Structural Classification of Proteins

Fold: TIM beta/alpha-barrel

: contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: TIM beta/alpha-barrel [51350]
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites

Superfamilies:

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)
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
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
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)
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
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
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)
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
(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
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)
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
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
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
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)
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
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
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
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
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
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
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)
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)
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
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
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
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)
(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
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
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
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
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
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
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