    1. Phosphatidylinositol-specific phospholipase C [51700]
      1. Bacillus cereus [TaxId: 1396] [51701] (9)
      2. Listeria monocytogenes [TaxId: 1639] [51702] (2)
  3. Glycerophosphoryl diester phosphodiesterase [89508] (4)
    Pfam 03009
    1. Hypothetical protein TM1621 [89509]
      1. Thermotoga maritima [TaxId: 2336] [89510] (1)
    2. Glycerophosphodiester phosphodiesterase GlpQ [110382]
      1. Escherichia coli [TaxId: 562] [110383] (3)
        SQ P09394
    3. Putative glycerophosphodiester phosphodiesterase TTHB141 [141864]
      1. Thermus thermophilus [TaxId: 274] [141865] (2)
        SQ Q53W25 8-224
    4. Glycerophosphodiester phosphodiesterase UgpQ [141866]
      1. Agrobacterium tumefaciens [TaxId: 358] [141867] (4)
        SQ Q8U887 1-240
20. Cobalamin (vitamin B12)-dependent enzymes [51703] (4)
  uperfamily
  1. Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [51704] (2)
    the subunits are clearly related but only one (alpha) is active
    1. Methylmalonyl-CoA mutase alpha subunit, domain 1 [88709]
      1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88710] (8)
    2. Methylmalonyl-CoA mutase beta subunit, domain 1 [88711]
      the subunits are clearly related but only one (alpha) is active
      1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88712] (8)
  2. Glutamate mutase, large subunit [51707] (1)
    1. Glutamate mutase, large subunit [51708]
      1. Clostridium cochlearium [TaxId: 1494] [51709] (3)
  3. Diol dehydratase, alpha subunit [51710] (2)
    1. Diol dehydratase, alpha subunit [51711]
      1. Klebsiella oxytoca [TaxId: 571] [51712] (7)
      2. Klebsiella pneumoniae [TaxId: 573] [82278] (2)
  4. D-lysine 5,6-aminomutase alpha subunit, KamD [117392] (1)
    most similar to the glutamate mutase subunit; contains second cofactor, PLP
    1. D-lysine 5,6-aminomutase alpha subunit, KamD [117393]
      1. Clostridium sticklandii [TaxId: 1511] [117394] (1)
        SQ Q9ZFE6
21. tRNA-guanine transglycosylase [51713] (1)
  uperfamily
  1. tRNA-guanine transglycosylase [51714] (2)
    1. Queosine tRNA-guanine transglycosylase [51715]
      contains zinc-binding subdomain
      1. Zymomonas mobilis [TaxId: 542] [51716] (34)
        SQ P28720
    2. Archaeosine tRNA-guanine transglycosylase, N-terminal domain [75096]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75097] (4)
22. Dihydropteroate synthetase-like [51717] (2)
  uperfamily
  1. Dihydropteroate synthetase [51718] (4)
    1. Dihydropteroate synthetase [51719]
      1. Escherichia coli [TaxId: 562] [51720] (3)
      2. Staphylococcus aureus [TaxId: 1280] [51721] (2)
      3. Mycobacterium tuberculosis [TaxId: 1773] [51722] (1)
      4. Bacillus anthracis [TaxId: 1392] [102103] (5)
        SQ Q81VW8
  2. Methyltetrahydrofolate-utiluzing methyltransferases [51723] (2)
    1. Methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase MetR [51724]
      1. Moorella thermoacetica [TaxId: 1525] [51725] (1)
    2. Cobalamin-dependent methionine synthase MetH, C-terminal domain [102104]
      5-methyltetrahydrofolate homocysteine S-methyltransferase
      1. Thermotoga maritima [TaxId: 2336] [102105] (10)
23. UROD/MetE-like [51726] (2)
  uperfamily
  1. Uroporphyrinogen decarboxylase, UROD [51727] (2)
    1. Uroporphyrinogen decarboxylase, UROD [51728]
      1. Human (Homo sapiens) [TaxId: 9606] [51729] (11)
      2. Tobacco (Nicotiana tabacum), UROD-III [TaxId: 4097] [69405] (1)
  2. Cobalamin-independent methionine synthase [110384] (1)
    Pfam 01717; duplication; consists of two related domains
    1. 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE [110385]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110386] (4)
        SQ O50008
24. FAD-linked oxidoreductase [51730] (2)
  distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation
  uperfamily
  1. Methylenetetrahydrofolate reductase [51731] (2)
    1. Methylenetetrahydrofolate reductase [51732]
      1. Escherichia coli [TaxId: 562] [51733] (1)
      2. Thermus thermophilus [TaxId: 274] [102106] (1)
  2. Proline dehydrohenase domain of bifunctional PutA protein [82279] (1)
    1. Proline dehydrohenase domain of bifunctional PutA protein [82280]
      1. Escherichia coli [TaxId: 562] [82281] (7)
        SQ P09546 87-610
25. Monomethylamine methyltransferase MtmB [75098] (1)
  uperfamily
  1. Monomethylamine methyltransferase MtmB [75099] (1)
    1. Monomethylamine methyltransferase MtmB [75100]
      contains a UAG-encoded L-pyrrolysine residue
      1. Archaeon Methanosarcina barkeri [TaxId: 2208] [75101] (5)
        SQ O30642
26. Homocysteine S-methyltransferase [82282] (1)
  uperfamily
  1. Homocysteine S-methyltransferase [82283] (3)
    Pfam 02574
    1. Betaine-homocysteine S-methyltransferase [82284]
      1. Human (Homo sapiens) [TaxId: 9606] [82285] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [102107] (1)
    2. Cobalamin-dependent methionine synthase MetH, N-terminal domain [102108]
      5-methyltetrahydrofolate homocysteine S-methyltransferase
      1. Thermotoga maritima [TaxId: 2336] [102109] (10)
27. (2r)-phospho-3-sulfolactate synthase ComA [102110] (1)
  uperfamily
  1. (2r)-phospho-3-sulfolactate synthase ComA [102111] (2)
    1. (2r)-phospho-3-sulfolactate synthase ComA [102112]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [102113] (1)
      2. Bacillus subtilis [TaxId: 1423] [110387] (1)
        SQ O06739
28. Radical SAM enzymes [102114] (3)
  common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel
  uperfamily
  1. Biotin synthase [102115] (1)
    regular (beta/alpha)8 barrel
    1. Biotin synthase [102116]
      1. Escherichia coli [TaxId: 562] [102117] (1)
  2. Oxygen-independent coproporphyrinogen III oxidase HemN [102118] (1)
    open beta/alpha barrel decorated with additional structures
    1. Oxygen-independent coproporphyrinogen III oxidase HemN [102119]
      1. Escherichia coli [TaxId: 562] [102120] (1)
  3. MoCo biosynthesis proteins [110388] (1)
    open alpha/beta-barrel with a specific second FeS cluster-binding region corresponding to Pfam 06463
    1. Molybdenum cofactor biosynthesis protein A MoaA [110389]
      1. Staphylococcus aureus [TaxId: 1280] [110390] (4)
        SQ P69848
29. GlpP-like [110391] (1)
  uperfamily
  1. GlpP-like [110392] (1)
    Pfam 04309
    1. Glycerol uptake operon antiterminator-related protein TM1436 [110393]
      1. Thermotoga maritima [TaxId: 2336] [110394] (1)
        SQ Q9X1F0
30. CutC-like [110395] (1)
  uperfamily
  1. CutC-like [110396] (1)
    Pfam 03932
    1. Copper homeostasis protein CutC [110397]
      1. Shigella flexneri [TaxId: 623] [110398] (5)
        SQ P67825
31. ThiG-like [110399] (1)
  shares the common phosphate-binding site with other superfamilies
  uperfamily
  1. ThiG-like [110400] (2)
    Pfam 05690
    1. Thiazole biosynthesis protein ThiG [110401]
      1. Bacillus subtilis [TaxId: 1423] [110402] (2)
        SQ O31618
      2. Pseudomonas aeruginosa [TaxId: 287] [117395] (1)
        SQ Q9I6B4 9-251
32. TM1631-like [117396] (1)
  uperfamily
  1. TM1631-like [117397] (2)
    Pfam 01904; DUF72
    1. Hypothetical protein TM1631 [117398]
      1. Thermotoga maritima [TaxId: 2336] [117399] (1)
        SQ Q9X1W6
    2. Hypothetical protein EF0366 [117400]
      1. Enterococcus faecalis [TaxId: 1351] [117401] (1)
        SQ Q838R9 1-265
33. EAL domain-like [141868] (1)
  variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest
  uperfamily
  1. EAL domain [141869] (1)
    Pfam 00563
    1. Hypothetical protein YkuI, N-terminal domain [141870]
      1. Bacillus subtilis [TaxId: 1423] [141871] (2)
        SQ O35014 2-262
NAD(P)-binding Rossmann-fold domains [51734] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
The nucleotide-binding modes of this and the next two folds/superfamilies are similar
1. NAD(P)-binding Rossmann-fold domains [51735] (12)
  uperfamily
  1. Alcohol dehydrogenase-like, C-terminal domain [51736] (28)
    N-terminal all-beta domain defines family
    1. Alcohol dehydrogenase [51737]
      1. Horse (Equus caballus) [TaxId: 9796] [51738] (38)
        SQ P00327
      2. Human (Homo sapiens), different isozymes [TaxId: 9606] [51739] (26)
        SQ P00326 ! SQ P00325 ! SQ P07327
      3. Mouse (Mus musculus), class II [TaxId: 10090] [51740] (3)
      4. Frog (Rana perezi) [TaxId: 8403] [89511] (2)
      5. Cod (Gadus callarias) [TaxId: 8053] [51741] (1)
      6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82286] (4)
      7. Archaeon Aeropyrum pernix [TaxId: 56636] [102121] (1)
      8. Pseudomonas aeruginosa [TaxId: 287] [102122] (1)
      9. Bacillus stearothermophilus [TaxId: 1422] [102123] (1)
    2. Hypothetical protein TM0436 [102124]
      1. Thermotoga maritima [TaxId: 2336] [102125] (1)
    3. Hypothetical protein YhdH [102126]
      1. Escherichia coli [TaxId: 562] [102127] (2)
        SQ P26646
    4. Hypothetical protein YahK [102128]
      1. Escherichia coli [TaxId: 562] [102129] (1)
    5. Benzyl alcohol dehydrogenase [89512]
      1. Acinetobacter calcoaceticus [TaxId: 471] [89513] (1)
    6. Bacterial secondary alcohol dehydrogenase [51742]
      1. Clostridium beijerinckii [TaxId: 1520] [51743] (3)
      2. Thermoanaerobacter brockii [TaxId: 29323] [51744] (10)
    7. Ketose reductase (sorbitol dehydrogenase) [51745]
      1. Silverleaf whitefly (Bemisia argentifolii) [TaxId: 77855] [51746] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [102130] (3)
    8. Formaldehyde dehydrogenase [82287]
      1. Pseudomonas putida [TaxId: 303] [82288] (1)
    9. Quinone oxidoreductase [51747]
      1. Escherichia coli [TaxId: 562] [51748] (1)
      2. Thermus thermophilus [TaxId: 274] [89514] (2)
      3. Human (Homo sapiens) [TaxId: 9606] [117402] (1)
        SQ Q08257
    10. Putative enoyl reductase domain of polyketide synthase [89515]
      1. Mycobacterium tuberculosis [TaxId: 1773] [89516] (1)
    11. 2,4-dienoyl-CoA reductase [89517]
      1. Yeast (Candida tropicalis) [TaxId: 5482] [89518] (5)
    12. Putative zinc-binding alcohol dehydrogenase [102131]
      1. Mouse (Mus musculus) [TaxId: 10090] [102132] (1)
    13. Cinnamyl alcohol dehydrogenase, ADH6 [110403]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110404] (3)
        SQ Q04894
    14. Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase [110405]
      1. Guinea pig (Cavia porcellus) [TaxId: 10141] [110406] (5)
        SQ Q9EQZ5
    15. B. subtilis YhfP homologue [117403]
      1. Bacillus stearothermophilus [TaxId: 1422] [117404] (1)
        SQ Q5L022; 96% sequence identity; Geobacillus kaustophilus TaxID:1462
    16. Hypothetical protein YhfP [117405]
      1. Bacillus subtilis [TaxId: 1423] [117406] (2)
        SQ O07615
  2. Tyrosine-dependent oxidoreductases [51751] (108)
    also known as short-chain dehydrogenases and SDR family
    parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7
    1. Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase) [51752]
      1. Escherichia coli [TaxId: 562] [51753] (17)
      2. Human (Homo sapiens) [TaxId: 9606] [51754] (7)
      3. Trypanosoma brucei [TaxId: 5691] [89519] (5)
      4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141872] (1)
        SQ P04397 11-357
        N-terminal domain of bifunctional Gal10 protein
    2. dTDP-glucose 4,6-dehydratase (RmlB) [51755]
      1. Escherichia coli [TaxId: 562] [51756] (1)
      2. Salmonella enterica [TaxId: 28901] [63925] (1)
      3. Streptococcus suis, serotype 2 [TaxId: 1307] [69406] (6)
      4. Streptomyces venezuelae [TaxId: 54571] [102133] (2)
    3. dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) [75102]
      1. Salmonella enterica serovar typhimurium [TaxId: 90371] [75103] (4)
    4. GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase) [51757]
      1. Escherichia coli [TaxId: 562] [51758] (8)
    5. GDP-mannose 4,6-dehydratase [51759]
      1. Escherichia coli [TaxId: 562] [51760] (1)
      2. Pseudomonas aeruginosa [TaxId: 287] [102134] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [102135] (1)
      4. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [82289] (2)
    6. ADP-L-glycero-D-mannoheptose 6-epimerase [51761]
      1. Escherichia coli [TaxId: 562] [51762] (1)
    7. CDP-glucose-4,6-dehydratase [102136]
      1. Yersinia pseudotuberculosis [TaxId: 633] [102137] (1)
      2. Salmonella typhimurium [TaxId: 90371] [141873] (2)
        SQ P26397 2-356
    8. CDP-tyvelose-2-epimerase [102138]
      1. Salmonella typhi [TaxId: 90370] [102139] (1)
    9. Phenylcoumaran benzylic ether reductase [102140]
      1. Loblolly pine (Pinus taeda) [TaxId: 3352] [102141] (1)
    10. Pinoresinol-lariciresinol reductase [102142]
      1. Giant arborvitae (Thuja plicata) [TaxId: 3316] [102143] (1)
    11. Sulfolipid biosynthesis protein SQD1 [51763]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [51764] (4)
    12. Negative transcriptional regulator NmrA [69407]
      has an UDP-galactose 4-epimerase-like structure but evolved a different function
      1. Aspergillus nidulans [TaxId: 162425] [69408] (29)
        SQ O59919
    13. Carbonyl reductase [51765]
      1. Mouse (Mus musculus) [TaxId: 10090] [51766] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [102144] (5)
        dicarbonyl/L-xylulose reductase
    14. Sepiapterin reductase [51767]
      1. Mouse (Mus musculus) [TaxId: 10090] [51768] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [141874] (6)
        SQ P35270 5-261
    15. Dihydropteridin reductase (pteridine reductase) [51769]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51770] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [51771] (1)
      3. Leishmania major [TaxId: 5664] [63926] (35)
        SQ Q01782
      4. Leishmania tarentolae [TaxId: 5689] [102145] (1)
      5. Trypanosoma cruzi [TaxId: 5693] [102146] (2)
      6. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89520] (1)
    16. Human estrogenic 17beta-hydroxysteroid dehydrogenase [51772]
      1. Human (Homo sapiens) [TaxId: 9606] [51773] (16)
        SQ P14061
    17. 7-alpha-hydroxysteroid dehydrogenase [51774]
      1. Escherichia coli [TaxId: 562] [51775] (3)
    18. 3-alpha,20-beta-hydroxysteroid dehydrogenase [51776]
      1. Streptomyces hydrogenans [TaxId: 1905] [51777] (2)
    19. 3-alpha-hydroxysteroid dehydrogenase [51778]
      1. Comamonas testosteroni [TaxId: 285] [51779] (2)
    20. 3beta/17beta hydroxysteroid dehydrogenase [82290]
      1. Comamonas testosteroni [TaxId: 285] [82291] (1)
    21. Putative oxidoreductase Rv2002 [82292]
      1. Mycobacterium tuberculosis [TaxId: 1773] [82293] (3)
    22. R-specific alcohol dehydrogenase [89521]
      1. Lactobacillus brevis [TaxId: 1580] [89522] (15)
    23. Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase [51780]
      1. Pseudomonas sp., lb400 [TaxId: 306] [51781] (1)
    24. Drosophila alcohol dehydrogenase [51782]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102147] (1)
      2. Fly (Drosophila lebanonensis) [TaxId: 7225] [51783] (7)
    25. Glucose dehydrogenase [51784]
      1. Bacillus megaterium [TaxId: 1404] [51785] (4)
    26. Sorbitol dehydrogenase [102148]
      1. Rhodobacter sphaeroides [TaxId: 1063] [102149] (1)
    27. meso-2,3-butanediol dehydrogenase [51786]
      1. Klebsiella pneumoniae [TaxId: 573] [51787] (1)
    28. Levodione reductase [89523]
      1. Corynebacterium aquaticum [TaxId: 144185] [89524] (1)
    29. Mannitol dehydrogenase [63927]
      1. Mushroom (Agaricus bisporus) [TaxId: 5341] [63928] (1)
    30. (3R)-hydroxyacyl-CoA dehydrogenase domain of estradiol 17 beta-Dehydrogenase 4 [82294]
      peroxisomal multifunctional enzyme type 2
      segment swapping involving a C-terminal extension to the family fold
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82295] (1)
    31. beta-keto acyl carrier protein reductase [51788]
      1. Oil seed rape (Brassica napus) [TaxId: 3708] [51789] (7)
      2. Escherichia coli [TaxId: 562] [51790] (3)
      3. Thermotoga maritima [TaxId: 2336] [102150] (1)
        TM1169
      4. Thermus thermophilus [TaxId: 274] [117407] (1)
        SQ Q5SK98
      5. Streptomyces coelicolor [TaxId: 1902] [117408] (9)
        SQ P16544 #SP
      6. Mycobacterium tuberculosis [TaxId: 1773] [141875] (6)
        SQ P0A5Y4 9-245! SQ P0A5Y4 9-247
      7. Thermus thermophilus, TTHB020 [TaxId: 274] [141876] (2)
        SQ Q53WH2 2-242
      8. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141877] (1)
        SQ Q86RB1 54-304
    32. Enoyl-ACP reductase [51791]
      1. Oil seed rape (Brassica napus) [TaxId: 3708] [51792] (4)
      2. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [82296] (27)
        SQ Q9BJJ9 96-424 # fragment
      3. Mycobacterium tuberculosis, TB, gene InhA [TaxId: 1773] [51793] (44)
      4. Escherichia coli [TaxId: 562] [51794] (14)
      5. Helicobacter pylori [TaxId: 210] [102151] (8)
      6. Thermus thermophilus [TaxId: 274] [117409] (9)
        SQ Q5SLI9
    33. Tropinone reductase [51795]
      1. Jimsonweed (Datura stramonium), I [TaxId: 4076] [51796] (1)
      2. Jimsonweed (Datura stramonium), II [TaxId: 4076] [51797] (4)
      3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117410] (2)
        SQ Q9ASX2
    34. 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase) [51798]
      1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51799] (4)
    35. 1,3,6,8-tetrahydroxynaphthalene reductase [63929]
      1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [63930] (1)
    36. Biliverdin IX beta reductase [63931]
      Histidine in the active site instead of the Tyr-Lys dyad
      1. Human (Homo sapiens) [TaxId: 9606] [63932] (5)
    37. Type II 3-hydroxyacyl-CoA dehydrogenase [63933]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [63934] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [102152] (4)
        SQ Q99714
      3. Thermus thermophilus [TaxId: 274] [89525] (1)
    38. Carbonyl reductase/20beta-hydroxysteroid dehydrogenase [63935]
      1. Pig (Sus scrofa) [TaxId: 9823] [63936] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [141878] (4)
        SQ P16152 2-276
    39. Halohydrin dehalogenase HheC [102153]
      haloalcohol dehalogenase: evolved a new activity; lost the NAD-binding site
      1. Agrobacterium tumefaciens [TaxId: 358] [102154] (23)
    40. Glucose dehydrogenase (5l265) [102155]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102156] (1)
    41. UDP-N-acetylglucosamine 4-epimerase WbpP [110407]
      1. Pseudomonas aeruginosa [TaxId: 287] [110408] (2)
        SQ Q8KN66 # list: Q8GGB8 Q9RHD6 99% identity
    42. DTDP-4-dehydrorhamnose reductase RfbD [110409]
      1. Clostridium acetobutylicum [TaxId: 1488] [110410] (1)
        SQ Q97GQ1
    43. Gluconate 5-dehydrogenase [110411]
      1. Thermotoga maritima [TaxId: 2336] [110412] (1)
        SQ Q9WYS2
    44. Carbonyl reductase sniffer [110413]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110414] (1)
        SQ Q9W3H4 # cg10964-pa
    45. Hypothetical protein F25D1.5 [110415]
      1. Caenorhabditis elegans [TaxId: 6239] [110416] (1)
        SQ Q19774
    46. Putative dehydrogenase ARPG836 (MGC4172) [117411]
      1. Human (Homo sapiens) [TaxId: 9606] [117412] (1)
        SQ Q6UWP2
    47. Aldehyde reductase II [117413]
      1. Sporobolomyces salmonicolor [TaxId: 5005] [117414] (5)
        SQ Q9UUN9
    48. Hypothetical protein R05D8.7 [117415]
      1. Caenorhabditis elegans [TaxId: 6239] [117416] (1)
        SQ Q9N5G4
    49. Hypothetical protein At5g02240 (T7H20_290) [117417]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117418] (7)
        SQ Q94EG6
    50. Polymyxin resistance protein ArnA (PrmI) [117419]
      evolved new activities: UDP-glucuronic acid decarboxylase, UDP-4-amino-4-deoxy-L-arabinose formyltransferase
      1. Escherichia coli [TaxId: 562] [117420] (12)
        SQ P77398
    51. 2,4-dienoyl-CoA reductase, mitochondrial (DECR) [117421]
      1. Human (Homo sapiens), [TaxId: 9606] [117422] (3)
        SQ Q16698 35-328
    52. 11-beta-hydroxysteroid dehydrogenase 1 [117423]
      1. Human (Homo sapiens) [TaxId: 9606] [117424] (37)
        SQ P28845
      2. Guinea pig (Cavia porcellus) [TaxId: 10141] [117425] (1)
        SQ Q6QLL4 23-296
      3. Mouse (Mus musculus) [TaxId: 10090] [141879] (4)
        SQ P50172 24-298
    53. 17-beta-hydroxysteroid dehydrogenase type XI [117426]
      1. Human (Homo sapiens) [TaxId: 9606] [117427] (1)
        SQ Q8NBQ5 30-273
    54. UDP-glucuronate decarboxylase 1 [141880]
      1. Human (Homo sapiens) [TaxId: 9606] [141881] (1)
        SQ Q8NBZ7 87-398
    55. Xylitol dehydrogenase [141882]
      1. Gluconobacter oxydans [TaxId: 442] [141883] (8)
        SQ Q8GR61 3-262
    56. Peroxisomal trans 2-enoyl CoA reductase [141884]
      1. Human (Homo sapiens) [TaxId: 9606] [141885] (4)
        SQ Q9BY49 7-303
    57. D(-)-3-hydroxybutyrate dehydrogenase [141886]
      1. Pseudomonas fragi [TaxId: 296] [141887] (3)
        SQ Q5KST5 1-260
    58. 15-hydroxyprostaglandin dehydrogenase, PGDH [141888]
      1. Human (Homo sapiens) [TaxId: 9606] [141889] (1)
        SQ P15428 3-256
    59. GDP-mannose-3', 5'-epimerase [141890]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141891] (8)
        SQ Q93VR3 13-374! SQ Q93VR3 13-375
    60. Bacterial sepiapterin reductase [141892]
      1. Chlorobium tepidum [TaxId: 1097] [141893] (4)
        SQ Q8KES3 2-241
        CT0609
    61. Dehydrogenase/reductase SDR family member 6, DHRS6 [141894]
      Oxidoreductase UCPA
      1. Human (Homo sapiens) [TaxId: 9606] [141895] (4)
        SQ Q9BUT1 1-245
    62. Hypothetical protein TTHA0369 [141896]
      TT0321
      1. Thermus thermophilus [TaxId: 274] [141897] (4)
        SQ Q5SLC4 2-249
    63. Rhizome secoisolariciresinol dehydrogenase [141898]
      1. Mayapple (Podophyllum peltatum) [TaxId: 35933] [141899] (4)
        SQ Q94KL8 11-278
    64. Peroxisomal multifunctional enzyme type 2 [141900]
      17-beta-hydroxysteroid dehydrogenase 4
      1. Human (Homo sapiens) [TaxId: 9606] [141901] (6)
        SQ P51659 2-303
        the structure of C-terminal domain is also known, PDB entry 1S9C
    65. (s)-1-phenylethanol dehydrogenase [141902]
      1. Azoarcus sp. ebn1 [TaxId: 76114] [141903] (6)
        SQ Q5P5I4 3-249
    66. TAT-interacting protein TIP30 [141904]
      1. Human (Homo sapiens) [TaxId: 9606] [141905] (1)
        SQ Q9BUP3 5-236
      2. Mouse (Mus musculus) [TaxId: 10090] [141906] (1)
        SQ Q9Z2G9 7-236
    67. Retinal dehydrogenase/reductase 3 [141907]
      1. Human (Homo sapiens) [TaxId: 9606] [141908] (16)
        SQ Q9BPX1 4-253
    68. Erythromycin synthase, eryAI, 1st ketoreductase module [141909]
      tandem repeat of two SDR-like modules resembling a dimer commonly founf in the family; only the second module retains the coenzyme-binding site
      1. Saccharopolyspora erythraea [TaxId: 1836] [141910] (4)
        SQ Q5UNP6 1448-1656! SQ Q5UNP6 1657-1915
    69. Hypothetical protein PA4017 [141911]
      unknown function; the active site region is blocked by a loop; strong sequence similarity to mammalian TAT-interacting protein TIP30
      1. Pseudomonas aeruginosa [TaxId: 287] [141912] (2)
        SQ Q9HX10 4-215
    70. Putative carbonyl reductase sniffer [141913]
      1. Caenorhabditis elegans [TaxId: 6239] [141914] (6)
        SQ P90780 1-250
  3. Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain [51800] (52)
    family members also share a common alpha+beta fold in C-terminal domain
    1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [51801]
      1. Escherichia coli [TaxId: 562] [51802] (13)
        SQ P06977
      2. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [51803] (14)
      3. Achromobacter xylosoxidans [TaxId: 85698] [89526] (1)
        formerly Alcaligenes xylosoxidans
      4. Thermus aquaticus [TaxId: 271] [51804] (13)
      5. Thermus thermophilus [TaxId: 274] [102157] (1)
      6. Thermotoga maritima [TaxId: 2336] [51805] (1)
      7. Archaeon Sulfolobus solfataricus [TaxId: 2287] [51806] (1)
      8. Archaeon Methanothermus fervidus [TaxId: 2180] [51807] (1)
      9. Trypanosoma brucei brucei, glycosome [TaxId: 5702] [51808] (1)
      10. Trypanosoma cruzi [TaxId: 5693] [75104] (7)
      11. Leishmania mexicana [TaxId: 5665] [51809] (5)
      12. American lobster (Homarus americanus) [TaxId: 6706] [51810] (2)
      13. South China Sea lobster (Palinurus versicolor) [TaxId: 150436] [51811] (5)
      14. Human (Homo sapiens) [TaxId: 9606] [51812] (1)
      15. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [102158] (1)
      16. Spinach (Spinacia oleracea) [TaxId: 3562] [69409] (24)
        SQ P19866
      17. Human(Homo sapiens), liver isoform [TaxId: 9606] [141915] (8)
        SQ P04406 2-150,315-334
      18. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141916] (12)
        SQ Q8IKK7 4-152,319-335! SQ Q8T6B1 1-152,319-337
      19. Archaeon Pyrococcus horikoshii [TaxId: 53953] [159423] (4)
        SQ O59494 1-139,302-334
    2. Aspartate beta-semialdehyde dehydrogenase [51813]
      1. Escherichia coli [TaxId: 562] [51814] (4)
        SQ P00353
      2. Vibrio cholerae [TaxId: 666] [82297] (2)
      3. Haemophilus influenzae [TaxId: 727] [102159] (12)
        SQ P44801
      4. Streptococcus pneumoniae [TaxId: 1313] [141917] (11)
        SQ Q8DQ00 2-127,330-357
    3. Acetaldehyde dehydrogenase (acylating) [89527]
      1. Pseudomonas sp. [TaxId: 306] [89528] (1)
    4. Homoserine dehydrogenase [51815]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51816] (4)
        SQ P31116
    5. Saccharopine reductase [51817]
      1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51818] (3)
    6. Diaminopimelic acid dehydrogenase (DAPDH) [51819]
      1. Corynebacterium glutamicum [TaxId: 1718] [51820] (4)
    7. Dihydrodipicolinate reductase [51821]
      1. Escherichia coli [TaxId: 562] [51822] (5)
      2. Mycobacterium tuberculosis [TaxId: 1773] [102160] (14)
      3. Thermotoga maritima [TaxId: 2336] [110417] (1)
        SQ Q9X1K8
    8. Myo-inositol 1-phosphate synthase [75105]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75106] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75107] (9)
        SQ P11986
      3. Archaeoglobus fulgidus [TaxId: 2234] [110418] (1)
        SQ O28480
      4. Caenorhabditis elegans [TaxId: 6239] [110419] (1)
        SQ Q18664
    9. Hypothetical protein TM1419 [102161]
      myo-inositol 1-phosphate synthase-related protein
      1. Thermotoga maritima [TaxId: 2336] [102162] (1)
    10. Hypothetical protein TM1643 [75108]
      1. Thermotoga maritima [TaxId: 2336] [75109] (2)
    11. 1-deoxy-D-xylulose-5-phosphate reductoisomerase [69410]
      1. Escherichia coli [TaxId: 562] [69411] (12)
        SQ P45568
      2. Zymomonas mobilis [TaxId: 542] [110420] (2)
        SQ Q9X5F2
    12. Biliverdin reductase [51823]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51824] (3)
    13. Glucose-fructose oxidoreductase, N-terminal domain [51825]
      1. Zymomonas mobilis [TaxId: 542] [51826] (12)
    14. Glucose 6-phosphate dehydrogenase, N-terminal domain [51827]
      1. Leuconostoc mesenteroides [TaxId: 1245] [51828] (9)
      2. Human (Homo sapiens) [TaxId: 9606] [51829] (1)
    15. Virulence factor MviM [110421]
      1. Escherichia coli [TaxId: 562] [110422] (1)
        SQ P75931
    16. N-acetyl-gamma-glutamyl-phosphate reductase ArgC [110423]
      1. Thermotoga maritima [TaxId: 2336] [110424] (1)
        SQ Q9X2A2
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117428] (5)
        SQ O82187 15-359
      3. Salmonella typhimurium [TaxId: 90371] [141918] (1)
        SQ Q8ZKL8 1-153,309-334
    17. Putative oxidoreductase VCA1048 [110425]
      1. Vibrio cholerae [TaxId: 666] [110426] (1)
        SQ Q9KKQ4
    18. Probable oxidoreductase At4g09670 [117429]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117430] (1)
        SQ Q9SZ83
    19. Putative semialdehyde dehydrogenase [141919]
      1. Rice (Oryza sativa) [TaxId: 4530] [141920] (4)
        SQ Q6AV34 68-218,384-415
    20. Galactose/lactose metabolism regulatory protein GAL80 [141921]
      1. Yeast (Kluyveromyces lactis) [TaxId: 28985] [141922] (9)
        SQ Q06433 2-154,374-457
    21. Usg-1 protein homolog PA3116 [141923]
      1. Pseudomonas aeruginosa [TaxId: 287] [141924] (1)
        SQ O87014 3-129,320-336
    22. Hypothetical protein TM0312 [141925]
      1. Thermotoga maritima [TaxId: 2336] [141926] (2)
        SQ Q9WYE8 4-131,276-328
  4. Formate/glycerate dehydrogenases, NAD-domain [51830] (14)
    this domain interrupts the other domain which defines family
    1. Formate dehydrogenase [51831]
      1. Pseudomonas sp., strain 101 [TaxId: 306] [51832] (2)
    2. Putative formate dehydrogenase [51833]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [51834] (1)
    3. Transcription corepressor CtbP [82298]
      C-terminal binding protein 1; a dehydrogenase
      1. Human (Homo sapiens), Ctbp1 [TaxId: 9606] [82299] (1)
      2. Rat (Rattus norvegicus), Ctbp3 [TaxId: 10116] [89529] (2)
    4. D-2-hydroxyisocaproate dehydrogenase [51835]
      1. Lactobacillus casei [TaxId: 1582] [51836] (1)
    5. D-glycerate dehydrogenase [51837]
      1. Hyphomicrobium methylovorum [TaxId: 84] [51838] (1)
    6. Phosphoglycerate dehydrogenase [51839]
      has additional C-terminal domain of the ferredoxin fold
      1. Escherichia coli [TaxId: 562] [51840] (18)
      2. Mycobacterium tuberculosis [TaxId: 1773] [141927] (2)
        SQ P0A544 98-281
    7. D-lactate dehydrogenase [51841]
      1. Lactobacillus helveticus [TaxId: 1587] [51842] (3)
    8. L-alanine dehydrogenase [51843]
      1. Phormidium lapideum [TaxId: 32060] [51844] (3)
    9. Nicotinamide nucleotide transhydrogenase dI component [63937]
      L-alanine dehydrogenase homologue
      1. Rhodospirillum rubrum [TaxId: 1085] [63938] (28)
    10. S-adenosylhomocystein hydrolase [51845]
      1. Human (Homo sapiens) [TaxId: 9606] [51846] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [51847] (17)
      3. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117431] (1)
        SQ P50250
  5. Siroheme synthase N-terminal domain-like [75110] (2)
    1. Siroheme synthase CysG, domain 1 [102163]
      1. Salmonella typhimurium [TaxId: 90371] [102164] (3)
    2. Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain [75111]
      involved in siroheme synthesis
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75112] (1)
  6. LDH N-terminal domain-like [51848] (33)
    1. Malate dehydrogenase [51849]
      1. Pig (Sus scrofa) [TaxId: 9823] [51850] (3)
      2. Sorghum (Sorghum vulgare), chloroplast [TaxId: 4558] [51851] (1)
      3. Flaveria bidentis, chloroplast [TaxId: 4224] [51852] (1)
      4. Escherichia coli [TaxId: 562] [51853] (8)
      5. Thermus flavus [TaxId: 274] [51854] (2)
      6. Thermus thermophilus [TaxId: 274] [82300] (9)
        identical sequence to that from the Thermus flavus enzyme
      7. Archaeon Haloarcula marismortui [TaxId: 2238] [51855] (17)
      8. Aquaspirillum arcticum [TaxId: 87645] [51856] (3)
      9. Chloroflexus aurantiacus [TaxId: 1108] [69415] (7)
        SQ P80040
      10. Chlorobium tepidum [TaxId: 1097] [69416] (1)
      11. Chlorobium vibrioforme [TaxId: 1098] [69417] (2)
      12. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110427] (2)
        SQ O08349
    2. L-2-hydroxyisocapronate dehydrogenase, L-HICDH [51857]
      1. Lactobacillus confusus [TaxId: 1583] [51858] (1)
    3. Lactate dehydrogenase [51859]
      1. Pig (Sus scrofa) [TaxId: 9823] [51860] (3)
      2. Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606] [63939] (2)
      3. Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606] [63940] (1)
      4. Mouse (Mus musculus) [TaxId: 10090] [51861] (4)
      5. Dogfish (Squalus acanthias) [TaxId: 7797] [51862] (3)
      6. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [51863] (9)
      7. Plasmodium berghei [TaxId: 5821] [102165] (7)
      8. Toxoplasma gondii [TaxId: 5811] [102166] (4)
      9. Bacillus stearothermophilus [TaxId: 1422] [51864] (9)
      10. Lactobacillus casei [TaxId: 1582] [51865] (1)
      11. Lactobacillus pentosus [TaxId: 1589] [69418] (1)
      12. Bifidobacterium longum, strain am101-2 [TaxId: 216816] [51866] (2)
      13. Thermotoga maritima [TaxId: 2336] [51867] (1)
      14. Clostridium thermocellum [TaxId: 1515] [117432] (1)
        SQ Q4CDK5
    4. MJ0490, lactate/malate dehydrogenase [63941]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63942] (2)
    5. Alpha-glucosidase AglA [89530]
      1. Thermotoga maritima [TaxId: 2336] [89531] (1)
        TM1834
    6. Putative alpha-glucosidase TM0752 [102167]
      1. Thermotoga maritima [TaxId: 2336] [102168] (1)
    7. Maltose-6'-phosphate glucosidase GlvA [102169]
      1. Bacillus subtilis [TaxId: 1423] [102170] (1)
        SQ P54716
    8. 6-phospho-beta-glucosidase [110428]
      1. Bacillus stearothermophilus [TaxId: 1422] [110429] (1)
        SQ P84135
      2. Thermotoga maritima [TaxId: 2336] [110430] (3)
        SQ Q9X108
  7. 6-phosphogluconate dehydrogenase-like, N-terminal domain [51868] (26)
    the beta-sheet is extended to 8 strands, order 32145678; strands 7 & 8 are antiparallel to the rest
    C-terminal domains also show some similarity
    1. Class I ketol-acid reductoisomerase (KARI) [89532]
      1. Pseudomonas aeruginosa [TaxId: 287] [89533] (1)
    2. Class II ketol-acid reductoisomerase (KARI) [51869]
      contains additional subdomain at the N-terminus, partly ordered
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [51870] (2)
    3. 6-phosphogluconate dehydrogenase [51871]
      1. Sheep (Ovis orientalis aries) [TaxId: 9940] [51872] (5)
      2. Trypanosoma brucei [TaxId: 5691] [51873] (1)
    4. Hydroxyisobutyrate dehydrogenase [102171]
      1. Thermus thermophilus [TaxId: 274] [102172] (8)
        structural genomics
      2. Salmonella typhimurium [TaxId: 90371] [110431] (1)
        SQ Q8ZLV8
      3. Pseudomonas aeruginosa [TaxId: 287] [159424] (1)
        SQ Q9I5I6 1-162
    5. Mannitol 2-dehydrogenase [82301]
      1. Pseudomonas fluorescens [TaxId: 294] [82302] (2)
    6. Short chain L-3-hydroxyacyl CoA dehydrogenase [51874]
      1. Human (Homo sapiens) [TaxId: 9606] [51875] (11)
      2. Pig (Sus scrofa) [TaxId: 9823] [51876] (1)
    7. Conserved hypothetical protein MTH1747 [75113]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75114] (1)
    8. UDP-glucose dehydrogenase (UDPGDH) [51877]
      1. Streptococcus pyogenes [TaxId: 1314] [51878] (2)
    9. GDP-mannose 6-dehydrogenase [89534]
      1. Pseudomonas aeruginosa [TaxId: 287] [89535] (3)
    10. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [51879]
      1. Arthrobacter, strain 1c [TaxId: 1663] [51880] (1)
    11. Glycerol-3- phosphate dehydrogenase [51881]
      1. Trypanosome (Leishmania mexicana) [TaxId: 5665] [51882] (7)
      2. Archaeoglobus fulgidus [TaxId: 2234] [117433] (1)
        SQ O29390
    12. Ketopantoate reductase PanE [69419]
      1. Escherichia coli [TaxId: 562] [69420] (5)
    13. Coenzyme F420H2:NADP+ oxidoreductase (FNO) [69421]
      lacks all but the first helix of the C-terminal all-alpha domain
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69422] (2)
    14. Fatty oxidation complex alpha subunit, middle domain [110432]
      1. Pseudomonas fragi [TaxId: 296] [110433] (4)
        SQ P28793
    15. Pyrroline-5-carboxylate reductase ProC [117434]
      1. Neisseria meningitidis, serogroup B [TaxId: 487] [117435] (2)
        SQ Q9K1N1
      2. Streptococcus pyogenes [TaxId: 1314] [141928] (10)
        SQ Q9A1S9 1-152
    16. Prephenate dehydrogenase TyrA [141929]
      1. Aquifex aeolicus [TaxId: 63363] [141930] (4)
        SQ O67636 30-200
      2. Synechocystis sp. pcc 6803 [TaxId: 1148] [141931] (4)
        SQ P73906 1-165
      3. Haemophilus influenzae [TaxId: 727] [159425] (2)
        SQ P43902 92-243
    17. 5,10-methenyltetrahydromethanopterin hydrogenase, HMD [141932]
      1. Archaeon Methanocaldococcus jannaschii [TaxId: 2190] [141933] (1)
        SQ Q58194 1-242
    18. Hypothetical protein TM1727 [159426]
      ProC structural homologue
      1. Thermotoga maritima [TaxId: 2336] [159427] (2)
        SQ Q9X250 2-154
  8. Aminoacid dehydrogenase-like, C-terminal domain [51883] (24)
    extra N-terminal helix displaces the C-terminal helix (following strand 6) from its usual position creating a family nicotineamide-binding site
    1. Glutamate dehydrogenase [51884]
      1. Clostridium symbiosum [TaxId: 1512] [51885] (4)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [51886] (1)
      3. Archaeon Thermococcus profundus [TaxId: 49899] [63943] (1)
      4. Archaeon Thermococcus litoralis [TaxId: 2265] [51887] (1)
      5. Thermotoga maritima [TaxId: 2336] [51888] (3)
      6. Cow (Bos taurus) [TaxId: 9913] [51889] (5)
      7. Human (Homo sapiens) [TaxId: 9606] [75115] (2)
      8. Pyrobaculum islandicum [TaxId: 2277] [117436] (1)
        SQ Q9Y8I4
    2. Leucine dehydrogenase [51890]
      1. Bacillus sphaericus [TaxId: 1421] [51891] (1)
    3. Phenylalanine dehydrogenase [51892]
      1. Rhodococcus sp., M4 [TaxId: 1831] [51893] (4)
    4. Methylenetetrahydrofolate dehydrogenase/cyclohydrolase [51894]
      the two-domain organization is similar to that of aminoacid dehydrogenases, but both domains are truncated
      1. Human (Homo sapiens) [TaxId: 9606] [51895] (4)
      2. Escherichia coli [TaxId: 562] [51896] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51897] (2)
    5. Methylene-tetrahydromethanopterin dehydrogenase [82303]
      1. Methylobacterium extorquens [TaxId: 408] [82304] (2)
    6. Putative shikimate dehydrogenase YdiB [82305]
      1. Escherichia coli [TaxId: 562] [82306] (3)
    7. Shikimate 5-dehydrogenase-like protein HI0607 [89536]
      1. Haemophilus influenzae [TaxId: 727] [89537] (1)
    8. Shikimate 5-dehydrogenase AroE [89538]
      1. Escherichia coli [TaxId: 562] [89539] (1)
      2. Haemophilus influenzae [TaxId: 727] [102173] (2)
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [89540] (1)
        MJ1084
    9. Glutamyl tRNA-reductase middle domain [69413]
      other domains of this protein are distinct from those usually associated with the family domain
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [69414] (1)
    10. Mitochondrial NAD(P)-dependent malic enzyme [51898]
      includes C-terminal additional subdomains
      1. Human (Homo sapiens) [TaxId: 9606] [51899] (10)
      2. Domestic pigeon (Columba livia) [TaxId: 8932] [75116] (1)
      3. Pig roundworm (Ascaris suum) [TaxId: 6253] [75117] (2)
    11. Malate oxidoreductase (malic enzyme) [110434]
      1. Thermotoga maritima [TaxId: 2336] [110435] (5)
        SQ Q9WZ12
  9. Potassium channel NAD-binding domain [63944] (4)
    1. Rck domain from putative potassium channel Kch [63945]
      1. Escherichia coli [TaxId: 562] [63946] (1)
    2. Ktn bsu222 [75118]
      1. Bacillus subtilis [TaxId: 1423] [75119] (13)
    3. Ktn Mja218 [75120]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75121] (1)
    4. Potassium channel-related protein MthK [75122]
      1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75123] (9)
  10. Transcriptional repressor Rex, C-terminal domain [102174] (1)
    1. Transcriptional repressor Rex, C-terminal domain [102175]
      forms swapped dimer with C-terminal helices
      1. Thermus aquaticus [TaxId: 271] [102176] (3)
        SQ Q9X2V5
        CASP5
  11. CoA-binding domain [51900] (7)
    1. Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain [51901]
      1. Escherichia coli [TaxId: 562] [51902] (18)
      2. Thermus thermophilus [TaxId: 274] [89541] (1)
      3. Pig (Sus scrofa) [TaxId: 9823] [51903] (6)
    2. Hypothetical protein TT1466 [89542]
      putative CoA-binding protein
      1. Thermus thermophilus [TaxId: 274] [89543] (2)
    3. Hypothetical protein PH1109 [141934]
      1. Pyrococcus horikoshii [TaxId: 53953] [141935] (3)
        SQ O58836 1-142
    4. Acetate-CoA ligase alpha chain, AcdA, N-terminal domain [141936]
      1. Pyrococcus horikoshii [TaxId: 53953] [141937] (2)
        SQ O58493 1-129
    5. Hypothetical protein PF0725 [141938]
      1. Pyrococcus furiosus [TaxId: 2261] [141939] (1)
        SQ Q8U2V3 6-121
  12. Ornithine cyclodeaminase-like [110436] (2)
    Pfam 02423; contains additional alpha+beta dimerisation subdomain mostly formed by the N-terminal meander beta-sheet
    1. Archaeal alanine dehydrogenase [110437]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110438] (2)
        SQ O28608 # Rossmann-fold core (101-292) begins with an N-terminal helix and ends with a beta-strand
    2. Ornithine cyclodeaminase [117437]
      1. Pseudomonas putida [TaxId: 303] [117438] (2)
        SQ Q88H32
FAD/NAD(P)-binding domain [51904] (1)
core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
1. FAD/NAD(P)-binding domain [51905] (8)
  uperfamily
  1. C-terminal domain of adrenodoxin reductase-like [51906] (5)
    1. Trimethylamine dehydrogenase, C-terminal domain [51907]
      N-terminal domain is beta/alpha barrel and the middle domain is alpha/beta Rossmann-fold
      1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51908] (5)
    2. 2,4-dienoyl-CoA reductase, C-terminal domain [102177]
      1. Escherichia coli [TaxId: 562] [102178] (1)
    3. Adrenodoxin reductase of mitochondrial p450 systems [51909]
      1. Cow (Bos taurus) [TaxId: 9913] [51910] (6)
    4. Ferredoxin:NADP reductase FprA [75124]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75125] (2)
    5. Dihydropyrimidine dehydrogenase, domain 3 [51911]
      1. Pig (Sus scrofa) [TaxId: 9823] [51912] (5)
  2. FAD-linked reductases, N-terminal domain [51913] (25)
    C-terminal domain is alpha+beta is common for the family
    1. Cholesterol oxidase of GMC family [51914]
      1. Brevibacterium sterolicum [TaxId: 1702] [51915] (2)
      2. Streptomyces sp. [TaxId: 1931] [51916] (13)
      3. Streptomyces sp. (strain SA-COO) (Streptomyces sp. SA-COO) [TaxId: 74576] [159428] (1)
    2. Glucose oxidase [51924]
      1. Aspergillus niger [TaxId: 5061] [51925] (2)
      2. Penicillium amagasakiense [TaxId: 63559] [51926] (1)
    3. Hydroxynitrile lyase [82307]
      1. Almond (Prunus dulcis) [TaxId: 3755] [82308] (1)
    4. Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), FAD-binding domain [82309]
      1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [82310] (2)
    5. p-Hydroxybenzoate hydroxylase, PHBH [51917]
      1. Pseudomonas fluorescens [TaxId: 294] [51918] (17)
      2. Pseudomonas aeruginosa [TaxId: 287] [51919] (19)
    6. Sarcosine oxidase [51920]
      1. Bacillus sp., strain b0618 [TaxId: 1409] [51921] (18)
    7. Glycine oxidase ThiO [89544]
      1. Bacillus sp. [TaxId: 1409] [89545] (6)
    8. Phenol hydroxylase [51922]
      structurally very similar to PHBH, but contains additional C-terminal domain of the thioredoxin-like fold
      1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [51923] (2)
    9. Polyamine oxidase [51927]
      1. Maize (Zea mays) [TaxId: 4577] [51928] (7)
    10. L-aminoacid oxidase [51929]
      1. Malayan pit viper (Calloselasma rhodostoma) [TaxId: 8717] [51930] (6)
      2. Halys viper (Agkistrodon halys) [TaxId: 8714] [102179] (4)
        SQ Q90W54 21-504
    11. Monoamine oxidase B [69423]
      1. Human (Homo sapiens) [TaxId: 9606] [69424] (20)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [102180] (27)
    12. N,N-dimethylglycine oxidase [102181]
      1. Arthrobacter globiformis [TaxId: 1665] [102182] (3)
    13. Protoporphyrinogen oxidase [102183]
      1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [102184] (1)
      2. Myxococcus xanthus [TaxId: 34] [159429] (4)
        SQ P56601 10-306,415-464
    14. Pyranose 2-oxidase [117439]
      1. White-rot fungus (Peniophora sp. SG) [TaxId: 204723] [117440] (19)
        SQ Q8J136 43-619
    15. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [141940]
      1. Pig (Sus scrofa) [TaxId: 9823] [141941] (4)
        SQ P55931 27-259,359-505
    16. Dihydroxypyridine hydroxylase DhpH [159430]
      1. Arthrobacter nicotinovorans [TaxId: 29320] [159431] (3)
        SQ Q93NG3 2-163,292-394
    17. Lysine-specific histone demethylase 1, LSD1 [159432]
      1. Human (Homo sapiens) [TaxId: 9606] [159433] (8)
        SQ O60341 274-654,764-836
    18. Monooxygenase PhzS [159434]
      1. Pseudomonas aeruginosa [TaxId: 287] [159435] (1)
        SQ Q9HWG9 4-182,294-402
  3. GDI-like N domain [51931] (3)
    Similar to FAD-linked reductases in both domains but does not bind FAD
    1. Guanine nucleotide dissociation inhibitor, GDI [51932]
      the inhibition function is probably associated with an insert subdomain, residues 120-220
      1. Cow (Bos taurus) [TaxId: 9913] [51933] (3)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110439] (13)
        SQ P39958 5-446
    2. Rab escort protein 1 [89546]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89547] (3)
        SQ P37727
  4. Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain [51934] (7)
    1. L-aspartate oxidase [51935]
      1. Escherichia coli [TaxId: 562] [51936] (3)
    2. Succinate dehydogenase [82311]
      1. Escherichia coli [TaxId: 562] [82312] (2)
    3. Fumarate reductase [51937]
      1. Escherichia coli [TaxId: 562] [51938] (7)
      2. Wolinella succinogenes [TaxId: 844] [51939] (8)
    4. Flavocytochrome c3 (respiratory fumarate reductase) [51940]
      contains additional N-terminal multiheme domain
      1. Shewanella frigidimarina [TaxId: 56812] [51941] (16)
      2. Shewanella putrefaciens [TaxId: 24] [51942] (3)
    5. Adenylylsulfate reductase A subunit [69425]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69426] (2)
  5. FAD/NAD-linked reductases, N-terminal and central domains [51943] (28)
    duplication: both domains have similar folds and functions
    most members of the family contain common C-terminal alpha+beta domain
    1. Glutathione reductase [51944]
      1. Human (Homo sapiens) [TaxId: 9606] [51945] (17)
      2. Plasmodium falciparum [TaxId: 5833] [89548] (1)
      3. Escherichia coli [TaxId: 562] [51946] (4)
    2. Trypanothione reductase [51947]
      1. Crithidia fasciculata [TaxId: 5656] [51948] (6)
      2. Trypanosoma cruzi [TaxId: 5693] [51949] (8)
    3. Mammalian thioredoxin reductase [63947]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [63948] (1)
    4. Thioredoxin reductase [51950]
      lacks the "interface" C-terminal alpha+beta domain
      1. Escherichia coli [TaxId: 562] [51951] (5)
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [51952] (1)
    5. Apoptosis-inducing factor (AIF) [75126]
      1. Human (Homo sapiens) [TaxId: 9606] [75127] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [75128] (1)
    6. Alkyl hydroperoxide reductase subunit F (AhpF), C-terminal domains [51953]
      1. Salmonella typhimurium [TaxId: 90371] [51954] (1)
      2. Escherichia coli [TaxId: 562] [63949] (1)
    7. NADH peroxidase [51955]
      1. Enterococcus faecalis [TaxId: 1351] [51956] (8)
    8. NADH-dependent ferredoxin reductase, BphA4 [51957]
      1. Pseudomonas sp., KKS102 [TaxId: 306] [51958] (2)
    9. Putidaredoxin reductase [102185]
      1. Pseudomonas putida [TaxId: 303] [102186] (2)
    10. Dihydrolipoamide dehydrogenase [51959]
      1. Pseudomonas putida [TaxId: 303] [51960] (1)
      2. Pseudomonas fluorescens [TaxId: 294] [51961] (1)
      3. Azotobacter vinelandii [TaxId: 354] [51962] (1)
      4. Bacillus stearothermophilus [TaxId: 1422] [51963] (1)
      5. Neisseria meningitidis [TaxId: 487] [51964] (2)
      6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63950] (5)
      7. Garden pea (Pisum sativum) [TaxId: 3888] [51965] (1)
      8. Mycobacterium tuberculosis [TaxId: 1773] [117441] (1)
        SQ O53355
    11. NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase [82313]
      1. Xanthobacter sp., py2 [TaxId: 35809] [82314] (10)
    12. Flavocytochrome c sulfide dehydrogenase, FCSD, flavin-binding subunit [51966]
      has a smaller C-terminal alpha+beta domain instead the "interface" domain
      1. Purple phototrophic bacterium (Chromatium vinosum) [TaxId: 1049] [51967] (1)
    13. Phenylacetone monooxygenase [110440]
      1. Thermobifida fusca [TaxId: 2021] [110441] (1)
        SQ Q5YS95 # 55% sequence identity; Nocardia farcinica TaxID:37329
    14. NADH oxidase /nitrite reductase [117442]
      1. Pyrococcus furiosus [TaxId: 2261] [117443] (1)
        SQ Q8U1K9
    15. Flavin-dependent monoxygenase SPBP16F5.08c [117444]
      1. Schizosaccharomyces pombe [TaxId: 4896] [117445] (13)
        SQ Q9HFE4
  6. Thi4-like [141942] (2)
    Pfam 01946; stand-alone, moderately decorated domain
    1. Thiazole biosynthetic enzyme Thi4 [141943]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141944] (2)
        SQ P32318 16-326
        mitochondrial
      2. Thale cress(Arabidopsis thaliana) [TaxId: 3702] [141945] (1)
        SQ Q38814 51-328
        chloroplast
  7. GidA-like [141946] (1)
    part of Pfam 01266
    1. GidA-related protein TTHA1897 [141947]
      1. Thermus thermophilus [TaxId: 274] [141948] (1)
        SQ Q5SH33 2-231
  8. HI0933 N-terminal domain-like [159436] (2)
    N-terminal part of Pfam 03486
    1. Hypothetical protein HI0933 [159437]
      1. Haemophilus influenzae [TaxId: 727] [159438] (1)
        SQ P44941 1-194,343-401
    2. Flavoprotein BC4706 [159439]
      1. Bacillus cereus [TaxId: 1396] [159440] (1)
        SQ Q816V9 1-192,362-420
Nucleotide-binding domain [51970] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Nucleotide-binding domain [51971] (3)
  this superfamily shares the common nucleotide-binding site with and provides a link between the Rossmann-fold NAD(P)-binding and FAD/NAD(P)-binding domains
  uperfamily
  1. N-terminal domain of adrenodoxin reductase-like [51972] (5)
    1. Trimethylamine dehydrogenase, middle domain [51973]
      1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51974] (5)
    2. 2,4-dienoyl-CoA reductase, middle domain [102187]
      1. Escherichia coli [TaxId: 562] [102188] (1)
    3. Adrenodoxin reductase of mitochondrial p450 systems [51975]
      1. Cow (Bos taurus) [TaxId: 9913] [51976] (6)
    4. Ferredoxin:NADP reductase FprA [75129]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75130] (2)
    5. Dihydropyrimidine dehydrogenase, domain 2 [51977]
      1. Pig (Sus scrofa) [TaxId: 9823] [51978] (5)
  2. D-aminoacid oxidase, N-terminal domain [51979] (2)
    This family is probably related to the FAD-linked reductases and shares with them the C-terminal domain fold
    1. D-aminoacid oxidase, N-terminal domain [51980]
      1. Pig (Sus scrofa) [TaxId: 9823] [51981] (6)
      2. Rhodotorula gracilis [TaxId: 5286] [51982] (4)
  3. UDP-galactopyranose mutase, N-terminal domain [69427] (2)
    domain structure is similar to that of D-aminoacid oxidase
    1. UDP-galactopyranose mutase, N-terminal domain [69428]
      1. Escherichia coli [TaxId: 562] [69429] (1)
      2. Klebsiella pneumoniae [TaxId: 573] [117446] (3)
        SQ Q48485
MurCD N-terminal domain [51983] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
1. MurCD N-terminal domain [51984] (1)
  uperfamily
  1. MurCD N-terminal domain [51985] (3)
    1. UDP-N-acetylmuramate-alanine ligase MurC [82315]
      1. Thermotoga maritima [TaxId: 2336] [82316] (1)
        TM0231
      2. Haemophilus influenzae [TaxId: 727] [89549] (4)
    2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [51986]
      1. Escherichia coli [TaxId: 562] [51987] (11)
7-stranded beta/alpha barrel [51988] (3)
variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
1. Glycosyl hydrolases family 6, cellulases [51989] (1)
  uperfamily
  1. Glycosyl hydrolases family 6, cellulases [51990] (5)
    Pfam 01341
    1. Cellulase E2 [51991]
      1. Thermomonospora fusca, strain yx [TaxId: 2021] [51992] (2)
    2. Cellobiohydrolase II (Cel6) [51993]
      1. Trichoderma reesei, Cel6a [TaxId: 51453] [51994] (7)
      2. Humicola insolens, Cel6a [TaxId: 34413] [51995] (9)
      3. Humicola insolens, Cel6b [TaxId: 34413] [51996] (1)
    3. Putative cellulase Rv0062 (Cel6, CelA1) [117447]
      1. Mycobacterium tuberculosis [TaxId: 1773] [117448] (4)
        SQ Q79G13 88-380
2. PHP domain-like [89550] (2)
  uperfamily
  1. PHP domain [89551] (2)
    putative phosphoesterase domain; contains trinuclear metal-binding site; some similarity to the metallohydrolases of TIM-barrel fold
    1. Hypothetical protein YcdX [89552]
      1. Escherichia coli [TaxId: 562] [89553] (3)
        SQ P75914
    2. Hypothetical protein TM0559 [141949]
      1. Thermotoga maritima [TaxId: 2336] [141950] (6)
        SQ Q9WZ29 5-233
  2. RNase P subunit p30 [110442] (1)
    Pfam 01876
    1. Ribonuclease P protein component 3, Rnp3 [110443]
      1. Pyrococcus horikoshii [TaxId: 53953] [110444] (3)
        SQ O59543 # PH1877
3. Glycoside hydrolase/deacetylase [88713] (8)
  in the different families beta-barrels are similarly distorted but may vary in the number of strands
  uperfamily
  1. 4-alpha-glucanotransferase, N-terminal domain [89554] (1)
    family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
    1. 4-alpha-glucanotransferase, N-terminal domain [89555]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [89556] (3)
  2. alpha-mannosidase [88714] (2)
    family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
    1. Golgi alpha-mannosidase II [88715]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [88716] (46)
        SQ Q24451 94-1107
    2. Lysosomal alpha-mannosidase [89557]
      the single-chain precursor is processed into 5 peptides; heavily glycosylated
      1. Cow (Bos taurus) [TaxId: 9913] [89558] (1)
  3. AmyC N-terminal domain-like [102189] (2)
    1. Hypothetical protein TT1467, N-terminal domain [102190]
      1. Thermus thermophilus [TaxId: 274] [102191] (1)
    2. Alpha-amylase AmyC [141951]
      1. Thermotoga maritima [TaxId: 2336] [141952] (1)
        SQ A1GKL6 1-404
  4. NodB-like polysaccharide deacetylase [89559] (6)
    variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=6, S=8; strand order 123456
    1. Probable polysaccharide deacetylase PdaA [89560]
      1. Bacillus subtilis [TaxId: 1423] [89561] (7)
    2. Chitin deacetylase [141953]
      1. Bean anthracnose fungus (Colletotrichum lindemuthianum) [TaxId: 290576] [141954] (1)
        SQ Q6DWK3 29-248
    3. Xylanase XynA C-terminal domain [141955]
      1. Clostridium thermocellum [TaxId: 1515] [141956] (2)
        SQ O87119 480-683
    4. Putative polysaccharide deacetylase BA0424 [141957]
      1. Bacillus anthracis [TaxId: 1392] [141958] (1)
        SQ Q81Z49 54-258
    5. Peptidoglycan GlcNAc deacetylase C-terminal domain [141959]
      1. Streptococcus pneumoniae [TaxId: 1313] [141960] (2)
        SQ Q8DP63 268-463
    6. Acetyl-xylan esterase [141961]
      1. Streptomyces lividans [TaxId: 1916] [141962] (2)
        SQ Q54413 42-233
  5. LamB/YcsF-like [117449] (3)
    Pfam 03746
    1. Hypothetical protein YbgL [117450]
      1. Escherichia coli [TaxId: 562] [117451] (1)
        SQ P75746
    2. Hypothetical protein PH0986 [117452]
      1. Pyrococcus horikoshii [TaxId: 53953] [117453] (1)
        SQ O58714
    3. Hypothetical protein TTHB195 [141963]
      1. Thermus thermophilus [TaxId: 274] [141964] (1)
        SQ Q53WG6 1-250
  6. PA1517-like [141965] (1)
    seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel NodB-like family; member of the same Pfam family (Pfam 01522)
    1. Hypothetical protein PA1517 [141966]
      1. Pseudomonas aeruginosa [TaxId: 287] [141967] (8)
        SQ Q9I3J6 4-304
  7. Divergent polysaccharide deacetylase [141968] (1)
    Pfam 04748
    1. Hypothetical protein BH1492 [141969]
      1. Bacillus halodurans [TaxId: 86665] [141970] (1)
        SQ Q9KCS7 31-254
  8. YdjC-like [159441] (1)
    Pfam 04794
    1. Uncharacterized protein EF3048 [159442]
      1. Enterococcus faecalis [TaxId: 1351] [159443] (2)
        SQ P59745 2-262
PFL-like glycyl radical enzymes [51997] (1)
contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
1. PFL-like glycyl radical enzymes [51998] (5)
  duplication: the N- and C-terminal halves have similar topologies
  uperfamily
  1. PFL-like [51999] (2)
    Pfam 02901; except the C-terminal ~100 residues covered by Pfam 01228
    1. Pyruvate formate-lyase, PFL [52000]
      1. Escherichia coli [TaxId: 562] [52001] (8)
    2. Glycerol dehydratase DhaB1 [110445]
      1. Clostridium butyricum [TaxId: 1492] [110446] (3)
        SQ Q8GEZ8
  2. R1 subunit of ribonucleotide reductase, C-terminal domain [52002] (2)
    1. R1 subunit of ribonucleotide reductase, C-terminal domain [52003]
      1. Escherichia coli [TaxId: 562] [52004] (8)
      2. Salmonella typhimurium [TaxId: 90371] [110447] (6)
        SQ Q08698
  3. B12-dependent (class II) ribonucleotide reductase [75131] (1)
    1. B12-dependent (class II) ribonucleotide reductase [75132]
      1. Lactobacillus leichmannii [TaxId: 28039] [75133] (1)
  4. Class III anaerobic ribonucleotide reductase NRDD subunit [52005] (1)
    1. Class III anaerobic ribonucleotide reductase NRDD subunit [52006]
      1. Bacteriophage T4 [TaxId: 10665] [52007] (5)
  5. SP0239-like [159444] (1)
    Pfam 05167; DUF771
    1. Uncharacterized protein SP0239 [159445]
      1. Streptococcus pneumoniae [TaxId: 1313] [159446] (2)
        SQ Q97ST4 1-440
The "swivelling" beta/beta/alpha domain [52008] (10)
3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
this domain is thought to be mobile in most multi-domain proteins known to contain it
1. Phosphohistidine domain [52009] (2)
  contains barrel, closed, n=7, S=10
  uperfamily
  1. Pyruvate phosphate dikinase, central domain [52010] (3)
    1. Pyruvate phosphate dikinase, central domain [52011]
      1. Clostridium symbiosum [TaxId: 1512] [52012] (8)
      2. Trypanosoma brucei [TaxId: 5691] [75134] (1)
      3. Maize (Zea mays) [TaxId: 4577] [141971] (2)
        SQ P11155 454-588
  2. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52013] (1)
    1. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52014]
      contains 4-helical insert domain, residues 22-144
      1. Escherichia coli [TaxId: 562] [52015] (11)
2. RraA-like [89562] (1)
  structural similarity and possible distant homology to the phosphohistidine domain of pyruvate phosphate dikinase
  uperfamily
  1. RraA-like [89563] (4)
    aka MenG-like; characterized as regulator of RNase E activity A (RraA) that globally modulates RNA abundance in E. coli
    1. Hypothetical protein Rv3853 [89564]
      RraA homologue; (mis)annotated as a probable MenG-like demethylmenaquinone methyltransferase
      1. Mycobacterium tuberculosis [TaxId: 1773] [89565] (1)
    2. Regulator of RNase E activity RraA (MenG) [102192]
      1. Escherichia coli [TaxId: 562] [102193] (1)
    3. Hypothetical protein VC2366 [102194]
      RraA homologue
      1. Vibrio cholerae [TaxId: 666] [102195] (1)
    4. Demethylmenaquinone methyltransferase [102196]
      as (mis)annotated in the PDB entry; RraA homologue
      1. Thermus thermophilus [TaxId: 274] [102197] (1)
3. Putative cyclase [102198] (1)
  contains mixed beta-sheet barrel, closed n=7, S=10
  uperfamily
  1. Putative cyclase [102199] (2)
    Pfam 04199; COG1878: predicted metal-dependent hydrolase
    1. Unnamed protein [102200]
      not in the sequence database yet; closest homologue is TTE1006 from Thermoanaerobacter tengcongensis
      1. Bacillus stearothermophilus [TaxId: 1422] [102201] (1)
        conflict: annotated in PDB as from Escherichia coli
    2. Hypothetical protein MJ0783 [141972]
      1. Methanococcus jannaschii [TaxId: 2190] [141973] (1)
        SQ Q58193 1-186
4. LeuD/IlvD-like [52016] (3)
  contains mixed beta-sheet barrel, closed n=7, S=10
  uperfamily
  1. LeuD-like [52017] (5)
    Pfam 00694; permutation of the domain order in the proteins containing this family domain
    1. Aconitase A, C-terminal domain [52018]
      other three domains have alpha/beta folds
      1. Pig (Sus scrofa) [TaxId: 9823] [52019] (6)
      2. Cow (Bos taurus) [TaxId: 9913] [52020] (9)
    2. Aconitase B, second N-terminal domain [75135]
      1. Escherichia coli [TaxId: 562] [75136] (1)
    3. Isopropylmalate isomerase LeuD [117454]
      3-isopropylmalate dehydratase small subunit
      1. Pyrococcus horikoshii [TaxId: 53953] [117455] (1)
        SQ O59393
    4. ron-responsive element binding protein 1, C-terminal domain [141974]
      1. Human (Homo sapiens) [TaxId: 9606] [141975] (3)
        SQ P21399 631-889
  2. IlvD/EDD C-terminal domain-like [141976] (1)
    C-terminal part of Pfam 00920
    1. 6-phosphogluconate dehydratase EDD [141977]
      1. Shewanella oneidensis [TaxId: 70863] [141978] (2)
        SQ Q8EEA0 419-608
  3. AF0055-like [141979] (1)
    PF01989; DUF126; probable link between the LeuD-like and Phosphohistidine domain superfamilies (sequence similarity crosshits)
    1. Hypothetical protein AF0055 [141980]
      1. Archaeoglobus fulgidus [TaxId: 2234] [141981] (1)
        SQ O30181 1-132
5. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52021] (1)
  uperfamily
  1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52022] (1)
    1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52023]
      1. Escherichia coli [TaxId: 562] [52024] (10)
        SQ P00907
6. Swiveling domain of dehydratase reactivase alpha subunit [82317] (1)
  uperfamily
  1. Swiveling domain of dehydratase reactivase alpha subunit [82318] (2)
    1. Swiveling domain of the glycerol dehydratase reactivase alpha subunit [82319]
      1. Klebsiella pneumoniae [TaxId: 573] [82320] (1)
    2. Diol dehydratase-reactivating factor large subunit DdrA [141982]
      1. Klebsiella oxytoca [TaxId: 571] [141983] (4)
        SQ O68195 93-254
7. PA domain [52025] (1)
  uperfamily
  1. PA domain [52026] (2)
    1. Transferrin receptor ectodomain, apical domain [52027]
      1. Human (Homo sapiens) [TaxId: 9606] [52028] (4)
    2. Glutamate carboxypeptidase II [141984]
      1. Human (Homo sapiens) [TaxId: 9606] [141985] (17)
        SQ Q04609 118-350
8. GroEL apical domain-like [52029] (2)
  uperfamily
  1. GroEL-like chaperone, apical domain [52030] (4)
    1. GroEL, A domain [52031]
      1. Escherichia coli [TaxId: 562] [52032] (22)
      2. Paracoccus denitrificans [TaxId: 266] [69430] (1)
      3. Thermus thermophilus [TaxId: 274] [52033] (3)
        SQ P61491
      4. Mycobacterium tuberculosis, GroEL2 [TaxId: 1773] [117456] (1)
        SQ P0A520 60-514
  2. Group II chaperonin (CCT, TRIC), apical domain [52034] (4)
    1. Thermosome, A-domain [52035]
      1. Archaeon Thermoplasma acidophilum, alpha chain [TaxId: 2303] [100946] (4)
      2. Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679] [102202] (4)
      3. Archaeon Thermoplasma acidophilum, beta chain [TaxId: 2303] [100947] (3)
      4. Mouse (Mus musculus), gamma chain [TaxId: 10090] [75137] (2)
9. FumA C-terminal domain-like [117457] (1)
  uperfamily
  1. FumA C-terminal domain-like [117458] (1)
    Pfam 05683
    1. Fumarate hydratase class I beta subunit [117459]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117460] (1)
        SQ O29167 # AF1098
10. LD-carboxypeptidase A C-terminal domain-like [141986] (1)
  uperfamily
  1. LD-carboxypeptidase A C-terminal domain-like [141987] (1)
    C-terminal half of Pfam 02016
    1. LD-carboxypeptidase A, C-terminal domain [141988]
      1. Pseudomonas aeruginosa [TaxId: 287] [141989] (8)
        SQ Q9HTZ1 152-307! SQ Q9HTZ1 170-307
Barstar-like [52037] (2)
2 layers, a/b; parallel beta-sheet of 3 strands, order 123
1. Barstar-related [52038] (1)
  uperfamily
  1. Barstar-related [52039] (2)
    1. Barstar (barnase inhibitor) [52040]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [52041] (23)
    2. Hypothetical protein YhcO [141990]
      1. Escherichia coli [TaxId: 562] [141991] (2)
        SQ P64618 1-90
2. Ribosomal protein L32e [52042] (1)
  uperfamily
  1. Ribosomal protein L32e [52043] (1)
    contains irregular N-terminal extension to the common fold
    1. Ribosomal protein L32e [52044]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [52045] (58)
        SQ P12736
MurF and HprK N-domain-like [63417] (2)
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core.
1. MurE/MurF N-terminal domain [63418] (1)
  binds UDP group
  uperfamily
  1. MurE/MurF N-terminal domain [63419] (2)
    1. UDP-N-acetylmuramyl tripeptide synthetase MurE [63951]
      1. Escherichia coli [TaxId: 562] [63952] (1)
    2. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [63420]
      1. Escherichia coli [TaxId: 562] [63421] (1)
2. HprK N-terminal domain-like [75138] (2)
  probable phosphatase
  uperfamily
  1. HPr kinase/phoshatase HprK N-terminal domain [75139] (2)
    1. HPr kinase/phoshatase HprK N-terminal domain [75140]
      1. Staphylococcus xylosus [TaxId: 1288] [75141] (1)
      2. Mycoplasma pneumoniae [TaxId: 2104] [82321] (1)
  2. DRTGG domain [159447] (1)
    Pfam 07085
    1. Hypothetical protein AF1212 [159448]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159449] (2)
        SQ O29056 206-329
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [52046] (3)
2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies
1. RNI-like [52047] (3)
  regular structure consisting of similar repeats
  uperfamily
  1. 28-residue LRR [52048] (4)
    1. Ribonuclease inhibitor [52049]
      duplication: consists of 16 repeats
      1. Pig (Sus scrofa) [TaxId: 9823] [52050] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [52051] (7)
    2. Tropomodulin C-terminal domain [82322]
      duplication: consists of 5 repeats
      1. Chicken (Gallus gallus) [TaxId: 9031] [82323] (1)
      2. nematode (Caenorhabditis elegans) [TaxId: 6239] [89566] (1)
  2. Rna1p (RanGAP1), N-terminal domain [52052] (1)
    1. Rna1p (RanGAP1), N-terminal domain [52053]
      GTPase-activating protein for SpI1, ortologue of Ran
      duplication: consists of 11 repeats
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [52054] (5)
  3. Cyclin A/CDK2-associated p19, Skp2 [52055] (1)
    1. Cyclin A/CDK2-associated p19, Skp2 [52056]
      1. Human (Homo sapiens) [TaxId: 9606] [52057] (4)
2. L domain-like [52058] (8)
  less regular structure consisting of variable repeats
  uperfamily
  1. Internalin LRR domain [52059] (3)
    capped at the N-end with a truncated EF-hand subdomain
    1. Internalin A [82324]
      1. Listeria monocytogenes [TaxId: 1639] [82325] (7)
    2. Internalin B [52060]
      1. Listeria monocytogenes [TaxId: 1639] [52061] (9)
    3. Internalin H [69431]
      1. Listeria monocytogenes [TaxId: 1639] [69432] (1)
  2. Leucine rich effector protein YopM [69433] (1)
    1. Leucine rich effector protein YopM [69434]
      1. Yersinia pestis [TaxId: 632] [69435] (2)
  3. Ngr ectodomain-like [75142] (6)
    1. von Willebrand factor binding domain of glycoprotein Ib alpha [75143]
      1. Human (Homo sapiens) [TaxId: 9606] [75144] (9)
    2. Reticulon 4 receptor (Nogo-66 receptor, Ngr) [89567]
      1. Human (Homo sapiens) [TaxId: 9606] [89568] (2)
    3. Slit [117461]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [117462] (1)
        SQ P24014 542-733
    4. Decorin [117463]
      1. Cow (Bos taurus) [TaxId: 9913] [117464] (3)
        SQ P21793 52-356
    5. High affinity nerve growth factor receptor, N-terminal domain [141992]
      1. Human (Homo sapiens) [TaxId: 9606] [141993] (2)
        SQ P04629 36-191
    6. Follicle-stimulating hormone receptor [159450]
      1. Human (Homo sapiens) [TaxId: 9606] [159451] (1)
        SQ P23945 18-259
  4. Polygalacturonase inhibiting protein PGIP [89569] (1)
    1. Polygalacturonase inhibiting protein PGIP [89570]
      1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [89571] (1)
  5. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52062] (1)
    1. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52063]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52064] (2)
  6. mRNA export factor tap [52065] (1)
    1. mRNA export factor tap [52066]
      1. Human (Homo sapiens) [TaxId: 9606] [52067] (8)
  7. U2A'-like [52068] (1)
    duplication: consists of 5-6 partly irregular repeats
    1. Splicesomal U2A' protein [52069]
      1. Human (Homo sapiens) [TaxId: 9606] [52070] (1)
  8. L domain [52071] (6)
    1. Type 1 insulin-like growth factor receptor extracellular domain [52072]
      1. Human (Homo sapiens) [TaxId: 9606] [52073] (1)
        L1 and L2 domains
    2. Receptor protein-tyrosine kinase Erbb-3 extracellular domain [75145]
      1. Human (Homo sapiens) [TaxId: 9606] [75146] (1)
    3. EGF receptor extracellular domain [82326]
      1. Human (Homo sapiens) [TaxId: 9606] [82327] (15)
    4. Protooncoprotein Her2 extracellular domain [82328]
      1. Human (Homo sapiens) [TaxId: 9606] [82329] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82330] (1)
    5. Insulin receptor [159452]
      1. Human (Homo sapiens) [TaxId: 9606] [159453] (2)
        SQ P06213 31-183! SQ P06213 339-494
3. Outer arm dynein light chain 1 [52075] (1)
  (beta-beta-alpha)n superhelix
  uperfamily
  1. Outer arm dynein light chain 1 [52076] (1)
    1. Outer arm dynein light chain 1 [52077]
      1. Green algae (Chlamydomonas reinhardtii) [TaxId: 3055] [52078] (2)
Ribosomal proteins L15p and L18e [52079] (1)
core: three turns of irregular (beta-beta-alpha)n superhelix
1. Ribosomal proteins L15p and L18e [52080] (1)
  uperfamily
  1. Ribosomal proteins L15p and L18e [52081] (5)
    1. Ribosomal protein L15 (L15p) [52082]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [52083] (40)
        SQ P12737
      2. Escherichia coli [TaxId: 562] [141994] (29)
        SQ P02413 1-144
      3. Thermus thermophilus [TaxId: 274] [159454] (11)
        SQ Q72I23 5-150
      4. Deinococcus radiodurans [TaxId: 1299] [159455] (6)
        SQ Q9RSK9 4-144
    2. Ribosomal protein L18e [52084]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [52085] (40)
        SQ P12733
SpoIIaa-like [52086] (2)
core: 4 turns of a (beta-alpha)n superhelix
1. CRAL/TRIO domain [52087] (1)
  uperfamily
  1. CRAL/TRIO domain [52088] (3)
    Pfam 00650
    1. C-terminal domain of phosphatidylinositol transfer protein sec14p [52089]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52090] (1)
    2. Alpha-tocopherol transfer protein [102203]
      1. Human (Homo sapiens) [TaxId: 9606] [102204] (3)
    3. Supernatant protein factor (SPF), middle domain [102205]
      Sec14-like protein 2; contains extra C-terminal beta-sandwich domain
      1. Human (Homo sapiens) [TaxId: 9606] [102206] (2)
        SQ O76054
2. SpoIIaa-like [52091] (2)
  uperfamily
  1. Anti-sigma factor antagonist SpoIIaa [52092] (4)
    1. Anti-sigma factor antagonist SpoIIaa [52093]
      1. Bacillus sphaericus [TaxId: 1421] [63953] (3)
      2. Bacillus subtilis [TaxId: 1423] [52094] (2)
      3. Bacillus stearothermophilus [TaxId: 1422] [110448] (4)
        SQ O32726 # 90% sequence identity
      4. Thermotoga maritima [TaxId: 2336] [110449] (3)
        SQ Q9X1F5; TM1442
  2. Sfri0576-like [159456] (2)
    significant structural variability despite high sequence similarity
    1. Uncharacterized protein Shew3102 [159457]
      1. Shewanella loihica [TaxId: 359303] [159458] (2)
        SQ A3QHM0 1-125
    2. Hypothetical protein Sfri0576 [159459]
      1. Shewanella frigidimarina [TaxId: 56812] [159460] (2)
        SQ Q087X8 2-126
ClpP/crotonase [52095] (1)
core: 4 turns of (beta-beta-alpha)n superhelix
1. ClpP/crotonase [52096] (4)
  uperfamily
  1. Clp protease, ClpP subunit [52097] (5)
    1. Clp protease, ClpP subunit [52098]
      1. Escherichia coli [TaxId: 562] [52099] (55)
      2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [141995] (7)
        SQ Q16740 57-249
      3. Plasmodium falciparum [TaxId: 5833] [141996] (7)
        SQ O97252 177-366
      4. Mycobacterium tuberculosis [TaxId: 1773] [141997] (21)
        SQ P0A526 15-193
      5. Streptococcus pneumoniae [TaxId: 1313] [141998] (7)
        SQ P63788 2-193
  2. Tail specific protease, catalytic domain [52100] (3)
    includes N-terminal all-alpha subdomain
    1. Photosystem II D1 C-terminal processing protease [68935]
      1. Algae (Scenedesmus obliquus) [TaxId: 3088] [52102] (4)
    2. Tricorn protease [69436]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69437] (4)
    3. Interphotoreceptor retinoid-binding protein IRBP [69438]
      very similar to the tail-specific protease domain; lacks the PDZ insertion domain and hydrolytic activity
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [69439] (1)
  3. Crotonase-like [52103] (17)
    1. 4-Chlorobenzoyl-CoA dehalogenase [52104]
      1. Pseudomonas sp., strain CBS-3 [TaxId: 306] [52105] (2)
    2. Enoyl-CoA hydratase (crotonase) [52106]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52107] (4)
      2. Thermus thermophilus [TaxId: 274] [102207] (1)
    3. Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase) [52108]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52109] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63954] (4)
      3. Rat (Rattus norvegicus), mitochondrial [TaxId: 10116] [117465] (1)
        SQ P23965
      4. Human (Homo sapiens), mitochondrial [TaxId: 9606] [141999] (3)
        SQ P42126 44-292
    4. Naphthoate synthase MenB [102208]
      1. Mycobacterium tuberculosis [TaxId: 1773] [102209] (4)
        SQ O06414 18-285
    5. AUH protein [69440]
      an RNA-binding homologue of enoyl-CoA hydratase
      1. Human (Homo sapiens) [TaxId: 9606] [69441] (1)
    6. Methylmalonyl CoA decarboxylase [52110]
      1. Escherichia coli [TaxId: 562] [52111] (2)
    7. 6-oxo camphor hydrolase [82331]
      1. Rhodococcus erythropolis [TaxId: 1833] [82332] (2)
        SQ Q93TU6
    8. Fatty oxidation complex alpha subunit, N-terminal domain [110450]
      1. Pseudomonas fragi [TaxId: 296] [110451] (4)
        SQ P28793
    9. Probable enoyl-CoA hydratase TTHA0218 [142000]
      1. Thermus thermophilus [TaxId: 274] [142001] (6)
        SQ Q5SLS5 2-264
    10. Chromodomain protein CDY2A [142002]
      1. Human (Homo sapiens) [TaxId: 9606] [142003] (6)
        SQ Q9Y6F7 284-541
    11. Carbapenem biosynthes protein CarB [142004]
      1. Pectobacterium carotovorum [TaxId: 554] [142005] (12)
        SQ Q9XB60 1-230
    12. Peroxisomal 3,2-trans-enoyl-CoA isomerase [142006]
      1. Human (Homo sapiens) [TaxId: 9606] [142007] (3)
        SQ O75521 103-347
    13. Chromodomain protein CDY1, C-terminal domain [142008]
      1. Human (Homo sapiens) [TaxId: 9606] [142009] (3)
        SQ Q9Y6F8 282-532
  4. Biotin dependent carboxylase carboxyltransferase domain [89572] (8)
    Pfam 01039
    the active site is formed by two different homologous subunits or domains of this fold
    1. Acetyl-coenzyme A carboxylase [89573]
      duplication: consists of two similar structural domains forming a functional domain of a larger multifunctional enzyme
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89574] (7)
        SQ Q00955 1482-2196
    2. Methylmalonyl-CoA carboxyltransferase (transcarboxylase 12S) [89575]
      1. Propionibacterium freudenreichii [TaxId: 1744] [89576] (2)
    3. Glutaconyl-CoA decarboxylase A subunit [102210]
      1. Acidaminococcus fermentans [TaxId: 905] [102211] (1)
    4. Propionyl-CoA carboxylase complex B subunit, PccB [117466]
      1. Streptomyces coelicolor [TaxId: 1902] [117467] (4)
        SQ Q9X4K7
      2. Mycobacterium tuberculosis [TaxId: 1773] [142010] (12)
        SQ P96885 20-277! SQ P96885 278-548
      3. Thermotoga maritima [TaxId: 2336] [142011] (12)
        SQ Q9WZH5 1-251! SQ Q9WZH5 252-515
    5. Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha, AccA [142012]
      1. Escherichia coli [TaxId: 562] [142013] (1)
        SQ P0ABD5 4-319
    6. Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD [142014]
      1. Escherichia coli [TaxId: 562] [142015] (1)
        SQ P0A9Q6 23-285
BRCT domain [52112] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. BRCT domain [52113] (5)
  Pfam 00533
  uperfamily
  1. BRCT domain [63955] (2)
    1. Breast cancer associated protein, BRCA1 [63956]
      duplication: tandem repeat of BRCT domain
      1. Human (Homo sapiens) [TaxId: 9606] [63957] (25)
        SQ P38398 1649-1863
      2. Rat (Rattus norvegicus) [TaxId: 10116] [75147] (3)
  2. 53BP1 [75148] (1)
    1. 53BP1 [75149]
      1. Human (Homo sapiens) [TaxId: 9606] [75150] (2)
  3. DNA-repair protein XRCC1 [52114] (1)
    1. DNA-repair protein XRCC1 [52115]
      1. Human (Homo sapiens) [TaxId: 9606] [52116] (1)
  4. DNA ligase [52117] (2)
    1. DNA ligase III alpha [63958]
      1. Human (Homo sapiens) [TaxId: 9606] [63959] (2)
    2. NAD+-dependent DNA ligase, domain 4 [52118]
      1. Thermus thermophilus [TaxId: 274] [100975] (1)
  5. DNA topoisomerase II binding protein 1, TopBP1 [117468] (1)
    1. DNA topoisomerase II binding protein 1, TopBP1 [117469]
      1. Human (Homo sapiens) [TaxId: 9606] [117470] (1)
        SQ Q92547 326-444
Lumazine synthase [52120] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Lumazine synthase [52121] (1)
  uperfamily
  1. Lumazine synthase [52122] (7)
    1. Lumazine synthase [52123]
      1. Bacillus subtilis [TaxId: 1423] [52124] (11)
        beta-subunit of the lumazine synthase/riboflavin synthase complex; 60 subunits form an icosahedral shell
      2. Brucella abortus [TaxId: 235] [52125] (1)
      3. Aquifex aeolicus [TaxId: 63363] [69442] (5)
      4. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [52126] (1)
      5. Spinach (Spinacia oleracea) [TaxId: 3562] [52127] (1)
      6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63960] (1)
      7. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [75151] (7)
Uracil-DNA glycosylase-like [52140] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Uracil-DNA glycosylase-like [52141] (4)
  uperfamily
  1. Uracil-DNA glycosylase [52142] (5)
    1. Uracil-DNA glycosylase [52143]
      1. Human (Homo sapiens) [TaxId: 9606] [52144] (11)
      2. Atlantic cod (Gadus morhua) [TaxId: 8049] [102212] (1)
      3. Herpes simplex virus type 1 [TaxId: 10298] [52145] (4)
      4. Escherichia coli [TaxId: 562] [52146] (12)
      5. Epstein-Barr virus [TaxId: 10376] [159461] (2)
        SQ Q777D9 26-255
  2. Mug-like [52147] (4)
    1. G:T/U mismatch-specific DNA glycosylase, Mug [52148]
      1. Escherichia coli [TaxId: 562] [52149] (4)
    2. Thermophilic uracil-DNA glycosylase [89577]
      1. Thermotoga maritima [TaxId: 2336] [89578] (2)
        gene TM0511
      2. Thermus thermophilus [TaxId: 274] [102213] (2)
    3. G/T mismatch-specific thymine DNA glycosylase [159462]
      1. Human (Homo sapiens) [TaxId: 9606] [159463] (2)
        SQ Q13569 117-132
  3. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89579] (1)
    1. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89580]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [89581] (3)
  4. AF0587 domain-like [159464] (1)
    a middle domain in the founder protein
    1. Uncharacterized protein AF0587 [159465]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159466] (1)
        SQ O29668 244-383
Creatininase [102214] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Creatininase [102215] (1)
  uperfamily
  1. Creatininase [102216] (1)
    1. Creatininase [102217]
      1. Pseudomonas putida [TaxId: 303] [102218] (4)
DNA polymerase III psi subunit [102219] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
1. DNA polymerase III psi subunit [102220] (1)
  uperfamily
  1. DNA polymerase III psi subunit [102221] (1)
    1. DNA polymerase III psi subunit [102222]
      1. Escherichia coli [TaxId: 562] [102223] (1)
Initiation factor IF2/eIF5b, domain 3 [52155] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Initiation factor IF2/eIF5b, domain 3 [52156] (1)
  uperfamily
  1. Initiation factor IF2/eIF5b, domain 3 [52157] (1)
    1. Initiation factor IF2/eIF5b, domain 3 [52158]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52159] (3)
Aminoacid dehydrogenase-like, N-terminal domain [53222] (1)
core: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134
1. Aminoacid dehydrogenase-like, N-terminal domain [53223] (5)
  uperfamily
  1. Aminoacid dehydrogenases [53224] (10)
    dimerisation domain; contains additional structures including two extra N-terminal strands in the beta-sheet
    1. Glutamate dehydrogenase [53225]
      1. Clostridium symbiosum [TaxId: 1512] [53226] (4)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [53227] (1)
      3. Archaeon Thermococcus profundus [TaxId: 49899] [64106] (1)
      4. Archaeon Thermococcus litoralis [TaxId: 2265] [53228] (1)
      5. Thermotoga maritima [TaxId: 2336] [53229] (3)
      6. Cow (Bos taurus) [TaxId: 9913] [53230] (5)
      7. Human (Homo sapiens) [TaxId: 9606] [75252] (2)
      8. Pyrobaculum islandicum [TaxId: 2277] [117471] (1)
        SQ Q9Y8I4
    2. Leucine dehydrogenase [53231]
      1. Bacillus sphaericus [TaxId: 1421] [53232] (1)
    3. Phenylalanine dehydrogenase [53233]
      1. Rhodococcus sp., M4 [TaxId: 1831] [53234] (4)
  2. Tetrahydrofolate dehydrogenase/cyclohydrolase [53235] (3)
    1. Tetrahydrofolate dehydrogenase/cyclohydrolase [53236]
      the two-domain organization is similar to that of aminoacid dehydrogenases, but both domains are truncated
      1. Human (Homo sapiens) [TaxId: 9606] [53237] (4)
      2. Escherichia coli [TaxId: 562] [53238] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53239] (2)
  3. Methylene-tetrahydromethanopterin dehydrogenase [82333] (1)
    1. Methylene-tetrahydromethanopterin dehydrogenase [82334]
      1. Methylobacterium extorquens [TaxId: 408] [82335] (2)
  4. Shikimate dehydrogenase-like [82336] (5)
    1. Putative shikimate dehydrogenase YdiB [82337]
      1. Escherichia coli [TaxId: 562] [82338] (3)
    2. Shikimate 5-dehydrogenase-like protein HI0607 [89582]
      1. Haemophilus influenzae [TaxId: 727] [89583] (1)
    3. Shikimate 5-dehydrogenase AroE [89584]
      1. Escherichia coli [TaxId: 562] [89585] (1)
      2. Haemophilus influenzae [TaxId: 727] [102224] (2)
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [89586] (1)
        MJ1084
  5. Malic enzyme N-domain [53240] (4)
    Pfam 00390; decorated with additional structures; includes N-terminal additional subdomains and extra N-terminal strand
    1. Mitochondrial NAD(P)-dependent malic enzyme [53241]
      1. Human (Homo sapiens) [TaxId: 9606] [53242] (10)
      2. Domestic pigeon (Columba livia) [TaxId: 8932] [75253] (1)
      3. Pig roundworm (Ascaris suum) [TaxId: 6253] [75254] (2)
    2. Malate oxidoreductase (malic enzyme) [110452]
      1. Thermotoga maritima [TaxId: 2336] [110453] (5)
        SQ Q9WZ12
Toprim domain [110454] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
1. Toprim domain [110455] (1)
  this domain is also present in several multidomain proteins that are not split in scop yet: scop_sf 56712, scop_sf 56719, scop_sf 56726, scop_sf 56731
  uperfamily
  1. Toprim domain [110456] (2)
    Pfam 01751
    1. Hypothetical protein aq_2086 [110457]
      1. Aquifex aeolicus [TaxId: 63363] [110458] (1)
        SQ O67859
    2. Hypothetical protein RBSTP2199 [142016]
      B. subtilis YusF homolog
      1. Bacillus stearothermophilus [TaxId: 1422] [142017] (6)
        SQ Q5KVJ9 1-114
AtpF-like [159467] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. AtpF-like [159468] (1)
  1. AtpF-like [159469] (2)
    Pfam 01990; segment-swapping in some members
    1. V-type ATP synthase subunit F, AtpF [159470]
      1. Thermus thermophilus [TaxId: 274] [159471] (6)
        SQ P74903 1-104
      2. Archaeoglobus fulgidus [TaxId: 2234] [159472] (2)
        SQ O29102 4-79
Ribosomal protein L13 [52160] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
1. Ribosomal protein L13 [52161] (1)
  uperfamily
  1. Ribosomal protein L13 [52162] (5)
    1. Ribosomal protein L13 [52163]
      synonym: 50S ribosomal protein L13p, HMAL13
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82339] (1)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [52164] (44)
        SQ P29198
      3. Thermus thermophilus [TaxId: 274] [159473] (10)
        SQ P60488 1-139
      4. Escherichia coli [TaxId: 562] [159474] (29)
        SQ P02410 1-140
      5. Deinococcus radiodurans [TaxId: 1299] [159475] (6)
        SQ Q9RXY1 30-171
Ribosomal protein L4 [52165] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
1. Ribosomal protein L4 [52166] (1)
  uperfamily
  1. Ribosomal protein L4 [52167] (5)
    1. Ribosomal protein L4 [52168]
      synonym: 50S ribosomal protein L4e, HMAL4, HL6
      1. Thermotoga maritima [TaxId: 2336] [52169] (1)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [52170] (46)
        SQ P12735
      3. Thermus thermophilus [TaxId: 274] [159476] (7)
        SQ Q5SHN9 1-208
      4. Escherichia coli [TaxId: 562] [159477] (29)
        SQ P60723 1-201
      5. Deinococcus radiodurans [TaxId: 1299] [159478] (6)
        SQ Q9RXK1 2-198
Nqo1 FMN-binding domain-like [142018] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
1. Nqo1 FMN-binding domain-like [142019] (1)
  uperfamily
  1. Nqo1 FMN-binding domain-like [142020] (1)
    N-terminal part of Pfam 01512
    1. NADH-quinone oxidoreductase chain 1, Nqo1 [142021]
      1. Thermus thermophilus [TaxId: 274] [142022] (4)
        SQ Q56222 7-249
Flavodoxin-like [52171] (15)
3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
1. CheY-like [52172] (7)
  uperfamily
  1. CheY-related [52173] (32)
    1. CheY protein [52174]
      1. Escherichia coli [TaxId: 562] [52175] (35)
        SQ P06143
      2. Salmonella typhimurium [TaxId: 90371] [52176] (18)
      3. Thermotoga maritima [TaxId: 2336] [52177] (5)
        SQ Q56312
      4. Sinorhizobium meliloti, CheY2 [TaxId: 382] [102225] (2)
        SQ Q52884
    2. Nitrate/nitrite response regulator (NarL), receiver domain [52178]
      1. Escherichia coli [TaxId: 562] [52179] (2)
    3. NTRC receiver domain [52180]
      1. Salmonella typhimurium [TaxId: 90371] [52181] (6)
    4. Transcriptional regulatory protein FixJ, receiver domain [52182]
      1. Rhizobium meliloti [TaxId: 382] [52183] (4)
    5. Transcriptional regulatory protein DctD, receiver domain [52184]
      1. Sinorhizobium meliloti [TaxId: 382] [52185] (3)
    6. Sporulation response regulator Spo0A [52186]
      1. Bacillus stearothermophilus [TaxId: 1422] [52187] (2)
    7. Sporulation response regulator Spo0F [52188]
      1. Bacillus subtilis [TaxId: 1423] [52189] (11)
        SQ P06628
    8. Methylesterase CheB, N-terminal domain [52190]
      1. Salmonella typhimurium [TaxId: 90371] [52191] (1)
    9. PhoB receiver domain [52192]
      1. Thermotoga maritima [TaxId: 2336] [69445] (1)
      2. Escherichia coli [TaxId: 562] [52193] (7)
    10. PhoP receiver domain [82340]
      1. Bacillus subtilis [TaxId: 1423] [82341] (1)
      2. Escherichia coli [TaxId: 562] [159479] (3)
        SQ P23836 1-119
    11. Response regulator DrrB [89587]
      1. Thermotoga maritima [TaxId: 2336] [89588] (1)
    12. Response regulator for cyanobacterial phytochrome [75152]
      1. Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148] [75153] (2)
      2. Calothrix sp. pcc 7601, RcpA [TaxId: 1188] [102226] (1)
      3. Calothrix sp. pcc 7601, RcpB [TaxId: 1188] [102227] (1)
    13. Cell division response regulator DivK [82342]
      1. Caulobacter crescentus [TaxId: 155892] [82343] (5)
    14. Response regulator Sin1 [102228]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102229] (3)
    15. Transcriptional activator sigm54 (NtrC1), N-terminal domain [102230]
      1. Aquifex aeolicus [TaxId: 63363] [102231] (2)
    16. DNA-binding response regulator MicA, N-terminal domain [102232]
      1. Streptococcus pneumoniae [TaxId: 1313] [102233] (11)
    17. Probable two-component system transcriptional regulator Rv1626 [110464]
      contains extra C-terminal all-alpha subdomain (144-20), 3-helical bundle
      1. Mycobacterium tuberculosis [TaxId: 1773] [110465] (2)
        SQ O06143
    18. Response regulator PleD, receiver domain [117472]
      duplication: tandem repeat of 2 CheY-like domains
      1. Caulobacter crescentus [TaxId: 155892] [117473] (5)
        SQ Q9A5I5
    19. Sensor kinase protein RcsC, C-terminal domain [142023]
      1. Escherichia coli [TaxId: 562] [142024] (2)
        SQ P14376 817-949
    20. Transcriptional regulatory protein KdpE, N-terminal domain [142025]
      1. Escherichia coli [TaxId: 562] [142026] (4)
        SQ P21866 2-120
    21. Response regulatory protein StyR, N-terminal domain [142027]
      1. Pseudomonas fluorescens [TaxId: 294] [142028] (2)
        SQ O30989 3-130
    22. Hypothetical protein BH3024 [142029]
      1. Bacillus halodurans [TaxId: 86665] [142030] (1)
        SQ Q9K8I2 2-119
    23. Transcriptional regulatory protein PrrA, N-terminal domain [142031]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142032] (4)
        SQ P0A5Z6 7-127
    24. TorCAD operon transcriptional regulator TorD, N-terminal domain [142033]
      1. Escherichia coli [TaxId: 562] [142034] (4)
        SQ P38684 2-121
    25. Aerobic respiration control protein ArcA, N-terminal domain [142035]
      1. Escherichia coli [TaxId: 562] [142036] (4)
        SQ P0A9Q1 2-122
  2. Receiver domain of the ethylene receptor [52194] (1)
    1. Receiver domain of the ethylene receptor [52195]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [52196] (1)
  3. Positive regulator of the amidase operon AmiR [52197] (1)
    1. Positive regulator of the amidase operon AmiR [52198]
      contains coiled coil and small all-alpha subdomains in the C-terminal extension
      1. Pseudomonas aeruginosa [TaxId: 287] [52199] (1)
  4. Ornithine decarboxylase N-terminal "wing" domain [52252] (1)
    1. Ornithine decarboxylase N-terminal "wing" domain [52253]
      1. Lactobacillus sp., strain 30a [TaxId: 1591] [52254] (2)
  5. N-terminal domain of the circadian clock protein KaiA [82344] (1)
    lacks canonical receiver domains features
    1. N-terminal domain of the circadian clock protein KaiA [82345]
      1. Synechococcus elongatus [TaxId: 32046] [82346] (3)
        SQ Q79PF6
  6. RcsC linker domain-like [142037] (1)
    PfamB 016190; probable rudiment CheY-like domain; precedes the C-terminal CheY-related domain of similar structure
    1. Sensor kinase protein RcsC [142038]
      1. Escherichia coli [TaxId: 562] [142039] (2)
        SQ P14376 700-816
  7. AF1403 C-terminal domain-like [142040] (1)
    1. Hypothetical protein AF1403, C-terminal domain [142041]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [142042] (3)
        SQ O28869 79-217
2. Toll/Interleukin receptor TIR domain [52200] (1)
  uperfamily
  1. Toll/Interleukin receptor TIR domain [52201] (2)
    1. Toll-like receptor 1, TLR1 [52202]
      1. Human (Homo sapiens) [TaxId: 9606] [52203] (1)
    2. Toll-like receptor 2, TLR2 [52204]
      1. Human (Homo sapiens) [TaxId: 9606] [52205] (3)
3. Hypothetical protein MTH538 [52206] (1)
  uperfamily
  1. Hypothetical protein MTH538 [52207] (1)
    1. Hypothetical protein MTH538 [52208]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52209] (1)
4. Succinyl-CoA synthetase domains [52210] (1)
  uperfamily
  1. Succinyl-CoA synthetase domains [52211] (6)
    contain additional N-terminal strand "0", antiparallel to strand 2
    1. Succinyl-CoA synthetase, alpha-chain, C-terminal domain [52212]
      1. Escherichia coli [TaxId: 562] [52213] (18)
      2. Thermus thermophilus [TaxId: 274] [89589] (1)
      3. Pig (Sus scrofa) [TaxId: 9823] [52214] (6)
    2. Succinyl-CoA synthetase, beta-chain, C-terminal domain [52215]
      1. Escherichia coli [TaxId: 562] [52216] (18)
      2. Pig (Sus scrofa) [TaxId: 9823] [52217] (6)
    3. Acetate-CoA ligase alpha chain, AcdA, domains 2 and 3 [142043]
      duplication: tandem repeat of two similar domains, structurally and functionally related to the C-terminal domains of Succinyl-CoA synthetase subunits; the first domain (2) is related to the alpha-chain domain, whereas the second domain (3) is related to the beta-chain domain
      1. Pyrococcus horikoshii [TaxId: 53953] [142044] (4)
        SQ O58493 130-290! SQ O58493 291-453
        PH0766
5. Flavoproteins [52218] (8)
  uperfamily
  1. Flavodoxin-related [52219] (13)
    binds FMN
    1. Flavodoxin [52220]
      1. Chondrus crispus [TaxId: 2769] [52221] (1)
      2. Desulfovibrio vulgaris [TaxId: 881] [52222] (25)
        SQ P00323
      3. Anabaena, pcc 7119 and 7120 [TaxId: 1163] [52223] (7)
      4. Escherichia coli [TaxId: 562] [52224] (2)
      5. Synechococcus elongatus PCC 7942 [TaxId: 1140] [52225] (10)
      6. Clostridium beijerinckii [TaxId: 1520] [52226] (16)
      7. Helicobacter pylori [TaxId: 210] [69446] (1)
      8. Megasphaera elsdenii [TaxId: 907] [142045] (1)
        SQ P00321 1-137
      9. Azotobacter vinelandii [TaxId: 354] [142046] (2)
        SQ P00324 1-179
    2. FMN-binding domain of the cytochrome P450bm-3 [52227]
      1. Bacillus megaterium [TaxId: 1404] [52228] (1)
    3. Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain [52229]
      1. Desulfovibrio gigas [TaxId: 879] [52230] (1)
    4. ROO-like flavoprotein TM0755, C-terminal domain [110466]
      1. Thermotoga maritima [TaxId: 2336] [110467] (1)
        SQ Q9WZL4
    5. Nitric oxide reductase C-terminal domain [142047]
      1. Moorella thermoacetica [TaxId: 1525] [142048] (12)
        SQ Q9FDN7 251-399
  2. Cytochrome p450 reductase N-terminal domain-like [52231] (4)
    1. NADPH-cytochrome p450 reductase, N-terminal domain [52232]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52233] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [52234] (1)
    2. Nitric oxide (NO) synthase FMN domain [110468]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110469] (1)
        SQ P29476 750-1413
    3. Sulfite reductase alpha-component CysJ N-terminal domain [142049]
      1. Escherichia coli [TaxId: 562] [142050] (1)
        SQ P38038 63-208
  3. Quinone reductase [52235] (6)
    binds FAD
    1. NAD(P)H:quinone reductase [52236]
      1. Mouse (Mus musculus) [TaxId: 10090] [52237] (1)
      2. Rat (Rattus rattus) [TaxId: 10117] [52238] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [52239] (16)
    2. Quinone reductase type 2 (menadione reductase) [52240]
      1. Human (Homo sapiens) [TaxId: 9606] [52241] (24)
    3. ACP phosphodiesterase AcpD [110470]
      evolved new enzymatic activity
      1. Escherichia coli [TaxId: 562] [110471] (8)
        SQ P41407
      2. Salmonella typhimurium [TaxId: 90371] [110472] (1)
        SQ Q8XFP4
  4. Hypothetical protein SP1951 [102234] (1)
    1. Hypothetical protein SP1951 [102235]
      1. (Streptococcus pneumoniae) [TaxId: 1313] [102236] (3)
  5. Hypothetical protein YwqN [102237] (1)
    1. Hypothetical protein YwqN [102238]
      Trp repressor binding protein
      1. Bacillus subtilis [TaxId: 1423] [102239] (1)
  6. NADPH-dependent FMN reductase [89590] (4)
    Pfam 03358
    1. Azobenzene reductase [89591]
      1. Bacillus subtilis [TaxId: 1423] [89592] (5)
        YhdA gene product
    2. Hypothetical protein Ylr011wp [110473]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110474] (1)
        SQ Q07923
    3. Hypothetical protein PA1204 [110475]
      1. Pseudomonas aeruginosa [TaxId: 287] [110476] (2)
        SQ Q9I4D4 5-167
    4. Putative arsenical resistance protein [142051]
      1. Shigella flexneri [TaxId: 623] [142052] (4)
        SQ Q7UC03 1-233
  7. Flavoprotein NrdI [110477] (1)
    1. Flavoprotein NrdI [110478]
      1. Bacillus subtilis [TaxId: 1423] [110479] (1)
        SQ P50618
  8. WrbA-like [117474] (3)
    1. Trp repressor binding protein WrbA [117475]
      1. Deinococcus radiodurans [TaxId: 1299] [117476] (9)
        SQ Q9RYU4
      2. Pseudomonas aeruginosa [TaxId: 287] [142053] (5)
        SQ Q9I509 3-198! SQ Q9I509 4-196
    2. Flavodoxin FldA [142054]
      1. Aquifex aeolicus [TaxId: 63363] [142055] (6)
        SQ O67866 1-184
6. Cobalamin (vitamin B12)-binding domain [52242] (1)
  uperfamily
  1. Cobalamin (vitamin B12)-binding domain [52243] (6)
    1. Methionine synthase, C-terminal domain [52244]
      1. Escherichia coli [TaxId: 562] [52245] (4)
    2. Glutamate mutase, small subunit [52246]
      1. Clostridium tetanomorphum [TaxId: 1553] [52247] (3)
      2. Clostridium cochlearium [TaxId: 1494] [52248] (4)
    3. Methylmalonyl-CoA mutase alpha subunit, C-terminal domain [88717]
      active subunit; binds B12
      1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88718] (8)
    4. Methylmalonyl-CoA mutase beta subunit, C-terminal domain [88719]
      inactive subunit
      1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [88720] (8)
    5. D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain [117477]
      most similar to the glutamate mutase subunit
      1. Clostridium sticklandii [TaxId: 1511] [117478] (1)
        SQ Q9ZFE5
7. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52255] (1)
  uperfamily
  1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52256] (4)
    1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52257]
      1. Escherichia coli [TaxId: 562] [52258] (3)
      2. Thermotoga maritima [TaxId: 2336] [89593] (1)
        TM0446
      3. Acetobacter aceti [TaxId: 435] [110480] (5)
        SQ Q72LC1
      4. Bacillus anthracis [TaxId: 1392] [117479] (1)
        SQ Q81ZH8
8. SGNH hydrolase [52266] (9)
  uperfamily
  1. Esterase [52267] (1)
    1. Esterase [52268]
      1. Streptomyces scabies [TaxId: 1930] [52269] (3)
  2. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52270] (1)
    1. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52271]
      includes irregular N- and C-terminal extensions
      1. Influenza C virus [TaxId: 11552] [52272] (1)
  3. Acetylhydrolase [52273] (3)
    1. Platelet-activating factor acetylhydrolase [52274]
      1. Cow (Bos taurus), alpha1 [TaxId: 9913] [52275] (6)
      2. Cow (Bos taurus), alpha2 [TaxId: 9913] [88721] (11)
    2. Uncharacterized protein SP1450 [159480]
      Putative platelet activating factor
      1. Streptococcus pneumoniae [TaxId: 1313] [159481] (4)
        SQ Q97PY9 1-211
  4. Rhamnogalacturonan acetylesterase [52276] (1)
    1. Rhamnogalacturonan acetylesterase [52277]
      1. Fungus (Aspergillus aculeatus) [TaxId: 5053] [52278] (4)
  5. TAP-like [89594] (2)
    1. Thioesterase I, TAP [89595]
      multifunctional enzyme with thioesterase, esterase, protease and lysophospholiase activities
      1. Escherichia coli [TaxId: 562] [89596] (5)
        SQ P29679 27-205
    2. Lipase/acylhydrolase [142056]
      1. Enterococcus faecalis [TaxId: 1351] [142057] (1)
        SQ Q839J6 1-195
  6. Hypothetical protein alr1529 [102240] (1)
    1. Hypothetical protein alr1529 [102241]
      putative lipase
      1. Nostoc sp. pcc 7120 [TaxId: 103690] [102242] (5)
  7. Putative acetylxylan esterase-like [142058] (2)
    Pfam 03629 (DUF303); contains a characteristic zinc(less) finger-like insertion after strand 1; lacks the conserved in other families Asn residue
    1. Putative acetylxylan esterase At4g34215 [142059]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142060] (4)
        SQ Q8L9J9 17-260
    2. Acetylxylan esterase related enzyme [142061]
      1. Clostridium acetobutylicum [TaxId: 1488] [142062] (6)
        SQ Q97LM8 1-282
  8. YxiM C-terminal domain-like [159482] (1)
    subfamily of Pfam 00657
    1. Hypothetical protein YxiM [159483]
      1. Bacillus subtilis [TaxId: 1423] [159484] (1)
        SQ P42304 175-382
  9. BT2961-like [159485] (2)
    PfamB 005894;homotrimeric assembly
    1. Uncharacterized protein BT2961 [159486]
      putative lipase
      1. Bacteroides thetaiotaomicron [TaxId: 818] [159487] (6)
        SQ Q8A3J3 38-285
    2. Uncharacterized protein Lp3323 [159488]
      1. Lactobacillus plantarum [TaxId: 1590] [159489] (3)
        SQ Q88SR8 18-224
9. Beta-D-glucan exohydrolase, C-terminal domain [52279] (1)
  uperfamily
  1. Beta-D-glucan exohydrolase, C-terminal domain [52280] (1)
    1. Beta-D-glucan exohydrolase, C-terminal domain [52281]
      interdomain linker forms an additional, N-terminal strand
      1. Barley (Hordeum vulgare) [TaxId: 4513] [52282] (9)
10. Formate/glycerate dehydrogenase catalytic domain-like [52283] (3)
  uperfamily
  1. Formate/glycerate dehydrogenases, substrate-binding domain [52284] (9)
    this domain is interrupted by the Rossmann-fold domain
    1. Formate dehydrogenase [52285]
      contains an additional beta-hairpin after the common fold
      1. Pseudomonas sp., strain 101 [TaxId: 306] [52286] (2)
    2. Putative formate dehydrogenase [52287]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [52288] (1)
    3. Transcription corepressor CtbP [82347]
      C-terminal binding protein 1; a dehydrogenase
      1. Human (Homo sapiens), Ctbp1 [TaxId: 9606] [82348] (1)
      2. Rat (Rattus norvegicus), Ctbp3 [TaxId: 10116] [89597] (2)
    4. D-2-hydroxyisocaproate dehydrogenase [52289]
      1. Lactobacillus casei [TaxId: 1582] [52290] (1)
    5. D-glycerate dehydrogenase [52291]
      1. Hyphomicrobium methylovorum [TaxId: 84] [52292] (1)
    6. Phosphoglycerate dehydrogenase [52293]
      has additional C-terminal domain of the ferredoxin fold
      1. Escherichia coli [TaxId: 562] [52294] (18)
      2. Mycobacterium tuberculosis [TaxId: 1773] [142063] (2)
        SQ P0A544 2-97,282-315
        there is an intervening domain between this domain and regulatory (C-terminal) domain
    7. D-lactate dehydrogenase [52295]
      1. Lactobacillus helveticus [TaxId: 1587] [52296] (3)
  2. L-alanine dehydrogenase-like [52297] (2)
    1. L-alanine dehydrogenase [52298]
      1. Phormidium lapideum [TaxId: 32060] [52299] (3)
    2. Nicotinamide nucleotide transhydrogenase dI component [63963]
      L-alanine dehydrogenase homologue
      1. Rhodospirillum rubrum [TaxId: 1085] [63964] (28)
  3. S-adenosylhomocystein hydrolase [52300] (3)
    1. S-adenosylhomocystein hydrolase [52301]
      contains additional secondary structures disguising the superfamily fold
      1. Human (Homo sapiens) [TaxId: 9606] [52302] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52303] (17)
      3. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117480] (1)
        SQ P50250
11. Type II 3-dehydroquinate dehydratase [52304] (1)
  uperfamily
  1. Type II 3-dehydroquinate dehydratase [52305] (5)
    1. Type II 3-dehydroquinate dehydratase [52306]
      1. Mycobacterium tuberculosis [TaxId: 1773] [52307] (4)
      2. Streptomyces coelicolor [TaxId: 1902] [52308] (40)
      3. Bacillus subtilis [TaxId: 1423] [82349] (1)
      4. Helicobacter pylori [TaxId: 210] [89598] (14)
      5. Actinobacillus pleuropneumoniae [TaxId: 715] [102243] (1)
12. N-(deoxy)ribosyltransferase-like [52309] (3)
  there are similar active site architectures as well as the catalytic mechanisms of functionally characterised members
  uperfamily
  1. N-deoxyribosyltransferase [52310] (3)
    1. Nucleoside 2-deoxyribosyltransferase [52311]
      class II N-deoxyribosyltransferase
      1. Lactobacillus leichmannii [TaxId: 28039] [52312] (2)
      2. Trypanosoma brucei [TaxId: 5691] [142064] (10)
        SQ Q57VC7 1-152
    2. Purine transdeoxyribosylase [102244]
      class I N-deoxyribosyltransferase
      1. Lactobacillus helveticus [TaxId: 1587] [102245] (5)
  2. Hypothetical protein PA1492 [110461] (1)
    lacks the last strand; monomer; predicted deoxyribosyltransferase activity
    1. Hypothetical protein PA1492 [110462]
      1. Pseudomonas aeruginosa [TaxId: 287] [110463] (1)
        SQ Q9I3M0
  3. ADP ribosyl cyclase-like [56630] (3)
    contains extra N-terminal all-alpha subdomain
    1. ADP ribosyl cyclase [56631]
      1. California sea hare (Aplysia californica) [TaxId: 6500] [56632] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [159490] (2)
        SQ P28907 45-291
    2. Bone marror stromal cell antigen 1, BST-1/CD157 (ADP ribosyl cyclase-2) [75597]
      1. Human (Homo sapiens) [TaxId: 9606] [75598] (6)
13. Ribosomal protein S2 [52313] (1)
  fold elaborated with additional structures
  uperfamily
  1. Ribosomal protein S2 [52314] (3)
    1. Ribosomal protein S2 [52315]
      1. Thermus thermophilus [TaxId: 274] [52316] (46)
        SQ P80371
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102246] (2)
      3. Escherichia coli [TaxId: 562] [159491] (26)
        SQ P0A7V0 8-225
14. Precorrin-8X methylmutase CbiC/CobH [63965] (1)
  fold elaborated with additional structures
  uperfamily
  1. Precorrin-8X methylmutase CbiC/CobH [63966] (3)
    1. Precorrin-8x methylmutase [63967]
      1. Pseudomonas denitrificans [TaxId: 43306] [63968] (2)
      2. Thermus thermophilus [TaxId: 274] [102247] (1)
    2. Precorrin-8x methylmutase related protein [102248]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102249] (1)
15. Class I glutamine amidotransferase-like [52317] (9)
  conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
  uperfamily
  1. Class I glutamine amidotransferases (GAT) [52318] (18)
    contains a catalytic Cys-His-Glu triad
    1. GMP synthetase [52319]
      1. Escherichia coli [TaxId: 562] [52320] (1)
    2. Carbamoyl phosphate synthetase, small subunit C-terminal domain [52321]
      1. Escherichia coli [TaxId: 562] [52322] (10)
        SQ P00907
    3. Anthranilate synthase GAT subunit, TrpG [52323]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [52324] (1)
      2. Salmonella typhimurium [TaxId: 90371] [63969] (1)
      3. Serratia marcescens [TaxId: 615] [63970] (2)
    4. GAT subunit, HisH, (or domain) of imidazoleglycerolphosphate synthase HisF [69447]
      1. Thermotoga maritima [TaxId: 2336] [69448] (3)
      2. Thermus thermophilus [TaxId: 274] [82350] (1)
      3. Baker's yeast (Saccharomyces cerevisiae), His7 [TaxId: 4932] [69449] (4)
    5. gamma-glutamyl hydrolase [75154]
      1. Human (Homo sapiens) [TaxId: 9606] [75155] (1)
    6. Hypothetical protein TM1158 [89599]
      1. Thermotoga maritima [TaxId: 2336] [89600] (1)
    7. Hypothetical protein YaaE [102250]
      glutamine amidotransferase of SNO/PDX2 family implicated in pyridoxine biosynthesis
      1. Bacillus subtilis [TaxId: 1423] [102251] (3)
      2. Bacillus stearothermophilus [TaxId: 1422] [102252] (1)
    8. CTP synthase PyrG, C-terminal domain [110481]
      1. Escherichia coli [TaxId: 562] [110482] (1)
        SQ P08398
      2. Thermus thermophilus [TaxId: 274] [110483] (3)
        SQ Q5SIA8
    9. FGAM synthase PurL, amidotransferase domain [110484]
      1. Salmonella typhimurium [TaxId: 90371] [110485] (1)
        SQ P74881
    10. GMP synthase subunit A, GuaAA [142065]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142066] (4)
        SQ Q9HJM3 1-196
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142067] (1)
        SQ O59071 1-188
    11. Pyridoxine biosynthesis protein 2, Pdx2 [142068]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [142069] (2)
        SQ Q5ND68 2-219
  2. A4 beta-galactosidase middle domain [82351] (1)
    probable non-catalytic branch of the class I GAT family; overall fold is very similar but the active site is not conserved
    1. A4 beta-galactosidase middle domain [82352]
      1. Thermus thermophilus [TaxId: 274] [82353] (2)
  3. DJ-1/PfpI [52325] (9)
    contains a catalytic triad or dyad different from the class I GAT triad
    1. Intracellular protease [52326]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [52327] (1)
    2. Hypothetical protein YhbO [89601]
      1. Escherichia coli [TaxId: 562] [89602] (1)
    3. DJ-1 [89603]
      RNA-binding protein regulatory subunit
      1. Human (Homo sapiens) [TaxId: 9606] [89604] (20)
        SQ Q99497
    4. Putative sigma cross-reacting protein 27A (SCRP-27A, EllB) [89606]
      involved in an early stage of isoprenoid biosynthesis; contains a Cys-Glu putative catalytic dyad
      1. Escherichia coli [TaxId: 562] [89607] (2)
    5. HSP31 (HchA; YedU) [89609]
      contains a buried Cys-His-Asp triad within one subunit
      1. Escherichia coli [TaxId: 562] [89610] (5)
    6. Hypothetical protein Ydr533Cp [102253]
      contains a buried Cys-His-Glu triad within one subunit
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102254] (4)
    7. GK2698 ortholog [117481]
      1. Bacillus stearothermophilus [TaxId: 1422] [117482] (1)
        SQ Q5KWF3; 96% sequence identity; Geobacillus kaustophilus TaxID: 1462
    8. Protein ThiJ (YajL) [142070]
      1. Escherichia coli [TaxId: 562] [142071] (2)
        SQ Q46948 2-196
    9. Hypothetical protein Atu0886 [142072]
      1. Agrobacterium tumefaciens [TaxId: 358] [142073] (3)
        SQ Q8UGZ9 1-188
  4. Catalase, C-terminal domain [52328] (2)
    1. Catalase, C-terminal domain [52329]
      1. Escherichia coli, HPII [TaxId: 562] [52330] (14)
      2. Neurospora crassa [TaxId: 5141] [117483] (1)
        SQ Q9C168 68-765
  5. Aspartyl dipeptidase PepE [52331] (1)
    probable circular permutation in the common core; contains a catalytic Ser-His-Glu triad
    1. Aspartyl dipeptidase PepE [52332]
      1. Salmonella typhimurium [TaxId: 90371] [52333] (2)
  6. ThuA-like [110486] (1)
    Pfam 06283; overall fold is very similar the class I GAT family but the putative active site has a different structure
    1. GK2113 homologue [110487]
      1. Bacillus stearothermophilus [TaxId: 1422] [110488] (1)
        SQ Q5KY38 # 99% sequence identity (Geobacillus kaustophilus TaxID:1462)
  7. LD-carboxypeptidase A N-terminal domain-like [142074] (1)
    N-terminal half of Pfam 02016
    1. LD-carboxypeptidase A, N-terminal domain [142075]
      1. Pseudomonas aeruginosa [TaxId: 287] [142076] (8)
        SQ Q9HTZ1 3-169! SQ Q9HTZ1 5-142! SQ Q9HTZ1 5-169
  8. HTS-like [142077] (1)
    Pfam 04204
    1. Homoserine O-succinyltransferase HTS (MetA) [142078]
      1. Bacillus cereus [TaxId: 1396] [142079] (1)
        SQ Q72X44 17-297
  9. STM3548-like [159492] (1)
    Pfam 07090; DUF1355
    1. Putative cytoplasmic protein STM3548 [159493]
      1. Salmonella typhimurium [TaxId: 90371] [159494] (6)
        SQ Q8ZLF9 8-253
Methylglyoxal synthase-like [52334] (1)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
1. Methylglyoxal synthase-like [52335] (3)
  contains a common phosphate-binding site
  uperfamily
  1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52336] (1)
    1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52337]
      1. Escherichia coli [TaxId: 562] [52338] (10)
        SQ P00968
  2. Methylglyoxal synthase, MgsA [52339] (3)
    1. Methylglyoxal synthase, MgsA [52340]
      1. Escherichia coli [TaxId: 562] [52341] (5)
      2. Thermotoga maritima [TaxId: 2336] [110489] (1)
        SQ Q9X0R7 #
      3. Thermus thermophilus [TaxId: 274] [142080] (6)
        SQ Q5SHD6 1-126
  3. Inosicase [63971] (3)
    1. IMP cyclohydrolase domain of bifunctional purine biosynthesis enzyme ATIC [63972]
      1. Chicken (Gallus gallus) [TaxId: 9031] [63973] (4)
        SQ P31335
      2. Human (Homo sapiens) [TaxId: 9606] [102255] (3)
      3. Thermotoga maritima [TaxId: 2336] [142081] (2)
        SQ Q9X0X6 1-157
Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
1. Ferredoxin reductase-like, C-terminal NADP-linked domain [52343] (5)
  binds NADP differently than classical Rossmann-fold
  N-terminal FAD-linked domain contains (6,10) barrel
  uperfamily
  1. Reductases [52344] (13)
    1. Ferredoxin reductase (flavodoxin reductase) [52345]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [52346] (7)
      2. Garden pea (Pisum sativum) [TaxId: 3888] [52347] (4)
      3. Paprika (Capsicum annuum) [TaxId: 4072] [52348] (1)
      4. Maize (Zea mays), leaf isoform [TaxId: 4577] [52349] (2)
      5. Maize (Zea mays), root isoform [TaxId: 4577] [63974] (1)
      6. Cyanobacterium (Anabaena sp.), pcc 7119 [TaxId: 1167] [52350] (25)
      7. Escherichia coli [TaxId: 562] [52351] (1)
      8. Azotobacter vinelandii [TaxId: 354] [52352] (1)
    2. NAD(P)H:flavin oxidoreductase [52353]
      1. Escherichia coli [TaxId: 562] [52354] (1)
    3. Nitrate reductase [52355]
      1. Corn (Zea mays) [TaxId: 4577] [52356] (3)
    4. cytochrome b5 reductase [52357]
      1. Pig (Sus scrofa), liver [TaxId: 9823] [52358] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [69450] (3)
        SQ P20070 33-300
      3. Human (Homo sapiens) [TaxId: 9606] [117484] (1)
        SQ P00387 30-300
  2. Aromatic dioxygenase reductase-like [52359] (3)
    contains additional 2Fe-2S ferredoxin domain at one of the termini
    1. Phthalate dioxygenase reductase [52360]
      1. Pseudomonas cepacia, db01 [TaxId: 292] [52361] (1)
    2. Benzoate dioxygenase reductase [75156]
      1. Acinetobacter sp. [TaxId: 472] [75157] (1)
    3. Methane monooxygenase component C, MmoC [117485]
      1. Methylococcus capsulatus [TaxId: 414] [117486] (1)
        SQ P22868 99-348 # structure of the N-terminal, 2Fe-2S ferredoxin domain is also known (1JQ4; scop_sp 69669)
  3. Dihydroorotate dehydrogenase B, PyrK subunit [52362] (1)
    contains 2Fe-2S cluster in the C-terminal extension
    1. Dihydroorotate dehydrogenase B, PyrK subunit [52363]
      1. Lactococcus lactis, isozyme B [TaxId: 1358] [52364] (3)
  4. NADPH-cytochrome p450 reductase-like [52365] (3)
    1. NADPH-cytochrome p450 reductase [52366]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52367] (4)
    2. Sulfite reductase flavoprotein [52368]
      1. Escherichia coli [TaxId: 562] [52369] (2)
    3. Neuronal nitric-oxide synthase FAD/NADP+ domain [69451]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69452] (2)
        SQ P29476 750-1413
  5. Flavohemoglobin, C-terminal domain [52370] (2)
    contains additional globin domain
    1. Flavohemoglobin, C-terminal domain [52371]
      1. Alcaligenes eutrophus [TaxId: 106590] [52372] (1)
      2. Escherichia coli [TaxId: 562] [75158] (1)
Adenine nucleotide alpha hydrolase-like [52373] (3)
core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
1. Nucleotidylyl transferase [52374] (5)
  uperfamily
  1. Class I aminoacyl-tRNA synthetases (RS), catalytic domain [52375] (22)
    contains a conserved all-alpha subdomain at the C-terminal extension
    1. Tyrosyl-tRNA synthetase (TyrRS) [52376]
      1. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [52377] (7)
      2. Staphylococcus aureus [TaxId: 1280] [69453] (4)
      3. Thermus thermophilus [TaxId: 274] [82354] (2)
      4. Archaeon Methanococcus jannaschii [TaxId: 2190] [89611] (3)
      5. Human (Homo sapiens) [TaxId: 9606] [82355] (2)
    2. Tryptophanyl-tRNA synthetase (TrpRS) [52378]
      overall structure is similar to TyrRS
      1. Bacillus stearothermophilus [TaxId: 1422] [52379] (9)
      2. Human (Homo sapiens) [TaxId: 9606] [102256] (16)
        SQ P23381 94-471
    3. Glutaminyl-tRNA synthetase (GlnRS) [52380]
      1. Escherichia coli [TaxId: 562] [52381] (14)
      2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159495] (2)
    4. Glutamyl-tRNA synthetase (GluRS) [52382]
      Catalytic domain is very similar to that of GlnRS
      1. Thermus thermophilus [TaxId: 274] [52383] (15)
    5. Glutamyl-Q tRNA-Asp synthetase YadB [102257]
      truncated GluRS and GlnRS homologue lacking the anticodon-binding domain; glutamylates the modified base queuosine (Q) of tRNA-Asp
      1. Escherichia coli [TaxId: 562] [102258] (2)
    6. Class I lysyl-tRNA synthetase [75159]
      similar domain organization to GluRS
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75160] (1)
    7. Methionyl-tRNA synthetase (MetRS) [52384]
      1. Thermus thermophilus [TaxId: 274] [52385] (4)
      2. Escherichia coli [TaxId: 562] [52386] (9)
      3. Pyrococcus abyssi [TaxId: 29292] [110490] (1)
        SQ Q9V011 1-606 # C-domain 616-722 is solved separately: 1MKH
    8. Cysteinyl-tRNA synthetase (CysRS) [75161]
      1. Escherichia coli [TaxId: 562] [75162] (3)
        SQ P21888
    9. Isoleucyl-tRNA synthetase (IleRS) [52387]
      1. Thermus thermophilus [TaxId: 274] [52388] (3)
      2. Staphylococcus aureus [TaxId: 1280] [52389] (3)
    10. Valyl-tRNA synthetase (ValRS) [52390]
      1. Thermus thermophilus [TaxId: 274] [52391] (3)
    11. Leucyl-tRNA synthetase (LeuRS) [82356]
      1. Thermus thermophilus [TaxId: 274] [82357] (3)
        contains a non-conserved insertion (residues 581-633) that forms a separate subdomain; possible rudiment Zn finger
    12. Arginyl-tRNA synthetase (ArgRS) [52392]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52393] (3)
      2. Thermus thermophilus [TaxId: 274] [69454] (1)
  2. Cytidylyltransferase [52394] (1)
    1. CTP:glycerol-3-phosphate cytidylyltransferase [52395]
      1. Bacillus subtilis [TaxId: 1423] [52396] (2)
  3. Adenylyltransferase [52397] (13)
    1. Phosphopantetheine adenylyltransferase [52398]
      1. Escherichia coli [TaxId: 562] [52399] (4)
      2. Thermus thermophilus [TaxId: 274] [89612] (1)
      3. Bacillus subtilis [TaxId: 1423] [102259] (1)
      4. Thermotoga maritima [TaxId: 2336] [110491] (1)
        SQ Q9WZK0
      5. Mycobacterium tuberculosis [TaxId: 1773] [110492] (1)
        SQ Q50452
    2. Cytosolic NMN/NAMN adenylyltransferase [89613]
      1. Human (Homo sapiens), FKSG76 [TaxId: 9606] [89614] (6)
    3. Nicotinamide mononucleotide (NMN) adenylyltransferase [52400]
      1. Human (Homo sapiens) [TaxId: 9606] [75163] (5)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [52401] (1)
      3. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63975] (6)
      4. Bacillus subtilis [TaxId: 1423] [75164] (2)
      5. Escherichia coli [TaxId: 562] [82358] (2)
    4. Transcriptional regulator NadR, NMN-adenylyltransferase domain [75165]
      1. Haemophilus influenzae [TaxId: 727] [75166] (1)
    5. FMN adenylyltransferase domain of bifunctional FAD synthetase [102260]
      1. Thermotoga maritima [TaxId: 2336] [102261] (7)
        SQ Q9WZW1
        TM0379
  4. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63976] (3)
    contains C-terminal subdomain similar to one structural repeat of the Creatinase/aminopeptidase family
    1. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63977]
      1. Escherichia coli [TaxId: 562] [63978] (1)
      2. Mycobacterium tuberculosis [TaxId: 1773] [89615] (21)
      3. Thermus thermophilus [TaxId: 274] [89616] (2)
  5. ATP sulfurylase catalytic domain [63979] (5)
    1. ATP sulfurylase catalytic domain [63980]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63981] (8)
      2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [63982] (2)
      3. Sulfur-oxidizing endosymbiont of Riftia pachyptila [TaxId: 35843] [69455] (1)
        lacks the C-terminal domain
      4. Thermus thermophilus [TaxId: 274] [102262] (1)
        lacks the C-terminal domain
      5. Human (Homo sapiens) [TaxId: 9606] [142082] (6)
        SQ O43252 390-624
2. Adenine nucleotide alpha hydrolases-like [52402] (6)
  share similar mode of ligand (Adenosine group) binding
  can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group
  uperfamily
  1. N-type ATP pyrophosphatases [52403] (13)
    1. GMP synthetase, central domain [52404]
      1. Escherichia coli [TaxId: 562] [52405] (1)
    2. NH3-dependent NAD+-synthetase [52406]
      1. Bacillus subtilis [TaxId: 1423] [52407] (7)
      2. Escherichia coli [TaxId: 562] [142083] (5)
        SQ P18843 2-275
      3. Helicobacter pylori [TaxId: 210] [142084] (3)
        SQ O25096 3-257
    3. Asparagine synthetase B, C-terminal domain [52408]
      1. Escherichia coli [TaxId: 562] [52409] (1)
    4. beta-Lactam synthetase [69456]
      Asparagine synthetase B homologue
      1. Streptomyces clavuligerus [TaxId: 1901] [69457] (5)
      2. Pectobacterium carotovorum [TaxId: 554] [102263] (2)
        carbapenam synthetase CarA
    5. Argininosuccinate synthetase, N-terminal domain [69458]
      1. Escherichia coli [TaxId: 562] [69459] (4)
      2. Thermus thermophilus [TaxId: 274] [75167] (7)
      3. Thermotoga maritima [TaxId: 2336] [110493] (1)
        SQ Q9X2A1
    6. Putative N-type ATP pyrophosphatase PF0828 [102264]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [102265] (1)
    7. Hypothetical protein PH1257 [142085]
      probable orthologue of PF0828
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142086] (4)
        SQ O58996 2-227
    8. Queuosine biosynthesis protein QueC [159496]
      1. Erwinia carotovora [TaxId: 554] [159497] (1)
        SQ Q6D820 1-230
  2. PP-loop ATPase [82359] (2)
    1. tRNA-Ile-lysidine synthetase, TilS, N-terminal domain [82360]
      formerly putative cell cycle protein MesJ
      1. Escherichia coli [TaxId: 562] [82361] (1)
    2. TilS-like protein Aq_1887 [142087]
      1. Aquifex aeolicus [TaxId: 63363] [142088] (10)
        SQ O67728 1-216
  3. PAPS reductase-like [52410] (2)
    1. Phosphoadenylyl sulphate (PAPS) reductase [52411]
      1. Escherichia coli [TaxId: 562] [52412] (1)
    2. Sulfate adenylyltransferase subunit 2, CysD [142089]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [142090] (1)
        SQ Q87WW0 1-211
  4. ETFP subunits [52432] (6)
    alpha/beta heterodimer of homologous subunits; contains additional strands on both edges of the core sheet
    1. Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain [81393]
      contains an additional FAD-binding domain of DHS-like fold
      1. Human (Homo sapiens) [TaxId: 9606] [81389] (4)
        SQ P13804 20-203
      2. Paracoccus denitrificans [TaxId: 266] [81391] (1)
      3. Methylophilus methylotrophus [TaxId: 17] [82362] (8)
    2. Small, beta subunit of electron transfer flavoprotein ETFP [81394]
      binds AMP
      1. Human (Homo sapiens) [TaxId: 9606] [81390] (4)
        SQ P38117
      2. Paracoccus denitrificans [TaxId: 266] [81392] (1)
      3. Methylophilus methylotrophus [TaxId: 17] [82363] (8)
  5. Universal stress protein-like [52436] (7)
    Pfam 00582
    1. "Hypothetical" protein MJ0577 [52437]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52438] (1)
    2. Universal stress protein A, UspA [69461]
      1. Haemophilus influenzae [TaxId: 727] [69462] (1)
        the nucleotide-binding is not known
    3. Hypothetical protein Aq_178 [102266]
      putative universal stress protein
      1. Aquifex aeolicus [TaxId: 63363] [102267] (1)
    4. Hypothetical protein Rv1636 [110494]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110495] (1)
        SQ O06153
    5. Hypothetical protein TTHA0895 [117487]
      1. Thermus thermophilus [TaxId: 274] [117488] (4)
        SQ Q5SJV7
    6. Putative ethylene-responsive protein AT3g01520/F4P13_7 [142091]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142092] (6)
        SQ Q940U0 5-175
    7. Hypothetical protein TTC0031 [159498]
      TT0030
      1. Thermus thermophilus [TaxId: 274] [159499] (2)
        SQ Q72LM7 2-135
  6. ThiI-like [142093] (2)
    Pfam 02568
    1. Thiamine biosynthesis protein ThiI, C-terminal domain [142094]
      1. Bacillus anthracis [TaxId: 1392] [142095] (1)
        SQ Q81KU0 174-391
    2. Hypothetical protein PH1313, C-terminal domain [142096]
      overal structure is similar to ThiI
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142097] (2)
        SQ O59053 176-307
3. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52413] (1)
  uperfamily
  1. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52414] (2)
    1. UDP-glucose dehydrogenase (UDPGDH), C-terminal (UDP-binding) domain [52415]
      1. Streptococcus pyogenes [TaxId: 1314] [52416] (2)
    2. GDP-mannose 6-dehydrogenase, GDP-binding domain [89617]
      1. Pseudomonas aeruginosa [TaxId: 287] [89618] (3)
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52418] (1)
  uperfamily
  1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52419] (6)
    1. Thymidine phosphorylase [52420]
      1. Escherichia coli [TaxId: 562] [52421] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [102268] (1)
    2. Pyrimidine nucleoside phosphorylase [52422]
      1. Bacillus stearothermophilus [TaxId: 1422] [52423] (1)
    3. Anthranilate phosphoribosyltransferase (TrpD) [82364]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82365] (14)
      2. Pectobacterium carotovorum [TaxId: 554] [82366] (2)
      3. Thermus thermophilus [TaxId: 274] [102269] (5)
Cryptochrome/photolyase, N-terminal domain [52424] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Cryptochrome/photolyase, N-terminal domain [52425] (1)
  uperfamily
  1. Cryptochrome/photolyase, N-terminal domain [52426] (5)
    1. DNA photolyase [52427]
      binds a light-harvesting cofactor
      1. Escherichia coli [TaxId: 562] [52428] (1)
        cofactor is MHTF
      2. Thermus thermophilus [TaxId: 274] [69460] (5)
      3. Synechococcus elongatus [TaxId: 32046] [52429] (7)
        SQ P05327 1-474
        cofactor is HDF
    2. Cryptochrome [82367]
      1. Synechocystis sp., pcc 6803 [TaxId: 1143] [82368] (1)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110496] (2)
        SQ Q43125 13-497
DsrEFH-like [75168] (1)
3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215
1. DsrEFH-like [75169] (2)
  uperfamily
  1. DsrEF-like [75170] (6)
    Pfam 02635
    1. Hypothetical protein YchN [82369]
      1. Escherichia coli [TaxId: 562] [82370] (1)
    2. Hypothetical protein MTH1491 [75171]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75172] (1)
    3. Sulfurtransferase DsrE [142098]
      1. Chromatium vinosum [TaxId: 1049] [142099] (7)
        SQ O87896 1-130
    4. tRNA 2-thiouridine synthesizing protein D, TusD [142100]
      formerly hypothetical protein YheN
      1. Escherichia coli [TaxId: 562] [142101] (3)
        SQ P45532 1-128
    5. Intracellular sulfur oxidation protein DsrF [142102]
      1. Chromatium vinosum [TaxId: 1049] [142103] (7)
        SQ O87897 5-136
    6. tRNA 2-thiouridine synthesizing protein C, TusC [142104]
      formerly hypothetical protein YheM
      1. Escherichia coli [TaxId: 562] [142105] (3)
        SQ P45531 1-119
  2. DsrH-like [117489] (3)
    Pfam 04077
    1. Hypothetical protein TM0979 [117490]
      1. Thermotoga maritima [TaxId: 2336] [117491] (2)
        SQ Q9X074
    2. tRNA 2-thiouridine synthesizing protein B, TusB [142106]
      formerly hypothetical protein YheL
      1. Escherichia coli [TaxId: 562] [142107] (3)
        SQ P45530 1-95
    3. DsrH [142108]
      1. Chromatium vinosum [TaxId: 1049] [142109] (7)
        SQ O87898 2-102
PIN domain-like [88722] (1)
3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145
1. PIN domain-like [88723] (2)
  uperfamily
  1. PIN domain [89619] (7)
    Pfam 01850
    1. Hypothetical protein AF0591 [89620]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89621] (1)
    2. Hypothetical protein PAE2754 [102270]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [102271] (2)
    3. Hypothetical protein AF1683 [117492]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117493] (1)
        SQ O28590
    4. Trafficking protein B [142110]
      1. Neisseria gonorrhoeae [TaxId: 485] [142111] (9)
        SQ Q5F882 1-138! SQ Q9RF91 1-138
    5. Hypothetical protein PH0500 [142112]
      1. Pyrococcus horikoshii [TaxId: 53953] [142113] (4)
        SQ O58236 2-149
    6. Conserved hypothetical protein PAE0151 [142114]
      1. Pyrobaculum aerophilum [TaxId: 13773] [142115] (1)
        SQ Q8ZZP3 1-130
    7. Hypothetical protein PF0355 [142116]
      PH0500 ortholog
      1. Pyrococcus furiosus [TaxId: 2261] [142117] (4)
        SQ Q8U3V0 2-148
  2. 5' to 3' exonuclease catalytic domain [53045] (8)
    contains an alpha-helical arch and additional strand 6 antiparallel to the rest; strand order 321456; similarity to the resolvase-like fold
    1. T4 RNase H [53046]
      1. Bacteriophage T4 [TaxId: 10665] [53047] (2)
    2. 5' to 3' exonuclease domain of DNA polymerase Taq [53048]
      1. Thermus aquaticus [TaxId: 271] [53049] (4)
    3. T5 5'-exonuclease [53050]
      1. Bacteriophage T5 [TaxId: 10726] [53051] (4)
    4. Flap endonuclease-1 (Fen-1 nuclease) [53052]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53053] (2)
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82436] (1)
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53055] (1)
      4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102272] (2)
      5. Human (Homo sapiens) [TaxId: 9606] [142118] (3)
        SQ P39748 2-217
Ribose/Galactose isomerase RpiB/AlsB [89622] (1)
3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topological similarity to a part of the arginase/deacetylase fold
1. Ribose/Galactose isomerase RpiB/AlsB [89623] (1)
  uperfamily
  1. Ribose/Galactose isomerase RpiB/AlsB [89624] (3)
    1. Alternate ribose 5-phosphate isomerase B, RpiB [89625]
      1. Escherichia coli [TaxId: 562] [89626] (1)
      2. Mycobacterium tuberculosis [TaxId: 1773] [102273] (18)
        SQ Q79FD7
        Rv2465c
    2. Putative sugar-phosphate isomerase [89627]
      1. Thermotoga maritima [TaxId: 2336] [89628] (1)
        TM1080
EreA/ChaN-like [159500] (1)
Core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order:51423;
1. EreA/ChaN-like [159501] (3)
  there are four conserved residues in the putative active site: two His and two Glu
  1. ChaN-like [159502] (1)
    Pfam 04187; DUF399; Ferric uptake regulator CjrA
    1. Heme transport protein ChaN [159503]
      1. Campylobacter jejuni [TaxId: 197] [159504] (1)
        SQ Q0PBW2 27-281
  2. PMT domain-like [159505] (1)
    This is the second from the PMT C-terminus; it retains the superfamily fold and the active site mainchain conformation but lacks the conserved in the other two families His and Glu residues
    1. Dermonecrotic toxin, ToxA [159506]
      Synonym: Mitogenic toxin PMT
      1. Pasteurella multocida [TaxId: 747] [159507] (4)
        SQ P17452 875-1093
  3. EreA-like [159508] (2)
    Pfam 05139; Erythromycin esterase-like; the superfamily core is decorated with insertion of a four-helical bundle and a C-terminal alpha+beta extension
    1. Succinoglycan biosynthesis protein BC3120 [159509]
      1. Bacillus cereus [TaxId: 1396] [159510] (3)
        SQ Q81BN2 40-442
    2. Succinoglycan biosynthesis protein BC3205 [159511]
      1. Bacillus cereus [TaxId: 1396] [159512] (1)
        SQ Q81BF7 33-445
alpha/beta knot [75216] (1)
core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot
1. alpha/beta knot [75217] (8)
  known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
  all known members have dimeric structures
  uperfamily
  1. YbeA-like [82371] (4)
    Pfam 02590
    1. Hypothetical protein YbeA [82372]
      1. Escherichia coli [TaxId: 562] [82373] (1)
    2. Hypothetical protein TM0844 [102274]
      1. Thermotoga maritima [TaxId: 2336] [102275] (1)
    3. Hypothetical protein SAV0024/SA0023 [102276]
      1. Staphylococcus aureus [TaxId: 1280] [102277] (1)
    4. Hypothetical protein YydA [110497]
      1. Bacillus subtilis [TaxId: 1423] [110498] (1)
        SQ Q45601
  2. tRNA(m1G37)-methyltransferase TrmD [89629] (3)
    fold and dimerisation mode are similar to those of the YbeA-like family; contains additional C-terminal all-alpha subdomain
    1. tRNA(m1G37)-methyltransferase TrmD [89630]
      1. Haemophilus influenzae [TaxId: 727] [89631] (4)
      2. Aquifex aeolicus [TaxId: 63363] [102278] (1)
      3. Escherichia coli [TaxId: 562] [110499] (1)
        SQ P07020
  3. SpoU-like RNA 2'-O ribose methyltransferase [75218] (4)
    contains extra strand (3) in the parallel beta-sheet, order 321546
    1. tRNA (Gm18) methyltransferase TrmH [102279]
      1. Thermus thermophilus [TaxId: 274] [102280] (1)
    2. Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) [82374]
      1. Haemophilus influenzae [TaxId: 727] [82375] (2)
    3. RrmA (RrmH), C-terminal domain [75219]
      23S rRNA methyltransferase; proposed gene names are as appear in the original publication (and the PDB entry)
      1. Thermus thermophilus [TaxId: 274] [75220] (1)
    4. RlmB, C-terminal domain [82376]
      23S rRNA G2251 2'O-methytransferase
      1. Escherichia coli [TaxId: 562] [82377] (1)
  4. Hypothetical protein MTH1 (MT0001), dimerisation domain [75221] (1)
    contains extra strand (3) in the parallel beta-sheet, order 321546; interrupted by an insert OB-fold domain
    1. Hypothetical protein MTH1 (MT0001), dimerisation domain [75222]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75223] (1)
  5. YggJ C-terminal domain-like [89632] (3)
    contains extra strand (3) in the parallel beta-sheet, order 321546; similar dimerisation to the MTH1 domain
    1. Hypothetical protein HI0303 [89633]
      1. Haemophilus influenzae [TaxId: 727] [89634] (2)
    2. Hypothetical protein YqeU [102281]
      1. Bacillus subtilis [TaxId: 1423] [102282] (1)
    3. Hypothetical protein TTHA0657 (TT1575) [117494]
      1. Thermus thermophilus [TaxId: 274] [117495] (3)
        SQ Q5SKI6
  6. EMG1/NEP1-like [159513] (2)
    Pfam 03587; structurally most similar to the AF1056-like family, but more decorated
    1. Ribosome biogenesis protein NEP1 [159514]
      1. Methanococcus jannaschii [TaxId: 2190] [159515] (6)
        SQ Q57977 2-205
    2. Essential for mitotic growth 1, EMG1 [159516]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159517] (2)
        SQ Q06287 23-251
  7. AF1056-like [159518] (2)
    Pfam 04013; DUF358
    1. Uncharacterized protein AF1056 [159519]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159520] (2)
        SQ O29206 95-288
    2. Uncharacterized protein VCA1059 [159521]
      1. Vibrio cholerae [TaxId: 666] [159522] (2)
        SQ Q9KKP3 1-201
  8. AF0751-like [159523] (1)
    Pfam 01994; DUF127
    1. Uncharacterized protein AF0751 [159524]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159525] (2)
        SQ O29507 1-167
PreATP-grasp domain [52439] (1)
3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
possible rudiment form of Rossmann-fold domain
1. PreATP-grasp domain [52440] (8)
  precedes the ATP-grasp domain common to all superfamily members, can contain a substrate-binding function
  uperfamily
  1. BC N-terminal domain-like [52441] (8)
    1. Biotin carboxylase (BC), N-terminal domain [52442]
      subunit of acetyl-CoA and pyruvate carboxylases
      1. Escherichia coli [TaxId: 562] [52443] (13)
      2. Aquifex aeolicus [TaxId: 63363] [102283] (1)
    2. Glycinamide ribonucleotide synthetase (GAR-syn), N-domain [52444]
      1. Escherichia coli [TaxId: 562] [52445] (1)
      2. Thermotoga maritima [TaxId: 2336] [110500] (1)
        SQ Q9X0X7
    3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), N-domain [52446]
      1. Escherichia coli [TaxId: 562] [52447] (6)
    4. Glycinamide ribonucleotide transformylase PurT, N-domain [52448]
      1. Escherichia coli [TaxId: 562] [52449] (7)
    5. Carbamoyl phosphate synthetase (CPS), large subunit PreATP-grasp domains [52450]
      duplication: CPS large subunit contains two full BC-like lobes: carboxyphosphate and carbamoyl phosphate domains
      1. Escherichia coli [TaxId: 562] [52451] (10)
        SQ P00968
    6. Acetyl-CoA carboxylase, BC-N subdomain [117496]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117497] (2)
        SQ Q00955 13-566
  2. D-Alanine ligase N-terminal domain [52452] (3)
    1. D-Ala-D-Ala ligase, N-domain [52453]
      1. Escherichia coli, gene ddlB [TaxId: 562] [52454] (3)
    2. D-alanine:D-lactate ligase VanA, N-domain [52455]
      1. Leuconostoc mesenteroides, Ddl2 [TaxId: 1245] [52456] (1)
      2. Enterococcus faecium [TaxId: 1352] [63983] (1)
  3. Lysine biosynthesis enzyme LysX, N-terminal domain [102284] (1)
    1. Lysine biosynthesis enzyme LysX, N-terminal domain [102285]
      1. Thermus thermophilus [TaxId: 274] [102286] (2)
  4. Prokaryotic glutathione synthetase, N-terminal domain [52457] (1)
    1. Prokaryotic glutathione synthetase, N-terminal domain [52458]
      1. Escherichia coli [TaxId: 562] [52459] (4)
  5. Eukaryotic glutathione synthetase, substrate-binding domain [52460] (2)
    circularly permuted version of prokaryotic enzyme
    1. Eukaryotic glutathione synthetase, substrate-binding domain [52461]
      1. Human (Homo sapiens) [TaxId: 9606] [52462] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82378] (2)
  6. Synapsin domain [52463] (3)
    1. Synapsin I [52464]
      1. Cow (Bos taurus) [TaxId: 9913] [52465] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [102287] (2)
    2. Synapsin II [89635]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89636] (2)
  7. Glutathionylspermidine synthase substrate-binding domain-like [142119] (1)
    central part of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
    1. Glutathionylspermidine synthase, synthetase domain [142120]
      1. Escherichia coli [TaxId: 562] [142121] (10)
        SQ P0AES0 379-496
  8. PurP N-terminal domain-like [159526] (3)
    Pfam 06849; DUF1246
    1. 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP [159527]
      1. Pyrococcus furiosus [TaxId: 2261] [159528] (12)
        SQ Q8U0R7 1-99
      2. Thermococcus kodakaraensis [TaxId: 311400] [159529] (3)
        SQ Q5JD28 2-97
      3. Methanocaldococcus jannaschii [TaxId: 2190] [159530] (4)
        SQ Q57600 1-123
DHS-like NAD/FAD-binding domain [52466] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
1. DHS-like NAD/FAD-binding domain [52467] (6)
  binds cofactor molecules in the opposite direction than classical Rossmann fold
  uperfamily
  1. Deoxyhypusine synthase, DHS [52468] (1)
    1. Deoxyhypusine synthase, DHS [52469]
      1. Human (Homo sapiens) [TaxId: 9606] [52470] (4)
        SQ P49366
  2. C-terminal domain of the electron transfer flavoprotein alpha subunit [52471] (3)
    lacks strand 3; shares the FAD-binding mode with the pyruvate oxidase domain
    1. C-terminal domain of the electron transfer flavoprotein alpha subunit [52472]
      1. Human (Homo sapiens) [TaxId: 9606] [52473] (3)
      2. Paracoccus denitrificans [TaxId: 266] [52474] (1)
      3. Methylophilus methylotrophus [TaxId: 17] [82379] (6)
  3. Pyruvate oxidase and decarboxylase, middle domain [52475] (12)
    N-terminal domain is Pyr module, and C-terminal domain is PP module of thiamin diphosphate-binding fold
    1. Pyruvate oxidase [52476]
      binds FAD
      1. Lactobacillus plantarum [TaxId: 1590] [52477] (12)
      2. Aerococcus viridans [TaxId: 1377] [142122] (4)
    2. Pyruvate decarboxylase [52478]
      rudiment domain with a variant fold, lacks FAD-binding
      1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [52479] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52480] (2)
      3. Zymomonas mobilis [TaxId: 542] [52481] (1)
    3. Indole-3-pyruvate decarboxylase [89637]
      1. Enterobacter cloacae [TaxId: 550] [89638] (1)
    4. Benzoylformate decarboxylase [52482]
      1. Pseudomonas putida [TaxId: 303] [52483] (12)
        SQ P20906
    5. Acetohydroxyacid synthase catalytic subunit [69463]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69464] (6)
        SQ P07342 84-687
      2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142123] (6)
        SQ P17597 281-459
    6. Catabolic acetolactate synthase [102288]
      1. Klebsiella pneumoniae [TaxId: 573] [102289] (3)
    7. Carboxyethylarginine synthase [102290]
      1. Streptomyces clavuligerus [TaxId: 1901] [102291] (11)
    8. Oxalyl-CoA decarboxylase [142124]
      1. Oxalobacter formigenes [TaxId: 847] [142125] (12)
        SQ P40149 195-369
  4. Transhydrogenase domain III (dIII) [52484] (3)
    binds NADP, shares with the pyruvate oxidase FAD-binding domain a common ADP-binding mode
    1. Transhydrogenase domain III (dIII) [52485]
      1. Human (Homo sapiens) [TaxId: 9606] [52486] (4)
      2. Cow (Bos taurus) [TaxId: 9913] [52487] (1)
      3. Rhodospirillum rubrum [TaxId: 1085] [52488] (17)
  5. Sir2 family of transcriptional regulators [63984] (7)
    silent information regulator 2; contains insertion of a rubredoxin-like zinc finger domain
    1. AF1676, Sir2 homolog (Sir2-AF1?) [63985]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [63986] (6)
    2. AF0112, Sir2 homolog (Sir2-AF2) [82380]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [82381] (7)
    3. NAD-dependent deacetylase CobB [102292]
      1. Escherichia coli [TaxId: 562] [102293] (1)
    4. Sirt2 histone deacetylase [63987]
      1. Human (Homo sapiens) [TaxId: 9606] [63988] (1)
    5. Hst2 [102294]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102295] (5)
        SQ P53686 1-293
    6. NAD-dependent deacetylase NpdA [142126]
      1. Thermotoga maritima [TaxId: 2336] [142127] (10)
        SQ Q9WYW0 1-245
    7. NAD-dependent deacetylase sirtuin-5 [142128]
      1. Human (Homo sapiens) [TaxId: 9606] [142129] (6)
        SQ Q9NXA8 36-302
  6. ACDE2-like [142130] (1)
    Pfam 02552
    1. Acetyl-CoA decarbonylase/synthase complex epsilon subunit 2, ACDE2 [142131]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142132] (4)
        SQ O30273 17-174
Tubulin nucleotide-binding domain-like [52489] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Tubulin nucleotide-binding domain-like [52490] (1)
  uperfamily
  1. Tubulin, GTPase domain [52491] (9)
    1. Cell-division protein FtsZ [52492]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52493] (7)
        SQ Q57816 23-360
      2. Pseudomonas aeruginosa [TaxId: 287] [89639] (2)
      3. Mycobacterium tuberculosis [TaxId: 1773] [110501] (7)
        SQ O08378
      4. Thermotoga maritima [TaxId: 2336] [117498] (1)
        SQ O08398 22-335
    2. Tubulin alpha-subunit [52494]
      1. Pig (Sus scrofa) [TaxId: 9823] [52495] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [63989] (5)
      3. Prosthecobacter dejongeii [TaxId: 48465] [159531] (3)
        SQ Q8GCC5 3-246
        bacterial tubulin BtubA
    3. Tubulin beta-subunit [52496]
      1. Pig (Sus scrofa) [TaxId: 9823] [52497] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [63990] (9)
        SQ P02550 ! SQ P02554
Isochorismatase-like hydrolases [52498] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Isochorismatase-like hydrolases [52499] (1)
  uperfamily
  1. Isochorismatase-like hydrolases [100948] (7)
    1. N-carbamoylsarcosine amidohydrolase [52501]
      1. Arthrobacter sp. [TaxId: 1667] [52502] (1)
    2. Pyrazinamidase/nicotinamidase [69465]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [69466] (2)
    3. Phenazine biosynthesis protein PhzD [89643]
      1. Pseudomonas aeruginosa [TaxId: 287] [89644] (2)
    4. YcaC [52504]
      octameric hydrolase of unknown specificity
      1. Escherichia coli [TaxId: 562] [52505] (1)
    5. Hypothetical protein YecD [102298]
      1. Escherichia coli [TaxId: 562] [102299] (1)
    6. Ribonuclease MAR1 [110502]
      1. Leishmania donovani [TaxId: 5661] [110503] (1)
        SQ O77166 # 89% sequence identity; Leishmania tarentolae TaxID:5689
      2. Leishmania major [TaxId: 5664] [117499] (1)
        SQ Q4QGT7 # ! Structural genomics target
Dipeptide transport protein [63991] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain
1. Dipeptide transport protein [63992] (1)
  uperfamily
  1. Dipeptide transport protein [63993] (1)
    1. Zn-dependent D-aminopeptidase DppA [63994]
      1. Bacillus subtilis [TaxId: 1423] [63995] (1)
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52506] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52507] (1)
  uperfamily
  1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52508] (5)
    Pfam 02441; formerly DFP, DNA/pantothenate metabolism flavoprotein family
    1. 4'-phosphopantothenoylcysteine decarboxylase (PPC decarboxylase, halotolerance protein Hal3a) [52509]
      involved in signal transduction; binds FMN
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52510] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [102300] (1)
        hypothetical protein mds018
    2. Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD [63996]
      binds FMN
      1. Staphylococcus epidermidis [TaxId: 1282] [63997] (2)
    3. MrsD [102301]
      binds FAD
      1. Bacillus sp. hil-y85/54728 [TaxId: 69002] [102302] (1)
    4. Probable aromatic acid decarboxylase Pad1 [117500]
      1. Escherichia coli O157:H7 [TaxId: 83334] [117501] (1)
        SQ Q9X728
HAD-like [56783] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. HAD-like [56784] (25)
  usually contains an insertion (sub)domain after strand 1
  uperfamily
  1. Probable phosphatase YrbI [69467] (1)
    the insertion subdomain is a beta-hairpin involved into tetramerisation
    1. Probable phosphatase YrbI [69468]
      1. Haemophilus influenzae, HI1679 [TaxId: 727] [69469] (2)
  2. HAD-related [56785] (3)
    the insertion subdomain is a 4-helical bundle
    1. L-2-Haloacid dehalogenase, HAD [56786]
      1. Pseudomonas sp., strain YL [TaxId: 306] [56787] (4)
      2. Xanthobacter autotrophicus [TaxId: 280] [56788] (4)
    2. Hypothetical protein PH0459 [142133]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142134] (1)
        SQ O58216 1-230
  3. beta-Phosphoglucomutase-like [75173] (9)
    the insertion subdomain is a 4-helical bundle
    1. beta-Phosphoglucomutase [75174]
      1. Lactococcus lactis [TaxId: 1358] [75175] (8)
    2. Phosphatase YniC [110504]
      1. Escherichia coli [TaxId: 562] [110505] (1)
        SQ P77247
    3. Phosphoglycolate phosphatase [142135]
      1. Lactobacillus plantarum [TaxId: 1590] [142136] (1)
        SQ Q88YA8 1-207
    4. N-acylneuraminate-9-phosphatase NANP [142137]
      1. Mouse (Mus musculus) [TaxId: 10090] [142138] (1)
        SQ Q9CPT3 1-247
    5. Hypothetical protein SP2064 [142139]
      1. Streptococcus pneumoniae [TaxId: 1313] [142140] (4)
        SQ Q97NG6 3-206
    6. Hypothetical protein Atu0790 [142141]
      1. Agrobacterium tumefaciens [TaxId: 358] [142142] (1)
        SQ Q8UH93 3-224
    7. Phosphoglycolate phosphatase Gph [142143]
      1. Haemophilus somnus [TaxId: 731] [142144] (2)
        SQ Q0I1W8 1-224
    8. predicted phosphatase SP0104 [142145]
      1. Streptococcus pneumoniae [TaxId: 1313] [142146] (1)
        SQ Q97T51 1-210
    9. Hypothetical protein CT1708 [142147]
      1. Chlorobium tepidum [TaxId: 1097] [142148] (1)
        SQ Q8KBS5 2-229
  4. YihX-like [56789] (3)
    the insertion subdomain is a 4-helical bundle
    1. Epoxide hydrolase, N-terminal domain [56790]
      has a lipid phosphatase activity
      1. Mouse (Mus musculus) [TaxId: 10090] [56791] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [102303] (6)
    2. Putative phosphatase YihX [142149]
      1. Escherichia coli [TaxId: 562] [142150] (1)
        SQ P0A8Y3 1-197
  5. Phosphonoacetaldehyde hydrolase-like [56792] (2)
    the insertion subdomain is a 4-helical bundle
    1. Phosphonoacetaldehyde hydrolase [56793]
      1. Bacillus cereus [TaxId: 1396] [56794] (6)
        SQ O31156
    2. Putative hydrolase SP0805 [142151]
      1. Streptococcus pneumoniae [TaxId: 1313] [142152] (1)
        SQ Q97RK1 4-190
  6. Phosphoserine phosphatase [64511] (2)
    the insertion subdomain is a 4-helical bundle
    1. Phosphoserine phosphatase [64512]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64513] (6)
      2. Human (Homo sapiens) [TaxId: 9606] [89645] (3)
  7. 5'(3')-deoxyribonucleotidase (dNT-2) [82382] (1)
    the insertion subdomain is a 4-helical bundle; dephosphorylates dUMP and dTMP
    1. 5'(3')-deoxyribonucleotidase (dNT-2) [82383]
      1. Human (Homo sapiens) [TaxId: 9606] [82384] (12)
  8. Homoserine kinase ThrH [102304] (1)
    the insertion subdomain is a rudiment 4-helical bundle
    1. Homoserine kinase ThrH [102305]
      1. Pseudomonas aeruginosa [TaxId: 287] [102306] (2)
  9. Class B acid phosphatase, AphA [102307] (2)
    the insertion subdomain is a helical hairpin
    1. Class B acid phosphatase, AphA [102308]
      1. Escherichia coli [TaxId: 562] [102309] (15)
        SQ P32697 27-237
      2. Salmonella typhimurium [TaxId: 90371] [142153] (12)
        SQ P58683 30-237
  10. Hypothetical protein MW1667 (SA1546) [102310] (1)
    the insertion subdomain is multi-helical
    1. Hypothetical protein MW1667 (SA1546) [102311]
      1. Staphylococcus aureus [TaxId: 1280] [102312] (1)
  11. phosphatase domain of polynucleotide kinase [82385] (2)
    no insertion subdomains
    1. Polynucleotide kinase, phosphatase domain [82386]
      1. Bacteriophage T4 [TaxId: 10665] [82387] (16)
    2. 5' polynucleotide kinase-3' phosphatase, middle domain [142154]
      1. Mouse (Mus musculus) [TaxId: 10090] [142155] (2)
        SQ Q9JLV6 144-338
  12. Predicted hydrolases Cof [82388] (13)
    contains an alpha+beta subdomain inserted into a new site after strand 3
    1. Phosphoglycolate phosphatase, PGPase [82389]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [82390] (2)
      2. Pyrococcus horikoshii [TaxId: 53953] [117502] (1)
        SQ O50129 # PH1421
    2. Hypothetical protein YwpJ [89646]
      1. Bacillus subtilis [TaxId: 1423] [89647] (1)
    3. Hypothetical protein TM0651 [102313]
      1. Thermotoga maritima [TaxId: 2336] [102314] (1)
    4. Hypothetical protein YidA [102315]
      1. Escherichia coli [TaxId: 562] [102316] (1)
    5. Sugar phosphatase SupH (YbiV) [117503]
      1. Escherichia coli [TaxId: 562] [117504] (3)
        SQ P75792
    6. Putative mannosyl-3-phosphoglycerate phosphatase MPGP (YedP) [117505]
      1. Escherichia coli [TaxId: 562] [117506] (1)
        SQ P76329 4-235
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142156] (2)
        SQ O58690 1-243
    7. Sugar-phosphate phosphatase BT4131 [142157]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [142158] (3)
        SQ Q8A090 2-261
    8. Phosphomannomutase 2 [142159]
      1. Human (Homo sapiens) [TaxId: 9606] [142160] (2)
        SQ O15305 4-246
    9. Phosphomannomutase 1 [142161]
      1. Human (Homo sapiens) [TaxId: 9606] [142162] (2)
        SQ Q92871 12-256
    10. Sucrose-phosphatase Slr0953 [142163]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [142164] (9)
        SQ P74325 1-244
    11. PFL1270w orthologue [142165]
      1. Plasmodium vivax [TaxId: 5855] [142166] (4)
        SQ Q8I5F4 11-293
  13. NagD-like [102317] (6)
    duplication: consists of two segment-swapped domains of this fold; this results in the insertion of a circularly permuted domain after strand 3, analogously to the Cof family
    1. Hypothetical protein TM1742 [102318]
      putative NagD protein
      1. Thermotoga maritima [TaxId: 2336] [102319] (2)
    2. Putative phosphatase SMU.1415c [117507]
      1. Streptococcus mutans [TaxId: 1309] [117508] (1)
        SQ Q8DTD6
    3. Hypothetical protein SPy1043 [142167]
      1. Streptococcus pyogenes [TaxId: 1314] [142168] (1)
        SQ Q99ZW4 2-254
    4. NagD [142169]
      1. Escherichia coli [TaxId: 562] [142170] (1)
        SQ P0AF24 1-250
    5. Putative hydrolase SP1407 [142171]
      1. Streptococcus pneumoniae [TaxId: 1313] [142172] (1)
        SQ Q97Q24 3-255
    6. Putative hydrolase EF1188 [142173]
      1. Enterococcus faecalis [TaxId: 1351] [142174] (2)
        SQ Q836C7 4-256
  14. Meta-cation ATPase, catalytic domain P [81656] (2)
    interrupted by a large insertion, domain N
    1. Calcium ATPase, catalytic domain P [81655]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81654] (17)
        SQ P04191
    2. Cation-transporting ATPase [142175]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [142176] (3)
        SQ O29777 416-434,548-663
  15. Trehalose-phosphatase [110506] (1)
    Pfam 02358; contains an insert alpha+beta subdomain; similar overall fold to the Cof family
    1. Trehalose-6-phosphate phosphatase related protein [110507]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [110508] (1)
        SQ Q9HIW7
  16. NLI interacting factor-like phosphatase [110509] (1)
    Pfam 03031; NIF; the insertion subdomain is a 3-stranded beta-sheet;
    1. Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1, NRAMP1 [110510]
      1. Human (Homo sapiens) [TaxId: 9606] [110511] (2)
        SQ Q9GZU7 76-256
  17. Magnesium-dependent phosphatase-1, Mdp1 [117509] (1)
    the insertion subdomain is a 3-stranded beta-sheet different from the NIF family
    1. Magnesium-dependent phosphatase-1, Mdp1 [117510]
      1. Mouse (Mus musculus) [TaxId: 10090] [117511] (2)
        SQ Q9D967
  18. Hypothetical protein VC0232 [117512] (1)
    contains a deletion in the common fold; segment-swapped tetramer
    1. Hypothetical protein VC0232 [117513]
      1. Vibrio cholerae [TaxId: 666] [117514] (1)
        SQ Q9KVB4
  19. Histidinol phosphatase-like [142177] (3)
    no insertion subdomains
    1. Histidine biosynthesis bifunctional protein HisB, phosphatase domain [142178]
      1. Escherichia coli [TaxId: 562] [142179] (10)
        SQ Q9S5G5 3-163
    2. Hypothetical protein Mll2559 [159532]
      1. Mesorhizobium loti [TaxId: 381] [159533] (1)
        SQ Q98I56 8-216
    3. D,D-heptose 1,7-bisphosphate phosphatase GmhB [159534]
      1. Escherichia coli [TaxId: 562] [159535] (4)
        SQ P63228 4-185
  20. MtnX-like [142180] (1)
    Pfam 06888; the insertion subdomain is a rudiment 4-helical bundle
    1. 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase MtnX [142181]
      1. Bacillus subtilis [TaxId: 1423] [142182] (2)
        SQ O31667 2-227
  21. Pyrimidine 5'-nucleotidase (UMPH-1) [142183] (2)
    Pfam 05822; the insertion subdomain is a rudiment 4-helical bundle
    1. Cytosolic 5'-nucleotidase III [142184]
      1. Human (Homo sapiens) [TaxId: 9606] [142185] (2)
        SQ Q9H0P0 64-336
      2. Mouse (Mus musculus) [TaxId: 10090] [159536] (1)
        SQ Q9D020 7-297
  22. Enolase-phosphatase E1 [142186] (2)
    the insertion subdomain is a 4-helical bundle
    1. Protein UTR4 [142187]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142188] (4)
        SQ P32626 17-241
    2. E-1 enzyme [142189]
      1. Human(Homo sapiens) [TaxId: 9606] [142190] (2)
        SQ Q9UHY7 4-256
  23. 5' nucleotidase-like [142191] (1)
    Pfam 05761; the insertion domain cosists of 3-helical bundle and a pseudo beta-barrel; contains extra C-terminal long alpha hairpin subdomain (scop_cf 46556)
    1. Cytosolic IMP-GMP specific 5'-nucleotidase [142192]
      1. Legionella pneumophila [TaxId: 446] [142193] (1)
        SQ Q5ZZB6 2-459
  24. AF1437-like [159537] (1)
    the insertion subdomain is a rudiment 4-helical bundle; extra alpha-hairpin insertion after strand 3
    1. Hypothetical protein AF1437 [159538]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [159539] (1)
        SQ O28835 1-308
  25. BT0820-like [159540] (1)
    PfamB 073209; deletion in the common fold; segment-swapped dimer
    1. Hypothetical protein BT0820 [159541]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [159542] (1)
        SQ Q8A9J5 1-122
NagB/RpiA/CoA transferase-like [100949] (1)
core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
1. NagB/RpiA/CoA transferase-like [100950] (8)
  uperfamily
  1. NagB-like [52513] (3)
    share a common phosphate-binding site with the RpiA family
    1. Glucosamine 6-phosphate deaminase/isomerase NagB [52514]
      1. Escherichia coli [TaxId: 562] [52515] (10)
      2. Human (Homo sapiens) [TaxId: 9606] [102320] (1)
    2. 6-phosphogluconolactonase [102321]
      1. Thermotoga maritima [TaxId: 2336] [102322] (2)
        SQ Q9X0N8 # TM1154
  2. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75176] (4)
    share a common phosphate-binding site with the NagB-like family; part of sheet is folded upon itself and forms a barrel-like structure like the CoA transferase subunits
    1. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75177]
      1. Escherichia coli [TaxId: 562] [75178] (3)
      2. Haemophilus influenzae [TaxId: 727] [82391] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75179] (2)
      4. Thermus thermophilus [TaxId: 274] [110512] (3)
        SQ Q72J47
  3. CoA transferase beta subunit-like [74657] (3)
    catalytic subunit: similar active site structure to the NagB and RpiA families; mixed beta-sheet of 7 strands, order 4321567; strand 3 is antiparallel to the rest
    1. Glutaconate:CoA transferase beta [53320]
      1. Acidaminococcus fermentans [TaxId: 905] [53321] (1)
    2. Succinate:CoA transferase, C-terminal domain [82466]
      1. Pig (Sus scrofa) [TaxId: 9823] [82467] (13)
    3. Putative enzyme YdiF C-terminal domain [142194]
      1. Escherichia coli [TaxId: 562] [142195] (12)
        SQ P37766 283-529
  4. CoA transferase alpha subunit-like [74656] (6)
    parallel beta-sheet of 7 strands, order 4321567
    1. Glutaconate:CoA transferase alpha [53318]
      1. Acidaminococcus fermentans [TaxId: 905] [53319] (1)
    2. Acetate:CoA transferase alpha [75257]
      1. Escherichia coli [TaxId: 562] [75258] (1)
    3. Succinate:CoA transferase, N-terminal domain [82464]
      1. Pig (Sus scrofa) [TaxId: 9823] [82465] (13)
    4. Putative citrate lyase alpha chain, citF2 [117515]
      duplication: consists of two topologically similar domains
      1. Salmonella typhimurium [TaxId: 90371] [117516] (1)
        SQ Q8ZRY1
    5. Acetyl-CoA hydrolase (PA5445) [142196]
      duplication: consists of two topologically similar domains; overall similarity to CitF2
      1. Pseudomonas aeruginosa [TaxId: 287] [142197] (4)
        SQ Q9HTC2 224-497! SQ Q9HTC2 3-223
    6. Putative enzyme YdiF N-terminal domain [142198]
      1. Escherichia coli [TaxId: 562] [142199] (12)
        SQ P37766 4-276
  5. IF2B-like [110513] (5)
    Pfam 01008; contains extra N-terminal alpha+beta domain (1-126); beta(3)-alpha(5); 3 layers: b/a/a
    1. Probable methylthioribose-1-phosphate isomerase TM0911 [110514]
      1. Thermotoga maritima [TaxId: 2336] [110515] (1)
        SQ Q9X013
    2. Putative methylthioribose-1-phosphate isomerase Ypr118W [110516]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110517] (1)
        SQ Q06489
    3. Putative eIF-2B delta-subunit [110518]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110519] (1)
        SQ O29877 # AF0370
    4. Putative eIF-2B subunit 2-like protein PH0440 [117517]
      1. Pyrococcus horikoshii [TaxId: 53953] [117518] (1)
        SQ O58185
    5. Initiation factor 2b [159543]
      1. Leishmania major [TaxId: 5664] [159544] (2)
        SQ Q4Q0R9 133-506,133-506
  6. Methenyltetrahydrofolate synthetase [110520] (3)
    Pfam 01812; 5-FTHF cyclo-ligase
    1. Hypothetical protein aq_1731 [110521]
      1. Aquifex aeolicus [TaxId: 63363] [110522] (1)
        SQ O67621
    2. 5,10-methenyltetrahydrofolate synthetase homolog MPN348 [110523]
      1. Mycoplasma pneumoniae [TaxId: 2104] [110524] (3)
        SQ P75430
    3. Hypothetical protein TTHA1611 [117519]
      1. Thermus thermophilus [TaxId: 274] [117520] (1)
        SQ Q5SHW9 1-175
  7. YkgG-like [142200] (1)
    Pfam 02589; DUF162
    1. Hypothetical protein DR1909 [142201]
      1. Deinococcus radiodurans [TaxId: 1299] [142202] (1)
        SQ Q9RT57 38-212
  8. SorC sugar-binding domain-like [159545] (5)
    Pfam 04198
    1. Transcriptional regulator PSPTO2395 [159546]
      1. Pseudomonas syringae [TaxId: 317] [159547] (1)
        SQ Q883G8 59-316
    2. Transcriptional regulator SP0247 [159548]
      1. Streptococcus pneumoniae [TaxId: 1313] [159549] (1)
        SQ Q97SS7 56-317
    3. Transcriptional regulator EF1965 [159550]
      1. Enterococcus faecalis [TaxId: 1351] [159551] (1)
        SQ Q833I7 95-341
    4. Sor-operon regulator SorC [159552]
      1. Shigella flexneri [TaxId: 623] [159553] (4)
        SQ Q83PA8 61-315
    5. Central glycolytic gene regulator CggR [159554]
      formerly hypothetical protein YvbQ
      1. Bacillus subtilis [TaxId: 1423] [159555] (10)
        SQ O32253 89-338
Hypothetical protein MTH777 (MT0777) [75180] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Hypothetical protein MTH777 (MT0777) [75181] (1)
  uperfamily
  1. Hypothetical protein MTH777 (MT0777) [75182] (1)
    1. Hypothetical protein MTH777 (MT0777) [75183]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75184] (1)
Thiamin pyrophosphokinase, catalytic domain [63998] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156
1. Thiamin pyrophosphokinase, catalytic domain [63999] (1)
  uperfamily
  1. Thiamin pyrophosphokinase, catalytic domain [64000] (2)
    1. Thiamin pyrophosphokinase, catalytic domain [64001]
      1. Mouse (Mus musculus) [TaxId: 10090] [64002] (2)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64003] (1)
Undecaprenyl diphosphate synthase [64004] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156
1. Undecaprenyl diphosphate synthase [64005] (1)
  the sheet topology is similar to those of the N-terminal domain of phosphoglycerate kinase and carbamate kinase
  uperfamily
  1. Undecaprenyl diphosphate synthase [64006] (2)
    1. Undecaprenyl diphosphate synthase [64007]
      1. Micrococcus luteus [TaxId: 1270] [64008] (1)
      2. Escherichia coli [TaxId: 562] [64009] (15)
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102323] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456
1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102324] (1)
  the sheet topology is similar to those of the Periplasmic binding protein-like I domains
  uperfamily
  1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102325] (1)
    1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102326]
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [102327] (28)
Thiamin diphosphate-binding fold (THDP-binding) [52517] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
1. Thiamin diphosphate-binding fold (THDP-binding) [52518] (8)
  there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
  two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
  uperfamily
  1. Pyruvate oxidase and decarboxylase Pyr module [88724] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpha/beta domain of Rossmann-like topology
    1. Pyruvate decarboxylase [88725]
      1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88726] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88727] (2)
      3. Zymomonas mobilis [TaxId: 542] [88728] (1)
    2. Indole-3-pyruvate decarboxylase [89648]
      1. Enterobacter cloacae [TaxId: 550] [89649] (1)
    3. Pyruvate oxidase [88729]
      1. Lactobacillus plantarum [TaxId: 1590] [88730] (12)
      2. Aerococcus viridans [TaxId: 1377] [142203] (4)
    4. Benzoylformate decarboxylase [88731]
      1. Pseudomonas putida [TaxId: 303] [88732] (12)
        SQ P20906
    5. Acetohydroxyacid synthase catalytic subunit [88733]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88734] (6)
        SQ P07342 84-687
      2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142204] (6)
        SQ P17597 86-280
    6. Catabolic acetolactate synthase [102328]
      1. Klebsiella pneumoniae [TaxId: 573] [102329] (3)
    7. Carboxyethylarginine synthase [102330]
      1. Streptomyces clavuligerus [TaxId: 1901] [102331] (11)
    8. Oxalyl-CoA decarboxylase [142205]
      1. Oxalobacter formigenes [TaxId: 847] [142206] (12)
        SQ P40149 7-194
  2. TK-like Pyr module [88735] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    1. Transketolase (TK), Pyr module [88736]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88737] (7)
      2. Maize (Zea mays) [TaxId: 4577] [88738] (1)
      3. Escherichia coli [TaxId: 562] [89650] (7)
      4. Leishmania mexicana mexicana [TaxId: 44270] [117521] (1)
        SQ Q8MPM3
    2. Pyruvate dehydrogenase E1 component, Pyr module [88739]
      E1A and E1B fused together in a single-chain protein
      1. Escherichia coli [TaxId: 562] [88740] (14)
  3. Branched-chain alpha-keto acid dehydrogenase Pyr module [88741] (6)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    1. Branched-chain alpha-keto acid dehydrogenase, Pyr module [88742]
      1. Human (Homo sapiens) [TaxId: 9606] [88743] (21)
        SQ P21953 52-392
      2. Thermus thermophilus [TaxId: 274] [102332] (4)
    2. 2-oxoisovalerate dehydrogenase (E1B), Pyr module [88744]
      chain A is alpha-subunit and chain B is beta-subunit
      1. Pseudomonas putida [TaxId: 303] [88745] (5)
    3. E1-beta subunit of pyruvate dehydrogenase, Pyr module [69472]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69473] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [89653] (3)
    4. Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain [117522]
      1. Bacillus stearothermophilus [TaxId: 1422] [117523] (2)
        SQ P21874
  4. PFOR Pyr module [88746] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain I [88747]
      1. Desulfovibrio africanus [TaxId: 873] [88748] (17)
  5. Pyruvate oxidase and decarboxylase PP module [88749] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpa/beta domain of Rossmann-like topology
    1. Pyruvate decarboxylase [88750]
      1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88751] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88752] (2)
      3. Zymomonas mobilis [TaxId: 542] [88753] (1)
    2. Indole-3-pyruvate decarboxylase [89654]
      1. Enterobacter cloacae [TaxId: 550] [89655] (1)
    3. Pyruvate oxidase [88754]
      1. Lactobacillus plantarum [TaxId: 1590] [88755] (12)
      2. Aerococcus viridans [TaxId: 1377] [142207] (4)
    4. Benzoylformate decarboxylase [88756]
      1. Pseudomonas putida [TaxId: 303] [88757] (12)
        SQ P20906
    5. Acetohydroxyacid synthase catalytic subunit [88758]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88759] (6)
        SQ P07342 84-687
      2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142208] (6)
        SQ P17597 460-667
    6. Catabolic acetolactate synthase [102333]
      1. Klebsiella pneumoniae [TaxId: 573] [102334] (3)
    7. Carboxyethylarginine synthase [102335]
      1. Streptomyces clavuligerus [TaxId: 1901] [102336] (11)
    8. Oxalyl-CoA decarboxylase [142209]
      1. Oxalobacter formigenes [TaxId: 847] [142210] (12)
        SQ P40149 370-552
  6. TK-like PP module [88760] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    1. Transketolase (TK), PP module [88761]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88762] (7)
      2. Maize (Zea mays) [TaxId: 4577] [88763] (1)
      3. Escherichia coli [TaxId: 562] [89656] (7)
      4. Leishmania mexicana mexicana [TaxId: 44270] [117524] (1)
        SQ Q8MPM3
    2. Pyruvate dehydrogenase E1 component, PP module [88764]
      E1A and E1B fused together in a single-chain protein
      1. Escherichia coli [TaxId: 562] [88765] (14)
  7. Branched-chain alpha-keto acid dehydrogenase PP module [88766] (5)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    1. Branched-chain alpha-keto acid dehydrogenase, PP module [88767]
      1. Human (Homo sapiens) [TaxId: 9606] [88768] (23)
        SQ P12694 52-445
      2. Thermus thermophilus [TaxId: 274] [102337] (4)
    2. E1-beta subunit of pyruvate dehydrogenase (PP module) [89651]
      1. Human (Homo sapiens) [TaxId: 9606] [89652] (3)
    3. 2-oxoisovalerate dehydrogenase (E1B), PP module [88769]
      chain A is alpha-subunit and chain B is beta-subunit
      1. Pseudomonas putida [TaxId: 303] [88770] (5)
    4. Pyruvate dehydrogenase E1-alpha, PdhA [117525]
      1. Bacillus stearothermophilus [TaxId: 1422] [117526] (2)
        SQ P21873
  8. PFOR PP module [88771] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI [88772]
      1. Desulfovibrio africanus [TaxId: 873] [88773] (17)
P-loop containing nucleoside triphosphate hydrolases [52539] (1)
3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
1. P-loop containing nucleoside triphosphate hydrolases [52540] (24)
  division into families based on beta-sheet topologies
  uperfamily
  1. Nucleotide and nucleoside kinases [52541] (46)
    parallel beta-sheet of 5 strands, order 23145
    1. Guanylate kinase [52542]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52543] (3)
      2. Mouse (Mus musculus) [TaxId: 10090] [82393] (1)
      3. Escherichia coli [TaxId: 562] [102338] (18)
      4. Mycobacterium tuberculosis [TaxId: 1773] [102339] (5)
        Rv1389
    2. Guanylate kinase-like domain of Cask [69474]
      1. Human (Homo sapiens) [TaxId: 9606] [69475] (1)
    3. Guanylate kinase-like domain of Psd-95 [69476]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69477] (3)
    4. Uridylate kinase [52544]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52545] (2)
    5. Deoxynucleoside monophosphate kinase [52546]
      contains insert 4-helical bundle subdomain, residues 35-145
      1. Bacteriophage T4 [TaxId: 10665] [52547] (2)
    6. Deoxyribonucleoside kinase [69478]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [69479] (37)
    7. Deoxycytidine kinase [89657]
      1. Human (Homo sapiens) [TaxId: 9606] [89658] (13)
    8. Deoxyguanosine kinase [69480]
      1. Human (Homo sapiens) [TaxId: 9606] [69481] (8)
    9. CMP kinase [52548]
      1. Escherichia coli [TaxId: 562] [52549] (6)
      2. Streptococcus pneumoniae [TaxId: 1313] [110525] (1)
        SQ Q97PK6
    10. UMP/CMP kinase [52550]
      1. Dictyostelium discoideum [TaxId: 44689] [52551] (6)
      2. Human (Homo sapiens) [TaxId: 9606] [110526] (1)
        SQ P30085
    11. Thymidine kinase [52552]
      contains insert all-alpha subdomain, res. 251-322
      1. Herpes simplex virus type 1, different strains [TaxId: 10298] [52553] (22)
        SQ P03176 46-375
      2. Equine herpesvirus type 4 [TaxId: 10331] [102340] (4)
      3. Varicella-zoster virus [TaxId: 10335] [89659] (1)
    12. Adenylate kinase [52554]
      1. Pig (Sus scrofa) [TaxId: 9823] [52555] (1)
      2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [52556] (1)
      3. Archaeon Methanococcus voltae [TaxId: 2188] [89660] (1)
      4. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [89661] (1)
      5. Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913] [52557] (1)
        contains a rudiment "zinc-finger" subdomain, residue 125-161
      6. Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913] [52558] (2)
        contains a rudiment "zinc-finger" subdomain, residue 147-176
      7. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52559] (4)
        contains a rudiment "zinc-finger" subdomain, residue 131-168
      8. Escherichia coli [TaxId: 562] [52560] (6)
        contains a rudiment "zinc-finger" subdomain, residue 122-156
      9. Maize (Zea mays) [TaxId: 4577] [52561] (1)
      10. Bacillus stearothermophilus [TaxId: 1422] [52562] (3)
        contains a zinc-finger subdomain, residues 126-160
      11. Bacillus subtilis [TaxId: 1423] [102341] (1)
        contains a zinc-finger subdomain, residues 126-160
      12. Bacillus globisporus [TaxId: 1459] [102342] (1)
        contains a zinc-finger subdomain, residues 126-160
      13. Mycobacterium tuberculosis [TaxId: 1773] [102343] (2)
        contains no zinc finger-like insertion
      14. Human (Homo sapiens), isoenzyme 6 [TaxId: 9606] [117527] (1)
        SQ Q9Y3D8
    13. Thymidylate kinase [52563]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52564] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [64010] (20)
      3. Escherichia coli [TaxId: 562] [52565] (2)
      4. Mycobacterium tuberculosis [TaxId: 1773] [69482] (13)
    14. Dephospho-CoA kinase [75187]
      1. Haemophilus influenzae [TaxId: 727] [75188] (1)
      2. Escherichia coli [TaxId: 562] [82394] (5)
      3. Thermus thermophilus [TaxId: 274] [102344] (1)
        TT1252
    15. Transcriptional regulator NadR, ribosylnicotinamide kinase domain [75189]
      1. Haemophilus influenzae [TaxId: 727] [75190] (1)
    16. Polynucleotide kinase, kinase domain [75191]
      1. Bacteriophage T4 [TaxId: 10665] [75192] (17)
    17. Guanylate kinase-like domain of the L-type calcium channel [110527]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110528] (4)
        SQ P54288 234-451
      2. Rat (Rattus norvegicus) [TaxId: 10116] [110529] (3)
        SQ P54287 38-362
    18. Probable kinase LmjF30.1890 [117528]
      1. Leishmania major [TaxId: 5664] [117529] (1)
        SQ Q4Q7A6
    19. Hypothetical protein YorR [142211]
      1. Bacillus subtilis [TaxId: 1423] [142212] (2)
        SQ O31896 2-165
    20. 5' polynucleotide kinase-3' phosphatase, C-terminal domain [142213]
      1. Mouse (Mus musculus) [TaxId: 10090] [142214] (2)
        SQ Q9JLV6 351-522
  2. Shikimate kinase (AroK) [52566] (4)
    similar to the nucleotide/nucleoside kinases but acts on different substrate
    1. Shikimate kinase (AroK) [52567]
      1. Escherichia coli [TaxId: 562] [75193] (1)
      2. Erwinia chrysanthemi [TaxId: 556] [52568] (3)
      3. Mycobacterium tuberculosis [TaxId: 1773] [75194] (24)
        SQ P95014
      4. Campylobacter jejuni [TaxId: 197] [102345] (1)
  3. Chloramphenicol phosphotransferase [52569] (1)
    similar to the nucleotide/nucleoside kinases but acts on different substrate
    1. Chloramphenicol phosphotransferase [52570]
      1. Streptomyces venezuelae [TaxId: 54571] [52571] (6)
  4. Gluconate kinase [75195] (1)
    similar to the nucleotide/nucleoside kinases
    1. Gluconate kinase [75196]
      1. Escherichia coli [TaxId: 562] [75197] (6)
  5. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82395] (1)
    similar to the nucleotide/nucleoside kinases; extra N- and C-terminal structures
    1. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82396]
      1. Streptococcus pyogenes [TaxId: 1314] [82397] (1)
  6. Adenosine-5'phosphosulfate kinase (APS kinase) [52572] (2)
    1. Adenosine-5'phosphosulfate kinase (APS kinase) [52573]
      1. Fungus (Penicillium chrysogenum) [TaxId: 5076] [52574] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [142215] (6)
        SQ O43252 34-228
  7. ATP sulfurylase C-terminal domain [64011] (2)
    1. ATP sulfurylase C-terminal domain [64012]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64013] (7)
      2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [64014] (2)
  8. PAPS sulfotransferase [52575] (15)
    Pfam 00685
    similar to the nucleotide/nucleoside kinases but transfer sulphate group
    1. Estrogen sulfotransferase (STE, sult1e1) [52576]
      1. Mouse (Mus musculus) [TaxId: 10090] [52577] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [75198] (2)
    2. Hydroxysteroid sulfotransferase sult2a1 [52578]
      1. Human (Homo sapiens) [TaxId: 9606] [52579] (3)
    3. Aryl sulfotransferase sult1a [102346]
      1. Human (Homo sapiens) [TaxId: 9606] [102347] (3)
    4. Aryl sulfotransferase sult1a3 [52580]
      1. Human (Homo sapiens) [TaxId: 9606] [52581] (3)
    5. Pregnenolone sulfotransferase sult2b1a [102348]
      1. Human (Homo sapiens) [TaxId: 9606] [102349] (1)
        cytosolic enzyme
    6. Cholesterol sulfotransferase sult2b1b [102350]
      1. Human (Homo sapiens) [TaxId: 9606] [102351] (3)
        cytosolic enzyme
    7. Putative steroid sulfotransferase rarO47 [102352]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102353] (2)
    8. Heparan sulfate N-deacetylase/N-sulfotransferase domain [52582]
      1. Human (Homo sapiens) [TaxId: 9606] [52583] (1)
    9. Heparan sulfate 3-O-sulfotransferase [102354]
      1. Mouse (Mus musculus) [TaxId: 10090] [102355] (1)
        SQ O35310 48-311
    10. Retinol dehydratase [64015]
      1. Fall armyworm (Spodoptera frugiperda) [TaxId: 7108] [64016] (2)
    11. Stf0 sulfotransferase [110530]
      1. Mycobacterium smegmatis [TaxId: 1772] [110531] (1)
        SQ P84151
    12. Heparan sulfate glucosamine 3-O-sulfotransferase 3 [110532]
      1. Human (Homo sapiens) [TaxId: 9606] [110533] (2)
        SQ Q9Y663 139-406 # isoform 3A1; 100% sequence identity to isoform 3B1 domain (SQ Q9Y662 133-390)
    13. Thyroid hormone sulfotransferase Sult1b1 [117530]
      1. Human (Homo sapiens) [TaxId: 9606] [117531] (1)
        SQ O43704
    14. Sulfotransferase Sult1c2 [159556]
      1. Human (Homo sapiens) [TaxId: 9606] [159557] (2)
        SQ O00338 12-296
  9. Phosphoribulokinase/pantothenate kinase [52584] (5)
    1. Phosphoribulokinase [52585]
      1. Rhodobacter sphaeroides [TaxId: 1063] [52586] (1)
    2. Pantothenate kinase PanK [52587]
      has a circularly permuted fold compared to the phosphoribulokinase fold
      1. Escherichia coli [TaxId: 562] [52588] (3)
        SQ P15044
    3. Hypothetical protein Ygr205W [102356]
      close structural similarity to PanK
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102357] (1)
    4. Hypothetical protein rbstp0775 [102358]
      structural similarity to PanK
      1. Bacillus stearothermophilus [TaxId: 1422] [102359] (1)
    5. Uridine-cytidine kinase 2 [102360]
      1. Human (Homo sapiens) [TaxId: 9606] [102361] (7)
  10. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52589] (2)
    1. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52590]
      bifunctional enzyme
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52591] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [82398] (1)
  11. G proteins [52592] (118)
    core: mixed beta-sheet of 6 strands, order 231456; strand 2 is antiparallel to the rest
    1. cH-p21 Ras protein [52593]
      1. Human (Homo sapiens) [TaxId: 9606] [52594] (57)
        SQ Q6P716
    2. Rac [52595]
      1. Human (Homo sapiens) [TaxId: 9606] [52596] (23)
    3. Ras-related protein RalA [89662]
      1. Human (Homo sapiens) [TaxId: 9606] [89663] (7)
      2. Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490] [117532] (3)
        SQ P63320 # 100% identical to the mouse and rat orthologs (SQ P63321 P63322)
    4. Rap1A [52597]
      1. Human (Homo sapiens) [TaxId: 9606] [52598] (2)
    5. Rap2a [52599]
      1. Human (Homo sapiens) [TaxId: 9606] [52600] (3)
    6. Rab3a [52601]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52602] (2)
    7. Rab5a [82399]
      1. Human (Homo sapiens) [TaxId: 9606] [82400] (11)
        SQ P20339 18-182
    8. Rab5c [52603]
      1. Mouse (Mus musculus) [TaxId: 10090] [52604] (4)
    9. Rab6 [52605]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [52606] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [142216] (1)
        SQ P20340 13-176
    10. Rab11a [102362]
      1. Human (Homo sapiens) [TaxId: 9606] [102363] (13)
      2. Saccharomyces cerevisiae [TaxId: 4932] [159558] (4)
    11. Rab-related protein Sec4 [52607]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52608] (5)
    12. Rab-related protein ypt7p [75199]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75200] (2)
    13. Ran [52609]
      1. Dog (Canis familiaris) [TaxId: 9615] [52610] (6)
        SQ P62825
      2. Human (Homo sapiens) [TaxId: 9606] [52611] (7)
    14. RhoA [52612]
      1. Human (Homo sapiens) [TaxId: 9606] [52613] (14)
        SQ P61586 2-181
    15. RhoE (RND3) [75201]
      1. Mouse (Mus musculus) [TaxId: 10090] [75202] (2)
    16. ADP-ribosylation factor [52614]
      1. Human (Homo sapiens), ARF1 [TaxId: 9606] [52615] (14)
        SQ P32889
      2. Rat (Rattus norvegicus), ARF1 [TaxId: 10116] [52616] (2)
      3. Human (Homo sapiens), ARF6 [TaxId: 9606] [52617] (6)
      4. Mouse (Mus musculus), ARL3 [TaxId: 10090] [52618] (2)
      5. Mouse (Mus musculus), ARL2 [TaxId: 10090] [75203] (3)
      6. Baker's yeast (Saccharomyces cerevisiae), ARF2 [TaxId: 4932] [82401] (1)
      7. Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932] [82402] (1)
      8. Human (Homo sapiens), ARL1 [TaxId: 9606] [102364] (2)
      9. Human (Homo sapiens), ARF4 [TaxId: 9606] [142217] (2)
        SQ P18085 3-177
      10. Human (Homo sapiens), ARL5A [TaxId: 9606] [142218] (3)
        SQ Q9Y689 2-178
      11. Human (Homo sapiens), ARL8A [TaxId: 9606] [142219] (1)
        SQ Q96BM9 18-181
      12. Human (Homo sapiens) [TaxId: 9606] [142220] (1)
        SQ P84085 6-179
      13. Human (Homo sapiens), ARL5B [TaxId: 9606] [142221] (1)
        SQ Q96KC2 6-173
      14. Human(Homo sapiens), ARL8B [TaxId: 9606] [142222] (1)
        SQ Q9NVJ2 18-182
    17. SAR1 [69483]
      1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [69484] (3)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82403] (2)
      3. Human (Homo sapiens) [TaxId: 9606] [142223] (2)
        SQ Q9NR31 13-198
    18. CDC42 [52619]
      1. Human (Homo sapiens) [TaxId: 9606] [52620] (21)
      2. Mus musculus [TaxId: 10090] [159559] (2)
    19. Ypt51 [52621]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52622] (1)
    20. Chloroplast protein translocon GTPase Toc34 [69485]
      1. Garden pea (Pisum sativum) [TaxId: 3888] [69486] (1)
    21. Signal recognition particle receptor beta-subunit [89664]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89665] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [142224] (2)
        SQ P47758 63-269
    22. Transducin (alpha subunit) [52623]
      common fold is interrupted with an all-alpha domain
      1. Cow (Bos taurus) [TaxId: 9913] [52624] (15)
        SQ P04896 39-388
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52625] (33)
        SQ P10824
      3. Mouse (Mus musculus) [TaxId: 10090] [142225] (6)
        SQ P21279 38-66,184-354! SQ P27600 53-81,204-370! SQ P27601 47-75,202-372
      4. Homo sapiens [TaxId: 9606] [159560] (4)
    23. Elongation factor Tu (EF-Tu), N-terminal (G) domain [52626]
      1. Escherichia coli [TaxId: 562] [52627] (10)
        SQ P02990
      2. Thermus aquaticus [TaxId: 271] [52628] (4)
      3. Thermus thermophilus [TaxId: 274] [52629] (9)
      4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [52630] (2)
        SQ P49410 56-452
    24. Elongation factor eEF-1alpha, N-terminal (G) domain [52631]
      eukaryotic and archaeal homologue of EF-Tu
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52632] (6)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69487] (2)
        SQ P35021
    25. Elongation factor G (EF-G), N-terminal (G) domain [52633]
      has internal nucleotide exchange factor built in as an insertion subdomain
      1. Thermus thermophilus [TaxId: 274] [52634] (9)
        residues 160-252 comprise insertion subdomain
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142226] (2)
        SQ Q5SI76 1-267
        TTHA1498
    26. Elongation factor 2 (eEF-2), N-terminal (G) domain [82404]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82405] (22)
        SQ P32324
    27. Initiation factor IF2/eIF5b, N-terminal (G) domain [52635]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52636] (3)
    28. Initiation factor eIF2 gamma subunit, N-terminal (G) domain [75204]
      includes rubredoxin-like zinc finger insert domain, res. 56-83, similar that of the Nop10-like family (scop_fa 144211)
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [75205] (5)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [102365] (1)
      3. Sulfolobus solfataricus [TaxId: 2287] [142227] (6)
        SQ Q980A5 2-206
    29. GTPase Era, N-terminal domain [52637]
      1. Escherichia coli [TaxId: 562] [52638] (3)
      2. Thermus thermophilus [TaxId: 274] [117533] (1)
        SQ Q5SM23
    30. Probable tRNA modification GTPase TrmE (MnmE), G domain [102366]
      1. Escherichia coli [TaxId: 562] [102367] (11)
    31. Probable GTPase Der, N-terminal and middle domains [82406]
      member of EngA subfamily of GTPases; contains two G domains
      1. Thermotoga maritima [TaxId: 2336] [82407] (1)
    32. Obg GTP-binding protein middle domain [82408]
      1. Bacillus subtilis [TaxId: 1423] [82409] (1)
      2. Thermus thermophilus [TaxId: 274] [102368] (1)
        TT1381
    33. YchF GTP-binding protein N-terminal domain [82410]
      Member of the Obg family of GTPases; contains an alpha-hairpin insert subdomain
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82411] (1)
      2. Haemophilus influenzae [TaxId: 727] [89666] (1)
        HI0393
    34. Probable GTPase EngB [89667]
      1. Escherichia coli [TaxId: 562] [89668] (1)
      2. Bacillus subtilis [TaxId: 1423] [110534] (3)
        SQ P38424
    35. Probable GTPase YlqF [89669]
      naturally occurring circular permutation of G-domain; includes C-terminal all-alpha subdomain
      1. Bacillus subtilis [TaxId: 1423] [89670] (1)
    36. Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain [52639]
      1. Human (Homo sapiens) [TaxId: 9606] [52640] (2)
    37. Dynamin G domain [69488]
      the family common core is decorated with large insertions
      1. Dictyostelium discoideum [TaxId: 44689] [69489] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [142228] (1)
        SQ P21575 6-304
        Dynamin-1
    38. Eukaryotic peptide chain release factor ERF2, G domain [110535]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110536] (3)
        SQ O74718
    39. Rab9a [110537]
      1. Dog (Canis familiaris) [TaxId: 9615] [110538] (1)
        SQ P24408
      2. Human (Homo sapiens) [TaxId: 9606] [110539] (1)
        SQ P51151 2-175 # 100% sequence identity do the dog protein (SQ P24408 2-175)
      3. Mouse (Mus musculus) [TaxId: 10090] [142229] (1)
        SQ Q9R0M6 4-175
    40. Rab7 [110540]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110541] (4)
        SQ P09527
      2. Human (Homo sapiens) [TaxId: 9606] [142230] (5)
        SQ P51149 7-182
    41. Probable GTPase EngC (YjeQ), C-terminal domain [110542]
      circularly permuted G-domain similar to B. sutilis YlqF; distinct extra C-terminal all-alpha subdomain
      1. Thermotoga maritima [TaxId: 2336] [110543] (1)
        SQ Q9X242 # TM1717
      2. Bacillus subtilis [TaxId: 1423] [117534] (1)
        SQ O34530
    42. GTPase Ytp1 [110544]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110545] (2)
        SQ P01123
    43. Interferon-inducible GTPase [110546]
      G domain is inserted in all-alpha domain
      1. Mouse (Mus musculus) [TaxId: 10090] [110547] (5)
        SQ Q9QZ85 # all-alpha domain (14-68,252-415)
    44. TrmE GTPase domain [117535]
      1. Thermotoga maritima [TaxId: 2336] [117536] (2)
        SQ Q9WYA4
    45. Elongation factor SelB, N-terminal domain [117537]
      1. Methanococcus maripaludis [TaxId: 39152] [117538] (3)
        SQ Q8J307
    46. Rab23 [142231]
      1. Mouse (Mus musculus) [TaxId: 10090] [142232] (2)
        SQ P35288 8-171
    47. Rab18 [142233]
      1. Human (Homo sapiens) [TaxId: 9606] [142234] (1)
        SQ Q9NP72 2-178
    48. Rab31 [142235]
      1. Human (Homo sapiens) [TaxId: 9606] [142236] (1)
        SQ Q13636 3-167
    49. Rab11b [142237]
      1. Human (Homo sapiens) [TaxId: 9606] [142238] (2)
        SQ Q15907 7-181
    50. Rab30 [142239]
      1. Human (Homo sapiens) [TaxId: 9606] [142240] (1)
        SQ Q15771 5-175
    51. Rab1a [142241]
      1. Human (Homo sapiens) [TaxId: 9606] [142242] (1)
        SQ P62820 7-175
    52. RhoB [142243]
      1. Human (Homo sapiens) [TaxId: 9606] [142244] (1)
        SQ P62745 4-185
    53. RhoC [142245]
      1. Human (Homo sapiens) [TaxId: 9606] [142246] (2)
        SQ P08134 1-179
    54. Rab4a [142247]
      1. Human (Homo sapiens) [TaxId: 9606] [142248] (5)
        SQ P20338 2-172! SQ P20338 4-172! SQ P20338 4-184
    55. Centaurin gamma 1, G domain [142249]
      1. Human (Homo sapiens) [TaxId: 9606] [142250] (1)
        SQ Q99490 402-576
    56. GTP-binding protein PH0525 [142251]
      Member of the Obg family of GTPases; contains an alpha-hairpin insert subdomain
      1. Pyrococcus horikoshii [TaxId: 53953] [142252] (1)
        SQ O58261 1-319
    57. Rab-22a [142253]
      1. Mouse (Mus musculus) [TaxId: 10090] [142254] (2)
        SQ P35285 2-167! SQ P35285 2-168
    58. Rac3 [142255]
      1. Human (Homo sapiens) [TaxId: 9606] [142256] (2)
        SQ P60763 3-177
    59. GTP-binding protein engB [142257]
      1. Pyrococcus horikoshii [TaxId: 53953] [142258] (3)
        SQ O57939 28-211
        PH0200
    60. Rab26 [142259]
      1. Human (Homo sapiens) [TaxId: 9606] [142260] (1)
        SQ Q9ULW5 58-227
    61. RhoQ [142261]
      1. Human (Homo sapiens) [TaxId: 9606] [142262] (2)
        SQ P17081 1-185
    62. Rab27b [142263]
      1. Human (Homo sapiens) [TaxId: 9606] [142264] (2)
        SQ O00194 4-189
    63. Rab2a [142265]
      1. Human (Homo sapiens) [TaxId: 9606] [142266] (4)
        SQ P61019 2-170
    64. di-Ras2 [142267]
      1. Human (Homo sapiens) [TaxId: 9606] [142268] (2)
        SQ Q96HU8 6-176
    65. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain [142269]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [142270] (1)
        SQ Q87WW1 16-237
    66. Rab14 [142271]
      1. Human (Homo sapiens) [TaxId: 9606] [142272] (2)
        SQ P61106 7-174
    67. r-Ras [142273]
      1. Human (Homo sapiens) [TaxId: 9606] [142274] (1)
        SQ P10301 24-196
    68. GTP-binding protein RheB [142275]
      1. Human (Homo sapiens) [TaxId: 9606] [142276] (3)
        SQ Q15382 3-169
    69. di-Ras1 [142277]
      1. Human (Homo sapiens) [TaxId: 9606] [142278] (4)
        SQ O95057 4-176
    70. Rab-33b [142279]
      1. Mouse (Mus musculus) [TaxId: 10090] [142280] (2)
        SQ O35963 32-196
    71. r-Ras2 [142281]
      1. Human (Homo sapiens) [TaxId: 9606] [142282] (2)
        SQ P62070 10-180
    72. Ras-related protein M-Ras (XRas) [142283]
      1. Mouse (Mus musculus) [TaxId: 10090] [142284] (2)
        SQ O08989 10-178
    73. Rab21 [142285]
      1. Human (Homo sapiens) [TaxId: 9606] [142286] (10)
        SQ Q9UL25 16-182
    74. Rab2b [142287]
      1. Human (Homo sapiens) [TaxId: 9606] [142288] (1)
        SQ Q8WUD1 4-176
    75. GTP-binding protein GEM [142289]
      1. Human (Homo sapiens) [TaxId: 9606] [142290] (1)
        SQ P55040 73-244
    76. Ras-like estrogen-regulated growth inhibitor, RERG [142291]
      1. Human (Homo sapiens) [TaxId: 9606] [142292] (1)
        SQ Q96A58 5-172
    77. Rab8a [142293]
      1. Mouse (Mus musculus) [TaxId: 10090] [142294] (2)
        SQ P55258 3-175
    78. Rad [142295]
      1. Human (Homo sapiens) [TaxId: 9606] [142296] (2)
        SQ P55042 91-258
  12. Motor proteins [52641] (15)
    1. Myosin S1, motor domain [52642]
      common fold is interrupted with some all-alpha subdomains
      1. Chicken (Gallus gallus), pectoral muscle [TaxId: 9031] [52643] (4)
      2. Chicken (Gallus gallus), Va isoform [TaxId: 9031] [102369] (3)
      3. Bay scallop (Aequipecten irradians) [TaxId: 31199] [52644] (11)
        SQ P24733 3-836 ! SQ P24733 6-837
      4. Dictyostelium discoideum [TaxId: 44689] [52645] (18)
      5. Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689] [75206] (1)
        lacks the SH3-like insert domain
    2. Kinesin [52646]
      1. Human (Homo sapiens) [TaxId: 9606] [52647] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52648] (2)
      3. Mouse (Mus musculus), kif1a [TaxId: 10090] [64017] (12)
        SQ P33173 3-355
      4. Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606] [64018] (34)
      5. Mouse (Mus musculus), kif2c [TaxId: 10090] [102370] (2)
      6. Neurospora crassa [TaxId: 5141] [69490] (1)
      7. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102371] (1)
    3. Kinesin motor Ncd (non-claret disjunctional) [52649]
      contains coiled-coil neck
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [52650] (3)
      2. Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932] [52651] (5)
        kinesin-like protein
    4. Kinesin heavy chain-like protein [110548]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [110549] (5)
        SQ Q41460 884-1252
  13. Nitrogenase iron protein-like [52652] (29)
    core: parallel beta-sheet of 7 strands; order 3241567
    1. Dethiobiotin synthetase [52653]
      1. Escherichia coli [TaxId: 562] [52654] (13)
    2. Adenylosuccinate synthetase, PurA [52655]
      common fold is interrupted by an all-alpha subdomain, residues 100-200
      1. Escherichia coli [TaxId: 562] [52656] (24)
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52657] (1)
      3. Bread wheat (Triticum aestivum) [TaxId: 4565] [52658] (1)
      4. Mouse (Mus musculus) [TaxId: 10090] [69491] (9)
      5. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102372] (1)
    3. Formyltetrahydrofolate synthetase [52659]
      modified P-loop; there are many insertions in the common fold
      1. Moorella thermoacetica [TaxId: 1525] [52660] (3)
    4. Nitrogenase iron protein [52661]
      1. Azotobacter vinelandii [TaxId: 354] [52662] (19)
      2. Clostridium pasteurianum [TaxId: 1501] [52663] (1)
    5. Cell division regulator MinD [64019]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64020] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [64021] (2)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [64022] (1)
    6. GTPase domain of the signal sequence recognition protein Ffh [52664]
      1. Thermus aquaticus [TaxId: 271] [52665] (25)
      2. Archaeon Acidianus ambivalens [TaxId: 2283] [64023] (2)
      3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [102373] (2)
    7. GTPase domain of the signal recognition particle receptor FtsY [52666]
      1. Escherichia coli [TaxId: 562] [52667] (2)
      2. Thermus aquaticus [TaxId: 271] [102374] (8)
      3. Thermotoga maritima [TaxId: 2336] [110550] (1)
        SQ Q9WZ40
    8. Arsenite-translocating ATPase ArsA [52668]
      Duplication: consists of two domains of this fold arranged as the NIP subunits in the dimer
      1. Escherichia coli [TaxId: 562] [52669] (4)
    9. Hypothetical protein YjiA, N-terminal domain [89671]
      homologue of the cobalamin biosynthesis protein CobW
      1. Escherichia coli [TaxId: 562] [89672] (1)
    10. Molybdopterin-guanine dinucleotide biosynthesis protein MobB [89673]
      forms segment-swapped dimer
      1. Escherichia coli [TaxId: 562] [89674] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [117539] (1)
        SQ Q5L1X2 # 91% sequence identity
    11. CTP synthase PyrG, N-terminal domain [110551]
      1. Escherichia coli [TaxId: 562] [110552] (1)
        SQ P08398
      2. Thermus thermophilus [TaxId: 274] [110553] (3)
        SQ Q5SIA8
      3. Human (Homo sapiens) [TaxId: 9606] [159561] (2)
        SQ Q5VW67 1-273
    12. ATP(GTP)-binding protein PAB0955 [142297]
      PYRAB14380; belongs to Pfam 03029
      1. Pyrococcus abyssi [TaxId: 29292] [142298] (9)
        SQ Q9UYR9 30-273
    13. Hypothetical protein TM0796 [142299]
      member of Pfam 07755; DUF1611; contains extra N-terminal alpha/beta fold of Rossmann-fold topology, parallel beta-sheet, strand order 312456
      1. Thermotoga maritima [TaxId: 2336] [142300] (2)
        SQ Q9WZQ3 1-338
    14. LAO/AO transport system kinase ArgK [159562]
      member of Pfam 03308; contains extra N-terminal 3-helical bundle and extra C-terminal helical dimerisation domain
      1. Escherichia coli [TaxId: 562] [159563] (1)
        SQ P27254 1-327
    15. Metallochaperone MeaB [159564]
      ArgK-like (sub)family; Pfam 03308
      1. Methylobacterium extorquens [TaxId: 408] [159565] (4)
        SQ Q8RPA0 5-327
  14. RecA protein-like (ATPase-domain) [52670] (29)
    core: mixed beta-sheet of 8 strands, order 32451678; strand 7 is antiparallel to the rest
    1. RecA protein, ATPase-domain [52671]
      C-terminal domain is alpha+beta
      1. Escherichia coli [TaxId: 562] [52672] (7)
        SQ P0A7G6 P03017
      2. Mycobacterium tuberculosis [TaxId: 1773] [52673] (6)
      3. Mycobacterium smegmatis [TaxId: 1772] [89675] (4)
      4. Deinococcus radiodurans [TaxId: 1299] [117540] (1)
        SQ P42443 15-341
    2. Gene 4 protein (g4p, DNA primase), helicase domain [52674]
      1. Bacteriophage T7 [TaxId: 10760] [52675] (7)
    3. Hexameric replicative helicase repA [52676]
      1. Escherichia coli [TaxId: 562] [52677] (3)
    4. Bacterial conjugative coupling protein TrwB [69492]
      1. Escherichia coli [TaxId: 562] [69493] (5)
    5. Hexameric traffic ATPase, HP0525 [52719]
      type II/IV secretion system protein; includes N-terminal alpha+beta domain of a profilin-like topology
      1. Helicobacter pylori [TaxId: 210] [52720] (6)
    6. Extracellular secretion NTPase EpsE [102375]
      type II/IV secretion system protein; overall structure is similar to HP0525
      1. Vibrio cholerae [TaxId: 666] [102376] (2)
    7. DNA repair protein Rad51, catalytic domain [82412]
      1. Human (Homo sapiens) [TaxId: 9606] [82413] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102377] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110554] (1)
        SQ P25454 81-395
      4. Archaeon Methanococcus voltae [TaxId: 2188] [110555] (8)
        SQ O73948
    8. Central domain of alpha subunit of F1 ATP synthase [88774]
      1. Cow (Bos taurus) [TaxId: 9913] [88775] (18)
        SQ P19483
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88776] (2)
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88777] (1)
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88778] (2)
    9. Central domain of beta subunit of F1 ATP synthase [88779]
      1. Cow (Bos taurus) [TaxId: 9913] [88780] (12)
        SQ P00829
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88781] (8)
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88782] (1)
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88783] (2)
    10. Transcription termination factor Rho, ATPase domain [89676]
      1. Escherichia coli [TaxId: 562] [89677] (10)
        SQ P03002
    11. Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU [52682]
      lacks the last strand 8
      1. Salmonella typhimurium [TaxId: 90371] [52683] (2)
    12. ATP:corrinoid adenosyltransferase CobA [52684]
      lacks the two last strands
      1. Salmonella typhimurium [TaxId: 90371] [52685] (3)
    13. Meiotic recombination protein DMC1/LIM15 homolog [110556]
      1. Human (Homo sapiens) [TaxId: 9606] [110557] (1)
        SQ Q14565
    14. Circadian clock protein KaiC [110558]
      duplication: contains two copies of this domain
      1. Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140] [110559] (25)
        SQ Q79PF4 14-497
    15. NTPase P4 [117541]
      contains extra N-terminal subdomain (~100 residues): [contains pseudo beta-barrel]
      1. Bacteriophage phi-12 [TaxId: 161736] [117542] (8)
        SQ Q94M05
    16. Hypothetical kinase-like protein Aq_1292 [142301]
      member of Pfam 03266 (DUF265)
      1. Aquifex aeolicus [TaxId: 63363] [142302] (1)
        SQ O67322 1-178
    17. Cancer-related NTPase, C1orf57 [159566]
      member of Pfam 03266; DUF265
      1. Human (Homo sapiens) [TaxId: 9606] [159567] (1)
        SQ Q5TDE9 2-190
  15. Bacterial cell division inhibitor SulA [89678] (1)
    homologous to RecA but lacks its P-loop motif; the fold is C-terminally truncated; 5-stranded parallel beta-sheet, order: 15423
    1. Hypothetical protein PA3008 [89679]
      1. Pseudomonas aeruginosa [TaxId: 287] [89680] (2)
  16. ABC transporter ATPase domain-like [52686] (29)
    there are two additional subdomains inserted into the central core that has a RecA-like topology
    1. ATP-binding subunit of the histidine permease [52687]
      1. Salmonella typhimurium [TaxId: 90371] [52688] (1)
    2. Branched chain aminoacid ABC transporter [75207]
      1. Thermotoga maritima, TM1139 [TaxId: 2336] [75208] (1)
    3. MJ1267 [64025]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64026] (3)
    4. MJ0796 [64027]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64028] (2)
    5. Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain [102378]
      1. Mouse (Mus musculus) [TaxId: 10090] [102379] (8)
        SQ P26361 390-670
      2. Human (Homo sapiens) [TaxId: 9606] [117543] (2)
        SQ P13569 389-671
    6. Peptide transporter Tap1, C-terminal ABC domain [64029]
      1. Human (Homo sapiens) [TaxId: 9606] [64030] (1)
    7. Maltose transport protein MalK, N-terminal domain [52689]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [52690] (1)
      2. Escherichia coli [TaxId: 562] [102380] (13)
    8. Glucose transport protein GlcV, N-terminal domain [89681]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89682] (5)
    9. ABC transporter involved in vitamin B12 uptake, BtuD [75209]
      1. Escherichia coli [TaxId: 562] [75210] (1)
    10. Haemolysin B ATP-binding protein [89683]
      1. Escherichia coli [TaxId: 562] [89684] (3)
    11. Multidrug resistance ABC transporter MsbA, C-terminal domain [89685]
      a low-resolution structure of the E. coli MsbA in an open conformation is also available (f.35.1.1)
      1. Vibrio cholerae [TaxId: 666] [89686] (1)
      2. Salmonella typhimurium [TaxId: 90371] [159568] (12)
        SQ P63359 329-581
    12. Multidrug resistance ABC transporter LmrA, C-terminal domain [102381]
      1. Lactococcus lactis [TaxId: 1358] [102382] (1)
    13. Rad50 [52691]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [52692] (4)
    14. Smc head domain [52693]
      1. Thermotoga maritima [TaxId: 2336] [52694] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117544] (1)
        SQ P32908 2-214,1024-1223
      3. Pyrococcus furiosus [TaxId: 2261] [117545] (2)
        SQ Q877I1 1-167,1012-1173
    15. Cell division protein MukB [52695]
      1. Escherichia coli [TaxId: 562] [52696] (1)
    16. DNA repair protein MutS, the C-terminal domain [52697]
      1. Thermus aquaticus [TaxId: 271] [52698] (4)
      2. Escherichia coli [TaxId: 562] [52699] (10)
        SQ P23909 2-800
    17. Putative ABC transporter PF0895 [110560]
      1. Pyrococcus furiosus [TaxId: 2261] [110561] (1)
        SQ Q8U2E3
    18. Hypothetical protein PH0022, N-terminal domain [117546]
      1. Pyrococcus horikoshii [TaxId: 53953] [117547] (2)
        SQ O57758
    19. Putative ABC transporter TM0544 [117548]
      1. Thermotoga maritima [TaxId: 2336] [117549] (1)
        SQ Q9WZ14
    20. Putative multidrug export ATP-binding/permease protein SAV1866 [142303]
      1. Staphylococcus aureus [TaxId: 1280] [142304] (4)
        SQ Q99T13 324-578
    21. Molybdate/tungstate import ATP-binding protein WtpC (ModC) [159569]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159570] (4)
        SQ O30144 1-240
    22. Methionine import ATP-binding protein MetN [159571]
      1. Escherichia coli [TaxId: 562] [159572] (4)
        SQ P30750 1-240
    23. Sulfate/molybdate ABC transporter, ATP-binding protein [159573]
      1. Methanosarcina acetivorans [TaxId: 2214] [159574] (2)
        SQ Q8TTZ3 1-229
  17. Tandem AAA-ATPase domain [81268] (27)
    duplication: tandem repeat of two RecA-like (AAA) domains
    1. DEXX box DNA helicase [52701]
      each AAA domain contains an all-alpha insert subdomain
      1. Bacillus stearothermophilus, PcrA [TaxId: 1422] [52702] (5)
      2. Escherichia coli, RepD [TaxId: 562] [52703] (1)
    2. Putative DEAD box RNA helicase [52704]
      homologous to eIF4a and UvrB
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52705] (1)
    3. Probable DEAD box RNA helicase YqfR [102383]
      1. Bacillus stearothermophilus [TaxId: 1422] [102384] (1)
    4. RecQ helicase domain [102385]
      1. Escherichia coli [TaxId: 562] [102386] (2)
    5. DEAD box RNA helicase rck/p54 [102387]
      1. Human (Homo sapiens) [TaxId: 9606] [102388] (1)
    6. RecG helicase domain [69494]
      1. Thermotoga maritima [TaxId: 2336] [69495] (1)
    7. Initiation factor 4a [52706]
      homologous to UvrB
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52707] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [142305] (2)
        SQ P60842 21-238
        4A-I
    8. Nucleotide excision repair enzyme UvrB [52708]
      contains large insertions in the first AAA domain
      1. Thermus thermophilus [TaxId: 274] [52709] (2)
      2. Bacillus caldotenax [TaxId: 1395] [52710] (7)
        SQ P56981
    9. Translocation ATPase SecA, nucleotide-binding domains [82414]
      a pre-protein crosslinking domain inserted in the first AAA domain
      1. Bacillus subtilis [TaxId: 1423] [82415] (4)
        SQ P28366
      2. Mycobacterium tuberculosis [TaxId: 1773] [89687] (2)
    10. Spliceosome RNA helicase BAT1 (UAP56) [110562]
      1. Human (Homo sapiens) [TaxId: 9606] [110563] (5)
        SQ Q13838 45-428
    11. Exodeoxyribonuclease V beta chain (RecB), N-terminal domain [117550]
      each AAA domain contains an all-alpha insert subdomain
      1. Escherichia coli [TaxId: 562] [117551] (1)
        SQ P08394
    12. Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain [117552]
      each AAA domain contains an all-alpha insert subdomain
      1. Escherichia coli [TaxId: 562] [117553] (1)
        SQ P07648
    13. Exodeoxyribonuclease V alpha chain (RecD) [117554]
      contains extra N-terminal alpha+beta (sub)domain (~100 residues)
      1. Escherichia coli [TaxId: 562] [117555] (1)
        SQ P04993
    14. putative ATP-dependent RNA helicase VlgB [142306]
      1. Flatworm (Dugesia japonica) [TaxId: 6161] [142307] (2)
        SQ O97032 164-401
    15. putative ATP-dependent RNA helicase PF2015 [142308]
      separate structures of other domains are known: the middle nuclease domain (scop_sp 89718) and the C-terminal RuvA-like HhH domain (PDB 1x2i)
      1. Pyrococcus furiosus [TaxId: 2261] [142309] (2)
        SQ Q8TZH8 2-201! SQ Q8TZH8 202-487
    16. ATP-dependent RNA helicase DDX25 [142310]
      1. Human (Homo sapiens) [TaxId: 9606] [142311] (4)
        SQ Q9UHL0 307-474
    17. Helicase of the SNF2/Rad54 hamily [142312]
      1. Sulfolobus solfataricus [TaxId: 2287] [142313] (8)
        SQ Q97XQ7 432-661! SQ Q97XQ7 662-802! SQ Q97XQ7 663-802
    18. Probable ATP-dependent RNA helicase DDX48 [142314]
      Eukaryotic translation initiation factor 4A isoform 3
      1. Human (Homo sapiens) [TaxId: 9606] [142315] (10)
        SQ P38919 22-243! SQ P38919 244-411
    19. Rad54-like, Rad54L [142316]
      1. Zebra fish (Danio rerio) [TaxId: 7955] [142317] (2)
        SQ Q7ZV09 390-735! SQ Q7ZV09 92-389
    20. DNA repair protein RAD25 [142318]
      shares with the DNA helicase UvsW (scop_fa 102396) extra N-terminal alpha+beta subdomain that might be related to the DNA repair protein MutS domain I (scop_sf 55271)
      1. Archaeoglobus fulgidus [TaxId: 2234] [142319] (10)
        SQ O29889 237-436! SQ O29889 238-434! SQ O29889 3-236! SQ O29889 4-209
    21. Transcription-repair coupling factor, TRCF [142320]
      similar to UvrB in the N-terminal part and DEAD helicases in the C-terminal part; also contains CarD-like domain in the middle and TRCF domain at the C-terminus
      1. Escherichia coli [TaxId: 562] [142321] (10)
        SQ P30958 2-348! SQ P30958 26-333! SQ P30958 349-465! SQ P30958 546-778! SQ P30958 779-989
    22. Putative ATP-dependent RNA helicase DHH1 [142322]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142323] (2)
        SQ P39517 252-422! SQ P39517 46-251
    23. Hel308 helicase [159575]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159576] (4)
  18. Extended AAA-ATPase domain [81269] (34)
    fold is similar to that of RecA, but lacks the last two strands, followed by a family-specific Arg-finger domain
    1. gamma subunit of DNA polymerase III, N-domain [64031]
      1. Escherichia coli [TaxId: 562] [64032] (3)
        SQ P06710 5-368
      2. Thermotoga maritima [TaxId: 2336] [142324] (1)
        SQ Q9WZM9 11-208
    2. delta prime subunit of DNA polymerase III, N-domain [52711]
      contains additional alpha-helical domain after the family specific domains
      1. Escherichia coli [TaxId: 562] [52712] (6)
        SQ P28631
    3. delta subunit of DNA polymerase III, N-domain [64033]
      1. Escherichia coli [TaxId: 562] [64034] (5)
        SQ P28630
    4. Replication factor C [64035]
      contains additional alpha-helical domain after the family specific domains
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64036] (1)
    5. Chromosomal replication initiation factor DnaA [82416]
      contains TrpR-like DNA-binding domain after the family specific domains
      1. Aquifex aeolicus [TaxId: 63363] [82417] (5)
    6. Holliday junction helicase RuvB [52713]
      contains "winged helix" DNA-binding domain after the family specific domains
      1. Thermus thermophilus [TaxId: 274] [52714] (3)
      2. Thermotoga maritima [TaxId: 2336] [64037] (6)
    7. Transcriptional activator sigm54 (NtrC1), C-terminal domain [102389]
      1. Aquifex aeolicus [TaxId: 63363] [102390] (2)
    8. CDC6, N-domain [52715]
      contains "winged helix" DNA-binding domain after the family specific domains
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [52716] (1)
    9. Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein [52717]
      1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [52718] (2)
    10. Membrane fusion ATPase VCP/p97 [64038]
      1. Mouse (Mus musculus) [TaxId: 10090] [64039] (4)
    11. AAA domain of cell division protein FtsH [82418]
      ATP-dependent protease
      1. Escherichia coli [TaxId: 562] [82419] (1)
      2. Thermus thermophilus [TaxId: 274] [82420] (4)
      3. Thermotoga maritima [TaxId: 2336] [142325] (12)
        SQ Q9WZ49 150-402
    12. HslU [52721]
      ATPase subunit of ATP-dependent protease
      1. Escherichia coli [TaxId: 562] [52722] (10)
      2. Haemophilus influenzae [TaxId: 727] [52723] (6)
    13. ClpX [102391]
      ATPase subunit of ATP-dependent protease
      1. Helicobacter pylori [TaxId: 210] [102392] (1)
    14. ATPase domain of protease Lon (La) [102393]
      1. Escherichia coli [TaxId: 562] [102394] (1)
    15. ClpA, an Hsp100 chaperone, AAA+ modules [82421]
      duplication: two AAA+ modules; the first module is structurally similar to the CDC6 module whereas the second module to the HslU module
      1. Escherichia coli [TaxId: 562] [82422] (2)
        SQ Q83LR6
    16. ClpB, AAA+ modules [75211]
      ATPase subunit of ATP-dependent protease; similar domain organization to ClpA
      1. Thermus thermophilus [TaxId: 274] [102395] (1)
      2. Escherichia coli [TaxId: 562] [75212] (1)
    17. ATPase subunit of magnesium chelatase, BchI [64040]
      1. Rhodobacter capsulatus [TaxId: 1061] [64041] (1)
    18. Papillomavirus large T antigen helicase domain [89688]
      1. Simian virus 40 [TaxId: 10633] [89689] (16)
        SQ P03070 265-627
    19. Rep 40 protein helicase domain [110564]
      1. Adeno-associated virus 2, AAV2 [TaxId: 10804] [110565] (2)
        SQ P03132 225-490
    20. Replication factor C1 [110566]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110567] (1)
        SQ P38630 295-696
    21. Replication factor C4 [110568]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110569] (1)
        SQ P40339
    22. Replication factor C3 [110570]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110571] (1)
        SQ P38629
    23. Replication factor C2 [110572]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110573] (1)
        SQ P40348
    24. Replication factor C5 [110574]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110575] (1)
        SQ P38251
    25. Replication protein E1 helicase domain [110576]
      1. Human papillomavirus type 18 [TaxId: 333761] [110577] (1)
        SQ P06789 428-629 # structure of the origin-binding domain (210-354) is also known, 1r9w (scop_sp 103119)
    26. CDC6-like protein APE0152, N-terminal domain [117556]
      1. Aeropyrum pernix [TaxId: 56636] [117557] (2)
        SQ Q9YFU8
    27. Archaeal ATPase SSO1545 [142326]
      member of Pfam 01637 family; overall structural similarity to the archael CDC6-like protein APE0102
      1. Sulfolobus solfataricus [TaxId: 2287] [142327] (2)
        SQ Q97Y08 1-283
    28. CED-4, NB-ARC domain [159577]
      belongs to Pfam 00931
      1. Caenorhabditis elegans [TaxId: 6239] [159578] (1)
        SQ P30429 109-385
  19. RNA helicase [52724] (3)
    duplication: consists of two similar domains, one binds NTP and the other binds RNA; also contains an all-alpha subdomain in the C-terminal extension
    1. HCV helicase domain [52725]
      1. Human hepatitis C virus (HCV), different isolates [TaxId: 11103] [52726] (6)
    2. Dengue virus helicase [142328]
      1. Dengue virus type 2 [TaxId: 11060] [142329] (8)
        SQ Q91H74 1653-1957! SQ Q91H74 1958-2093
    3. YFV helicase domain [142330]
      1. Yellow fever virus [TaxId: 11089] [142331] (2)
        SQ P19901 1669-1842! SQ P19901 1843-2107
  20. Helicase-like "domain" of reverse gyrase [69496] (1)
    1. Helicase-like "domain" of reverse gyrase [69497]
      contains a mobile insertion of LEM/SAP-like HeH motif, residues 354-423
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69498] (2)
  21. DNA helicase UvsW [102396] (1)
    contains extra N-terminal alpha+beta subdomain
    1. DNA helicase UvsW [102397]
      1. Bacteriophage T4 [TaxId: 10665] [102398] (1)
  22. YjeE-like [75213] (1)
    mixed beta-sheet; order 234156(0), strands 2 and 6 are antiparallel to the rest
    1. Hypothetical protein HI0065 [75214]
      1. Haemophilus influenzae [TaxId: 727] [75215] (2)
  23. Type II thymidine kinase [117558] (3)
    N-terminal part of Pfam 00265; parallel beta-sheet of 6 strands, order 324516; topological similarity to the RecA-like proteins, especially CobA (scop_pr 52684)
    1. Thymidine kinase, TK1, N-terminal domain [117559]
      1. Human (Homo sapiens) [TaxId: 9606] [117560] (3)
        SQ P04183 18-191
      2. Ureaplasma urealyticum [TaxId: 2130] [117561] (8)
        SQ Q9PPP5 11-211
      3. Clostridium acetobutylicum [TaxId: 1488] [117562] (1)
        SQ Q97F65
  24. Atu3015-like [142332] (2)
    unknown function; similar to the nucleotide/nucleoside kinases
    1. Hypothetical protein BH3686 [142333]
      annotated as putative gluconate kinase by NESG
      1. Bacillus halodurans [TaxId: 86665] [142334] (1)
        SQ Q9K6P2 1-176
    2. Hypothetical protein Atu3015 [142335]
      1. Agrobacterium tumefaciens [TaxId: 358] [142336] (1)
        SQ Q8UBK1 6-181
PTS IIb component [52727] (1)
3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
1. PTS IIb component [52728] (1)
  uperfamily
  1. PTS IIb component [52729] (2)
    1. Fructose permease, subunit IIb [52730]
      1. Bacillus subtilis [TaxId: 1423] [52731] (1)
    2. Sorbose permease subunit IIb , EIIb-sor [89690]
      1. Klebsiella pneumoniae [TaxId: 573] [89691] (1)
DNA polymerase III chi subunit [102399] (1)
3 layers, a/b/a; parallel beta-sheet of 7 strands, order 7165243
1. DNA polymerase III chi subunit [102400] (1)
  structural similarity and possible evolutionary relationship to the AAA domain; lacks the P-loop motif
  uperfamily
  1. DNA polymerase III chi subunit [102401] (1)
    1. DNA polymerase III chi subunit [102402]
      1. Escherichia coli [TaxId: 562] [102403] (1)
Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52733] (1)
  uperfamily
  1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52734] (2)
    1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52735]
      1. Salmonella typhimurium [TaxId: 90371] [52736] (28)
      2. Thermus thermophilus [TaxId: 274] [82423] (1)
CofD-like [142337] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (scop_cf 52732)
1. CofD-like [142338] (1)
  uperfamily
  1. CofD-like [142339] (2)
    Pfam 01933; UPF0052
    1. LPPG:FO 2-phospho-L-lactate transferase CofD [142340]
      1. Methanosarcina mazei [TaxId: 2209] [142341] (1)
        SQ Q8PVT6 1-309
    2. Hypothetical protein BH3568 [142342]
      1. Bacillus halodurans [TaxId: 86665] [142343] (4)
        SQ Q9K706 2-312
MCP/YpsA-like [102404] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567
1. MCP/YpsA-like [102405] (2)
  uperfamily
  1. MoCo carrier protein-like [102406] (6)
    Pfam 03641
    1. Hypothetical protein TM1055 [102407]
      1. Thermotoga maritima [TaxId: 2336] [102408] (1)
        structural genomics; NESG target VT76
    2. Hypothetical protein YvdD [102409]
      1. Bacillus subtilis [TaxId: 1423] [102410] (1)
    3. Hypothetical protein TT1887 (TTHA0294) [117563]
      1. Thermus thermophilus [TaxId: 274] [117564] (1)
        SQ Q5SLJ9
    4. Hypothetical protein TT1465 (TTHA1644) [117565]
      1. Thermus thermophilus [TaxId: 274] [117566] (1)
        SQ Q5SHT6
    5. Hypothetical protein At5g11950 [117567]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117568] (3)
        SQ Q84MC2
    6. Hypothetical protein At2g37210/T2N18.3 [142344]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142345] (4)
        SQ Q8L8B8 8-190
  2. YpsA-like [159579] (1)
    Pfam 06908; DUF1273; lacking the last strand 7; different set of conserved residues in the putative active site than in the MoCo carrier protein-like family
    1. Hypothetical protein YpsA [159580]
      1. Bacillus subtilis [TaxId: 1423] [159581] (1)
        SQ P50838 1-177
Methylesterase CheB, C-terminal domain [52737] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
1. Methylesterase CheB, C-terminal domain [52738] (1)
  uperfamily
  1. Methylesterase CheB, C-terminal domain [52739] (1)
    1. Methylesterase CheB, C-terminal domain [52740]
      1. Salmonella typhimurium [TaxId: 90371] [52741] (2)
Subtilisin-like [52742] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
1. Subtilisin-like [52743] (2)
  uperfamily
  1. Subtilases [52744] (18)
    1. Subtilisin [52745]
      1. Bacillus subtilis, carlsberg [TaxId: 1423] [52746] (6)
      2. Bacillus subtilis, E [TaxId: 1423] [52747] (1)
      3. Bacillus licheniformis [TaxId: 1402] [52748] (17)
      4. Bacillus lentus, savinase (TM) [TaxId: 1467] [52749] (2)
        SQ P29600
      5. Bacillus lentus [TaxId: 1467] [52750] (11)
      6. Bacillus amyloliquefaciens, Novo/BPN' [TaxId: 1390] [52751] (52)
        SQ P00782 108-382
    2. Messentericopeptidase [52752]
      1. Bacillus mesentericus [TaxId: 1408] [52753] (1)
    3. M-proteinase [52754]
      1. Bacillus sp., strain ksm-k16 [TaxId: 1409] [52755] (2)
        SQ Q99405 112-380
    4. Serine protease PB92 (subtilisin PB92) [52756]
      1. Bacillus alcalophilus [TaxId: 1445] [52757] (2)
        identical sequence to Bacillus lentus, TaxId: 1467
    5. Thermostable serine protease [52758]
      1. Bacillus sp., AK.1 [TaxId: 1409] [52759] (1)
    6. Sphericase [75224]
      1. Bacillus sphaericus [TaxId: 1421] [75225] (3)
    7. Thermitase [52760]
      1. Thermoactinomyces vulgaris [TaxId: 2026] [52761] (4)
    8. Proteinase K [52762]
      1. Fungus (Tritirachium album), strain limber [TaxId: 37998] [52763] (28)
        SQ P06873
    9. Kexin, N-terminal domain [89692]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89693] (4)
    10. Furin, N-terminal domain [89694]
      1. Mouse (Mus musculus) [TaxId: 10090] [89695] (1)
    11. Alkaline serine protease kp-43, N-terminal domain [110578]
      1. Bacillus sp. KSM-KP43 [TaxId: 109322] [110579] (3)
        SQ Q93UV9 207-640
    12. Fervidolysin [117569]
      1. Fervidobacterium pennivorans [TaxId: 93466] [117570] (1)
        SQ Q93LQ6
    13. Alkaline serine protease Apa1 [117571]
      1. Pseudoalteromonas sp. AS-11 [TaxId: 247492] [117572] (1)
        SQ Q65Z69 145-579
  2. Serine-carboxyl proteinase, SCP [52764] (3)
    elaborated with additional structures
    1. Serine-carboxyl proteinase, SCP [52765]
      1. Pseudomonas sp., sedolisin [TaxId: 306] [52766] (9)
      2. Bacillus novosp. MN-32, kumamolisin [TaxId: 198803] [75226] (7)
        SQ Q8RR56 ! SQ Q8RR56
      3. Alicyclobacillus sendaiensis, kumamolisin-as [TaxId: 192387] [102411] (3)
        SQ Q8GB88
Indigoidine synthase A-like [110580] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756
1. Indigoidine synthase A-like [110581] (1)
  uperfamily
  1. Indigoidine synthase A-like [110582] (1)
    Pfam 04227
    1. Hypothetical protein TM1464 [110583]
      1. Thermotoga maritima [TaxId: 2336] [110584] (1)
        SQ Q9X1H5
Arginase/deacetylase [52767] (1)
3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
1. Arginase/deacetylase [52768] (2)
  uperfamily
  1. Arginase-like amidino hydrolases [52769] (8)
    Pfam 00491
    1. Arginase [52770]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52771] (51)
        SQ P07824
      2. Human (Homo sapiens), isoform II, mitochondrial [TaxId: 9606] [102412] (1)
      3. Bacillus caldovelox [TaxId: 33931] [52772] (5)
      4. Human (Homo sapiens) [TaxId: 9606] [142346] (16)
        SQ P05089 5-313
      5. Trypanosoma cruzi [TaxId: 5693] [142347] (1)
        SQ Q4DSA0 5-302
    2. Proclavaminate amidino hydrolase [75227]
      1. Streptomyces clavuligerus [TaxId: 1901] [75228] (2)
    3. Agmatinase [110585]
      1. Deinococcus radiodurans [TaxId: 1299] [110586] (3)
        SQ Q9RZ04 # DRA0149
    4. Formimidoylglutamase HutG [117573]
      1. Vibrio cholerae [TaxId: 666] [117574] (1)
        SQ Q9KSQ2
  2. Histone deacetylase, HDAC [52773] (3)
    1. HDAC homologue [52774]
      1. Aquifex aeolicus [TaxId: 63363] [52775] (3)
    2. Histone deacetylase 8, HDAC8 [110587]
      1. Human (Homo sapiens) [TaxId: 9606] [110588] (5)
        SQ Q9BY41 13-375 ! SQ Q9BY41
    3. Histone deacetylase 7, HDAC7 [159582]
      HDAC7a
      1. Human (Homo sapiens) [TaxId: 9606] [159583] (9)
        SQ Q8WUI4 515-900
Alpha-2,3/8-sialyltransferase CstII [102413] (1)
3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678
1. Alpha-2,3/8-sialyltransferase CstII [102414] (1)
  uperfamily
  1. Alpha-2,3/8-sialyltransferase CstII [102415] (1)
    1. Alpha-2,3/8-sialyltransferase CstII [102416]
      1. Campylobacter jejuni [TaxId: 197] [102417] (2)
Cell-division inhibitor MinC, N-terminal domain [64042] (1)
beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest
1. Cell-division inhibitor MinC, N-terminal domain [64043] (1)
  uperfamily
  1. Cell-division inhibitor MinC, N-terminal domain [64044] (1)
    1. Cell-division inhibitor MinC, N-terminal domain [64045]
      1. Thermotoga maritima [TaxId: 2336] [64046] (1)
DTD-like [69499] (1)
beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC
1. DTD-like [69500] (1)
  active form is a dimer
  uperfamily
  1. DTD-like [69501] (3)
    Pfam 02580
    1. D-Tyr tRNAtyr deacylase, DTD [69502]
      formerly hypothetical protein YihZ
      1. Escherichia coli [TaxId: 562] [69503] (1)
      2. Haemophilus influenzae [TaxId: 727] [89696] (1)
        YihZ homologue HI0670
    2. probable eukaryotic D-amino acid tRNA deacylase [110589]
      1. Leishmania major [TaxId: 5664] [110590] (1)
        SQ P84066
CoA-dependent acyltransferases [52776] (1)
core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
1. CoA-dependent acyltransferases [52777] (3)
  uperfamily
  1. CAT-like [52778] (5)
    trimeric enzymes with the active sites being located in between subunits
    1. Chloramphenicol acetyltransferase, CAT [52779]
      1. Escherichia coli [TaxId: 562] [52780] (8)
        SQ P00483
      2. Shigella flexneri [TaxId: 623] [52781] (1)
    2. Dihydrolipoamide acetyltransferase [52782]
      1. Azotobacter vinelandii [TaxId: 354] [52783] (9)
      2. Bacillus stearothermophilus [TaxId: 1422] [52784] (1)
    3. Dihydrolipoamide succinyltransferase [52785]
      1. Escherichia coli [TaxId: 562] [52786] (3)
  2. Choline/Carnitine O-acyltransferase [82424] (4)
    Pfam 00755; monomeric enzyme containing tandem repeat of two CAT subunit-like domains
    1. Carnitine acetyltransferase [82425]
      relative spatial position of the domains is similar to the monomers in CAT trimer
      1. Mouse (Mus musculus) [TaxId: 10090] [82426] (18)
        SQ P47934
      2. Human (Homo sapiens) [TaxId: 9606] [89697] (2)
    2. Choline O-acetyltransferase [110591]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110592] (3)
        SQ P32738
    3. Peroxisomal carnitine O-octanoyltransferase, COT [117575]
      1. Mouse (Mus musculus) [TaxId: 10090] [117576] (4)
        SQ Q9DC50 11-612
  3. NRPS condensation domain (amide synthase) [75229] (2)
    Pfam 00668; functional domain of multifunctional enzyme containing tandem repeat of two CAT subunit-like domains
    1. VibH [75230]
      relative spatial position of the domains is similar to the monomers in CAT trimer
      1. Vibrio cholerae [TaxId: 666] [75231] (1)
    2. Polyketide synthase associated protein 5, PapA5 [110593]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110594] (1)
        SQ P96208
Phosphotyrosine protein phosphatases I-like [52787] (2)
3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
1. Phosphotyrosine protein phosphatases I [52788] (1)
  share the common active site structure with the family II
  uperfamily
  1. Low-molecular-weight phosphotyrosine protein phosphatases [52789] (7)
    1. Tyrosine phosphatase [52790]
      1. Cow (Bos taurus) [TaxId: 9913] [52791] (7)
      2. Human (Homo sapiens) [TaxId: 9606] [52792] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52793] (3)
      4. Tritrichomonas foetus [TaxId: 5724] [110595] (1)
        SQ O00810
    2. Arsenate reductase ArsC [69504]
      also has a phosphotyrosine phosphatase activity
      1. Staphylococcus aureus [TaxId: 1280] [69505] (8)
        SQ P30330
      2. Bacillus subtilis [TaxId: 1423] [69506] (3)
      3. Archaeoglobus fulgidus [TaxId: 2234] [117577] (1)
        SQ O28910
2. PTS system IIB component-like [52794] (2)
  uperfamily
  1. PTS system, Lactose/Cellobiose specific IIB subunit [52795] (2)
    Pfam 02302
    1. Enzyme IIB-cellobiose [52796]
      of the phosphoenol-pyruvate dependent phosphotransferase system
      1. Escherichia coli [TaxId: 562] [52797] (3)
    2. PTS system mannitol-specific EIICBA component [110596]
      1. Escherichia coli [TaxId: 562] [110597] (1)
        SQ P00550 375-471
  2. PTS system, Fructose specific IIB subunit-like [159584] (2)
    Pfam 02379
    1. Fructose-specific enzyme IIABC component FruA, middle domain [159585]
      1. Bacillus subtilis [TaxId: 1423] [159586] (1)
        SQ P71012 171-273
    2. Mannose-specific enzyme IIBCA component ManP, N-terminal domain [159587]
      1. Bacillus subtilis [TaxId: 1423] [159588] (1)
        SQ O31645 2-104
(Phosphotyrosine protein) phosphatases II [52798] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
1. (Phosphotyrosine protein) phosphatases II [52799] (5)
  share with the family I the common active site structure with a circularly permuted topology
  uperfamily
  1. Dual specificity phosphatase-like [52800] (10)
    1. VH1-related dual-specificity phosphatase, VHR [52801]
      1. Human (Homo sapiens) [TaxId: 9606] [52802] (2)
    2. Mapk phosphatase [52803]
      1. Human (Homo sapiens), pyst1 (mkp3) [TaxId: 9606] [52804] (1)
      2. Human (Homo sapiens), pac-1 [TaxId: 9606] [75232] (1)
    3. Phoshphoinositide phosphatase Pten (Pten tumor suppressor), N-terminal domain [52818]
      1. Human (Homo sapiens) [TaxId: 9606] [52819] (1)
    4. Proline directed phosphatase CDC14b2 [89698]
      duplication: consists of two structurally similar domains with the catalytic site being in the C-terminal domain
      1. Human (Homo sapiens) [TaxId: 9606] [89699] (3)
    5. Protein tyrosine phosphatase type IVa [102418]
      1. Human (Homo sapiens), pr-3 [TaxId: 9606] [102419] (2)
        SQ O75365 1-162 # 99% sequence identity
      2. Human (Homo sapiens), pr-1 [TaxId: 9606] [117578] (1)
        SQ Q93096 9-160
    6. mRNA capping enzyme, triphosphatase domain [64047]
      1. Mouse (Mus musculus) [TaxId: 10090] [64048] (2)
    7. Kinase associated phosphatase (kap) [64049]
      1. Human (Homo sapiens) [TaxId: 9606] [64050] (2)
    8. Putative phosphatase At1g05000 [117579]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117580] (3)
        SQ Q9ZVN4 52-201
  2. Higher-molecular-weight phosphotyrosine protein phosphatases [52805] (12)
    has an extension to the beta-sheet of 3 antiparallel strands before strand 4
    1. Tyrosine phosphatase [52806]
      1. Human (Homo sapiens), 1B [TaxId: 9606] [52807] (92)
        SQ P18031 2-300 ! SQ P18031 1-298 ! SQ P18031 2-299
      2. Human (Homo sapiens), mu [TaxId: 9606] [52808] (1)
        receptor protein tyrosine phosphatase mu, domain 1
      3. Mouse (Mus musculus) [TaxId: 10090] [52809] (1)
        receptor protein tyrosine phosphatase alpha, domain 1
      4. Human (Homo sapiens), shp-2 [TaxId: 9606] [52810] (1)
      5. Human (Homo sapiens), shp-1 [TaxId: 9606] [52811] (2)
      6. Mouse (Mus musculus), ptp-sl/br7 [TaxId: 10090] [64051] (1)
      7. Human (Homo sapiens), T-cell [TaxId: 9606] [75233] (1)
        non-receptor type 2
    2. Protein-tyrosine phosphatase YopH, catalytic domain [100952]
      1. Yersinia enterocolitica [TaxId: 630] [52812] (13)
    3. SptP tyrosine phosphatase, catalytic domain [52813]
      1. Salmonella typhimurium [TaxId: 90371] [52814] (2)
    4. RPTP Lar [52815]
      duplication: tandem repeat of the phosphatase domain
      1. Human (Homo sapiens) [TaxId: 9606] [52816] (1)
    5. Protein-tyrosine phosphatase alpha [102420]
      1. Mouse (Mus musculus) [TaxId: 10090] [102421] (1)
    6. Tyrosine-protein phosphatase, non-receptor type 13 (PTPL1) [117581]
      1. Human (Homo sapiens) [TaxId: 9606] [117582] (1)
        SQ Q12923 2170-2477 # structure of a PDZ domain (1361-1456) is also known (scop_sp 50169)
  3. Myotubularin-like phosphatases [102422] (1)
    common fold is decorated with additional structures
    1. Myotubularin-related protein 2, C-terminal domain [102423]
      1. Human (Homo sapiens) [TaxId: 9606] [102424] (4)
  4. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117583] (1)
    1. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117584]
      1. Selenomonas ruminantium [TaxId: 971] [117585] (13)
        SQ Q7WUJ1 34-346
  5. Mycobacterial PtpB-like [142348] (1)
    1. Phosphotyrosine protein phosphatase PtpB [142349]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142350] (3)
        SQ P96830 4-275
Rhodanese/Cell cycle control phosphatase [52820] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
1. Rhodanese/Cell cycle control phosphatase [52821] (4)
  Pfam 00581
  the active site structure is similar to those of the families I and II protein phosphatases; the topology can be related by a different circular permutation to the family I topology
  uperfamily
  1. Cell cycle control phosphatase, catalytic domain [52822] (4)
    1. CDC25a [52823]
      1. Human (Homo sapiens) [TaxId: 9606] [52824] (1)
    2. CDC25b [52825]
      1. Human (Homo sapiens) [TaxId: 9606] [52826] (15)
    3. Erk2 binding domain of Mapk phosphatase mkp-3 [69507]
      1. Human (Homo sapiens) [TaxId: 9606] [69508] (1)
    4. Dual specificity phosphatase Cdc25 [110598]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110599] (1)
        SQ Q8GY31
  2. Single-domain sulfurtransferase [69509] (3)
    1. Sulfurtransferase GlpE [69510]
      single-domain rhodanese
      1. Escherichia coli [TaxId: 562] [69511] (2)
    2. Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) [102425]
      1. Wolinella succinogenes [TaxId: 844] [102426] (1)
    3. Thiosulfate sulfurtransferase/Senescence-associated protein [110600]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110601] (1)
        SQ Q39129
  3. Multidomain sulfurtransferase (rhodanese) [52827] (6)
    duplication: consists of two domains of this fold
    1. Rhodanese [52828]
      1. Cow (Bos taurus) [TaxId: 9913] [52829] (7)
    2. Sulfurtransferase [52830]
      1. Azotobacter vinelandii [TaxId: 354] [52831] (3)
      2. Thermus thermophilus [TaxId: 274] [110602] (1)
        SQ Q5SJI0
    3. 3-mercaptopyruvate sulfurtransferase [102427]
      1. Leishmania major [TaxId: 5664] [102428] (1)
      2. Escherichia coli [TaxId: 562] [102429] (1)
    4. Thiosulfate sulfurtransferase PA2603 [142351]
      1. Pseudomonas aeruginosa [TaxId: 287] [142352] (4)
        SQ Q9I0N4 105-240! SQ Q9I0N4 241-370! SQ Q9I0N4 371-527! SQ Q9I0N4 4-104
  4. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117586] (1)
    1. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117587]
      1. Human (Homo sapiens) [TaxId: 9606] [117588] (4)
        SQ P40818 174-317
Thioredoxin fold [52832] (2)
core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
1. Thioredoxin-like [52833] (23)
  uperfamily
  1. Thioltransferase [52834] (31)
    1. Thioredoxin [52835]
      1. Escherichia coli [TaxId: 562] [52836] (31)
        SQ P00274 ! SQ P00581
      2. Anabaena sp., pcc 7120 [TaxId: 1167] [52837] (1)
        thioredoxin H
      3. Chlamydomonas reinhardtii [TaxId: 3055] [52838] (4)
      4. Alicyclobacillus acidocaldarius, formerly Bacillus acidocaldarius [TaxId: 405212] [52839] (4)
        SQ P80579
      5. Spinach (Spinacia oleracea), thioredoxin F [TaxId: 3562] [52840] (2)
      6. Spinach (Spinacia oleracea), thioredoxin M [TaxId: 3562] [52841] (3)
      7. Human (Homo sapiens) [TaxId: 9606] [52842] (26)
      8. Trypanosoma brucei [TaxId: 5691] [102430] (1)
      9. Malarial parasite (Plasmodium falciparum) [TaxId: 5833] [102431] (1)
      10. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110603] (1)
        SQ P29448 #
      11. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [117589] (4)
        SQ Q9V429
      12. European aspen (Populus tremula), thioredoxin H [TaxId: 113636] [117590] (1)
        SQ Q8S3L3
    2. Glutaredoxin (Grx, thioltransferase) [52843]
      1. Bacteriophage T4 [TaxId: 10665] [52844] (4)
      2. Escherichia coli [TaxId: 562] [52845] (4)
      3. Escherichia coli, Grx3 [TaxId: 562] [52846] (2)
      4. Pig (Sus scrofa) [TaxId: 9823] [52847] (1)
      5. Human (Homo sapiens) [TaxId: 9606] [52848] (2)
    3. C-terminal, Grx domain of Hybrid-Prx5 [89700]
      1. Haemophilus influenzae [TaxId: 727] [89701] (1)
        HI0572
    4. Glutaredoxin-like NRDH-redoxin [64052]
      1. Escherichia coli [TaxId: 562] [64053] (1)
      2. Corynebacterium ammoniagenes [TaxId: 1697] [102432] (1)
    5. MJ0307, thioredoxin/glutaredoxin-like protein [64054]
      single-domain PDI
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64055] (1)
    6. MTH807, thioredoxin/glutaredoxin-like protein [102433]
      behaves as true thioredoxin; probable MJ0307 ortholog
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102434] (1)
    7. MTH985, a thioredoxin [69512]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69513] (1)
    8. Thioredoxin-like protein, N-terminal domain [64056]
      1. Human (Homo sapiens) [TaxId: 9606] [64057] (1)
    9. Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma) [102435]
      1. Escherichia coli [TaxId: 562] [102436] (8)
    10. Thioredoxin-like protein p19, TLP19 [110604]
      1. Human (Homo sapiens) [TaxId: 9606] [110605] (1)
        SQ O95881 23-172
    11. Hypothetical protein XCC2852 [110606]
      1. Xanthomonas campestris [TaxId: 339] [110607] (2)
        SQ Q8P6W3
    12. Thioredoxin-like protein 2 [117591]
      1. Mouse (Mus musculus) [TaxId: 10090] [117592] (1)
        SQ Q9CQM9 241-336
    13. Thioredoxin-like structure containing protein C330018D20Rik [117593]
      1. Mouse (Mus musculus) [TaxId: 10090] [117594] (1)
        SQ Q9CWB7 21-107
    14. Hypothetical protein PA1234 [142353]
      1. Pseudomonas aeruginosa [TaxId: 287] [142354] (1)
        SQ Q9I4A4 1-166
    15. Bacterocin transport accessory protein Bta [142355]
      1. Streptococcus pneumoniae [TaxId: 1313] [142356] (1)
        SQ Q97PU4 1-115
  2. PDI-like [52849] (6)
    duplication: contains two tandem repeats of this fold
    1. Protein disulfide isomerase, PDI [52850]
      1. Human (Homo sapiens) [TaxId: 9606] [52851] (3)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [52852] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [89702] (1)
        glutaredoxin-like protein
      4. Fungi (Humicola insolens) [TaxId: 34413] [142357] (2)
        SQ P55059 227-355! SQ P55059 350-459
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142358] (4)
        SQ P17967 142-239! SQ P17967 23-141! SQ P17967 240-364! SQ P17967 365-504
    2. Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain [52853]
      1. Salmonella typhimurium [TaxId: 90371] [52854] (9)
  3. Calsequestrin [52855] (1)
    duplication: contains three tandem repeats of this fold
    1. Calsequestrin [52856]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [52857] (1)
  4. DsbA-like [100953] (4)
    contains an all-alpha subdomain insertion
    1. Disulfide-bond formation facilitator (DsbA) [100954]
      the insert subdomain is a 4-helical bundle
      1. Escherichia coli [TaxId: 562] [100955] (22)
      2. Vibrio cholerae [TaxId: 666] [100956] (1)
        TcpG, periplasmic enzyme required for the maturation of secreted virulence factors
    2. Mitochondrial class kappa glutathione S-transferase [102437]
      contains larger and less compact insertion in the common fold than DsbA
      1. Rat (Rattus norvegicus) [TaxId: 10116] [102438] (1)
    3. Hypothetical protein EF0770 [142359]
      1. Enterococcus faecalis [TaxId: 1351] [142360] (1)
        SQ Q837R1 1-172
  5. Glutathione S-transferase (GST), N-terminal domain [52862] (44)
    1. Class pi GST [81358]
      1. Human (Homo sapiens) [TaxId: 9606] [52864] (49)
      2. Pig (Sus scrofa) [TaxId: 9823] [52865] (1)
      3. Mouse (Mus musculus) [TaxId: 10090] [52866] (12)
      4. Onchocerca volvulus [TaxId: 6282] [117595] (2)
        SQ P46427
    2. Class mu GST [81359]
      1. Human (Homo sapiens) [TaxId: 9606] [52867] (29)
        SQ P09488 ! SQ P28161
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52868] (16)
      3. Chicken (Gallus gallus) [TaxId: 9031] [52869] (2)
    3. Class alpha GST [81360]
      1. Human (Homo sapiens), (a1-1) [TaxId: 9606] [52870] (29)
        SQ P08263
      2. Rat (Rattus norvegicus), (a1-1) [TaxId: 10116] [52871] (2)
      3. Mouse (Mus musculus), (a1-1) [TaxId: 10090] [52872] (2)
      4. Mouse (Mus musculus), (a1-4) [TaxId: 10090] [52873] (2)
      5. Mouse (Mus musculus), (a2-2) [TaxId: 10090] [89703] (1)
      6. Schistosoma japonicum [TaxId: 6182] [52878] (14)
        SQ P08515
      7. Blood fluke (Schistosoma haematobium) [TaxId: 6185] [89704] (12)
      8. Fasciola hepatica [TaxId: 6192] [52879] (2)
    4. Class theta GST [81361]
      1. Human (Homo sapiens) [TaxId: 9606] [52874] (3)
    5. Class sigma GST [81362]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52875] (1)
        synonym: hematopoietic prostaglandin D synthase
      2. Human (Homo sapiens) [TaxId: 9606] [89705] (33)
        SQ O60760
        synonym: hematopoietic prostaglandin D synthase
      3. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [82427] (1)
      4. Squid (Ommastrephes sloani pacificus) [TaxId: 6634] [52876] (2)
      5. Heligmosomoides polygyrus [TaxId: 6339] [110608] (1)
        SQ Q9NJQ6 # Fragment
    6. Class omega GST [81363]
      1. Human (Homo sapiens) [TaxId: 9606] [52877] (1)
    7. Class zeta GST [81364]
      1. Human (Homo sapiens) [TaxId: 9606] [64058] (1)
        maleylacetoacetate isomerase
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [64059] (1)
    8. Class delta GST [81366]
      formerly a part of class theta enzymes
      1. Mosquito (Anopheles dirus b), isozyme 1-3 [TaxId: 123217] [75234] (1)
      2. Mosquito (Anopheles dirus b), isozyme 1-4 [TaxId: 123217] [75235] (1)
      3. Mosquito (Anopheles dirus b), isozyme 1-5 [TaxId: 123217] [102439] (1)
      4. Mosquito (Anopheles dirus b), isozyme 1-6 [TaxId: 123217] [102440] (1)
      5. African malaria mosquito (Anopheles gambiae), isozyme 1-6 [TaxId: 7165] [102441] (1)
    9. Class tau GST [81365]
      1. Aegilops tauschii, also known as Triticum tauschii [TaxId: 37682] [75236] (1)
      2. Rice (Oryza sativa) [TaxId: 4530] [89706] (1)
    10. Class phi GST [81367]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52880] (2)
      2. Maize (Zea mays), type I [TaxId: 4577] [52881] (2)
      3. Maize (Zea mays), type III [TaxId: 4577] [52882] (1)
    11. Class beta GST [81368]
      1. Escherichia coli [TaxId: 562] [52883] (3)
      2. Proteus mirabilis [TaxId: 584] [52884] (2)
      3. Sphingomonas paucimobilis [TaxId: 13689] [52885] (1)
    12. Pf GST [102442]
      cannot be assigned to any of the known GST classes
      1. Malarial parasite (Plasmodium falciparum) [TaxId: 5833] [102443] (5)
    13. Glutaredoxin 2 [64060]
      similar to class zeta enzymes
      1. Escherichia coli [TaxId: 562] [64061] (1)
    14. Yeast prion protein ure2p, nitrogen regulation fragment [52886]
      similar to class phi enzymes
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52887] (8)
    15. GST-like domain of elongation factor 1-gamma [82428]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82429] (1)
    16. Chloride intracellular channel 1 (clic1) [69514]
      similar to class theta enzymes; the N-domain undergoes a redox-controlled structural transition
      1. Human (Homo sapiens) [TaxId: 9606] [69515] (4)
    17. Hypothetical protein AGR_pAT_752p/Atu5508 [142361]
      putative glutathione S-transferase
      1. Agrobacterium tumefaciens [TaxId: 358] [142362] (2)
        SQ Q7D2W7 1-87
    18. Microsomal prostaglandin E synthase-2 [142363]
      1. Crab-eating macaque (Macaca fascicularis) [TaxId: 9541] [142364] (8)
        SQ Q9N0A4 100-212
  6. Phosducin [52888] (2)
    1. Phosducin [52889]
      the transducin beta subunit-binding subdomain is an irregular array of helices in the N-terminal extension
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52890] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [52891] (1)
  7. ERP29 N domain-like [52892] (2)
    1. Endoplasmic reticulum protein ERP29, N-terminal domain [52893]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52894] (1)
    2. Windbeutel, N-terminal domain [102444]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102445] (8)
  8. spliceosomal protein U5-15Kd [52895] (1)
    1. spliceosomal protein U5-15Kd [52896]
      1. Human (Homo sapiens) [TaxId: 9606] [52897] (5)
  9. SH3BGR (SH3-binding, glutamic acid-rich protein-like) [102446] (1)
    related to glutaredoxin 1 (GRX1) but lacks both conserved cysteine residues
    1. SH3BGRL3 [102447]
      1. Mouse (Mus musculus) [TaxId: 10090] [102448] (2)
        SQ Q91VW3
  10. KaiB-like [102449] (2)
    Pfam 07689; contains members with alternative folds
    1. Circadian oscillation regulator KaiB [102450]
      the differently folded C-terminal half facilitates oligomerization
      1. Cyanobacterium (Nostoc sp.) pcc 7120 [TaxId: 1180] [102451] (1)
    2. Adaptive-response sensory-kinase SasA, N-terminal domain [117596]
      has a canonical thioredoxin fold
      1. Synechococcus elongatus [TaxId: 32046] [117597] (2)
        SQ Q06904 19-109 # 97% sequence identity
  11. DsbC/DsbG C-terminal domain-like [52898] (3)
    elaborated common fold
    1. Disulfide bond isomerase, DsbC, C-terminal domain [52899]
      1. Escherichia coli [TaxId: 562] [52900] (5)
        SQ P21892
      2. Haemophilus influenzae [TaxId: 727] [110609] (1)
        SQ P45111 20-228
    2. Thiol:disulfide interchange protein DsbG, C-terminal domain [110610]
      1. Escherichia coli [TaxId: 562] [110611] (8)
        SQ P77202
  12. Glutathione peroxidase-like [52901] (42)
    1. Glutathione peroxidase [52902]
      contains many insertions in the common fold
      1. Cow (Bos taurus) [TaxId: 9913] [52903] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [142365] (2)
        SQ P07203 12-195
    2. Tryparedoxin I [52904]
      1. Crithidia fasciculata [TaxId: 5656] [52905] (8)
      2. Trypanosoma brucei brucei [TaxId: 5702] [89707] (1)
    3. Tryparedoxin II [64062]
      1. Crithidia fasciculata [TaxId: 5656] [64063] (6)
    4. Tryparedoxin peroxidase (thioredoxin peroxidase homologue) [64064]
      1. Crithidia fasciculata [TaxId: 5656] [64065] (1)
      2. Trypanosoma cruzi [TaxId: 5693] [117598] (1)
        SQ O96763
    5. Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin) [52906]
      1. Norway rat (Rattus norvegicus) [TaxId: 10116] [52907] (1)
        heme-binding protein 23, HBP23
      2. Human (Homo sapiens) [TaxId: 9606] [52908] (1)
      3. Plasmodium yoelii [TaxId: 5861] [142366] (1)
        SQ Q86SB2 8-177
    6. Peroxiredoxin 5 [64066]
      1. Human (Homo sapiens) [TaxId: 9606] [64067] (10)
        SQ P30044
    7. 1-Cys peroxiredoxin [52909]
      1. Human (Homo sapiens) [TaxId: 9606] [52910] (1)
      2. Plasmodium yoelii yoelii [TaxId: 73239] [117599] (1)
        SQ Q7RGR1
      3. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [142367] (2)
        SQ Q5MYR6 60-238
    8. Alkyl hydroperoxide reductase AhpC [69516]
      1. Salmonella typhimurium [TaxId: 90371] [69517] (26)
      2. Mycobacterium tuberculosis [TaxId: 1773] [142368] (3)
        SQ Q7BHK8 2-170
      3. Amphibacillus xylanus [TaxId: 1449] [142369] (10)
        SQ O87200 2-167
    9. N-terminal, Prx domain of Hybrid-Prx5 [89708]
      1. Haemophilus influenzae [TaxId: 727] [89709] (1)
        HI0572
    10. Probable thiol peroxidase PsaD [89710]
      1. Streptococcus pneumoniae [TaxId: 1313] [89711] (1)
    11. Thiol peroxidase Tpx [102452]
      1. Escherichia coli [TaxId: 562] [102453] (1)
      2. Haemophilus influenzae [TaxId: 727] [102454] (1)
        HI0751
      3. Mycobacterium tuberculosis [TaxId: 1773] [117600] (3)
        SQ P66952
    12. Membrane-anchored thioredoxin-like protein TlpA, soluble domain [64068]
      1. Bradyrhizobium japonicum [TaxId: 375] [64069] (1)
    13. Thioredoxin-like protein CcmG (CycY, DsbE) [75237]
      1. Bradyrhizobium japonicum [TaxId: 375] [75238] (1)
      2. Escherichia coli [TaxId: 562] [142370] (1)
        SQ P0AA86 49-184
    14. Thiol-disulfide oxidoreductase ResA [102455]
      1. Bacillus subtilis [TaxId: 1423] [102456] (6)
    15. Soluble secreted antigen MPT53 [102457]
      1. Mycobacterium tuberculosis [TaxId: 1773] [102458] (1)
    16. Thioredoxin-like protein Sco1 (YpmQ), soluble domain [102459]
      1. Bacillus subtilis [TaxId: 1423] [102460] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [142371] (5)
        SQ O75880 138-297
      3. Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932] [142372] (8)
        SQ P23833 111-262
    17. Phenol hydroxylase, C-terminal domain [52911]
      1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [52912] (2)
    18. Peroxiredoxin [117601]
      1. Aeropyrum pernix [TaxId: 56636] [117602] (50)
        SQ Q9Y9L0 # APE2278
    19. thiol:disulfide oxidoreductase YkuV [142373]
      1. Bacillus subtilis [TaxId: 1423] [142374] (2)
        SQ O31699 1-143
    20. Lipoprotein DsbF [142375]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142376] (1)
        SQ O53924 47-180
    21. Bacterioferritin comigratory protein [142377]
      1. Archaeon Aeropyrum pernix [TaxId: 56636] [142378] (12)
        SQ Q9YA14 4-163
    22. Plant peroxiredoxin [142379]
      1. Western balsam poplar(Populus trichocarpa) [TaxId: 3694] [142380] (4)
        SQ Q8S3L0 1-162
    23. Putative peroxiredoxin Rv2238c/MT2298 [142381]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142382] (6)
        SQ P65688 1-153
    24. Thioredoxin reductase TsaA [142383]
      1. Helicobacter pylori [TaxId: 210] [142384] (10)
        SQ P56876 1-170
    25. Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain [142385]
      1. Neisseria meningitidis serogroup A [TaxId: 65699] [142386] (3)
        SQ Q9JWM8 33-175
    26. Peroxiredoxin dot5 [142387]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142388] (1)
        SQ P40553 59-214
    27. Probable thiol-disulfide isomerase/thioredoxin TTHA0593 [142389]
      1. Thermus thermophilus [TaxId: 274] [142390] (2)
        SQ Q5SKQ0 2-188
    28. Peroxiredoxin-3 (AOP-1, SP-22) [142391]
      1. Cow (Bos taurus) [TaxId: 9913] [142392] (12)
        SQ P35705 63-220
  13. Thioredoxin-like 2Fe-2S ferredoxin [52918] (1)
    1. Thioredoxin-like 2Fe-2S ferredoxin [52919]
      1. Aquifex aeolicus [TaxId: 63363] [52920] (4)
  14. ArsC-like [69518] (3)
    Pfam 03960
    1. Arsenate reductase ArsC [69519]
      1. Escherichia coli [TaxId: 562] [69520] (3)
    2. Hypothetical protein PA3664 (YffB) [117603]
      1. Pseudomonas aeruginosa [TaxId: 287] [117604] (1)
        SQ Q9HXX5
    3. Regulatory protein Spx [142393]
      1. Bacillus subtilis [TaxId: 1423] [142394] (1)
        SQ O31602 1-114
  15. Txnl5-like [110612] (2)
    Pfam 06110
    1. Putative 42-9-9 protein (thioredoxin containing protein Txnl5) [110613]
      1. Mouse (Mus musculus) [TaxId: 10090] [110614] (1)
        SQ Q9D0Y4
      2. Human (Homo sapiens) [TaxId: 9606] [110615] (1)
        SQ Q9BRA2
  16. YuzD-like [117605] (1)
    Pfam 07315
    1. Hypothetical protein SA0798 [117606]
      1. Staphylococcus aureus [TaxId: 1280] [117607] (1)
        SQ Q7A6J8
  17. YKR049C-like [142395] (1)
    Pfam 07955; DUF1687; contains an all-alpha insert subdomain
    1. Hypothetical protein YKR049C [142396]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142397] (1)
        SQ P36141 1-133
  18. Atu2684-like [142398] (1)
    Pfam 06764; DUF1223; contains extra C-terminal domain of Immunoglobulin-like fold (scop_cf 48725), intimately associated with the N-terminal thioredixin-like domain and contributing to the active site
    1. Hypothetical protein Atu2684 [142399]
      1. Agrobacterium tumefaciens [TaxId: 358] [142400] (1)
        SQ Q8UC14 38-262
  19. HyaE-like [142401] (2)
    Pfam 07449; have evolved a different function; contains no conserved cysteine residues
    1. Hydrogenase-1 operon protein HyaE [142402]
      1. Escherichia coli [TaxId: 562] [142403] (1)
        SQ P19931 1-132
      2. Salmonella typhimurium [TaxId: 90371] [142404] (5)
        SQ Q8ZP25 7-125
  20. NQO2-like [142405] (1)
    complex I 24 kDa subunit; contains 2Fe-2S cluster in the active site; includes extra N-terminal four-helical bundle
    1. NADH-quinone oxidoreductase chain 2, NQO2 [142406]
      1. Thermus thermophilus [TaxId: 274] [142407] (4)
        SQ Q56221 2-179
  21. Mitochondrial ribosomal protein L51/S25/CI-B8 domain [142408] (1)
    Pfam 05047; "minimalized" version of the thioredoxin-like fold; variable positions for cysteine residues in the putative active site
    1. NADH-ubiquinone oxidoreductase b8 subunit, CI-B8 [142409]
      1. Human (Homo sapiens) [TaxId: 9606] [142410] (1)
        SQ O43678 14-98
  22. Selenoprotein W-related [142411] (3)
    Pfam 05169; "minimalized" version of the thioredoxin-like fold
    1. Selenoprotein sep15 [142412]
      1. Drosophila melanogaster [TaxId: 7227] [142413] (1)
        SQ Q9VVJ7 62-178
    2. Hypothetical protein Atu0228 [142414]
      1. Agrobacterium tumefaciens [TaxId: 358] [142415] (4)
        SQ Q8UIR5 4-89
    3. Selenoprotein M [142416]
      1. Mouse (Mus musculus) [TaxId: 10090] [142417] (1)
        SQ Q8VHC3 25-144
  23. UAS domain [159589] (1)
    SMART 00594
    1. UBX domain-containing protein 7 [159590]
      1. Human (Homo sapiens) [TaxId: 9606] [159591] (1)
        SQ O94888 131-270
2. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52913] (1)
  uperfamily
  1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52914] (1)
    1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52915]
      1. Escherichia coli [TaxId: 562] [52916] (2)
Peptidyl-tRNA hydrolase II [102461] (1)
3 layers: a/b/a; mixed beta-sheet of 4 strands, order 2143, strand 4 is antiparallel to the rest
1. Peptidyl-tRNA hydrolase II [102462] (1)
  uperfamily
  1. Peptidyl-tRNA hydrolase II [102463] (4)
    Pfam 01981; UPF0099
    1. Bit1 (Cgi-147) [102464]
      Peptidyl-tRNA hydrolase; involved in apoptosis
      1. Human (Homo sapiens) [TaxId: 9606] [102465] (1)
    2. Hypothetical protein TA0108 [102466]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102467] (1)
    3. Hypothetical protein AF2095 [117608]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117609] (3)
        SQ O28185
    4. Hypothetical protein Atu0240 [159592]
      1. Agrobacterium tumefaciens [TaxId: 358] [159593] (2)
        SQ Q8UIQ3 1-135
TK C-terminal domain-like [52921] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
1. TK C-terminal domain-like [52922] (3)
  uperfamily
  1. Transketolase C-terminal domain-like [52923] (5)
    1. Transketolase (TK), C-domain [52924]
      two N-terminal domains are PP and Pyr modules of thiamin-binding fold
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52925] (7)
      2. Maize (Zea mays) [TaxId: 4577] [82430] (1)
      3. Escherichia coli [TaxId: 562] [89712] (7)
      4. Leishmania mexicana mexicana [TaxId: 44270] [117610] (1)
        SQ Q8MPM3
    2. Pyruvate dehydrogenase E1 component, C-domain [75239]
      E1A and E1B fused together in a single-chain protein
      1. Escherichia coli [TaxId: 562] [75240] (14)
  2. Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain [52926] (6)
    1. Branched-chain alpha-keto acid dehydrogenase [52927]
      1. Human (Homo sapiens) [TaxId: 9606] [52928] (21)
        SQ P21953 52-392
      2. Thermus thermophilus [TaxId: 274] [102468] (4)
    2. 2-oxoisovalerate dehydrogenase E1b, C-domain [52929]
      1. Pseudomonas putida [TaxId: 303] [52930] (5)
    3. E1-beta subunit of pyruvate dehydrogenase, C-domain [69521]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69522] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [89713] (3)
    4. Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain [117611]
      1. Bacillus stearothermophilus [TaxId: 1422] [117612] (2)
        SQ P21874
  3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52931] (1)
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52932]
      1. Desulfovibrio africanus [TaxId: 873] [52933] (17)
Pyruvate kinase C-terminal domain-like [52934] (2)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
1. PK C-terminal domain-like [52935] (2)
  uperfamily
  1. Pyruvate kinase, C-terminal domain [52936] (6)
    1. Pyruvate kinase, C-terminal domain [52937]
      1. Cat (Felis catus) [TaxId: 9685] [52938] (1)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [52939] (14)
      3. Human (Homo sapiens) [TaxId: 9606] [82431] (4)
      4. Leishmania mexicana [TaxId: 5665] [52940] (8)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52941] (2)
      6. Escherichia coli [TaxId: 562] [52942] (3)
  2. MTH1675-like [110616] (2)
    PfamB 019040; probable flavoenzyme, binds FMN; the phosphoribityl group binds in the equivalent site to the binding site of the PK allosteric regulator FBP
    1. Hypothetical protein MTH1675 [110617]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [110618] (1)
        SQ O27711
    2. Hypothetical protein AF0103 [117613]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117614] (1)
        SQ O30133
2. ATP synthase (F1-ATPase), gamma subunit [52943] (1)
  contains an antiparallel coiled coil formed by N- and C-terminal extensions to the common fold
  uperfamily
  1. ATP synthase (F1-ATPase), gamma subunit [52944] (3)
    1. ATP synthase (F1-ATPase), gamma subunit [52945]
      1. Cow (Bos taurus) [TaxId: 9913] [52946] (14)
        SQ P05631
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52947] (2)
      3. Escherichia coli [TaxId: 562] [64070] (1)
Anticodon-binding domain-like [52953] (6)
3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
1. Class II aaRS ABD-related [52954] (2)
  uperfamily
  1. Anticodon-binding domain of Class II aaRS [52955] (13)
    1. Histidyl-tRNA synthetase (HisRS), C-terminal domain [52956]
      1. Escherichia coli [TaxId: 562] [52957] (7)
      2. Staphylococcus aureus [TaxId: 1280] [52958] (1)
      3. Thermus thermophilus [TaxId: 274] [52959] (3)
      4. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142418] (2)
        SQ Q9HLX5 330-426
    2. Glycyl-tRNA synthetase (GlyRS), C-terminal domain [52960]
      1. Thermus thermophilus [TaxId: 274] [52961] (3)
    3. Threonyl-tRNA synthetase (ThrRS), C-terminal domain [52962]
      1. Escherichia coli [TaxId: 562] [52963] (5)
      2. Staphylococcus aureus [TaxId: 1280] [102469] (2)
    4. Prolyl-tRNA synthetase (ProRS) domain [64071]
      1. Thermus thermophilus [TaxId: 274] [64072] (4)
      2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [89714] (4)
      3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [89715] (1)
    5. The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain [64073]
      1. Mouse (Mus musculus) [TaxId: 10090] [64074] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [142419] (4)
        SQ Q9UHN1 369-485
    6. Nuclear receptor coactivator 5 (KIAA1637) [110619]
      1. Human (Homo sapiens) [TaxId: 9606] [110620] (1)
        SQ Q9HCD5 197-313
  2. Brix domain [142420] (2)
    Pfam 04427; tandem repeat of two ABD-like structural repeats, which are associated together with the formation of single beta-sheet, folded into half-barrel
    1. Probable ribosomal biogenesis protein [142421]
      comprises stand-alone brix domain
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [142422] (2)
        SQ O26776 1-154
        MTH680
      2. Archaeon Aeropyrum pernix [TaxId: 56636] [142423] (1)
        SQ Q9YC08 13-192
        APE1443
2. TolB, N-terminal domain [52964] (1)
  uperfamily
  1. TolB, N-terminal domain [52965] (1)
    1. TolB, N-terminal domain [52966]
      1. Escherichia coli [TaxId: 562] [52967] (10)
3. B12-dependent dehydatase associated subunit [52968] (2)
  uperfamily
  1. Diol dehydratase, beta subunit [52969] (2)
    contains additional structures in the C-terminal extension
    1. Diol dehydratase, beta subunit [52970]
      1. Klebsiella oxytoca [TaxId: 571] [52971] (7)
      2. Klebsiella pneumoniae [TaxId: 573] [82432] (2)
  2. Dehydratase-reactivating factor beta subunit [82433] (2)
    1. Glycerol dehydratase reactivase, beta subunit [82434]
      1. Klebsiella pneumoniae [TaxId: 573] [82435] (1)
    2. Diol dehydratase-reactivating factor small subunit DdrB [142424]
      1. Klebsiella oxytoca [TaxId: 571] [142425] (4)
        SQ O68196 5-112
4. ITPase-like [52972] (3)
  formerly Maf/Ham1; elaborated with additional structures inserted in the common fold
  uperfamily
  1. ITPase (Ham1) [52973] (5)
    Pfam 01725
    1. XTP pyrophosphatase [52974]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52975] (2)
        MJ0226
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102470] (6)
        PH1917
    2. Hypothetical protein YggV [75242]
      annotated as putative ribosomal protein
      1. Escherichia coli [TaxId: 562] [75243] (1)
    3. Putative inosine/xanthosine triphosphate pyrophosphatase TM0159 [117615]
      1. Thermotoga maritima [TaxId: 2336] [117616] (1)
        SQ Q9WY06
    4. Inosine triphosphate pyrophosphatase, ITPase [142426]
      1. Human (Homo sapiens) [TaxId: 9606] [142427] (11)
        SQ Q9BY32 1-194
  2. Maf-like [52976] (2)
    1. Maf protein [52977]
      1. Bacillus subtilis [TaxId: 1423] [52978] (2)
    2. Maf homologue Tb11.01.5890 [142428]
      1. Trypanosoma brucei [TaxId: 5691] [142429] (1)
        SQ Q382A9 3-203
  3. YjjX-like [110621] (3)
    Pfam 01931
    1. Hypothetical protein YjjX [110622]
      1. Salmonella typhimurium [TaxId: 90371] [110623] (1)
        SQ P39432
      2. Escherichia coli [TaxId: 562] [142430] (8)
        SQ P39411 1-170
    2. Hypothetical protein VC0702 [142431]
      1. Vibrio cholerae [TaxId: 666] [142432] (6)
        SQ Q9KU27 9-181
5. CinA-like [142433] (1)
  uperfamily
  1. CinA-like [142434] (1)
    Pfam 02464
    1. Competence/damage-inducible protein CinA [142435]
      1. Agrobacterium tumefaciens [TaxId: 358] [142436] (2)
        SQ Q8UFF5 1-167
6. XCC0632-like [159594] (2)
  short crossover loop between strands 2 and 3; the antiparallel part of the beta-sheet (strands 3, 4 and 5) and the C-terminal helix are quite long
  1. NLBH-like [159595] (1)
    Pfam 05211; Neuraminyllactose-binding hemagglutinin
    1. Hypothetical protein HP0492 [159596]
      1. Helicobacter pylori [TaxId: 210] [159597] (1)
        SQ O25234 51-271
  2. XCC0632-like [159598] (1)
    Pfam 03886; DUF330
    1. Hypothetical protein XCC0632 [159599]
      1. Xanthomonas campestris pv. campestris [TaxId: 340] [159600] (8)
        SQ Q8PCT0 32-209
MTH938-like [64075] (1)
core: 3 layers, b+a/b/a ; the central mixed sheet of 5 strands: order 21534; strand 2 is antiparallel to the rest
1. MTH938-like [64076] (1)
  uperfamily
  1. MTH938-like [64077] (5)
    1. Hypothetical protein MT938 (MTH938) [64078]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [64079] (1)
    2. Hypothetical protein RPA2829 [142437]
      1. Rhodopseudomonas palustris [TaxId: 1076] [142438] (1)
        SQ Q6N5Y9 1-127
    3. Hypothetical outer membrane protein BH05650 [142439]
      1. Bartonella henselae [TaxId: 38323] [142440] (1)
        SQ Q8RIU4 11-128
    4. Hypothetical protein PH1505 [142441]
      1. Pyrococcus horikoshii [TaxId: 53953] [142442] (1)
        SQ O59174 1-118
    5. Hypothetical protein PTD015 (C11orf67) [142443]
      1. Human (Homo sapiens) [TaxId: 9606] [142444] (4)
        SQ Q9H7C9 2-122
Restriction endonuclease-like [52979] (4)
core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
1. Restriction endonuclease-like [52980] (33)
  uperfamily
  1. Restriction endonuclease EcoRI [52981] (1)
    1. Restriction endonuclease EcoRI [52982]
      1. Escherichia coli [TaxId: 562] [52983] (7)
  2. Restriction endonuclease EcoRV [52984] (1)
    1. Restriction endonuclease EcoRV [52985]
      1. Escherichia coli [TaxId: 562] [52986] (31)
  3. Restriction endonuclease BamHI [52987] (1)
    1. Restriction endonuclease BamHI [52988]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [52989] (5)
  4. Restriction endonuclease BglI [52990] (1)
    1. Restriction endonuclease BglI [52991]
      1. Bacillus subtilis [TaxId: 1423] [52992] (1)
  5. Restriction endonuclease BglII [52993] (1)
    1. Restriction endonuclease BglII [52994]
      1. Bacillus subtilis [TaxId: 1423] [52995] (3)
  6. Restriction endonuclease BstyI [102471] (1)
    1. Restriction endonuclease BstyI [102472]
      local sequence similarity to BglII
      1. Geobacillus stearothermophilus [TaxId: 1422] [102473] (5)
  7. Restriction endonuclease PvuII [52996] (1)
    1. Restriction endonuclease PvuII [52997]
      1. Proteus vulgaris [TaxId: 585] [52998] (9)
  8. Cfr10I/Bse634I [52999] (2)
    1. Restriction endonuclease Cfr10I [53000]
      1. Citrobacter freundii [TaxId: 546] [53001] (1)
    2. Restriction endonuclease Bse634I [69523]
      1. Bacillus stearothermophilus [TaxId: 1422] [69524] (1)
  9. Restriction endonuclease MunI [53002] (1)
    1. Restriction endonuclease MunI [53003]
      1. Mycoplasma, unidentified species [TaxId: 2093] [53004] (1)
  10. Restriction endonuclease NaeI [53005] (1)
    1. Restriction endonuclease NaeI [53006]
      1. Nocardia aerocolonigenes [TaxId: 68170] [53007] (2)
  11. Restriction endonuclease NgoIV [53008] (1)
    1. Restriction endonuclease NgoIV [53009]
      1. Neisseria gonorrhoeae [TaxId: 485] [53010] (1)
  12. Restriction endonuclease BsobI [53011] (1)
    1. Restriction endonuclease BsobI [53012]
      1. Bacillus stearothermophilus [TaxId: 1422] [53013] (1)
  13. Restriction endonuclease HincII [69525] (1)
    1. Restriction endonuclease HincII [69526]
      1. Haemophilus influenzae [TaxId: 727] [69527] (12)
        SQ P17743 ! SQ P44413
  14. Restriction endonuclease FokI, C-terminal (catalytic) domain [53014] (1)
    1. Restriction endonuclease FokI, C-terminal (catalytic) domain [53015]
      1. Flavobacterium okeanokoites [TaxId: 244] [53016] (2)
  15. Type II restriction endonuclease catalytic domain [102474] (1)
    1. Restriction endonuclease EcoRII, C-terminal domain [102475]
      1. Escherichia coli [TaxId: 562] [102476] (1)
  16. lambda exonuclease [53017] (1)
    1. lambda exonuclease [53018]
      1. Bacteriophage lambda [TaxId: 10710] [53019] (1)
  17. DNA mismatch repair protein MutH from [53020] (1)
    1. DNA mismatch repair protein MutH from [53021]
      1. Escherichia coli [TaxId: 562] [53022] (2)
  18. Very short patch repair (VSR) endonuclease [53023] (1)
    1. Very short patch repair (VSR) endonuclease [53024]
      1. Escherichia coli [TaxId: 562] [53025] (3)
  19. TnsA endonuclease, N-terminal domain [53026] (1)
    1. TnsA endonuclease, N-terminal domain [53027]
      a catalytic component of the tn7 transposition system
      1. Escherichia coli [TaxId: 562] [53028] (2)
        SQ P13988
  20. Endonuclease I (Holliday junction resolvase) [53029] (1)
    1. Endonuclease I (Holliday junction resolvase) [53030]
      forms dimer by swapping the common core elements
      1. Bacteriophage T7 [TaxId: 10760] [53031] (3)
  21. Hjc-like [64080] (3)
    Pfam 01870
    1. Archaeal Holliday junction resolvase Hjc [64081]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64082] (2)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [64083] (1)
    2. Holliday-junction resolvase SSO1176 [117617]
      1. Sulfolobus solfataricus [TaxId: 2287] [117618] (2)
        SQ Q97YX6
  22. XPF/Rad1/Mus81 nuclease [89716] (3)
    1. Putative ATP-dependent RNA helicase Hef, nuclease domain [89717]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89718] (4)
    2. DNA excision repair protein ERCC-1 [142445]
      1. Human (Homo sapiens) [TaxId: 9606] [142446] (3)
        SQ P07992 99-227
    3. XPF endonuclease [142447]
      1. Aeropyrum pernix [TaxId: 56636] [142448] (6)
        SQ Q9YC15 16-148
  23. Restriction endonuclease MspI [110624] (1)
    1. Restriction endonuclease MspI [110625]
      1. Moraxella sp. [TaxId: 479] [110626] (3)
        SQ P11405
  24. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117619] (1)
    related to the RecC domain
    1. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117620]
      1. Escherichia coli [TaxId: 562] [117621] (1)
        SQ P08394
  25. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117622] (1)
    related to the RecB domain
    1. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117623]
      1. Escherichia coli [TaxId: 562] [117624] (1)
        SQ P07648
  26. Hypothetical protein VC1899 [117625] (1)
    contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
    1. Hypothetical protein VC1899 [117626]
      1. Vibrio cholerae [TaxId: 666] [117627] (1)
        SQ Q9KQU9 # d1 (1-156); d2 (161-249); putative catalytic domain d3 (250-383)
  27. Hypothetical protein TT1808 (TTHA1514) [117628] (1)
    Pfam 05685; DUF820
    1. Hypothetical protein TT1808 (TTHA1514) [117629]
      1. Thermus thermophilus [TaxId: 274] [117630] (1)
        SQ Q5SI60
  28. RecU-like [117631] (2)
    Pfam 03838
    1. Recombination protein U (RecU)/PBP related factor A (PrfA) [117632]
      1. Bacillus subtilis [TaxId: 1423] [117633] (1)
        SQ P39792 34-196
      2. Bacillus stearothermophilus [TaxId: 1422] [117634] (1)
        SQ Q5KXY4 31-198 # 99% sequence identity; Geobacillus kaustophilus TaxID: 1462
  29. Restriction endonuclease EcoO109IR [117635] (1)
    1. Restriction endonuclease EcoO109IR [117636]
      1. Escherichia coli [TaxId: 562] [117637] (2)
        SQ Q9RPJ3
  30. MRR-like [117638] (1)
    Pfam 04471
    1. Hypothetical protein AF1548, N-terminal domain [117639]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117640] (1)
        SQ 28724
  31. PA4535-like [142449] (1)
    contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix
    1. Hypothetical protein PA4535 [142450]
      1. Pseudomonas aeruginosa [TaxId: 287] [142451] (1)
        SQ Q9HVP2 1-209
  32. XisH-like [159601] (2)
    Pfam 08814
    1. FdxN element excision controlling factor protein [159602]
      1. Nostoc punctiforme [TaxId: 272131] [159603] (1)
      2. Anabaena variabilis [TaxId: 1172] [159604] (2)
        SQ Q3M7W6 4-139
  33. YaeQ-like [159605] (2)
    Pfam 07152; contains extra N- and C-terminal beta-structures forming additional five-stranded beta-sheet; retains the PD motif in the putative active site
    1. Hypothetical protein XAC2396 [159606]
      1. Xanthomonas axonopodis pv. citri [TaxId: 92829] [159607] (2)
        SQ Q8PJY1 4-182
    2. Hypothetical protein PSPTO1487 [159608]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [159609] (1)
        SQ Q886T9 2-180
2. tRNA-intron endonuclease catalytic domain-like [53032] (1)
  uperfamily
  1. tRNA-intron endonuclease catalytic domain-like [53033] (3)
    1. Tetrameric tRNA splicing endonuclease, C-terminal domain [53034]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53035] (1)
    2. Dimeric tRNA splicing endonuclease, domains 2 and 4 [102477]
      duplication: one subunit consists of two tetrameric tRNA splicing endonuclease subunit-like repeats
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102478] (11)
    3. tRNA-splicing endonuclease subunit Sen15 [159610]
      1. Human (Homo sapiens) [TaxId: 9606] [159611] (2)
        SQ Q8WW01 36-157
3. Eukaryotic RPB5 N-terminal domain [53036] (1)
  uperfamily
  1. Eukaryotic RPB5 N-terminal domain [53037] (1)
    1. Eukaryotic RPB5 N-terminal domain [53038]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53039] (26)
        SQ P20434; part of multichain biological unit
4. TBP-interacting protein-like [159612] (1)
  contains extra C-terminal alpha+beta domain of complex fold with an embeded C2H2 zinc-finger
  1. TBP-interacting protein-like [159613] (1)
    PfamB 059845 (N-terminal domain) and Pfam B059846 (C-terminal region)
    1. TBP-interacting protein [159614]
      1. Thermococcus kodakaraensis [TaxId: 311400] [159615] (1)
        SQ Q9V2W6 1-218
        TK1172
Resolvase-like [53040] (2)
Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
1. Resolvase-like [53041] (1)
  uperfamily
  1. gamma,delta resolvase, catalytic domain [53042] (1)
    1. gamma,delta resolvase, catalytic domain [53043]
      1. Escherichia coli [TaxId: 562] [53044] (13)
2. beta-carbonic anhydrase, cab [53056] (1)
  uperfamily
  1. beta-carbonic anhydrase, cab [53057] (4)
    1. beta-carbonic anhydrase [53058]
      1. Pea (Pisum sativum) [TaxId: 3888] [53059] (1)
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [64084] (1)
      3. Escherichia coli [TaxId: 562] [64085] (5)
        SQ P61517
      4. Red alga (Porphyridium purpureum) [TaxId: 35688] [53060] (1)
        duplication: consists of two similar domains
PTS system fructose IIA component-like [53061] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
1. PTS system fructose IIA component-like [53062] (2)
  active dimer is formed by strand 5 swapping
  uperfamily
  1. EIIA-man component-like [53063] (2)
    1. IIA domain of mannose transporter, IIA-Man [53064]
      1. Escherichia coli [TaxId: 562] [53065] (7)
    2. PTS system, IIA subunit [159616]
      1. Enterococcus faecalis [TaxId: 1351] [159617] (2)
        SQ Q838I6 1-132
  2. DhaM-like [159618] (2)
    probable link between the PTS system fructose IIA component-like superfamily and the DAK1/DegV-like superfamily (scop_sf 82549)
    1. Uncharacterized protein EF1359 [159619]
      1. Enterococcus faecalis [TaxId: 1351] [159620] (6)
        SQ Q835L8 1-132
    2. PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM [159621]
      1. Lactococcus lactis [TaxId: 1358] [159622] (4)
        SQ Q9CIV6 1-123
Ribonuclease H-like motif [53066] (7)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
1. Actin-like ATPase domain [53067] (14)
  duplication contains two domains of this fold
  uperfamily
  1. Actin/HSP70 [53068] (14)
    1. Heat shock protein 70kDa, ATPase fragment [53069]
      1. Cow (Bos taurus) [TaxId: 9913] [53070] (51)
      2. Human (Homo sapiens) [TaxId: 9606] [53071] (14)
      3. Escherichia coli, gene dnaK [TaxId: 562] [53072] (1)
    2. Actin [53073]
      1. Cow (Bos taurus) [TaxId: 9913] [53074] (68)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53075] (20)
        SQ P02568 ! SQ 02568
      3. Chicken (Gallus gallus) [TaxId: 9031] [82437] (1)
        sequence identical to the rabbit actin
      4. Nematode (Caenorhabditis elegans) [TaxId: 6239] [64086] (1)
      5. Dictyostelium discoideum [TaxId: 44689] [53076] (6)
      6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53077] (2)
    3. Prokaryotic actin homolog MreB [64087]
      1. Thermotoga maritima [TaxId: 2336] [64088] (3)
    4. Actin-related protein 3, Arp3 [69528]
      part of Arp2/3 complex
      1. Cow (Bos taurus) [TaxId: 9913] [69529] (17)
        SQ P61158
    5. Actin-related protein 2, Arp2 [69530]
      part of Arp2/3 complex
      1. Cow (Bos taurus) [TaxId: 9913] [69531] (3)
        SQ P61160 143-350 # 100% sequence identity
    6. Cell division protein FtsA [53078]
      1. Thermotoga maritima [TaxId: 2336] [53079] (2)
    7. Plasmid segregation protein ParM [82438]
      1. Escherichia coli [TaxId: 562] [82439] (14)
  2. BadF/BadG/BcrA/BcrD-like [64089] (5)
    1. Hydroxyglutaryl-CoA dehydratase component A [64090]
      1. Acidaminococcus fermentans [TaxId: 905] [64091] (1)
    2. Hypothetical protein PG1100 [142452]
      1. Porphyromonas gingivalis [TaxId: 837] [142453] (2)
        SQ Q7MVG4 1-107! SQ Q7MVG4 108-283
    3. Probable N-acetylglucosamine kinase CV2896 [142454]
      1. Chromobacterium violaceum [TaxId: 536] [142455] (4)
        SQ Q7NU07 122-292! SQ Q7NU07 8-121
    4. Hypothetical protein BT3618 [142456]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [142457] (12)
        SQ Q8A1P1 107-280! SQ Q8A1P1 3-106
    5. N-acetylglucosamine kinase, NAGK [142458]
      1. Human (Homo sapiens) [TaxId: 9606] [142459] (16)
        SQ Q9UJ70 1-117! SQ Q9UJ70 118-344
  3. Acetokinase-like [53080] (3)
    1. Acetate kinase [53081]
      1. Archaeon Methanosarcina thermophila [TaxId: 2210] [53082] (6)
        SQ P38502 1-399
    2. butyrate kinase 2 [142460]
      1. Thermotoga maritima [TaxId: 2336] [142461] (18)
        SQ Q9X278 1-172! SQ Q9X278 173-375
    3. Propionate kinase [142462]
      1. Salmonella typhimurium [TaxId: 90371] [142463] (10)
        SQ O06961 193-397! SQ O06961 4-192
  4. ATPase domain of dehydratase reactivase alpha subunit [82440] (2)
    1. ATPase domain of the glycerol dehydratase reactivase alpha subunit [82441]
      includes the insert and linker domains
      1. Klebsiella pneumoniae [TaxId: 573] [82442] (1)
    2. Diol dehydratase-reactivating factor large subunit DdrA [142464]
      1. Klebsiella oxytoca [TaxId: 571] [142465] (8)
        SQ O68195 1-92,255-403! SQ O68195 404-606
  5. Hexokinase [53083] (5)
    1. Hexokinase [53084]
      1. Baker's yeast (Saccharomyces cerevisiae), pII [TaxId: 4932] [64092] (1)
      2. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [53085] (1)
    2. Glucokinase [102479]
      Hexokinase D
      1. Human (Homo sapiens) [TaxId: 9606] [102480] (2)
    3. Mammalian type I hexokinase [53086]
      further duplication: consists of two very similar lobes
      1. Human (Homo sapiens) [TaxId: 9606] [53087] (5)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [53088] (1)
  6. Glycerol kinase [53089] (2)
    1. Glycerol kinase [53090]
      1. Escherichia coli [TaxId: 562] [53091] (28)
      2. Enterococcus casseliflavus [TaxId: 37734] [117641] (2)
        SQ O34153 5-491
  7. Glucokinase [110627] (1)
    Pfam 02685
    1. Glucokinase Glk [110628]
      1. Escherichia coli [TaxId: 562] [110629] (2)
        SQ P46880 P0A6V8
  8. Ppx/GppA phosphatase [110630] (2)
    Pfam 02541
    1. Exopolyphosphatase Ppx [110631]
      1. Aquifex aeolicus [TaxId: 63363] [110632] (6)
        SQ O67040
      2. Escherichia coli [TaxId: 562] [142466] (12)
        SQ P0AFL6 11-134! SQ P0AFL6 135-311
  9. YeaZ-like [110633] (2)
    Pfam 00814; ubiquitous cytoplasmic protein; annotated as Glycoprotease (Peptidase_M22 family) on the basis of one member's known extracellular activity
    1. Hypothetical protein YeaZ [110634]
      1. Escherichia coli [TaxId: 562] [110635] (1)
        SQ P76256
    2. Hypothetical protein TM0874 [142467]
      1. Thermotoga maritima [TaxId: 2336] [142468] (4)
        SQ Q9WZX7 1-103! SQ Q9WZX7 104-193
  10. ROK [110636] (8)
    Pfam 00480
    1. Inorganic polyphosphate/ATP-glucomannokinase PPGMK [110637]
      1. Arthrobacter sp. KM [TaxId: 184230] [110638] (1)
        SQ Q7WT42 11-263 # Fragment
    2. Putative fructokinase YhdR [117642]
      1. Bacillus subtilis [TaxId: 1423] [117643] (1)
        SQ O05510
    3. N-acetylglucosamine kinase [142469]
      Transcriptional regulator, XylR-related
      1. Thermotoga maritima [TaxId: 2336] [142470] (2)
        SQ Q9X0V1 200-368! SQ Q9X0V1 72-199
        TM1224
    4. N-acetylmannosamine kinase NanK [142471]
      1. Escherichia coli [TaxId: 562] [142472] (4)
        SQ P45425 1-119! SQ P45425 120-289
    5. Mlc protein [142473]
      Making large colonies protein
      1. Escherichia coli [TaxId: 562] [142474] (12)
        SQ P50456 211-406! SQ P50456 82-210
    6. Putative regulator protein YcfX [142475]
      1. Salmonella typhimurium [TaxId: 90371] [142476] (2)
        SQ Q8ZPZ9 1-117! SQ Q8ZPZ9 118-303
    7. Hypothetical protein SP2142 [142477]
      1. Streptococcus pneumoniae [TaxId: 1313] [142478] (2)
        SQ Q97NB0 1-114! SQ Q97NB0 115-289
    8. Transcriptional regulator VC2007 [142479]
      1. Vibrio cholerae [TaxId: 666] [142480] (2)
        SQ Q9KQJ1 209-405! SQ Q9KQJ1 81-208
  11. Cyto-EpsL domain [117644] (1)
    N-terminal part of Pfam 05134
    1. Cytoplasmic domain of general secretion pathway protein L, EpsL [117645]
      1. Vibrio cholerae [TaxId: 666] [117646] (7)
        SQ P45782 6-244
  12. Ta0583-like [142481] (1)
    1. Hypothetical protein Ta0583 [142482]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [142483] (10)
        SQ Q9HKL4 1-164! SQ Q9HKL4 165-325
  13. CoaX-like [142484] (3)
    Pfam 03309; Bordetella pertussis Bvg accessory factor family, Baf
    1. Type III pantothenate kinase, CoaX [142485]
      1. Thermotoga maritima [TaxId: 2336] [142486] (48)
        SQ Q9WZY5 1-118! SQ Q9WZY5 119-245
      2. Pseudomonas aeruginosa [TaxId: 287] [142487] (8)
        SQ Q9HWC1 1-114! SQ Q9HWC1 115-248
      3. Campylobacter jejuni [TaxId: 197] [142488] (4)
        SQ Q5HW73 1-82! SQ Q5HW73 83-208
  14. Fumble-like [159623] (3)
    Pfam 03630; type II pantothenate kinase-like
    1. Pantothenate kinase 3, PANK3 [159624]
      1. Human (Homo sapiens) [TaxId: 9606] [159625] (8)
        SQ Q9H999 12-152! SQ Q9H999 157-368
    2. Type II pantothenate kinase, CoaW [159626]
      1. Staphylococcus aureus [TaxId: 1280] [159627] (2)
        SQ Q8NVG0 1-267
    3. Pantothenate kinase 1, PANK1 [159628]
      1. Human (Homo sapiens) [TaxId: 9606] [159629] (4)
        SQ Q8TE04 236-381! SQ Q8TE04 382-593
2. Creatinase/prolidase N-terminal domain [53092] (1)
  uperfamily
  1. Creatinase/prolidase N-terminal domain [53093] (4)
    1. Creatinase [53094]
      1. Pseudomonas putida [TaxId: 303] [53095] (1)
      2. Actinobacillus sp. [TaxId: 41114] [75244] (1)
    2. Aminopeptidase P [53096]
      synonym: Xaa-Pro dipeptidase, prolidase
      1. Escherichia coli [TaxId: 562] [53097] (37)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102481] (1)
3. Ribonuclease H-like [53098] (14)
  consists of one domain of this fold
  uperfamily
  1. Ribonuclease H [53099] (11)
    1. RNase H (RNase HI) [53100]
      1. Escherichia coli [TaxId: 562] [53101] (37)
        SQ P0A7Y4
      2. Thermus thermophilus [TaxId: 274] [53102] (1)
      3. synthetic, Escherichia coli/Thermus thermophilus chimera [69532] (1)
    2. Class II ribonuclease H (RNase HII) [53103]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53104] (1)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64093] (2)
      3. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [64094] (2)
      4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [110639] (2)
        SQ O59351
      5. Thermotoga maritima [TaxId: 2336] [142489] (1)
        SQ Q9X017 1-221
    3. HIV RNase H (Domain of reverse transcriptase) [53105]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [53106] (88)
        SQ P04585 159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ P03366 186-725 # chain A coverage; chain B coverage: 156-584 ! SQ P04585 158-698 # chain A coverage; chain B is shorter: 159-595
      2. Human immunodeficiency virus type 2 [TaxId: 11709] [82443] (1)
    4. BH0863-like Ribonuclease H [142490]
      new class of RNase H
      1. Bacillus halodurans [TaxId: 86665] [142491] (15)
        SQ Q9KEI9 61-193! SQ Q9KEI9 62-193
        BH0863
  2. Retroviral integrase, catalytic domain [53107] (3)
    1. Retroviral integrase, catalytic domain [53108]
      1. Rous sarcoma virus RSV [TaxId: 11886] [53109] (21)
      2. Human immunodeficiency virus type 1 [TaxId: 11676] [53110] (19)
      3. Simian immunodeficiency virus [TaxId: 11723] [53111] (1)
  3. mu transposase, core domain [53112] (1)
    1. mu transposase, core domain [53113]
      1. Bacteriophage mu [TaxId: 10677] [53114] (2)
  4. Transposase inhibitor (Tn5 transposase) [53115] (1)
    1. Transposase inhibitor (Tn5 transposase) [53116]
      contains additional all-alpha subdomains in both N- and C-terminal regions
      1. Escherichia coli [TaxId: 562] [53117] (6)
  5. DnaQ-like 3'-5' exonuclease [53118] (26)
    contains Pfam 00929
    1. Exonuclease domain of prokaryotic DNA polymerase [53119]
      part of Klenow fragment, KF
      1. Escherichia coli [TaxId: 562] [53120] (14)
      2. Thermus aquaticus [TaxId: 271] [53121] (13)
      3. Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] [53122] (45)
        SQ Q45458 298-876 # 88% sequence identity ! SQ Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
    2. Exonuclease domain of T7 DNA polymerase [53123]
      1. Bacteriophage T7 [TaxId: 10760] [53124] (16)
        SQ P00581
    3. Exonuclease domain of family B DNA polymerases [53125]
      elaborated with additional structures and the N-terminal subdomain
      1. Escherichia coli [TaxId: 562] [102482] (1)
        DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
      2. Bacteriophage T4 [TaxId: 10665] [53126] (2)
        additional N-terminal subdomain contains rudimental OB-fold
      3. Bacteriophage RB69 [TaxId: 12353] [53127] (27)
        additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
      4. Archaeon Thermococcus gorgonarius [TaxId: 71997] [53128] (3)
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      5. Archaeon Thermococcus sp., 9on-7 [TaxId: 35749] [53129] (1)
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      6. Archaeon Desulfurococcus tok [TaxId: 108142] [53130] (2)
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      7. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [53131] (2)
        SQ P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
        additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
      8. Sulfolobus solfataricus [TaxId: 2287] [117647] (1)
        SQ P26811 40-864
    4. N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444]
      1. Escherichia coli [TaxId: 562] [82445] (5)
    5. Exonuclease I [53132]
      also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region
      1. Escherichia coli [TaxId: 562] [53133] (1)
      2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159630] (3)
    6. Oligoribonuclease [89719]
      1. Haemophilus influenzae [TaxId: 727] [89720] (1)
        HI1715
      2. Escherichia coli [TaxId: 562] [142492] (6)
        SQ P0A784 1-180
    7. Hypothetical protein AT5G06450 [102483]
      forms a ring-shaped hexamer; function unknown
      1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [102484] (7)
    8. Exonuclease ERI1 [117648]
      1. Human (Homo sapiens) [TaxId: 9606] [117649] (1)
        SQ Q8IV48 122-321
    9. Exonuclease domain of phi29 DNA polymerase [117650]
      1. Bacteriophage phi-29 [TaxId: 10756] [117651] (18)
        SQ P03680
    10. Interferon-stimulated gene 20 kDa protein, ISG20 [117652]
      1. Human (Homo sapiens) [TaxId: 9606] [117653] (1)
        SQ Q96AZ6 6-178
    11. Exosome complex exonuclease RRP6 [142493]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142494] (4)
        SQ Q12149 129-420
    12. Ribonuclease D, catalytic domain [142495]
      1. Escherichia coli [TaxId: 562] [142496] (1)
        SQ P09155 1-193
    13. Ribonuclease T [142497]
      1. Pseudomonas aeruginosa [TaxId: 287] [142498] (2)
        SQ Q9HY82 19-220
    14. Three prime repair exonuclease 2, TREX2 [142499]
      1. Human (Homo sapiens) [TaxId: 9606] [142500] (2)
        SQ Q9BQ50 44-271
    15. Three prime repair exonuclease 1, TREX1 [159631]
      1. Mouse (Mus musculus) [TaxId: 10090] [159632] (18)
        SQ Q91XB0 5-234! SQ Q91XB0 9-234
  6. RuvC resolvase [53134] (1)
    1. RuvC resolvase [53135]
      Holliday junction-specific endonuclease
      1. Escherichia coli [TaxId: 562] [53136] (1)
  7. Mitochondrial resolvase ydc2 catalytic domain [69533] (1)
    1. Mitochondrial resolvase ydc2 catalytic domain [69534]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [69535] (1)
  8. Putative Holliday junction resolvase RuvX [102485] (3)
    1. Hypothetical protein YqgF (RuvX) [102486]
      1. Escherichia coli [TaxId: 562] [102487] (3)
    2. Hypothetical protein YrrK (RuvX) [102488]
      1. Bacillus subtilis [TaxId: 1423] [102489] (1)
    3. Hypothetical protein, YqgF homologue [102490]
      1. Thermus thermophilus [TaxId: 274] [102491] (1)
  9. CAF1-like ribonuclease [102492] (2)
    1. Pop2 RNase D domain [102493]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102494] (1)
    2. CCR4-NOT transcription complex subunit 7, CAF1 [159633]
      1. Human (Homo sapiens) [TaxId: 9606] [159634] (1)
        SQ Q9UIV1 11-262
  10. PIWI domain [110640] (3)
    Pfam 02171
    1. Argonaute homologue PF0537 [110641]
      includes the middle domain
      1. Pyrococcus furiosus [TaxId: 2261] [110642] (3)
        SQ Q8U3D2
    2. Argonaute homologue Aq_1447 [142501]
      includes the middle domain
      1. Aquifex aeolicus [TaxId: 63363] [142502] (6)
        SQ O67434 315-706
    3. Hypothetical protein AF1318 [142503]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142504] (5)
        SQ O28951 11-427
  11. TM1739-like [142505] (1)
    Pfam 04251; DUF430; particular similarity to the PIWI domain family
    1. Hypothetical protein TM1739 [142506]
      1. Thermotoga maritima [TaxId: 2336] [142507] (2)
        SQ Q9X261 1-301
  12. Hermes transposase-like [142508] (1)
    1. Transposase Hermes, catalytic domain [142509]
      1. House fly (Musca domestica) [TaxId: 7370] [142510] (1)
        SQ Q25442 163-609
  13. Tex RuvX-like domain-like [159635] (1)
    1. Transcriptional accessory factor Tex [159636]
      1. Pseudomonas aeruginosa [TaxId: 287] [159637] (3)
        SQ Q9HTY8 325-473
  14. Prp8 beta-finger domain-like [159638] (2)
    1. Pre-mRNA-splicing factor 8, Prp8 [159639]
      1. Human (Homo sapiens) [TaxId: 9606] [159640] (3)
        SQ Q6P2Q9 1760-2016! SQ Q6P2Q9 1771-1989
      2. Saccharomyces cerevisiae [TaxId: 4932] [159641] (5)
        SQ P33334 1833-2087! SQ P33334 1835-2087
4. Translational machinery components [53137] (2)
  uperfamily
  1. Ribosomal protein L18 and S11 [53138] (7)
    1. Ribosomal protein L18 (L18p) [53139]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [53140] (40)
        SQ P14123
      2. Thermus thermophilus [TaxId: 274] [75245] (7)
      3. Bacillus stearothermophilus [TaxId: 1422] [102495] (1)
      4. Escherichia coli [TaxId: 562] [159642] (29)
        SQ P0C018 1-117
      5. Deinococcus radiodurans [TaxId: 1299] [159643] (6)
        SQ Q9RSL2 8-111
    2. Ribosomal protein S11 [53141]
      1. Thermus thermophilus [TaxId: 274] [53142] (46)
        SQ P80376
      2. Escherichia coli [TaxId: 562] [159644] (24)
        SQ P0A7R9 12-128
  2. ERF1/Dom34 middle domain-like [53143] (3)
    1. Middle domain of eukaryotic peptide chain release factor subunit 1, ERF1 [53144]
      1. Human (Homo sapiens) [TaxId: 9606] [53145] (2)
    2. Dom34 [159645]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159646] (3)
        SQ P33309 136-277
    3. Cell division protein pelota [159647]
      1. Thermoplasma acidophilum [TaxId: 2303] [159648] (1)
        SQ Q9HJ74 127-243
5. Nitrogenase accessory factor-like [53146] (2)
  uperfamily
  1. MTH1175-like [53147] (3)
    1. Hypothetical protein MTH1175 [53148]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [53149] (1)
    2. Hypothetical protein TM1816 [82446]
      1. Thermotoga maritima [TaxId: 2336] [82447] (2)
        SQ Q9X2D6 1-115
    3. Hypothetical protein TM1290 [110643]
      1. Thermotoga maritima [TaxId: 2336] [110644] (1)
        SQ Q9X116
  2. Nitrogenase accessory factor [102496] (1)
    capable of binding the iron molybdenum cofactor, FeMo-co
    1. NafY core domain [102497]
      1. Azotobacter vinelandii [TaxId: 354] [102498] (1)
6. DNA repair protein MutS, domain II [53150] (1)
  uperfamily
  1. DNA repair protein MutS, domain II [53151] (2)
    1. DNA repair protein MutS, domain II [53152]
      1. Thermus aquaticus [TaxId: 271] [53153] (4)
      2. Escherichia coli [TaxId: 562] [53154] (10)
        SQ P23909 2-800
7. Methylated DNA-protein cysteine methyltransferase domain [53155] (1)
  uperfamily
  1. Methylated DNA-protein cysteine methyltransferase domain [53156] (3)
    1. Ada DNA repair protein [53157]
      1. Escherichia coli [TaxId: 562] [53158] (1)
    2. O6-alkylguanine-DNA alkyltransferase [53159]
      1. Human (Homo sapiens) [TaxId: 9606] [53160] (9)
        SQ P16455 6-176
      2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [53161] (1)
Phosphorylase/hydrolase-like [53162] (8)
core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
1. HybD-like [53163] (2)
  the HybD fold coincides with the consensus core structure
  uperfamily
  1. Hydrogenase maturating endopeptidase HybD [53164] (1)
    1. Hydrogenase maturating endopeptidase HybD [53165]
      1. Escherichia coli [TaxId: 562] [53166] (1)
  2. Germination protease [64095] (1)
    elaborated with the N-terminal alpha+beta subdomain and the insertion all-alpha dimerisation subdomain
    1. Germination protease [64096]
      1. Bacillus megaterium [TaxId: 1404] [64097] (1)
2. Purine and uridine phosphorylases [53167] (1)
  complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8
  uperfamily
  1. Purine and uridine phosphorylases [53168] (18)
    1. Purine nucleoside phosphorylase, PNP [53169]
      1. Human (Homo sapiens) [TaxId: 9606] [53170] (17)
        SQ P00491
      2. Cow (Bos taurus) [TaxId: 9913] [53171] (20)
        SQ P55859
      3. Escherichia coli [TaxId: 562] [53172] (19)
      4. Vibrio cholerae [TaxId: 666] [102499] (2)
      5. Cellulomonas sp. [TaxId: 40001] [53173] (2)
      6. Mycobacterium tuberculosis [TaxId: 1773] [64098] (3)
      7. Thermus thermophilus [TaxId: 274] [89721] (4)
      8. Thermotoga maritima [TaxId: 2336] [117654] (1)
        SQ Q9X1T2
      9. Bacillus anthracis [TaxId: 1392] [117655] (3)
        SQ Q81T09
    2. Uridine phosphorylase [53176]
      1. Escherichia coli [TaxId: 562] [53177] (40)
        also includes the PDB entry (1rxs) where protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
      2. Salmonella typhimurium [TaxId: 90371] [117656] (1)
        SQ P0A1F6
    3. Putative uridine phosphorylase [102500]
      1. Plasmodium falciparum [TaxId: 5833] [102501] (4)
    4. 5'-deoxy-5'-methylthioadenosine phosphorylase [53174]
      1. Human (Homo sapiens) [TaxId: 9606] [53175] (5)
        SQ Q13126
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69536] (9)
      3. Sulfolobus tokodaii [TaxId: 111955] [117657] (1)
        SQ Q975C3
    5. 5'-Methylthioadenosine/S-Adenosylhomocysteine nucleosidase [82448]
      1. Escherichia coli [TaxId: 562] [82449] (8)
    6. AMP nucleosidase [110645]
      contains extra N-terminal oligomerisation (sub)domain (8-153)
      1. Escherichia coli [TaxId: 562] [110646] (4)
        SQ P15272
      2. Bacteroides thetaiotaomicron [TaxId: 818] [117658] (1)
        SQ Q7MVU1
3. Peptidyl-tRNA hydrolase-like [53178] (1)
  uperfamily
  1. Peptidyl-tRNA hydrolase-like [53179] (2)
    1. Peptidyl-tRNA hydrolase [53180]
      1. Escherichia coli [TaxId: 562] [53181] (1)
    2. Chloroplast group II intron splicing factor Crs2 [102502]
      1. Maize (Zea mays) [TaxId: 4577] [102503] (3)
4. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53182] (1)
  uperfamily
  1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53183] (4)
    1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53184]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [53185] (1)
      2. Bacillus amyloliquefaciens [TaxId: 1390] [53186] (1)
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [64099] (2)
      4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75246] (1)
5. Zn-dependent exopeptidases [53187] (9)
  core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest
  uperfamily
  1. Pancreatic carboxypeptidases [53188] (10)
    1. Carboxypeptidase A [53189]
      1. Cow (Bos taurus) [TaxId: 9913] [53190] (30)
      2. Pig (Sus scrofa) [TaxId: 9823] [53191] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [53192] (7)
      4. Cotton bollworm (Helicoverpa armigera) [TaxId: 29058] [75247] (1)
    2. Carboxypeptidase B [53193]
      1. Pig (Sus scrofa) [TaxId: 9823] [53194] (54)
      2. Human (Homo sapiens) [TaxId: 9606] [75248] (2)
      3. Cow (Bos taurus) [TaxId: 9913] [53195] (1)
      4. Corn earworm (Helicoverpa zea) [TaxId: 7113] [142511] (2)
        SQ Q3T905 117-428
    3. Carboxypeptidase D, catalytic domain [53196]
      1. Crested duck (Lophonetta specularioides) [TaxId: 8836] [53197] (2)
    4. Carboxypeptidase M, catalytic domain [102504]
      1. Human (Homo sapiens) [TaxId: 9606] [102505] (1)
  2. Carboxypeptidase T [53198] (1)
    1. Carboxypeptidase T [53199]
      1. Thermoactinomyces vulgaris [TaxId: 2026] [53200] (1)
  3. Leucine aminopeptidase, C-terminal domain [53201] (2)
    1. Leucine aminopeptidase, C-terminal domain [53202]
      1. Cow (Bos taurus) [TaxId: 9913] [53203] (9)
      2. Escherichia coli, PepA [TaxId: 562] [75249] (1)
  4. Bacterial dinuclear zinc exopeptidases [53204] (19)
    1. Aminopeptidase [53205]
      1. Aeromonas proteolytica [TaxId: 671] [53206] (13)
        SQ Q01693
        synonym: Vibrio proteolyticus
      2. Streptomyces griseus [TaxId: 1911] [53207] (11)
    2. Aminopeptidase PepV [82450]
      unspecific amino dipeptidase
      1. Lactobacillus delbrueckii [TaxId: 1584] [82451] (1)
    3. Carboxypeptidase G2, catalytic domain [53208]
      1. Pseudomonas sp., strain rs-16 [TaxId: 306] [53209] (1)
    4. Peptidase T (tripeptidase), catalytic domain [75250]
      1. Salmonella typhimurium [TaxId: 90371] [75251] (1)
      2. Escherichia coli [TaxId: 562] [102506] (1)
    5. Peptidase-like beta-alanine synthase, catalytic domain [102507]
      1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [102508] (2)
    6. Succinyl-diaminopimelate desuccinylase, catalytic domain [102509]
      1. Neisseria meningitidis [TaxId: 487] [102510] (1)
    7. Aminoacylase-1, catalytic domain [102511]
      1. Human (Homo sapiens) [TaxId: 9606] [102512] (1)
    8. Hypothetical protein YsdC, catalytic domain [102513]
      contains insert beta-barrel domain
      1. Bacillus subtilis [TaxId: 1423] [102514] (1)
    9. Putative endoglucanase TM1048, catalytic domain [102515]
      contains insert beta-barrel domain
      1. Thermotoga maritima [TaxId: 2336] [102516] (1)
    10. Frv operon protein FrvX, catalytic domain [117659]
      1. Pyrococcus horikoshii [TaxId: 53953] [117660] (3)
        SQ O59196 # PH1527
    11. Probable aminopeptidase ApeA [117661]
      contains insert beta-barrel domain
      1. Borrelia burgdorferi [TaxId: 139] [117662] (1)
        SQ Q45055
    12. IAA-amino acid hydrolase, catalytic domain [117663]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [117664] (2)
        SQ P54970 37-428
    13. Deblocking aminopeptidase YhfE [142512]
      contains insert beta-barrel domain
      1. Bacillus cereus [TaxId: 1396] [142513] (16)
        SQ Q81HB5 3-73,187-348
        BC0901
    14. Allantoate amidohydrolase AllC catalytic domain [142514]
      1. Escherichia coli [TaxId: 562] [142515] (4)
        SQ P77425 2-210,328-411
    15. Endoglucanase TM1049 [142516]
      1. Thermotoga maritima [TaxId: 2336] [142517] (1)
        SQ Q9X0D9 1-64,149-339
    16. Protein YxeP [142518]
      1. Bacillus subtilis [TaxId: 1423] [142519] (2)
        SQ P54955 4-177,293-379
    17. Aminopeptidase YpdE [142520]
      1. Shigella flexneri [TaxId: 623] [142521] (6)
        SQ Q83K87 1-66,148-345
        hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)
  5. FolH catalytic domain-like [53210] (2)
    1. Transferrin receptor ectodomain, protease-like domain [53211]
      1. Human (Homo sapiens) [TaxId: 9606] [53212] (4)
    2. Glutamate carboxypeptidase II FOLH1 [142522]
      Folate hydrolase 1, FolH homologue
      1. Human (Homo sapiens) [TaxId: 9606] [142523] (17)
        SQ Q04609 57-117,351-593
  6. N-acetylmuramoyl-L-alanine amidase-like [102517] (2)
    1. N-acetylmuramoyl-L-alanine amidase CwlV [102518]
      1. Paenibacillus polymyxa [TaxId: 1406] [102519] (1)
    2. Endolysin Ply, catalytic domain [142524]
      1. Bacteriophage Psa [TaxId: 171618] [142525] (1)
        SQ Q8W5Y8 1-180
  7. AstE/AspA-like [142526] (6)
    Pfam 04952; Succinylglutamate desuccinylase / Aspartoacylase family; contains extra C-terminal domain, new variant of the Barrel-sandwich hybrid fold (scop_cf 51229)
    1. Succinylglutamate desuccinylase AstE [142527]
      1. Vibrio cholerae [TaxId: 666] [142528] (1)
        SQ Q9KSL4 3-342
      2. Vibrio parahaemolyticus [TaxId: 670] [142529] (2)
        SQ Q87Q40 4-342
      3. Escherichia coli [TaxId: 562] [142530] (2)
        SQ P76215 1-322
      4. Chromobacterium violaceum [TaxId: 536] [142531] (1)
        SQ Q7NU26 2-332
    2. Aspartoacylase AspA [159649]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [159650] (1)
        SQ Q6AZ03 4-310
      2. Human (Homo sapiens) [TaxId: 9606] [159651] (1)
        SQ P45381 9-310
  8. Glutaminyl-peptide cyclotransferase-like [142532] (1)
    part of Pfam 04389
    1. Glutaminyl-peptide cyclotransferase, QPCT [142533]
      Glutaminyl cyclase
      1. Human (Homo sapiens) [TaxId: 9606] [142534] (16)
        SQ Q16769 33-361
  9. FGase-like [159652] (2)
    Pfam 05013; N-formylglutamate amidohydrolase
    1. N-formylglutamate amidohydrolase [159653]
      1. Ralstonia eutropha [TaxId: 106590] [159654] (2)
        SQ Q46VW8 10-289
    2. Hypothetical protein Atu2144 [159655]
      1. Agrobacterium tumefaciens [TaxId: 358] [159656] (8)
        SQ Q8UDI1 6-257
6. LigB-like [53213] (1)
  circular permutation of the common fold, most similar to the PNP fold
  uperfamily
  1. LigB-like [53214] (2)
    1. LigB subunit of an aromatic-ring-opening dioxygenase LigAB [53215]
      1. Pseudomonas paucimobilis [TaxId: 13689] [53216] (2)
    2. Uncharacterized protein YgiD [159657]
      1. Escherichia coli [TaxId: 562] [159658] (1)
        SQ P24197 14-271
7. AF0625-like [142535] (1)
  contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
  uperfamily
  1. AF0625-like [142536] (2)
    Pfam 04414; DUF516, binds magnesium ion and pyrophosphate in the putative active site
    1. Hypothetical protein PH0006 [142537]
      1. Pyrococcus horikoshii [TaxId: 53953] [142538] (3)
        SQ O57774 1-274
    2. Hypothetical protein AF0625 [142539]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142540] (1)
        SQ O29630 1-278
8. Cgl1923-like [159659] (1)
  1. Cgl1923-like [159660] (1)
    Pfam 01908; DUF75
    1. Hypothetical protein Cgl1923 [159661]
      1. Corynebacterium glutamicum [TaxId: 1718] [159662] (3)
        SQ Q8NP93 6-274
Molybdenum cofactor biosynthesis proteins [53217] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
1. Molybdenum cofactor biosynthesis proteins [53218] (2)
  uperfamily
  1. MogA-like [53219] (8)
    1. MogA [53220]
      1. Escherichia coli [TaxId: 562] [53221] (2)
      2. Shewanella oneidensis [TaxId: 70863] [142541] (12)
        SQ Q8EKM7 2-174
    2. MoaB [89722]
      1. Escherichia coli [TaxId: 562] [89723] (2)
        SQ P30746
      2. Bacillus cereus [TaxId: 1396] [142542] (3)
        SQ Q816R0 12-166
    3. Gephyrin N-terminal domain [64100]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [64101] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [64102] (1)
        the human neuroreceptor anchoring protein
    4. Plant CNX1 G domain [69537]
      gephyrin homologue
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [69538] (6)
        SQ Q39054 464-623
    5. Putative molybdenum cofactor biosynthesis protein DIP0503 [142543]
      1. Corynebacterium diphtheriae [TaxId: 1717] [142544] (1)
        SQ Q6NJA6 1-163
  2. MoeA central domain-like [64103] (5)
    1. MoeA, central domain [64104]
      1. Escherichia coli [TaxId: 562] [64105] (27)
      2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102520] (1)
      3. Pyrococcus furiosus [TaxId: 2261] [117665] (1)
        SQ Q8U034
      4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117666] (1)
        SQ O59354
    2. Gephyrin, domain 5 [110647]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110648] (4)
        SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
CobE/GbiG C-terminal domain-like [159663] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32154; strand 5 is antiparallel to the rest
1. CobE/GbiG C-terminal domain-like [159664] (1)
  probably involved in deacylation steps in both anaerobic and aerobic pathways of cobalamin biosynthesis
  1. CobE/GbiG C-terminal domain-like [159665] (3)
    C-terminal part of Pfam 01890 (CbiG); corresponds to standalone protein CobE in the aerobic pathway; also includes resent structure 3BY5
    1. Cobalamin biosynthesis protein CobE [159666]
      predicted to facilitate the deacylation of precorrin-5 intermediate; this step can proceed non-enzymatically in vitro
      1. Agrobacterium tumefaciens [TaxId: 358] [159667] (1)
        SQ A9CHC6 8-130
        CobE orthologue Atu2797/ChiG; typo in the (mis)annotation
      2. Pseudomonas aeruginosa [TaxId: 287] [159668] (1)
        SQ Q9HZQ0 1-139
    2. Cobalamin biosynthesis protein G, CbiG [159669]
      1. Sulfolobus solfataricus [TaxId: 2287] [159670] (2)
        SQ Q97WD0 215-335
CbiG N-terminal domain-like [159671] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 213456, strand 5 is antiparallel to the rest
1. CbiG N-terminal domain-like [159672] (1)
  probable biological unit is a homodimer; putative active site is formed by residues from both subunits
  1. CbiG N-terminal domain-like [159673] (1)
    N-terminal part of Pfam 01890; also includes variable linker domain to CobE-like C-terminal domain; the linker domain may be in a rudimentary form or missing
    1. Cobalamin biosynthesis protein G, CbiG [159674]
      1. Sulfolobus solfataricus [TaxId: 2287] [159675] (2)
        SQ Q97WD0 8-215
Bacterial fluorinating enzyme, N-terminal domain [102521] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands; order: 213546, strand 5 is antiparallel to the rest; topological similarity to the MogA-like family fold
1. Bacterial fluorinating enzyme, N-terminal domain [102522] (1)
  uperfamily
  1. Bacterial fluorinating enzyme, N-terminal domain [102523] (1)
    1. 5'-fluoro-5'-deoxyadenosine synthase [102524]
      1. Streptomyces cattleya [TaxId: 29303] [102525] (41)
Caspase-like [52128] (1)
3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest
1. Caspase-like [52129] (2)
  mature protein may be composed of two chains folded in a single domain
  uperfamily
  1. Caspase catalytic domain [52130] (7)
    1. Apopain (caspase-3, cpp32) [52131]
      1. Human (Homo sapiens) [TaxId: 9606] [52132] (31)
    2. Interleukin-1beta converting enzyme (a cysteine protease) [52133]
      1. Human (Homo sapiens) [TaxId: 9606] [52134] (14)
        SQ P29466 125-297,317-404
    3. Caspase-1 [102526]
      1. Fall armyworm (Spodoptera frugiperda) [TaxId: 7108] [102527] (1)
    4. Caspase-2 [102528]
      1. Human (Homo sapiens) [TaxId: 9606] [102529] (1)
    5. Caspase-7 [63961]
      1. Human (Homo sapiens) [TaxId: 9606] [63962] (9)
        SQ P55210 57-303
    6. Caspase-8 [52135]
      1. Human (Homo sapiens) [TaxId: 9606] [52136] (6)
    7. Caspase-9 [69443]
      1. Human (Homo sapiens) [TaxId: 9606] [69444] (2)
  2. Gingipain R (RgpB), N-terminal domain [52137] (1)
    contains extra N-terminal alpha/beta subdomain
    1. Gingipain R (RgpB), N-terminal domain [52138]
      Arginine-specific cysteine proteinase
      1. Porphyromonas gingivalis [TaxId: 837] [52139] (1)
Macro domain-like [52948] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 is antiparallel to the rest
1. Macro domain-like [52949] (2)
  uperfamily
  1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52950] (2)
    1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52951]
      1. Cow (Bos taurus) [TaxId: 9913] [52952] (9)
      2. Escherichia coli, PepA [TaxId: 562] [75241] (1)
        involved in Xer site-specific recombination; probable DNA-binding domain
  2. Macro domain [89724] (7)
    found in different proteins, including macro-H2a histone and the Appr-1"-p processing enzyme
    1. Hypothetical protein AF1521 [89725]
      contains extra N-terminal strand
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89726] (4)
        SQ O28751
    2. Hypothetical protein YmbD [102530]
      1. Escherichia coli [TaxId: 562] [102531] (1)
    3. Hypothetical protein Ymr087W [110654]
      contains structural variations at both termini
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110655] (3)
        SQ Q04299
    4. Hypothetical protein BT1257 [142545]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [142546] (3)
        SQ Q8A8B0 2-155
    5. Histone macro-H2a1.1 [142547]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [142548] (4)
        SQ Q02874 180-370
      2. Human (Homo sapiens) [TaxId: 9606] [142549] (8)
        SQ O75367 179-367! SQ O75367 181-371
    6. Replicase polyprotein 1ab [142550]
      1. SARS coronavirus [TaxId: 227859] [142551] (4)
        SQ P59641 1002-1169
MurD-like peptide ligases, peptide-binding domain [53243] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
1. MurD-like peptide ligases, peptide-binding domain [53244] (2)
  uperfamily
  1. MurCDEF C-terminal domain [53245] (5)
    1. UDP-N-acetylmuramate-alanine ligase MurC [82452]
      1. Thermotoga maritima [TaxId: 2336] [82453] (1)
        TM0231
      2. Haemophilus influenzae [TaxId: 727] [89727] (4)
    2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [53246]
      1. Escherichia coli [TaxId: 562] [53247] (11)
    3. UDP-N-acetylmuramyl tripeptide synthetase MurE [64107]
      1. Escherichia coli [TaxId: 562] [64108] (1)
    4. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [53248]
      1. Escherichia coli [TaxId: 562] [53249] (1)
  2. Folylpolyglutamate synthetase, C-terminal domain [53250] (2)
    1. Folylpolyglutamate synthetase, C-terminal domain [53251]
      1. Lactobacillus casei [TaxId: 1582] [53252] (7)
      2. Thermotoga maritima [TaxId: 2336] [102532] (1)
        TM0166
Phosphoglycerate mutase-like [53253] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
1. Phosphoglycerate mutase-like [53254] (3)
  uperfamily
  1. Cofactor-dependent phosphoglycerate mutase [53255] (8)
    1. Phosphoglycerate mutase [53256]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53257] (7)
      2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64109] (1)
      3. Escherichia coli [TaxId: 562] [64110] (2)
      4. Human (Homo sapiens) [TaxId: 9606] [110656] (13)
        SQ P07738
      5. Mycobacterium tuberculosis [TaxId: 1773] [117667] (1)
        SQ Q11140
      6. Plasmodium falciparum [TaxId: 5833] [117668] (1)
        SQ Q8IIG6
    2. Broad specificity phosphatase PhoE (YhfR) [69539]
      1. Bacillus stearothermophilus [TaxId: 1422] [69540] (3)
    3. Alpha-ribazole-5'-phosphate phosphatase [117669]
      1. Thermus thermophilus [TaxId: 274] [117670] (2)
        SQ Q53WB3
  2. Histidine acid phosphatase [53258] (7)
    1. Prostatic acid phosphatase [53259]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53260] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [53261] (4)
    2. Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase) [53263]
      1. Aspergillus ficuum [TaxId: 5058] [53264] (1)
      2. Aspergillus niger [TaxId: 5061] [53265] (1)
      3. Escherichia coli [TaxId: 562] [53266] (6)
      4. Aspergillus fumigatus [TaxId: 5085] [110657] (5)
        SQ O00092 30-464 ! SQ O00092
    3. Glucose-1-phosphatase [102533]
      1. Escherichia coli [TaxId: 562] [102534] (1)
  3. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53267] (2)
    1. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53268]
      bifunctional enzyme
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53269] (8)
      2. Human (Homo sapiens) [TaxId: 9606] [82454] (1)
PRTase-like [53270] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
1. PRTase-like [53271] (2)
  uperfamily
  1. Phosphoribosyltransferases (PRTases) [53272] (36)
    1. Xanthine-guanine PRTase (XPRTase) [53273]
      1. Escherichia coli [TaxId: 562] [53274] (5)
      2. Thermoanaerobacter tengcongensis [TaxId: 119072] [142552] (2)
        SQ Q8R7L0 3-180
    2. Hypoxanthine-guanine-xanthine PRTase [53275]
      1. Tritrichomonas foetus [TaxId: 5724] [53276] (1)
      2. Toxoplasma gondii [TaxId: 5811] [53277] (5)
      3. Leishmania tarentolae [TaxId: 5689] [110658] (1)
        SQ Q9NJI5
    3. Glutamine PRPP amidotransferase, C-terminal domain [53278]
      1. Bacillus subtilis [TaxId: 1423] [53279] (2)
      2. Escherichia coli [TaxId: 562] [53280] (5)
    4. Guanine PRTase [53281]
      1. Giardia lamblia [TaxId: 5741] [53282] (2)
    5. Hypoxanthine-guanine PRTase (HGPRTase) [53283]
      1. Human (Homo sapiens) [TaxId: 9606] [53284] (7)
      2. Plasmodium falciparum [TaxId: 5833] [53285] (1)
      3. Thermoanaerobacter tengcongensis [TaxId: 119072] [117671] (1)
        SQ Q8R7L0
    6. Hypoxanthine PRTase [53286]
      1. Trypanosoma cruzi [TaxId: 5693] [53287] (9)
        SQ Q27796
      2. Escherichia coli [TaxId: 562] [75255] (3)
      3. Salmonella typhimurium [TaxId: 90371] [89728] (1)
    7. Adenine PRTase [53288]
      1. Leishmania donovani [TaxId: 5661] [53289] (4)
      2. Leishmania tarentolae [TaxId: 5689] [102535] (1)
      3. Giardia lamblia [TaxId: 5741] [82455] (2)
      4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69541] (2)
      5. Human (Homo sapiens) [TaxId: 9606] [102536] (7)
    8. Orotate PRTase [53290]
      1. Salmonella typhimurium [TaxId: 90371] [53291] (3)
      2. Escherichia coli [TaxId: 562] [53292] (1)
      3. Streptococcus pyogenes [TaxId: 1314] [142553] (2)
        SQ Q9A076 1-208
    9. Uracil PRTase, Upp [53293]
      1. Bacillus caldolyticus [TaxId: 1394] [75256] (1)
      2. Thermotoga maritima [TaxId: 2336] [102538] (1)
        TM0721
      3. Toxoplasma gondii [TaxId: 5811] [53295] (6)
      4. Thermus thermophilus [TaxId: 274] [142554] (4)
        SQ Q72J35 1-208
      5. Sulfolobus solfataricus [TaxId: 2287] [142555] (20)
        SQ Q980Q4 2-216
    10. Pyrimidine operon regulator PyrR [109612]
      bifunctional protein; contains the uracil PRTase and Pyr RNA-binding activities
      1. Bacillus subtilis [TaxId: 1423] [53294] (2)
      2. Thermus thermophilus [TaxId: 274] [102537] (1)
        TT1027
      3. Bacillus caldolyticus [TaxId: 1394] [110659] (7)
        SQ P41007
      4. Mycobacterium tuberculosis [TaxId: 1773] [117672] (1)
        SQ P71807
    11. Pur operon repressor (PurR), C-terminal domain [102539]
      1. Bacillus subtilis [TaxId: 1423] [102540] (2)
    12. Putative phosphoribosyltransferase TT1426 (TTHA1462) [117673]
      1. Thermus thermophilus [TaxId: 274] [117674] (1)
        SQ Q5SIB2
    13. Xanthine phosphoribosyltransferase [142556]
      1. Bacillus subtilis [TaxId: 1423] [142557] (6)
        SQ P42085 1-191
    14. Putative phosphoribosyltransferase TTHA1613 [142558]
      putative APRTase in UniProt
      1. Thermus thermophilus [TaxId: 274] [142559] (5)
        SQ Q5SHW7 2-175
    15. Pprobable purine phosphoribosyltransferase PH0095 [142560]
      1. Pyrococcus horikoshii [TaxId: 53953] [142561] (12)
        SQ O57827 1-153
  2. Phosphoribosylpyrophosphate synthetase-like [53296] (3)
    duplication: consists of two domains of this fold
    1. Phosphoribosylpyrophosphate synthetase [53297]
      1. Bacillus subtilis [TaxId: 1423] [53298] (3)
      2. Methanocaldococcus jannaschii [TaxId: 2190] [142562] (16)
        SQ Q58761 1-155! SQ Q58761 156-284
    2. PRPP synthetase-associated protein 1 [142563]
      1. Human (Homo sapiens) [TaxId: 9606] [142564] (12)
        SQ Q14558 167-350! SQ Q14558 7-166
vWA-like [53299] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
1. vWA-like [53300] (5)
  uperfamily
  1. Integrin A (or I) domain [53301] (12)
    1. Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) [53302]
      1. Human (Homo sapiens) [TaxId: 9606] [53303] (23)
        SQ P20701 153-334
    2. von Willebrand factor A3 domain, vWA3 [53304]
      1. Human (Homo sapiens) [TaxId: 9606] [53305] (4)
    3. von Willebrand factor A1 domain, vWA1 [53306]
      1. Human (Homo sapiens) [TaxId: 9606] [53307] (9)
      2. Mouse (Mus musculus) [TaxId: 10090] [159676] (1)
        SQ Q8CIZ8 1270-1465
    4. Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit) [53308]
      1. Human (Homo sapiens) [TaxId: 9606] [53309] (9)
    5. Integrin alpha1-beta1 [53310]
      1. Human (Homo sapiens) [TaxId: 9606] [53311] (3)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [53312] (4)
    6. Integrin alpha2-beta1 [53313]
      1. Human (Homo sapiens) [TaxId: 9606] [53314] (3)
        SQ P17301 172-364
    7. Integrin alpha-x beta2 [82456]
      Leukocyte adhesion glycoprotein P150,95 alpha chain
      1. Human (Homo sapiens) [TaxId: 9606] [82457] (1)
    8. Integrin beta A domain [69542]
      1. Human (Homo sapiens) [TaxId: 9606] [69543] (5)
        SQ P05106 27-716 ! SQ P05106 27-466
    9. Complement factor B domain [102541]
      1. Human (Homo sapiens) [TaxId: 9606] [102542] (5)
        SQ P00751 268-764
    10. Capillary morphogenesis protein 2 domain [102543]
      Anthrax toxin receptor 2
      1. Human (Homo sapiens) [TaxId: 9606] [102544] (3)
        SQ P58335 41-210
  2. Trunk domain of Sec23/24 [82458] (2)
    1. Sec23 [82459]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82460] (3)
    2. Sec24 [82461]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82462] (4)
  3. Ku70 subunit N-terminal domain [100959] (1)
    1. Ku70 subunit N-terminal domain [100960]
      1. Human (Homo sapiens) [TaxId: 9606] [100961] (2)
  4. Ku80 subunit N-terminal domain [100962] (1)
    1. Ku80 subunit N-terminal domain [100963]
      1. Human (Homo sapiens) [TaxId: 9606] [100964] (2)
  5. RoRNP C-terminal domain-like [142565] (1)
    1. 60-kda SS-A/Ro ribonucleoprotein, RoRNP [142566]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [142567] (5)
        SQ P42700 364-537
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53322] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53323] (1)
  uperfamily
  1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53324] (1)
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53325]
      also includes linker domain IV
      1. Desulfovibrio africanus [TaxId: 873] [53326] (17)
RbsD-like [102545] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 251634; strand 6 is antiparallel to the rest
1. RbsD-like [102546] (1)
  uperfamily
  1. RbsD-like [102547] (2)
    1. Ribose transport protein RbsD [102548]
      1. Bacillus subtilis [TaxId: 1423] [102549] (4)
    2. Hypothetical protein Atu2016 [159677]
      1. Agrobacterium tumefaciens [TaxId: 358] [159678] (1)
        SQ Q8UDV3 1-147
FabD/lysophospholipase-like [52150] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
1. FabD/lysophospholipase-like [52151] (3)
  uperfamily
  1. FabD-like [52152] (2)
    the superfamily common core covers almost all of the family fold
    1. Catalytic domain of malonyl-CoA ACP transacylase FabD [52153]
      1. Escherichia coli [TaxId: 562] [52154] (1)
      2. Streptomyces coelicolor A3(2) [TaxId: 100226] [82463] (1)
  2. Lysophospholipase [53645] (1)
    common core is decorated with many additional structures; mixed beta-sheet of 9 strands, order 654321798; strands 4, 6 and 8 are antiparallel to the rest
    1. Cytosolic phospholipase A2 catalytic domain [53646]
      1. Human (Homo sapiens) [TaxId: 9606] [53647] (1)
  3. Patatin [89729] (1)
    plant proteins; structurally and functionally related to animal cytosolic phospholipase A2
    1. Patatin [89730]
      1. Heartleaf nightshade (Solanum cardiophyllum) [TaxId: 160510] [89731] (1)
L-sulfolactate dehydrogenase-like [89732] (1)
core: 3 layers, a/b/a; mixed sheet of 7 strands, order 1237456; strands 1, 6 and 7 are antiparallel to the rest
1. L-sulfolactate dehydrogenase-like [89733] (1)
  topological similarity to the domain 2 of TM1585
  uperfamily
  1. L-sulfolactate dehydrogenase-like [89734] (3)
    Pfam 02615; type II malate/L-lactate dehydrogenase;
    1. 2,3-diketogulonate oxidoreductase (YiaK) [89735]
      1. Escherichia coli [TaxId: 562] [89736] (2)
    2. L-sulfolactate dehydrogenase [102550]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [102551] (1)
    3. Ureidoglycolate dehydrogenase AllD [117675]
      1. Escherichia coli [TaxId: 562] [117676] (1)
        SQ P77555
Formyltransferase [53327] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
1. Formyltransferase [53328] (1)
  uperfamily
  1. Formyltransferase [53329] (7)
    1. Glycinamide ribonucleotide transformylase, GART [53330]
      1. Escherichia coli [TaxId: 562] [53331] (12)
      2. Human (Homo sapiens) [TaxId: 9606] [82468] (22)
    2. Methionyl-tRNAfmet formyltransferase [53332]
      1. Escherichia coli [TaxId: 562] [53333] (2)
      2. Clostridium thermocellum [TaxId: 1515] [117677] (1)
        SQ Q4HJX2 47% sequence identity
        Structural genomics target; GI:67850689
    3. 10-formyltetrahydrofolate dehydrogenase domain 1 [102552]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [102553] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [142568] (2)
        SQ O75891 1-203
    4. Polymyxin resistance protein ArnA, N-terminal domain [142569]
      1. Escherichia coli [TaxId: 562] [142570] (9)
        SQ P77398 1-200! SQ P77398 1-203
S-adenosyl-L-methionine-dependent methyltransferases [53334] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
1. S-adenosyl-L-methionine-dependent methyltransferases [53335] (57)
  uperfamily
  1. COMT-like [53336] (3)
    1. Catechol O-methyltransferase, COMT [53337]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53338] (6)
    2. COMT domain-containing protein 1, COMTD1 [142571]
      1. Human (Homo sapiens) [TaxId: 9606] [142572] (2)
        SQ Q86VU5 44-262
    3. Caffeoyl-CoA O-methyltransferase [142573]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [142574] (8)
        SQ Q40313 21-247
  2. Plant O-methyltransferase, C-terminal domain [64111] (5)
    1. Chalcone O-methyltransferase [64112]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [64113] (2)
    2. Isoflavone O-methyltransferase [64114]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [64115] (2)
    3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [75259]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [75260] (2)
    4. Aclacinomycin-10-hydroxylase RdmB [102554]
      evolved a different function; binds SAM and SAH
      1. Streptomyces purpurascens [TaxId: 1924] [102555] (4)
        SQ Q54527
    5. Carminomycin 4-O-methyltransferase [110660]
      1. Streptomyces peucetius [TaxId: 1950] [110661] (2)
        SQ Q06528
  3. RNA methyltransferase FtsJ [53339] (1)
    1. RNA methyltransferase FtsJ [53340]
      1. Escherichia coli [TaxId: 562] [53341] (2)
  4. Fibrillarin homologue [53342] (3)
    1. Fibrillarin homologue [53343]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53344] (2)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89737] (1)
        AF2087
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102556] (2)
  5. rRNA methyltransferase RlmA [102557] (1)
    1. rRNA methyltransferase RlmA [102558]
      23S rRNA N1-G745 methyltransferase
      1. Escherichia coli [TaxId: 562] [102559] (1)
  6. rRNA methyltransferase AviRa [89738] (1)
    1. rRNA methyltransferase AviRa [89739]
      1. Streptomyces viridochromogenes [TaxId: 1938] [89740] (2)
  7. rRNA adenine dimethylase-like [88784] (5)
    1. rRNA adenine dimethylase [53363]
      contains additional all-alpha C-terminal domain (res.181-248)
      1. Streptococcus pneumoniae, Ermam [TaxId: 1313] [53364] (1)
      2. Bacillus subtilis, Ermc' [TaxId: 1423] [53365] (5)
    2. Transcription factor sc-mtTFB [69555]
      overall structure is very similar to those of Ermc' and Ermam
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69556] (1)
    3. High level kasugamycin resistance protein KsgA [110662]
      1. Escherichia coli [TaxId: 562] [110663] (1)
        SQ P06992
    4. Probable dimethyladenosine transferase [142575]
      1. Human (Homo sapiens) [TaxId: 9606] [142576] (2)
        SQ Q9UNQ2 36-313
  8. mRNA cap methylase [88785] (3)
    1. Polymerase regulatory subunit VP39 [53361]
      1. Vaccinia virus [TaxId: 10245] [53362] (19)
    2. An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5 [89741]
      structurally and functionally similar to VP39
      1. Flavivirus (Dengue virus type 2) [TaxId: 12637] [89742] (3)
        SQ P12823 2495-2756
      2. Dengue virus 2 [TaxId: 11060] [159679] (5)
  9. mRNA cap (Guanine N-7) methyltransferase [102560] (1)
    mRNA capping enzyme
    1. mRNA cap (Guanine N-7) methyltransferase [102561]
      1. Fungus (Encephalitozoon cuniculi) [TaxId: 6035] [102562] (7)
  10. Hypothetical protein MJ0882 [53345] (1)
    1. Hypothetical protein MJ0882 [53346]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53347] (1)
  11. Hypothetical protein HI0319 (YecO) [69544] (1)
    1. Hypothetical protein HI0319 (YecO) [69545]
      1. Haemophilus influenzae [TaxId: 727] [69546] (1)
        structural genomics
  12. Glycine N-methyltransferase [53348] (3)
    1. Glycine N-methyltransferase [53349]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53350] (16)
      2. Human (Homo sapiens) [TaxId: 9606] [110664] (1)
        SQ Q14749
      3. Mouse (Mus musculus) [TaxId: 10090] [110665] (2)
        SQ Q9QXF8
  13. Arylamine N-methyltransferase [69547] (2)
    1. Phenylethanolamine N-methyltransferase, PNMTase [69548]
      1. Human (Homo sapiens) [TaxId: 9606] [69549] (21)
    2. Indolethylamine N-methyltransferase, INMT [142577]
      1. Human (Homo sapiens) [TaxId: 9606] [142578] (1)
        SQ O95050 5-261
  14. Histamine methyltransferase [75261] (1)
    1. Histamine methyltransferase [75262]
      1. Human (Homo sapiens) [TaxId: 9606] [75263] (12)
  15. Hypothetical Protein YjhP [82469] (1)
    1. Hypothetical Protein YjhP [82470]
      1. Escherichia coli [TaxId: 562] [82471] (1)
  16. Salicylic acid carboxyl methyltransferase (SAMT) [102563] (1)
    1. Salicylic acid carboxyl methyltransferase (SAMT) [102564]
      1. Clarkia breweri [TaxId: 36903] [102565] (1)
  17. Thiopurine S-methyltransferase [102566] (2)
    1. Thiopurine S-methyltransferase [102567]
      1. Pseudomonas syringae [TaxId: 317] [102568] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [142579] (3)
        SQ P51580 17-245
  18. Leucine carboxy methyltransferase Ppm1 [102569] (1)
    1. Leucine carboxy methyltransferase Ppm1 [102570]
      involved in the regulation of protein phosphatase 2a activity
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102571] (7)
  19. Precorrin-6Y methyltransferase (CbiT) [82472] (1)
    1. Precorrin-6Y methyltransferase (CbiT) [82473]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [82474] (5)
        MTH146
  20. MraW-like putative methyltransferases [82475] (2)
    1. TM0872, methyltransferase domain [82476]
      contains an inserted alpha helical subdomain
      1. Thermotoga maritima [TaxId: 2336] [82477] (2)
      2. Thermus thermophilus [TaxId: 274] [117678] (1)
        SQ Q5SJD8
  21. N5-glutamine methyltransferase, HemK [89743] (2)
    1. N5-glutamine methyltransferase, HemK [89744]
      contains an N-terminal alpha helical subdomain; res. 13-84
      1. Thermotoga maritima [TaxId: 2336] [89745] (5)
        SQ Q9WYV8
      2. Escherichia coli [TaxId: 562] [110666] (2)
        SQ P37186
  22. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89746] (2)
    1. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89747]
      a non-SET domain nucleosomal histone methyltransferase
      1. Human (Homo sapiens) [TaxId: 9606] [89748] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110667] (1)
        SQ Q04089 176-581
  23. Guanidinoacetate methyltransferase [69550] (2)
    1. Guanidinoacetate methyltransferase [69551]
      a template structure of protein arginine methyltransferase
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69552] (5)
        SQ P10868
      2. Human (Homo sapiens) [TaxId: 9606] [142580] (3)
        SQ Q14353 8-236
  24. Arginine methyltransferase [53351] (4)
    lacks the last two strands of the common fold replaced with a beta-sandwich oligomerisation subdomain
    1. Arginine methyltransferase, HMT1 [53352]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53353] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [64116] (1)
    2. Protein arginine N-methyltransferase 1, PRMT1 [89749]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89750] (3)
    3. Protein arginine N-methyltransferase 3, PRMT3 [142581]
      1. Human (Homo sapiens) [TaxId: 9606] [142582] (1)
        SQ O60678 221-531
  25. Protein-L-isoaspartyl O-methyltransferase [53354] (5)
    topological variant; strand order 3214567; strand 6 is antiparallel to the rest
    1. Protein-L-isoaspartyl O-methyltransferase [68927]
      1. Thermotoga maritima [TaxId: 2336] [68928] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [69553] (4)
      3. Human (Homo sapiens) [TaxId: 9606] [69554] (2)
      4. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102572] (1)
      5. Sulfolobus tokodaii [TaxId: 111955] [110668] (1)
        SQ Q972K9
  26. Glucose-inhibited division protein B (GidB) [75264] (2)
    1. Glucose-inhibited division protein B (GidB) [75265]
      function unknown
      1. Escherichia coli [TaxId: 562] [75266] (1)
      2. Bacillus subtilis [TaxId: 1423] [117679] (1)
        SQ P25813
  27. tRNA(1-methyladenosine) methyltransferase-like [64117] (4)
    contains additional N-terminal beta-sandwich domain
    1. Probable methyltransferase Rv2118c [64118]
      1. Mycobacterium tuberculosis [TaxId: 1773] [64119] (1)
    2. Hypothetical protein TM0748 [102573]
      1. Thermotoga maritima [TaxId: 2336] [102574] (1)
    3. Hypothetical protein FLJ20628 [142583]
      1. Human (Homo sapiens) [TaxId: 9606] [142584] (2)
        SQ Q9BVS5 149-472
    4. Hypothetical protein Ta0852 [142585]
      forms dimer similar to half-tetramer of the other members but with swapped N-terminal domains; variant topology of the N-terminal domain
      1. Thermoplasma acidophilum [TaxId: 2303] [142586] (1)
        SQ Q9HJW1 6-255
  28. NOL1/NOP2/sun [102575] (3)
    Pfam 01189; contains additional N-terminal 3-helical and ferredoxin-like domains
    1. Hypothetical methyltransferase PH1374 [102576]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102577] (1)
    2. Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), C-terminal domain [110669]
      1. Escherichia coli [TaxId: 562] [110670] (2)
        SQ P36929
    3. NOL1R [142587]
      1. Human (Homo sapiens) [TaxId: 9606] [142588] (1)
        SQ Q96P11 133-425
  29. Ribosomal protein L11 methyltransferase PrmA [102578] (1)
    contains additional N-terminal ferredoxin-like domain
    1. PrmA-like protein TTHA0656 (TT0836) [102579]
      1. Thermus thermophilus [TaxId: 274] [102580] (12)
  30. (Uracil-5-)-methyltransferase [102581] (1)
    Pfam 05958
    1. rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain [102582]
      includes an iron-sulfur cluster-binding, alpha+beta sudbomain
      1. Escherichia coli [TaxId: 562] [102583] (3)
  31. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53357] (1)
    contains additional N-terminal all-alpha domain, res. 11-91
    1. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53358]
      1. Salmonella typhimurium [TaxId: 90371] [53359] (2)
  32. C5 cytosine-specific DNA methylase, DCM [88786] (3)
    1. DNA methylase HhaI [53367]
      1. Haemophilus haemolyticus [TaxId: 726] [53368] (20)
        SQ P05102
    2. DNA methylase HaeIII [53371]
      1. Haemophilus aegyptius [TaxId: 197575] [53372] (1)
    3. DNMT2 [53375]
      an enigmatic DNA methyltransferase homologue from mitochondria
      1. Human (Homo sapiens) [TaxId: 9606] [53376] (1)
  33. DNA methylase TaqI, N-terminal domain [88787] (1)
    1. DNA methylase TaqI, N-terminal domain [53369]
      1. Thermus aquaticus [TaxId: 271] [53370] (18)
  34. N6 adenine-specific DNA methylase, DAM [88788] (2)
    1. DNA methylase DpnM [53373]
      1. Streptococcus pneumoniae [TaxId: 1313] [53374] (1)
    2. DNA methylase T4DAM [102584]
      1. Bacteriophage T4 [TaxId: 10665] [102585] (14)
  35. Type II DNA methylase [53377] (3)
    circularly permuted version of the common fold
    1. m.PvuII N4 cytosine-specific DNA methyltransferase [53378]
      1. Proteus vulgaris [TaxId: 585] [53379] (1)
    2. m.RsrI N6 adenosine-specific DNA methyltransferase [53380]
      1. Rhodobacter sphaeroides [TaxId: 1063] [53381] (5)
    3. Methyltransferase mboII [75267]
      1. Moraxella bovis [TaxId: 476] [75268] (1)
  36. Spermidine synthase [69557] (7)
    contains additional N-terminal tetramerisation all-beta domain, res. 1-71
    1. Spermidine synthase [69558]
      polyamine aminopropyltransferase
      1. Thermus thermophilus [TaxId: 274] [102586] (1)
      2. Thermotoga maritima [TaxId: 2336] [69559] (2)
      3. Bacillus subtilis [TaxId: 1423] [82478] (1)
      4. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117680] (5)
        SQ Q9ZUB3
      5. Caenorhabditis elegans [TaxId: 6239] [142589] (2)
        SQ Q9U2F0 3-314
      6. Human (Homo sapiens) [TaxId: 9606] [142590] (8)
        SQ P19623 15-300
    2. Putative spermidine synthetase PF0127 (SpeE) [82479]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82480] (1)
  37. Mycolic acid cyclopropane synthase [69560] (6)
    1. CmaA1 [69561]
      1. Mycobacterium tuberculosis [TaxId: 1773] [69562] (3)
    2. CmaA2 [116723]
      1. Mycobacterium tuberculosis [TaxId: 1773] [116724] (1)
    3. PccA [75269]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75270] (1)
    4. Methoxy mycolic acid synthase 2, Mma2 [117681]
      1. Mycobacterium tuberculosis [TaxId: 1773] [117682] (1)
        SQ P72026 33-317
    5. Methoxy mycolic acid synthase 4, Mma4 [142591]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142592] (2)
        SQ Q79FX8 22-301
    6. Putative sarcosine dimethylglycine methyltransferase [159680]
      sequence similarity to other families with less structural similarity
      1. Red algae (Galdieria sulphuraria) [TaxId: 130081] [159681] (1)
  38. Ta1320-like [89751] (2)
    1. Hypothetical protein Ta1320 [89752]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89753] (1)
    2. Hypothetical protein PH1948 [142593]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142594] (4)
        SQ O59611 4-204
  39. UbiE/COQ5-like [110671] (5)
    Pfam 01209
    1. Hypothetical protein BH2331 [110672]
      1. Bacillus halodurans [TaxId: 86665] [110673] (1)
        SQ Q9KAF6
    2. Possible histamine N-methyltransferase TM1293 [110674]
      1. Thermotoga maritima [TaxId: 2336] [110675] (1)
        SQ Q9X119
    3. Hypothetical protein YcgJ [117683]
      1. Bacillus subtilis [TaxId: 1423] [117684] (3)
        SQ O31474
    4. Hypothetical methyltransferase TM1389 [142595]
      1. Thermotoga maritima [TaxId: 2336] [142596] (2)
        SQ Q9X1A9 1-246
    5. Hypothetical protein ECA1738 [159682]
      1. Erwinia carotovora [TaxId: 554] [159683] (6)
        SQ Q6D6E7 21-249
  40. AD-003 protein-like [117685] (2)
    Pfam 05891; DUF858
    1. Hypothetical protein Lmaj004091aaa (LmjF30.0810) [117686]
      1. Leishmania major [TaxId: 5664] [117687] (1)
        SQ Q4Q7M2
    2. Adrenal gland protein AD-003 (C9orf32) [142597]
      1. Human (Homo sapiens) [TaxId: 9606] [142598] (2)
        SQ Q9BV86 1-222
  41. CAC2371-like [117688] (3)
    similar overall fold to the Glycine N-methyltransferase (scop_fa 53348) and mRNA cap (Guanine N-7) methyltransferase (scop_fa 102560) families
    1. Putative methyltransferase CAC2371 [117689]
      1. Clostridium acetobutylicum [TaxId: 1488] [117690] (1)
        SQ Q97GJ5
    2. Hypothetical protein PH0226 [142599]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142600] (2)
        SQ O57965 2-227
    3. Hypothetical methyltransferase PH1305 [142601]
      the beta-sheet insertion makes trimerization subdomain
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142602] (3)
        SQ O59000 1-251
  42. TehB-like [142603] (1)
    Pfam 03848; overall structural similarity to Thiopurine S-methyltransferase (Pfam 05724)
    1. Putative methyltransferase TehB [142604]
      Tellurite resistance protein
      1. Salmonella typhimurium [TaxId: 90371] [142605] (2)
        SQ Q8ZPC3 1-198
        sequence similarity to Hypothetical methyltransferase PH1305 of the CAC2371-like family (scop_fa 117688)
  43. N-6 DNA Methylase-like [142606] (3)
    Pfam 02384; contains C-terminal extension to the canonical fold and extra N-terminal all-alpha domain similar to the insert domain of the DAM family (scop_fa 88788)
    1. Hypothetical protein Lmo1582 [142607]
      1. Listeria monocytogenes [TaxId: 1639] [142608] (1)
        SQ Q8Y6U9 2-329
    2. M.EcoKI [142609]
      contains extra C-terminal structured region
      1. Escherichia coli [TaxId: 562] [142610] (2)
        SQ P08957 4-527
    3. Type I restriction enzyme StySJI M protein [159684]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [159685] (2)
        SQ Q89Z59 9-433
  44. YhhF-like [142611] (5)
    Pfam 03602
    1. Putative methylase EF2452 [142612]
      1. Enterococcus faecalis [TaxId: 1351] [142613] (2)
        SQ Q831P8 1-182
    2. Methyltransferase TTHA0928 [142614]
      1. Thermus thermophilus [TaxId: 274] [142615] (1)
        SQ Q5SJT0 15-185
    3. Putative methylase HI0767 [142616]
      YhhF homologue
      1. Haemophilus influenzae [TaxId: 727] [142617] (1)
        SQ P44869 11-193
    4. Putative methyltransferase SPy1538 [142618]
      1. Streptococcus pyogenes [TaxId: 1314] [142619] (2)
        SQ Q99YU1 28-179
    5. Methylase YhhF [142620]
      1. Escherichia coli [TaxId: 562] [142621] (6)
        SQ P0ADX9 10-192
  45. Met-10+ protein-like [142622] (1)
    Pfam 02475; contains extra N-terminal alpha+beta domain: beta(2)-alpha-beta(2); mixed beta-sheet; order: 1234; cf scop_fold 102740
    1. Hypothetical protein PH0793 [142623]
      1. Pyrococcus horikoshii [TaxId: 53953] [142624] (1)
        SQ O58523 19-278
  46. Nsp15 N-terminal domain-like [142625] (2)
    rudiment methyltransferase fold that probably has lost the enzymatic activity; contains extra N-terminal alpha+beta subdomain
    1. Nsp15 [142626]
      1. Murine hepatitis virus, MHV [TaxId: 11138] [142627] (2)
        SQ P16342 6504-6697! SQ P16342 6697-6872
      2. SARS coronavirus [TaxId: 227859] [142628] (11)
        SQ Q6VA80 6619-6774
  47. BC2162-like [142629] (1)
    contains extra helical regions inserted after strands 5 and 6 of the canonical fold
    1. Methyltransferase BC2162 [142630]
      1. Bacillus cereus [TaxId: 1396] [142631] (2)
        SQ Q81E32 13-293
  48. CmcI-like [142632] (1)
    Pfam 04989; may have evolved different enzymatic activity
    1. Cephalosporin hydroxylase CmcI [142633]
      1. Streptomyces clavuligerus [TaxId: 1901] [142634] (34)
        SQ O85726 2-233
  49. hypothetical RNA methyltransferase [142635] (4)
    C-terminal part of Pfam 03602; similar to (Uracil-5-)-methyltransferase (Pfam 05958)
    1. Putative methyltransferase Atu0340 [142636]
      there is no associated PUA domain; rudiment extra N-terminal subdomain
      1. Agrobacterium tumefaciens [TaxId: 358] [142637] (3)
        SQ Q8UIF7 1-309
    2. Hypothetical protein TTHA1280, middle and C-terminal domains [142638]
      1. Thermus thermophilus [TaxId: 274] [142639] (10)
        SQ Q5SIT4 65-382
    3. Hypothetical protein SMu776, middle and C-terminal domains [142640]
      1. Streptococcus mutans [TaxId: 1309] [142641] (1)
        SQ Q8DUW5 69-385
    4. Hypothetical protein PH1915, middle and C-terminal domains [142642]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142643] (2)
        SQ O59578 73-396
  50. RPA4359-like [142644] (1)
    Pfam 02636; DUF185
    1. Hypothetical protein RPA4359 [142645]
      1. Rhodopseudomonas palustris [TaxId: 1076] [142646] (2)
        SQ Q6N1P6 2-366
  51. TrmB-like [142647] (2)
    Pfam 02390
    1. tRNA (guanine-N(7)-)-methyltransferase TrmB [142648]
      1. Streptococcus pneumoniae [TaxId: 1313] [142649] (2)
        SQ P67506 8-211
      2. Bacillus subtilis [TaxId: 1423] [142650] (2)
        SQ O34522 10-213
  52. Methyltransferase 10 domain [142651] (1)
    Pfam 05971; DUF890
    1. Methyltransferase 10 domain containing protein METT10D [142652]
      1. Human (Homo sapiens) [TaxId: 9606] [142653] (3)
        SQ Q86W50 42-291
  53. YhiQ-like [159686] (3)
    Pfam 04445; DUF548; contains extra N-terminal alpha+beta subdomain [beta-alpha-beta(4)]
    1. Hypothetical protein YhiQ [159687]
      1. Escherichia coli [TaxId: 562] [159688] (1)
        SQ P68568 1-250
      2. Salmonella typhimurium [TaxId: 90371] [159689] (1)
        SQ Q9X6G2 1-252
      3. Shigella flexneri [TaxId: 623] [159690] (1)
        SQ Q7UAV7 1-250
  54. FkbM-like [159691] (1)
    contains extra N-terminal alpha/beta and all-alpha subdomains
    1. Methyltransferase FkbM [159692]
      1. Methylobacillus flagellatus [TaxId: 405] [159693] (1)
        SQ Q1GXX6 14-408
  55. ML2640-like [159694] (1)
    Pfam 02409; O-methyltransferase N-terminus (DUF142); most similar structure to the Leucine carboxy methyltransferase Ppm1 family
    1. Putative methyltransferase ML2640 [159695]
      1. Mycobacterium leprae [TaxId: 1769] [159696] (4)
        SQ Q9CCZ4 8-310
  56. TRM1-like [159697] (1)
    Pfam 02005; contains extra C-terminal alpha+beta subdomain
    1. N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1 [159698]
      1. Pyrococcus horikoshii [TaxId: 53953] [159699] (5)
        SQ O59493 3-377
  57. LPG1296-like [159700] (1)
    Pfam 04378; DUF519
    1. Uncharacterized protein LPG1296 [159701]
      involved in catabolism of external DNA
      1. Legionella pneumophila [TaxId: 446] [159702] (1)
        SQ Q5ZVZ2 14-284
LmbE-like [102587] (1)
3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest; topological similarity to SAM-dependent methyltransferases
1. LmbE-like [102588] (1)
  uperfamily
  1. LmbE-like [102589] (2)
    putative deacetylases
    1. 1D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase MshD [102590]
      1. Mycobacterium tuberculosis [TaxId: 1773] [102591] (2)
        gene Rv1170
    2. Hypothetical protein TT1542 [102592]
      1. Thermus thermophilus [TaxId: 274] [102593] (1)
PLP-dependent transferase-like [53382] (3)
main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
1. PLP-dependent transferases [53383] (9)
  uperfamily
  1. AAT-like [53384] (28)
    1. Aspartate aminotransferase, AAT [53385]
      1. Chicken (Gallus gallus), mitochondria [TaxId: 9031] [53386] (15)
      2. Chicken (Gallus gallus), cytosolic form [TaxId: 9031] [53387] (3)
      3. Pig (Sus scrofa), cytosolic form [TaxId: 9823] [53388] (2)
      4. Baker's yeast (Saccharomyces cerevisiae), cytosolic form [TaxId: 4932] [53389] (1)
      5. Escherichia coli [TaxId: 562] [53390] (65)
        SQ P00509
      6. Thermus thermophilus [TaxId: 274] [53391] (9)
      7. Phormidium lapideum [TaxId: 32060] [82481] (1)
      8. Thermotoga maritima [TaxId: 2336] [89754] (1)
        TM1255
    2. Aromatic aminoacid aminotransferase, AroAT [53392]
      1. Paracoccus denitrificans [TaxId: 266] [53393] (12)
      2. Escherichia coli [TaxId: 562] [53394] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [64120] (3)
    3. Tyrosine aminotransferase (TAT) [53395]
      1. Trypanosoma cruzi [TaxId: 5693] [53396] (1)
    4. Histidinol-phosphate aminotransferase HisC [64121]
      1. Escherichia coli [TaxId: 562] [64122] (6)
      2. Thermotoga maritima [TaxId: 2336] [102594] (8)
        SQ Q9X0D0
        TM1040
    5. L-threonine-O-3-phosphate decarboxylase CobD [69563]
      1. Salmonella enterica [TaxId: 28901] [69564] (4)
    6. Low-specificity threonine aldolase [64123]
      1. Thermotoga maritima [TaxId: 2336] [64124] (8)
      2. Leishmania major [TaxId: 5664] [110676] (1)
        SQ O15839
    7. Alliinase [82482]
      cysteine sulphoxide lyase
      1. Garlic (Allium sativum) [TaxId: 4682] [82483] (6)
    8. Glutamine aminotransferase [110677]
      1. Thermus thermophilus [TaxId: 274] [110678] (3)
        SQ Q75WK2
    9. Putative methionine aminotransferase YdbL [110679]
      1. Escherichia coli [TaxId: 562] [110680] (1)
        SQ P77806
    10. Kynurenine--oxoglutarate transaminase I [110681]
      1. Human (Homo sapiens) [TaxId: 9606] [110682] (3)
        SQ Q16773
      2. Yellowfever mosquito (Aedes aegypti) [TaxId: 7159] [142654] (8)
        SQ Q95VY4 61-477
    11. Putative aminotransferase TM1131 [117691]
      1. Thermotoga maritima [TaxId: 2336] [117692] (1)
        SQ Q9X0L5
    12. Putative alanine aminotransferase [117693]
      1. Pyrococcus furiosus [TaxId: 2261] [117694] (1)
        SQ Q9P9M8
    13. Multiple substrate aminotransferase, MSAT [142655]
      1. Thermococcus profundus [TaxId: 49899] [142656] (1)
        SQ Q9V2W5 13-415
    14. Hypothetical aminotransferase PH0207 [142657]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142658] (1)
        SQ O57946 26-428
    15. Phenylserine aldolase PSALD [142659]
      most similar to the low-specificity threonine aldolase
      1. Pseudomonas putida [TaxId: 303] [142660] (1)
        SQ Q59IT3 7-351
    16. AAT homologue TM1698 [142661]
      1. Thermotoga maritima [TaxId: 2336] [142662] (6)
        SQ Q9X224 4-392
  2. Beta-eliminating lyases [53397] (4)
    1. Tyrosine phenol-lyase [53398]
      1. Citrobacter intermedius [TaxId: 66695] [53399] (2)
      2. Erwinia herbicola [TaxId: 549] [102595] (1)
    2. Tryptophan indol-lyase (tryptophanase) [53400]
      1. Proteus vulgaris [TaxId: 585] [53401] (1)
      2. Escherichia coli [TaxId: 562] [159703] (7)
        SQ P0A853 5-471! SQ Q8XB34 5-471
  3. Pyridoxal-dependent decarboxylase [69565] (3)
    1. DOPA decarboxylase [69566]
      1. Pig (Sus scrofa) [TaxId: 9823] [69567] (2)
    2. Glutamate decarboxylase beta, GadB [102596]
      1. Escherichia coli [TaxId: 562] [102597] (14)
    3. Glutamate decarboxylase alpha, GadA [117695]
      1. Escherichia coli [TaxId: 562] [117696] (1)
        SQ P69908
  4. Cystathionine synthase-like [53402] (24)
    1. Cystathionine beta-lyase, CBL [53403]
      1. Escherichia coli [TaxId: 562] [53404] (6)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [64125] (1)
    2. Cystathionine gamma-synthase, CGS [53405]
      1. Escherichia coli [TaxId: 562] [53406] (1)
      2. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [53407] (4)
    3. Cystathionine gamma-lyase (CYS3) [82484]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82485] (1)
    4. Methionine gamma-lyase, MGL [64126]
      1. Trichomonas vaginalis, MGL1 [TaxId: 5722] [64127] (2)
      2. Pseudomonas putida [TaxId: 303] [75271] (8)
        SQ P13254
      3. Trichomonas vaginalis, MGL2 [TaxId: 5722] [110683] (1)
        SQ O15565
      4. Citrobacter freundii [TaxId: 546] [142663] (1)
        SQ Q84AR1 2-398
    5. Modulator in mal gene expression, MalY [53408]
      1. Escherichia coli [TaxId: 562] [53409] (1)
    6. Cystalysin [53410]
      PLP-dependent haemolytic enzyme
      1. Treponema denticola [TaxId: 158] [53411] (2)
    7. NifS-like protein/selenocysteine lyase [53412]
      1. Thermotoga maritima [TaxId: 2336] [53413] (2)
      2. Escherichia coli [TaxId: 562] [53414] (5)
        gene product CsdB
    8. Cysteine desulfurase IscS [89755]
      1. Escherichia coli [TaxId: 562] [89756] (1)
    9. Alanine-glyoxylate aminotransferase [89757]
      1. Human (Homo sapiens) [TaxId: 9606] [89758] (2)
      2. Cyanobacteria (Nostoc sp. pcc 7120) [TaxId: 103690] [102598] (1)
        alr1004
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142664] (1)
        SQ P43567 3-384
    10. Subgroup IV putative aspartate aminotransferase [102599]
      1. Thermus thermophilus [TaxId: 274] [102600] (1)
    11. Kynureninase [102601]
      1. Pseudomonas fluorescens [TaxId: 294] [102602] (1)
    12. 2-aminoethylphosphonate transaminase [82486]
      1. Salmonella typhimurium [TaxId: 90371] [82487] (1)
    13. Cystine C-S lyase C-des [53415]
      1. Synechocystis sp. [TaxId: 1143] [53416] (4)
    14. Probable cysteine desulfurase SufS [110684]
      1. Synechocystis sp. PCC 6803 [TaxId: 1148] [110685] (1)
        SQ Q55793 # slr0077
    15. O-acetyl-L-homoserine sulfhydrylase [142665]
      1. Thermus thermophilus [TaxId: 274] [142666] (2)
        SQ Q93I77 1-421
    16. 3-hydroxykynurenine transaminase [142667]
      1. Malaria mosquito (Anopheles gambiae) [TaxId: 7165] [142668] (8)
        SQ Q4LAM2 2-389
  5. GABA-aminotransferase-like [53417] (27)
    formerly omega-Aminoacid:pyruvate aminotransferase-like
    1. Dialkylglycine decarboxylase [53418]
      1. Pseudomonas cepacia [TaxId: 292] [53419] (16)
    2. Glutamate-1-semialdehyde aminomutase (aminotransferase) [53420]
      1. Synechococcus sp., strain GR6 [TaxId: 1131] [53421] (3)
      2. Synechococcus elongatus [TaxId: 32046] [142669] (1)
        SQ Q8DLK8 45-437
    3. Ornithine aminotransferase [53422]
      1. Human (Homo sapiens) [TaxId: 9606] [53423] (10)
      2. Plasmodium yoelii yoelii [TaxId: 73239] [142670] (6)
        SQ Q7RT90 7-410
    4. 4-aminobutyrate aminotransferase, GABA-aminotransferase [53424]
      1. Pig (Sus scrofa) [TaxId: 9823] [53425] (3)
      2. Escherichia coli [TaxId: 562] [110686] (14)
        SQ P22256
    5. Phosphoserine aminotransferase, PSAT [53426]
      1. Bacillus circulans, subsp. alkalophilus [TaxId: 1397] [53427] (4)
        SQ Q59196
      2. Escherichia coli [TaxId: 562] [53428] (2)
      3. Bacillus alcalophilus [TaxId: 1445] [117697] (19)
        SQ Q9RME2
    6. Serine hydroxymethyltransferase [53429]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53430] (6)
        SQ P07511
      2. Mouse (Mus musculus) [TaxId: 10090] [53431] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [53432] (1)
      4. Escherichia coli [TaxId: 562] [53433] (2)
      5. Bacillus stearothermophilus [TaxId: 1422] [75272] (7)
      6. Human (Homo sapiens), mitochondrial [TaxId: 9606] [142671] (1)
        SQ P34897 42-504
    7. 3-amino-5-hydroxybenzoic acid synthase (AHBA synthase) [53434]
      1. Amycolatopsis mediterranei [TaxId: 33910] [53435] (2)
    8. Aminotransferase ArnB [82488]
      4-amino-4-deoxy-L-arabinose liposaccharide modifying enzyme
      1. Salmonella typhimurium [TaxId: 90371] [82489] (3)
    9. 2-amino-3-ketobutyrate CoA ligase [64128]
      1. Escherichia coli [TaxId: 562] [64129] (1)
    10. PLP-dependent acyl-CoA synthase (8-amino-7-oxonanoate synthase, AONS) [53436]
      1. Escherichia coli [TaxId: 562] [53437] (4)
    11. Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA [53438]
      synonym: 7,8-diaminopelargonic acid synthase
      1. Escherichia coli [TaxId: 562] [53439] (11)
    12. 1-aminocyclopropane-1-carboxylate synthase (ACC synthase) [53440]
      1. Apple (Malus domestica) [TaxId: 3750] [53441] (4)
      2. Tomato (Lycopersicon esculentum) [TaxId: 4081] [64130] (2)
    13. Aminotransferase homolog WlaK (PglE, Cj1121c) [102603]
      1. Campylobacter jejuni [TaxId: 197] [102604] (3)
    14. Spore coat polysaccharide biosynthesis protein C [142672]
      1. Helicobacter pylori [TaxId: 210] [142673] (6)
        SQ O25130 2-372
    15. Acetylornithine/acetyl-lysine aminotransferase ArgD [142674]
      1. Thermus thermophilus [TaxId: 274] [142675] (6)
        SQ Q93R93 9-395
    16. 5-aminolevulinate synthase [142676]
      1. Rhodobacter capsulatus [TaxId: 1061] [142677] (12)
        SQ P18079 2-397
  6. Ornithine decarboxylase major domain [53444] (1)
    1. Ornithine decarboxylase major domain [53445]
      1. Lactobacillus sp., strain 30a [TaxId: 1591] [53446] (2)
  7. Glycine dehydrogenase subunits (GDC-P) [142678] (2)
    Pfam 02347
    1. Glycine dehydrogenase (decarboxylating) subunit 1 [142679]
      1. Thermus thermophilus [TaxId: 274] [142680] (10)
        SQ Q5SKW8 1-437
    2. Glycine dehydrogenase subunit 2 (P-protein) [142681]
      1. Thermus thermophilus [TaxId: 274] [142682] (10)
        SQ Q5SKW7 2-472
  8. SelA-like [142683] (1)
    Pfam 03841
    1. Hypothetical protein MJ0158 [142684]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [142685] (2)
        SQ Q57622 9-374
  9. SepSecS-like [159704] (3)
    Pfam 05889
    1. Selenocysteinyl-tRNA synthase (SepSecS) [159705]
      1. Mouse (Mus musculus) [TaxId: 10090] [159706] (3)
        SQ Q6P6M7 23-467
      2. Archaeoglobus fulgidus [TaxId: 2234] [159707] (4)
        SQ O30207 8-371
      3. Methanococcus maripaludis [TaxId: 39152] [159708] (4)
        SQ Q6LZM9 1-434
2. PhnH-like [159709] (1)
  single domain protein of similar topology to the core domain of PLP-transferases
  1. PhnH-like [159710] (1)
    Pfam 05845; Bacterial phosphonate metabolism protein (PhnH)
    1. Phosphonate metabolism protein PhnH [159711]
      1. Escherichia coli [TaxId: 562] [159712] (1)
        SQ P16686 12-194
3. Dhaf3308-like [159713] (1)
  not known to bind PLP cofactor; the extra N-terminal subdomain has a enolase N-terminal domain-like fold (scop_cf 54825)
  1. Dhaf3308-like [159714] (1)
    Pfam 04016; DUF364
    1. Hypothetical protein Dhaf_3308 [159715]
      1. Desulfitobacterium hafniense [TaxId: 49338] [159716] (2)
        SQ Q18YZ7 1-251
Nucleotide-diphospho-sugar transferases [53447] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
1. Nucleotide-diphospho-sugar transferases [53448] (19)
  uperfamily
  1. Spore coat polysaccharide biosynthesis protein SpsA [53449] (1)
    1. Spore coat polysaccharide biosynthesis protein SpsA [53450]
      1. Bacillus subtilis [TaxId: 1423] [53451] (5)
  2. beta 1,4 galactosyltransferase (b4GalT1) [53452] (1)
    1. beta 1,4 galactosyltransferase (b4GalT1) [53453]
      1. Cow (Bos taurus) [TaxId: 9913] [53454] (22)
        SQ P08037 131-402
  3. Galactosyltransferase LgtC [53458] (1)
    1. Galactosyltransferase LgtC [53459]
      1. Neisseria meningitidis [TaxId: 487] [53460] (3)
        SQ Q93EK7
  4. Glycogenin [75273] (1)
    1. Glycogenin [75274]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [75275] (10)
  5. alpha-1,3-galactosyltransferase-like [64131] (3)
    1. alpha-1,3-galactosyltransferase catalytic domain [64132]
      1. Cow (Bos taurus) [TaxId: 9913] [64133] (23)
        SQ P14769
    2. Glycosyltransferase A catalytic domain [75276]
      involved in blood group antigen biosynthesis
      1. Human (Homo sapiens) [TaxId: 9606] [75277] (19)
        SQ P16442 64-345
    3. Glycosyltransferase B [75278]
      involved in blood group antigen biosynthesis
      1. Human (Homo sapiens) [TaxId: 9606] [75279] (18)
  6. UDP-glucose pyrophosphorylase [53461] (6)
    1. N-acetylglucosamine 1-phosphate uridyltransferase GlmU, N-terminal domain [53462]
      1. Escherichia coli [TaxId: 562] [53463] (9)
      2. Streptococcus pneumoniae [TaxId: 1313] [64134] (5)
    2. UDP-N-acetylglucosamine pyrophosphorylase [75280]
      1. Human (Homo sapiens), AGX1 [TaxId: 9606] [75281] (2)
      2. Human (Homo sapiens), AGX2 [TaxId: 9606] [82490] (2)
      3. Mouse (Mus musculus), AGX2 [TaxId: 10090] [117698] (1)
        SQ Q91YN5
    3. UDP-glucose pyrophosphorylase 2 (UDPGP 2) [142686]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142687] (8)
        SQ Q9M9P3 6-383
  7. glucose-1-phosphate thymidylyltransferase [53464] (6)
    1. RmlA (RfbA) [53465]
      1. Pseudomonas aeruginosa [TaxId: 287] [53466] (7)
      2. Salmonella enterica [TaxId: 28901] [64135] (5)
      3. Escherichia coli [TaxId: 562] [69568] (3)
      4. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89759] (1)
    2. RffH [82491]
      1. Escherichia coli [TaxId: 562] [82492] (1)
    3. Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain [142688]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [142689] (12)
        SQ P23509 80-386
  8. 1,3-glucuronyltransferase [53467] (2)
    1. 1,3-Glucuronyltransferase I (glcAT-I) [53468]
      1. Human (Homo sapiens) [TaxId: 9606] [53469] (4)
    2. Beta-1,3-glucuronyltransferase 1, GlcAT-P [110687]
      1. Human (Homo sapiens) [TaxId: 9606] [110688] (3)
        SQ Q9P2W7
  9. N-acetylglucosaminyltransferase I [64136] (1)
    1. N-acetylglucosaminyltransferase I [64137]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [64138] (7)
  10. Exostosin [89760] (1)
    1. Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2) [89761]
      1. Mouse (Mus musculus) [TaxId: 10090] [89762] (4)
  11. Molybdenum cofactor biosynthesis protein MobA [53470] (1)
    1. Molybdenum cofactor biosynthesis protein MobA [53471]
      1. Escherichia coli [TaxId: 562] [53472] (8)
  12. Cytidylytransferase [68901] (12)
    1. 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) [64140]
      1. Escherichia coli [TaxId: 562] [64141] (6)
      2. Neisseria gonorrhoeae [TaxId: 485] [102605] (2)
      3. Thermotoga maritima [TaxId: 2336] [117699] (1)
        SQ Q9X1B3
      4. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142690] (1)
        SQ P69834 75-300
    2. CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase [64143]
      1. Escherichia coli, KpsU [TaxId: 562] [64144] (8)
        capsule-specific enzyme
      2. Escherichia coli, KdsB [TaxId: 562] [102606] (1)
      3. Haemophilus influenzae [TaxId: 727] [102607] (2)
    3. CTP:phosphocholine cytidylytransferase LicC [69569]
      1. Streptococcus pneumoniae [TaxId: 1313] [69570] (2)
    4. CMP acylneuraminate synthetase [53456]
      a sialic acid activating synthetase
      1. Neisseria meningitidis [TaxId: 487] [53457] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [102608] (1)
    5. Glucose-1-phosphate cytidylyltransferase RfbF [110689]
      1. Salmonella typhimurium [TaxId: 90371] [110690] (2)
        SQ P26396 2-257
    6. IspD/IspF bifunctional enzyme, CDP-me synthase domain [117700]
      1. Campylobacter jejuni [TaxId: 197] [117701] (2)
        SQ Q9PM68
  13. Glycolipid 2-alpha-mannosyltransferase [102609] (1)
    1. Glycolipid 2-alpha-mannosyltransferase [102610]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102611] (3)
  14. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117702] (1)
    1. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117703]
      1. Mouse (Mus musculus) [TaxId: 10090] [117704] (1)
        SQ O08912
  15. MGS-like [142691] (1)
    contains extra C-terminal all-alpha subdomain: 5 helices, orthogonal array
    1. Mannosylglycerate synthase, MGS [142692]
      1. Rhodothermus marinus [TaxId: 29549] [142693] (28)
        SQ Q9RFR0 2-382
  16. TTHA0179-like [159717] (1)
    1. Uncharacterized protein TTHA0179 [159718]
      1. Thermus thermophilus [TaxId: 274] [159719] (1)
        SQ Q5SLW4 1-231
  17. mannose-1-phosphate guanylyl transferase [159720] (1)
    1. Putative mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase TTHA1750 [159721]
      1. Thermus thermophilus [TaxId: 274] [159722] (1)
        SQ Q5SHI0 1-268
  18. MM2497-like [159723] (1)
    Pfam 01983; DUF121
    1. Hypothetical protein MM2497 [159724]
      1. Methanosarcina mazei [TaxId: 2209] [159725] (2)
        SQ Q8PU52 1-208
  19. Glycosylating toxin catalytic domain-like [159726] (3)
    contains Glycosyltransferase sugar-binding region containing DXD motif, Pfam 04488
    1. Cytotoxin L [159727]
      1. Clostridium sordellii [TaxId: 1505] [159728] (9)
        SQ Q46342 1-542
    2. Alpha-toxin [159729]
      1. Clostridium novyi [TaxId: 1542] [159730] (1)
        SQ Q46149 2-541
    3. Toxin B [159731]
      1. Clostridium difficile [TaxId: 1496] [159732] (2)
        SQ P18177 1-542
RibA-like [142694] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 1235467, strands 1 and 3 are antiparallel to the rest; partial topological similarity to some alpha/beta hydrolases (scop_cf 53473)
1. RibA-like [142695] (1)
  uperfamily
  1. RibA-like [142696] (1)
    Pfam 00925; GTP cyclohydrolase II
    1. GTP cyclohydrolase II, RibA [142697]
      1. Escherichia coli [TaxId: 562] [142698] (3)
        SQ P0A7I7 1-174
Activating enzymes of the ubiquitin-like proteins [69571] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
1. Activating enzymes of the ubiquitin-like proteins [69572] (2)
  transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins
  the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
  uperfamily
  1. Molybdenum cofactor biosynthesis protein MoeB [69573] (1)
    1. Molybdenum cofactor biosynthesis protein MoeB [69574]
      1. Escherichia coli [TaxId: 562] [69575] (3)
  2. Ubiquitin activating enzymes (UBA) [89763] (2)
    the common fold is elaborated with additional (sub)domains
    1. UBA3 [89764]
      a subunit of the heterodimeric E1 enzyme for NEDD8; contains an all-alpha insert subdomain of the FF-like fold (residues 210-288) and an extra C-terminal alpha+beta subdomain (partly disordered)
      1. Human (Homo sapiens) [TaxId: 9606] [89765] (11)
        SQ Q8TBC4 33-458
    2. Amyloid beta precursor protein-binding protein 1, APPBP1 [89766]
      a subunit of the heterodimeric E1 enzyme for NEDD8; contains a large insertion (residues 170-487) that can be divided into 3 units similar to the UBA3 insertion
      1. Human (Homo sapiens) [TaxId: 9606] [89767] (18)
        SQ Q13564
alpha/beta-Hydrolases [53473] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
1. alpha/beta-Hydrolases [53474] (41)
  many members have left-handed crossover connection between strand 8 and additional strand 9
  uperfamily
  1. Acetylcholinesterase-like [53475] (11)
    1. Acetylcholinesterase [53476]
      1. Pacific electric ray (Torpedo californica) [TaxId: 7787] [53477] (79)
        SQ P04058 25-556
      2. Electric eel (Electrophorus electricus) [TaxId: 8005] [53478] (3)
      3. Mouse (Mus musculus) [TaxId: 10090] [53479] (31)
      4. Human (Homo sapiens) [TaxId: 9606] [53480] (2)
      5. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [53481] (3)
    2. Butyryl cholinesterase [102612]
      1. Human (Homo sapiens) [TaxId: 9606] [102613] (9)
    3. Bile-salt activated lipase (cholesterol esterase) [53482]
      1. Cow (Bos taurus) [TaxId: 9913] [53483] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [53484] (2)
    4. Mammalian carboxylesterase (liver carboxylesterase I) [75282]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [75283] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [89768] (48)
    5. Thermophilic para-nitrobenzyl esterase (PNB esterase) [53485]
      1. Bacillus subtilis [TaxId: 1423] [53486] (3)
  2. Carboxylesterase [53487] (9)
    1. Carboxylesterase [53488]
      bacterial homologue of human hormone sensitive lipase
      1. Bacillus subtilis, brefeldin A esterase [TaxId: 1423] [53489] (1)
      2. Alicyclobacillus acidocaldarius [TaxId: 405212] [53490] (3)
        SQ Q7SIG1
      3. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69576] (1)
    2. Feruloyl esterase domain of the cellulosomal xylanase z [69577]
      1. Clostridium thermocellum [TaxId: 1515] [69578] (2)
    3. Feruloyl esterase domain of the cellulosomal xylanase y [69579]
      1. Clostridium thermocellum [TaxId: 1515] [69580] (8)
    4. Heroin esterase [82493]
      1. Rhodococcus sp. [TaxId: 1831] [82494] (2)
    5. Enterochelin esterase, catalytic domain [142699]
      1. Shigella flexneri [TaxId: 623] [142700] (1)
        SQ Q83SB9 151-397
      2. Shigella flexneri 2a str. 2457T [TaxId: 198215] [159733] (10)
    6. Uncharacterized protein TM1040_2492 [159734]
      1. Silicibacter sp. tm1040 [TaxId: 292414] [159735] (4)
        SQ Q1GDP2 1-261
  3. Mycobacterial antigens [53491] (4)
    1. Antigen 85b [53492]
      1. Mycobacterium tuberculosis [TaxId: 1773] [53493] (2)
    2. Antigen 85c [53494]
      1. Mycobacterium tuberculosis [TaxId: 1773] [53495] (3)
        SQ P31953
    3. Antigen pt51/mpb51 [102614]
      1. Mycobacterium tuberculosis [TaxId: 1773] [102615] (1)
    4. Antigen 85a [110691]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110692] (1)
        SQ P17944 43-330
  4. Hypothetical protein TT1662 [102616] (1)
    1. Hypothetical protein TT1662 [102617]
      1. Thermus thermophilus [TaxId: 274] [102618] (1)
  5. PepX catalytic domain-like [69581] (4)
    1. Bacterial cocaine esterase N-terminal domain [69582]
      1. Rhodococcus sp. mb1 [TaxId: 51612] [69583] (4)
    2. Alpha-amino acid ester hydrolase [89769]
      1. Xanthomonas citri [TaxId: 346] [89770] (1)
      2. Acetobacter pasteurianus [TaxId: 438] [102619] (29)
    3. X-Prolyl dipeptidyl aminopeptidase PepX, middle domain [82495]
      1. Lactococcus lactis [TaxId: 1358] [82496] (1)
  6. Prolyl oligopeptidase, C-terminal domain [53496] (1)
    N-terminal domain is a 7-bladed beta-propeller
    1. Prolyl oligopeptidase, C-terminal domain [53497]
      1. Pig (Sus scrofa) [TaxId: 9823] [53498] (16)
        SQ P23687
  7. DPP6 catalytic domain-like [82497] (3)
    N-terminal domain is a 8-bladed beta-propeller
    1. Dipeptidyl peptidase IV/CD26, C-terminal domain [82498]
      1. Human (Homo sapiens) [TaxId: 9606] [82499] (58)
        SQ P27487 39-776 ! SQ P27487 ! SQ P27487
      2. Pig (Sus scrofa) [TaxId: 9823] [89771] (76)
    2. Dipeptidyl aminopeptidase-like protein 6, DPP6, C-terminal domain [117705]
      1. Human (Homo sapiens) [TaxId: 9606] [117706] (1)
        SQ P42658 127-849
  8. Serine carboxypeptidase-like [53499] (5)
    1. Serine carboxypeptidase II [53500]
      1. Wheat (Triticum vulgare) [TaxId: 4565] [53501] (5)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53502] (3)
      3. Baker's yeast (Saccharomyces cerevisiae), kex1(delta)p [TaxId: 4932] [53503] (1)
        prohormone-processing carboxypeptidase
    2. Human 'protective protein', HPP [53504]
      synonyms: cathepsin A, carboxypeptidase L
      1. Human (Homo sapiens) [TaxId: 9606] [53505] (1)
    3. Hydroxynitrile lyase [82500]
      a novel cyanogenic enzyme
      1. Sorghum (Sorghum bicolor) [TaxId: 4558] [82501] (1)
  9. Gastric lipase [53506] (2)
    1. Gastric lipase [53507]
      1. Human (Homo sapiens) [TaxId: 9606] [53508] (1)
      2. Dog (Canis familiaris) [TaxId: 9615] [75284] (1)
  10. Proline iminopeptidase-like [53509] (3)
    1. Proline iminopeptidase [53510]
      1. Xanthomonas campestris, pv. citri [TaxId: 339] [53511] (1)
    2. Proline aminopeptidase [81303]
      1. Serratia marcescens [TaxId: 615] [81304] (4)
        SQ O32449
    3. Tricorn interacting factor F1 [82502]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [82503] (3)
  11. Acetyl xylan esterase-like [82504] (2)
    Pfam 05448; AXE1
    1. Cephalosporin C deacetylase [82505]
      1. Bacillus subtilis [TaxId: 1423] [82506] (3)
    2. Acetyl xylan esterase TM0077 [110693]
      1. Thermotoga maritima [TaxId: 2336] [110694] (1)
        SQ Q9WXT2
  12. Haloalkane dehalogenase [53513] (3)
    1. Haloalkane dehalogenase [53514]
      1. Xanthobacter autotrophicus [TaxId: 280] [53515] (17)
      2. Rhodococcus sp. [TaxId: 1831] [53516] (3)
      3. Sphingomonas paucimobilis, UT26, LinB [TaxId: 13689] [53517] (12)
  13. Dienelactone hydrolase [53518] (2)
    1. Dienelactone hydrolase [53519]
      1. Pseudomonas sp., B13 [TaxId: 306] [53520] (1)
      2. Pseudomonas putida [TaxId: 303] [53521] (1)
  14. Carbon-carbon bond hydrolase [53522] (4)
    closely related to the Proline iminopeptidase-like family
    1. 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (BPHD) [53523]
      1. Rhodococcus sp., strain rha1 [TaxId: 1831] [53524] (1)
      2. Burkholderia xenovorans [TaxId: 36873] [159736] (4)
        SQ P47229 4-286
    2. Meta-cleavage product hydrolase CumD [82507]
      2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
      1. Pseudomonas fluorescens [TaxId: 294] [82508] (9)
        SQ P96965 3-273
    3. Meta cleavage compound hydrolase CarC [89772]
      involved in carbazole degradation
      1. Janthinobacterium sp. J3 [TaxId: 213804] [89773] (1)
  15. Biotin biosynthesis protein BioH [82509] (1)
    1. Biotin biosynthesis protein BioH [82510]
      1. Escherichia coli [TaxId: 562] [82511] (1)
  16. Aclacinomycin methylesterase RdmC [102620] (1)
    1. Aclacinomycin methylesterase RdmC [102621]
      1. Streptomyces purpurascens [TaxId: 1924] [102622] (2)
  17. Carboxylesterase/lipase [102623] (1)
    1. Carboxylesterase Est [102624]
      1. Bacillus stearothermophilus [TaxId: 1422] [102625] (2)
        SQ Q06174
  18. Epoxide hydrolase [53525] (4)
    1. Mammalian epoxide hydrolase, C-terminal domain [53526]
      1. Mouse (Mus musculus) [TaxId: 10090] [53527] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [102626] (6)
    2. Bacterial epoxide hydrolase [53528]
      1. Agrobacterium radiobacter [TaxId: 358] [53529] (1)
      2. Aspergillus niger [TaxId: 5061] [53530] (1)
  19. Haloperoxidase [53531] (7)
    1. Bromoperoxidase A2 [53532]
      1. Streptomyces aureofaciens [TaxId: 1894] [53533] (2)
    2. Bromoperoxidase A1 [53534]
      1. Streptomyces aureofaciens [TaxId: 1894] [53535] (1)
    3. Chloroperoxidase T [53536]
      1. Streptomyces aureofaciens [TaxId: 1894] [53537] (2)
    4. Chloroperoxidase L [53538]
      1. Streptomyces lividans [TaxId: 1916] [53539] (1)
    5. Chloroperoxidase F [53540]
      1. Pseudomonas fluorescens [TaxId: 294] [53541] (1)
    6. Gamma-lactamase [102627]
      haloperoxidase homologue
      1. Aureobacterium sp. [TaxId: 51671] [102628] (2)
    7. Arylesterase [110695]
      haloperoxidase homologue
      1. Pseudomonas fluorescens [TaxId: 294] [110696] (1)
        SQ P22862
  20. Thioesterases [53542] (3)
    1. Myristoyl-ACP-specific thioesterase [53543]
      1. Vibrio harveyi [TaxId: 669] [53544] (1)
    2. Palmitoyl protein thioesterase 1 [53545]
      1. Cow (Bos taurus) [TaxId: 9913] [53546] (3)
    3. Palmitoyl protein thioesterase 2 [102629]
      1. Human (Homo sapiens) [TaxId: 9606] [102630] (1)
  21. Carboxylesterase/thioesterase 1 [53547] (5)
    1. Carboxylesterase [53548]
      1. Pseudomonas fluorescens [TaxId: 294] [53549] (2)
      2. Bacillus cereus [TaxId: 1396] [159737] (3)
        SQ Q81AD5 1-202
        similar fold and function to the Pseudomonas fluorescens enzyme despite low sequence identity
    2. Acyl protein thioesterase 1 [53550]
      1. Human (Homo sapiens) [TaxId: 9606] [53551] (1)
    3. Uncharacterized protein Mll8374 [159738]
      1. Mesorhizobium loti [TaxId: 381] [159739] (2)
        SQ Q983D6 7-215
    4. Uncharacterized protein Atu2452 [159740]
      1. Agrobacterium tumefaciens [TaxId: 358] [159741] (2)
        SQ A9CHT9 1-203
  22. Ccg1/TafII250-interacting factor B (Cib) [75285] (1)
    1. Ccg1/TafII250-interacting factor B (Cib) [75286]
      1. Human (Homo sapiens) [TaxId: 9606] [75287] (1)
  23. A novel bacterial esterase [53552] (1)
    1. A novel bacterial esterase [53553]
      1. Alcaligenes sp. [TaxId: 512] [53554] (1)
  24. Lipase [53555] (1)
    1. Lipase [53556]
      1. Streptomyces exfoliatus [TaxId: 1905] [53557] (1)
  25. Fungal lipases [53558] (12)
    1. Triacylglycerol lipase [53559]
      1. Yeast (Candida antarctica), form b [TaxId: 34362] [53560] (11)
      2. Rhizomucor miehei [TaxId: 4839] [53561] (4)
      3. Penicillium camembertii [TaxId: 5075] [53562] (1)
      4. Thermomyces lanuginosus, formerly Humicola lanuginosa [TaxId: 5541] [53563] (7)
      5. Rhizopus niveus [TaxId: 4844] [53564] (1)
      6. Rhizopus delemar [TaxId: 64495] [53565] (1)
    2. Feruloyl esterase A [102631]
      Triacylglycerol lipase homologue
      1. Aspergillus niger [TaxId: 5061] [102632] (7)
        SQ O42807 23-281
    3. Type-B carboxylesterase/lipase [53566]
      1. Fungus (Geotrichum candidum), ATCC 34614 [TaxId: 27317] [53567] (1)
      2. Fungus (Candida rugosa), formerly Cylindracea [TaxId: 5481] [53568] (7)
      3. Candida rugosa, lipase 2 isoform [TaxId: 5481] [89774] (1)
      4. Candida cylindracea, cholesterol esterase [TaxId: 44322] [53569] (2)
    4. Esterase EstA [110697]
      1. Aspergillus niger [TaxId: 5061] [110698] (1)
        SQ Q6ED33
  26. Bacterial lipase [53570] (7)
    lack the first two strands of the common fold
    1. Lipase A [64145]
      minimal alpha/beta hydrolase fold;
      1. Bacillus subtilis [TaxId: 1423] [64146] (16)
        SQ P37957 34-212
    2. Lipase [53571]
      1. Pseudomonas glumae, also known as Pseudomonas gladioli [TaxId: 337] [53572] (2)
      2. Burkholderia cepacia, formerly Pseudomonas cepacia [TaxId: 292] [63399] (7)
      3. Pseudomonas aeruginosa [TaxId: 287] [53575] (1)
      4. Chromobacterium viscosum [TaxId: 42739] [53576] (3)
    3. Lipase L1 [75288]
      1. Bacillus stearothermophilus [TaxId: 1422] [75289] (1)
      2. Bacillus stearothermophilus, P1 [TaxId: 1422] [82512] (1)
        the first thermostable bacterial lipase
  27. Pancreatic lipase, N-terminal domain [53577] (6)
    1. Pancreatic lipase, N-terminal domain [53578]
      contains additional, colipase-binding domain
      1. Horse (Equus caballus) [TaxId: 9796] [53579] (1)
      2. Pig (Sus scrofa) [TaxId: 9823] [53580] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [53581] (3)
      4. Guinea pig (Cavia porcellus) [TaxId: 10141] [53582] (1)
      5. Dog (Canis familiaris) [TaxId: 9615] [53583] (1)
        pancreatic lipase related protein 1
      6. Rat (Rattus norvegicus) [TaxId: 10116] [53584] (1)
        pancreatic lipase related protein 2
  28. Hydroxynitrile lyase-like [53585] (3)
    1. Hydroxynitrile lyase [53586]
      1. Rubber tree (Hevea brasiliensis) [TaxId: 3981] [53587] (19)
        SQ P52704
      2. Cassava (Manihot esculenta) [TaxId: 3983] [53588] (7)
    2. Salicylic acid-binding protein 2 (SABP2) [117707]
      1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [117708] (3)
        SQ Q6RYA0
  29. Thioesterase domain of polypeptide, polyketide and fatty acid synthases [69584] (4)
    Pfam 00975
    1. Erythromycin polyketide synthase [69585]
      synonym: 6-deoxyerythronolide synthase
      1. Saccharopolyspora erythraea [TaxId: 1836] [69586] (2)
    2. Picromycin polyketide synthase [82513]
      1. Streptomyces venezuelae [TaxId: 54571] [82514] (9)
    3. Surfactin synthetase, SrfA [75290]
      1. Bacillus subtilis [TaxId: 1423] [75291] (1)
    4. Fatty acid synthase [117709]
      1. Human (Homo sapiens) [TaxId: 9606] [117710] (1)
        SQ P49327 2212-2496
  30. Cutinase-like [52260] (3)
    minimal alpha/beta hydrolase lacking peripheral secondary structures; similar to a flavodoxin-like fold
    1. Cutinase [52261]
      1. Fungus (Fusarium solani), subsp. pisi [TaxId: 169388] [52262] (39)
    2. Acetylxylan esterase [52263]
      1. Penicillium purpurogenum [TaxId: 28575] [52264] (3)
      2. Trichoderma reesei [TaxId: 51453] [52265] (1)
  31. YdeN-like [110699] (1)
    Pfam 06821; DUF1234; lack the first two strands of the common fold
    1. Hypothetical protein YdeN [110700]
      1. Bacillus subtilis [TaxId: 1423] [110701] (1)
        SQ P96671
  32. Putative serine hydrolase Ydr428c [110702] (1)
    1. Putative serine hydrolase Ydr428c [110703]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110704] (1)
        SQ Q04066
  33. Acylamino-acid-releasing enzyme, C-terminal donain [117711] (1)
    closely related to the prolyl peptidase and DPP6 domains (scop_fa 53496 and 82497)
    1. Acylamino-acid-releasing enzyme, C-terminal donain [117712]
      1. Aeropyrum pernix [TaxId: 56636] [117713] (12)
        SQ Q9YBQ2
  34. Hypothetical esterase YJL068C [117714] (1)
    part of Pfam 00756
    1. Hypothetical esterase YJL068C [117715]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117716] (1)
        SQ P40363
  35. Hypothetical protein VC1974 [117717] (1)
    1. Hypothetical protein VC1974 [117718]
      1. Vibrio cholerae [TaxId: 666] [117719] (1)
        SQ Q9KQM4
  36. Atu1826-like [159742] (2)
    1. XC6422 protein [159743]
      XCC0260 orthologue
      1. Xanthomonas campestris [TaxId: 339] [159744] (1)
        SQ Q8PDS5 3-220
    2. Hypothetical protein Atu1826 [159745]
      1. Agrobacterium tumefaciens [TaxId: 358] [159746] (2)
        SQ Q8UED4 2-219
  37. PHB depolymerase-like [159747] (1)
    1. Polyhydroxybutyrate depolymerase [159748]
      1. Penicillium funiculosum [TaxId: 28572] [159749] (2)
  38. IroE-like [159750] (1)
    1. Enterobactin and salmochelin hydrolase IroE [159751]
      1. Escherichia coli [TaxId: 562] [159752] (2)
        SQ Q6KD95 41-305
  39. TTHA1544-like [159753] (1)
    minimal hydrolase fold (one strand less than the cutinase-like family); there is neither catalytic triad, nor nucleopilic residue in the elbow motif
    1. Hypothetical protein TTHA1544 [159754]
      1. Thermus thermophilus [TaxId: 274] [159755] (2)
        SQ Q5SI36 2-123
  40. O-acetyltransferase [159756] (3)
    1. Acetyl-CoA:deacetylcephalosporin C acetyltransferase CefG [159757]
      1. Acremonium chrysogenum [TaxId: 5044] [159758] (36)
        SQ P39058 66-441
    2. Homoserine O-acetyltransferase [159759]
      1. Leptospira interrogans [TaxId: 173] [159760] (1)
        SQ Q8F4I0 5-366
      2. Haemophilus influenzae [TaxId: 727] [159761] (1)
        SQ P45131 2-358
  41. 2,6-dihydropseudooxynicotine hydrolase-like [159762] (1)
    Pfam 06500; DUF1100
    1. 2,6-dihydropseudooxynicotine hydrolase [159763]
      1. Arthrobacter nicotinovorans [TaxId: 29320] [159764] (1)
        SQ Q93NG6 8-367
Nucleoside hydrolase [53589] (1)
core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
1. Nucleoside hydrolase [53590] (1)
  uperfamily
  1. Nucleoside hydrolase [53591] (4)
    1. Inosine-uridine nucleoside N-ribohydrolase, IU-NH [53592]
      1. Crithidia fasciculata [TaxId: 5656] [53593] (2)
    2. Nucleoside hydrolase [53594]
      1. Leishmania major [TaxId: 5664] [53595] (1)
    3. Inosine-adenosine-guanosine preferring nucleoside hydrolase [69587]
      1. Trypanosoma vivax [TaxId: 5699] [69588] (9)
    4. Pyrimidine nucleoside hydrolase YeiK [102633]
      1. Escherichia coli [TaxId: 562] [102634] (5)
Dihydrofolate reductase-like [53596] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
1. Dihydrofolate reductase-like [53597] (2)
  uperfamily
  1. Dihydrofolate reductases [53598] (12)
    1. Dihydrofolate reductase, prokaryotic type [53599]
      1. Escherichia coli [TaxId: 562] [53600] (46)
      2. Lactobacillus casei [TaxId: 1582] [53601] (8)
      3. Mycobacterium tuberculosis [TaxId: 1773] [53602] (4)
      4. Thermotoga maritima [TaxId: 2336] [53603] (2)
      5. Haloferax volcanii [TaxId: 2246] [53604] (1)
      6. Bacteriophage T4 [TaxId: 10665] [102635] (1)
    2. Dihydrofolate reductases, eukaryotic type [53605]
      1. Chicken (Gallus gallus) [TaxId: 9031] [53606] (8)
      2. Human (Homo sapiens) [TaxId: 9606] [53607] (27)
      3. Fungus (Pneumocystis carinii) [TaxId: 4754] [53608] (14)
      4. Yeast (Candida albicans) [TaxId: 5476] [53609] (9)
    3. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, DFR domain [53610]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [88963] (3)
      2. Cryptosporidium hominis [TaxId: 237895] [102636] (7)
        SQ Q5CGA3 Q27552
  2. RibD C-terminal domain-like [142701] (3)
    Pfam 01872
    1. Riboflavin biosynthesis protein RibD [142702]
      1. Bacillus subtilis [TaxId: 1423] [142703] (8)
        SQ P17618 146-359
      2. Thermotoga maritima [TaxId: 2336] [142704] (1)
        SQ Q9X2E8 148-345
    2. HTP reductase [142705]
      monofunctional 5-amino-6-(5-phosphoribosylamino)uracil reductase
      1. Methanococcus jannaschii [TaxId: 2190] [142706] (6)
        SQ Q58085 6-224
Ribokinase-like [53612] (3)
core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
potential superfamily: members of this fold have similar functions but different ATP-binding sites
1. Ribokinase-like [53613] (5)
  has extra strand located between strands 2 and 3
  uperfamily
  1. Thiamin biosynthesis kinases [53620] (4)
    1. Hydroxyethylthiazole kinase (THZ kinase, ThiK) [53621]
      1. Bacillus subtilis [TaxId: 1423] [53622] (5)
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102637] (1)
    2. 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) [69589]
      1. Salmonella typhimurium [TaxId: 90371] [69590] (2)
      2. Thermus thermophilus [TaxId: 274] [89775] (1)
  2. YjeF C-terminal domain-like [75292] (2)
    1. Hypothetical protein YxkO [75293]
      1. Bacillus subtilis [TaxId: 1423] [75294] (1)
    2. Hypothetical protein TM0922, C-terminal domain [142707]
      YjeF homolog
      1. Thermotoga maritima [TaxId: 2336] [142708] (1)
        SQ Q9X024 212-489
  3. PfkB-like kinase [82515] (2)
    includes a variety of carbohydrate and pyrimidine kinases
    1. Pyridoxal kinase [82516]
      1. Sheep (Ovis aries) [TaxId: 9940] [82517] (8)
    2. Pyridoxamine kinase [102638]
      1. Escherichia coli [TaxId: 562] [102639] (2)
        SQ P77150
  4. Ribokinase-like [53614] (13)
    1. Ribokinase [53615]
      1. Escherichia coli [TaxId: 562] [53616] (5)
      2. Thermotoga maritima [TaxId: 2336] [110706] (1)
        SQ Q9X055
      3. Human (Homo sapiens) [TaxId: 9606] [142709] (2)
        SQ Q9H477 15-322
    2. 2-keto-3-deoxygluconate kinase [75295]
      1. Thermotoga maritima, TM0067 [TaxId: 2336] [75296] (2)
      2. Thermus thermophilus [TaxId: 274] [102640] (4)
    3. Hypothetical protein TM0415 [102641]
      1. Thermotoga maritima [TaxId: 2336] [102642] (1)
    4. Putative sugar kinase TM0828 [82518]
      1. Thermotoga maritima [TaxId: 2336] [82519] (2)
    5. Adenosine kinase [53617]
      1. Human (Homo sapiens) [TaxId: 9606] [53618] (5)
      2. Toxoplasma gondii [TaxId: 5811] [53619] (10)
    6. Aminoimidazole riboside kinase [117720]
      1. Salmonella typhimurium [TaxId: 90371] [117721] (3)
        SQ Q8ZKR2
    7. Tagatose-6-phosphate kinase LacC [142710]
      1. Enterococcus faecalis [TaxId: 1351] [142711] (4)
        SQ Q833W9 1-313
    8. Fructose 1-phosphate kinase FruB [142712]
      1. Bacillus halodurans [TaxId: 86665] [142713] (2)
        SQ Q9KEM5 1-306
    9. Hypothetical fructokinase ST2478 [142714]
      1. Sulfolobus tokodaii [TaxId: 111955] [142715] (18)
        SQ Q96XN9 2-309
  5. ADP-specific Phosphofructokinase/Glucokinase [64147] (3)
    Pfam 04587
    1. ADP-dependent glucokinase [64148]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [64149] (2)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102643] (1)
    2. ADP-specific phosphofructokinase [110707]
      1. Pyrococcus horikoshii [TaxId: 53953] [110708] (1)
        SQ O59355 # PH1645
2. MurD-like peptide ligases, catalytic domain [53623] (2)
  has extra strand located between strands 1 and 2
  uperfamily
  1. MurCDEF [53624] (5)
    1. UDP-N-acetylmuramate-alanine ligase MurC [82520]
      1. Thermotoga maritima [TaxId: 2336] [82521] (1)
        TM0231
      2. Haemophilus influenzae [TaxId: 727] [89776] (4)
    2. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD [53625]
      1. Escherichia coli [TaxId: 562] [53626] (11)
    3. UDP-N-acetylmuramyl tripeptide synthetase MurE [64150]
      1. Escherichia coli [TaxId: 562] [64151] (1)
    4. UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF [53627]
      1. Escherichia coli [TaxId: 562] [53628] (1)
  2. Folylpolyglutamate synthetase [53629] (2)
    1. Folylpolyglutamate synthetase [53630]
      1. Lactobacillus casei [TaxId: 1582] [53631] (7)
      2. Thermotoga maritima [TaxId: 2336] [102644] (1)
        TM0166
3. CoaB-like [102645] (1)
  combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest
  uperfamily
  1. CoaB-like [102646] (2)
    Pfam 04127
    1. Phosphopantothenoylcysteine synthetase [102647]
      1. Human (Homo sapiens) [TaxId: 9606] [102648] (1)
    2. Coenzyme A biosynthesis bifunctional protein CoaBC, phosphopantothenoylcysteine synthase domain (CoaB) [117722]
      1. Escherichia coli [TaxId: 562] [117723] (4)
        SQ P24285 181-404
YjeF N-terminal domain-like [64152] (1)
3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest
1. YjeF N-terminal domain-like [64153] (1)
  possible circular permutation of the ribokinase-like fold (of the YjeF C-terminal domain)
  uperfamily
  1. YjeF N-terminal domain-like [64154] (2)
    1. Hypothetical protein YNL200c (YNU0_YEAST) [64155]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64156] (1)
    2. Hypothetical protein TM0922, N-terminal domain [142716]
      YjeF homolog
      1. Thermotoga maritima [TaxId: 2336] [142717] (1)
        SQ Q9X024 1-211
Carbamate kinase-like [53632] (1)
3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
1. Carbamate kinase-like [53633] (3)
  the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase
  uperfamily
  1. Carbamate kinase [53634] (2)
    1. Carbamate kinase [53635]
      1. Enterococcus faecium [TaxId: 1352] [53636] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [53637] (1)
  2. N-acetyl-l-glutamate kinase [75297] (4)
    1. N-acetyl-l-glutamate kinase [75298]
      1. Escherichia coli [TaxId: 562] [75299] (5)
      2. Pseudomonas aeruginosa [TaxId: 287] [142718] (12)
        SQ Q9HTN2 1-300
      3. Mycobacterium tuberculosis [TaxId: 1773] [142719] (6)
        SQ P0A4Y6 4-294
      4. Thermotoga maritima [TaxId: 2336] [142720] (3)
        SQ Q9X2A4 1-282
  3. PyrH-like [142721] (10)
    part of Pfam 00696
    1. Glutamate 5-kinase [142722]
      1. Campylobacter jejuni [TaxId: 197] [142723] (4)
        SQ Q9PJ29 2-251
    2. Aspartokinase [142724]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142725] (2)
        SQ Q9LYU8 84-387
      2. Methanococcus jannaschii [TaxId: 2190] [142726] (4)
        SQ Q57991 2-303
      3. Escherichia coli [TaxId: 562] [142727] (3)
        SQ P08660 3-294
        Lysine-sensitive aspartokinase 3
    3. Uridylate kinase PyrH [142728]
      1. Streptococcus pyogenes [TaxId: 1314] [142729] (3)
        SQ P65938 2-239
      2. Escherichia coli [TaxId: 562] [142730] (12)
        SQ P0A7E9 4-240
      3. Pyrococcus furiosus [TaxId: 2261] [142731] (6)
        SQ Q8U122 1-225
      4. Archaeoglobus fulgidus [TaxId: 2234] [142732] (2)
        SQ O28237 1-219
      5. Haemophilus influenzae [TaxId: 727] [142733] (6)
        SQ P43890 2-237
      6. Neisseria meningitidis [TaxId: 487] [142734] (3)
        SQ P65932 4-239
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64157] (1)
core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest
1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64158] (1)
  uperfamily
  1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64159] (1)
    1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64160]
      1. Bacillus stearothermophilus [TaxId: 1422] [64161] (4)
Alkaline phosphatase-like [53648] (1)
core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
1. Alkaline phosphatase-like [53649] (5)
  uperfamily
  1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64162] (1)
    1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64163]
      1. Bacillus stearothermophilus [TaxId: 1422] [64164] (4)
  2. Alkaline phosphatase [53650] (3)
    common fold is decorated with several large insertions
    1. Alkaline phosphatase [53651]
      1. Escherichia coli [TaxId: 562] [53652] (33)
      2. Human (Homo sapiens) [TaxId: 9606] [64165] (5)
      3. Northern shrimp (Pandalus borealis) [TaxId: 6703] [75300] (3)
        SQ Q9BHT8 # fragment
  3. Arylsulfatase [53653] (4)
    includes additional C-terminal alpha+beta (sub)domain
    1. Arylsulfatase A [53654]
      1. Human (Homo sapiens) [TaxId: 9606] [53655] (7)
    2. Arylsulfatase B (4-sulfatase) [53656]
      1. Human (Homo sapiens) [TaxId: 9606] [53657] (1)
      2. Pseudomonas aeruginosa [TaxId: 287] [69591] (1)
    3. Steryl-sulfatase [102649]
      contains membrane-anchoring alpha-hairpin insertion
      1. Human (Homo sapiens) [TaxId: 9606] [102650] (1)
        placental estrone/DHEA sulfatase
  4. Phosphonoacetate hydrolase [102651] (1)
    contains alpha+beta subdomain inserted near C-terminus
    1. Phosphonoacetate hydrolase [102652]
      1. Pseudomonas fluorescens [TaxId: 294] [102653] (1)
  5. DeoB catalytic domain-like [142735] (1)
    Pfam 08342 in the N-terminal part; Pfam 01676 in the C-terminal part; there is an alpha+beta domain between the two parts, inserted in the same location as the substrate-binding domain of 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
    1. Phosphopentomutase DeoB [142736]
      1. Streptococcus mutans [TaxId: 1309] [142737] (2)
        SQ Q8DTU0 2-107,227-403
TTHA0583/YokD-like [110709] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 78612354; strands 3, 4 and 8 are antiparallel to the rest
1. TTHA0583/YokD-like [110710] (2)
  uperfamily
  1. Hypothetical protein TT1679 [110711] (1)
    Pfam 04260, DUF436
    1. Hypothetical protein TT1679 [110712]
      UPF0340 protein TTHA0583
      1. Thermus thermophilus [TaxId: 274] [110713] (1)
        SQ P68591
  2. Aminoglycoside 3-N-acetyltransferase-like [159765] (1)
    Pfam 02522; CoA-dependent enzymes
    1. Uncharacterized protein YokD [159766]
      1. Bacillus subtilis [TaxId: 1423] [159767] (3)
        SQ O32003 2-271
Glycerol-3-phosphate (1)-acyltransferase [69592] (1)
3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8 are antiparallel to the rest
1. Glycerol-3-phosphate (1)-acyltransferase [69593] (1)
  some topological similarity to the dihydrofolate reductase fold
  uperfamily
  1. Glycerol-3-phosphate (1)-acyltransferase [69594] (1)
    1. Glycerol-3-phosphate (1)-acyltransferase [69595]
      1. Cushaw squash (Cucurbita moschata) [TaxId: 3662] [69596] (2)
AraD/HMP-PK domain-like [53638] (1)
3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
1. AraD/HMP-PK domain-like [53639] (2)
  uperfamily
  1. AraD-like aldolase/epimerase [53640] (4)
    metal (zinc)-ion dependent
    1. L-fuculose-1-phosphate aldolase [53641]
      class II aldolase
      1. Escherichia coli [TaxId: 562] [53642] (17)
    2. L-ribulose-5-phosphate 4-epimerase [69597]
      1. Escherichia coli [TaxId: 562] [69598] (2)
    3. L-rhamnulose-1-phosphate aldolase [75301]
      1. Escherichia coli [TaxId: 562] [75302] (2)
    4. Putative sugar-phosphate aldolase [102654]
      1. Thermotoga maritima [TaxId: 2336] [102655] (1)
  2. Phosphomethylpyrimidine kinase C-terminal domain-like [159768] (2)
    1. Phosphomethylpyrimidine kinase [159769]
      1. Pyrococcus furiosus [TaxId: 2261] [159770] (2)
        SQ Q8U193 268-451
    2. Uncharacterized protein MJ0236 [159771]
      1. Methanocaldococcus jannaschii [TaxId: 2190] [159772] (4)
        SQ Q57688 241-420
SurE-like [64166] (1)
3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7
1. SurE-like [64167] (1)
  some topological similarity to the N-terminal domain of Glutaminase/Asparaginase family
  uperfamily
  1. SurE-like [64168] (2)
    1. SurE homolog TM1662 [64169]
      has a phosphatase activity
      1. Thermotoga maritima [TaxId: 2336] [64170] (4)
    2. SurE homolog PAE2908 (SurE-alpha) [82522]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [82523] (1)
YerB-like [159773] (1)
3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4
1. YerB-like [159774] (1)
  1. YerB-like [159775] (1)
    PfamB 028118
    1. Uncharacterized protein YerB [159776]
      1. Bacillus subtilis [TaxId: 1423] [159777] (1)
        SQ O34968 32-327
CdCA1 repeat-like [159778] (1)
contains two parallel beta-strands of four strands each; the sheets contact each other with edges at a right angle
1. CdCA1 repeat-like [159779] (1)
  1. CdCA1 repeat-like [159780] (1)
    Pfam 10563
    1. Cadmium-specific carbonic anhydrase CdCA1 [159781]
      1. Thalassiosira weissflogii [TaxId: 67004] [159782] (6)
        SQ Q50EL4 1-196! SQ Q50EL4 198-406
Isocitrate/Isopropylmalate dehydrogenase-like [53658] (1)
consists of two intertwined (sub)domains related by pseudo dyad; duplication
3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
1. Isocitrate/Isopropylmalate dehydrogenase-like [53659] (5)
  the constituent families form similar dimers
  uperfamily
  1. Dimeric isocitrate & isopropylmalate dehydrogenases [53660] (13)
    the active site is between the two identical subunits
    1. 3-isopropylmalate dehydrogenase, IPMDH [53661]
      1. Thermus thermophilus [TaxId: 274] [53662] (14)
      2. Chimera (Thermus thermophilus) and (Bacillus subtilis) [TaxId: 274] [53663] (2)
      3. Bacillus coagulans [TaxId: 1398] [53664] (3)
      4. Thiobacillus ferrooxidans [TaxId: 920] [53665] (1)
      5. Salmonella typhimurium [TaxId: 90371] [53666] (1)
      6. Escherichia coli [TaxId: 562] [53667] (1)
      7. Thermotoga maritima [TaxId: 2336] [110714] (1)
        SQ Q9WZ26
      8. Sulfolobus tokodaii [TaxId: 111955] [117724] (1)
        SQ P50455
      9. Mycobacterium tuberculosis [TaxId: 1773] [117725] (5)
        SQ P95313
    2. Isocitrate dehydrogenase, ICDH [53668]
      1. Escherichia coli [TaxId: 562] [53669] (26)
      2. Bacillus subtilis [TaxId: 1423] [64171] (1)
    3. NADP-dependent isocitrate dehydrogenase [82524]
      1. Pig (Sus scrofa) [TaxId: 9823] [82525] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [110715] (2)
        SQ O75874
  2. PdxA-like [102656] (2)
    Pfam 04166; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PlsX-like and phosphotransacetylase families
    1. 4-hydroxythreonine-4-phosphate dehydrogenase PdxA [102657]
      pyridoxal phosphate biosynthetic protein
      1. Escherichia coli [TaxId: 562] [102658] (3)
      2. Salmonella typhimurium [TaxId: 90371] [102659] (1)
  3. PlsX-like [102660] (2)
    Pfam 02504; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and phosphotransacetylase families
    1. Fatty acid/phospholipid synthesis protein PlsX [102661]
      1. Bacillus subtilis [TaxId: 1423] [102662] (1)
      2. Enterococcus faecalis [TaxId: 1351] [110716] (1)
        SQ Q82ZE8
  4. Phosphotransacetylase [102663] (4)
    Pfam 01515; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and PlsX-like families
    1. Phosphotransacetylase Pta [110717]
      1. Methanosarcina thermophila [TaxId: 2210] [110718] (5)
        SQ P38503
      2. Streptococcus pyogenes [TaxId: 1314] [102665] (1)
      3. Bacillus subtilis [TaxId: 1423] [117726] (2)
        SQ P39646
    2. Ethanolamine utilization protein EutD [117727]
      1. Escherichia coli [TaxId: 562] [117728] (1)
        SQ P77218 2-323
  5. Monomeric isocitrate dehydrogenase [82526] (1)
    the active site is contained within one subunit between the canonical ICDH fold and a large insert domain that itself is a probable rudiment form of ICDH fold resulted from duplication, domain swapping and deletion
    1. Monomeric isocitrate dehydrogenase [82527]
      1. Azotobacter vinelandii [TaxId: 354] [82528] (1)
        the insert region spans residues 150-404
Amidase signature (AS) enzymes [75303] (1)
possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest
1. Amidase signature (AS) enzymes [75304] (1)
  uperfamily
  1. Amidase signature (AS) enzymes [75305] (5)
    1. Malonamidase E2 [75306]
      1. Bradyrhizobium japonicum [TaxId: 375] [75307] (12)
    2. Peptide amidase Pam [82529]
      1. Stenotrophomonas maltophilia [TaxId: 40324] [82530] (2)
    3. Fatty acid amide hydrolase (oleamide hydrolase) [82531]
      elaborated fold with additional helices
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82532] (1)
    4. Glutamyl-tRNA(Gln) amidotransferase subunit A [142738]
      1. Staphylococcus aureus [TaxId: 1280] [142739] (5)
        SQ P63488 1-485
      2. Thermotoga maritima [TaxId: 2336] [142740] (1)
        SQ Q9X0Z9 1-475
ATC-like [53670] (2)
consists of two similar domains related by pseudo dyad; duplication
core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
1. Aspartate/ornithine carbamoyltransferase [53671] (1)
  uperfamily
  1. Aspartate/ornithine carbamoyltransferase [53672] (11)
    1. Aspartate carbamoyltransferase catalytic subunit [53673]
      1. Escherichia coli [TaxId: 562] [53674] (94)
        SQ P00479
      2. Bacillus subtilis [TaxId: 1423] [53675] (1)
      3. Archaeon Pyrococcus abyssi [TaxId: 29292] [82533] (1)
      4. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [110719] (3)
        SQ Q55338
    2. Ornithine transcarbamoylase [53676]
      1. Pseudomonas aeruginosa [TaxId: 287] [53677] (2)
      2. Escherichia coli [TaxId: 562] [53678] (3)
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53679] (2)
      4. Human (Homo sapiens) [TaxId: 9606] [53680] (4)
      5. Sheep (Ovis aries) [TaxId: 9940] [102666] (1)
      6. Thermotoga maritima [TaxId: 2336] [110720] (1)
        SQ P96108
    3. Transcarbamylase-like protein [75308]
      1. Bacteroides fragilis [TaxId: 817] [75309] (25)
2. Aspartate/glutamate racemase [53681] (1)
  uperfamily
  1. Aspartate/glutamate racemase [53682] (3)
    C-terminal extension is added to the N-terminal domain
    1. Glutamate racemase [53683]
      1. Aquifex pyrophilus [TaxId: 2714] [53684] (2)
    2. Aspartate racemase [75310]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75311] (2)
      2. Pyrococcus horikoshii OT3 [TaxId: 70601] [159783] (2)
Tryptophan synthase beta subunit-like PLP-dependent enzymes [53685] (1)
consists of two similar domains related by pseudo dyad; duplication
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53686] (1)
  uperfamily
  1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53687] (22)
    1. Tryptophan synthase, beta-subunit [53688]
      1. Salmonella typhimurium [TaxId: 90371] [53689] (47)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [142741] (10)
        SQ Q8U093 1-386
    2. O-acetylserine sulfhydrylase (Cysteine synthase) [53690]
      1. Salmonella typhimurium [TaxId: 90371] [53691] (3)
      2. Thermotoga maritima [TaxId: 2336] [75312] (1)
        TM0665
      3. Archaeon Aeropyrum pernix [TaxId: 56636] [142742] (2)
        SQ Q9YBL2 1-382
      4. Thermus thermophilus [TaxId: 274] [142743] (5)
        SQ Q5SLE6 1-302
      5. Escherichia coli, isoform B (CysM) [TaxId: 562] [142744] (8)
        SQ P16703 2-293
      6. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142745] (2)
        SQ P47998 3-322
      7. Haemophilus influenzae [TaxId: 727] [142746] (1)
        SQ P45040 2-311
    3. Threonine deaminase [53692]
      1. Escherichia coli [TaxId: 562] [53693] (1)
      2. Thermus thermophilus [TaxId: 274] [142747] (4)
        SQ Q5SLL4 2-311
    4. Threonine synthase [64172]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [64173] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75313] (1)
      3. Thermus thermophilus [TaxId: 274] [102667] (3)
      4. Escherichia coli [TaxId: 562] [142748] (1)
        SQ P00934 1-428
    5. L-serine dehydratase [102668]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [102669] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [110721] (1)
        SQ P20132
    6. 1-aminocyclopropane-1-carboxylate deaminase [53694]
      1. Yeast (Hansenula saturnus) [TaxId: 4906] [53695] (4)
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [89777] (2)
      3. Pseudomonas sp., strain ACP [TaxId: 306] [110722] (6)
        SQ Q00740
    7. Cystathionine beta-synthase [64174]
      PLP-dependent hemoprotein
      1. Human (Homo sapiens) [TaxId: 9606] [64175] (2)
    8. Hypothetical protein C320.14 (SPCC320.14, SPCC330.15c) [142749]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [142750] (2)
        SQ O59791 6-323
SIS domain [53696] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
1. SIS domain [53697] (3)
  uperfamily
  1. mono-SIS domain [69599] (8)
    dimer of mono-domain subunits
    1. Probable 3-hexulose-6-phosphate isomerase MJ1247 [69600]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [69601] (1)
    2. Hypothetical protein YckF [82534]
      1. Bacillus subtilis [TaxId: 1423] [82535] (2)
    3. Hypothetical protein HI0754 [89778]
      1. Haemophilus influenzae [TaxId: 727] [89779] (1)
    4. Hypothetical protein AF1796 [102670]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102671] (1)
    5. Phosphoheptose isomerase GmhA1 [110723]
      1. Campylobacter jejuni [TaxId: 197] [110724] (1)
        SQ Q9PNE6
      2. Vibrio cholerae [TaxId: 666] [110725] (1)
        SQ Q9KPY2
      3. Pseudomonas aeruginosa [TaxId: 287] [117729] (1)
        SQ Q9HVZ0
      4. Pseudomonas aeruginosa str. PAO1 (Pseudomonas aeruginosa PAO1) [TaxId: 208964] [159784] (4)
  2. double-SIS domain [53698] (4)
    duplication: consists of two SIS domains related by pseudo dyad
    1. Hypothetical protein TM0813 [75314]
      1. Thermotoga maritima [TaxId: 2336] [75315] (1)
    2. "Isomerase domain" of glucosamine 6-phosphate synthase (GLMS) [53699]
      1. Escherichia coli [TaxId: 562] [53700] (11)
    3. Glucose-6-phosphate isomerase, conjectural [110726]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [110727] (4)
        SQ Q8ZWV0
    4. Glucose-6-phosphate isomerase-like protein TTHA1346 [117730]
      1. Thermus thermophilus [TaxId: 274] [117731] (1)
        SQ Q5SIM3
  3. Phosphoglucose isomerase, PGI [53701] (6)
    permutation of the double-SIS domain fold
    1. Phosphoglucose isomerase, PGI [53702]
      moonlights as neuroleukin, autocrine motility factor, and differentiation mediator
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53703] (8)
      2. Human (Homo sapiens) [TaxId: 9606] [64176] (5)
      3. Pig (Sus scrofa) [TaxId: 9823] [75316] (2)
      4. Bacillus stearothermophilus [TaxId: 1422] [53704] (4)
      5. Leishmania mexicana [TaxId: 5665] [110728] (2)
        SQ P42861
      6. Mouse (Mus musculus) [TaxId: 10090] [117732] (3)
        SQ P06745
Formate dehydrogenase/DMSO reductase, domains 1-3 [53705] (1)
contains of two similar intertwined domains related by pseudo dyad; duplication
core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53706] (1)
  molybdopterine enzyme
  uperfamily
  1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53707] (12)
    domain 1 (residues 1-55) binds Fe4S4 cluster in FDH but not DMSO reductase
    1. Dimethylsulfoxide reductase (DMSO reductase) [53708]
      1. Rhodobacter sphaeroides [TaxId: 1063] [53709] (1)
      2. Rhodobacter capsulatus [TaxId: 1061] [53710] (10)
    2. Formate dehydrogenase H [53711]
      1. Escherichia coli [TaxId: 562] [53712] (4)
    3. Formate dehydrogenase N, alpha subunit [75317]
      1. Escherichia coli [TaxId: 562] [75318] (2)
    4. Tungsten containing formate dehydrogenase, large subunit [82536]
      1. Desulfovibrio gigas [TaxId: 879] [82537] (1)
    5. Trimethylamine N-oxide reductase [53713]
      1. Shewanella massilia [TaxId: 76854] [53714] (1)
    6. Arsenite oxidase large subunit [53715]
      1. Alcaligenes faecalis [TaxId: 511] [53716] (2)
    7. Periplasmic nitrate reductase alpha chain [53717]
      1. Desulfovibrio desulfuricans [TaxId: 876] [53718] (8)
        dissimilatory nitrate reductase (NAP)
      2. Rhodobacter sphaeroides [TaxId: 1063] [102672] (1)
    8. Respiratory nitrate reductase 1 alpha chain [102673]
      1. Escherichia coli [TaxId: 562] [102674] (7)
        SQ P09152
    9. Transhydroxylase alpha subunit, AthL [110729]
      1. Pelobacter acidigallici [TaxId: 35816] [110730] (6)
        SQ P80563
    10. NADH-quinone oxidoreductase chain 3, Nqo3 [142751]
      1. Thermus thermophilus [TaxId: 274] [142752] (4)
        SQ Q56223 247-685
ALDH-like [53719] (1)
consists of two similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
1. ALDH-like [53720] (2)
  binds NAD differently from other NAD(P)-dependent oxidoreductases
  uperfamily
  1. ALDH-like [53721] (14)
    1. Aldehyde reductase (dehydrogenase), ALDH [53722]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53723] (1)
      2. Rat (Rattus norvegicus), retinal type II [TaxId: 10116] [53724] (1)
      3. Cow (Bos taurus), mitochondrial [TaxId: 9913] [53725] (2)
      4. Human (Homo sapiens), mitochondrial [TaxId: 9606] [53726] (17)
        SQ P05091
      5. Sheep (Ovis aries) [TaxId: 9940] [53727] (1)
      6. Elephant shrew (Elephantulus edwardii) [TaxId: 28737] [89780] (1)
        cytosolic form; eta-crystallin
      7. Baltic cod (Gadus callarias) [TaxId: 8053] [53728] (2)
      8. Streptococcus mutans [TaxId: 1309] [53729] (4)
      9. Vibrio harveyi [TaxId: 669] [53730] (2)
    2. Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN [82538]
      1. Archaeon Thermoproteus tenax [TaxId: 2271] [82539] (8)
        SQ O57693
    3. Gamma-glutamyl phosphate reductase [89781]
      1. Thermotoga maritima [TaxId: 2336] [89782] (1)
        TM0293
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110731] (1)
        SQ P54885
    4. 1-pyrroline-5-carboxylate dehydrogenase [102675]
      1. Thermus thermophilus [TaxId: 274] [102676] (3)
    5. Putative betaine aldehyde dehydrogenase YdcW [117733]
      1. Escherichia coli [TaxId: 562] [117734] (2)
        SQ P77674
  2. L-histidinol dehydrogenase HisD [69602] (1)
    1. L-histidinol dehydrogenase HisD [69603]
      1. Escherichia coli [TaxId: 562] [69604] (4)
NadA-like [142753] (1)
duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134
1. NadA-like [142754] (1)
  uperfamily
  1. NadA-like [142755] (1)
    Pfam 02445
    1. Quinolinate synthetase A, NadA [142756]
      1. Pyrococcus horikoshii [TaxId: 53953] [142757] (1)
        SQ O57767 1-298
Aconitase iron-sulfur domain [53731] (1)
consists of three similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
1. Aconitase iron-sulfur domain [53732] (1)
  uperfamily
  1. Aconitase iron-sulfur domain [53733] (4)
    duplication: consists of three structurally similar subdomains with subdomains 1 and 3 being related by pseudo twofold symmetry
    1. Aconitase A, N-terminal domain [53734]
      1. Pig (Sus scrofa) [TaxId: 9823] [53735] (6)
      2. Cow (Bos taurus) [TaxId: 9913] [53736] (9)
    2. Aconitase B, C-terminal domain [75319]
      1. Escherichia coli [TaxId: 562] [75320] (1)
    3. Iron-responsive element binding protein 1, N-terminal domain [142758]
      1. Human (Homo sapiens) [TaxId: 9606] [142759] (3)
        SQ P21399 2-630
Phosphoglucomutase, first 3 domains [53737] (1)
consists of three similar domains with 3 layers (a/b/a) each; duplication
core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
1. Phosphoglucomutase, first 3 domains [53738] (1)
  uperfamily
  1. Phosphoglucomutase, first 3 domains [53739] (3)
    1. Phosphoglucomutase [53740]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53741] (6)
    2. Exocytosis-sensitive phosphoprotein, pp63/parafusin [69605]
      1. Paramecium tetraurelia [TaxId: 5888] [69606] (2)
    3. Phosphomannomutase/phosphoglucomutase [69607]
      1. Pseudomonas aeruginosa [TaxId: 287] [69608] (24)
FucI/AraA N-terminal and middle domains [53742] (1)
consists of two domains of similar topology, 3 layers (a/b/a) each
Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
1. FucI/AraA N-terminal and middle domains [53743] (2)
  uperfamily
  1. L-fucose isomerase, N-terminal and second domains [53744] (1)
    1. L-fucose isomerase, N-terminal and second domains [53745]
      1. Escherichia coli [TaxId: 562] [53746] (1)
  2. AraA N-terminal and middle domain-like [142760] (1)
    N-terminal part of Pfam 02610
    1. L-arabinose isomerase AraA [142761]
      1. Escherichia coli [TaxId: 562] [142762] (6)
        SQ P08202 1-328
YgbK-like [142763] (1)
consists of two domains with partial topological similarity to the P-loop kinases but without the P-loop motif; the domain association results in the formation of a single mixed beta-sheet of 15 strands
1. YgbK-like [142764] (1)
  uperfamily
  1. YgbK-like [142765] (1)
    Pfam 07005; DUF1537; the B-fam model-covered region is non-compact in structure and distributed between the two domains
    1. Hypothetical protein HI1011 [142766]
      1. Haemophilus influenzae [TaxId: 727] [142767] (2)
        SQ P44093 2-413
Phosphoglycerate kinase [53747] (1)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has parallel beta-sheet of 6 strands, order 342156
Domain 2 has parallel beta-sheet of 6 strands, order 321456
1. Phosphoglycerate kinase [53748] (1)
  uperfamily
  1. Phosphoglycerate kinase [53749] (7)
    Domain 2 binds ATP
    1. Phosphoglycerate kinase [53750]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53751] (3)
      2. Bacillus stearothermophilus [TaxId: 1422] [53752] (1)
      3. Thermus thermophilus [TaxId: 274] [102677] (1)
      4. Thermotoga maritima [TaxId: 2336] [53753] (1)
      5. Trypanosoma brucei [TaxId: 5691] [53754] (2)
      6. Pig (Sus scrofa) [TaxId: 9823] [64177] (4)
      7. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [89783] (1)
UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1)
consists of two non-similar domains with 3 layers (a/b/a) each
domain 1: parallel beta-sheet of 7 strands, order 3214567
domain 2: parallel beta-sheet of 6 strands, order 321456
1. UDP-Glycosyltransferase/glycogen phosphorylase [53756] (11)
  uperfamily
  1. beta-Glucosyltransferase (DNA-modifying) [53757] (1)
    1. beta-Glucosyltransferase (DNA-modifying) [53758]
      1. Bacteriophage T4 [TaxId: 10665] [53759] (20)
        SQ P04547
  2. Peptidoglycan biosynthesis glycosyltransferase MurG [53760] (1)
    1. Peptidoglycan biosynthesis glycosyltransferase MurG [53761]
      UDP-N-acetylglucosamine:N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
      1. Escherichia coli [TaxId: 562] [53762] (2)
  3. UDP-N-acetylglucosamine 2-epimerase [53763] (3)
    1. UDP-N-acetylglucosamine 2-epimerase [53764]
      1. Escherichia coli [TaxId: 562] [53765] (2)
      2. Bacillus subtilis [TaxId: 1423] [102678] (1)
      3. Thermus thermophilus [TaxId: 274] [102679] (1)
  4. Gtf glycosyltransferase [64178] (3)
    Glycosyltransferase family 28
    1. UDP-glucosyltransferase GtfB [64179]
      1. Amycolatopsis orientalis [TaxId: 31958] [64180] (1)
    2. TDP-epi-vancosaminyltransferase GtfA [102680]
      1. Amycolatopsis orientalis [TaxId: 31958] [102681] (2)
    3. TDP-vancosaminyltransferase GftD [110732]
      1. Amycolatopsis orientalis [TaxId: 31958] [110733] (1)
        SQ Q9AFC7
  5. ADP-heptose LPS heptosyltransferase II [89784] (1)
    1. ADP-heptose LPS heptosyltransferase II [89785]
      1. Escherichia coli [TaxId: 562] [89786] (1)
  6. Trehalose-6-phosphate synthase, OtsA [82540] (1)
    family 20 glycosyltransferase; good structural similarity in the active site to the Oligosaccharide phosphorylases
    1. Trehalose-6-phosphate synthase, OtsA [82541]
      1. Escherichia coli [TaxId: 562] [82542] (3)
  7. Oligosaccharide phosphorylase [53766] (4)
    1. Glycogen phosphorylase [53767]
      both domains are elaborated with many insertions
      1. Human (Homo sapiens) [TaxId: 9606] [53768] (17)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53769] (106)
        SQ P00489 ! SQ P00489
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53770] (1)
    2. Maltodextrin phosphorylase (MALP) [53771]
      1. Escherichia coli [TaxId: 562] [53772] (15)
  8. Glycosyl transferases group 1 [110734] (4)
    Pfam 00534
    1. Glycogen synthase 1, GlgA [110735]
      1. Agrobacterium tumefaciens [TaxId: 358] [110736] (2)
        SQ P39670
      2. Pyrococcus abyssi [TaxId: 29292] [142768] (4)
        SQ Q9V2J8 1-437! SQ Q9V2J8 218-413
    2. First mannosyl transferase WbaZ [142769]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142770] (1)
        SQ O30192 173-338
    3. Lipopolysaccharide core biosynthesis protein RfaG [142771]
      Glucosyltransferase I
      1. Escherichia coli [TaxId: 562] [142772] (2)
        SQ P25740 2-371
  9. Sialyltransferase-like [142773] (1)
    1. Alpha-2,3/2,6-sialyltransferase/sialidase [142774]
      1. Pasteurella multocida [TaxId: 747] [142775] (9)
        SQ Q15KI8 26-412
  10. UDPGT-like [159785] (4)
    Pfam 00201
    1. UDP glucose:flavonoid 3-o-glucosyltransferase [159786]
      1. Grape (Vitis vinifera) [TaxId: 29760] [159787] (3)
        SQ O22304 7-456
    2. Triterpene UDP-glucosyl transferase UGT71G1 [159788]
      1. Medicago truncatula [TaxId: 3880] [159789] (4)
        SQ Q5IFH7 3-463
    3. (Iso)flavonoid glycosyltransferase [159790]
      1. Medicago truncatula [TaxId: 3880] [159791] (1)
        SQ A6XNC5 8-480
    4. Hydroquinone glucosyltransferase [159792]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [159793] (3)
        SQ Q9M156 6-476
  11. FucT-like [159794] (1)
    Pfam 00852; Glycosyltransferase family 10 (fucosyltransferase)
    1. Alpha1,3-fucosyltransferase FucT [159795]
      1. Helicobacter pylori [TaxId: 210] [159796] (9)
        SQ O30511 1-349
Glutaminase/Asparaginase [53773] (1)
consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
Domain 2 has parallel beta-sheet of 4 strands, order 1234
1. Glutaminase/Asparaginase [53774] (1)
  uperfamily
  1. Glutaminase/Asparaginase [53775] (8)
    1. Asparaginase type II [53776]
      1. Escherichia coli [TaxId: 562] [53777] (7)
      2. Wolinella succinogenes [TaxId: 844] [53778] (1)
      3. Erwinia chrysanthemi [TaxId: 556] [53779] (8)
      4. Vibrio cholerae [TaxId: 666] [159797] (4)
        SQ Q9KQK3 2-337
    2. Glutaminase-asparaginase [53780]
      1. Acinetobacter glutaminasificans [TaxId: 474] [53781] (1)
      2. Pseudomonas sp., 7A [TaxId: 306] [53782] (4)
    3. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [142776]
      1. Pyrococcus abyssi [TaxId: 29292] [142777] (2)
        SQ Q9V0T9 76-438
      2. Methanobacterium thermoautotrophicum [TaxId: 145262] [142778] (2)
        SQ O26802 84-435
Phosphofructokinase [53783] (1)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
Domain 2 has parallel sheet of 4 strands, order 2314
1. Phosphofructokinase [53784] (1)
  uperfamily
  1. Phosphofructokinase [53785] (3)
    1. ATP-dependent phosphofructokinase [53786]
      Domain 1 binds ATP
      1. Escherichia coli [TaxId: 562] [53787] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [53788] (4)
    2. Pyrophosphate-dependent phosphofructokinase [75321]
      1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [75322] (3)
Tetrapyrrole methylase [53789] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 5 strands, order 32415
Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
1. Tetrapyrrole methylase [53790] (1)
  uperfamily
  1. Tetrapyrrole methylase [53791] (10)
    Pfam 00590
    1. Cobalt precorrin-4 methyltransferase CbiF [53792]
      1. Bacillus megaterium [TaxId: 1404] [53793] (2)
    2. Siroheme synthase CysG, domains 4 and 5 [102682]
      1. Salmonella typhimurium [TaxId: 90371] [102683] (3)
    3. Diphthine synthase, DphB [102684]
      diphthamide biosynthesis methyltransferase
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102685] (1)
      2. Aeropyrum pernix [TaxId: 56636] [117735] (1)
        SQ Q9YDI2; APE0931
      3. Pyrococcus horikoshii [TaxId: 53953] [142779] (6)
        SQ O58456 1-265
    4. Uroporphyrin-III C-methyltransferase (SUMT, UROM, CobA) [117736]
      1. Pseudomonas denitrificans [TaxId: 43306] [117737] (1)
        SQ P21631
      2. Thermus thermophilus [TaxId: 274] [142780] (2)
        SQ Q53WA2 1-235
    5. Hypothetical protein TTHA0667 [142781]
      strong sequence similarity to the CysG domain
      1. Thermus thermophilus [TaxId: 274] [142782] (4)
        SQ Q5SKH6 2-226
    6. Putative methytransferase BT4190 [142783]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [142784] (4)
        SQ Q8A031 2-234
    7. Precorrin-6y methylase CbiE [142785]
      1. Archaeoglobus fulgidus [TaxId: 2234] [142786] (2)
        SQ O29536 1-195
GckA/TtuD-like [82543] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology
Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2
1. GckA/TtuD-like [82544] (1)
  uperfamily
  1. GckA/TtuD-like [82545] (1)
    1. Putative glycerate kinase (hypothetical protein TM1585) [82546]
      1. Thermotoga maritima [TaxId: 2336] [82547] (2)
DAK1/DegV-like [82548] (1)
2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order: 2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest]
1. DAK1/DegV-like [82549] (2)
  domain folds and architecture show some similarity to the tubulin-like GTPases; the nucleotide-binding sites of the Dihydroxyacetone kinase and tubulin families are different
  uperfamily
  1. DegV-like [82550] (2)
    Pfam 02645, DUF194
    1. Hypothetical protein TM841 [82551]
      reveals fatty acid binding function
      1. Thermotoga maritima [TaxId: 2336] [82552] (2)
        SQ Q9X1H9
    2. Hypothetical protein apc36103 [102686]
      lipid-binding protein; Bacilus subtilis YitS ortholog
      1. Bacillus stearothermophilus [TaxId: 1422] [102687] (1)
  2. DAK1 [109613] (2)
    Pfam 02733
    1. Dihydroxyacetone kinase subunit K, DhaK [109614]
      1. Escherichia coli [TaxId: 562] [109615] (4)
        SQ P76015 20-366
        gene product YcgT
    2. Dihydroxyacetone kinase [109616]
      contains additional alpha-helical, ATP-binding domain
      1. Citrobacter freundii [TaxId: 546] [109617] (2)
DHH phosphoesterases [64181] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456
Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest
1. DHH phosphoesterases [64182] (2)
  constituent families have similar domain organization with variable interdomain linker and spatial arrangement of the domains
  uperfamily
  1. Manganese-dependent inorganic pyrophosphatase (family II) [64183] (3)
    1. Manganese-dependent inorganic pyrophosphatase (family II) [64184]
      1. Streptococcus mutans [TaxId: 1309] [64185] (1)
      2. Streptococcus gordonii [TaxId: 1302] [69609] (2)
        SQ P95765
      3. Bacillus subtilis [TaxId: 1423] [69610] (5)
        SQ P37487
  2. Exonuclease RecJ [75323] (1)
    1. Exonuclease RecJ [75324]
      1. Thermus thermophilus [TaxId: 274] [75325] (1)
Glycerate kinase I [110737] (1)
consists of two different alpha/beta domains; (1) of the Flavodoxin-like fold (scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf 52979), inserted into domain 1
1. Glycerate kinase I [110738] (1)
  uperfamily
  1. Glycerate kinase I [110739] (1)
    Pfam 02595
    1. Glycerate kinase GlxK [110740]
      1. Neisseria meningitidis, (serogroup A) [TaxId: 487] [110741] (1)
        SQ P57098
PEP carboxykinase-like [53794] (1)
contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
1. PEP carboxykinase-like [53795] (2)
  uperfamily
  1. PEP carboxykinase C-terminal domain [53796] (4)
    1. Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) [68921]
      1. Escherichia coli [TaxId: 562] [53798] (10)
      2. Thermus thermophilus [TaxId: 274] [82553] (7)
        SQ Q7SIC6
      3. Trypanosoma cruzi [TaxId: 5693] [69611] (1)
    2. Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing) [69612]
      1. Human (Homo sapiens) [TaxId: 9606] [69613] (8)
  2. HPr kinase HprK C-terminal domain [64186] (3)
    1. HPr kinase HprK C-terminal domain [64187]
      1. Lactobacillus casei [TaxId: 1582] [64188] (3)
      2. Staphylococcus xylosus [TaxId: 1288] [75326] (1)
      3. Mycoplasma pneumoniae [TaxId: 2104] [82554] (1)
PEP carboxykinase N-terminal domain [68922] (1)
contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain
1. PEP carboxykinase N-terminal domain [68923] (1)
  uperfamily
  1. PEP carboxykinase N-terminal domain [68924] (4)
    1. Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) [68925]
      1. Escherichia coli [TaxId: 562] [68926] (10)
      2. Thermus thermophilus [TaxId: 274] [82555] (7)
        SQ Q7SIC6
      3. Trypanosoma cruzi [TaxId: 5693] [69614] (1)
    2. Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing) [69615]
      1. Human (Homo sapiens) [TaxId: 9606] [69616] (8)
Chelatase-like [53799] (3)
duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
1. Chelatase [53800] (3)
  interdomain linker is short; swapping of C-terminal helices between the two domains
  uperfamily
  1. Ferrochelatase [53801] (3)
    1. Ferrochelatase [53802]
      1. Bacillus subtilis [TaxId: 1423] [53803] (8)
      2. Human (Homo sapiens) [TaxId: 9606] [64189] (3)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82556] (2)
  2. Cobalt chelatase CbiK [53804] (1)
    1. Cobalt chelatase CbiK [53805]
      1. Salmonella typhimurium [TaxId: 90371] [53806] (1)
  3. CbiX-like [110742] (1)
    Pfam 01903; single-domain protein; forms the C-terminal helix-swapped dimer similar to the CbiK subunit
    1. Sirohydrochlorin cobaltochelatase CbiX [110743]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110744] (3)
        SQ O29537
2. "Helical backbone" metal receptor [53807] (4)
  contains a long alpha helical insertion in the interdomain linker
  uperfamily
  1. Periplasmic ferric siderophore binding protein FhuD [53808] (1)
    1. Periplasmic ferric siderophore binding protein FhuD [53809]
      1. Escherichia coli [TaxId: 562] [53810] (4)
  2. TroA-like [53811] (5)
    1. Periplasmic zinc binding protein TroA [53812]
      1. Treponema pallidum [TaxId: 160] [53813] (2)
    2. Periplasmic zinc binding protein ZnuA [102688]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [102689] (1)
    3. Pneumococcal surface antigen PssA [53814]
      1. Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] [53815] (1)
    4. Vitamin B12 binding protein BtuF [82557]
      1. Escherichia coli [TaxId: 562] [82558] (4)
    5. Mn transporter MntC [142787]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [142788] (2)
        SQ Q79EF9 49-327
  3. Nitrogenase iron-molybdenum protein [53816] (6)
    contains three domains of this fold; "Helical backbone" holds domains 2 and 3
    both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
    1. Nitrogenase iron-molybdenum protein, alpha chain [81402]
      1. Clostridium pasteurianum [TaxId: 1501] [81396] (1)
      2. Azotobacter vinelandii [TaxId: 354] [81398] (18)
      3. Klebsiella pneumoniae [TaxId: 573] [81400] (4)
    2. Nitrogenase iron-molybdenum protein, beta chain [81401]
      both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
      1. Clostridium pasteurianum [TaxId: 1501] [81395] (1)
      2. Azotobacter vinelandii [TaxId: 354] [81397] (18)
      3. Klebsiella pneumoniae [TaxId: 573] [81399] (4)
  4. TM0189-like [142789] (3)
    Part of Pfam 01497 that include some other superfamily members
    1. Putative iron(III) transporter TM0189 [142790]
      1. Thermotoga maritima [TaxId: 2336] [142791] (2)
        SQ Q9WY32 25-358
    2. Enterochelin uptake protein CeuE [142792]
      1. Campylobacter jejuni [TaxId: 197] [142793] (2)
        SQ Q0P8Q4 44-330
    3. Iron-uptake system-binding protein FeuA [159798]
      1. Bacillus subtilis [TaxId: 1423] [159799] (1)
        SQ P40409 39-315
3. PrpR receptor domain-like [159800] (1)
  recent PDB entry 2q5c belongs to this superfamily
  1. PrpR receptor domain-like [159801] (1)
    N-terminal domain corresponds to Pfam 06506; C-terminal domain, assigned to Pfam 00158, is distinct from other structures of this Pfam family
    1. Propionate catabolism operon regulatory protein PrpR [159802]
      1. Escherichia coli [TaxId: 562] [159803] (4)
        SQ P77743 11-196
HemD-like [69617] (1)
duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345
1. HemD-like [69618] (1)
  uperfamily
  1. HemD-like [69619] (2)
    Pfam 02602
    1. Uroporphyrinogen III synthase (U3S, HemD) [69620]
      1. Human (Homo sapiens) [TaxId: 9606] [69621] (1)
    2. Probable uroporphyrinogen-III synthase [117738]
      1. Thermus thermophilus [TaxId: 274] [117739] (1)
        SQ Q5SKH2; TTHA0671
CAC2185-like [142794] (1)
consists of two non-similar domains, 3 layers (a/b/a) each; d1 has parallel sheet of 4 strands, order 2134; d2 has parallel sheet of 5 strands, order 21345, and antiparallel meander sheet of 3 strands
1. CAC2185-like [142795] (1)
  uperfamily
  1. CAC2185-like [142796] (1)
    1. Hypothetical protein CAC2185 [142797]
      1. Clostridium acetobutylicum [TaxId: 1488] [142798] (2)
        SQ Q97H28 1-305
Periplasmic binding protein-like I [53821] (1)
consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
parallel beta-sheet of 6 strands, order 213456
1. Periplasmic binding protein-like I [53822] (1)
  Similar in architecture to the superfamily II but partly differs in topology
  uperfamily
  1. L-arabinose binding protein-like [53823] (18)
    1. D-ribose-binding protein [53824]
      1. Escherichia coli, strain k-12 [TaxId: 562] [53825] (6)
    2. L-arabinose-binding protein [53826]
      1. Escherichia coli [TaxId: 562] [53827] (9)
    3. D-allose-binding protein [53828]
      1. Escherichia coli [TaxId: 562] [53829] (3)
    4. Galactose/glucose-binding protein [53830]
      1. Escherichia coli [TaxId: 562] [53831] (6)
      2. Salmonella typhimurium, strain lt2 [TaxId: 90371] [53832] (3)
    5. Amide receptor/negative regulator of the amidase operon (AmiC) [53833]
      1. Pseudomonas aeruginosa [TaxId: 287] [53834] (3)
    6. Quorum-sensing signal (autoinducer-2) binding protein LuxP [69622]
      1. Vibrio harveyi [TaxId: 669] [69623] (4)
    7. Purine repressor (PurR), C-terminal domain [53835]
      1. Escherichia coli [TaxId: 562] [53836] (24)
    8. Lac-repressor (lacR) core (C-terminal domain) [53837]
      1. Escherichia coli [TaxId: 562] [53838] (16)
    9. Trehalose repressor, C-terminal domain [53839]
      1. Escherichia coli [TaxId: 562] [53840] (1)
    10. Leucine-,isoleucine-,valine-binding (LIV) protein [53841]
      1. Escherichia coli [TaxId: 562] [53842] (1)
    11. Leucine-binding protein [53843]
      1. Escherichia coli [TaxId: 562] [53844] (4)
    12. Hormone binding domain of the atrial natriuretic peptide receptor [53845]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53846] (2)
        SQ P18910 29-454
      2. Human (Homo sapiens) [TaxId: 9606] [64190] (2)
    13. Metabotropic glutamate receptor subtype 1 [53847]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [53848] (5)
    14. AI-2 receptor LsrB [110745]
      1. Salmonella typhi [TaxId: 90370] [110746] (2)
        SQ Q8Z2X8 27-340
    15. Glucose-resistance amylase regulator CcpA, C-terminal domain [117740]
      1. Bacillus megaterium [TaxId: 1404] [117741] (11)
        SQ P46828 58-322 ! SQ P46828
    16. YraM C-terminal domain [159804]
      1. Haemophilus influenzae [TaxId: 727] [159805] (1)
        SQ P45299 257-573
        HI1655
Periplasmic binding protein-like II [53849] (1)
consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
1. Periplasmic binding protein-like II [53850] (3)
  Similar in architecture to the superfamily I but partly differs in topology
  uperfamily
  1. Phosphate binding protein-like [53851] (65)
    1. Oligo-peptide binding protein (OPPA) [53852]
      contains an additional alpha+beta domain inserted in the N-terminal domain
      1. Salmonella typhimurium [TaxId: 90371] [53853] (32)
      2. Bacillus subtilis [TaxId: 1423] [142799] (1)
        SQ P42061 40-543
      3. Thermotoga maritima [TaxId: 2336] [142800] (2)
        SQ Q9X0V0 23-557
        TM1223
    2. Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain [53854]
      1. Escherichia coli [TaxId: 562] [53855] (5)
    3. Lysine-,arginine-,ornithine-binding (LAO) protein [53856]
      1. Salmonella typhimurium [TaxId: 90371] [53857] (5)
    4. Sulphate-binding protein [53858]
      1. Salmonella typhimurium [TaxId: 90371] [53859] (1)
    5. Phosphate-binding protein [53860]
      1. Escherichia coli [TaxId: 562] [53861] (13)
      2. Mycobacterium tuberculosis [TaxId: 1773] [110747] (1)
        SQ P15712
    6. D-maltodextrin-binding protein, MBP [53862]
      contains a few additional helices in the C-terminal extension; homologous to thiaminase I
      1. Escherichia coli [TaxId: 562] [53863] (47)
        SQ P02928
      2. Alicyclobacillus acidocaldarius [TaxId: 405212] [102690] (3)
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53864] (1)
      4. Archaeon Thermococcus litoralis [TaxId: 2265] [64191] (1)
        trehalose maltose-binding protein
      5. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159806] (1)
    7. Thiaminase I [53865]
      contains a few additional helices in the C-terminal extension; homologous to MBP
      1. Paenibacillus thiaminolyticus [TaxId: 49283] [53866] (3)
    8. Ferric-binding protein FbpA [53867]
      1. Haemophilus influenzae [TaxId: 727] [53868] (5)
      2. Mannheimia haemolytica [TaxId: 75985] [102691] (3)
        SQ Q9Z4N6
      3. Neisseria gonorrhoeae [TaxId: 485] [53869] (4)
        SQ Q50964 23-331
      4. Yersinia enterocolitica, YfuA [TaxId: 630] [117742] (1)
        SQ Q56925 28-338
      5. Serratia marcescens, SfuA [TaxId: 615] [117743] (1)
        SQ P21408 32-338
      6. Campylobacter jejuni [TaxId: 197] [117744] (1)
        SQ Q9PIV4 17-334
      7. Bordetella pertussis [TaxId: 520] [117745] (3)
        SQ Q7VXW9 31-349
    9. Dipeptide-binding protein [53870]
      similar domain organization to oligopeptide-binding protein, OPPA
      1. Escherichia coli [TaxId: 562] [53871] (2)
    10. Hypothetical protein YliB [102692]
      similar domain organization to oligo- and dipeptide-binding protein
      1. Escherichia coli [TaxId: 562] [102693] (1)
    11. Nickel-binding periplasmic protein NikA [102694]
      similar domain organization to oligo- and dipeptide-binding protein
      1. Escherichia coli [TaxId: 562] [102695] (10)
    12. Histidine-binding protein [53872]
      1. Escherichia coli [TaxId: 562] [53873] (1)
      2. Salmonella typhimurium [TaxId: 90371] [53874] (1)
    13. Spermidine/putrescine-binding protein PotD [53875]
      1. Escherichia coli [TaxId: 562] [53876] (2)
    14. Putrescine receptor (PotF) [53877]
      1. Escherichia coli [TaxId: 562] [53878] (1)
    15. Glutamine-binding protein [53879]
      1. Escherichia coli [TaxId: 562] [53880] (2)
    16. Glutamate receptor ligand binding core [53881]
      1. Rat (Rattus norvegicus), GluR2 [TaxId: 10116] [53882] (80)
      2. Synechocystis sp., GluR0 [TaxId: 1143] [64192] (3)
      3. Rat (Rattus norvegicus), GluR6 [TaxId: 10116] [142801] (14)
        SQ P42260 421-544,668-804! SQ P42260 429-544,667-806
      4. Rat (Rattus norvegicus), GluR5 [TaxId: 10116] [142802] (13)
        SQ P22756 429-546,667-799! SQ P22756 433-544,682-815
    17. Putative GluR0 ligand binding core [102696]
      1. Thermus thermophilus [TaxId: 274] [102697] (2)
    18. N-methyl-D-aspartate receptor subunit 1 [89787]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89788] (9)
      2. Rat (Rattus norvegicus), subtype 2A [TaxId: 10116] [142803] (2)
        SQ Q00959 404-539,661-801
    19. ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain [82559]
      there is an additional C-terminal allosteric domain in some species
      1. Mycobacterium tuberculosis [TaxId: 1773] [82560] (2)
      2. Escherichia coli [TaxId: 562] [102698] (2)
      3. Thermotoga maritima [TaxId: 2336] [102699] (3)
        SQ Q9X0D2
      4. Lactococcus lactis [TaxId: 1358] [142804] (8)
        SQ Q02129 1-204
      5. Thermus thermophilus [TaxId: 274] [142805] (1)
        SQ Q5SM15 1-206
    20. Molybdate-binding protein, ModA [53883]
      1. Escherichia coli [TaxId: 562] [53884] (2)
      2. Azotobacter vinelandii [TaxId: 354] [53885] (1)
      3. Archaeoglobus fulgidus [TaxId: 2234] [159807] (4)
        SQ O30142 32-342
    21. Cofactor-binding fragment of LysR-type protein CysB [53886]
      1. Klebsiella aerogenes [TaxId: 28451] [53887] (1)
    22. Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain [64193]
      1. Escherichia coli [TaxId: 562] [64194] (2)
    23. LysR-type regulatory protein CbnR [89789]
      1. Ralstonia eutropha [TaxId: 106590] [89790] (2)
    24. Alginate-binding periplasmic protein AlgQ2 [69624]
      1. Sphingomonas sp. [TaxId: 28214] [69625] (2)
    25. Putative lipoprotein (NlpA family) [102700]
      aka PG110, TpN32
      1. Staphylococcus aureus [TaxId: 1280] [102701] (1)
      2. Treponema pallidum [TaxId: 160] [117746] (1)
        SQ O07950 28-267
    26. Glycine betaine-binding periplasmic protein ProX [102702]
      1. Escherichia coli [TaxId: 562] [102703] (2)
    27. LysR-type regulatory protein DntR [110748]
      1. Burkholderia sp. [TaxId: 36773] [110749] (2)
        SQ Q7WT50 75-301
    28. Osmoprotection protein ProX [110750]
      functionally related to the bacterial ProX
      1. Archaeoglobus fulgidus [TaxId: 2234] [110751] (4)
        SQ O29280 # AF0982
    29. ABC transporter, periplasmic substrate-binding protein VCA0807 [117747]
      1. Vibrio cholerae [TaxId: 666] [117748] (1)
        SQ Q9KLD9 26-274
    30. Hypothetical protein TTHA1568 [142806]
      member of Pfam 02642 (DUF191)
      1. Thermus thermophilus [TaxId: 274] [142807] (2)
        SQ Q5SI12 3-272
    31. Alginate-binding periplasmic protein AlgQ1 [142808]
      1. Sphingomonas sp. [TaxId: 28214] [142809] (3)
        SQ Q9KWT6 25-514
    32. Hypothetical protein AF1704 [142810]
      member of Pfam 02642 (DUF191)
      1. Archaeoglobus fulgidus [TaxId: 2234] [142811] (1)
        SQ O28569 2-261
    33. Probable LysR-type transcriptional regulator PA0477 [142812]
      1. Pseudomonas aeruginosa [TaxId: 287] [142813] (4)
        SQ Q9I641 92-303
    34. Putative amino-acid transporter CjaA [142814]
      1. Campylobacter jejuni [TaxId: 197] [142815] (2)
        SQ Q0P9S0 29-276
    35. LysR-type regulatory protein Cbl [142816]
      1. Escherichia coli [TaxId: 562] [142817] (4)
        SQ Q47083 88-307
    36. Prephenate dehydratase [159808]
      1. Staphylococcus aureus [TaxId: 1280] [159809] (2)
        SQ Q99SX2 1-184
    37. Hypothetical protein SCo4506 [159810]
      1. Streptomyces coelicolor [TaxId: 1902] [159811] (4)
        SQ Q9L0T8 6-282
    38. Hypothetical protein YhfZ [159812]
      1. Shigella flexneri [TaxId: 623] [159813] (1)
        SQ Q83JA6 1-228
    39. Hypothetical protein DR0370 [159814]
      1. Deinococcus radiodurans [TaxId: 1299] [159815] (8)
        SQ Q9RXE3 14-285
    40. PstS-like phosphate-binding protein [159816]
      1. Human (Homo sapiens) [TaxId: 9606] [159817] (1)
        SQ P85173 1-376
  2. Transferrin [53888] (11)
    further duplication: composed of two two-domain lobes
    1. Lactoferrin [53889]
      1. Human (Homo sapiens) [TaxId: 9606] [53890] (23)
      2. Cow (Bos taurus) [TaxId: 9913] [53891] (44)
      3. Domestic water buffalo (Bubalus arnee bubalis) [TaxId: 89462] [53892] (2)
      4. Goat (Capra hircus) [TaxId: 9925] [89791] (1)
      5. Horse (Equus caballus) [TaxId: 9796] [53893] (8)
      6. Arabian camel (Camelus dromedarius) [TaxId: 9838] [64195] (2)
    2. Ovotransferrin [53894]
      1. Duck (Anas platyrhynchos) [TaxId: 8839] [53895] (5)
      2. Chicken (Gallus gallus) [TaxId: 9031] [53896] (11)
        SQ P02789
    3. Transferrin [53897]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53898] (6)
      2. Human (Homo sapiens) [TaxId: 9606] [53899] (17)
      3. Pig (Sus scrofa) [TaxId: 9823] [69626] (1)
  3. PG0945 N-terminal domain-like [159818] (1)
    truncated to one domain; extra C-terminal region provides dimerisation interface
    1. Uncharacterized protein PG0945 [159819]
      putative ABC transporter, permease
      1. Porphyromonas gingivalis [TaxId: 837] [159820] (1)
        SQ Q7MVU4 48-183
Thiolase-like [53900] (1)
consists of two similar domains related by pseudo dyad; duplication
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
1. Thiolase-like [53901] (2)
  uperfamily
  1. Thiolase-related [53902] (12)
    1. Thiolase [53903]
      topology of each domain is similar to the first domain of phosphoglucomutase
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53904] (2)
    2. Biosynthetic thiolase [53905]
      1. Zoogloea ramigera [TaxId: 350] [53906] (12)
        SQ P07097
    3. Beta-ketoacyl-ACP synthase I [53907]
      1. Escherichia coli [TaxId: 562] [53908] (135)
        SQ P14926
    4. Beta-ketoacyl-ACP synthase II [53909]
      1. Escherichia coli [TaxId: 562] [53910] (10)
      2. Synechocystis sp. [TaxId: 1143] [53911] (1)
      3. Thermus thermophilus [TaxId: 274] [89792] (1)
      4. Streptococcus pneumoniae [TaxId: 1313] [89793] (4)
      5. Thale cress (Arabidopsis thaliana), mitochondrial isoform [TaxId: 3702] [117749] (5)
        SQ Q8L3X9
    5. Actinorhodin polyketide putative beta-ketoacyl synthase 1, KasA [110752]
      1. Streptomyces coelicolor [TaxId: 1902] [110753] (1)
        SQ Q02059
    6. Actinorhodin polyketide putative beta-ketoacyl synthase 2, KasB [110754]
      1. Streptomyces coelicolor [TaxId: 1902] [110755] (1)
        SQ Q02062
    7. Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase) [110756]
      1. Pseudomonas fragi [TaxId: 296] [110757] (7)
        SQ P28790
    8. Beta-ketoadipyl CoA thiolase [117750]
      1. Thermus thermophilus [TaxId: 274] [117751] (1)
        SQ Q5SJM1
  2. Chalcone synthase-like [53914] (10)
    1. Chalcone synthase [53915]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [53916] (16)
        SQ P30074
    2. Pyrone synthase (PyS, chalcone synthase 2) [53917]
      1. Gerbera hybrid cultivar [TaxId: 18101] [53918] (2)
    3. Ketoacyl-ACP synthase III (FabH) [53912]
      1. Escherichia coli [TaxId: 562] [53913] (15)
      2. Mycobacterium tuberculosis [TaxId: 1773] [64196] (42)
      3. Thermus thermophilus [TaxId: 274] [89794] (1)
    4. Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway [82561]
      1. Streptomyces sp. r1128 [TaxId: 140437] [82562] (1)
    5. Polyketide synthase PKS18 [110758]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110759] (2)
        SQ Q79FQ0
    6. 3-hydroxy-3-methylglutaryl CoA synthase MvaS [110760]
      most similar to FabH
      1. Staphylococcus aureus [TaxId: 1280] [110761] (5)
        SQ Q7A3F6
    7. Putative polyketide synthase SCO1206 [110762]
      1. Streptomyces coelicolor [TaxId: 1902] [110763] (1)
        SQ Q9FCA7
    8. Dihydropinosylvin synthase [117752]
      1. Scots pine (Pinus sylvestris) [TaxId: 3349] [117753] (1)
        SQ Q02323
NIF3 (NGG1p interacting factor 3)-like [102704] (1)
consist of two intertwined domains; duplication: contains two structural repeats of alpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 is antiparallel to the rest
1. NIF3 (NGG1p interacting factor 3)-like [102705] (1)
  di-iron binding protein
  uperfamily
  1. NIF3 (NGG1p interacting factor 3)-like [102706] (3)
    Pfam 01784
    1. Hypothetical protein YbgI [102707]
      1. Escherichia coli [TaxId: 562] [102708] (2)
    2. Nif3-related protein BC4286 [142818]
      1. Bacillus cereus [TaxId: 1396] [142819] (3)
        SQ Q818H0 4-373
    3. Hypothetical protein SP1609 [142820]
      1. Streptococcus pneumoniae [TaxId: 1313] [142821] (3)
        SQ Q97PK0 1-265
Fe-only hydrogenase [53919] (1)
consist of two intertwined domains; contains partial duplication
1. Fe-only hydrogenase [53920] (1)
  uperfamily
  1. Fe-only hydrogenase [53921] (2)
    1. Fe-only hydrogenase, catalytic domain [53922]
      includes C-terminal region homologous to the smaller subunit of Desulfovidrio hydrogenase
      1. Clostridium pasteurianum [TaxId: 1501] [53923] (4)
    2. Fe-only hydrogenase larger subunit, C-domain [53924]
      1. Desulfovibrio desulfuricans [TaxId: 876] [53925] (1)
ComB-like [142822] (1)
contains of two similar intertwined domains related by pseudo dyad; duplication; core: 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 1423
1. ComB-like [142823] (1)
  uperfamily
  1. ComB-like [142824] (1)
    Pfam 04029; 2-phosphosulpholactate phosphatase
    1. 2-phosphosulfolactate phosphatase ComB [142825]
      1. Clostridium acetobutylicum [TaxId: 1488] [142826] (3)
        SQ Q97E82 1-235
CoA-transferase family III (CaiB/BaiF) [89795] (1)
consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit
1. CoA-transferase family III (CaiB/BaiF) [89796] (1)
  uperfamily
  1. CoA-transferase family III (CaiB/BaiF) [89797] (4)
    forms interlocked homodimer of two ring-like subunits
    1. Formyl-CoA transferase [89798]
      1. Oxalobacter formigenes [TaxId: 847] [89799] (11)
        SQ O06644
    2. Hypothetical protein YfdW [102709]
      1. Escherichia coli [TaxId: 562] [102710] (6)
    3. Crotonobetainyl-CoA:carnitine CoA-transferase, CaiB [117754]
      1. Escherichia coli [TaxId: 562] [117755] (12)
        SQ P31572
    4. 2-methylacyl-CoA racemase Mcr [142827]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142828] (24)
        SQ O06543 2-360
Cytidine deaminase-like [53926] (2)
core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 1 is antiparallel to the rest
1. Cytidine deaminase-like [53927] (5)
  contains extra C-terminal strand 5, order 21345
  uperfamily
  1. Cytidine deaminase [53928] (7)
    strand 5 is antiparallel to strand 4
    1. mono-domain cytidine deaminase [75327]
      1. Bacillus subtilis [TaxId: 1423] [75328] (4)
        SQ P19079
      2. Human (Homo sapiens) [TaxId: 9606] [102711] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110764] (1)
        SQ Q06549
      4. Bacillus anthracis [TaxId: 1392] [142829] (2)
        SQ Q81LT6 1-124
      5. Mouse (Mus musculus) [TaxId: 10090] [142830] (12)
        SQ P56389 10-146
    2. Two-domain cytidine deaminase [53929]
      duplication: consists of two similar domains; contains extra helices in the N-terminal domain
      1. Escherichia coli [TaxId: 562] [53930] (4)
    3. Blasticidin-S deaminase [142831]
      1. Aspergillus terreus [TaxId: 33178] [142832] (14)
        SQ P78986 2-126
  2. Deoxycytidylate deaminase-like [89800] (10)
    strand 5 is parallel to strand 4
    1. Cytosine deaminase [89801]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89802] (8)
    2. Guanine deaminase GuaD [110765]
      1. Bacillus subtilis [TaxId: 1423] [110766] (2)
        SQ O34598
    3. Deoxycytidylate deaminase [117756]
      1. Bacteriophage T4 [TaxId: 10665] [117757] (1)
        SQ P16006
    4. Putative deaminase NE0047 [142833]
      1. Nitrosomonas europaea [TaxId: 915] [142834] (1)
        SQ Q82Y41 1-189
    5. Cytidine and deoxycytidylate deaminase CodA [142835]
      1. Agrobacterium tumefaciens [TaxId: 358] [142836] (2)
        SQ Q8UHJ4 2-131
    6. Riboflavin biosynthesis protein RibD [142837]
      1. Bacillus subtilis [TaxId: 1423] [142838] (8)
        SQ P17618 1-145
      2. Thermotoga maritima [TaxId: 2336] [142839] (1)
        SQ Q9X2E8 1-147
    7. tRNA adenosine deaminase TadA [142840]
      1. Staphylococcus aureus [TaxId: 1280] [142841] (4)
        SQ Q99W51 1-151
      2. Escherichia coli [TaxId: 562] [142842] (2)
        SQ P68398 13-168
      3. Aquifex aeolicus [TaxId: 63363] [142843] (4)
        SQ O67050 1-151
  3. Hypothetical protein TM1506 [110651] (1)
    strand 5 is parallel to strand 4
    1. Hypothetical protein TM1506 [110652]
      1. Thermotoga maritima [TaxId: 2336] [110653] (1)
        SQ Q9X1J4
  4. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64198] (3)
    duplication: consists of two domains of this fold with extra secondary structures within and in between the two core motifs
    1. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64199]
      1. Chicken (Gallus gallus) [TaxId: 9031] [64200] (4)
        SQ P31335
      2. Human (Homo sapiens) [TaxId: 9606] [102716] (3)
      3. Thermotoga maritima [TaxId: 2336] [142844] (2)
        SQ Q9X0X6 158-452
  5. FdhD/NarQ [159821] (1)
    Pfam 02634; contains extra N-terminal beta-hairpin arm, involved in dimerization, and an alpha+beta subdomain of beta-grasp fold (scop_cf 54235)
    1. Uncharacterized protein DP1777 [159822]
      Related to formate dehydrogenase accessory protein FdhD
      1. Desulfotalea psychrophila [TaxId: 84980] [159823] (4)
        SQ Q6AMB9 7-257
2. JAB1/MPN domain [102712] (1)
  uperfamily
  1. JAB1/MPN domain [102713] (1)
    Pfam 01398; synonyms Mov34, PAD-1;
    1. Hypothetical protein AF2198 [102714]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102715] (2)