Structural Classification of Proteins

Class: Multi-domain proteins (alpha and beta)

: Folds consisting of two or more domains belonging to different classes

Lineage:

Root: scop
Class: Multi-domain proteins (alpha and beta) [56572]
Folds consisting of two or more domains belonging to different classes

Folds:

Serpins [56573] (1)
contains a cluster of helices and a beta-sandwich
1. Serpins [56574] (1)
  uperfamily
  1. Serpins [56575] (17)
    1. Elastase inhibitor [56576]
      1. Horse (Equus caballus) [TaxId: 9796] [56577] (1)
    2. Ovalbumin [56578]
      1. Hen (Gallus gallus) [TaxId: 9031] [56579] (3)
    3. Antichymotrypsin, alpha-1 [56580]
      1. Human (Homo sapiens) [TaxId: 9606] [56581] (5)
    4. Antitrypsin, alpha-1 [56582]
      1. Human (Homo sapiens) [TaxId: 9606] [56583] (15)
    5. Antithrombin [56584]
      1. Cow (Bos taurus) [TaxId: 9913] [56585] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [56586] (33)
        SQ P01008
    6. Plasminogen activator inhibitor-1 [56587]
      1. Human (Homo sapiens) [TaxId: 9606] [56588] (9)
    7. Plasminogen activator inhibitor-2 [56589]
      1. Human (Homo sapiens) [TaxId: 9606] [56590] (2)
    8. Heparin cofactor II (Hc-II, leuserpin 2) [82833]
      1. Human (Homo sapiens) [TaxId: 9606] [82834] (2)
    9. Protein C inhibitor [82835]
      1. Human (Homo sapiens) [TaxId: 9606] [82836] (1)
    10. Neuroserpin [69871]
      1. Mouse (Mus musculus) [TaxId: 10090] [69872] (1)
    11. Serpin K [56591]
      1. Tobacco hawkmoth (Manduca sexta) [TaxId: 7130] [56592] (1)
    12. Alaserpin (serpin 1) [64469]
      1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [64470] (1)
        Michaelis serpin-trypsin complex
    13. Viral serpin crmA (cytokine response modifier protein) [56593]
      1. Cowpox virus [TaxId: 10243] [56594] (3)
    14. Pigment epithelium-derived factor, PEDF [64471]
      1. Human (Homo sapiens) [TaxId: 9606] [64472] (1)
    15. Thermopin [90080]
      Serpin from a thermophilic prokaryote
      1. Thermobifida fusca [TaxId: 2021] [90081] (2)
        SQ Q47NK3
    16. Maspin [118179]
      1. Human (Homo sapiens) [TaxId: 9606] [118180] (2)
        SQ P36952
FdhE-like [144019] (1)
consists on the N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and the C-terminal helix packed together
1. FdhE-like [144020] (1)
  uperfamily
  1. FdhE-like [144021] (1)
    Pfam 04216
    1. FdhE homolog PA4809 [144022]
      1. Pseudomonas aeruginosa [TaxId: 287] [144023] (1)
        SQ Q9HV00 19-308
FlhC-like [160929] (1)
3 domains; d1 & d2 are similar three-helical bundles, with d1 containing an HTH motif; d3: zinc finger of a rubredoxin-like fold
1. FlhC-like [160930] (1)
  1. FlhC-like [160931] (1)
    Pfam 05280
    1. Flagellar transcriptional activator FlhC [160932]
      1. Escherichia coli [TaxId: 562] [160933] (2)
        SQ P0ABY7 5-160
Replication terminator protein (Tus) [56595] (1)
contains a cluster of helices and a beta-sandwich
1. Replication terminator protein (Tus) [56596] (1)
  uperfamily
  1. Replication terminator protein (Tus) [56597] (1)
    1. Replication terminator protein (Tus) [56598]
      1. Escherichia coli [TaxId: 562] [56599] (4)
VPA0735-like [160934] (1)
consists of a cluster of helices and two beta-sandwich domains of similar topology; probable duplication
1. VPA0735-like [160935] (1)
  1. VPA0735-like [160936] (1)
    the N-terminal beta-sandwich domain corresponds to Pfam 06863 (DUF1254); the C-terminal beta-sandwich domains corresponds to Pfam 06742 (DUF1214); the two Pfam families are structurally related
    1. Hypothetical protein VPA0735 [160937]
      1. Vibrio parahaemolyticus [TaxId: 670] [160938] (2)
        SQ Q87I71 22-482
2-methylcitrate dehydratase PrpD [103377] (1)
consists of an all-alpha and alpha+beta domains
1. 2-methylcitrate dehydratase PrpD [103378] (1)
  uperfamily
  1. 2-methylcitrate dehydratase PrpD [103379] (1)
    1. 2-methylcitrate dehydratase PrpD [103380]
      1. Escherichia coli [TaxId: 562] [103381] (1)
Antivirulence factor [103382] (1)
contains a helical bundle with a buried helix and an alpha+beta insert domain
1. Antivirulence factor [103383] (1)
  uperfamily
  1. Antivirulence factor [103384] (1)
    1. Type III effector AvrB [103385]
      1. Pseudomonas syringae [TaxId: 317] [103386] (4)
Api92-like [160939] (1)
2 domains; d1: [alpha+beta with similarity to ferredoxin-like fold]; d2: [6 helices, bundle, one buried central helix], inserted into d1
1. Api92-like [160940] (1)
  1. Api92-like [160941] (1)
    Pfam 06924; DUF1281
    1. Hypothetical protein api92 [160942]
      1. Yersinia pseudotuberculosis [TaxId: 633] [160943] (1)
        SQ Q6EVP2 3-282
PH0156-like [160944] (1)
2 (sub)domains; d1: [alpha/beta with central mixed beta-sheet, order: 23415876, similarity to the G protein but no P-loop]; d2: [all-alpha, 5 helices, provides dimerization interface]
1. PH0156-like [160945] (1)
  1. PH0156-like [160946] (1)
    PfamB 117416
    1. Hypothetical protein PH0156 [160947]
      1. Pyrococcus horikoshii [TaxId: 53953] [160948] (2)
        SQ O57895 1-241
YacF-like [160949] (1)
2 domains; d1: kinked four-helical bundle, inserted in d2: beta-sandwich of 7 strands in two sheets
1. YacF-like [160950] (1)
  probable biological unit is a dimer
  1. YacF-like [160951] (1)
    Pfam 07072; DUF1342
    1. Uncharacterized protein VP2528 [160952]
      1. Vibrio parahaemolyticus [TaxId: 670] [160953] (2)
        SQ Q87LT3 1-245
Virulence-associated V antigen [103387] (1)
consists of an all-alpha and alpha+beta domains connected by antiparallel coiled coil
1. Virulence-associated V antigen [103388] (1)
  uperfamily
  1. Virulence-associated V antigen [103389] (1)
    1. Low calcium response locus protein V, LcrV [103390]
      1. Yersinia pestis [TaxId: 632] [103391] (1)
Heme-dependent catalase-like [56633] (1)
contains an (8,10) beta-barrel and an all-alpha domain
1. Heme-dependent catalase-like [56634] (2)
  uperfamily
  1. Heme-dependent catalases [56635] (9)
    1. Catalase I [56636]
      1. Cow (Bos taurus) [TaxId: 9913] [56637] (20)
      2. Human (Homo sapiens) [TaxId: 9606] [56638] (6)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56639] (1)
      4. Proteus mirabilis [TaxId: 584] [56640] (8)
      5. Helicobacter pylori [TaxId: 210] [103392] (6)
      6. Enterococcus faecalis [TaxId: 1351] [103393] (1)
      7. Micrococcus lysodeikticus [TaxId: 1270] [56641] (4)
      8. Pseudomonas syringae [TaxId: 317] [75599] (1)
    2. Catalase II [56642]
      contains additional flavodoxin-like domain at C-terminus
      1. Escherichia coli, HPII [TaxId: 562] [56643] (14)
  2. Allene oxide synthase [118183] (1)
    1. Allene oxide synthase-lipoxygenase protein, N-terminal domain [118184]
      1. Black sea rod (Plexaura homomalla) [TaxId: 47982] [118185] (1)
        SQ O16025 1-374
Acyl-CoA dehydrogenase NM domain-like [56644] (1)
2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
1. Acyl-CoA dehydrogenase NM domain-like [56645] (2)
  flavoprotein: binds FAD; constituent families differ in the numbers of C-terminal domains (four-helical bundles)
  uperfamily
  1. Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains [56646] (12)
    1. Butyryl-CoA dehydrogenase, NM domains [56647]
      1. Megasphaera elsdenii [TaxId: 907] [56648] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [69877] (1)
    2. Medium chain acyl-CoA dehydrogenase, NM domains [56649]
      1. Pig (Sus scrofa) [TaxId: 9823] [56650] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [56651] (8)
        SQ P11310 34-421
      3. Thermus thermophilus [TaxId: 274] [118186] (1)
        SQ Q5SJ70 32-409
    3. Isovaleryl-coa dehydrogenase, NM domains [56652]
      1. Human (Homo sapiens) [TaxId: 9606] [56653] (1)
    4. Isobutyryl-CoA dehydrogenase [103394]
      1. Human (Homo sapiens) [TaxId: 9606] [103395] (1)
    5. Protein FkbI [103396]
      involved in biosynthesis of methoxymalonyl extender unit of fk520 polyketide immunosuppressant
      1. Streptomyces hygroscopicus [TaxId: 1912] [103397] (1)
    6. Glutaryl-CoA dehydrogenase GCDH [111293]
      1. Human (Homo sapiens) [TaxId: 9606] [111294] (4)
        SQ Q92947
    7. 4-hydroxybutyryl-CoA dehydratase AbfD, NM domains [118187]
      1. Clostridium aminobutyricum [TaxId: 33953] [118188] (1)
        SQ P55792
    8. Acyl-CoA dehydrogenase [144024]
      1. Thermus thermophilus [TaxId: 274] [144025] (8)
        SQ Q5SGZ2 2-234
    9. Nitroalkane oxidase [144026]
      1. Fusarium oxysporum [TaxId: 5507] [144027] (18)
        SQ Q8X1D8 2-260
  2. acyl-CoA oxidase N-terminal domains [75600] (2)
    1. Peroxisomal acyl-CoA oxidase-II, domains 1 and 2 [75601]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [75602] (2)
    2. Acyl-coenzyme A oxidase 1, domains 1 and 2 [118189]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118190] (1)
        SQ O65202
Carbohydrate phosphatase [56654] (1)
N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
1. Carbohydrate phosphatase [56655] (2)
  uperfamily
  1. Inositol monophosphatase/fructose-1,6-bisphosphatase-like [56656] (14)
    1. Fructose-1,6-bisphosphatase [56657]
      1. Pig (Sus scrofa) [TaxId: 9823] [56658] (54)
      2. Human (Homo sapiens) [TaxId: 9606] [56659] (1)
      3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [56660] (1)
      4. Spinach (Spinacia oleracea) [TaxId: 3562] [56661] (1)
      5. Garden pea (Pisum sativum) [TaxId: 3888] [56662] (3)
    2. Inositol monophosphatase [56663]
      1. Human (Homo sapiens) [TaxId: 9606] [56664] (8)
    3. Archaeal inositol monophosphatase/fructose-1,6-bisphosphatase [56665]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [56666] (3)
        MJ0109
        structural genomics
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75608] (5)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103398] (1)
        PH1897
      4. Pyrococcus furiosus [TaxId: 2261] [118191] (1)
        SQ Q8TZH9
    4. Inositol polyphosphate 1-phosphatase [56667]
      1. Cow (Bos taurus), brain [TaxId: 9913] [56668] (1)
    5. 3';5'-adenosine bisphosphatase, PAP phosphatase [56669]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69878] (4)
      2. Yeast (Candida albicans) [TaxId: 5476] [56670] (1)
        sequence identical to that of Saccharomyces cerevisiae
    6. PIPase [64475]
      enzyme displaying both inositol-polyphosphate 1-phosphatase and 3'-phosphoadenosine-5'-phosphate phosphatase activities
      1. Rat (Rattus norvegicus) [TaxId: 10116] [64476] (1)
  2. GlpX-like bacterial fructose-1,6-bisphosphatase [90087] (1)
    similar to the other family in overall domain architecture but each domain has a permuted topology
    1. Glycerol metabolism protein GlpX [90088]
      1. Escherichia coli [TaxId: 562] [90089] (1)
DNA/RNA polymerases [56671] (1)
divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
1. DNA/RNA polymerases [56672] (6)
  "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain
  uperfamily
  1. DNA polymerase I [56673] (12)
    1. DNA polymerase I (Klenow fragment) [56674]
      1. Escherichia coli [TaxId: 562] [56675] (14)
      2. Thermus aquaticus [TaxId: 271] [56676] (13)
      3. Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] [56677] (45)
        SQ Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
        SQ Q45458 298-876 # 88% sequence identity
    2. T7 phage DNA polymerase [56678]
      1. Bacteriophage T7 [TaxId: 10760] [56679] (16)
        SQ P00581
    3. Family B DNA polymerase [56680]
      1. Escherichia coli [TaxId: 562] [103399] (1)
      2. Bacteriophage RB69 [TaxId: 12353] [56681] (27)
      3. Archaeon Thermococcus gorgonarius [TaxId: 71997] [56682] (3)
      4. Archaeon Thermococcus sp., 9on-7 [TaxId: 35749] [56683] (1)
      5. Archaeon Desulfurococcus tok [TaxId: 108142] [56684] (2)
      6. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [56685] (2)
        SQ P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
      7. Sulfolobus solfataricus [TaxId: 2287] [118192] (1)
        SQ P26811 40-864
    4. phi29 DNA polymerase [118193]
      1. Bacteriophage phi-29 [TaxId: 10756] [118194] (18)
        SQ P03680
  2. Lesion bypass DNA polymerase (Y-family), catalytic domain [100888] (6)
    contains a distinct 'fingers' domain possibly related to the C-terminal subdomain of hypothetical protein Ta1206 (1qw2)
    1. DinB homolog (DBH) [100889]
      1. Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287] [100890] (62)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [100891] (3)
      3. Sulfolobus acidocaldarius Brock et al. 1972 (Sulfolobus acidocaldarius) [TaxId: 2285] [160954] (3)
    2. DNA polymerase eta [100892]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [100893] (5)
    3. DNA polymerase iota [111295]
      1. Human (Homo sapiens) [TaxId: 9606] [111296] (8)
        SQ Q9UNA4
    4. DNA polymerase kappa [111297]
      1. Human (Homo sapiens) [TaxId: 9606] [111298] (1)
        SQ Q9UBT6 71-517
  3. Reverse transcriptase [56686] (3)
    1. MMLV reverse transcriptase [56687]
      1. Moloney murine leukemia virus, MoMLV [TaxId: 11801] [56688] (22)
        SQ P03355 RE 144-594
    2. HIV-1 reverse transcriptase [56689]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [56690] (191)
        SQ P04585 159-692 # chain A coverage; chain B is shorter: 162-582 ! SQ P03366 186-725 # chain A coverage; chain B coverage: 156-584 ! SQ P04585 158-698 # chain A coverage; chain B is shorter: 159-595
      2. Human immunodeficiency virus type 2 [TaxId: 11709] [82840] (2)
  4. T7 RNA polymerase [56691] (1)
    1. T7 RNA polymerase [56692]
      multidomain; mostly alpha
      1. Bacteriophage T7 [TaxId: 10760] [56693] (11)
  5. RNA-dependent RNA-polymerase [56694] (11)
    1. Viral RNA polymerase [56695]
      1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [56696] (13)
        SQ P03300 1748-2208
      2. Hepatitis C virus [TaxId: 11103] [56697] (30)
      3. Rabbit hemorrhagic disease virus [TaxId: 11976] [69882] (2)
      4. Norwalk virus [TaxId: 11983] [103400] (3)
      5. Bovine viral diarrhea virus [TaxId: 11099] [103401] (3)
      6. Human rhinovirus 1B, HRV-1B [TaxId: 12129] [111299] (1)
        SQ P12916 1698-2157
      7. Human rhinovirus 16, HRV-16 [TaxId: 31708] [111300] (1)
        SQ Q82122 1694-2153
      8. Human rhinovirus 14, HRV-14 [TaxId: 12131] [111301] (1)
        SQ P03303 1720-2179
      9. Foot-and-mouth disease virus [TaxId: 12110] [111302] (10)
        SQ Q9QCE4 1858-2327
      10. Avian infectious bursal disease virus [TaxId: 10995] [160955] (1)
        SQ Q9Q6Q5 31-804
    2. Reovirus polymerase lambda3 [82841]
      contains additional N-terminal domain (res. 1-380) and C-terminal "bracelet" domain (res. 891-1267)
      1. Reovirus [TaxId: 10891] [82842] (5)
  6. dsRNA phage RNA-dependent RNA-polymerase [64480] (1)
    1. dsRNA phage RNA-dependent RNA-polymerase [64481]
      1. Bacteriophage PHI-6 [TaxId: 10879] [64482] (11)
beta and beta-prime subunits of DNA dependent RNA-polymerase [64483] (1)
Multidomain subunits of complex domain organization
1. beta and beta-prime subunits of DNA dependent RNA-polymerase [64484] (2)
  The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit
  uperfamily
  1. RNA-polymerase beta [64485] (3)
    1. RBP2 [64491]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64492] (30)
        SQ P08518; part of multichain biological unit
    2. RNA-polymerase beta [64488]
      1. Thermus aquaticus [TaxId: 271] [64489] (4)
      2. Thermus thermophilus [TaxId: 274] [75609] (24)
        SQ Q8RQE9; part of multichain biological unit
  2. RNA-polymerase beta-prime [64490] (3)
    1. RBP1 [64486]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64487] (25)
        SQ P04050; part of multichain biological unit
    2. RNA-polymerase beta-prime [64493]
      1. Thermus aquaticus [TaxId: 271] [64494] (4)
      2. Thermus thermophilus [TaxId: 274] [75610] (24)
        SQ Q8RQE8; part of multichain biological unit
Poly(A) polymerase catalytic subunit-like [160956] (1)
3 domains; d1: all-alpha, contains HhH motif; d2: alpha+beta of nucleotidyltransferase fold (scop_cf 81302); d3: [alpha+beta; beta(3)-alpha-beta(3)-alpha(2); 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 123654, strands 2 and 5 are antiparallel to the rest
1. Poly(A) polymerase catalytic subunit-like [160957] (1)
  Central domain d2 is distantly related to the nucleotidyltransferase superfamily (scop_sf 81301)
  1. Poxvirus poly(A) polymerase catalytic subunit-like [160958] (1)
    Pfam 03296
    1. Poly(A) polymerase catalytic subunit, PAPL [160959]
      1. Vaccinia virus [TaxId: 10245] [160960] (2)
        SQ P23371 12-479
Adenylylcyclase toxin (the edema factor) [81299] (1)
3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
1. Adenylylcyclase toxin (the edema factor) [81298] (1)
  Domain 1 has topological and active site similarity to the Nucleotidyltransferases (eg. 1kny N-domain); domain 3 binds calmodulin
  uperfamily
  1. Adenylylcyclase toxin (the edema factor) [69887] (1)
    decorated with many insertions and the C-terminal domain
    1. Adenylylcyclase toxin (the edema factor) [69888]
      1. Bacillus anthracis [TaxId: 1392] [69889] (7)
        SQ P40136
Prokaryotic type I DNA topoisomerase [56711] (1)
4 domains: (1) Toprim alpha/beta; (2&4) "winged helix"-like; (3) barrel: n=6, S=8
1. Prokaryotic type I DNA topoisomerase [56712] (1)
  duplication: the protein chain passing through the domains 2-4 makes two structural repeats
  The active site is formed by the toprim and "winged helix" domains (domains 1 and 4); these two domains are also found in the type II topoisomerase (DNA gyrase A) and in the alpha subunit of topoisomerase IV
  uperfamily
  1. Prokaryotic type I DNA topoisomerase [56713] (3)
    domain 4 contains the catalytic tyrosine residue
    1. DNA topoisomerase I, 67K N-terminal domain [56714]
      1. Escherichia coli [TaxId: 562] [56715] (12)
    2. DNA topoisomerase III [56716]
      1. Escherichia coli [TaxId: 562] [56717] (2)
    3. Topoisomerase "domain" of reverse gyrase [69890]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69891] (2)
Type II DNA topoisomerase [56718] (1)
4 domains: (1) toprim alpha/beta; (2) "winged helix"-like; (3) alpha+beta; (4) all-alpha
1. Type II DNA topoisomerase [56719] (1)
  uperfamily
  1. Type II DNA topoisomerase [56720] (2)
    domain 2 contains the catalytic tyrosine residue
    1. DNA topoisomerase II, C-terminal fragment (residues 410-1202) [56721]
      the N-terminal fragment is homologous to known structure of DNA gyrase B
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56722] (3)
    2. DNA Gyrase A [56723]
      1. Escherichia coli [TaxId: 562] [56724] (3)
DNA topoisomerase IV, alpha subunit [56725] (1)
2 domains: (1) toprim alpha/beta; (2) "winged helix"-like
1. DNA topoisomerase IV, alpha subunit [56726] (1)
  uperfamily
  1. DNA topoisomerase IV, alpha subunit [56727] (1)
    domain 2 contains the catalytic tyrosine residue
    1. DNA topoisomerase IV, alpha subunit [56728]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [56729] (1)
DNA primase core [56730] (1)
2 domains: (1) alpha+beta; (2) toprim alpha/beta
1. DNA primase core [56731] (2)
  uperfamily
  1. DNA primase DnaG catalytic core [56732] (1)
    1. DNA primase DnaG catalytic core [56733]
      1. Escherichia coli [TaxId: 562] [56734] (3)
  2. Primase fragment of primase-helicase protein [90090] (1)
    1. Primase fragment of primase-helicase protein [90091]
      1. Bacteriophage T7 [TaxId: 10760] [90092] (2)
Recombination protein RecR [111303] (1)
consists of three domains: alpha-helical dimerisation domain (res. 1-53) with HhH motif; 'treble cleft' C4 zinc-finger domain (54-76); and Toprim domain (76-199; segment-swapped dimer)
1. Recombination protein RecR [111304] (1)
  uperfamily
  1. Recombination protein RecR [111305] (1)
    three sequential domains correspond to Pfam 00633, Pfam 02132 and Pfam 01751, respectively
    1. Recombination protein RecR [111306]
      1. Deinococcus radiodurans [TaxId: 1299] [111307] (3)
        SQ Q9ZNA2
Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56740] (1)
2 domains: alpha+beta and all-beta
1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56741] (1)
  uperfamily
  1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56742] (2)
    1. Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment [56743]
      1. Human (Homo sapiens) [TaxId: 9606] [56744] (15)
        SQ P11387 203-765 ! SQ P11387 203-767
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56745] (1)
D-aminoacid aminotransferase-like PLP-dependent enzymes [56751] (1)
2 domains: (1) alpha+beta: beta3-alpha2-beta2; (2) alpha/beta, a part of its mixed sheet forms barrel: n=6, S=8
1. D-aminoacid aminotransferase-like PLP-dependent enzymes [56752] (1)
  uperfamily
  1. D-aminoacid aminotransferase-like PLP-dependent enzymes [56753] (5)
    1. D-aminoacid aminotransferase [56754]
      1. Bacillus sp., strain YM-1 [TaxId: 1409] [56755] (7)
        domain 1: 1-120; domain 2: 121-277
      2. Bacillus stearothermophilus [TaxId: 1422] [56756] (1)
    2. Branched-chain aminoacid aminotransferase [56757]
      1. Escherichia coli [TaxId: 562] [56758] (6)
        domain 1: 4-126; domain 2: 137-308
      2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [64508] (9)
    3. Aminodeoxychorismate lyase [56759]
      1. Escherichia coli [TaxId: 562] [56760] (3)
HydB/Nqo4-like [56761] (1)
3 domains: (1) all-alpha; (2&3) alpha+beta
1. HydB/Nqo4-like [56762] (2)
  uperfamily
  1. Nickel-iron hydrogenase, large subunit [56763] (5)
    1. Nickel-iron hydrogenase, large subunit [56764]
      1. Desulfovibrio gigas [TaxId: 879] [56765] (4)
      2. Desulfovibrio vulgaris [TaxId: 881] [56766] (16)
      3. Desulfovibrio fructosovorans [TaxId: 878] [56767] (1)
      4. Desulfomicrobium baculatum [TaxId: 899] [56768] (1)
      5. Desulfovibrio desulfuricans [TaxId: 876] [64509] (1)
  2. Nqo4-like [144028] (1)
    Pfam 00346; Respiratory-chain NADH dehydrogenase, 49 Kd subunit
    1. NADH-quinone oxidoreductase chain 4, Nqo4 [144029]
      1. Thermus thermophilus [TaxId: 274] [144030] (4)
        SQ Q56220 35-409
HydA/Nqo6-like [56769] (1)
2 domains: (1) alpa/beta; (2) Fe-S cluster-bound
1. HydA/Nqo6-like [56770] (2)
  uperfamily
  1. Nickel-iron hydrogenase, small subunit [56771] (5)
    1. Nickel-iron hydrogenase, small subunit [56772]
      1. Desulfovibrio gigas [TaxId: 879] [56773] (4)
      2. Desulfovibrio vulgaris [TaxId: 881] [56774] (16)
      3. Desulfovibrio fructosovorans [TaxId: 878] [56775] (1)
      4. Desulfomicrobium baculatum [TaxId: 899] [56776] (1)
      5. Desulfovibrio desulfuricans [TaxId: 876] [64510] (1)
  2. Nq06-like [144031] (1)
    Pfam 01058
    1. NAD-quinone oxidoreductase chain 6, Nqo6 [144032]
      1. Thermus thermophilus [TaxId: 274] [144033] (4)
        SQ Q56218 14-174
Dehydroquinate synthase-like [56795] (1)
2 domains: (1) alpha/beta of a Rossmann-fold topology, binds NAD (2) multihelical array
1. Dehydroquinate synthase-like [56796] (2)
  uperfamily
  1. Dehydroquinate synthase, DHQS [56797] (2)
    1. Dehydroquinate synthase, DHQS [56798]
      1. Aspergillus nidulans [TaxId: 162425] [56799] (10)
        SQ P07547
      2. Thermus thermophilus [TaxId: 274] [103402] (1)
  2. Iron-containing alcohol dehydrogenase [69892] (6)
    Pfam 00465
    1. Glycerol dehydrogenase [69893]
      1. Bacillus stearothermophilus [TaxId: 1422] [69894] (3)
      2. Thermotoga maritima [TaxId: 2336] [69895] (1)
        TM0423
    2. Alcohol dehydrogenase TM0920 [75612]
      1. Thermotoga maritima [TaxId: 2336] [75613] (2)
    3. Hypothetical oxidoreductase yqhD [111308]
      1. Escherichia coli [TaxId: 562] [111309] (1)
        SQ Q46856
    4. Lactaldehyde reductase FucO [111310]
      1. Escherichia coli [TaxId: 562] [111311] (5)
        SQ P11549
    5. NADH-dependent butanol dehydrogenase A (TM0820) [111312]
      1. Thermotoga maritima [TaxId: 2336] [111313] (1)
        SQ Q9WZS7
Siroheme synthase middle domains-like [75614] (1)
2 domains: (1) alpha+beta, 2 layers; (2) 3/4-helical bundle, right-handed twist, left-handed superhelix
1. Siroheme synthase middle domains-like [75615] (1)
  uperfamily
  1. Siroheme synthase middle domains-like [75616] (2)
    1. Siroheme synthase CysG, domains 2 and 3 [103403]
      1. Salmonella typhimurium [TaxId: 90371] [103404] (3)
    2. Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains [75617]
      involved in siroheme synthesis
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75618] (1)
Acetyl-CoA synthetase-like [56800] (1)
4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta
1. Acetyl-CoA synthetase-like [56801] (1)
  uperfamily
  1. Acetyl-CoA synthetase-like [56802] (8)
    1. Luciferase [56803]
      1. Firefly (Photinus pyralis) [TaxId: 7054] [56804] (2)
    2. Dihydroxybenzoate-AMP ligase DhbE [82843]
      1. Bacillus subtilis [TaxId: 1423] [82844] (3)
    3. Phenylalanine activating domain of gramicidin synthetase 1 [56805]
      1. Bacillus brevis [TaxId: 1393] [56806] (1)
    4. Acetyl-CoA synthetase [90093]
      1. Salmonella enterica [TaxId: 28901] [90094] (2)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103405] (1)
    5. Long chain fatty acid-CoA ligase TT0168 [111314]
      1. Thermus thermophilus [TaxId: 274] [111315] (3)
        SQ Q6L8F0
    6. 4-chlorobenzoyl CoA ligase [111316]
      1. Alcaligenes sp. AL3007 [TaxId: 206162] [111317] (2)
        SQ Q8GN86
      2. Alcaligenes sp. [TaxId: 512] [160961] (2)
Ribosomal protein L1 [56807] (1)
2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
1. Ribosomal protein L1 [56808] (1)
  uperfamily
  1. Ribosomal protein L1 [56809] (4)
    1. Ribosomal protein L1 [56810]
      1. Thermus thermophilus [TaxId: 274] [56811] (16)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [56812] (4)
      3. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [56813] (1)
      4. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82845] (1)
Release factor [75619] (1)
4 domains: (1) 3-helical bundle; (2) alpha+beta of ferredoxin-like fold (3 and 4) alpha+beta of dsRDB-like fold
1. Release factor [75620] (1)
  uperfamily
  1. Release factor [75621] (3)
    Pfam 00472
    1. Polypeptide chain release factor 2 (RF2) [75622]
      1. Escherichia coli [TaxId: 562] [75623] (1)
    2. Peptide chain release factor 1, RF1 [111318]
      1. Thermotoga maritima [TaxId: 2336] [111319] (2)
        SQ Q9X183
      2. Escherichia coli [TaxId: 562] [160962] (1)
        SQ P0A7I0 7-354
YaeB-like [118195] (1)
2 domains; d1: [beta-barrel (n=6, S=10), similar to the Reductase/isomerase/elongation factor common domain fold (scop_cf 50412), provides homodimerisation interface]; d2: [alpha+beta (disordered)]
1. YaeB-like [118196] (1)
  uperfamily
  1. YaeB-like [118197] (1)
    Pfam 01980
    1. Hypothetical protein HI0510 [118198]
      1. Haemophilus influenzae [TaxId: 727] [118199] (1)
        SQ P44740
MalF N-terminal region-like [160963] (1)
consists of 3 N-terminal transmembrane helices, an alpha+beta linker domain and a beta-barrel (n=7; S=8) with one overside loop
1. MalF N-terminal region-like [160964] (1)
  1. MalF N-terminal region-like [160965] (1)
    PfamB 001917
    1. Maltose transport system permease protein MalF [160966]
      1. Escherichia coli [TaxId: 562] [160967] (1)
        SQ P02916 13-260
YebC-like [75624] (1)
3 domains: (1) 3-helical bundle; (2 and 3 ) alpha+beta of different folds: domain 3 has a ferredoxin-like fold and is inserted in domain 2
1. YebC-like [75625] (1)
  uperfamily
  1. YebC-like [75626] (3)
    1. Hypothetical protein YebC [75627]
      1. Escherichia coli [TaxId: 562] [75628] (1)
    2. Hypothetical protein aq1575 [75629]
      1. Aquifex aeolicus [TaxId: 63363] [75630] (1)
    3. Hypothetical protein HP0162 [82846]
      1. Helicobacter pylori [TaxId: 210] [82847] (1)
Cullin homology domain [75631] (1)
3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
1. Cullin homology domain [75632] (1)
  uperfamily
  1. Cullin homology domain [75633] (2)
    1. Cullin homolog 1, cul-1 [75634]
      1. Human (Homo sapiens) [TaxId: 9606] [75635] (3)
        SQ Q13616 17-776
    2. Cullin-4A [160968]
      1. Human (Homo sapiens) [TaxId: 9606] [160969] (1)
        SQ Q13619 402-675
Sec1/munc18-like (SM) proteins [56814] (1)
3 domains: (1 and 2) alpha+beta; (3) mostly alpha, inserted in domain 2
1. Sec1/munc18-like (SM) proteins [56815] (1)
  uperfamily
  1. Sec1/munc18-like (SM) proteins [56816] (3)
    1. Neuronal Sec1, NSec1 [56817]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [56818] (1)
      2. Longfin inshore squid (Loligo pealei) [TaxId: 6621] [56819] (3)
    2. Sly1P protein [82848]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82849] (1)
Prismane protein-like [56820] (1)
3 domains: (1) spectrin repeat-like 3-helical bundle; (2 and 3) alpha/beta: Rossmann-fold topology
1. Prismane protein-like [56821] (3)
  uperfamily
  1. Carbon monoxide dehydrogenase [64514] (3)
    1. Ni-containing carbon monoxide dehydrogenase [64515]
      1. Carboxydothermus hydrogenoformans [TaxId: 129958] [64516] (7)
      2. Rhodospirillum rubrum [TaxId: 1085] [69896] (1)
    2. Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) beta (CODH) subunit [82850]
      1. Moorella thermoacetica [TaxId: 1525] [82851] (6)
  2. Hybrid cluster protein (prismane protein) [56822] (2)
    contains extra N-terminal 3-helical bundle domain
    1. Hybrid cluster protein (prismane protein) [56823]
      1. Desulfovibrio vulgaris [TaxId: 881] [56824] (6)
      2. Desulfovibrio desulfuricans [TaxId: 876] [75636] (4)
  3. Acetyl-CoA synthase [82852] (2)
    4 domains: structures and assembly of domains 1 and 2 are similar to those of domains 1 and 3 of the CODH subunit; (3 and 4) alpha+beta
    1. Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) alpha (ACS) subunit [82853]
      1. Moorella thermoacetica [TaxId: 1525] [82854] (6)
    2. Monomeric acetyl-CoA synthase [103406]
      1. Carboxydothermus hydrogenoformans [TaxId: 129958] [103407] (1)
Subunits of heterodimeric actin filament capping protein Capz [90095] (1)
3 domains: (1) protozoan pheromone-like alpha-helical bundle; (2) rubredoxin-like domain lacking metal-binding site; (3) alpha+beta heterodimerisation domain: alpha-beta(5)-alpha
1. Subunits of heterodimeric actin filament capping protein Capz [90096] (2)
  uperfamily
  1. Capz alpha-1 subunit [90097] (1)
    1. Capz alpha-1 subunit [90098]
      1. Chicken (Gallus gallus) [TaxId: 9031] [90099] (1)
  2. Capz beta-1 subunit [90100] (1)
    1. Capz beta-1 subunit [90101]
      1. Chicken (Gallus gallus) [TaxId: 9031] [90102] (1)
beta-lactamase/transpeptidase-like [56600] (1)
contains a cluster of helices and an alpha+beta sandwich
1. beta-lactamase/transpeptidase-like [56601] (3)
  uperfamily
  1. beta-Lactamase/D-ala carboxypeptidase [56602] (38)
    1. D-ala carboxypeptidase/transpeptidase [56603]
      1. Streptomyces sp., K15 [TaxId: 1931] [56604] (7)
      2. Streptomyces sp., R61 [TaxId: 1931] [56605] (15)
        SQ P15555 34-378 ! SQ P15555
    2. Esterase EstB [69873]
      1. Burkholderia gladioli [TaxId: 28095] [69874] (2)
    3. beta-Lactamase, class A [56606]
      1. Escherichia coli, TEM-1 [TaxId: 562] [56607] (35)
      2. Klebsiella pneumoniae, TEM52 [TaxId: 573] [64473] (1)
      3. Escherichia coli, TOHO-1 [TaxId: 562] [56608] (5)
      4. Proteus vulgaris [TaxId: 585] [75596] (1)
      5. Klebsiella pneumoniae, SHV-1 [TaxId: 573] [56609] (15)
        SQ Q5PSW7 ! SQ P14557 22-286
        inhibited by tazobactam
      6. Klebsiella pneumoniae, SHV-2 [TaxId: 573] [90082] (1)
        almost identical sequence to SHV-1
      7. Pseudomonas aeruginosa, PSE-4 carbenicillinase [TaxId: 287] [56610] (2)
      8. Staphylococcus aureus [TaxId: 1280] [56611] (16)
      9. Bacillus licheniformis [TaxId: 1402] [56612] (5)
      10. Enterobacter cloacae, NMC-A carbapenemase [TaxId: 550] [56613] (2)
      11. Streptomyces albus G [TaxId: 1962] [56614] (1)
      12. Mycobacterium fortuitum [TaxId: 1766] [56615] (1)
      13. Pseudomonas aeruginosa, PER-1 [TaxId: 287] [56616] (1)
      14. Serratia marcescens, Sme-1 [TaxId: 615] [56617] (1)
        imipenem-hydrolyzing
      15. Stenotrophomonas maltophilia, L2 [TaxId: 40324] [103374] (2)
    4. AMPC beta-Lactamase, class C [56618]
      contains small alpha+beta subdomain inserted in the common fold
      1. Citrobacter freundii [TaxId: 546] [56619] (3)
      2. Enterobacter cloacae, P99, cephalosporinase [TaxId: 550] [56620] (10)
        SQ P05364 22-380 ! SQ P05364 22-381
      3. Escherichia coli, cephalosporinase [TaxId: 562] [56621] (60)
    5. Class D beta-lactamase [56622]
      1. Escherichia coli, OXA-1 [TaxId: 562] [82837] (1)
      2. Salmonella typhimurium, OXA-2 [TaxId: 90371] [90083] (1)
      3. Pseudomonas aeruginosa, OXA-10 [TaxId: 287] [56623] (12)
      4. Pseudomonas aeruginosa, OXA-13 [TaxId: 287] [64474] (3)
    6. Penicillin receptor BlaR, C-terminal domain [103375]
      closely related to class D beta-lactamase
      1. Bacillus licheniformis [TaxId: 1402] [103376] (1)
    7. Penicillin-binding protein 2x (pbp-2x), transpeptidase domain [56624]
      1. Streptococcus pneumoniae [TaxId: 1313] [56625] (14)
    8. Penicillin binding protein 2a (PBP2A), C-terminal domain [82838]
      1. Staphylococcus aureus [TaxId: 1280] [82839] (5)
        SQ O54286 27-668
    9. Penicillin-binding protein 5, N-terminal domain [69875]
      1. Escherichia coli [TaxId: 562] [69876] (8)
    10. D-aminopeptidase, N-terminal domain [56626]
      1. Ochrobactrum anthropi [TaxId: 529] [56627] (1)
    11. Pencillin binding protein 4 (PbpD), N-terminal domain [111287]
      1. Staphylococcus aureus [TaxId: 1280] [111288] (1)
        SQ Q53613 21-383
    12. Regulatory protein BlaR1 [111289]
      1. Staphylococcus aureus [TaxId: 1280] [111290] (3)
        SQ P18357 338-582 ! SQ P18357 334-581 ! SQ P18357 338-583
    13. D,D-carboxypeptidase DacA, N-terminal domain [118181]
      1. Streptococcus pneumoniae [TaxId: 1313] [118182] (1)
        SQ P72518 25-393
    14. Penicillin-binding protein 1a, transpeptidase domain [144034]
      1. Streptococcus pneumoniae [TaxId: 1313] [144035] (2)
        SQ Q8DR59 266-650! SQ Q8DR59 267-650
    15. Penicillin-binding protein 1b, transpeptidase domain [144036]
      1. Streptococcus pneumoniae [TaxId: 1313] [144037] (3)
        SQ O70038 337-789! SQ O70038 337-791
    16. D-Amino acid amidase DaaA [144038]
      1. Ochrobactrum anthropi [TaxId: 529] [144039] (24)
        SQ Q9LCC8 2-363
    17. Penicillin-binding protein 2, PBP2 [160970]
      1. Staphylococcus aureus [TaxId: 1280] [160971] (7)
        SQ Q2YY56 293-692
    18. 6-aminohexanoate-dimer hydrolase NylC [160972]
      NylB'
      1. Flavobacterium sp. [TaxId: 239] [160973] (3)
        SQ P07062 5-392
  2. Glutaminase [90084] (2)
    Pfam 04960
    1. Probable glutaminase YbgJ [90085]
      1. Bacillus subtilis [TaxId: 1423] [90086] (5)
    2. Probable glutaminase YbaS [111291]
      1. Escherichia coli [TaxId: 562] [111292] (1)
        SQ P77454
  3. Dac-like [144040] (3)
    Pfam 02113; D-Ala-D-Ala carboxypeptidase 3 (S13) family; contains a large insertion comprising two subdomains: (d1) aplha+beta with topological similarity to one subunit of the DTD-like family (scop_fa 69501) and (d2) six-stranded beta-sandwich with a crossed-loop topology
    1. Penicillin-binding protein DacC [144041]
      1. Bacillus subtilis [TaxId: 1423] [144042] (3)
        SQ P39844 34-491
    2. D-alanyl-D-alanine carboxypeptidase Dac [144043]
      1. Actinomadura sp. [TaxId: 1989] [144044] (12)
        SQ P39045 50-516
    3. DD-carboxypeptidase DacB [144045]
      Penicillin-binding protein 4
      1. Escherichia coli [TaxId: 562] [144046] (6)
        SQ P24228 22-477
Upper collar protein gp10 (connector protein) [56825] (1)
2 domains: (1) alpha-helical bundle; (2) beta-barrel (n=5, S=8)
1. Upper collar protein gp10 (connector protein) [56826] (1)
  uperfamily
  1. Upper collar protein gp10 (connector protein) [56827] (1)
    1. Upper collar protein gp10 (connector protein) [56828]
      1. Bacteriophage phi-29 [TaxId: 10756] [56829] (4)
AF1531-like [160974] (1)
2 domains; d1: incomplete barrel similar to the OB-fold domain of ribosomal L2 protein, d2: six helices, array
1. AF1531-like [160975] (1)
  1. AF1531-like [160976] (1)
    Pfam 04919; DUF655
    1. Hypothetical protein AF1531 [160977]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160978] (1)
        SQ O28741 16-195
Phase 1 flagellin [64517] (1)
3 domains: (1) alpha-helical bundle; (2&3) complex all-beta folds
1. Phase 1 flagellin [64518] (1)
  uperfamily
  1. Phase 1 flagellin [64519] (1)
    1. Phase 1 flagellin [64520]
      1. Salmonella typhimurium [TaxId: 90371] [64521] (2)
39 kda initiator binding protein, IBP39, C-terminal domains [103408] (1)
2 closely associated domains: (1) all-alpha, EF-hand like; (2) alpha+beta, Frataxin-like
1. 39 kda initiator binding protein, IBP39, C-terminal domains [103409] (1)
  uperfamily
  1. 39 kda initiator binding protein, IBP39, C-terminal domains [103410] (1)
    1. 39 kda initiator binding protein, IBP39, C-terminal domains [103411]
      1. Trichomonas vaginalis [TaxId: 5722] [103412] (3)
AF1104-like [111320] (1)
2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
1. AF1104-like [111321] (1)
  uperfamily
  1. AF1104-like [111322] (3)
    Pfam 01937
    1. Hypothetical protein At2g17340 [111323]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111324] (2)
        SQ Q949P3; d1: 36-117; d2: 118-365
    2. Hypothetical protein AF1104 [144047]
      1. Archaeoglobus fulgidus [TaxId: 2234] [144048] (2)
        SQ O29161 7-288
    3. Hypothetical protein PH1575 [144049]
      1. Pyrococcus horikoshii [TaxId: 53953] [144050] (2)
        SQ O59272 1-284
SSO1389-like [160979] (1)
2 domains; d1: [alpha/beta, central parallel beta-sheet of 6 strands, order 321456, Rossmann-like]; d2: [alpha+beta, cluster of helices and a small 4-stranded beta-sheet]
1. SSO1389-like [160980] (1)
  1. Cas_DxTHG [160981] (1)
    Pfam 09455; CRISPR-associated DxTHG family
    1. Hypothetical protein SSO1389 [160982]
      1. Sulfolobus solfataricus [TaxId: 2287] [160983] (2)
        SQ Q97YD5 1-377
Urocanase [111325] (1)
3 domains; d1: alpha+beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta of the NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar to scop_fa 51883 and scop_fa 51736); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheet
1. Urocanase [111326] (1)
  uperfamily
  1. Urocanase [111327] (2)
    Pfam 01175
    1. Urocanate hydratase HutU [111328]
      1. Pseudomonas putida [TaxId: 303] [111329] (3)
        SQ P25080; d1:4-138; d2:135-350; d3: 351-557
      2. Bacillus stearothermophilus [TaxId: 1422] [118200] (1)
        SQ Q5L084 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462
NAD kinase/diacylglycerol kinase-like [111330] (1)
2 domains: d1 [alpha/beta; related to the PFK N-terminal domain (scop_sf 53784)]; d2 [all-beta; atypical beta-sandwich made of 4 structural repeats of beta(3) unit]
1. NAD kinase/diacylglycerol kinase-like [111331] (2)
  uperfamily
  1. NAD kinase-like [111332] (2)
    Pfam 01513
    1. Inorganic polyphosphate/ATP-NAD kinase PpnK [111333]
      1. Archaeoglobus fulgidus [TaxId: 2234] [111334] (11)
        SQ O30297; d1:1-96; d2:101-227
      2. Mycobacterium tuberculosis [TaxId: 1773] [111335] (4)
        SQ O33196; d1:5-132; d2:140-275
  2. Diacylglycerol kinase-like [160984] (3)
    N-terminal, catalytic domain is covered by Pfam 00781
    1. Lipid kinase YegS [160985]
      1. Salmonella typhimurium [TaxId: 90371] [160986] (4)
        SQ Q8ZNP1 1-299
      2. Escherichia coli [TaxId: 562] [160987] (3)
        SQ P76407 4-299! SQ P76407 5-299
    2. Diacylglycerol kinase DgkB [160988]
      1. Staphylococcus aureus [TaxId: 1280] [160989] (2)
        SQ Q6GFF9 1-312
QueA-like [111336] (1)
2 domains; d1 (1-64,174-335) [alpha/beta; 3 layers, a/b/a; mixed beta sheet of 9 strands, order: 219863457; strands 1, 5 and 8 are antiparallel to the rest]; d2 (65-142) [all-beta; barrel, closed (n=6, S=10); greek-key; topologically similar to the split barrel fold (scop_cf 50474)
1. QueA-like [111337] (1)
  uperfamily
  1. QueA-like [111338] (2)
    Pfam 02547
    1. Queuosine biosynthesis protein queA [111339]
      1. Thermotoga maritima [TaxId: 2336] [111340] (1)
        SQ Q9WZ44
      2. Thermus thermophilus [TaxId: 274] [118201] (1)
        SQ Q5SMH0
CbiD-like [111341] (1)
2 domains; (1) alpha+beta (res 1-192), a circularly permuted rS5 domain 2-like fold (scop_cf 54210); (2) alpha/beta with parallel beta-sheet of 4 strands, order 2134
1. CbiD-like [111342] (1)
  uperfamily
  1. CbiD-like [111343] (1)
    Pfam 01888
    1. Cobalamin biosynthesis protein CbiD [111344]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111345] (1)
        SQ O29535
Rap/Ran-GAP [111346] (1)
consists of two domains; d1: alpha+beta (78-190; alpha-beta(4)-alpha-beta-alpha; 3 layers; antiparallel beta-sheet of 5 strands; order 51234); d2: alpha/beta similar to the G-domain fold (191-381; scop_fa 52592)
1. Rap/Ran-GAP [111347] (1)
  uperfamily
  1. Rap/Ran-GAP [111348] (1)
    Pfam 02145
    1. Rap1 GTPase-activating protein 1, Rap1GAP [111349]
      1. Human (Homo sapiens) [TaxId: 9606] [111350] (1)
        SQ P47736
Vacuolar ATP synthase subunit C [118202] (1)
2 alpha+beta (sub)domains [each has a ferredoxin-like fold; scop_cf 54861], connected with 3-helical bundle; duplication: two repeats of beta-alpha-beta-[alpha coiled-coil]-beta-alpha-beta motif
1. Vacuolar ATP synthase subunit C [118203] (1)
  uperfamily
  1. Vacuolar ATP synthase subunit C [118204] (1)
    Pfam 03223
    1. Vacuolar ATP synthase subunit C [118205]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118206] (1)
        SQ P31412
Thermophilic metalloprotease-like [144051] (1)
consists of two domains; d1: alpha/beta (3 layers, a/b/a; parralel beta-sheet, order 2134); d2: pseudo beta-barrel capped by helices
1. Thermophilic metalloprotease-like [144052] (1)
  uperfamily
  1. Thermophilic metalloprotease (M29) [144053] (2)
    Pfam 02073
    1. Aminopeptidase T [144054]
      1. Thermus thermophilus [TaxId: 274] [144055] (5)
        SQ P42778 3-408
    2. Aminopeptidase S, AMPS [144056]
      1. Staphylococcus aureus [TaxId: 1280] [144057] (1)
        SQ Q8NVU1 3-415
ImpE-like [144058] (1)
consists of two domains; d1: right-handed superhelix of five helices; d2: pseudo beta-barrel containing structurally similar part to the "Histone-like" proteins from archaea (scop_fa 54161)
1. ImpE-like [144059] (1)
  uperfamily
  1. ImpE-like [144060] (1)
    Pfam 07024
    1. Hypothetical protein VPA1032 [144061]
      1. Vibrio parahaemolyticus [TaxId: 670] [144062] (1)
        SQ Q87HD3 2-265
CV3147-like [160990] (1)
2 domains; d1: [alpha/beta; 3 layers, a/b/a, mixed beta-sheet of 8 strands, order 12543876, strands 1, 7 and 8 are antiparallel to the rest]; d2: [pseudo beta-barrel of 6 strands, meander]
1. CV3147-like [160991] (1)
  1. CV3147-like [160992] (1)
    Pfam 06032; DUF917
    1. Hypothetical protein CV3147 [160993]
      1. Chromobacterium violaceum [TaxId: 536] [160994] (2)
        SQ Q7NTB2 2-390
Heme iron utilization protein-like [144063] (1)
2 domains; d1 - 3-helical bundle similar to the homeodomain-like fold; d2 - 6-stranded beta-barrel capped by two helices at one end, similar topology to the PH-like fold
1. Heme iron utilization protein-like [144064] (2)
  uperfamily
  1. HemS/ChuS-like [144065] (2)
    Pfam 05171; Haemin-degrading proteins; duplication: consists of thandem repeat of this fold joined at the 'free' ends of their PH-like barrels
    1. Hemin transport protein HemS [144066]
      1. Yersinia enterocolitica [TaxId: 630] [144067] (2)
        SQ P31517 3-341! SQ P31517 4-341
    2. Heme oxygenase ChuS [144068]
      1. Escherichia coli O157:H7 [TaxId: 83334] [144069] (2)
        SQ Q8X5N8 1-337
  2. ChuX-like [144070] (1)
    Pfam 06228; DUF1008; single-domain subunits form a dimer similar to the HemS/ChuS subunits
    1. Hypothetical protein AGR_C_4470p [144071]
      1. Agrobacterium tumefaciens [TaxId: 358] [144072] (1)
        SQ Q7CX01 11-186
HI0933 insert domain-like [160995] (1)
2 domains; d1: barrel, closed, n=6, S=12, greek-key; d2: four-helical bundle, inserted in d1
1. HI0933 insert domain-like [160996] (1)
  1. HI0933 insert domain-like [160997] (2)
    C-terminal part of Pfam 03486
    1. Hypothetical protein HI0933 [160998]
      1. Haemophilus influenzae [TaxId: 727] [160999] (1)
        SQ P44941 195-342
    2. Flavoprotein BC4706 [161000]
      1. Bacillus cereus [TaxId: 1396] [161001] (1)
        SQ Q816V9 193-361
NSP3 homodimer [69902] (1)
2 domains: (1) all-alpha, (2) alpha+beta; asymmetric homodimer with each domain intertwining with its counterpart
1. NSP3 homodimer [69903] (1)
  uperfamily
  1. NSP3 homodimer [69904] (1)
    1. NSP3 homodimer [69905]
      non-structural RNA-binding protein
      1. Simian 11 rotavirus [TaxId: 10923] [69906] (1)
E2F-DP heterodimerization region [144073] (1)
heterodimeric fold with the N-terminal long helices of both chains forming a parallel coiled coil and their C-terminal folded beta-hairpins interlocking together in a beta-sandwich
1. E2F-DP heterodimerization region [144074] (2)
  uperfamily
  1. DP dimerization segment [144075] (1)
    Pfam 08781
    1. Transcription factor DP-1 [144076]
      1. Human (Homo sapiens) [TaxId: 9606] [144077] (1)
        SQ Q14186 199-346
  2. E2F dimerization segment [144078] (1)
    PfamB 001971
    1. Transcription factor E2F1 [144079]
      1. Human (Homo sapiens) [TaxId: 9606] [144080] (1)
        SQ Q01094 201-301
Membrane penetration protein mu1 [69907] (1)
4 domains: three intertwined predominately alpha domains and one jelly-roll beta-sandwich
1. Membrane penetration protein mu1 [69908] (1)
  uperfamily
  1. Membrane penetration protein mu1 [69909] (1)
    1. Membrane penetration protein mu1 [69910]
      1. Reovirus [TaxId: 10891] [69911] (1)
Flu NP-like [161002] (1)
consists of alpha+beta and all-alpha domains; biological unit is a trimer
1. flu NP-like [161003] (1)
  1. Flu NP-like [161004] (1)
    Pfam 00506; Influenza virus nucleoprotein
    1. Nucleocapsid protein [161005]
      1. Influenza A virus [TaxId: 11320] [161006] (3)
        SQ Q1I2B5 21-489
Viral glycoprotein ectodomain-like [161007] (1)
complex fold; contains three rigid, mostly-beta domains and an alpha-helical region, acting as a conformatiomal switch ("fusion stalk")
1. Viral glycoprotein ectodomain-like [161008] (2)
  1. Glycoprotein B-like [161009] (1)
    Pfam 00606; Herpesvirus Glycoprotein B
    1. Glycoprotein B [161010]
      1. Human herpesvirus 1 [TaxId: 10298] [161011] (3)
        SQ P06437 111-725
  2. Spike glycoprotein-like [161012] (1)
    Pfam 00974; Rhabdovirus spike glycoprotein
    1. Spike glycoprotein [161013]
      1. Vesicular stomatitis indiana virus [TaxId: 11277] [161014] (4)
        SQ P04883 17-425
        representative prefusion form 2CMZ; representative acidic conformation 2J6J
Reovirus inner layer core protein p3 [56830] (1)
large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
1. Reovirus inner layer core protein p3 [56831] (2)
  uperfamily
  1. Orbivirus core [56832] (1)
    1. BTV vp3 [56833]
      1. Bluetongue virus, strain 1 [TaxId: 40051] [56834] (1)
  2. Phytoreovirus core [103413] (1)
    1. RDV p3 [103414]
      1. Rice dwarf virus [TaxId: 10991] [103415] (1)
L-A virus major coat protein [82855] (1)
large protein without apparent domain division
1. L-A virus major coat protein [82856] (1)
  uperfamily
  1. L-A virus major coat protein [82857] (1)
    1. L-A virus major coat protein [82858]
      1. Saccharomyces cerevisiae virus L-A [TaxId: 11008] [82859] (1)
Major capsid protein VP5 [103416] (1)
large protein without apparent domain division
1. Major capsid protein VP5 [103417] (1)
  uperfamily
  1. Major capsid protein VP5 [103418] (1)
    1. Major capsid protein VP5 [103419]
      1. Herpes simplex virus 1 [TaxId: 10298] [103420] (1)
Viral ssDNA binding protein [118207] (1)
2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array]
1. Viral ssDNA binding protein [118208] (1)
  uperfamily
  1. Viral ssDNA binding protein [118209] (1)
    Pfam 00747
    1. Infected cell protein 8, ICP8 [118210]
      1. Herpes simplex virus 1 [TaxId: 10298] [118211] (1)
        SQ P04296 9-1130 # d1: 9-1038; d2: 1048-1130