Structural Classification of Proteins
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Superfamily: P-loop containing nucleoside triphosphate hydrolases

division into families based on beta-sheet topologies
link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: P-loop containing nucleoside triphosphate hydrolases [52539]
    3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
  4. Superfamily: P-loop containing nucleoside triphosphate hydrolases [52540]
    division into families based on beta-sheet topologies
    link to SUPERFAMILY database - Superfamily

Families:

  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) picpic
      2. Mouse (Mus musculus) [TaxId: 10090] [82393] (1) picpic
      3. Escherichia coli [TaxId: 562] [102338] (18) picpic
      4. Mycobacterium tuberculosis [TaxId: 1773] [102339] (5) picpic
        Rv1389
    2. Guanylate kinase-like domain of Cask [69474]
      1. Human (Homo sapiens) [TaxId: 9606] [69475] (1) picpic
    3. Guanylate kinase-like domain of Psd-95 [69476]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69477] (3) picpic
    4. Uridylate kinase [52544]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52545] (2) picpic
    5. Deoxynucleoside monophosphate kinase [52546]
      contains insert 4-helical bundle subdomain, residues 35-145
      1. Bacteriophage T4 [TaxId: 10665] [52547] (2) picpic
    6. Deoxyribonucleoside kinase [69478]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [69479] (37) picpic
    7. Deoxycytidine kinase [89657]
      1. Human (Homo sapiens) [TaxId: 9606] [89658] (13) picpic
    8. Deoxyguanosine kinase [69480]
      1. Human (Homo sapiens) [TaxId: 9606] [69481] (8) picpic
    9. CMP kinase [52548]
      1. Escherichia coli [TaxId: 562] [52549] (6) picpic
      2. Streptococcus pneumoniae [TaxId: 1313] [110525] (1) picpic
        SQ Q97PK6
    10. UMP/CMP kinase [52550]
      1. Dictyostelium discoideum [TaxId: 44689] [52551] (6) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [110526] (1) picpic
        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) picpic
        SQ P03176 46-375
      2. Equine herpesvirus type 4 [TaxId: 10331] [102340] (4) picpic
      3. Varicella-zoster virus [TaxId: 10335] [89659] (1) picpic
    12. Adenylate kinase [52554]
      1. Pig (Sus scrofa) [TaxId: 9823] [52555] (1) picpic
      2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [52556] (1) picpic
      3. Archaeon Methanococcus voltae [TaxId: 2188] [89660] (1) picpic
      4. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [89661] (1) picpic
      5. Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913] [52557] (1) picpic
        contains a rudiment "zinc-finger" subdomain, residue 125-161
      6. Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913] [52558] (2) picpic
        contains a rudiment "zinc-finger" subdomain, residue 147-176
      7. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52559] (4) picpic
        contains a rudiment "zinc-finger" subdomain, residue 131-168
      8. Escherichia coli [TaxId: 562] [52560] (6) picpic
        contains a rudiment "zinc-finger" subdomain, residue 122-156
      9. Maize (Zea mays) [TaxId: 4577] [52561] (1) picpic
      10. Bacillus stearothermophilus [TaxId: 1422] [52562] (3) picpic
        contains a zinc-finger subdomain, residues 126-160
      11. Bacillus subtilis [TaxId: 1423] [102341] (1) picpic
        contains a zinc-finger subdomain, residues 126-160
      12. Bacillus globisporus [TaxId: 1459] [102342] (1) picpic
        contains a zinc-finger subdomain, residues 126-160
      13. Mycobacterium tuberculosis [TaxId: 1773] [102343] (2) picpic
        contains no zinc finger-like insertion
      14. Human (Homo sapiens), isoenzyme 6 [TaxId: 9606] [117527] (1) picpic
        SQ Q9Y3D8
    13. Thymidylate kinase [52563]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52564] (3) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [64010] (20) picpic
      3. Escherichia coli [TaxId: 562] [52565] (2) picpic
      4. Mycobacterium tuberculosis [TaxId: 1773] [69482] (13) picpic
    14. Dephospho-CoA kinase [75187]
      1. Haemophilus influenzae [TaxId: 727] [75188] (1) picpic
      2. Escherichia coli [TaxId: 562] [82394] (5) picpic
      3. Thermus thermophilus [TaxId: 274] [102344] (1) picpic
        TT1252
    15. Transcriptional regulator NadR, ribosylnicotinamide kinase domain [75189]
      1. Haemophilus influenzae [TaxId: 727] [75190] (1) picpic
    16. Polynucleotide kinase, kinase domain [75191]
      1. Bacteriophage T4 [TaxId: 10665] [75192] (17) picpic
    17. Guanylate kinase-like domain of the L-type calcium channel [110527]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110528] (4) picpic
        SQ P54288 234-451
      2. Rat (Rattus norvegicus) [TaxId: 10116] [110529] (3) picpic
        SQ P54287 38-362
    18. Probable kinase LmjF30.1890 [117528]
      1. Leishmania major [TaxId: 5664] [117529] (1) picpic
        SQ Q4Q7A6
    19. Hypothetical protein YorR [142211]
      1. Bacillus subtilis [TaxId: 1423] [142212] (2) picpic
        SQ O31896 2-165
    20. 5' polynucleotide kinase-3' phosphatase, C-terminal domain [142213]
      1. Mouse (Mus musculus) [TaxId: 10090] [142214] (2) picpic
        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) picpic
      2. Erwinia chrysanthemi [TaxId: 556] [52568] (3) picpic
      3. Mycobacterium tuberculosis [TaxId: 1773] [75194] (24) picpic
        SQ P95014
      4. Campylobacter jejuni [TaxId: 197] [102345] (1) picpic
  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) picpic
  4. Gluconate kinase [75195] (1)
    similar to the nucleotide/nucleoside kinases
    1. Gluconate kinase [75196]
      1. Escherichia coli [TaxId: 562] [75197] (6) picpic
  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) picpic
  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) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [142215] (6) picpic
        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) picpic
      2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [64014] (2) picpic
  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) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [75198] (2) picpic
    2. Hydroxysteroid sulfotransferase sult2a1 [52578]
      1. Human (Homo sapiens) [TaxId: 9606] [52579] (3) picpic
    3. Aryl sulfotransferase sult1a [102346]
      1. Human (Homo sapiens) [TaxId: 9606] [102347] (3) picpic
    4. Aryl sulfotransferase sult1a3 [52580]
      1. Human (Homo sapiens) [TaxId: 9606] [52581] (3) picpic
    5. Pregnenolone sulfotransferase sult2b1a [102348]
      1. Human (Homo sapiens) [TaxId: 9606] [102349] (1) picpic
        cytosolic enzyme
    6. Cholesterol sulfotransferase sult2b1b [102350]
      1. Human (Homo sapiens) [TaxId: 9606] [102351] (3) picpic
        cytosolic enzyme
    7. Putative steroid sulfotransferase rarO47 [102352]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102353] (2) picpic
    8. Heparan sulfate N-deacetylase/N-sulfotransferase domain [52582]
      1. Human (Homo sapiens) [TaxId: 9606] [52583] (1) picpic
    9. Heparan sulfate 3-O-sulfotransferase [102354]
      1. Mouse (Mus musculus) [TaxId: 10090] [102355] (1) picpic
        SQ O35310 48-311
    10. Retinol dehydratase [64015]
      1. Fall armyworm (Spodoptera frugiperda) [TaxId: 7108] [64016] (2) picpic
    11. Stf0 sulfotransferase [110530]
      1. Mycobacterium smegmatis [TaxId: 1772] [110531] (1) picpic
        SQ P84151
    12. Heparan sulfate glucosamine 3-O-sulfotransferase 3 [110532]
      1. Human (Homo sapiens) [TaxId: 9606] [110533] (2) picpic
        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) picpic
        SQ O43704
    14. Sulfotransferase Sult1c2 [159556]
      1. Human (Homo sapiens) [TaxId: 9606] [159557] (2) picpic
        SQ O00338 12-296
  9. Phosphoribulokinase/pantothenate kinase [52584] (5)
    1. Phosphoribulokinase [52585]
      1. Rhodobacter sphaeroides [TaxId: 1063] [52586] (1) picpic
    2. Pantothenate kinase PanK [52587]
      has a circularly permuted fold compared to the phosphoribulokinase fold
      1. Escherichia coli [TaxId: 562] [52588] (3) picpic
        SQ P15044
    3. Hypothetical protein Ygr205W [102356]
      close structural similarity to PanK
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102357] (1) picpic
    4. Hypothetical protein rbstp0775 [102358]
      structural similarity to PanK
      1. Bacillus stearothermophilus [TaxId: 1422] [102359] (1) picpic
    5. Uridine-cytidine kinase 2 [102360]
      1. Human (Homo sapiens) [TaxId: 9606] [102361] (7) picpic
  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) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [82398] (1) picpic
  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) picpic
        SQ Q6P716
    2. Rac [52595]
      1. Human (Homo sapiens) [TaxId: 9606] [52596] (23) picpic
    3. Ras-related protein RalA [89662]
      1. Human (Homo sapiens) [TaxId: 9606] [89663] (7) picpic
      2. Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490] [117532] (3) picpic
        SQ P63320 # 100% identical to the mouse and rat orthologs (SQ P63321 P63322)
    4. Rap1A [52597]
      1. Human (Homo sapiens) [TaxId: 9606] [52598] (2) picpic
    5. Rap2a [52599]
      1. Human (Homo sapiens) [TaxId: 9606] [52600] (3) picpic
    6. Rab3a [52601]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [52602] (2) picpic
    7. Rab5a [82399]
      1. Human (Homo sapiens) [TaxId: 9606] [82400] (11) picpic
        SQ P20339 18-182
    8. Rab5c [52603]
      1. Mouse (Mus musculus) [TaxId: 10090] [52604] (4) picpic
    9. Rab6 [52605]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [52606] (1) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [142216] (1) picpic
        SQ P20340 13-176
    10. Rab11a [102362]
      1. Human (Homo sapiens) [TaxId: 9606] [102363] (13) picpic
      2. Saccharomyces cerevisiae [TaxId: 4932] [159558] (4) picpic
    11. Rab-related protein Sec4 [52607]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52608] (5) picpic
    12. Rab-related protein ypt7p [75199]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75200] (2) picpic
    13. Ran [52609]
      1. Dog (Canis familiaris) [TaxId: 9615] [52610] (6) picpic
        SQ P62825
      2. Human (Homo sapiens) [TaxId: 9606] [52611] (7) picpic
    14. RhoA [52612]
      1. Human (Homo sapiens) [TaxId: 9606] [52613] (14) picpic
        SQ P61586 2-181
    15. RhoE (RND3) [75201]
      1. Mouse (Mus musculus) [TaxId: 10090] [75202] (2) picpic
    16. ADP-ribosylation factor [52614]
      1. Human (Homo sapiens), ARF1 [TaxId: 9606] [52615] (14) picpic
        SQ P32889
      2. Rat (Rattus norvegicus), ARF1 [TaxId: 10116] [52616] (2) picpic
      3. Human (Homo sapiens), ARF6 [TaxId: 9606] [52617] (6) picpic
      4. Mouse (Mus musculus), ARL3 [TaxId: 10090] [52618] (2) picpic
      5. Mouse (Mus musculus), ARL2 [TaxId: 10090] [75203] (3) picpic
      6. Baker's yeast (Saccharomyces cerevisiae), ARF2 [TaxId: 4932] [82401] (1) picpic
      7. Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932] [82402] (1) picpic
      8. Human (Homo sapiens), ARL1 [TaxId: 9606] [102364] (2) picpic
      9. Human (Homo sapiens), ARF4 [TaxId: 9606] [142217] (2) picpic
        SQ P18085 3-177
      10. Human (Homo sapiens), ARL5A [TaxId: 9606] [142218] (3) picpic
        SQ Q9Y689 2-178
      11. Human (Homo sapiens), ARL8A [TaxId: 9606] [142219] (1) picpic
        SQ Q96BM9 18-181
      12. Human (Homo sapiens) [TaxId: 9606] [142220] (1) picpic
        SQ P84085 6-179
      13. Human (Homo sapiens), ARL5B [TaxId: 9606] [142221] (1) picpic
        SQ Q96KC2 6-173
      14. Human(Homo sapiens), ARL8B [TaxId: 9606] [142222] (1) picpic
        SQ Q9NVJ2 18-182
    17. SAR1 [69483]
      1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [69484] (3) picpic
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82403] (2) picpic
      3. Human (Homo sapiens) [TaxId: 9606] [142223] (2) picpic
        SQ Q9NR31 13-198
    18. CDC42 [52619]
      1. Human (Homo sapiens) [TaxId: 9606] [52620] (21) picpic
      2. Mus musculus [TaxId: 10090] [159559] (2) picpic
    19. Ypt51 [52621]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52622] (1) picpic
    20. Chloroplast protein translocon GTPase Toc34 [69485]
      1. Garden pea (Pisum sativum) [TaxId: 3888] [69486] (1) picpic
    21. Signal recognition particle receptor beta-subunit [89664]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89665] (1) picpic
      2. Mouse (Mus musculus) [TaxId: 10090] [142224] (2) picpic
        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) picpic
        SQ P04896 39-388
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52625] (33) picpic
        SQ P10824
      3. Mouse (Mus musculus) [TaxId: 10090] [142225] (6) picpic
        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) picpic
    23. Elongation factor Tu (EF-Tu), N-terminal (G) domain [52626]
      1. Escherichia coli [TaxId: 562] [52627] (10) picpic
        SQ P02990
      2. Thermus aquaticus [TaxId: 271] [52628] (4) picpic
      3. Thermus thermophilus [TaxId: 274] [52629] (9) picpic
      4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [52630] (2) picpic
        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) picpic
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69487] (2) picpic
        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) picpic
        residues 160-252 comprise insertion subdomain
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142226] (2) picpic
        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) picpic
        SQ P32324
    27. Initiation factor IF2/eIF5b, N-terminal (G) domain [52635]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [52636] (3) picpic
    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) picpic
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [102365] (1) picpic
      3. Sulfolobus solfataricus [TaxId: 2287] [142227] (6) picpic
        SQ Q980A5 2-206
    29. GTPase Era, N-terminal domain [52637]
      1. Escherichia coli [TaxId: 562] [52638] (3) picpic
      2. Thermus thermophilus [TaxId: 274] [117533] (1) picpic
        SQ Q5SM23
    30. Probable tRNA modification GTPase TrmE (MnmE), G domain [102366]
      1. Escherichia coli [TaxId: 562] [102367] (11) picpic
    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) picpic
    32. Obg GTP-binding protein middle domain [82408]
      1. Bacillus subtilis [TaxId: 1423] [82409] (1) picpic
      2. Thermus thermophilus [TaxId: 274] [102368] (1) picpic
        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) picpic
      2. Haemophilus influenzae [TaxId: 727] [89666] (1) picpic
        HI0393
    34. Probable GTPase EngB [89667]
      1. Escherichia coli [TaxId: 562] [89668] (1) picpic
      2. Bacillus subtilis [TaxId: 1423] [110534] (3) picpic
        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) picpic
    36. Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain [52639]
      1. Human (Homo sapiens) [TaxId: 9606] [52640] (2) picpic
    37. Dynamin G domain [69488]
      the family common core is decorated with large insertions
      1. Dictyostelium discoideum [TaxId: 44689] [69489] (2) picpic
      2. Rat (Rattus norvegicus) [TaxId: 10116] [142228] (1) picpic
        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) picpic
        SQ O74718
    39. Rab9a [110537]
      1. Dog (Canis familiaris) [TaxId: 9615] [110538] (1) picpic
        SQ P24408
      2. Human (Homo sapiens) [TaxId: 9606] [110539] (1) picpic
        SQ P51151 2-175 # 100% sequence identity do the dog protein (SQ P24408 2-175)
      3. Mouse (Mus musculus) [TaxId: 10090] [142229] (1) picpic
        SQ Q9R0M6 4-175
    40. Rab7 [110540]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110541] (4) picpic
        SQ P09527
      2. Human (Homo sapiens) [TaxId: 9606] [142230] (5) picpic
        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) picpic
        SQ Q9X242 # TM1717
      2. Bacillus subtilis [TaxId: 1423] [117534] (1) picpic
        SQ O34530
    42. GTPase Ytp1 [110544]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110545] (2) picpic
        SQ P01123
    43. Interferon-inducible GTPase [110546]
      G domain is inserted in all-alpha domain
      1. Mouse (Mus musculus) [TaxId: 10090] [110547] (5) picpic
        SQ Q9QZ85 # all-alpha domain (14-68,252-415)
    44. TrmE GTPase domain [117535]
      1. Thermotoga maritima [TaxId: 2336] [117536] (2) picpic
        SQ Q9WYA4
    45. Elongation factor SelB, N-terminal domain [117537]
      1. Methanococcus maripaludis [TaxId: 39152] [117538] (3) picpic
        SQ Q8J307
    46. Rab23 [142231]
      1. Mouse (Mus musculus) [TaxId: 10090] [142232] (2) picpic
        SQ P35288 8-171
    47. Rab18 [142233]
      1. Human (Homo sapiens) [TaxId: 9606] [142234] (1) picpic
        SQ Q9NP72 2-178
    48. Rab31 [142235]
      1. Human (Homo sapiens) [TaxId: 9606] [142236] (1) picpic
        SQ Q13636 3-167
    49. Rab11b [142237]
      1. Human (Homo sapiens) [TaxId: 9606] [142238] (2) picpic
        SQ Q15907 7-181
    50. Rab30 [142239]
      1. Human (Homo sapiens) [TaxId: 9606] [142240] (1) picpic
        SQ Q15771 5-175
    51. Rab1a [142241]
      1. Human (Homo sapiens) [TaxId: 9606] [142242] (1) picpic
        SQ P62820 7-175
    52. RhoB [142243]
      1. Human (Homo sapiens) [TaxId: 9606] [142244] (1) picpic
        SQ P62745 4-185
    53. RhoC [142245]
      1. Human (Homo sapiens) [TaxId: 9606] [142246] (2) picpic
        SQ P08134 1-179
    54. Rab4a [142247]
      1. Human (Homo sapiens) [TaxId: 9606] [142248] (5) picpic
        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) picpic
        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) picpic
        SQ O58261 1-319
    57. Rab-22a [142253]
      1. Mouse (Mus musculus) [TaxId: 10090] [142254] (2) picpic
        SQ P35285 2-167! SQ P35285 2-168
    58. Rac3 [142255]
      1. Human (Homo sapiens) [TaxId: 9606] [142256] (2) picpic
        SQ P60763 3-177
    59. GTP-binding protein engB [142257]
      1. Pyrococcus horikoshii [TaxId: 53953] [142258] (3) picpic
        SQ O57939 28-211
        PH0200
    60. Rab26 [142259]
      1. Human (Homo sapiens) [TaxId: 9606] [142260] (1) picpic
        SQ Q9ULW5 58-227
    61. RhoQ [142261]
      1. Human (Homo sapiens) [TaxId: 9606] [142262] (2) picpic
        SQ P17081 1-185
    62. Rab27b [142263]
      1. Human (Homo sapiens) [TaxId: 9606] [142264] (2) picpic
        SQ O00194 4-189
    63. Rab2a [142265]
      1. Human (Homo sapiens) [TaxId: 9606] [142266] (4) picpic
        SQ P61019 2-170
    64. di-Ras2 [142267]
      1. Human (Homo sapiens) [TaxId: 9606] [142268] (2) picpic
        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) picpic
        SQ Q87WW1 16-237
    66. Rab14 [142271]
      1. Human (Homo sapiens) [TaxId: 9606] [142272] (2) picpic
        SQ P61106 7-174
    67. r-Ras [142273]
      1. Human (Homo sapiens) [TaxId: 9606] [142274] (1) picpic
        SQ P10301 24-196
    68. GTP-binding protein RheB [142275]
      1. Human (Homo sapiens) [TaxId: 9606] [142276] (3) picpic
        SQ Q15382 3-169
    69. di-Ras1 [142277]
      1. Human (Homo sapiens) [TaxId: 9606] [142278] (4) picpic
        SQ O95057 4-176
    70. Rab-33b [142279]
      1. Mouse (Mus musculus) [TaxId: 10090] [142280] (2) picpic
        SQ O35963 32-196
    71. r-Ras2 [142281]
      1. Human (Homo sapiens) [TaxId: 9606] [142282] (2) picpic
        SQ P62070 10-180
    72. Ras-related protein M-Ras (XRas) [142283]
      1. Mouse (Mus musculus) [TaxId: 10090] [142284] (2) picpic
        SQ O08989 10-178
    73. Rab21 [142285]
      1. Human (Homo sapiens) [TaxId: 9606] [142286] (10) picpic
        SQ Q9UL25 16-182
    74. Rab2b [142287]
      1. Human (Homo sapiens) [TaxId: 9606] [142288] (1) picpic
        SQ Q8WUD1 4-176
    75. GTP-binding protein GEM [142289]
      1. Human (Homo sapiens) [TaxId: 9606] [142290] (1) picpic
        SQ P55040 73-244
    76. Ras-like estrogen-regulated growth inhibitor, RERG [142291]
      1. Human (Homo sapiens) [TaxId: 9606] [142292] (1) picpic
        SQ Q96A58 5-172
    77. Rab8a [142293]
      1. Mouse (Mus musculus) [TaxId: 10090] [142294] (2) picpic
        SQ P55258 3-175
    78. Rad [142295]
      1. Human (Homo sapiens) [TaxId: 9606] [142296] (2) picpic
        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) picpic
      2. Chicken (Gallus gallus), Va isoform [TaxId: 9031] [102369] (3) picpic
      3. Bay scallop (Aequipecten irradians) [TaxId: 31199] [52644] (11) picpic
        SQ P24733 3-836 ! SQ P24733 6-837
      4. Dictyostelium discoideum [TaxId: 44689] [52645] (18) picpic
      5. Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689] [75206] (1) picpic
        lacks the SH3-like insert domain
    2. Kinesin [52646]
      1. Human (Homo sapiens) [TaxId: 9606] [52647] (2) picpic
      2. Rat (Rattus norvegicus) [TaxId: 10116] [52648] (2) picpic
      3. Mouse (Mus musculus), kif1a [TaxId: 10090] [64017] (12) picpic
        SQ P33173 3-355
      4. Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606] [64018] (34) picpic
      5. Mouse (Mus musculus), kif2c [TaxId: 10090] [102370] (2) picpic
      6. Neurospora crassa [TaxId: 5141] [69490] (1) picpic
      7. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102371] (1) picpic
    3. Kinesin motor Ncd (non-claret disjunctional) [52649]
      contains coiled-coil neck
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [52650] (3) picpic
      2. Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932] [52651] (5) picpic
        kinesin-like protein
    4. Kinesin heavy chain-like protein [110548]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [110549] (5) picpic
        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) picpic
    2. Adenylosuccinate synthetase, PurA [52655]
      common fold is interrupted by an all-alpha subdomain, residues 100-200
      1. Escherichia coli [TaxId: 562] [52656] (24) picpic
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [52657] (1) picpic
      3. Bread wheat (Triticum aestivum) [TaxId: 4565] [52658] (1) picpic
      4. Mouse (Mus musculus) [TaxId: 10090] [69491] (9) picpic
      5. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102372] (1) picpic
    3. Formyltetrahydrofolate synthetase [52659]
      modified P-loop; there are many insertions in the common fold
      1. Moorella thermoacetica [TaxId: 1525] [52660] (3) picpic
    4. Nitrogenase iron protein [52661]
      1. Azotobacter vinelandii [TaxId: 354] [52662] (19) picpic
      2. Clostridium pasteurianum [TaxId: 1501] [52663] (1) picpic
    5. Cell division regulator MinD [64019]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [64020] (1) picpic
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [64021] (2) picpic
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [64022] (1) picpic
    6. GTPase domain of the signal sequence recognition protein Ffh [52664]
      1. Thermus aquaticus [TaxId: 271] [52665] (25) picpic
      2. Archaeon Acidianus ambivalens [TaxId: 2283] [64023] (2) picpic
      3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [102373] (2) picpic
    7. GTPase domain of the signal recognition particle receptor FtsY [52666]
      1. Escherichia coli [TaxId: 562] [52667] (2) picpic
      2. Thermus aquaticus [TaxId: 271] [102374] (8) picpic
      3. Thermotoga maritima [TaxId: 2336] [110550] (1) picpic
        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) picpic
    9. Hypothetical protein YjiA, N-terminal domain [89671]
      homologue of the cobalamin biosynthesis protein CobW
      1. Escherichia coli [TaxId: 562] [89672] (1) picpic
    10. Molybdopterin-guanine dinucleotide biosynthesis protein MobB [89673]
      forms segment-swapped dimer
      1. Escherichia coli [TaxId: 562] [89674] (2) picpic
      2. Bacillus stearothermophilus [TaxId: 1422] [117539] (1) picpic
        SQ Q5L1X2 # 91% sequence identity
    11. CTP synthase PyrG, N-terminal domain [110551]
      1. Escherichia coli [TaxId: 562] [110552] (1) picpic
        SQ P08398
      2. Thermus thermophilus [TaxId: 274] [110553] (3) picpic
        SQ Q5SIA8
      3. Human (Homo sapiens) [TaxId: 9606] [159561] (2) picpic
        SQ Q5VW67 1-273
    12. ATP(GTP)-binding protein PAB0955 [142297]
      PYRAB14380; belongs to Pfam 03029
      1. Pyrococcus abyssi [TaxId: 29292] [142298] (9) picpic
        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) picpic
        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) picpic
        SQ P27254 1-327
    15. Metallochaperone MeaB [159564]
      ArgK-like (sub)family; Pfam 03308
      1. Methylobacterium extorquens [TaxId: 408] [159565] (4) picpic
        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) picpic
        SQ P0A7G6 P03017
      2. Mycobacterium tuberculosis [TaxId: 1773] [52673] (6) picpic
      3. Mycobacterium smegmatis [TaxId: 1772] [89675] (4) picpic
      4. Deinococcus radiodurans [TaxId: 1299] [117540] (1) picpic
        SQ P42443 15-341
    2. Gene 4 protein (g4p, DNA primase), helicase domain [52674]
      1. Bacteriophage T7 [TaxId: 10760] [52675] (7) picpic
    3. Hexameric replicative helicase repA [52676]
      1. Escherichia coli [TaxId: 562] [52677] (3) picpic
    4. Bacterial conjugative coupling protein TrwB [69492]
      1. Escherichia coli [TaxId: 562] [69493] (5) picpic
    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) picpic
    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) picpic
    7. DNA repair protein Rad51, catalytic domain [82412]
      1. Human (Homo sapiens) [TaxId: 9606] [82413] (1) picpic
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102377] (1) picpic
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110554] (1) picpic
        SQ P25454 81-395
      4. Archaeon Methanococcus voltae [TaxId: 2188] [110555] (8) picpic
        SQ O73948
    8. Central domain of alpha subunit of F1 ATP synthase [88774]
      1. Cow (Bos taurus) [TaxId: 9913] [88775] (18) picpic
        SQ P19483
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88776] (2) picpic
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88777] (1) picpic
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88778] (2) picpic
    9. Central domain of beta subunit of F1 ATP synthase [88779]
      1. Cow (Bos taurus) [TaxId: 9913] [88780] (12) picpic
        SQ P00829
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88781] (8) picpic
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88782] (1) picpic
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88783] (2) picpic
    10. Transcription termination factor Rho, ATPase domain [89676]
      1. Escherichia coli [TaxId: 562] [89677] (10) picpic
        SQ P03002
    11. Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU [52682]
      lacks the last strand 8
      1. Salmonella typhimurium [TaxId: 90371] [52683] (2) picpic
    12. ATP:corrinoid adenosyltransferase CobA [52684]
      lacks the two last strands
      1. Salmonella typhimurium [TaxId: 90371] [52685] (3) picpic
    13. Meiotic recombination protein DMC1/LIM15 homolog [110556]
      1. Human (Homo sapiens) [TaxId: 9606] [110557] (1) picpic
        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) picpic
        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) picpic
        SQ Q94M05
    16. Hypothetical kinase-like protein Aq_1292 [142301]
      member of Pfam 03266 (DUF265)
      1. Aquifex aeolicus [TaxId: 63363] [142302] (1) picpic
        SQ O67322 1-178
    17. Cancer-related NTPase, C1orf57 [159566]
      member of Pfam 03266; DUF265
      1. Human (Homo sapiens) [TaxId: 9606] [159567] (1) picpic
        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) picpic
  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) picpic
    2. Branched chain aminoacid ABC transporter [75207]
      1. Thermotoga maritima, TM1139 [TaxId: 2336] [75208] (1) picpic
    3. MJ1267 [64025]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64026] (3) picpic
    4. MJ0796 [64027]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64028] (2) picpic
    5. Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain [102378]
      1. Mouse (Mus musculus) [TaxId: 10090] [102379] (8) picpic
        SQ P26361 390-670
      2. Human (Homo sapiens) [TaxId: 9606] [117543] (2) picpic
        SQ P13569 389-671
    6. Peptide transporter Tap1, C-terminal ABC domain [64029]
      1. Human (Homo sapiens) [TaxId: 9606] [64030] (1) picpic
    7. Maltose transport protein MalK, N-terminal domain [52689]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [52690] (1) picpic
      2. Escherichia coli [TaxId: 562] [102380] (13) picpic
    8. Glucose transport protein GlcV, N-terminal domain [89681]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89682] (5) picpic
    9. ABC transporter involved in vitamin B12 uptake, BtuD [75209]
      1. Escherichia coli [TaxId: 562] [75210] (1) picpic
    10. Haemolysin B ATP-binding protein [89683]
      1. Escherichia coli [TaxId: 562] [89684] (3) picpic
    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) picpic
      2. Salmonella typhimurium [TaxId: 90371] [159568] (12) picpic
        SQ P63359 329-581
    12. Multidrug resistance ABC transporter LmrA, C-terminal domain [102381]
      1. Lactococcus lactis [TaxId: 1358] [102382] (1) picpic
    13. Rad50 [52691]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [52692] (4) picpic
    14. Smc head domain [52693]
      1. Thermotoga maritima [TaxId: 2336] [52694] (1) picpic
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117544] (1) picpic
        SQ P32908 2-214,1024-1223
      3. Pyrococcus furiosus [TaxId: 2261] [117545] (2) picpic
        SQ Q877I1 1-167,1012-1173
    15. Cell division protein MukB [52695]
      1. Escherichia coli [TaxId: 562] [52696] (1) picpic
    16. DNA repair protein MutS, the C-terminal domain [52697]
      1. Thermus aquaticus [TaxId: 271] [52698] (4) picpic
      2. Escherichia coli [TaxId: 562] [52699] (10) picpic
        SQ P23909 2-800
    17. Putative ABC transporter PF0895 [110560]
      1. Pyrococcus furiosus [TaxId: 2261] [110561] (1) picpic
        SQ Q8U2E3
    18. Hypothetical protein PH0022, N-terminal domain [117546]
      1. Pyrococcus horikoshii [TaxId: 53953] [117547] (2) picpic
        SQ O57758
    19. Putative ABC transporter TM0544 [117548]
      1. Thermotoga maritima [TaxId: 2336] [117549] (1) picpic
        SQ Q9WZ14
    20. Putative multidrug export ATP-binding/permease protein SAV1866 [142303]
      1. Staphylococcus aureus [TaxId: 1280] [142304] (4) picpic
        SQ Q99T13 324-578
    21. Molybdate/tungstate import ATP-binding protein WtpC (ModC) [159569]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159570] (4) picpic
        SQ O30144 1-240
    22. Methionine import ATP-binding protein MetN [159571]
      1. Escherichia coli [TaxId: 562] [159572] (4) picpic
        SQ P30750 1-240
    23. Sulfate/molybdate ABC transporter, ATP-binding protein [159573]
      1. Methanosarcina acetivorans [TaxId: 2214] [159574] (2) picpic
        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) picpic
      2. Escherichia coli, RepD [TaxId: 562] [52703] (1) picpic
    2. Putative DEAD box RNA helicase [52704]
      homologous to eIF4a and UvrB
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [52705] (1) picpic
    3. Probable DEAD box RNA helicase YqfR [102383]
      1. Bacillus stearothermophilus [TaxId: 1422] [102384] (1) picpic
    4. RecQ helicase domain [102385]
      1. Escherichia coli [TaxId: 562] [102386] (2) picpic
    5. DEAD box RNA helicase rck/p54 [102387]
      1. Human (Homo sapiens) [TaxId: 9606] [102388] (1) picpic
    6. RecG helicase domain [69494]
      1. Thermotoga maritima [TaxId: 2336] [69495] (1) picpic
    7. Initiation factor 4a [52706]
      homologous to UvrB
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [52707] (5) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [142305] (2) picpic
        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) picpic
      2. Bacillus caldotenax [TaxId: 1395] [52710] (7) picpic
        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) picpic
        SQ P28366
      2. Mycobacterium tuberculosis [TaxId: 1773] [89687] (2) picpic
    10. Spliceosome RNA helicase BAT1 (UAP56) [110562]
      1. Human (Homo sapiens) [TaxId: 9606] [110563] (5) picpic
        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) picpic
        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) picpic
        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) picpic
        SQ P04993
    14. putative ATP-dependent RNA helicase VlgB [142306]
      1. Flatworm (Dugesia japonica) [TaxId: 6161] [142307] (2) picpic
        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) picpic
        SQ Q8TZH8 2-201! SQ Q8TZH8 202-487
    16. ATP-dependent RNA helicase DDX25 [142310]
      1. Human (Homo sapiens) [TaxId: 9606] [142311] (4) picpic
        SQ Q9UHL0 307-474
    17. Helicase of the SNF2/Rad54 hamily [142312]
      1. Sulfolobus solfataricus [TaxId: 2287] [142313] (8) picpic
        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) picpic
        SQ P38919 22-243! SQ P38919 244-411
    19. Rad54-like, Rad54L [142316]
      1. Zebra fish (Danio rerio) [TaxId: 7955] [142317] (2) picpic
        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) picpic
        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) picpic
        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) picpic
        SQ P39517 252-422! SQ P39517 46-251
    23. Hel308 helicase [159575]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159576] (4) picpic
  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) picpic
        SQ P06710 5-368
      2. Thermotoga maritima [TaxId: 2336] [142324] (1) picpic
        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) picpic
        SQ P28631
    3. delta subunit of DNA polymerase III, N-domain [64033]
      1. Escherichia coli [TaxId: 562] [64034] (5) picpic
        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) picpic
    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) picpic
    6. Holliday junction helicase RuvB [52713]
      contains "winged helix" DNA-binding domain after the family specific domains
      1. Thermus thermophilus [TaxId: 274] [52714] (3) picpic
      2. Thermotoga maritima [TaxId: 2336] [64037] (6) picpic
    7. Transcriptional activator sigm54 (NtrC1), C-terminal domain [102389]
      1. Aquifex aeolicus [TaxId: 63363] [102390] (2) picpic
    8. CDC6, N-domain [52715]
      contains "winged helix" DNA-binding domain after the family specific domains
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [52716] (1) picpic
    9. Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein [52717]
      1. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [52718] (2) picpic
    10. Membrane fusion ATPase VCP/p97 [64038]
      1. Mouse (Mus musculus) [TaxId: 10090] [64039] (4) picpic
    11. AAA domain of cell division protein FtsH [82418]
      ATP-dependent protease
      1. Escherichia coli [TaxId: 562] [82419] (1) picpic
      2. Thermus thermophilus [TaxId: 274] [82420] (4) picpic
      3. Thermotoga maritima [TaxId: 2336] [142325] (12) picpic
        SQ Q9WZ49 150-402
    12. HslU [52721]
      ATPase subunit of ATP-dependent protease
      1. Escherichia coli [TaxId: 562] [52722] (10) picpic
      2. Haemophilus influenzae [TaxId: 727] [52723] (6) picpic
    13. ClpX [102391]
      ATPase subunit of ATP-dependent protease
      1. Helicobacter pylori [TaxId: 210] [102392] (1) picpic
    14. ATPase domain of protease Lon (La) [102393]
      1. Escherichia coli [TaxId: 562] [102394] (1) picpic
    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) picpic
        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) picpic
      2. Escherichia coli [TaxId: 562] [75212] (1) picpic
    17. ATPase subunit of magnesium chelatase, BchI [64040]
      1. Rhodobacter capsulatus [TaxId: 1061] [64041] (1) picpic
    18. Papillomavirus large T antigen helicase domain [89688]
      1. Simian virus 40 [TaxId: 10633] [89689] (16) picpic
        SQ P03070 265-627
    19. Rep 40 protein helicase domain [110564]
      1. Adeno-associated virus 2, AAV2 [TaxId: 10804] [110565] (2) picpic
        SQ P03132 225-490
    20. Replication factor C1 [110566]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110567] (1) picpic
        SQ P38630 295-696
    21. Replication factor C4 [110568]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110569] (1) picpic
        SQ P40339
    22. Replication factor C3 [110570]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110571] (1) picpic
        SQ P38629
    23. Replication factor C2 [110572]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110573] (1) picpic
        SQ P40348
    24. Replication factor C5 [110574]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110575] (1) picpic
        SQ P38251
    25. Replication protein E1 helicase domain [110576]
      1. Human papillomavirus type 18 [TaxId: 333761] [110577] (1) picpic
        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) picpic
        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) picpic
        SQ Q97Y08 1-283
    28. CED-4, NB-ARC domain [159577]
      belongs to Pfam 00931
      1. Caenorhabditis elegans [TaxId: 6239] [159578] (1) picpic
        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) picpic
    2. Dengue virus helicase [142328]
      1. Dengue virus type 2 [TaxId: 11060] [142329] (8) picpic
        SQ Q91H74 1653-1957! SQ Q91H74 1958-2093
    3. YFV helicase domain [142330]
      1. Yellow fever virus [TaxId: 11089] [142331] (2) picpic
        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) picpic
  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) picpic
  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) picpic
  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) picpic
        SQ P04183 18-191
      2. Ureaplasma urealyticum [TaxId: 2130] [117561] (8) picpic
        SQ Q9PPP5 11-211
      3. Clostridium acetobutylicum [TaxId: 1488] [117562] (1) picpic
        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) picpic
        SQ Q9K6P2 1-176
    2. Hypothetical protein Atu3015 [142335]
      1. Agrobacterium tumefaciens [TaxId: 358] [142336] (1) picpic
        SQ Q8UBK1 6-181
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk