Structural Classification of Proteins

Root: scop

Classes:

All alpha proteins [46456] (284)
1. Globin-like [46457] (2)
  core: 6 helices; folded leaf, partly opened
  1. Globin-like [46458] (4)
    uperfamily
    1. Truncated hemoglobin [46459] (6)
      lack the first helix (A)
    2. Nerve tissue mini-hemoglobin (neural globin) [74660] (1)
      lack the first helix but otherwise is more similar to conventional globins than the truncated ones
    3. Globins [46463] (81)
      Heme-binding protein
    4. Phycocyanin-like phycobilisome proteins [46532] (26)
      oligomers of two different types of globin-like subunits containing two extra helices at the N-terminus
      binds a bilin chromophore
  2. alpha-helical ferredoxin [46548] (2)
    contains two Fe4-S4 clusters
    uperfamily
    1. Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain [46549] (3)
    2. Dihydropyrimidine dehydrogenase, N-terminal domain [46553] (1)
2. Long alpha-hairpin [46556] (20)
  2 helices; antiparallel hairpin, left-handed twist
  1. GreA transcript cleavage protein, N-terminal domain [46557] (1)
    uperfamily
    1. GreA transcript cleavage protein, N-terminal domain [46558] (3)
  2. Ribosomal protein L29 (L29p) [46561] (1)
    uperfamily
    1. Ribosomal protein L29 (L29p) [46562] (5)
  3. Chaperone J-domain [46565] (1)
    uperfamily
    1. Chaperone J-domain [46566] (8)
      Pfam 00226
  4. Prefoldin [46579] (1)
    uperfamily
    1. Prefoldin [46580] (2)
      contains one or two beta-hairpins at the tip of alpha-hairpin
  5. HR1 repeat [46585] (1)
    uperfamily
    1. HR1 repeat [46586] (1)
      protein kinase effector domain
  6. tRNA-binding arm [46589] (4)
    formerly a class II aminoacyl-tRNA synthetase N-domain
    uperfamily
    1. Seryl-tRNA synthetase (SerRS) [46590] (1)
    2. Phenylalanyl-tRNA synthetase (PheRS) [46593] (1)
    3. Valyl-tRNA synthetase (ValRS) C-terminal domain [81635] (1)
    4. Methicillin resistance protein FemA probable tRNA-binding arm [81671] (1)
      inserted in the C-terminal NAT-like domain
  7. Eukaryotic DNA topoisomerase I, dispensable insert domain [46596] (1)
    uperfamily
    1. Eukaryotic DNA topoisomerase I, dispensable insert domain [46597] (1)
  8. C-terminal UvrC-binding domain of UvrB [46600] (1)
    uperfamily
    1. C-terminal UvrC-binding domain of UvrB [46601] (1)
  9. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46604] (1)
    uperfamily
    1. Epsilon subunit of F1F0-ATP synthase C-terminal domain [46605] (2)
  10. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46609] (1)
    uperfamily
    1. Fe,Mn superoxide dismutase (SOD), N-terminal domain [46610] (19)
  11. Sporulation inhibitor Sda [100985] (1)
    uperfamily
    1. Sporulation inhibitor Sda [100986] (1)
  12. Transcriptional repressor TraM [109631] (1)
    similar structure to L29p (scop_sf 46561); contains extra short helix; forms homodimer: an open bundle
    uperfamily
    1. Transcriptional repressor TraM [109632] (1)
  13. DnaK suppressor protein DksA, alpha-hairpin domain [109635] (1)
    uperfamily
    1. DnaK suppressor protein DksA, alpha-hairpin domain [109636] (1)
  14. ISY1 domain-like [140102] (1)
    uperfamily
    1. ISY1 N-terminal domain-like [140103] (1)
      N-terminal region of Pfam 06246
  15. Calcyclin-binding protein-like [140106] (1)
    uperfamily
    1. Siah interacting protein N terminal domain-like [140107] (2)
      Pfam 09032
  16. Endosomal sorting complex assembly domain [140111] (3)
    forms 'fan'-like heterooligomers, in which the domains of different subunit make similar interactions at the tip of the hairpin
    uperfamily
    1. VPS23 C-terminal domain [140112] (1)
    2. VPS28 N-terminal domain [140115] (1)
      includes structurally variable linker region
    3. VPS37 C-terminal domain-like [140118] (1)
      Pfam 07200; Modifier of rudimentary, Mod(r)
  17. SPy1572-like [140121] (1)
    forms homodimer: an open bundle, different from the TRAM dimer
    uperfamily
    1. SPy1572-like [140122] (1)
  18. Rabenosyn-5 Rab-binding domain-like [140125] (1)
    uperfamily
    1. Rabenosyn-5 Rab-binding domain-like [140126] (1)
  19. MxiH-like [140129] (1)
    Type III secretion system needle
    uperfamily
    1. MxiH-like [140130] (2)
  20. YnzC-like [158221] (1)
    1. YznC-like [158222] (1)
      Pfam 05979; DUF896
3. Type I dockerin domain [63445] (1)
  tandem repeat of two calcium-binding loop-helix motifs, distinct from the EF-hand
  1. Type I dockerin domain [63446] (1)
    uperfamily
    1. Type I dockerin domain [63447] (3)
4. LEM/SAP HeH motif [63450] (6)
  helix-extended loop-helix; parallel helices
  1. LEM domain [63451] (1)
    uperfamily
    1. LEM domain [63452] (2)
  2. SAP domain [68906] (1)
    uperfamily
    1. SAP domain [68907] (7)
      Pfam 02037
  3. Rho N-terminal domain-like [68912] (2)
    uperfamily
    1. Rho termination factor, N-terminal domain [68913] (1)
    2. YqbF C-terminal domain-like [158225] (2)
  4. Recombination endonuclease VII, C-terminal and dimerization domains [68918] (1)
    uperfamily
    1. Recombination endonuclease VII, C-terminal and dimerization domains [68919] (1)
  5. DNA-binding domain of EIN3-like [116768] (1)
    decorated with additional structures
    uperfamily
    1. DNA-binding domain of EIN3-like [116769] (1)
      middle part of Pfam 04873
  6. PRP4-like [158230] (1)
    1. PRP4-like [158231] (1)
      Pfam 08799; pre-mRNA processing factor 4 (PRP4) like
5. SOCS box-like [158234] (1)
  helix-loop-helix motif with orthogonally packed helices
  1. SOCS box-like [158235] (1)
    1. SOCS box-like [158236] (2)
      Pfam 07525
6. RPB6/omega subunit-like [63561] (1)
  core: 2 helices and adjacent loops
  1. RPB6/omega subunit-like [63562] (2)
    the bacterial omega and eukaryotic RPB6 subunits both function in polymerase assembly; the common core is involved in conserved interactions with other subunits
    uperfamily
    1. RNA polymerase omega subunit [63563] (3)
      4 helices; irregular array
    2. RPB6 [55294] (2)
7. KRAB domain (Kruppel-associated box) [109639] (1)
  2 helices: one short, one long; aromatic-rich iterface
  1. KRAB domain (Kruppel-associated box) [109640] (1)
    uperfamily
    1. KRAB domain (Kruppel-associated box) [109641] (1)
      Pfam 01352
8. Cytochrome c [46625] (1)
  core: 3 helices; folded leaf, opened
  1. Cytochrome c [46626] (8)
    covalently-bound heme completes the core
    uperfamily
    1. monodomain cytochrome c [46627] (44)
    2. N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [46671] (3)
    3. Quinoprotein alcohol dehydrogenase, C-terminal domain [68952] (2)
    4. Cytochrome bc1 domain [46676] (3)
    5. Two-domain cytochrome c [46680] (3)
      duplication: consists of two cytochrome c type domains
    6. Di-heme cytochrome c SoxA [81677] (1)
      two-domain cytochrome c with novel domain arrangement
    7. Di-heme cytochrome c peroxidase [46685] (3)
      duplication: contains two cytochrome c-type domains
    8. Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [68956] (2)
9. DNA/RNA-binding 3-helical bundle [46688] (14)
  core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
  1. Homeodomain-like [46689] (19)
    consists only of helices
    uperfamily
    1. Homeodomain [46690] (42)
      Pfam 00046
    2. Recombinase DNA-binding domain [46728] (5)
    3. Myb/SANT domain [46739] (15)
    4. SLIDE domain [100998] (1)
      myb-related probable DNA-binding motif
    5. GARP response regulators [81683] (1)
      plant myb-related DNA-binding motif
    6. DNA-binding domain of telomeric protein [46745] (2)
      part of Pfam 00249 (Myb/SANT domain)
    7. Paired domain [46748] (3)
      duplication: consists of two domains of this fold
    8. DNA-binding domain of rap1 [46753] (1)
      duplication: consist of two domains of this fold
    9. Centromere-binding [46756] (2)
      duplication: tandem repeat of two similar domains
    10. FIS-like [100918] (4)
    11. AraC type transcriptional activator [46759] (2)
      duplication: consists of two structural repeats bipartite HTH protein
    12. Tetracyclin repressor-like, N-terminal domain [46764] (34)
    13. Middle operon regulator, Mor [109659] (1)
      contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
    14. Psq domain [140213] (1)
      Pfam 05225
    15. Alr1493-like [140216] (1)
      Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
    16. Nanomeric phage protein-like [140219] (1)
      contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
    17. SWIRM domain [140222] (3)
      Pfam 04433; contains extra N-terminal helix
    18. Cgl2762-like [158260] (1)
      Pfam 01527; Transposase 8
    19. RpiR-like [158263] (1)
      Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
  2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
    uperfamily
    1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3)
  3. ARID-like [46774] (1)
    contains extra helices at both N- and C-termini
    uperfamily
    1. ARID domain [46775] (4)
  4. "Winged helix" DNA-binding domain [46785] (84)
    contains a small beta-sheet (wing)
    uperfamily
    1. Biotin repressor-like [46786] (2)
    2. LexA repressor, N-terminal DNA-binding domain [46789] (1)
    3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
    4. Transcriptional repressor Rex, N-terminal domain [101007] (1)
    5. CAP C-terminal domain-like [46796] (9)
    6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
      Swapped dimer with the "wing" C-terminal strands
    7. ArsR-like transcriptional regulators [46801] (4)
      The N- and C-terminal helical extensions to the common fold form the dimer interface
    8. Transcriptional regulator IclR, N-terminal domain [74676] (1)
    9. MarR-like transcriptional regulators [63379] (20)
      The N- and C-terminal helical extensions to the common fold form the dimer interface
    10. DNA-binding protein Mj223 [81690] (1)
      homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold
    11. Penicillinase repressor [101016] (4)
      homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
    12. GntR-like transcriptional regulators [46804] (4)
    13. N-terminal domain of Bacillus PurR [101021] (1)
    14. Replication terminator protein (RTP) [46807] (1)
    15. LysR-like transcriptional regulators [88979] (2)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
    16. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
      contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
    17. Transcription factor MotA, activation domain [46813] (1)
      The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
    18. Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
      contains extra N-terminal helix
    19. FUR-like [101027] (1)
      contains extra N-terminal helix and an alpha+beta dimerisation subdomain
    20. Replication initiation protein [46816] (3)
      duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
    21. Helicase DNA-binding domain [46819] (5)
      follows the extended AAA-ATPase domain
    22. RecQ helicase DNA-binding domain-like [101030] (3)
      follows the tandem AAA-ATPase domain
    23. SCF ubiquitin ligase complex WHB domain [74679] (4)
    24. C-terminal fragment of elongation factor SelB [74683] (1)
    25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
    26. TnsA endonuclease, C-terminal domain [46782] (1)
    27. Plant O-methyltransferase, N-terminal domain [63475] (5)
      unknown function
    28. Linker histone H1/H5 [46827] (3)
    29. Forkhead DNA-binding domain [46832] (6)
    30. DNA-binding domain from rap30 [46841] (1)
    31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
    32. C-terminal domain of RPA32 [46844] (1)
    33. DEP domain [63483] (5)
      membrane-binding domain
    34. Cell cycle transcription factor e2f-dp [46847] (2)
      heterodimer of two homologous chains
    35. The central core domain of TFIIE beta [46850] (1)
    36. Z-DNA binding domain [46853] (4)
      Pfam 02295
    37. P4 origin-binding domain-like [46856] (2)
      C-terminus passes through the first loop
    38. ets domain [46859] (9)
    39. Heat-shock transcription factor [46873] (2)
    40. Interferon regulatory factor [46877] (3)
      Pfam 00605
    41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
    42. Iron-dependent repressor protein [46882] (3)
    43. Dissimilatory sulfite reductase DsvD [101048] (1)
    44. La domain [101051] (3)
      Pfam 05383; RNA-binding domain
    45. Methionine aminopeptidase, insert domain [46887] (2)
      circularly permuted version of the "winged helix" fold
    46. PCI domain (PINT motif) [109671] (2)
      Pfam 01399
    47. F93-like [109674] (3)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
    48. Archaeal DNA-binding protein [109677] (1)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
    49. TrmB-like [109680] (2)
      The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
    50. Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
      similar domain organization to the transcriptional regulator IclR
    51. DNA replication factor Cdt1 [109686] (1)
    52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
      C-terminal part of Pfam 06272
    53. Vacuolar sorting protein domain [109692] (3)
      duplication: tandem repeat of two "winged-helix" domains
    54. Transcriptional regulator Rrf2 [109699] (2)
      Pfam 02082
    55. Rio2 serine protein kinase N-terminal domain [109702] (1)
    56. Rad21/Rec8-like [116795] (1)
      Pfam 04824
    57. Hypothetical protein PH1932 [116798] (1)
      contains new dimerisation all-alpha C-terminal subdomain
    58. An Obfc1 domain [116801] (1)
      helix-loop insertion in the HTH motif
    59. ScpB/YpuH-like [116804] (1)
      Pfam 04079
      duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
    60. PadR-like [116807] (3)
      Pfam 03551; related to the MarR-like family (Pfam 01047)
    61. Hypothetical protein YhgG [116812] (1)
    62. ROK associated domain [140279] (3)
      found N-terminal to ROK domain in some proteins
    63. PF1790-like [140286] (1)
      sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil
    64. MukF N-terminal domain-like [140289] (1)
      N-terminal part of Pfam 03882
    65. CodY HTH domain [140292] (1)
      Pfam 08222
    66. FtsK C-terminal domain-like [140295] (2)
      PfamB 000224
    67. Nudix-associated domain [140299] (2)
      PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
    68. HxlR-like [140304] (5)
      Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
    69. Marine metagenome family WH1 [158296] (1)
    70. ReutB4095-like [158299] (1)
      probable biological unit is a homohexamer
    71. PH0730 N-terminal domain-like [158302] (1)
    72. FaeA-like [158305] (1)
      Pfam 04703
    73. STY4665 C-terminal domain-like [158308] (1)
      Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
    74. PSPTO2686-like [158311] (1)
      Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
    75. RHA1_ro06458-like [158314] (1)
    76. YjcQ-like [158317] (1)
      Pfam 09639
    77. F112-like [158320] (1)
    78. MerB N-terminal domain-like [158323] (1)
    79. CED-4 C-terminal domain-like [158326] (1)
      similar domain architecture to AAA+ helicases
    80. ELL N2 domain-like [158329] (1)
      PfamB 026212; includes recent PDB entry 2e5n
    81. PF0610-like [158332] (1)
      PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
    82. Rv2827c N-terminal domain-like [158335] (1)
      ~80 N-terminal residues of Pfam 09407' DUF2005
    83. Rps19E-like [158338] (1)
      Pfam 01090; local sequence similarity to members of the GntR-like family
    84. RPO3F domain-like [158341] (2)
      middle region of Pfam 05158
  5. C-terminal effector domain of the bipartite response regulators [46894] (3)
    binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
    uperfamily
    1. PhoB-like [46895] (6)
      contains 4-stranded meander beta-sheet in the N-terminal extension
    2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5)
      contains additional, fourth helix in the C-terminal extension
    3. Spo0A [46903] (2)
      elaborated with additional helices
  6. TrpR-like [48295] (3)
    contains an extra shared helix after the HTH motif
    uperfamily
    1. Trp repressor, TrpR [48296] (1)
      intertwined dimer of identical 6-helical subunits
    2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2)
      monomeric; contains additional N-terminal helices
    3. SPO1678-like [158345] (1)
      Pfam 06627; DUF1153
  7. Ribosomal protein L11, C-terminal domain [46906] (1)
    uperfamily
    1. Ribosomal protein L11, C-terminal domain [46907] (6)
  8. Ribosomal protein S18 [46911] (1)
    uperfamily
    1. Ribosomal protein S18 [46912] (2)
  9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
    uperfamily
    1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2)
  10. N-terminal Zn binding domain of HIV integrase [46919] (1)
    uperfamily
    1. N-terminal Zn binding domain of HIV integrase [46920] (2)
      Zn-binding site is near the C-terminus
  11. RNA polymerase subunit RPB10 [46924] (1)
    uperfamily
    1. RNA polymerase subunit RPB10 [46925] (2)
      Zn-binding site is near the N-terminus
  12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
    uperfamily
    1. Sigma3 domain [88660] (3)
    2. Sigma4 domain [88665] (7)
    3. YlxM/p13-like [109706] (2)
      Pfam 04297; UPF0122
      structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers
  13. KorB DNA-binding domain-like [109709] (1)
    contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
    uperfamily
    1. KorB DNA-binding domain-like [109710] (2)
      [N-terminal half of Pfam 06613]
  14. Rps17e-like [116820] (1)
    uperfamily
    1. Rps17e-like [116821] (1)
      Pfam 00833
10. Another 3-helical bundle [81602] (5)
  topologically similar to the DNA/RNA-binding bundles; distinct packing
  1. FF domain [81698] (1)
    uperfamily
    1. FF domain [81699] (3)
  2. Protein serine/threonine phosphatase 2C, C-terminal domain [81601] (1)
    uperfamily
    1. Protein serine/threonine phosphatase 2C, C-terminal domain [81600] (1)
  3. B-form DNA mimic Ocr [101059] (1)
    uperfamily
    1. B-form DNA mimic Ocr [101060] (1)
  4. DEK C-terminal domain [109715] (1)
    uperfamily
    1. DEK C-terminal domain [109716] (1)
  5. IscX-like [140319] (1)
    uperfamily
    1. IscX-like [140320] (1)
      Pfam 04384; DUF528
11. RuvA C-terminal domain-like [46928] (9)
  3 helices; bundle, right-handed twist
  1. DNA helicase RuvA subunit, C-terminal domain [46929] (1)
    possibly related to UBA-like domains
    uperfamily
    1. DNA helicase RuvA subunit, C-terminal domain [46930] (3)
  2. UBA-like [46934] (4)
    uperfamily
    1. UBA domain [46935] (24)
    2. TS-N domain [63423] (4)
    3. TAP-C domain-like [68973] (2)
    4. CUE domain [88995] (4)
      Pfam 02845
  3. post-HMGL domain-like [89000] (2)
    uperfamily
    1. DmpG/LeuA communication domain-like [89001] (2)
    2. Conserved carboxylase domain [109725] (1)
      Pfam 02436
      duplication: contains two domains of this fold, connected with a helical linker
  4. CRAL/TRIO N-terminal domain [46938] (1)
    uperfamily
    1. CRAL/TRIO N-terminal domain [46939] (3)
  5. Elongation factor TFIIS domain 2 [46942] (1)
    uperfamily
    1. Elongation factor TFIIS domain 2 [46943] (1)
  6. Double-stranded DNA-binding domain [46950] (1)
    uperfamily
    1. Double-stranded DNA-binding domain [46951] (2)
  7. Hypothetical protein AF0491, middle domain [109728] (1)
    uperfamily
    1. Hypothetical protein AF0491, middle domain [109729] (1)
  8. HBS1-like domain [109732] (1)
    possibly related to UBA-like domains
    uperfamily
    1. HBS1-like domain [109733] (1)
  9. FGAM synthase PurL, linker domain [109736] (1)
    uperfamily
    1. FGAM synthase PurL, linker domain [109737] (1)
12. S13-like H2TH domain [81297] (1)
  core: 3-4 helices
  1. S13-like H2TH domain [46946] (3)
    contains a helix-two turns-helix (H2TH) motif
    uperfamily
    1. Ribosomal protein S13 [46947] (2)
      contains 3 helices and a beta-hairpin in the core and a non-globular C-terminal extension
    2. Middle domain of MutM-like DNA repair proteins [81626] (6)
      contains 4 helices in the core
    3. Topoisomerase VI-B subunit middle domain [81705] (1)
13. Putative DNA-binding domain [46954] (1)
  core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
  1. Putative DNA-binding domain [46955] (7)
    uperfamily
    1. Domains B1 and B5 of PheRS-beta, PheT [46956] (1)
      duplication: contains two such domains related by pseudo dyad
    2. DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [46959] (1)
    3. Dachshund-homology domain [74693] (2)
      Pfam 02437
    4. DNA-binding N-terminal domain of transcription activators [46962] (4)
      includes a dimerisation, antiparallel coiled-coil subdomain
    5. Terminase gpNU1 subunit domain [74696] (1)
    6. Excisionase-like [46891] (2)
      kinked C-terminal helix
    7. N-terminal subdomain of bacterial translation initiation factor IF2 [89006] (1)
14. Spectrin repeat-like [46965] (16)
  3 helices; bundle, closed, left-handed twist; up-and-down
  1. Spectrin repeat [46966] (1)
    uperfamily
    1. Spectrin repeat [46967] (5)
  2. Enzyme IIa from lactose specific PTS, IIa-lac [46973] (1)
    uperfamily
    1. Enzyme IIa from lactose specific PTS, IIa-lac [46974] (1)
      form trimers with 9 helices in a bundle
  3. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46977] (1)
    uperfamily
    1. Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain [46978] (5)
  4. Smac/diablo [46984] (1)
    uperfamily
    1. Smac/diablo [46985] (1)
  5. BAG domain [63491] (1)
    uperfamily
    1. BAG domain [63492] (6)
      Pfam 02179
  6. GAT-like domain [89009] (2)
    uperfamily
    1. GAT domain [89010] (3)
    2. Phosphoinositide-binding clathrin adaptor, domain 2 [100929] (2)
      this domain is associated with the N-terminal ENTH-like domain
  7. Tubulin chaperone cofactor A [46988] (1)
    uperfamily
    1. Tubulin chaperone cofactor A [46989] (2)
      the C-terminal helix is shorter that the other two helices
  8. Ribosomal protein S20 [46992] (1)
    uperfamily
    1. Ribosomal protein S20 [46993] (2)
  9. Glycogen synthesis protein GlgS [109747] (1)
    uperfamily
    1. Glycogen synthesis protein GlgS [109748] (1)
  10. Alpha-hemoglobin stabilizing protein AHSP [109751] (1)
    the bundle twist angle is close to zero (small positive value); similar to the RRF alpha-helical bundle, scop_sf 55194
    uperfamily
    1. Alpha-hemoglobin stabilizing protein AHSP [109752] (1)
  11. PhoU-like [109755] (1)
    duplication: consists of two sequence each repeats adopting this fold
    uperfamily
    1. PhoU-like [109756] (4)
      Pfam 01895
  12. XseB-like [116842] (1)
    helix-swapped homodimer
    uperfamily
    1. XseB-like [116843] (1)
      Pfam 02609
  13. MIT domain [116846] (1)
    uperfamily
    1. MIT domain [116847] (3)
      Pfam 04212
  14. PPK N-terminal domain-like [140356] (1)
    uperfamily
    1. PPK N-terminal domain-like [140357] (2)
      N-terminal part of Pfam 02503
  15. MIT domain-like [140361] (1)
    uperfamily
    1. MIT domain [140362] (1)
  16. Efb C-domain-like [158366] (1)
    1. Efb C-domain-like [158367] (2)
      PfamB 008033
15. immunoglobulin/albumin-binding domain-like [46996] (11)
  3 helices; bundle, closed, left-handed twist; up-and-down; mirror topology to the spectrin-like fold
  1. Bacterial immunoglobulin/albumin-binding domains [46997] (2)
    uperfamily
    1. Immunoglobulin-binding protein A modules [46998] (1)
    2. GA module, an albumin-binding domain [47001] (3)
      Pfam 01468; also includes FIVAR module, Pfam 07554
  2. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81710] (1)
    uperfamily
    1. Plasmid maintenance system epsilon/zeta, antidote epsilon subunit [81711] (1)
      dimeric
  3. Families 57/38 glycoside transferase middle domain [88688] (3)
    uperfamily
    1. 4-alpha-glucanotransferase, domain 2 [89013] (1)
      family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
    2. alpha-mannosidase, domain 2 [88693] (2)
      family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
    3. AmyC C-terminal domain-like [101086] (2)
  4. Phosphoprotein XD domain [101089] (1)
    uperfamily
    1. Phosphoprotein XD domain [101090] (2)
  5. Staphylocoagulase [101094] (1)
    duplication: consists of two domains of this fold
    uperfamily
    1. Staphylocoagulase [101095] (1)
  6. Heat shock protein 70kD (HSP70), C-terminal subdomain [100934] (1)
    uperfamily
    1. Heat shock protein 70kD (HSP70), C-terminal subdomain [100935] (3)
  7. Typo IV secretion system protein TraC [101082] (1)
    uperfamily
    1. Typo IV secretion system protein TraC [101083] (1)
  8. Avirulence protein AvrPto [116854] (1)
    uperfamily
    1. Avirulence protein AvrPto [116855] (1)
  9. Coronavirus NSP7-like [140367] (1)
    uperfamily
    1. Coronavirus NSP7-like [140368] (1)
  10. Vng1086c-like [140371] (1)
    homotetramer; comprises two dimers similar to the antidote epsilon subunit dimer
    uperfamily
    1. Vng1086c-like [140372] (1)
      Pfam 01893; UPF0058
  11. AF1782-like [158372] (1)
    1. AF1782-like [158373] (2)
      Pfam 04010; DUF357
16. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47004] (1)
  3 helices; bundle, closed, right-handed twist; up-and-down
  1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47005] (1)
    uperfamily
    1. Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex [47006] (3)
17. ChaB-like [140375] (1)
  3 helices, the first one is shorter than the other two; bundle, capped by a small, C-terminal beta-hairpin
  1. ChaB-like [140376] (1)
    uperfamily
    1. ChaB-like [140377] (1)
      Pfam 06150
18. Protozoan pheromone-like [47013] (2)
  3 helices; bundle, closed, left-handed twist, up-and-down
  1. Protozoan pheromone proteins [47014] (1)
    uperfamily
    1. Protozoan pheromone proteins [47015] (5)
  2. Hypothetical membrane protein Ta0354, soluble domain [116858] (1)
    uperfamily
    1. Hypothetical membrane protein Ta0354, soluble domain [116859] (1)
19. Acyl-CoA binding protein-like [47026] (2)
  core: 3 helices; bundle, closed, left-handed twist; up-and-down
  1. Acyl-CoA binding protein [47027] (1)
    uperfamily
    1. Acyl-CoA binding protein [47028] (2)
  2. Second domain of FERM [47031] (1)
    uperfamily
    1. Second domain of FERM [47032] (9)
20. YqgQ-like [158378] (1)
  3 helices, bundle, left-handed twist, extended overside connection between the first and second helices
  1. YqgQ-like [158379] (1)
    1. YqgQ-like [158380] (1)
      Pfam 06014; DUF910
21. Kix domain of CBP (creb binding protein) [47039] (1)
  3 helices; bundle, partly opened
  1. Kix domain of CBP (creb binding protein) [47040] (1)
    uperfamily
    1. Kix domain of CBP (creb binding protein) [47041] (1)
22. RAP domain-like [47044] (1)
  3 helices, the first one is shorter than the other two; bundle, partly opened
  1. RAP domain-like [47045] (1)
    uperfamily
    1. RAP domain [47046] (1)
23. VHP, Villin headpiece domain [47049] (1)
  3 short helices; irregular array
  1. VHP, Villin headpiece domain [47050] (1)
    uperfamily
    1. VHP, Villin headpiece domain [47051] (5)
24. BSD domain-like [140382] (1)
  core: 3 helices; triangular array; the extra N-terminal and C-terminal helices form a coiled coil structure
  1. BSD domain-like [140383] (1)
    uperfamily
    1. BSD domain [140384] (2)
      Pfam 03909
25. TAF(II)230 TBP-binding fragment [47054] (1)
  3 short helices; irregular array
  1. TAF(II)230 TBP-binding fragment [47055] (1)
    uperfamily
    1. TAF(II)230 TBP-binding fragment [47056] (1)
26. S15/NS1 RNA-binding domain [47059] (1)
  3 helices; irregular array
  1. S15/NS1 RNA-binding domain [47060] (3)
    uperfamily
    1. N-terminal, RNA-binding domain of nonstructural protein NS1 [47061] (2)
    2. Ribosomal protein S15 [47064] (3)
      contains additional N-terminal helix that forms a separate unit
    3. a tRNA synthase domain [47068] (3)
27. Frizzled cysteine-rich domain [63500] (1)
  Core: 3 helices; irregular array; disulfide-rich
  1. Frizzled cysteine-rich domain [63501] (1)
    uperfamily
    1. Frizzled cysteine-rich domain [63502] (2)
28. T4 endonuclease V [47076] (1)
  3 helices; irregular array
  1. T4 endonuclease V [47077] (1)
    uperfamily
    1. T4 endonuclease V [47078] (1)
29. Fertilization protein [47081] (1)
  core: 3 helices; bundle, closed, right-handed twist; up-and-down
  1. Fertilization protein [47082] (1)
    uperfamily
    1. Fertilization protein [47083] (3)
30. PGBD-like [47089] (1)
  core: 3 helices; bundle, closed, left-handed twist; parallel
  1. PGBD-like [47090] (2)
    uperfamily
    1. Peptidoglycan binding domain, PGBD [47091] (2)
    2. MMP N-terminal domain [63427] (4)
31. HMG-box [47094] (1)
  3 helices; irregular array
  1. HMG-box [47095] (1)
    uperfamily
    1. HMG-box [47096] (12)
32. Histone-fold [47112] (1)
  core: 3 helices; long middle helix is flanked at each end with shorter ones
  1. Histone-fold [47113] (4)
    uperfamily
    1. Nucleosome core histones [47114] (23)
      form octamers composed of two copies of each of the four histones
    2. Archaeal histone [47129] (4)
    3. TBP-associated factors, TAFs [47134] (13)
    4. Bacterial histone-fold protein [101318] (2)
      duplication: two repeats of histone fold are arranged as subunits in the archael histone dimer; new structure from Thermus thermophilus (1wws) comprised of dimers similar the to the H3-H4 tetramer
33. Open three-helical up-and-down bundle [47143] (7)
  core: 3 helices; bundle, open
  1. HSC20 (HSCB), C-terminal oligomerisation domain [47144] (1)
    uperfamily
    1. HSC20 (HSCB), C-terminal oligomerisation domain [47145] (1)
  2. Diol dehydratase, gamma subunit [47148] (1)
    contains irregular N-terminal subdomain
    uperfamily
    1. Diol dehydratase, gamma subunit [47149] (2)
  3. Methane monooxygenase hydrolase, gamma subunit [47152] (1)
    duplication: consists of two domains of this fold
    uperfamily
    1. Methane monooxygenase hydrolase, gamma subunit [47153] (2)
  4. Mitochondrial import receptor subunit Tom20 [47157] (1)
    uperfamily
    1. Mitochondrial import receptor subunit Tom20 [47158] (1)
  5. Hemolysin expression modulating protein HHA [68989] (1)
    uperfamily
    1. Hemolysin expression modulating protein HHA [68990] (1)
  6. EF2458-like [140404] (1)
    N-terminal helix swapped dimer; interrupted antiparallel coiled coil
    uperfamily
    1. EF2458-like [140405] (1)
      Pfam 07408; DUF1507
  7. YvfG-like [158388] (1)
    1. YvfG-like [158389] (1)
      Pfam 09628
34. beta-catenin-interacting protein ICAT [81729] (1)
  core: 3 helices; irregular array
  1. beta-catenin-interacting protein ICAT [81730] (1)
    uperfamily
    1. beta-catenin-interacting protein ICAT [81731] (1)
35. DNA polymerase III theta subunit-like [116730] (1)
  3 helices; irregular array
  1. DNA polymerase III theta subunit-like [46575] (1)
    uperfamily
    1. DNA polymerase III theta subunit-like [46576] (2)
      Pfam 06440
      independent solution structure determinations of different members resulted in similar secondary structures but different folds
36. Four-helical up-and-down bundle [47161] (28)
  core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down
  1. Apolipoprotein [47162] (1)
    uperfamily
    1. Apolipoprotein [47163] (3)
      Can exist in a coiled-coil oligomeric form, see PDB entry 1AV1
      family may also include the five-helical bundle protein Apolipophorin-III
  2. Aspartate receptor, ligand-binding domain [47170] (1)
    uperfamily
    1. Aspartate receptor, ligand-binding domain [47171] (2)
  3. Cytochromes [47175] (2)
    Heme-containing proteins
    uperfamily
    1. Cytochrome b562 [47176] (1)
    2. Cytochrome c'-like [47179] (9)
  4. Hemerythrin-like [47188] (1)
    uperfamily
    1. Hemerythrin-like [47189] (3)
      Iron-binding proteins
  5. TMV-like viral coat proteins [47195] (1)
    uperfamily
    1. TMV-like viral coat proteins [47196] (3)
  6. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47212] (1)
    uperfamily
    1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47213] (1)
  7. Proteasome activator [47216] (1)
    uperfamily
    1. Proteasome activator [47217] (2)
  8. alpha-catenin/vinculin-like [47220] (2)
    uperfamily
    1. alpha-catenin/vinculin [47221] (4)
      possible duplication: contains several domains of this fold
      The listed PDB entries contain different large fragments but not the whole proteins
    2. VBS domain [140408] (1)
      Pfam 08913; Vinculin Binding Site
  9. FAT domain of focal adhesion kinase [68993] (1)
    uperfamily
    1. FAT domain of focal adhesion kinase [68994] (3)
  10. Oxygen-evolving enhancer protein 3, [101112] (1)
    uperfamily
    1. Oxygen-evolving enhancer protein 3, [101113] (1)
  11. Histidine-containing phosphotransfer domain, HPT domain [47226] (6)
    contains additional, fifth helix at the N-terminus
    uperfamily
    1. Aerobic respiration control sensor protein, ArcB [47227] (1)
    2. Phosphorelay protein-like [47230] (3)
    3. Chemotaxis protein CheA P1 domain [63512] (2)
    4. Sensor-like histidine kinase YojN, C-terminal domain [116868] (1)
    5. Phosphorelay protein luxU [116871] (1)
    6. SphA-like [158394] (1)
  12. Bacterial GAP domain [47233] (1)
    contains extra helices in the loops at one end of the bundle
    uperfamily
    1. Bacterial GAP domain [47234] (3)
  13. Outer surface protein C (OspC) [63515] (1)
    uperfamily
    1. Outer surface protein C (OspC) [63516] (1)
  14. Flagellar export chaperone FliS [101116] (1)
    can form closed, open and helix-swapped bundles
    uperfamily
    1. Flagellar export chaperone FliS [101117] (2)
  15. Domain of the SRP/SRP receptor G-proteins [47364] (1)
    uperfamily
    1. Domain of the SRP/SRP receptor G-proteins [47365] (7)
  16. FAD-dependent thiol oxidase [69000] (1)
    uperfamily
    1. FAD-dependent thiol oxidase [69001] (2)
  17. Group V grass pollen allergen [81736] (1)
    uperfamily
    1. Group V grass pollen allergen [81737] (2)
  18. Nucleotidyltransferase substrate binding subunit/domain [81593] (4)
    uperfamily
    1. Family 1 bi-partite nucleotidyltransferase subunit [81740] (2)
    2. HEPN domain [89022] (2)
    3. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81592] (1)
      N-terminal catalytic domain is followed by an all-alpha domain
    4. Glutamine synthase adenylyltransferase GlnE, domain 2 [109767] (1)
  19. RecG, N-terminal domain [69008] (1)
    uperfamily
    1. RecG, N-terminal domain [69009] (1)
  20. Colicin D immunity protein [101125] (1)
    uperfamily
    1. Colicin D immunity protein [101126] (1)
  21. Nickel-containing superoxide dismutase, NiSOD [109770] (1)
    uperfamily
    1. Nickel-containing superoxide dismutase, NiSOD [109771] (2)
  22. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109775] (1)
    contains extra alpha+beta subdomain formed by the N- and C-termini.
    uperfamily
    1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109776] (1)
  23. Domain from hypothetical 2610208m17rik protein [109779] (1)
    uperfamily
    1. Domain from hypothetical 2610208m17rik protein [109780] (1)
  24. TrmE connector domain [116878] (1)
    uperfamily
    1. TrmE connector domain [116879] (1)
  25. YppE-like [140415] (1)
    flattened bundle at one end with helices 2 and coming in contact and separating helices 1 and 3
    uperfamily
    1. YppE-like [140416] (3)
      Pfam 08807; DUF1798
  26. MW0975(SA0943)-like [140423] (1)
    open bundle; there is a long groove between helices 1 and 4
    uperfamily
    1. MW0975(SA0943)-like [140424] (1)
  27. VPS28 C-terminal domain-like [140427] (1)
    uperfamily
    1. VPS28 C-terminal domain-like [140428] (1)
      C-terminal part of Pfam 03997
  28. TM1646-like [158397] (1)
    1. TM1646-like [158398] (1)
      Pfam 03885; DUF327
37. PTS-regulatory domain, PRD [63519] (1)
  core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection
  1. PTS-regulatory domain, PRD [63520] (1)
    duplication: consists of two domains of this fold
    uperfamily
    1. PTS-regulatory domain, PRD [63521] (1)
38. Ferritin-like [47239] (6)
  core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
  1. Ferritin-like [47240] (9)
    contains bimetal-ion centre in the middle of the bundle
    uperfamily
    1. Ferritin [47241] (34)
    2. Ribonucleotide reductase-like [47253] (18)
    3. Manganese catalase (T-catalase) [100951] (2)
    4. YciF-like [140445] (2)
      Pfam 05974; DUF892
    5. half-ferritin [140450] (1)
      comprise of alpha-hairpin subunits forming the ferritin-like four-helical bundle; assembles further in a homodecamer
    6. PMT1231-like [158402] (1)
      PfamB 016165
    7. MiaE-like [158405] (1)
      Pfam 06175; tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
    8. AMB4284-like [158408] (1)
      possible rubrerythrin
    9. Rv2844-like [158411] (1)
      PfamB 061364
  2. Cobalamin adenosyltransferase-like [89028] (2)
    crossover loop goes across a different side of the 4-helical bundle; no internal metal-binding site
    uperfamily
    1. Cobalamin adenosyltransferase [89032] (2)
    2. Hypothetical protein Ta1238 [89029] (1)
  3. EsxAB dimer-like [140453] (1)
    (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
    uperfamily
    1. ESAT-6 like [140454] (2)
      Pfam 06013; the conserwed WxG motif makes the turn at the alpha-hairpin tip
  4. PE/PPE dimer-like [140459] (2)
    (hetero)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals inside the bundle
    uperfamily
    1. PE [140460] (1)
      Pfam 00934; pairs with with the N-terminal hairpin of PPE
    2. PPE [140463] (1)
      Pfam 00823; contains extra C-terminal alpha-hairpin, unlike the PE family subunit
  5. HP0062-like [158414] (1)
    (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
    1. HP0062-like [158415] (1)
      Pfam 09647
  6. SO2669-like [158418] (1)
    (homo)dimer of alpha-hairpin subunits similar to that of the half-ferritin family; no bound metals
    1. SO2669-like [158419] (1)
39. 4-helical cytokines [47265] (1)
  core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
  1. 4-helical cytokines [47266] (3)
    there are two different topoisomers of this fold with different entanglements of the two crossover connections
    uperfamily
    1. Long-chain cytokines [47267] (14)
    2. Short-chain cytokines [47286] (14)
    3. Interferons/interleukin-10 (IL-10) [47305] (13)
      contains an additional helix in one of the crossover connections
40. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47322] (1)
  core: 4 helices; bundle; one loop crosses over one side of the bundle
  1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47323] (1)
    uperfamily
    1. Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [47324] (10)
41. Acyl carrier protein-like [47335] (3)
  4 helices, bundle; helix 3 is shorter than others; up-and-down
  1. ACP-like [47336] (3)
    uperfamily
    1. Acyl-carrier protein (ACP) [47337] (9)
    2. Peptidyl carrier domain [47342] (1)
    3. apo-D-alanyl carrier protein [63535] (1)
  2. Colicin E immunity proteins [47345] (1)
    uperfamily
    1. Colicin E immunity proteins [47346] (3)
  3. Retrovirus capsid dimerization domain-like [47353] (2)
    uperfamily
    1. Retrovirus capsid protein C-terminal domain [47354] (4)
    2. SCAN domain [140466] (2)
      Pfam 02023; forms segment-swapped dimers compared to the retroviral capsid domain
42. Bromodomain-like [47363] (15)
  4 helices; bundle; minor mirror variant of up-and-down topology
  1. Bromodomain [47370] (1)
    uperfamily
    1. Bromodomain [47371] (5)
  2. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69012] (1)
    uperfamily
    1. alpha-ketoacid dehydrogenase kinase, N-terminal domain [69013] (3)
  3. Acyl-CoA dehydrogenase C-terminal domain-like [47203] (2)
    multidomain flavoprotein; N-terminal domain is all-alpha; the middle domain is open (5,8) barrel
    uperfamily
    1. Medium chain acyl-CoA dehydrogenase-like, C-terminal domain [47204] (12)
    2. acyl-CoA oxidase C-terminal domains [74714] (2)
      duplication: tandem repeat of this fold
  4. Plant invertase/pectin methylesterase inhibitor [101148] (1)
    contains a short alpha-hairpin at the N-terminal extension
    uperfamily
    1. Plant invertase/pectin methylesterase inhibitor [101149] (2)
      Pfam 04043
  5. Mob1/phocein [101152] (1)
    common fold is elaborated with additional short helices; contains a zinc-binding site
    uperfamily
    1. Mob1/phocein [101153] (2)
  6. Bacteriocin immunity protein-like [109797] (2)
    uperfamily
    1. Carnobacteriocin B2 immunity protein [109798] (1)
    2. EntA-Im [140475] (1)
  7. LemA-like [140478] (1)
    helices 2 and 3 are shorther than helices 1 and 4
    uperfamily
    1. LemA-like [140479] (1)
      Pfam 04011
  8. MAST3 pre-PK domain-like [140482] (1)
    this domain precedes the Protein Kinase domain in Microtubule-associated serine/threonine-protein kinase 3 (MAST3)
    uperfamily
    1. MAST3 pre-PK domain-like [140483] (1)
  9. PA2201 N-terminal domain-like [140486] (1)
    uperfamily
    1. PA2201 N-terminal domain-like [140487] (1)
      trimerisation domain
  10. Nqo1C-terminal domain-like [140490] (1)
    contains extra C-terminal helix that caps the bundle at one end and Fe4-S4 cluster at the other end
    uperfamily
    1. Nqo1C-terminal domain-like [140491] (1)
      PfamB 000336; sequence similarity to the Fe4-S4 ferredoxins in the cluser-binding site
  11. Bacillus cereus metalloprotein-like [158430] (1)
    Duplication: tandem repeat of two domains of this fold with similar sequences; binds a dimetal ion cluster between the repeats
    1. Bacillus cereus metalloprotein-like [158431] (2)
  12. Ta0600-like [158436] (1)
    1. Ta0600-like [158437] (2)
      Pfam 03685; UPF0147
  13. DsbB-like [158442] (1)
    contains an extra helix in a long loop between helices 3 and 4
    1. DsbB-like [158443] (1)
      Pfam 02600
  14. IVS-encoded protein-like [158446] (1)
    IVS: Intervening sequence with conserved ORF in eubacterial 23S rRNA genes; forms a homopentamer with a toroid-shaped structure containing a tapered central channel
    1. IVS-encoded protein-like [158447] (2)
      Pfam 05635
  15. YqcC-like [158452] (1)
    1. YqcC-like [158453] (1)
      Pfam 04287; DUF446
43. ROP-like [47379] (8)
  4 helices; dimer of identical alpha-hairpin subunits; bundle, closed, left-handed twist
  1. ROP protein [47380] (1)
    uperfamily
    1. ROP protein [47381] (1)
  2. Homodimeric domain of signal transducing histidine kinase [47384] (1)
    uperfamily
    1. Homodimeric domain of signal transducing histidine kinase [47385] (3)
  3. Nonstructural protein ns2, Nep, M1-binding domain [101156] (1)
    uperfamily
    1. Nonstructural protein ns2, Nep, M1-binding domain [101157] (1)
  4. Dimerisation domain of CENP-B [101160] (1)
    uperfamily
    1. Dimerisation domain of CENP-B [101161] (1)
  5. Hypothetical protein D-63 [109801] (1)
    uperfamily
    1. Hypothetical protein D-63 [109802] (1)
  6. HP1531-like [140496] (1)
    contains short extra helix in the loop between the two bundle-forming helices
    uperfamily
    1. HP1531-like [140497] (1)
      Small sequence family, specific to Helicobacteraceae
  7. BAS1536-like [140500] (1)
    uperfamily
    1. BAS1536-like [140501] (2)
      PfamB 015565
  8. FHV B2 protein-like [140506] (1)
    uperfamily
    1. FHV B2 protein-like [140507] (1)
44. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47390] (1)
  4 helices; bundle, closed, right-handed twist
  1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47391] (1)
    dimer of identical alpha-hairpin motifs
    uperfamily
    1. Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit [47392] (2)
45. Orange domain-like [158456] (1)
  4 helices; dimer of identical alpha-hairpin subunits;
  1. Orange domain-like [158457] (1)
    1. Hairy Orange domain [158458] (1)
      Pfam 07527
46. Soluble domain of poliovirus core protein 3a [89042] (1)
  4 helices; bundle, closed, right-handed twist
  1. Soluble domain of poliovirus core protein 3a [89043] (1)
    dimer of identical alpha-hairpin motifs
    uperfamily
    1. Soluble domain of poliovirus core protein 3a [89044] (1)
47. Transcription factor IIA (TFIIA), alpha-helical domain [47395] (1)
  4 helices; bundle, closed, right-handed twist
  1. Transcription factor IIA (TFIIA), alpha-helical domain [47396] (1)
    dimer of non-identical alpha-hairpins
    uperfamily
    1. Transcription factor IIA (TFIIA), alpha-helical domain [47397] (4)
      heterodimer of two homologous chains
48. Ectatomin subunits [47400] (1)
  4 helices; bundle, closed, left-handed twist
  1. Ectatomin subunits [47401] (1)
    disulfide-linked heterodimer of similar alpha-hairpin subunits
    uperfamily
    1. Ectatomin subunits [47402] (2)
49. Dimerisation interlock [47405] (4)
  4 helices; bundle, closed, right-handed twist
  1. SinR repressor dimerisation domain-like [47406] (1)
    intertwined heterodimer of two homologous chains
    uperfamily
    1. SinR repressor dimerisation domain-like [47407] (2)
  2. Dimerization cofactor of HNF-1 alpha [100957] (1)
    uperfamily
    1. Dimerization cofactor of HNF-1 alpha [100958] (1)
  3. Docking domain A of the erythromycin polyketide synthase (DEBS) [101166] (1)
    uperfamily
    1. Docking domain A of the erythromycin polyketide synthase (DEBS) [101167] (1)
  4. Phenylalanine zipper [109805] (1)
    interlocking dimer with longer helices and aromatic-rich core
    uperfamily
    1. Adapter protein APS, dimerisation domain [109806] (1)
50. lambda repressor-like DNA-binding domains [47412] (1)
  core: 4 helices; folded leaf, closed
  1. lambda repressor-like DNA-binding domains [47413] (13)
    uperfamily
    1. POU-specific domain [47414] (3)
    2. Phage repressors [47419] (7)
      consists of different sequence families of HTH repressors of phage origins
    3. SinR domain-like [47432] (8)
    4. Cyanase N-terminal domain [47435] (1)
      probably does not bind to DNA
    5. GalR/LacI-like bacterial regulator [47438] (4)
      lacks the first helix of canonical fold
      3 helices; bundle, partly opened, right-handed twist
    6. YdiL-like [109813] (2)
      contains extra C-terminal all-alpha dimerization subdomain; the dimer may bind DNA
    7. CUT domain [116891] (4)
      Pfam 02376
    8. Probable transcriptional regulator VC1968, N-terminal domain [116898] (1)
    9. Bacteriophage CII protein [140520] (1)
      Pfam 05269; a compact helix-swapped dimer of the canonical fold; includes the extra C-terminal teramerisation region (alpha-helix); in the tetramer-DNA complex only two of the four HTH motifs interact with DNA
    10. NE0471 C-terminal domain-like [140523] (1)
    11. PrgX N-terminal domain-like [140526] (1)
      Part of Pfam 01381
    12. EDF1-like [140529] (1)
      part of Pfam 01381
    13. NE1354 [140532] (2)
      contains extra C-terminal dimerisation arm (beta-strand)
51. Signal peptide-binding domain [47445] (1)
  4 helices; orthogonal array
  1. Signal peptide-binding domain [47446] (1)
    uperfamily
    1. Signal peptide-binding domain [47447] (4)
52. A DNA-binding domain in eukaryotic transcription factors [47453] (1)
  4 helices; the long C-terminal helix protrudes from the domain and binds to DNA
  1. A DNA-binding domain in eukaryotic transcription factors [47454] (1)
    uperfamily
    1. A DNA-binding domain in eukaryotic transcription factors [47455] (2)
53. HLH-like [47458] (2)
  4-helices; bundle, closed, left-handed twist; 2 crossover connections
  1. HLH, helix-loop-helix DNA-binding domain [47459] (1)
    dimer of two identical helix-loop-helix subunits
    uperfamily
    1. HLH, helix-loop-helix DNA-binding domain [47460] (9)
  2. Docking domain B of the erythromycin polyketide synthase (DEBS) [101173] (1)
    uperfamily
    1. Docking domain B of the erythromycin polyketide synthase (DEBS) [101174] (1)
54. HAMP domain-like [158471] (1)
  dimer of helix-loop-helix segments; distict from the HLH-like fold; parallel four-helical bundle with two overside connections
  1. HAMP domain-like [158472] (1)
    1. HAMP domain [158473] (1)
      Pfam 00672
55. EF Hand-like [47472] (4)
  core: 4 helices; array of 2 hairpins, opened
  1. EF-hand [47473] (11)
    Duplication: consists of two EF-hand units: each is made of two helices connected with calcium-binding loop
    uperfamily
    1. Calbindin D9K [47474] (2)
      made of two EF-hands only
    2. S100 proteins [47478] (17)
      dimer: subunits are made of two EF-hands
    3. Polcalcin [89048] (3)
      calcium-binding pollen allergen; two EF-hands per subunit
    4. Osteonectin [47489] (1)
      5 helices; two EF-hands plus one of additional helices in the N-terminal part
    5. Parvalbumin [47492] (9)
      6-helices; array of 3 hairpins, closed
      made with two-helical hairpin and two EF-hands
    6. Calmodulin-like [47502] (49)
      Duplication: made with two pairs of EF-hands
    7. Eps15 homology domain (EH domain) [47543] (4)
    8. Cbp40 (plasmodial specific CaII-binding protein LAV1-2) [81758] (1)
      4 EF-hands assembled in a compact structure like the Penta-EF-hand proteins; contains additional N-terminal all-alpha subdomain
    9. Penta-EF-hand proteins [63550] (11)
    10. EF-hand modules in multidomain proteins [47547] (8)
    11. p25-alpha [140538] (2)
      Pfam 05517; comprises two degenerate EF-hands and extra C-terminal helix, packed agains the bundle end
  2. Insect pheromone/odorant-binding proteins [47565] (1)
    the N-terminal extension, containing a few short helices, forms a flexible lid for the binding cavity
    uperfamily
    1. Insect pheromone/odorant-binding proteins [47566] (6)
  3. Hypothetical protein MTH865 [69025] (1)
    uperfamily
    1. Hypothetical protein MTH865 [69026] (1)
  4. Cloroperoxidase [47571] (1)
    duplication: consists of 2 similar domains composed of 2 EF hand-like motifs each
    uperfamily
    1. Cloroperoxidase [47572] (1)
56. CH domain-like [47575] (3)
  core: 4 helices: bundle
  1. Calponin-homology domain, CH-domain [47576] (1)
    uperfamily
    1. Calponin-homology domain, CH-domain [47577] (12)
      Pfam 00307
  2. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81761] (1)
    uperfamily
    1. X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain [81762] (1)
  3. Hook domain [116907] (1)
    uperfamily
    1. Hook domain [116908] (1)
      N-terminal part of Pfam 05622
57. Domain of poly(ADP-ribose) polymerase [47586] (1)
  core: 4 helices: bundle; unusual topology
  1. Domain of poly(ADP-ribose) polymerase [47587] (1)
    duplication: consists of 2 helix-loop-helix structural repeats
    uperfamily
    1. Domain of poly(ADP-ribose) polymerase [47588] (3)
58. SWIB/MDM2 domain [47591] (1)
  core: 4 helices: open bundle; capped by two small 3-stranded beta-sheets
  duplication: consists of two structural repeats
  1. SWIB/MDM2 domain [47592] (1)
    binds to the transactivation domain of human p53
    uperfamily
    1. SWIB/MDM2 domain [47593] (5)
      Pfam 02201
59. Pre-protein crosslinking domain of SecA [81766] (1)
  core: 4 helices: bundle; flanked by two short beta-hairpins
  duplication: consists of two structural repeats
  1. Pre-protein crosslinking domain of SecA [81767] (1)
    uperfamily
    1. Pre-protein crosslinking domain of SecA [81768] (2)
60. Ribbon-helix-helix [47597] (1)
  core: 4 helices; array of 2 hairpins, opened
  1. Ribbon-helix-helix [47598] (11)
    formerly Met repressor-like; dimeric proteins; the N-termini form a small beta-sheet ribbon
    uperfamily
    1. Arc/Mnt-like phage repressors [47599] (2)
    2. CopG-like [100970] (5)
      similar to the phage repressor family
    3. Omega transcriptional repressor [100971] (1)
      plasmid-encoded, similar to the phage repressor family
    4. Met repressor, MetJ (MetR) [100972] (1)
    5. NE0241-like [140544] (1)
      contains extra C-terminal long helix; currently consists of an orphan protein
    6. SeqA N-terminal domain-like [140547] (1)
      N-terminal part of Pfam 03925
    7. Trafficking protein A-like [140550] (1)
    8. VCA0319-like [140553] (1)
      COG4453; extended and extra C-terminal helices; potential component of the bi-partite system also including an acetyltransferase
    9. VirC2-like [158482] (1)
      Pfam 07181; duplicated ribbon-helix-helix motif; fold forms a trefoil knot
    10. PutA pre-N-terminal region-like [158485] (1)
      in PutA it forms a separate ribbon-helix-helix domain connected to the N-terminal enzymatic domain by a flexible linker
    11. MJ0366-like [158488] (1)
      PfamB 022101; duplicated ribbon-helix-helix motif; forms trefoil knot; predicted DNA binding
61. GST C-terminal domain-like [47615] (1)
  core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
  1. GST C-terminal domain-like [47616] (2)
    this domains follows the thioredoxin-like N-terminal domain
    uperfamily
    1. Glutathione S-transferase (GST), C-terminal domain [47617] (44)
    2. Arc1p N-terminal domain-like [158491] (1)
      PfamB 021108
62. Methionine synthase domain-like [47643] (3)
  4 helices; bundle, left-handed twist; right-handed superhelix
  1. Methionine synthase domain [47644] (1)
    uperfamily
    1. Methionine synthase domain [47645] (1)
  2. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47648] (1)
    uperfamily
    1. Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain [47649] (6)
  3. TM0693-like [140560] (1)
    helix-swapped dimer; in which the two last helices of this fold form a single coiled-coil helix
    uperfamily
    1. TM0693-like [140561] (1)
63. KaiA/RbsU domain [101214] (1)
  4 helices; bundle, right-handed twist; right-handed superhelix
  1. KaiA/RbsU domain [101215] (2)
    uperfamily
    1. Circadian clock protein KaiA, C-terminal domain [101216] (3)
    2. Phosphoserine phosphatase RsbU, N-terminal domain [109836] (1)
      forms a helix-swapped dimer that otherwise is similar to the KaiA domain dimer
64. STAT-like [47654] (6)
  4 long helices; bundle, left-handed twist (coiled coil); right-handed superhelix
  1. STAT [47655] (1)
    uperfamily
    1. STAT [47656] (3)
  2. t-snare proteins [47661] (1)
    uperfamily
    1. t-snare proteins [47662] (6)
  3. Cag-Z [109839] (1)
    four-helical bundle without significant twist
    uperfamily
    1. Cag-Z [109840] (1)
  4. CAPPD, an extracellular domain of amyloid beta A4 protein [109843] (1)
    the first three helices are longer than the fourth one and, taken separately, adopt a Spectrin repeat-like fold (scop_cf 46965)
    uperfamily
    1. CAPPD, an extracellular domain of amyloid beta A4 protein [109844] (1)
  5. FlgN-like [140566] (1)
    the last helix is shorter than the three others; a short extra helix between helices 2 an 3 fills the gap in the bundle
    uperfamily
    1. FlgN-like [140567] (1)
      Pfam 05130
  6. MukF C-terminal domain-like [140570] (1)
    uperfamily
    1. MukF C-terminal domain-like [140571] (1)
      C-terminal part of Pfam 03882
65. N-cbl like [47667] (5)
  4 helices; bundle, left-handed twist; left-handed superhelix
  1. N-terminal domain of cbl (N-cbl) [47668] (1)
    uperfamily
    1. N-terminal domain of cbl (N-cbl) [47669] (1)
  2. Transferrin receptor-like dimerisation domain [47672] (1)
    uperfamily
    1. Transferrin receptor-like dimerisation domain [47673] (2)
  3. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47676] (1)
    uperfamily
    1. Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [47677] (2)
      Smart 00509
  4. HIV integrase-binding domain [140576] (1)
    uperfamily
    1. HIV integrase-binding domain [140577] (1)
      N-terminal part of PfamB 012949
  5. PG0775 C-terminal domain-like [158494] (1)
    1. PG0775 C-terminal domain-like [158495] (1)
      PfamB 133436
66. Replisome organizer (g39p helicase loader/inhibitor protein) [89063] (1)
  4 helices; bundle, right-handed twist; left-handed superhelix
  1. Replisome organizer (g39p helicase loader/inhibitor protein) [89064] (1)
    uperfamily
    1. Replisome organizer (g39p helicase loader/inhibitor protein) [89065] (1)
67. Hypothetical protein YqbG [116914] (1)
  core: 4 helices; bundle, right-handed twist; left-handed superhelix
  1. Hypothetical protein YqbG [116915] (1)
    uperfamily
    1. Hypothetical protein YqbG [116916] (1)
68. DnaD domain-like [158498] (1)
  4 helices; bundle, right-handed twist; left-handed superhelix
  1. DnaD domain-like [158499] (1)
    1. DnaD domain [158500] (1)
      Pfam 04271
69. C-terminal domain of B transposition protein [47680] (1)
  4 helices; irregular array
  1. C-terminal domain of B transposition protein [47681] (1)
    uperfamily
    1. C-terminal domain of B transposition protein [47682] (1)
70. HAND domain of the nucleosome remodeling ATPase ISWI [101223] (1)
  4 helices; irregular array
  1. HAND domain of the nucleosome remodeling ATPase ISWI [101224] (1)
    uperfamily
    1. HAND domain of the nucleosome remodeling ATPase ISWI [101225] (1)
71. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89068] (1)
  4 helices; irregular array
  1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89069] (1)
    uperfamily
    1. N-terminal, cytoplasmic domain of anti-sigmaE factor RseA [89070] (1)
72. Anaphylotoxins (complement system) [47685] (1)
  4 helices; irregular array, disulfide-linked
  1. Anaphylotoxins (complement system) [47686] (1)
    uperfamily
    1. Anaphylotoxins (complement system) [47687] (2)
      can be classified as disulfide-rich
73. Cytochrome c oxidase subunit h [47693] (1)
  4 helices; irregular array, disulfide-linked
  1. Cytochrome c oxidase subunit h [47694] (1)
    uperfamily
    1. Cytochrome c oxidase subunit h [47695] (1)
74. Crustacean CHH/MIH/GIH neurohormone [81777] (1)
  4 helices; irregular array, disulfide-linked
  1. Crustacean CHH/MIH/GIH neurohormone [81778] (1)
    uperfamily
    1. Crustacean CHH/MIH/GIH neurohormone [81779] (1)
75. C-terminal domain of DFF45/ICAD (DFF-C domain) [81782] (1)
  4 helices; folded leaf; right-handed superhelix
  1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81783] (1)
    uperfamily
    1. C-terminal domain of DFF45/ICAD (DFF-C domain) [81784] (1)
76. BH2638-like [158503] (1)
  4 helices, folded leaf, right-handed superhelix; some similarity to the DFF-C domain fold (scop_cf 81782)
  1. BH2638-like [158504] (1)
    1. BH2638-like [158505] (1)
      Pfam 05256; UPF0223
77. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47698] (1)
  4 helices; folded leaf; right-handed superhelix
  1. Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin [47699] (3)
    can be classified as disulfide-rich
    uperfamily
    1. Plant lipid-transfer and hydrophobic proteins [47700] (7)
    2. Proteinase/alpha-amylase inhibitors [47708] (3)
    3. Seed storage protein, 2S albumin [47715] (3)
      two chains result from a single-chain precursor
78. p53 tetramerization domain [47718] (1)
  core: 4 helices; bundle
  1. p53 tetramerization domain [47719] (1)
    homotetramer
    uperfamily
    1. p53 tetramerization domain [47720] (1)
79. Bcr-Abl oncoprotein oligomerization domain [69035] (1)
  core: 4 long helices; bundle
  1. Bcr-Abl oncoprotein oligomerization domain [69036] (1)
    homotetramer
    uperfamily
    1. Bcr-Abl oncoprotein oligomerization domain [69037] (1)
80. Domain of early E2A DNA-binding protein, ADDBP [47723] (1)
  4 helices; bundle, partly opened
  1. Domain of early E2A DNA-binding protein, ADDBP [47724] (1)
    this domain is the first in the fragment of known structure
    uperfamily
    1. Domain of early E2A DNA-binding protein, ADDBP [47725] (1)
81. IHF-like DNA-binding proteins [47728] (1)
  core: 4 helices; bundle, partly opened, capped with a beta-sheet
  1. IHF-like DNA-binding proteins [47729] (2)
    dimer of identical subunits
    uperfamily
    1. Prokaryotic DNA-bending protein [47730] (8)
    2. DNA-binding domain (fragment?) of the TraM protein [63566] (1)
      old provisional classification awaiting the entire protein structure; structure of a different fragment of this protein (PDB 2g7o) is classified into a different superfamily
82. TraM-like [140580] (1)
  multihelical oligomeric protein; structure of whole subunit is not known; the N-terminal part is implicated in DNA binding, the middle region forms tetrameric parallel coiled coil, surrounded by the C-terminal helices
  1. TraM-like [140581] (1)
    uperfamily
    1. TraM-like [140582] (2)
      Pfam 05261
83. CO dehydrogenase ISP C-domain like [47740] (1)
  core: 4 helices, bundle
  1. CO dehydrogenase ISP C-domain like [47741] (1)
    contains 2Fe-2S cluster
    uperfamily
    1. CO dehydrogenase ISP C-domain like [47742] (8)
84. Protein HNS-dependent expression A; HdeA [47751] (1)
  4 helices; the three last helices form a bundle similar to that of the RuvA C-domain
  1. Protein HNS-dependent expression A; HdeA [47752] (1)
    overall fold is similar to the fold of N-terminal subdomain of the GluRS anticodon-binding domain (1GLN)
    uperfamily
    1. Protein HNS-dependent expression A; HdeA [47753] (1)
85. PABP domain-like [63569] (2)
  4 helices; an orthogonal array
  1. PABC (PABP) domain [63570] (1)
    uperfamily
    1. PABC (PABP) domain [63571] (4)
  2. Ribosomal protein L20 [74731] (1)
    uperfamily
    1. Ribosomal protein L20 [74732] (4)
86. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47756] (1)
  4 helices; an orthogonal array
  1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47757] (1)
    uperfamily
    1. Chemotaxis receptor methyltransferase CheR, N-terminal domain [47758] (1)
87. Dcp2 domain-like [140585] (1)
  4 helices; orthogonal array of two alpha hairpins
  1. Dcp2 domain-like [140586] (1)
    uperfamily
    1. Dcp2 box A domain [140587] (1)
      Pfam 05026
88. Type III secretion system domain [140590] (1)
  core: 4 helices, orthogonal array; right-handed superhelix
  1. Type III secretion system domain [140591] (3)
    uperfamily
    1. TyeA-like [140592] (1)
      Pfam 09059
    2. YopR Core [140595] (1)
      Pfam 09025, contains extra N-terminal helix
    3. LcrE-like [140598] (1)
      Duplication; contains two domains of this fold; Pfam 07201 (HrpJ-like) covers the first domain and the N-terminal half of the second domain
89. YugE-like [116921] (1)
  4-helices; bundle; right-handed twist
  1. YugE-like [116922] (1)
    uperfamily
    1. YugE-like [116923] (1)
90. PWI domain [101232] (1)
  4 helices; up-and-down bundle; topological similarity to the bromodomain-like and SAM domain-like folds
  1. PWI domain [101233] (1)
    uperfamily
    1. PWI domain [101234] (1)
91. PAH2 domain [47761] (1)
  4 helices; open up-and-down bundle; binds alpha-helical peptides
  1. PAH2 domain [47762] (1)
    uperfamily
    1. PAH2 domain [47763] (2)
92. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81789] (1)
  4 helices; open up-and-down bundle; flexible N-terminal tail
  1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81790] (1)
    uperfamily
    1. Myosin phosphatase inhibitor 17kDa protein, CPI-17 [81791] (1)
93. XPC-binding domain [101237] (1)
  4 helices; array
  1. XPC-binding domain [101238] (1)
    uperfamily
    1. XPC-binding domain [101239] (3)
94. DinB/YfiT-like putative metalloenzymes [109853] (1)
  core: 4 helices; bundle, closed, left-handed twist; an unusual topology with a higher contact order
  1. DinB/YfiT-like putative metalloenzymes [109854] (4)
    contains metal-binding site on the bundle surface surrounded by loops
    uperfamily
    1. YfiT-like putative metal-dependent hydrolases [109855] (1)
      probably distantly related to the DinB family (Pfam 05163)
    2. DinB-like [140603] (4)
      Pfam 05163
    3. Sden0562-like [158519] (1)
      Pfam 09351; DUF1993
    4. Maleylpyruvate isomerase-like [158522] (1)
95. EspA/CesA-like [116926] (1)
  4 helices; bundle, closed, left ight-handed twist; interlocked (hetero)dimer of 2-helical subunits
  1. EspA/CesA-like [116927] (2)
    secreted protein and its chaperone both adopt similar substructures in the heterodimer
    uperfamily
    1. EspA-like [116928] (1)
      Pfam 03433
    2. EspA chaperone CesA [116931] (1)
96. NblA-like [109858] (1)
  4 helices; dimer of identical alpha-hairpin subunits; open bundle
  1. NblA-like [109859] (1)
    uperfamily
    1. NblA-like [109860] (1)
      Pfam 04485
97. EF2947-like [140606] (1)
  4 helices; "diamond" array; duplication: N-terminal and C-terminal pairs of helices are related by pseudo dyad
  1. EF2947-like [140607] (1)
    uperfamily
    1. EF2947-like [140608] (1)
98. EB1 dimerisation domain-like [140611] (1)
  dimeric 4-helical bundle with a coiled coil at one end formed by the longer N-terminal helices
  1. EB1 dimerisation domain-like [140612] (1)
    uperfamily
    1. EB1 dimerisation domain-like [140613] (1)
      Pfam 03271
99. SAM domain-like [47768] (16)
  4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
  1. SAM/Pointed domain [47769] (3)
    uperfamily
    1. Pointed domain [47770] (7)
    2. SAM (sterile alpha motif) domain [47773] (16)
    3. Variant SAM domain [158526] (2)
      shares a sequence motif with Pfam 07647, but has a distinct packing of helices
  2. RuvA domain 2-like [47781] (7)
    duplication: contains two helix-hairpin-helix (HhH) motifs
    uperfamily
    1. DNA helicase RuvA subunit, middle domain [47782] (3)
    2. Excinuclease UvrC C-terminal domain [81795] (1)
    3. NAD+-dependent DNA ligase, domain 3 [47786] (1)
    4. Topoisomerase V repeat domain [140626] (1)
    5. Hef domain-like [140629] (4)
      helicase/nuclease domain; forms homo and heterodimers; probably includes the Excinuclease UvrC C-terminal domain (scop_fa 81795, that contains a single NMR structure of a monomeric truncated domain, 1kft)
    6. Tex HhH-containing domain-like [158531] (1)
      tandem repeat of two Ruva_2-like domains
    7. ComEA-like [158534] (2)
      sequence similarity to the HhH-motif domains of the PsbU-like and Tex-like families
  3. C-terminal domain of RNA polymerase alpha subunit [47789] (1)
    contains one classic and one pseudo HhH motifs
    uperfamily
    1. C-terminal domain of RNA polymerase alpha subunit [47790] (3)
  4. Rad51 N-terminal domain-like [47794] (3)
    contains one classic and one pseudo HhH motifs
    uperfamily
    1. DNA repair protein Rad51, N-terminal domain [47795] (4)
    2. NusA extra C-terminal domains [109873] (1)
    3. Hypothetical protein AF1548, C-terminal domain [116936] (1)
  5. Barrier-to-autointegration factor, BAF [47798] (1)
    contains one classic and one pseudo HhH motifs
    uperfamily
    1. Barrier-to-autointegration factor, BAF [47799] (1)
  6. DNA polymerase beta, N-terminal domain-like [47802] (1)
    contains one classic and one pseudo HhH motifs
    uperfamily
    1. DNA polymerase beta, N-terminal domain-like [47803] (4)
  7. PsbU/PolX domain-like [81585] (2)
    contains one classic and one pseudo HhH motifs
    uperfamily
    1. DNA polymerase beta-like, second domain [81584] (4)
      topological similarity to the N-terminal domain
    2. PsbU-like [158539] (1)
      Pfam 06514
  8. 5' to 3' exonuclease, C-terminal subdomain [47807] (1)
    uperfamily
    1. 5' to 3' exonuclease, C-terminal subdomain [47808] (8)
  9. HRDC-like [47819] (4)
    uperfamily
    1. HRDC domain from helicases [47820] (3)
    2. RNA polymerase II subunit RBP4 (RpoF) [69044] (3)
    3. RNase D C-terminal domains [140643] (1)
      tandem repeat of two domains of this fold, the first domain belongs to Pfam 00570
    4. EXOSC10 HRDC domain-like [140646] (2)
  10. lambda integrase-like, N-terminal domain [47823] (1)
    uperfamily
    1. lambda integrase-like, N-terminal domain [47824] (3)
  11. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47831] (1)
    uperfamily
    1. Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain [47832] (1)
  12. Hypothetical protein YjbJ [69047] (1)
    uperfamily
    1. Hypothetical protein YjbJ [69048] (1)
  13. Putative methyltransferase TM0872, insert domain [81799] (1)
    uperfamily
    1. Putative methyltransferase TM0872, insert domain [81800] (2)
  14. eIF2alpha middle domain-like [116742] (1)
    uperfamily
    1. eIF2alpha middle domain-like [116743] (3)
  15. YozE-like [140652] (1)
    uperfamily
    1. YozE-like [140653] (2)
      Pfam 06855; DUF1250
  16. GspK insert domain-like [158544] (1)
    tandem repeat of two SAM-like domains iserted into pilin fold; domain 1 contains one classic HhH motif
    1. GspK insert domain-like [158545] (1)
      middle part of Pfam 03934
100. Retroviral matrix proteins [47835] (1)
  4-5 helices; right-handed superhelix
  1. Retroviral matrix proteins [47836] (6)
    the 5th, C-terminal helix is missing in some of the member structures
    uperfamily
    1. Immunodeficiency virus matrix proteins [47837] (2)
    2. HTLV-II matrix protein [47842] (1)
      the C-terminal helix region is disordered(?)
    3. Mason-Pfizer monkey virus matrix protein [47845] (1)
      the C-terminal helix region is missing(?)
    4. GAG polyprotein M-domain [47848] (1)
      the C-terminal helix region is missing(?)
    5. EIAV matrix antigen [69051] (1)
    6. MMLV matrix protein-like [81803] (2)
101. Flavivirus capsid protein C [101256] (1)
  core: 5 helices; right-handed superhelix; swapped dimer with the two long C-terminal helices
  1. Flavivirus capsid protein C [101257] (1)
    uperfamily
    1. Flavivirus capsid protein C [101258] (2)
102. Hepatitis B viral capsid (hbcag) [47851] (1)
  5 helices; array; two long helices form a hairpin that dimerizes into a 4-helical bundle
  1. Hepatitis B viral capsid (hbcag) [47852] (1)
    uperfamily
    1. Hepatitis B viral capsid (hbcag) [47853] (1)
103. Apolipophorin-III [47856] (1)
  5 helices; bundle, closed, left-handed twist
  1. Apolipophorin-III [47857] (1)
    uperfamily
    1. Apolipophorin-III [47858] (2)
104. Methenyltetrahydrofolate cyclohydrolase-like [101261] (1)
  5 helices; bundle, closed, left-handed twist
  1. Methenyltetrahydrofolate cyclohydrolase-like [101262] (1)
    uperfamily
    1. Methenyltetrahydrofolate cyclohydrolase-like [101263] (1)
      COG3404
105. A middle domain of Talin 1 [109879] (1)
  5 helices; bundle, closed, left-handed twist; helices 2-5 adopt the Four-helical up-and-down bundle fold (scop_cf 47161)
  1. A middle domain of Talin 1 [109880] (1)
    uperfamily
    1. A middle domain of Talin 1 [109881] (1)
106. I/LWEQ domain [109884] (1)
  5 helices; bundle, closed, left-handed twist
  1. I/LWEQ domain [109885] (1)
    uperfamily
    1. I/LWEQ domain [109886] (2)
      Pfam 01608
      actin-binding motif that adopts different folds; possibly refolds upon binding
107. RNA-binding protein She2p [116941] (1)
  5 helices; bundle, closed, left-handed twist; topological similarity to the middle domain of the L-aspartase-like fold (scop_cf 48556)
  1. RNA-binding protein She2p [116942] (1)
    uperfamily
    1. RNA-binding protein She2p [116943] (1)
108. Hyaluronidase domain-like [140656] (3)
  5 helices; bundle, closed, left-handed twist; up-and-down (meander) topology
  1. Hyaluronidase post-catalytic domain-like [140657] (1)
    uperfamily
    1. Hyaluronidase post-catalytic domain-like [140658] (2)
  2. TTHA0068-like [140663] (1)
    uperfamily
    1. TTHA0068-like [140664] (2)
      Pfam 03745; DUF309
  3. FLJ32549 domain-like [158548] (1)
    1. FLJ32549 domain-like [158549] (1)
      middle part of Pfam 09404; DUF2003
109. YoaC-like [140669] (1)
  5 helices; bundle, one crossover connection, the arrangement of the first four helices is similar to the KaiA/RbsU domain fold (scop_cf 101214)
  1. YoaC-like [140670] (1)
    uperfamily
    1. YoaC-like [140671] (1)
110. Saposin-like [47861] (2)
  5 helices; folded leaf, closed
  1. Saposin [47862] (4)
    Lipid-binding can promote conformational changes and oligomerisation in some members
    uperfamily
    1. Saposin B [81806] (1)
      the alternative subunit conformation is an open four-helical bundle; helices 3 and 4 form a contiguous helix
    2. NKL-like [47863] (3)
    3. Ameobapore A [101266] (1)
    4. Swaposin [47866] (1)
      circularly permuted saposin domain inserted in plant acid proteases
  2. Bacteriocin AS-48 [47869] (1)
    uperfamily
    1. Bacteriocin AS-48 [47870] (1)
111. Annexin [47873] (1)
  5 helices; folded leaf, closed
  1. Annexin [47874] (1)
    duplication: consists of four domains of the same fold
    uperfamily
    1. Annexin [47875] (14)
112. TAFH domain-like [158552] (1)
  5 helices; folded leaf, closed
  1. TAFH domain-like [158553] (1)
    1. TAFH domain-like [158554] (2)
      Pfam 07531
113. Transducin (alpha subunit), insertion domain [47894] (1)
  5 helices; folded leaf
  1. Transducin (alpha subunit), insertion domain [47895] (1)
    this domain interrupts the G-protein common fold
    uperfamily
    1. Transducin (alpha subunit), insertion domain [47896] (4)
114. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47911] (1)
  5 helices; irregular array; left-handed superhelix
  1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47912] (1)
    uperfamily
    1. Wiscott-Aldrich syndrome protein, WASP, C-terminal domain [47913] (1)
115. Left-handed superhelix [47916] (4)
  core: 4-5 helices; bundle; left-handed superhelix
  1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47917] (1)
    uperfamily
    1. C-terminal domain of alpha and beta subunits of F1 ATP synthase [47918] (8)
  2. Ypt/Rab-GAP domain of gyp1p [47923] (1)
    uperfamily
    1. Ypt/Rab-GAP domain of gyp1p [47924] (1)
      duplication: contains two similar domains of this fold
  3. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69055] (1)
    uperfamily
    1. 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain [69056] (2)
  4. BH3980-like [158560] (1)
    1. BH3980-like [158561] (3)
      Pfam 06304; DUF1048
116. ATPD N-terminal domain-like [47927] (2)
  core: 5 helices; bundle
  1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47928] (1)
    uperfamily
    1. N-terminal domain of the delta subunit of the F1F0-ATP synthase [47929] (1)
  2. AF1862-like [158568] (1)
    probable biological unit is a hexamer
    1. Cas Cmr5-like [158569] (1)
      Pfam 09701; CRISPR-associated protein
117. ERP29 C domain-like [47932] (2)
  5 helices; bundle
  1. ERP29 C domain-like [47933] (1)
    uperfamily
    1. ERP29 C domain-like [47934] (2)
  2. Helical domain of Sec23/24 [81811] (1)
    uperfamily
    1. Helical domain of Sec23/24 [81812] (2)
118. Functional domain of the splicing factor Prp18 [47937] (1)
  core: 5 helices; bundle
  1. Functional domain of the splicing factor Prp18 [47938] (1)
    uperfamily
    1. Functional domain of the splicing factor Prp18 [47939] (1)
119. Retrovirus capsid protein, N-terminal core domain [47942] (1)
  core: 5 helices; bundle
  1. Retrovirus capsid protein, N-terminal core domain [47943] (1)
    uperfamily
    1. Retrovirus capsid protein, N-terminal core domain [47944] (5)
120. GINS helical bundle-like [158572] (1)
  5 helices, staggered bundle;
  1. GINS helical bundle-like [158573] (4)
    common to all subunits of the GINS complex
    1. PSF1 N-terminal domain-like [158574] (1)
    2. PSF2 C-terminal domain-like [158577] (1)
      C-terminal part of PF04128
    3. PSF3 C-terminal domain-like [158580] (1)
      C-terminal part of Pfam 06425
    4. SLD5 N-terminal domain-like [158583] (1)
      N-terminal part of Pfam 05916
121. Jann4075-like [158586] (1)
  core: 5 helices; the C-terminal helix is surrounded by the others; similarity to some EF-hand domains
  1. Jann4075-like [158587] (1)
    1. Jann4075-like [158588] (1)
122. Cyclin-like [47953] (1)
  core: 5 helices; one helix is surrounded by the others
  1. Cyclin-like [47954] (3)
    duplication: consists of two domains of this fold
    uperfamily
    1. Cyclin [47955] (11)
    2. Transcription factor IIB (TFIIB), core domain [47965] (2)
    3. Retinoblastoma tumor suppressor domains [47969] (1)
123. Arp2/3 complex 21 kDa subunit ARPC3 [69059] (1)
  5 helices; one helix is surrounded by the others
  1. Arp2/3 complex 21 kDa subunit ARPC3 [69060] (1)
    uperfamily
    1. Arp2/3 complex 21 kDa subunit ARPC3 [69061] (1)
124. RNase III domain-like [69064] (1)
  core: 5 helices; one helix is surrounded by the others
  1. RNase III domain-like [69065] (2)
    uperfamily
    1. RNase III catalytic domain-like [69066] (3)
      Pfam 00636
    2. PF0609-like [140675] (1)
      specific to Thermococci; shares conserved carboxylic residues and similar dimerisation mode with the RNase III domain; contains integrated in the fold extra C-terminal helix, making it similar to the core fold of Ribosomal protein S7 (scop_cf 47972)
125. Ribosomal protein S7 [47972] (1)
  core: 5 helices; contains one more helix and a beta-hairpin outside the core
  1. Ribosomal protein S7 [47973] (1)
    uperfamily
    1. Ribosomal protein S7 [47974] (4)
126. post-AAA+ oligomerization domain-like [48018] (1)
  core: 5 helices: bundle
  1. post-AAA+ oligomerization domain-like [48019] (2)
    associated with N-terminal domain from the AAA+ family of P-loop hydrolases
    uperfamily
    1. DNA polymerase III clamp loader subunits, C-terminal domain [48020] (10)
      contains an extra helix
    2. MgsA/YrvN C-terminal domain-like [158600] (3)
127. PAP/OAS1 substrate-binding domain [81632] (1)
  core: 5-helical bundle; up-and-down; right-handed twist
  1. PAP/OAS1 substrate-binding domain [81631] (5)
    this domain follows the catalytic nucleotidyltransferase domain
    uperfamily
    1. Poly(A) polymerase, PAP, middle domain [81630] (2)
    2. 2'-5'-oligoadenylate synthetase 1, OAS1, second domain [101271] (1)
    3. Archaeal tRNA CCA-adding enzyme substrate-binding domain [101274] (1)
    4. RNA editing terminal uridyl transferase 2, RET2, domain 2 [140679] (1)
    5. AadK C-terminal domain-like [158607] (1)
      C-terminal part of Pfam 04439; Streptomycin adenylyltransferase; contains extra C-terminal helix
128. Anti-sigma factor AsiA [69069] (1)
  core: 5 helices: orthogonal array
  1. Anti-sigma factor AsiA [69070] (1)
    uperfamily
    1. Anti-sigma factor AsiA [69071] (1)
129. Antibiotic binding domain of TipA-like multidrug resistance regulators [89081] (1)
  5 helices: orthogonal array
  1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89082] (1)
    uperfamily
    1. Antibiotic binding domain of TipA-like multidrug resistance regulators [89083] (1)
130. Surp module (SWAP domain) [109904] (1)
  5 helices: irregular array
  1. Surp module (SWAP domain) [109905] (1)
    uperfamily
    1. Surp module (SWAP domain) [109906] (3)
      Pfam 01805
131. YgfY-like [109909] (1)
  5 helices; array; forms a tight dimer in crystals
  1. YgfY-like [109910] (1)
    uperfamily
    1. YgfY-like [109911] (1)
      Pfam 03937; despite the Pfam annotation, this family shows no topological similarity to the TPR repeat proteins
132. Hypothetical protein YhaI [109914] (1)
  core: 5 helices; orthogonal array; folding similarity to the TipA-S domain (1ny9)
  1. Hypothetical protein YhaI [109915] (1)
    oligomerizes via extra N-terminal helix forming trimeric coil-coiled
    uperfamily
    1. Hypothetical protein YhaI [109916] (1)
133. Hypothetical protein At3g22680 [109919] (1)
  5 helices; array; probable biological unit is a homodimer
  1. Hypothetical protein At3g22680 [109920] (1)
    uperfamily
    1. Hypothetical protein At3g22680 [109921] (1)
134. SP0561-like [140682] (1)
  5 helices; array; includes extra N-terminal and C-terminal short strands forming parrallel beta-sheet ladder
  1. SP0561-like [140683] (1)
    uperfamily
    1. SP0561-like [140684] (1)
      Pfam 08984; DUF1858
135. RbcX-like [158614] (1)
  5 helices per subunit; irregular array of short and long helices; swapping of the C-terminal helices in the dimer
  1. RbcX-like [158615] (1)
    1. RbcX-like [158616] (3)
      Pfam 02341 (note typo in the Pfam name: RcbX)
136. YheA-like [158621] (1)
  5 helices; "kinked" antiparallel coiled coil; forms flexible oligomeric assemblies via two different dimerisation interfaces
  1. YheA/YmcA-like [158622] (2)
    1. YmcA-like [158623] (1)
      N-terminal and C-terminal parts correspond to PfamB 012831 and PfamB 007043, respectively
    2. YheA-like [158626] (3)
      Pfam 06133; DUF964
137. RPA2825-like [158633] (1)
  5 helices, array; long flexible loop between helices 1 and 2; the remaining helices are arranged similar to the PGBD-like fold (scop_cf 47089)
  1. RPA2825-like [158634] (1)
    1. RPA2825-like [158635] (1)
      PfamB 041910
138. ENT-like [158638] (1)
  5 helices, irregular array, right-handed superhelix
  1. ENT-like [158639] (1)
    1. Emsy N terminal (ENT) domain-like [158640] (1)
      Pfam 03735
139. YfmB-like [140687] (1)
  5 helices, array; buried N-terminal helix; some topological similarity (circular permutation?) to the Nucleotidyltransferase substrate binding subunit/domain (scop_sf 81593)
  1. YfmB-like [140688] (1)
    uperfamily
    1. YfmB-like [140689] (1)
140. N-terminal domain of adenylylcyclase associated protein, CAP [101277] (1)
  6 helices: bundle; left-handed twist, up-and-down topology
  1. N-terminal domain of adenylylcyclase associated protein, CAP [101278] (1)
    uperfamily
    1. N-terminal domain of adenylylcyclase associated protein, CAP [101279] (1)
141. IpaD-like [140692] (1)
  6 helices; bundle, up-and-down; can be divided into two four-helical bundles sharing two helices (3 and 6), which are twice longer than the rest
  1. IpaD-like [140693] (1)
    uperfamily
    1. IpaD-like [140694] (2)
      Pfam 06511
142. Iron-dependent repressor protein, dimerization domain [47978] (1)
  6 helices, homodimer of 3-helical domains
  1. Iron-dependent repressor protein, dimerization domain [47979] (1)
    uperfamily
    1. Iron-dependent repressor protein, dimerization domain [47980] (3)
143. Glutamyl tRNA-reductase dimerization domain [69074] (1)
  6 helices, homodimer of 3-helical domains
  1. Glutamyl tRNA-reductase dimerization domain [69075] (1)
    uperfamily
    1. Glutamyl tRNA-reductase dimerization domain [69076] (1)
144. GRIP domain [101282] (1)
  6 helices, homodimer of 3-helical domains
  1. GRIP domain [101283] (1)
    uperfamily
    1. GRIP domain [101284] (1)
145. BAR/IMD domain-like [116747] (1)
  6 helices, homodimer of 3-helical domains
  1. BAR/IMD domain-like [103657] (4)
    core: dimeric six-helical bundle; protuding long helices form aniparallel coiled coils at both bundle ends
    uperfamily
    1. BAR domain [103658] (5)
      sensor of membrane curvature
    2. Arfaptin, Rac-binding fragment [64599] (1)
    3. IMD domain [140703] (1)
      Pfam 08397
    4. FCH domain [158645] (2)
      Pfam 00611; Fes/CIP4 homology domain
146. L27 domain [101287] (1)
  6 helices, heterodimer of 3-helical domains
  1. L27 domain [101288] (1)
    uperfamily
    1. L27 domain [101289] (9)
147. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109924] (1)
  dimer of 3-helical segments; consists of two subdomains: 4-helical bundle and coiled coil
  1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109925] (1)
    uperfamily
    1. Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain [109926] (1)
148. Phage replication organizer domain [140712] (1)
  6 helices, homodimer of 3-helical domains
  1. Phage replication organizer domain [140713] (1)
    DNA binding induces further oligomerization
    uperfamily
    1. Phage replication organizer domain [140714] (1)
      Pfam 06720
149. YejL-like [158650] (1)
  6 helices; intertwined homodimer of three-helical subunits, bundle
  1. YejL-like [158651] (1)
    1. YejL-like [158652] (5)
      Pfam 07208; DUF1414
150. Mediator hinge subcomplex-like [140717] (1)
  6 helices; heterodimer of structurally similar subunits; the N-terminal hairpins form a four-helical bundle, whereas the C-terminal helices form coiled coil structure
  1. Mediator hinge subcomplex-like [140718] (2)
    uperfamily
    1. CSE2-like [140719] (1)
      Pfam 07544
    2. MED7 hinge region [140722] (1)
      C-terminal part of Pfam 05983
151. DEATH domain [47985] (1)
  6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
  1. DEATH domain [47986] (4)
    uperfamily
    1. DEATH domain, DD [81312] (9)
      Pfam 00531
    2. DEATH effector domain, DED [81388] (2)
    3. Caspase recruitment domain, CARD [81313] (5)
    4. Pyrin domain, PYD [101298] (2)
152. GntR ligand-binding domain-like [48007] (1)
  core: 6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
  1. GntR ligand-binding domain-like [48008] (1)
    uperfamily
    1. GntR ligand-binding domain-like [48009] (2)
153. AF0941-like [140725] (1)
  6 helices, arranged into two interconnected 3-helical bundles; can also be described as a 'kinked' four-helical bundle; right-handed superhelix
  1. AF0941-like [140726] (1)
    uperfamily
    1. AF0941-like [140727] (1)
154. NusB-like [48012] (1)
  6 helices: bundle; one central helix is surrounded by 5 others
  1. NusB-like [48013] (3)
    uperfamily
    1. Antitermination factor NusB [48014] (3)
    2. Hypothetical protein MG027 [101303] (1)
    3. RmsB N-terminal domain-like [109930] (1)
155. YutG-like [101306] (1)
  core: 6 helices; bundle; one central helix is surrounded by 5 others
  1. YutG-like [101307] (1)
    uperfamily
    1. YutG-like [101308] (3)
      Pfam 01892; DUF64
156. N-terminal domain of DnaB helicase [48023] (1)
  6 helices: array
  1. N-terminal domain of DnaB helicase [48024] (1)
    uperfamily
    1. N-terminal domain of DnaB helicase [48025] (1)
157. Invasion protein A (SipA) , C-terminal actin binding domain [101311] (1)
  6 helices: orthogonal array
  1. Invasion protein A (SipA) , C-terminal actin binding domain [101312] (1)
    uperfamily
    1. Invasion protein A (SipA) , C-terminal actin binding domain [101313] (1)
158. MtlR-like [158667] (1)
  multihelical; 8-helical up-and-down bundle
  1. MtlR-like [158668] (1)
    1. MtlR-like [158669] (2)
      Pfam 05068; mannitol repressor
159. Guanido kinase N-terminal domain [48033] (1)
  irregular array of 6 short helices
  1. Guanido kinase N-terminal domain [48034] (1)
    uperfamily
    1. Guanido kinase N-terminal domain [48035] (8)
160. Scaffolding protein gpD of bacteriophage procapsid [48044] (1)
  core: 6 helices; one central helix is surrounded by 5 others
  1. Scaffolding protein gpD of bacteriophage procapsid [48045] (1)
    uperfamily
    1. Scaffolding protein gpD of bacteriophage procapsid [48046] (1)
161. Hemocyanin, N-terminal domain [48049] (1)
  6 helices; bundle; one central helix is surrounded by 5 others
  1. Hemocyanin, N-terminal domain [48050] (1)
    uperfamily
    1. Hemocyanin, N-terminal domain [48051] (2)
162. Sama2622-like [158674] (1)
  core: 6 helices; bundle; one central helix is surrounded by 5 others
  1. Sama2622-like [158675] (1)
    1. Sama2622-like [158676] (1)
163. Di-copper centre-containing domain [48055] (1)
  multihelical
  1. Di-copper centre-containing domain [48056] (2)
    duplication: contains two structural repeats
    uperfamily
    1. Hemocyanin middle domain [48057] (4)
    2. Catechol oxidase [48061] (1)
164. DBL homology domain (DH-domain) [48064] (1)
  multihelical; core: 5-helical bundle
  1. DBL homology domain (DH-domain) [48065] (1)
    uperfamily
    1. DBL homology domain (DH-domain) [48066] (10)
      Pfam 00621
165. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48075] (1)
  multihelical; contains compact array of 6 short helices
  1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48076] (1)
    uperfamily
    1. LigA subunit of an aromatic-ring-opening dioxygenase LigAB [48077] (1)
166. RuBisCo LSMT C-terminal, substrate-binding domain [81821] (1)
  multihelical; irregular array of long and short helices
  1. RuBisCo LSMT C-terminal, substrate-binding domain [81822] (1)
    uperfamily
    1. RuBisCo LSMT C-terminal, substrate-binding domain [81823] (1)
167. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48080] (1)
  multihelical bundle; contains buried central helix
  1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48081] (1)
    uperfamily
    1. Methyl-coenzyme M reductase alpha and beta chain C-terminal domain [48082] (6)
      C-terminal domain is all-alpha
168. YcfC-like [101321] (1)
  multihelical; contains two buried central helices
  1. YcfC-like [101322] (1)
    uperfamily
    1. YcfC-like [101323] (1)
      Pfam 04356; DUF489
169. PA2201 C-terminal domain-like [140730] (1)
  multihelical; seven-helical bundle with buried central helix
  1. PA2201 C-terminal domain-like [140731] (1)
    uperfamily
    1. PA2201 C-terminal domain-like [140732] (1)
170. Rv1873-like [140735] (1)
  multihelical; contains unusually short buried central helix
  1. Rv1873-like [140736] (1)
    uperfamily
    1. Rv1873-like [140737] (1)
      contains conserved motif HWuW at the beginning of the central helix
171. RUN domain-like [140740] (1)
  multihelical; 3-helical bundle similar to one half of the DEATH domain fold is flanked by two alpha-hairpins forming a four-helical bundle; the axes of the three-helical and four-helical bundles are aproximately orthogonal to each other
  1. RUN domain-like [140741] (1)
    uperfamily
    1. RUN domain [140742] (1)
      Pfam 02759
172. SipA N-terminal domain-like [140745] (1)
  multihelical; bundle; the last helix is buried inside the bundle
  1. SipA N-terminal domain-like [140746] (1)
    uperfamily
    1. SipA N-terminal domain-like [140747] (1)
      N-terminal part of Pfam 09052
173. Transcription factor STAT-4 N-domain [48091] (1)
  multihelical; can be divided into two subdomains
  1. Transcription factor STAT-4 N-domain [48092] (1)
    uperfamily
    1. Transcription factor STAT-4 N-domain [48093] (1)
174. TerB-like [158681] (1)
  multihelical; contains two central helices; duplication: there are two three-helical repeats related by pseudo twofold symmetry
  1. TerB-like [158682] (2)
    members of this superfamily probably related to the tellurite resistance protein TerB (Pfam 05099) of yet undetermined structure
    1. COG3793-like [158683] (1)
      Pfam 07049; DUF1332
    2. PG1108-like [158686] (1)
175. Regulator of G-protein signaling, RGS [48096] (1)
  multihelical; consists of two all-alpha subdomains
  contains a 4-helical bundle with left-handed twist and up-and-down topology
  1. Regulator of G-protein signaling, RGS [48097] (1)
    uperfamily
    1. Regulator of G-protein signaling, RGS [48098] (9)
176. SopE-like GEF domain [81831] (1)
  multihelical; consists of two all-alpha subdomains each containing a 3-helical bundle with right-handed twist
  1. SopE-like GEF domain [81832] (1)
    uperfamily
    1. SopE-like GEF domain [81833] (3)
      C-terminal part of Pfam 05364
177. Variable surface antigen VlsE [74747] (1)
  multihelical; consists of two all-alpha subdomains; contains a 4-helical bundle with left-handed twist and up-and-down topology
  1. Variable surface antigen VlsE [74748] (1)
    uperfamily
    1. Variable surface antigen VlsE [74749] (1)
178. YgfB-like [101326] (1)
  multihelical; consists of two tightly associated 3-helical bundles with different twists
  1. YgfB-like [101327] (1)
    uperfamily
    1. YgfB-like [101328] (1)
179. Hypothetical protein MTH393 [101331] (1)
  multihelical; consists of two all-alpha subdomains; dimer
  1. Hypothetical protein MTH393 [101332] (1)
    uperfamily
    1. Hypothetical protein MTH393 [101333] (1)
180. PG0816-like [140752] (1)
  multihelical; comprises two helical bundles, both are topologically similar to the RuvA C-terminal domain-like fold (scop_cf 46928)
  1. PG0816-like [140753] (1)
    uperfamily
    1. PG0816-like [140754] (1)
      Pfam 08989; DUF1896
181. UraD-like [158693] (1)
  multihelical; irregular array of long and short helices
  1. UraD-Like [158694] (1)
    1. UraD-like [158695] (3)
      Pfam 09349; OHCU decarboxylase (formerly DUF1991)
182. Sec63 N-terminal domain-like [158701] (1)
  multihelical; consists of two helical subdomains
  1. Sec63 N-terminal domain-like [158702] (2)
    1. Sec63 N-terminal domain [158703] (1)
      N-terminal part of Pfam 02889
    2. Achaeal helicase C-terminal domain [158706] (1)
183. Carbamoyl phosphate synthetase, large subunit connection domain [48107] (1)
  multihelical; consists of two all-alpha subdomains
  possible duplication: subdomains have similar topologies
  1. Carbamoyl phosphate synthetase, large subunit connection domain [48108] (1)
    uperfamily
    1. Carbamoyl phosphate synthetase, large subunit connection domain [48109] (1)
184. Heme-dependent peroxidases [48112] (1)
  multihelical; consists of two all-alpha domains
  1. Heme-dependent peroxidases [48113] (3)
    uperfamily
    1. CCP-like [48114] (14)
    2. Catalase-peroxidase KatG [74753] (4)
      duplication: tandem repeat of two CCP-like domains
    3. Myeloperoxidase-like [48132] (4)
185. Ribosomal protein L19 (L19e) [48139] (1)
  multihelical; consists of two different 3-helical domains connected by a long, partly helical linker
  1. Ribosomal protein L19 (L19e) [48140] (1)
    uperfamily
    1. Ribosomal protein L19 (L19e) [48141] (1)
186. PSPTO4464-like [158709] (1)
  multihelical; consists of two subdomains at the ends of a long connecting helix
  1. PSPTO4464-like [158710] (1)
    1. PSPTO4464-like [158711] (1)
      Pfam 04751; DUF615
187. GatB/YqeY motif [89094] (1)
  multihelical; consists of two different alpha-helical bundles (4-helical and 3-helical)
  1. GatB/YqeY motif [89095] (2)
    uperfamily
    1. GatB/YqeY domain [89096] (1)
    2. GatB/GatE C-terminal domain-like [140757] (3)
      assigned to the same Pfam 02637 family as YeqY by the presence of a common sequence motif with an alpha-hairpin structure
188. YfbU-like [116959] (1)
  multihelical; consist of two subdomains; forms 24-mer with the N-terminal sudbomains packing around the 4-fold axis and the C-terminal domains interacting at the 2-fold and 3-fold axes
  1. YfbU-like [116960] (1)
    uperfamily
    1. YfbU-like [116961] (1)
      Pfam 03887
189. MG296-like [158714] (1)
  multihelical; in crystal forms helical polymers by swapping the two N-terminal helices to the next subunit in polymer; three subunits per turn of polymer helix
  1. MG296-like [158715] (1)
    1. MG296-like [158716] (1)
      Pfam 09644
190. Hypothetical protein MPN330 [116964] (1)
  multihelical; consists of three different 4-helical bundles
  1. Hypothetical protein MPN330 [116965] (1)
    uperfamily
    1. Hypothetical protein MPN330 [116966] (1)
191. HD-domain/PDEase-like [109603] (1)
  multihelical; consists of two different alpha-helical bundles
  1. HD-domain/PDEase-like [109604] (5)
    uperfamily
    1. HD domain [101340] (13)
      Pfam 01966; metal dependent phosphohydrolases
    2. PDEase [48548] (6)
      Pfam 00233; multihelical; can be divided into three subdomains
    3. modified HD domain [116973] (1)
      retains the superfamily core fold but lacks the conserved metal-binding site
    4. MioX-like [140769] (2)
      Pfam 05153; DUF706
    5. Ppx associated domain [140773] (1)
      this domain is C-terminal to Ppx domain in some Exopolyphosphatases
192. Superantigen MAM [101343] (1)
  multihelical; consists of two different alpha-helical bundles
  1. Superantigen MAM [101344] (1)
    uperfamily
    1. Superantigen MAM [101345] (1)
193. Influenza virus matrix protein M1 [48144] (1)
  multihelical; consists of two different all-alpha subdomains, 4 helices each
  1. Influenza virus matrix protein M1 [48145] (1)
    superficially similar to membrane translocation domains
    uperfamily
    1. Influenza virus matrix protein M1 [48146] (1)
194. DNA-glycosylase [48149] (1)
  multihelical; consists of two all-alpha domains
  1. DNA-glycosylase [48150] (6)
    uperfamily
    1. Endonuclease III [48151] (1)
    2. Mismatch glycosylase [48154] (4)
    3. 3-Methyladenine DNA glycosylase I (Tag) [74756] (1)
    4. 3-Methyladenine DNA glycosylase III (MagIII) [101349] (1)
    5. DNA repair glycosylase, 2 C-terminal domains [48157] (2)
    6. AgoG-like [116976] (2)
195. An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48162] (1)
  multihelical; consists of two all-alpha domains
  1. An anticodon-binding domain of class I aminoacyl-tRNA synthetases [48163] (2)
    uperfamily
    1. C-terminal domain of glutamyl-tRNA synthetase (GluRS) [48164] (1)
    2. C-terminal domain of class I lysyl-tRNA synthetase [74759] (1)
196. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101352] (1)
  multihelical; consists of two all-alpha subdomains
  1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101353] (1)
    uperfamily
    1. Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) [101354] (1)
197. R1 subunit of ribonucleotide reductase, N-terminal domain [48167] (1)
  multihelical consists of two all-alpha subdomains
  subdomain 1 (residues 10-100) is a 4-helical bundle
  1. R1 subunit of ribonucleotide reductase, N-terminal domain [48168] (1)
    uperfamily
    1. R1 subunit of ribonucleotide reductase, N-terminal domain [48169] (2)
198. BEACH domain [81836] (1)
  multihelical, complex architecture
  1. BEACH domain [81837] (1)
    uperfamily
    1. BEACH domain [81838] (2)
      Pfam 02138
199. Cryptochrome/photolyase FAD-binding domain [48172] (1)
  multihelical; consists of two all-alpha subdomains
  1. Cryptochrome/photolyase FAD-binding domain [48173] (1)
    uperfamily
    1. Cryptochrome/photolyase FAD-binding domain [48174] (5)
200. 6-phosphogluconate dehydrogenase C-terminal domain-like [48178] (1)
  multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
  1. 6-phosphogluconate dehydrogenase C-terminal domain-like [48179] (12)
    N-terminal domain is Rossmann-fold with a family-specific C-terminal extension
    uperfamily
    1. Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain [48180] (5)
      Hydroxyisobutyrate dehydrogenase domain is similar to one structural repeat in the 6-phosphogluconate dehydrogenase domain
    2. Mannitol 2-dehydrogenase [81843] (1)
    3. Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) [48184] (2)
    4. HCDH C-domain-like [48187] (3)
    5. Conserved hypothetical protein MTH1747 [74762] (1)
    6. UDP-glucose/GDP-mannose dehydrogenase dimerisation domain [48191] (2)
    7. N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [48194] (1)
    8. Glycerol-3-phosphate dehydrogenase [48197] (2)
    9. Ketopantoate reductase PanE [69084] (1)
    10. ProC C-terminal domain-like [116984] (3)
      similar dimer to the class I KARI
    11. HMD dimerization domain-like [140777] (1)
      dimer similar to those of the GDP-mannose 6-dehydrogenase and class I KARI domains
    12. TyrA dimerization domain-like [140780] (3)
      new dimerisation mode with swapping of C-terminal helices
201. Uteroglobin-like [48200] (1)
  multihelical
  1. Uteroglobin-like [48201] (1)
    disulfide-linked dimer of two identical chains, 4 helices in each
    uperfamily
    1. Uteroglobin-like [48202] (4)
202. alpha/alpha toroid [48207] (6)
  multihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
  1. Six-hairpin glycosidases [48208] (9)
    uperfamily
    1. Glucoamylase [48209] (2)
    2. Cellulases catalytic domain [48213] (13)
    3. N-acylglucosamine (NAG) epimerase [48222] (2)
    4. Glycosyltransferase family 36 C-terminal domain [63588] (2)
      overall domain organization is similar to Bacterial glucoamylase
    5. Bacterial glucoamylase C-terminal domain-like [81850] (2)
      overall domain organization is similar to Lactobacillus maltose phosphorylase
    6. Hypothetical protein YteR [89108] (1)
      unknown function; weak sequence similarity to the catalytic domain of cellulases
    7. Glycosyl Hydrolase Family 88 [109953] (1)
      Pfam 07470
    8. CPF0428-like [158737] (2)
      Pfam 06824; DUF1237
    9. Trehalase-like [158742] (1)
      Pham 01204
  2. Seven-hairpin glycosidases [48225] (1)
    uperfamily
    1. Class I alpha-1;2-mannosidase, catalytic domain [48226] (5)
  3. Chondroitin AC/alginate lyase [48230] (2)
    incomplete toroid
    uperfamily
    1. Alginate lyase A1-III [48231] (1)
    2. Hyaluronate lyase-like catalytic, N-terminal domain [48234] (6)
  4. Family 10 polysaccharide lyase [81853] (1)
    uperfamily
    1. Family 10 polysaccharide lyase [81854] (2)
      incomplete toroid made of four hairpins
  5. Terpenoid cyclases/Protein prenyltransferases [48239] (4)
    uperfamily
    1. Terpenoid cyclase N-terminal domain [48240] (2)
      incomplete toroid made of four hairpins
    2. Terpene synthases [48243] (2)
      consists of two toroid domains: one of six and one of five hairpins
    3. Protein prenyltransferases [48246] (3)
    4. Complement components [48251] (3)
      probably related to other families, but has no known enzymatic activity
  6. LanC-like [158745] (1)
    comprises seven hairpins
    1. LanC-like [158746] (1)
      Pfam 05147; there are seven internal sequence repeats
203. Citrate synthase [48255] (1)
  multihelical; consists of two all-alpha domains
  1. Citrate synthase [48256] (1)
    uperfamily
    1. Citrate synthase [48257] (7)
      duplication: large domain consists of two structural repeats
      the second repeat is interrupted by the small domain
204. Cytochrome P450 [48263] (1)
  multihelical
  1. Cytochrome P450 [48264] (1)
    uperfamily
    1. Cytochrome P450 [48265] (23)
205. Flagellar transcriptional activator FlhD [63591] (1)
  multihelical; forms intertwined dimer of identical 5-helical subunits
  1. Flagellar transcriptional activator FlhD [63592] (1)
    uperfamily
    1. Flagellar transcriptional activator FlhD [63593] (1)
      contains an HTH motif
206. HP0242-like [158751] (1)
  multihelical; intertwined homodimer of four-helical subunits, forming catenated triangular ring-like structures; pseudo knot
  1. HP0242-like [158752] (1)
    1. HP0242-like [158753] (1)
      Pfam 09442; DUF2018
207. SMc04008-like [158756] (1)
  multihelcal; intertwined homodimer; there are 4 core helices in each subunits; contains putative metal ion-binding motif MxxxxxCxxC in the conserved surface site
  1. SMc04008-like [158757] (1)
    1. SMc04008-like [158758] (1)
      Pfam 06844; DUF1244
208. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48299] (1)
  multihelical; intertwined tetramer
  1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48300] (1)
    uperfamily
    1. Ribosomal protein L7/12, oligomerisation (N-terminal) domain [48301] (2)
209. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48304] (1)
  multihelical; intertwined trimer of identical 3-helical subunits
  1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48305] (1)
    uperfamily
    1. Class II MHC-associated invariant chain ectoplasmic trimerization domain [48306] (1)
210. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48309] (1)
  multihelical; consists of two all-alpha domains
  1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48310] (1)
    uperfamily
    1. Aldehyde ferredoxin oxidoreductase, C-terminal domains [48311] (2)
211. Acid phosphatase/Vanadium-dependent haloperoxidase [48316] (1)
  multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
  1. Acid phosphatase/Vanadium-dependent haloperoxidase [48317] (3)
    uperfamily
    1. Type 2 phosphatidic acid phosphatase, PAP2 [48318] (1)
    2. Haloperoxidase (bromoperoxidase) [48321] (3)
      contains one core bundle; forms dimer
    3. Chloroperoxidase [48325] (1)
      duplication: contains two core bundles arranged as in the other family dimer
212. BRCA2 helical domain [81871] (1)
  multihelical; contains a 3-helical bundle surrounded by several shorter helices
  1. BRCA2 helical domain [81872] (1)
    uperfamily
    1. BRCA2 helical domain [81873] (2)
213. BRCA2 tower domain [81877] (1)
  multihelical; contains a 3-helical Hin recombinase-like subdomain and two long dimerisation helices
  1. BRCA2 tower domain [81878] (1)
    uperfamily
    1. BRCA2 tower domain [81879] (2)
214. H-NS histone-like proteins [81274] (1)
  multihelical oligomeric protein; structure of whole subunit is not known yet but are probably composed of three different domains
  1. H-NS histone-like proteins [81273] (1)
    available NMR structures suggest two very different dimerisation modes of the N-terminal domain
    uperfamily
    1. H-NS histone-like proteins [81272] (2)
215. Sigma2 domain of RNA polymerase sigma factors [88945] (1)
  multihelical; consists of a conserved 4-helical core and a variable insert subdomain
  1. Sigma2 domain of RNA polymerase sigma factors [88946] (1)
    uperfamily
    1. Sigma2 domain of RNA polymerase sigma factors [88947] (6)
216. DNA repair protein MutS, domain III [48333] (1)
  multihelical; consists of 2 all-alpha subdomains
  1. DNA repair protein MutS, domain III [48334] (1)
    uperfamily
    1. DNA repair protein MutS, domain III [48335] (2)
217. Helical scaffold and wing domains of SecA [81885] (1)
  multihelical; consists of 2 all-alpha subdomains
  1. Helical scaffold and wing domains of SecA [81886] (1)
    uperfamily
    1. Helical scaffold and wing domains of SecA [81887] (2)
218. all-alpha NTP pyrophosphatases [101385] (1)
  multihelical: dimeric 4-helical bundle surrounded by other helices; oligomerizes further in a tetramer
  1. all-alpha NTP pyrophosphatases [101386] (4)
    basic module consist of 5 active site-forming helices; four from one subunit/structural repeat; the fifth from the other subunit/repeat
    uperfamily
    1. MazG-like [116993] (3)
      Pfam 03819
    2. AF0060-like [140794] (1)
      consists of a single member with an orphan sequence; "circular permutation" of putative active site residues: the catalytic lysine resides in the N-terminal helix instead of the missing in this family C-terminal helix; probable biological unit is a tertramer, distinct from the MazG family tetramer
    3. Type II deoxyuridine triphosphatase [101387] (2)
      one subunit comprises two degenerate structural repeats, organised into the "rigid" and "mobile" subdomains
    4. HisE-like (PRA-PH) [140797] (5)
      Pfam 01503
219. Hsp90 co-chaperone CDC37 [101390] (1)
  multihelical; consists of 2 all-alpha subdomains connected by a long helix
  1. Hsp90 co-chaperone CDC37 [101391] (1)
    uperfamily
    1. Hsp90 co-chaperone CDC37 [101392] (1)
220. Nop domain [89123] (1)
  multihelical; array of longer and shorter helices; contains an alpha-hairpin dimerisation subdomain
  1. Nop domain [89124] (1)
    uperfamily
    1. Nop domain [89125] (2)
      putative snoRNA binding domain
221. YidB-like [140803] (1)
  multihelical; three strings of short helices are packed across one longer helix
  1. YidB-like [140804] (1)
    uperfamily
    1. YidB-like [140805] (1)
      Pfam 06078; DUF937
222. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48339] (1)
  multihelical; bundle of longer and shorter helices
  1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48340] (1)
    uperfamily
    1. Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain [48341] (1)
223. A virus capsid protein alpha-helical domain [48344] (1)
  multihelical; three-helical bundle in the core is surrounded by non-conserved helices
  1. A virus capsid protein alpha-helical domain [48345] (3)
    this domain is interrupted by a jelly-roll beta-sandwich domain
    uperfamily
    1. Orbivirus capsid [48346] (1)
    2. Phytoreovirus capsid [101395] (1)
    3. vp6, the major capsid protein of group A rotavirus [63596] (1)
224. P40 nucleoprotein [101398] (1)
  multihelical; consists of two subdomains
  1. P40 nucleoprotein [101399] (1)
    uperfamily
    1. P40 nucleoprotein [101400] (1)
225. Rhabdovirus nucleoprotein-like [140808] (1)
  multihelical, consist of two helical domains; each domain contains a buried helix
  1. Rhabdovirus nucleoprotein-like [140809] (1)
    uperfamily
    1. Rhabdovirus nucleocapsid protein [140810] (2)
      Pfam 00945; RNA-binding homooligomeric protein
226. GTPase activation domain, GAP [48349] (1)
  multihelical
  1. GTPase activation domain, GAP [48350] (2)
    uperfamily
    1. BCR-homology GTPase activation domain (BH-domain) [48351] (5)
      Pfam 00620
    2. p120GAP domain-like [48360] (2)
227. Ras GEF [48365] (1)
  multihelical
  1. Ras GEF [48366] (1)
    uperfamily
    1. Ras GEF [48367] (1)
228. Telomeric repeat binding factor (TRF) dimerisation domain [63599] (1)
  multihelical; can be divided into an alpha-alpha superhelix domain and a long alpha-hairpin dimerization domain
  1. Telomeric repeat binding factor (TRF) dimerisation domain [63600] (1)
    uperfamily
    1. Telomeric repeat binding factor (TRF) dimerisation domain [63601] (2)
229. Poly A polymerase C-terminal region-like [81890] (1)
  multihelical; can be divided into three subdomains (neck, body and tail)
  1. Poly A polymerase C-terminal region-like [81891] (1)
    the neck subdomain is an alpha-alpha superhelix; the tail subdomain is similar to the RuvA C-terminal domain-like
    uperfamily
    1. Poly A polymerase C-terminal region-like [81892] (3)
      the 'neck' domain corresponds to the C-terminal part of Pfam 01743
230. alpha-alpha superhelix [48370] (24)
  multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
  1. ARM repeat [48371] (23)
    uperfamily
    1. Armadillo repeat [48372] (9)
    2. Clathrin adaptor core protein [74771] (2)
    3. HEAT repeat [48385] (2)
      Pfam 02985
    4. MIF4G domain-like [100908] (5)
      duplication: family members contains 2 or more structurally similar domains of this fold connected by unstructured linkers
    5. PHAT domain [89129] (1)
      pseudo-HEAT repeat
    6. Mo25 protein [101407] (1)
    7. Leukotriene A4 hydrolase C-terminal domain [63608] (1)
    8. Clathrin heavy chain proximal leg segment [48390] (1)
    9. Clathrin heavy-chain linker domain [48393] (1)
    10. Leucine-rich repeat variant [48396] (1)
    11. Phoshoinositide 3-kinase (PI3K) helical domain [48399] (2)
    12. Pumilio repeat [63611] (1)
    13. Regulatory subunit H of the V-type ATPase [63614] (1)
    14. PBS lyase HEAT-like repeat [101410] (2)
      Pfam 03130
    15. BC3264-like [109965] (2)
      Pfam 06352; DUF1061
    16. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain [109968] (1)
      N-terminal part of Pfam 06272
    17. Exportin HEAT-like repeat [117002] (1)
    18. B56-like [140819] (1)
      Pfam 01603; Protein phosphatase 2A regulatory B subunit family
    19. HspBP1 domain [140822] (1)
    20. GUN4-associated domain [140825] (2)
      PfamB 089177
    21. Diap1 N-terninal region-like [140830] (1)
      contains two consequitive Pfam domains in one superhelical segment: Pfam 06371 and Pfam 06367
    22. Plakophilin 1 helical region [140833] (1)
    23. RPA1889-like [158764] (1)
      Pfam 09450; DUF2019; similar to the BC3264-like family
  2. IP3 receptor type 1 binding core, domain 2 [100909] (1)
    uperfamily
    1. IP3 receptor type 1 binding core, domain 2 [81895] (1)
  3. Chemosensory protein Csp2 [100910] (1)
    uperfamily
    1. Chemosensory protein Csp2 [81898] (1)
  4. Sec7 domain [48425] (1)
    uperfamily
    1. Sec7 domain [48426] (6)
      Pfam 01369
  5. Lipovitellin-phosvitin complex, superhelical domain [48431] (1)
    uperfamily
    1. Lipovitellin-phosvitin complex, superhelical domain [48432] (1)
  6. Bacterial muramidases [48435] (1)
    uperfamily
    1. Bacterial muramidases [48436] (1)
  7. Aconitase B, N-terminal domain [74778] (1)
    uperfamily
    1. Aconitase B, N-terminal domain [74779] (1)
  8. HCP-like [81901] (1)
    uperfamily
    1. HCP-like [81902] (2)
      Helicobacter Cysteine-rich Protein
  9. Protein prenylyltransferase [48439] (1)
    uperfamily
    1. Protein prenylyltransferase [48440] (3)
  10. 14-3-3 protein [48445] (1)
    uperfamily
    1. 14-3-3 protein [48446] (5)
  11. TPR-like [48452] (8)
    uperfamily
    1. Tetratricopeptide repeat (TPR) [48453] (20)
    2. Transcription factor MalT domain III [69094] (1)
    3. BTAD-like [140845] (1)
      Pfam 03704; Bacterial transcriptional activator domain
    4. PrgX C-terminal domain-like [140848] (1)
    5. Atu0120-like [158772] (1)
      Pfam 06041; DUF924
    6. SusD-like [158775] (3)
      TPR-like structure resides in the N-terminal part; the C-terminal part is structurally unique and is covered by Pfam 07980
    7. HAT/Suf repeat [158782] (1)
      includes Pfam 05843
    8. CT2138-like [158785] (1)
      probable biological unit is a homohexamer
  12. ENTH/VHS domain [48464] (4)
    uperfamily
    1. ENTH domain [48465] (2)
    2. VHS domain [48468] (5)
    3. Phosphoinositide-binding clathrin adaptor, N-terminal domain [100911] (2)
    4. RPR domain (SMART 00582 ) [109975] (1)
      found in proteins involved in regulation of nuclear pre-mRNA; some sequence similarity to VHS domain
  13. Translin [74784] (1)
    uperfamily
    1. Translin [74785] (2)
  14. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69099] (1)
    uperfamily
    1. Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain [69100] (2)
  15. Arp2/3 complex 16 kDa subunit ARPC5 [69103] (1)
    uperfamily
    1. Arp2/3 complex 16 kDa subunit ARPC5 [69104] (1)
  16. FliG [48029] (1)
    fragmented superhelix; consist of 3/4-helical motifs and connecting helices
    uperfamily
    1. FliG [48030] (1)
  17. Cullin repeat-like [74788] (2)
    uperfamily
    1. Cullin repeat [74789] (2)
    2. Exocyst complex component [140851] (2)
      includes Pfam 03081
  18. C-terminal domain of Ku80 [101420] (1)
    uperfamily
    1. C-terminal domain of Ku80 [101421] (1)
  19. Hypothetical protein ST1625 [101424] (1)
    uperfamily
    1. Hypothetical protein ST1625 [101425] (1)
  20. Cytochrome c oxidase subunit E [48479] (1)
    uperfamily
    1. Cytochrome c oxidase subunit E [48480] (1)
  21. USP8 N-terminal domain-like [140856] (1)
    uperfamily
    1. USP8 N-terminal domain-like [140857] (1)
      PfamB 029795
  22. Pseudo ankyrin repeat-like [140860] (1)
    contains three helices per turn of the superhelix
    uperfamily
    1. Pseudo ankyrin repeat [140861] (1)
      one repeat consist of 3 helices; there are similarities in the repeat sequence and assembly with the ankyrin repeat (scop_fa 48404)
  23. TROVE domain-like [140864] (1)
    consist of two superhelical sections arranged like a horse-shoe
    uperfamily
    1. TROVE domain-like [140865] (1)
      Pfam 05731
  24. MgtE N-terminal domain-like [158791] (1)
    made of short helices; approximately 2.5 helices per turn of superhelix
    1. MgtE N-terminal domain-like [158792] (2)
      Pfam 03448
231. GUN4-like [140868] (1)
  multihelical; open array, trapping inside an extended region before the C-terminal helix
  1. GUN4-like [140869] (1)
    uperfamily
    1. GUN4-like [140870] (2)
      Pfam 05419
232. Lipoxigenase [48483] (1)
  multihelical
  large nearly all-alpha domain
  1. Lipoxigenase [48484] (2)
    uperfamily
    1. Plant lipoxigenases [48485] (2)
    2. Animal lipoxigenases [48489] (1)
233. gene 59 helicase assembly protein [48492] (1)
  multihelical; consists of two all-alpha subdomains
  1. gene 59 helicase assembly protein [48493] (1)
    uperfamily
    1. gene 59 helicase assembly protein [48494] (1)
234. Tetracyclin repressor-like, C-terminal domain [48497] (1)
  multihelical; interlocked (homo)dimer
  1. Tetracyclin repressor-like, C-terminal domain [48498] (1)
    uperfamily
    1. Tetracyclin repressor-like, C-terminal domain [48499] (34)
235. Skp1 dimerisation domain-like [81384] (1)
  multihelical; interlocked heterodimer with F-box proteins
  1. Skp1 dimerisation domain-like [81382] (1)
    uperfamily
    1. Skp1 dimerisation domain-like [81380] (2)
236. F-box domain [81385] (1)
  multihelical; interlocked heterodimer with the Skp1 dimerisation domain
  1. F-box domain [81383] (1)
    uperfamily
    1. F-box domain [81381] (4)
237. Nuclear receptor ligand-binding domain [48507] (1)
  multihelical; 3 layers or orthogonally packed helices
  1. Nuclear receptor ligand-binding domain [48508] (1)
    uperfamily
    1. Nuclear receptor ligand-binding domain [48509] (44)
238. Phospholipase C/P1 nuclease [48536] (1)
  multihelical
  1. Phospholipase C/P1 nuclease [48537] (2)
    duplication: all chain but the N-terminal helix forms two structural repeats
    uperfamily
    1. Phospholipase C [48538] (3)
    2. P1 nuclease [48543] (1)
239. ATP-dependent DNA ligase DNA-binding domain [117017] (1)
  multihelical; duplication: contains two intertwined structural repeats related by pseudo twofold symmetry
  1. ATP-dependent DNA ligase DNA-binding domain [117018] (1)
    uperfamily
    1. ATP-dependent DNA ligase DNA-binding domain [117019] (1)
      Pfam 04675
240. DNA primase DnaG, C-terminal domain [117022] (1)
  multihelical; segment-swapped dimer
  1. DNA primase DnaG, C-terminal domain [117023] (1)
    uperfamily
    1. DNA primase DnaG, C-terminal domain [117024] (1)
241. PriB N-terminal domain-like [140913] (1)
  multihelical bundle; contains buried central helix; also includes the PriA interface-forming insert subdomain (alpha+beta)
  1. PriB N-terminal domain-like [140914] (1)
    uperfamily
    1. PriB N-terminal domain-like [140915] (1)
242. VPS9 domain [109992] (1)
  multihelical; consist of two subdomains
  1. VPS9 domain [109993] (1)
    uperfamily
    1. VPS9 domain [109994] (1)
      Pfam 02204
243. Triger factor/SurA peptide-binding domain-like [109997] (1)
  multihelical; irregular array of long and short helices
  1. Triger factor/SurA peptide-binding domain-like [109998] (2)
    there are sequence and functional similarities between the families, but their structural similarity is obscured by conformational flexibility (in the TF family)
    uperfamily
    1. TF C-terminus [109999] (2)
      Pfam 05698; includes the upstream linker region not covered by the Pfam model
    2. Porin chaperone SurA, peptide-binding domain [81828] (1)
244. DNA terminal protein [140918] (1)
  multihelical, open array; contains the C-terminal four-helical bundle, left-handed superhelix
  1. DNA terminal protein [140919] (1)
    uperfamily
    1. DNA terminal protein [140920] (1)
      Pfam 05435
245. Glycolipid transfer protein, GLTP [110003] (1)
  multihelical; 2 layers or orthogonally packed helices
  1. Glycolipid transfer protein, GLTP [110004] (1)
    uperfamily
    1. Glycolipid transfer protein, GLTP [110005] (1)
246. Hypothetical protein MG354 [110008] (1)
  multihelical bundle; contains buried central helix
  1. Hypothetical protein MG354 [110009] (1)
    uperfamily
    1. Hypothetical protein MG354 [110010] (1)
247. Duffy binding domain-like [140923] (1)
  consist of two subdomains, each containing a three-helical bundle
  1. Duffy binding domain-like [140924] (1)
    uperfamily
    1. Duffy binding domain [140925] (2)
      Pfam 05424
248. Fic-like [140930] (1)
  multihelical; one central helix is surrounded by seven helices
  1. Fic-like [140931] (1)
    uperfamily
    1. Fic-like [140932] (2)
      Pfam 02661; the conserved motif HPFXXGNG is at the N-terminus of the central helix
249. Her-1 [110013] (1)
  multihelical; consists of two topologically similar alpha-helical bundles
  1. Her-1 [110014] (1)
    uperfamily
    1. Her-1 [110015] (1)
250. ERO1-like [110018] (1)
  multihelical; consists of 2 four-helical bundles
  1. ERO1-like [110019] (1)
    similar active site architecture to scop_sf 69000
    uperfamily
    1. ERO1-like [110020] (1)
      Pfam 04137
251. Serum albumin-like [48551] (1)
  multihelical; one domain consists of two similar disulfide-linked subdomains
  1. Serum albumin-like [48552] (1)
    uperfamily
    1. Serum albumin-like [48553] (2)
252. L-aspartase-like [48556] (1)
  multihelical, consists of three all-alpha domains
  1. L-aspartase-like [48557] (2)
    uperfamily
    1. L-aspartase/fumarase [48558] (14)
    2. HAL/PAL-like [48572] (3)
      Pfam 00221
253. Formin homology 2 domain (FH2 domain) [101446] (1)
  multihelical, consists of three all-alpha domains
  1. Formin homology 2 domain (FH2 domain) [101447] (1)
    uperfamily
    1. Formin homology 2 domain (FH2 domain) [101448] (2)
254. Terpenoid synthases [48575] (1)
  multihelical; core: 8 helices (C-J) are arranged in 2 parallel layers
  1. Terpenoid synthases [48576] (5)
    duplication: two metal-binding sites are related by a pseudo dyad that also relates helices C-F to helices G-J
    uperfamily
    1. Isoprenyl diphosphate synthases [48577] (5)
    2. Squalene synthase [48580] (1)
    3. Terpenoid cyclase C-terminal domain [48583] (2)
    4. Aristolochene/pentalenene synthase [48586] (2)
    5. Trichodiene synthase [69113] (1)
255. GroEL equatorial domain-like [48591] (1)
  multihelical; 8 helices arranged in 2 parallel layers
  1. GroEL equatorial domain-like [48592] (2)
    duplication: two 4-helical subdomains are related by a pseudo dyad passing through the ATP-binding site
    uperfamily
    1. GroEL chaperone, ATPase domain [48593] (4)
    2. Group II chaperonin (CCT, TRIC), ATPase domain [48596] (3)
256. TorD-like [89154] (1)
  multihelical; bundle
  1. TorD-like [89155] (1)
    uperfamily
    1. TorD-like [89156] (4)
      Pfam 06192
257. Chorismate mutase II [48599] (1)
  multihelical; core: 6 helices, bundle
  1. Chorismate mutase II [48600] (4)
    uperfamily
    1. Dimeric chorismate mutase [48601] (4)
      intertwined homodimer of 3-helical subunits
    2. Allosteric chorismate mutase [48604] (1)
      duplication: 2 weak structural repeats resembling subunits of E. coli protein
    3. monomeric chorismate mutase [140942] (1)
      "un-swapped" four-helical relative of the homodimeric chorismate mutase domain
    4. Secreted chorismate mutase-like [140945] (1)
      duplication; two structural repeats, like in the yeast enzyme, but with a different location of the remaining active site
258. Peridinin-chlorophyll protein [48607] (1)
  multihelical: forms a boat-shaped protein shell around cofactors
  1. Peridinin-chlorophyll protein [48608] (1)
    duplication: consists of two 8-helical repeats
    uperfamily
    1. Peridinin-chlorophyll protein [48609] (1)
259. Heme oxygenase-like [48612] (1)
  multihelical; bundle
  1. Heme oxygenase-like [48613] (4)
    duplication: contains two structural repeats of 3-helical motif
    uperfamily
    1. Eukaryotic type heme oxygenase [48614] (5)
    2. Heme oxygenase HemO (PigA) [63627] (2)
    3. TENA/THI-4 [101458] (8)
      Pfam 03070; HO-related family lacking the heme-binding site
    4. PqqC-like [101463] (2)
      Pfam 05312
260. Indolic compounds 2,3-dioxygenase-like [140958] (1)
  multihelical; bundle, contains interrupted helices
  1. Indolic compounds 2,3-dioxygenase-like [140959] (2)
    contains heme-dependent enzymes
    uperfamily
    1. Bacterial tryptophan 2,3-dioxygenase [140960] (1)
      Pfam 03301
    2. Indoleamine 2,3-dioxygenase-like [140963] (2)
      Pfam 01231; contains extra N-terminal all-alpha subdomain of similar fold to the GST C-terminal domain (scop_cf 47615)
261. AhpD-like [69117] (1)
  multihelical; contains 4-helical bundle and 2-helical arm
  1. AhpD-like [69118] (4)
    probable biological unit contains six domains of this fold arranged with 32 symmetry
    uperfamily
    1. CMD-like [101468] (2)
      Pfam 02627; hexamer of single-domain subunits
    2. AhpD [69119] (2)
      duplication: two-domain subunits form a helix-swapped trimer
    3. Atu0492-like [140970] (5)
      duplication: similar subunit structure to the AhpD family, but the putative active site is conserved in different relative location; new hexameric architecture; similar dimeric interface to the CMD-like family
    4. TTHA0727-like [140975] (2)
      similar to the CMD-like family by the subunit sequence and hexameric architecture; the segment-swapped subunit fold is similar to the AhpD domains
262. Double Clp-N motif [81922] (1)
  multihelical; array
  1. Double Clp-N motif [81923] (1)
    duplication: contains two structural repeats of 4-helical motif
    uperfamily
    1. Double Clp-N motif [81924] (3)
263. Orange carotenoid protein, N-terminal domain [81929] (1)
  multihelical; array
  1. Orange carotenoid protein, N-terminal domain [81930] (1)
    duplication: contains four structural repeats arranged into two intertwined 4-helical subdomains
    uperfamily
    1. Orange carotenoid protein, N-terminal domain [81931] (1)
264. DhaL-like [101472] (1)
  multihelical; bundle
  1. DhaL-like [101473] (1)
    uperfamily
    1. DhaL-like [101474] (2)
265. ADP-ribosylglycohydrolase [101477] (1)
  multihelical; bundle
  1. ADP-ribosylglycohydrolase [101478] (1)
    uperfamily
    1. ADP-ribosylglycohydrolase [101479] (1)
      Pfam 03747
266. Topoisomerase V catalytic domain-like [140978] (1)
  multihelical; irregular array; contains small amount of beta-structure and a 3-helical bundle with a variant homeofomain-like fold and HTH motif (scop_cf 46688)
  1. Topoisomerase V catalytic domain-like [140979] (1)
    uperfamily
    1. Topoisomerase V catalytic domain-like [140980] (1)
267. PTPA-like [140983] (1)
  multihelical
  1. PTPA-like [140984] (1)
    uperfamily
    1. PTPA-like [140985] (2)
      Pfam 03095
268. Tex N-terminal region-like [158831] (1)
  multihelical; irregular array of long and short helices; can be divided into several subdomains
  1. Tex N-terminal region-like [158832] (1)
    1. Tex N-terminal region-like [158833] (1)
      Pfam 09371
269. AGR_C_984p-like [158836] (1)
  multihelical, consists of two subdomains; duplication: there are two 5-helical structural repeats, one in each subdomain
  1. AGR_C_984p-like [158837] (1)
    1. AGR_C_984p-like [158838] (1)
      Pfam 06748; DUF1217
270. PMT central region-like [158841] (1)
  multihelical; comprises two four-helical bundles of different topologies and an irregular helical array packed against a small beta-sheet
  1. PMT central region-like [158842] (1)
    1. PMT central region-like [158843] (1)
271. FtsH protease domain-like [140989] (1)
  array of 6 helices and a 2-stranded beta-ribbon
  1. FtsH protease domain-like [140990] (1)
    contains zincin-like (scop_sf 55486) metal-binding motif HExxH, embedded into a topologically different fold
    uperfamily
    1. FtsH protease domain-like [140991] (2)
      Pfam 01434; Peptidase family M41
272. Gametocyte protein Pfg27 [89161] (1)
  multihelical; bundle
  1. Gametocyte protein Pfg27 [89162] (1)
    duplication: contains two structural repeats of four helices each
    uperfamily
    1. Gametocyte protein Pfg27 [89163] (1)
273. N-terminal domain of bifunctional PutA protein [81934] (1)
  multihelical; array
  1. N-terminal domain of bifunctional PutA protein [81935] (1)
    uperfamily
    1. N-terminal domain of bifunctional PutA protein [81936] (1)
274. Cysteine alpha-hairpin motif [47071] (1)
  core: alpha-hairpin crosslinked with two disulfides
  1. Cysteine alpha-hairpin motif [47072] (2)
    uperfamily
    1. p8-MTCP1 [47073] (1)
    2. COX17-like [117033] (1)
      Pfam 05051
275. Phospholipase A2, PLA2 [48618] (1)
  common core: 2 helices, disulfide-linked, and a calcium-binding loop
  1. Phospholipase A2, PLA2 [48619] (3)
    uperfamily
    1. Vertebrate phospholipase A2 [48623] (39)
    2. Insect phospholipase A2 [48620] (1)
    3. Prokaryotic phospholipase A2 [63630] (1)
276. Fungal elicitin [48646] (1)
  5 helices: irregular disulfide-linked array; also contains a small beta-hairpin
  1. Fungal elicitin [48647] (1)
    uperfamily
    1. Fungal elicitin [48648] (2)
277. Tetraspanin [48651] (1)
  5 helices: irregular disulfide-linked array; form homodimer
  1. Tetraspanin [48652] (1)
    uperfamily
    1. Tetraspanin [48653] (1)
278. GDNF receptor-like [110034] (1)
  5 helices: irregular disulfide-linked array; topological similarity to the Fungal elicitin fold (scop_cf 48646)
  1. GDNF receptor-like [110035] (1)
    uperfamily
    1. GDNF receptor-like [110036] (1)
      Pfam 02351
279. FinO-like [48656] (1)
  6 helices: irregular non-globular array; also contains two small beta-hairpins
  1. FinO-like [48657] (1)
    uperfamily
    1. FinO-like [48658] (2)
280. Nuclear receptor coactivator interlocking domain [69124] (1)
  3 helices, non-globular array; forms interlocked heterodimers with its targets
  1. Nuclear receptor coactivator interlocking domain [69125] (1)
    not a true superfamily
    uperfamily
    1. Nuclear receptor coactivator interlocking domain [69126] (3)
281. Hermes dimerisation domain [140995] (1)
  multihelical, intertwinned dimer of two 4-helical strings
  1. Hermes dimerisation domain [140996] (1)
    uperfamily
    1. Hermes dimerisation domain [140997] (1)
282. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101488] (1)
  5 helices, non-globular array; wraps around the N-terminal tail of its target
  1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101489] (1)
    not a true superfamily
    uperfamily
    1. Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain [101490] (1)
283. Non-globular all-alpha subunits of globular proteins [48661] (14)
  not a true fold
  1. Ribosomal protein L39e [48662] (1)
    interrupted alpha-helix
    uperfamily
    1. Ribosomal protein L39e [48663] (1)
  2. Methanol dehydrogenase subunit [48666] (1)
    consists of single alpha-helix and irregular N-terminal tail
    uperfamily
    1. Methanol dehydrogenase subunit [48667] (3)
  3. Transducin (heterotrimeric G protein), gamma chain [48670] (1)
    long alpha-helix interrupted in the middle
    uperfamily
    1. Transducin (heterotrimeric G protein), gamma chain [48671] (2)
  4. Fe-only hydrogenase smaller subunit [48674] (1)
    uperfamily
    1. Fe-only hydrogenase smaller subunit [48675] (1)
  5. Moesin tail domain [48678] (1)
    uperfamily
    1. Moesin tail domain [48679] (1)
  6. Proteinase A inhibitor IA3 [48686] (1)
    uperfamily
    1. Proteinase A inhibitor IA3 [48687] (1)
  7. Epsilon subunit of mitochondrial F1F0-ATP synthase [48690] (1)
    uperfamily
    1. Epsilon subunit of mitochondrial F1F0-ATP synthase [48691] (1)
  8. Quinohemoprotein amine dehydrogenase C chain [69131] (1)
    uperfamily
    1. Quinohemoprotein amine dehydrogenase C chain [69132] (2)
  9. Stathmin [101494] (1)
    single long helix crosslinking four tubulin subunits
    uperfamily
    1. Stathmin [101495] (1)
  10. Anti-sigma factor FlgM [101498] (1)
    uperfamily
    1. Anti-sigma factor FlgM [101499] (1)
  11. Glu-tRNAGln amidotransferase C subunit [141000] (1)
    uperfamily
    1. Glu-tRNAGln amidotransferase C subunit [141001] (1)
      Pfam 02686
  12. RelB-like [141004] (1)
    wraps around RelE subunit
    uperfamily
    1. RelB-like [141005] (1)
  13. Lag-3 N-terminal region [158851] (1)
    long kinked helix, part of the CSL-Notch-Mastermind ternary complex
    1. Lag-3 N-terminal region [158852] (1)
  14. Lipase chaperone-like [158855] (1)
    open single layer scaffold of 11 helices, which engulfs the substrate protein
    1. Lipase chaperone LifO-like [158856] (1)
      Pfam 03280
284. Multiheme cytochromes [48694] (1)
  variable number of helices and little beta structure; not a true fold
  1. Multiheme cytochromes [48695] (3)
    duplication: contains multiple CxxCH motifs
    uperfamily
    1. Cytochrome c3-like [48696] (13)
    2. Photosynthetic reaction centre (cytochrome subunit) [48707] (2)
      consists of four heme-binding repeats
    3. Di-heme elbow motif [48711] (13)
      the main characteristic feature of this motif is the packing of its two hemes
      many members contains one or more complete motifs flanked by incomplete motifs and/or other domains
All beta proteins [48724] (174)
1. Immunoglobulin-like beta-sandwich [48725] (28)
  sandwich; 7 strands in 2 sheets; greek-key
  some members of the fold have additional strands
  1. Immunoglobulin [48726] (4)
    uperfamily
    1. V set domains (antibody variable domain-like) [48727] (90)
    2. C1 set domains (antibody constant domain-like) [48942] (70)
    3. C2 set domains [49142] (10)
    4. I set domains [49159] (53)
  2. E set domains [81296] (23)
    "Early" Ig-like fold families possibly related to the immunoglobulin and/or fibronectin type III superfamilies
    uperfamily
    1. NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain [81279] (10)
      subgroup of the larger IPT/TIG domain family
    2. E-set domains of sugar-utilizing enzymes [81282] (30)
      domains of unknown function associated with different type of catalytic domains in a different sequential location
      subgroup of the larger IPT/TIG domain family
    3. Other IPT/TIG domains [89191] (1)
      apart from the domains of transcription factors and sugar-utilizing enzymes
    4. Arthropod hemocyanin, C-terminal domain [81283] (2)
    5. Class II viral fusion proteins C-terminal domain [81284] (6)
    6. Cytomegalovirus protein US2 [81285] (1)
    7. Molybdenum-containing oxidoreductases-like dimerisation domain [81286] (2)
    8. ML domain [81287] (3)
      implicated in lipid recognition, particularly in the recognition of pathogen related products
    9. RhoGDI-like [81288] (3)
    10. Cytoplasmic domain of inward rectifier potassium channel [81966] (3)
    11. Transglutaminase N-terminal domain [81289] (4)
    12. Filamin repeat (rod domain) [81290] (4)
      Pfam 00630
    13. Arrestin/Vps26-like [81291] (2)
    14. Gingipain R (RgpB), C-terminal domain [81292] (1)
    15. Copper resistance protein C (CopC, PcoC) [81969] (2)
    16. Cellulosomal scaffoldin protein CipC, module x2.1 [81293] (1)
    17. Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 [81294] (2)
    18. Internalin Ig-like domain [81295] (3)
      truncated fold fused to an LRR domain
    19. SoxZ-like [141027] (1)
    20. Enterochelin esterase N-terminal domain-like [141030] (2)
      PfamB 013071
    21. AMPK-beta glycogen binding domain-like [158886] (3)
      lacks the N-terminal strand (A) and contains a beta-hairpin insertion in the C-terminal strand (G)
    22. Sec63 C-terminal domain-like [158893] (1)
      C-terminal part of Pfam 02889
    23. SVA-like [158896] (1)
      Pfam 05326
  3. Fibronectin type III [49265] (1)
    uperfamily
    1. Fibronectin type III [49266] (53)
      Pfam 00041
  4. PKD domain [49299] (1)
    uperfamily
    1. PKD domain [49300] (3)
      Pfam 00801
  5. beta-Galactosidase/glucuronidase domain [49303] (1)
    uperfamily
    1. beta-Galactosidase/glucuronidase domain [49304] (5)
  6. Transglutaminase, two C-terminal domains [49309] (1)
    uperfamily
    1. Transglutaminase, two C-terminal domains [49310] (4)
  7. Cadherin-like [49313] (2)
    uperfamily
    1. Cadherin [49314] (4)
    2. Dystroglycan, N-terminal domain [110062] (1)
  8. Actinoxanthin-like [49319] (1)
    uperfamily
    1. Actinoxanthin-like [49320] (5)
  9. Cu,Zn superoxide dismutase-like [49329] (1)
    has additional strand at N-terminus
    uperfamily
    1. Cu,Zn superoxide dismutase-like [49330] (13)
  10. CBD9-like [49344] (3)
    has additional strand at N-terminus; the active site in a similar topological location as the Cu,Zn SOD site
    uperfamily
    1. Cytochrome domain of cellobiose dehydrogenase [49345] (1)
    2. Family 9 carbohydrate-binding module, CBD9 [63677] (1)
    3. Glucodextranase, domain C [101533] (1)
  11. Lamin A/C globular tail domain [74853] (1)
    uperfamily
    1. Lamin A/C globular tail domain [74854] (2)
  12. Clathrin adaptor appendage domain [49348] (3)
    contains an additional N-terminal strand
    uperfamily
    1. Alpha-adaptin ear subdomain-like [49349] (2)
      ear domain consists of two different subdomains
    2. gamma-adaptin C-terminal appendage domain-like [74857] (3)
      consist of a single subdomain
    3. Coatomer appendage domain [101536] (2)
  13. Integrin domains [69179] (1)
    uperfamily
    1. Integrin domains [69180] (2)
  14. PapD-like [49354] (2)
    contains PP switch between strands D and C'
    uperfamily
    1. Pilus chaperone [49355] (5)
    2. MSP-like [49360] (5)
      Pfam 00635
  15. Purple acid phosphatase, N-terminal domain [49363] (1)
    uperfamily
    1. Purple acid phosphatase, N-terminal domain [49364] (2)
  16. Fungal immunomodulatory protein, FIP [101542] (1)
    uperfamily
    1. Fungal immunomodulatory protein, FIP [101543] (1)
  17. Superoxide reductase-like [49367] (1)
    uperfamily
    1. Superoxide reductase-like [49368] (3)
      binds iron in the site that is topologically equivalent to the copper-binding site of cupredoxins
  18. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74863] (1)
    uperfamily
    1. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74864] (1)
  19. Invasin/intimin cell-adhesion fragments [49373] (1)
    uperfamily
    1. Invasin/intimin cell-adhesion fragments [49374] (2)
  20. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81982] (1)
    uperfamily
    1. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81983] (1)
  21. Tp47 lipoprotein, middle and C-terminal domains [81986] (1)
    uperfamily
    1. Tp47 lipoprotein, middle and C-terminal domains [81987] (1)
      contains two different domains of immunoglobulin-like fold
  22. ASF1-like [101546] (1)
    contains extra C-terminal strand
    uperfamily
    1. ASF1-like [101547] (3)
  23. ApaG-like [110069] (1)
    uperfamily
    1. ApaG-like [110070] (3)
      Pfam 04379; dimeric in crystals; this dimer is a probable biological unit
  24. Accessory protein X4 (ORF8, ORF7a) [117066] (1)
    uperfamily
    1. Accessory protein X4 (ORF8, ORF7a) [117067] (1)
  25. LEA14-like [117070] (1)
    uperfamily
    1. LEA14-like [117071] (1)
      Pfam 03168
  26. ICP-like [141066] (1)
    topological variant with similarity to the Cupredoxin-like fold (scop_cf 49502) in the N-terminal region
    uperfamily
    1. ICP-like [141067] (2)
      PfamB 014070
  27. CalX-like [141072] (1)
    uperfamily
    1. CalX-beta domain [141073] (1)
      Pfam 03160
  28. NEAT domain-like [158911] (1)
    1. NEAT domain [158912] (3)
      Pfam 05031; iron transport-associated domain
2. Common fold of diphtheria toxin/transcription factors/cytochrome f [49379] (10)
  sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
  1. Diphtheria toxin, C-terminal domain [49380] (1)
    uperfamily
    1. Diphtheria toxin, C-terminal domain [49381] (1)
  2. Carbohydrate-binding domain [49384] (3)
    uperfamily
    1. Cellulose-binding domain family II [49385] (2)
    2. Cellulose-binding domain family III [49390] (11)
      Pfam 00963
    3. Bacterial chitobiase, n-terminal domain [49398] (1)
  3. Bacterial adhesins [49401] (6)
    uperfamily
    1. Collagen-binding domain of adhesin [49402] (1)
    2. Fibrinogen-binding domain [89210] (2)
      duplication: contains two differently decorated domains of this fold
    3. Pilus subunits [49405] (8)
    4. PapG adhesin receptor-binding domain [63680] (1)
    5. F17c-type adhesin [89215] (2)
    6. Dr-family adhesin [110075] (1)
      Pfam 04619
  4. Alpha-macroglobulin receptor domain [49410] (1)
    uperfamily
    1. Alpha-macroglobulin receptor domain [49411] (3)
  5. p53-like transcription factors [49417] (7)
    uperfamily
    1. p53 DNA-binding domain-like [81314] (3)
    2. Rel/Dorsal transcription factors, DNA-binding domain [81315] (9)
    3. T-box [81316] (2)
    4. STAT DNA-binding domain [81317] (3)
    5. RUNT domain [81318] (2)
    6. DNA-binding domain from NDT80 [81992] (1)
    7. DNA-binding protein LAG-1 (CSL) [110080] (1)
  6. Cytochrome f, large domain [49441] (1)
    uperfamily
    1. Cytochrome f, large domain [49442] (5)
  7. beta-sandwich domain of Sec23/24 [81995] (1)
    uperfamily
    1. beta-sandwich domain of Sec23/24 [81996] (2)
  8. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49447] (1)
    duplication: one domain of this fold is inserted into another domain of the same fold
    uperfamily
    1. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49448] (2)
  9. Peptidylarginine deiminase Pad4, middle domain [110083] (1)
    uperfamily
    1. Peptidylarginine deiminase Pad4, middle domain [110084] (1)
  10. DR1885-like metal-binding protein [110087] (1)
    uperfamily
    1. DR1885-like metal-binding protein [110088] (1)
      Pfam 04314
3. Prealbumin-like [49451] (7)
  sandwich; 7 strands in 2 sheets, greek-key
  variations: some members have additional 1-2 strands to common fold
  1. Starch-binding domain-like [49452] (3)
    uperfamily
    1. Rhamnogalacturonase B, RhgB, middle domain [110091] (1)
    2. Starch-binding domain [49453] (8)
    3. PUD-like [158932] (4)
      Pfam 03714; bacterial pullanase-associated domain
  2. Carboxypeptidase regulatory domain-like [49464] (2)
    uperfamily
    1. Carboxypeptidase regulatory domain [49465] (2)
    2. Pre-dockerin domain [141082] (1)
      PfamB 085396
  3. VHL [49468] (1)
    uperfamily
    1. VHL [49469] (1)
  4. Transthyretin (synonym: prealbumin) [49472] (1)
    uperfamily
    1. Transthyretin (synonym: prealbumin) [49473] (4)
  5. Cna protein B-type domain [49478] (1)
    uperfamily
    1. Cna protein B-type domain [49479] (2)
      Pfam 05738
  6. Aromatic compound dioxygenase [49482] (1)
    uperfamily
    1. Aromatic compound dioxygenase [49483] (6)
      sandwich; 9 strands in 2 sheets
  7. Hypothetical protein PA1324 [117074] (1)
    uperfamily
    1. Hypothetical protein PA1324 [117075] (1)
4. HSP40/DnaJ peptide-binding domain [49492] (1)
  sandwich; 6 strands in 2 sheets
  1. HSP40/DnaJ peptide-binding domain [49493] (1)
    uperfamily
    1. HSP40/DnaJ peptide-binding domain [49494] (2)
5. Penicillin-binding protein associated domain [69188] (1)
  sandwich; 6 strands in 2 sheets
  1. Penicillin-binding protein associated domain [69189] (2)
    uperfamily
    1. PBP5 C-terminal domain-like [69190] (2)
    2. Pencillin binding protein 4 (PbpD), C-terminal domain [110098] (1)
      rudiment form of the PBP-5-like domain
6. alpha-Amylase inhibitor tendamistat [49497] (1)
  sandwich; 6 strands in 2 sheets
  1. alpha-Amylase inhibitor tendamistat [49498] (1)
    uperfamily
    1. alpha-Amylase inhibitor tendamistat [49499] (1)
7. C-terminal domain of mollusc hemocyanin [81278] (1)
  six-stranded beta-sandwich, jelly-roll/greek-key topology
  1. C-terminal domain of mollusc hemocyanin [81277] (1)
    analogous to the Ig-like domain of arthropod hemocyanin; similar sequential but different spatial position relative the shared domain
    uperfamily
    1. C-terminal domain of mollusc hemocyanin [81276] (2)
8. HPA-like [141085] (1)
  sandwich, 6 strands in 2 sheets; jelly-roll (truncated); also includes the pending PCSK9 V domain-like superfamily (the C-terminal domains of 2p4e and 2pmw)
  1. Agglutinin HPA-like [141086] (1)
    forms similar trimers to the PCSK9 V domain; strand directions of the subunit beta-sheets are parallel to the three-fold symmetry axis;
    uperfamily
    1. Agglutinin HPA-like [141087] (1)
9. L21p-like [141090] (1)
  core: sandwich, 6 strands in 2 sheets
  1. L21p-like [141091] (1)
    uperfamily
    1. Ribosomal protein L21p [141092] (3)
      Pfam 00829
10. Cupredoxin-like [49502] (2)
  sandwich; 7 strands in 2 sheets, greek-key
  variations: some members have additional 1-2 strands
  1. Cupredoxins [49503] (7)
    contains copper-binding site
    uperfamily
    1. Plastocyanin/azurin-like [49504] (32)
      mono-domain proteins
    2. Nitrosocyanin [63392] (3)
    3. Periplasmic domain of cytochrome c oxidase subunit II [49541] (5)
    4. Multidomain cupredoxins [49550] (15)
    5. Ephrin ectodomain [74874] (2)
      eukaryotic signaling domain probably related to cupredoxins but lacking the metal-binding site
    6. Peptidylarginine deiminase Pad4, N-terminal domain [110107] (1)
      probably related to cupredoxins but lacking the metal-binding site
    7. SO1698-like [141095] (1)
      probably related to cupredoxins but lacking the metal-binding site
  2. Major surface antigen p30, SAG1 [74877] (1)
    SS-crosslinked beta-sandwich of distinct geometry but topologically similar to cupredoxins
    uperfamily
    1. Major surface antigen p30, SAG1 [74878] (1)
11. Ctag/Cox11 [110110] (1)
  sandwich; 7 strands in 2 sheets, greek-key; permutation of the immunoglobulin-like fold
  1. Ctag/Cox11 [110111] (1)
    uperfamily
    1. Ctag/Cox11 [110112] (1)
      Pfam 04442
12. Atu1913-like [141098] (1)
  sandwich; 7 strands in two sheets, greek-key/jelly-roll; forms segment swapped dimers, swapping is probably facilitated by the helix insertion after strand 3
  1. Atu1913-like [141099] (1)
    uperfamily
    1. Atu1913-like [141100] (1)
13. C2 domain-like [49561] (5)
  sandwich; 8 strands in 2 sheets; greek-key
  1. C2 domain (Calcium/lipid-binding domain, CaLB) [49562] (2)
    two constituent families are related by circular permutation
    uperfamily
    1. PLC-like (P variant) [49563] (12)
    2. Synaptotagmin-like (S variant) [49575] (12)
      topologically similar to the C-terminal domain of PapD
  2. Periplasmic chaperone C-domain [49584] (1)
    uperfamily
    1. Periplasmic chaperone C-domain [49585] (5)
  3. PHL pollen allergen [49590] (1)
    uperfamily
    1. PHL pollen allergen [49591] (2)
  4. Rab geranylgeranyltransferase alpha-subunit, insert domain [49594] (1)
    uperfamily
    1. Rab geranylgeranyltransferase alpha-subunit, insert domain [49595] (1)
  5. Smr-associated domain-like [158949] (1)
    1. Smr-associated domain [158950] (1)
      Pfam 09640; DUF2027
14. TRAF domain-like [49598] (1)
  sandwich; 8 strands in 2 sheets; greek-key
  1. TRAF domain-like [49599] (2)
    has a circularly permuted immunoglobulin-fold topology with extra strand
    uperfamily
    1. MATH domain [49600] (4)
    2. SIAH, seven in absentia homolog [69198] (1)
15. Neurophysin II [49605] (1)
  sandwich; 8 strands in 2 sheets; meander
  1. Neurophysin II [49606] (1)
    duplication: composed of two structural repeats
    uperfamily
    1. Neurophysin II [49607] (1)
16. N-utilization substance G protein NusG, insert domain [82003] (1)
  sandwich; 8 strands in 2 sheets; meander
  1. N-utilization substance G protein NusG, insert domain [82004] (1)
    uperfamily
    1. N-utilization substance G protein NusG, insert domain [82005] (1)
17. Nucleoplasmin-like/VP (viral coat and capsid proteins) [88632] (7)
  sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands
  characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
  1. Nucleoplasmin-like core domain [69203] (1)
    oligomerizes into a pentameric ring structure
    uperfamily
    1. Nucleoplasmin-like core domain [69204] (3)
  2. Positive stranded ssRNA viruses [88633] (9)
    uperfamily
    1. Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [88634] (18)
      the order of the chains N-VP0-VP3-VP1-C is as in the polyprotein; VP0 is cleaved later upon capsid assembly to VP4 and VP2
      there is a different order in the shuffled genome of insect picorna-like proteins (Cricket paralysis virus)
    2. Comoviridae-like VP [88636] (3)
      duplication: mature coat protein consists of three similar domains that can be in a single chain or in two separate chains
    3. Caliciviridae-like VP [88637] (1)
    4. Nodaviridae-like VP [88638] (3)
    5. Tetraviridae-like VP [101568] (1)
    6. Bromoviridae-like VP [88639] (4)
    7. Tymoviridae-like VP [88641] (3)
    8. Tombusviridae-like VP [88643] (7)
    9. Birnaviridae-like VP [141109] (1)
      dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses; includes Pfam 01766; Birnavirus VP2 protein
  3. ssDNA viruses [88645] (3)
    uperfamily
    1. Microviridae-like VP [49612] (3)
    2. Parvoviridae-like VP [88646] (7)
    3. Densovirinae-like VP [88647] (1)
  4. Group I dsDNA viruses [88648] (1)
    uperfamily
    1. Papovaviridae-like VP [88649] (3)
  5. Group II dsDNA viruses VP [49749] (3)
    duplication: consists of two domains of this fold packed together like the nucleoplasmin subunits
    trimeric; in the trimers, the domains are arranged around pseudo six-fold axis
    uperfamily
    1. Coat protein p3 [49750] (1)
    2. Major capsid protein vp54 [82013] (1)
    3. Adenovirus hexon [49753] (2)
      each domain is heavily decorated with many insertions
  6. Satellite viruses [88650] (1)
    uperfamily
    1. Satellite viruses [88651] (3)
  7. PHM/PNGase F [49742] (2)
    members of this superfamily bind peptide substrates
    duplication: consists of two domains of this fold packed together like the adjacent nucleoplasmin subunits
    uperfamily
    1. Glycosyl-asparaginase [49743] (1)
    2. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [49746] (1)
18. gamma-Crystallin-like [49694] (1)
  sandwich; 8 strands in 2 sheets; greek-key
  duplication: has internal pseudo twofold symmetry
  1. gamma-Crystallin-like [49695] (6)
    uperfamily
    1. Crystallins/Ca-binding development proteins [49696] (13)
    2. Yeast killer toxin [49710] (1)
    3. Streptomyces metalloproteinase inhibitor, SMPI [49713] (1)
    4. Killer toxin-like protein SKLP [49716] (1)
    5. Antifungal protein AFP1 [63693] (1)
      shares putative chitin-binding site with SKLP
    6. Plant antimicrobial protein MIAMP1 [49719] (1)
19. Lipase/lipooxygenase domain (PLAT/LH2 domain) [49722] (1)
  sandwich; 8 strands in 2 sheets; complex topology
  duplication: has weak internal pseudo twofold symmetry
  1. Lipase/lipooxygenase domain (PLAT/LH2 domain) [49723] (3)
    uperfamily
    1. Lipoxigenase N-terminal domain [49724] (3)
    2. Colipase-binding domain [49730] (6)
    3. Alpha-toxin, C-terminal domain [49738] (2)
20. Calpain large subunit, middle domain (domain III) [49757] (1)
  sandwich; 8 strands in 2 sheets; jelly-roll
  1. Calpain large subunit, middle domain (domain III) [49758] (1)
    uperfamily
    1. Calpain large subunit, middle domain (domain III) [49759] (3)
21. Supernatant protein factor (SPF), C-terminal domain [101575] (1)
  sandwich; 8 strands in 2 sheets; jelly-roll; similarity to the Nucleoplasmin-like/VP fold
  1. Supernatant protein factor (SPF), C-terminal domain [101576] (1)
    uperfamily
    1. Supernatant protein factor (SPF), C-terminal domain [101577] (1)
22. Hypothetical protein TM1070 [89231] (1)
  sandwich; 8 strands in 2 sheets; jelly-roll
  1. Hypothetical protein TM1070 [89232] (1)
    uperfamily
    1. Hypothetical protein TM1070 [89233] (1)
23. Olfactory marker protein [63696] (1)
  sandwich; 8 strands in 2 sheets; jelly-roll
  1. Olfactory marker protein [63697] (1)
    uperfamily
    1. Olfactory marker protein [63698] (2)
24. HSP20-like chaperones [49763] (1)
  sandwich; 8 strands in 2 sheets; greek-key
  1. HSP20-like chaperones [49764] (4)
    uperfamily
    1. HSP20 [49765] (2)
    2. Co-chaperone p23-like [49768] (2)
    3. GS domain [101580] (2)
      Pfam 04969
    4. Nuclear movement domain [117092] (2)
      Pfam 03593
25. Heat shock protein 70kD (HSP70), peptide-binding domain [100919] (1)
  beta-sandwich: 8 strands in 2 sheets
  1. Heat shock protein 70kD (HSP70), peptide-binding domain [100920] (1)
    uperfamily
    1. Heat shock protein 70kD (HSP70), peptide-binding domain [100921] (4)
26. Ecotin, trypsin inhibitor [49771] (1)
  sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
  1. Ecotin, trypsin inhibitor [49772] (1)
    uperfamily
    1. Ecotin, trypsin inhibitor [49773] (1)
27. PEBP-like [49776] (1)
  sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
  1. PEBP-like [49777] (2)
    uperfamily
    1. Phosphatidylethanolamine binding protein [49778] (5)
    2. Prokaryotic PEBP-like proteins [63701] (2)
28. Ganglioside M2 (gm2) activator [63706] (1)
  sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
  1. Ganglioside M2 (gm2) activator [63707] (1)
    uperfamily
    1. Ganglioside M2 (gm2) activator [63708] (1)
29. Nicotinic receptor ligand binding domain-like [63711] (1)
  sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
  1. Nicotinic receptor ligand binding domain-like [63712] (1)
    uperfamily
    1. Nicotinic receptor ligand binding domain-like [63713] (1)
30. Beta-galactosidase LacA, domain 3 [117099] (1)
  sandwich; 8 strands in 2 sheets
  1. Beta-galactosidase LacA, domain 3 [117100] (1)
    uperfamily
    1. Beta-galactosidase LacA, domain 3 [117101] (1)
31. Galactose-binding domain-like [49784] (1)
  sandwich; 9 strands in 2 sheets; jelly-roll
  1. Galactose-binding domain-like [49785] (32)
    uperfamily
    1. Galactose-binding domain [49786] (4)
    2. Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) [49791] (4)
    3. APC10-like [69210] (3)
      Pfam 03256
    4. delta-Endotoxin, C-terminal domain [49796] (4)
    5. Ephrin receptor ligand binding domain [49800] (2)
    6. beta-Galactosidase/glucuronidase, N-terminal domain [49803] (5)
    7. Chondroitin ABC lyase I, N-terminal domain [89236] (1)
    8. CBM4/9 [74893] (3)
    9. Family 6 carbohydrate binding module, CBM6 [69213] (4)
    10. CBM15 [69216] (1)
    11. Family 17 carbohydrate binding module, CBM17 [69219] (1)
    12. CBM22 [49811] (1)
      CBM family 22, formerly x6b domain
    13. Family 27 carbohydrate binding module, CBM27 [89241] (2)
    14. Family 29 carbohydrate binding module, CBM29 [89244] (1)
    15. Fucose binding lectin [74896] (1)
    16. N-terminal domain of xrcc1 [49814] (1)
    17. F-box associated region, FBA [101585] (1)
    18. Allantoicase repeat [101588] (1)
    19. PepX C-terminal domain-like [69222] (4)
    20. PA-IL, galactose-binding lectin 1 [82022] (1)
      a truncated form of this fold lacking one of the N-terminal strands
    21. Proprotein convertase P-domain [89249] (3)
      a truncated form of this fold lacking one of the N-terminal strands
    22. Family 28 carbohydrate binding module, CBM28 [110122] (1)
    23. Family 30 carbohydrate binding module, CBM30 (PKD repeat) [110125] (1)
    24. Rhamnogalacturonase B, RhgB, C-terminal domain [110128] (1)
    25. Hypothetical protein AT3g04780/F7O18_27 [117108] (1)
      Pfam 06201; DUF1000
    26. Beta-galactosidase LacA, domains 4 and 5 [117111] (1)
      duplication: tandem repeat of two similar domains; some sequence similarity to the beta-Galactosidase/glucuronidase N-terminal domain (scop_fa 49803)
    27. Family 36 carbohydrate binding module, CBM36 [117114] (1)
    28. Extended PAW domain [141113] (1)
      single domain; the N-terminal half is covered by Pfam 04721; DUF750 (Smart 00613; PAW), the C-terminal half by PfamB 028386
    29. CBM11 [141116] (1)
      Pfam 03425; Carbohydrate binding domain (family 11)
    30. beta-mannanase CBM [141119] (1)
    31. YxiM N-terminal domain-like [158963] (1)
      PfamB 038265
    32. NPCBM-like [158966] (2)
      Pfam 08305
32. Viral protein domain [49817] (1)
  sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
  1. Viral protein domain [49818] (3)
    forms homotrimers
    uperfamily
    1. Top domain of virus capsid protein [49819] (4)
      this domain is inserted into a multihelical domain
    2. Influenza hemagglutinin headpiece [49823] (1)
    3. Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [49826] (1)
33. Calcium-mediated lectin [82025] (1)
  sandwich; 9 strands in 2 sheets; greek-key
  1. Calcium-mediated lectin [82026] (1)
    uperfamily
    1. Calcium-mediated lectin [82027] (2)
34. Dextranase, N-terminal domain [101595] (1)
  sandwich; 9 strands in 2 sheets; greek-key
  1. Dextranase, N-terminal domain [101596] (1)
    uperfamily
    1. Dextranase, N-terminal domain [101597] (1)
35. Smp-1-like [101600] (1)
  sandwich; 9 strands in 2 sheets; greek-key/jelly-roll
  1. Smp-1-like [101601] (1)
    uperfamily
    1. Smp-1-like [101602] (2)
36. Superantigen (mitogen) Ypm [101605] (1)
  sandwich; 9 strands in 2 sheets; jelly-roll
  1. Superantigen (mitogen) Ypm [101606] (1)
    uperfamily
    1. Superantigen (mitogen) Ypm [101607] (1)
37. ENV polyprotein, receptor-binding domain [49829] (1)
  sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
  1. ENV polyprotein, receptor-binding domain [49830] (1)
    uperfamily
    1. ENV polyprotein, receptor-binding domain [49831] (2)
38. BTV NS2-like ssRNA-binding domain [110131] (1)
  sandwich; 9 strands in 2 sheets; unusual topology with 2 crossover loops
  1. BTV NS2-like ssRNA-binding domain [110132] (1)
    uperfamily
    1. BTV NS2-like ssRNA-binding domain [110133] (1)
      N-terminal half of Pfam 04514
39. WSSV envelope protein-like [158973] (1)
  beta-sandwich; 9 strands in 2 sheets; greek-key
  1. WSSV envelope protein-like [158974] (1)
    1. WSSV envelope protein-like [158975] (2)
40. Virus attachment protein globular domain [49834] (1)
  sandwich, 10 strands in 2 sheets; greek-key
  1. Virus attachment protein globular domain [49835] (3)
    uperfamily
    1. Adenovirus fiber protein "knob" domain [49836] (7)
    2. Reovirus attachment protein sigma 1 head domain [69225] (1)
    3. Lactophage receptor-binding protein head domain [141122] (2)
41. TNF-like [49841] (1)
  sandwich, 10 strands in 2 sheets; jelly-roll
  1. TNF-like [49842] (1)
    uperfamily
    1. TNF-like [49843] (18)
42. CUB-like [49853] (3)
  sandwich, 10 strands in 2 sheets; jelly-roll
  1. Spermadhesin, CUB domain [49854] (1)
    uperfamily
    1. Spermadhesin, CUB domain [49855] (6)
  2. Collagen-binding domain [89260] (1)
    N-terminal strand appears only in calcium-free form
    uperfamily
    1. Collagen-binding domain [89261] (1)
  3. Acetamidase/Formamidase-like [141130] (1)
    decorated fold with additional structures; contains extra C-terminal alpha+beta subdomain: beta(2)-alpha(2)-beta(2): antiparallel beta-sheet, order 1243
    uperfamily
    1. Acetamidase/Formamidase-like [141131] (1)
      Pfam 03069
43. Hyaluronate lyase-like, C-terminal domain [49862] (1)
  sandwich, 10 strands in 2 sheets; "folded meander"
  1. Hyaluronate lyase-like, C-terminal domain [49863] (1)
    uperfamily
    1. Hyaluronate lyase-like, C-terminal domain [49864] (6)
44. Cytolysin/lectin [63723] (1)
  sandwich, 10 strands in 2 sheets;
  1. Cytolysin/lectin [63724] (2)
    some topological similarity to osmotin
    uperfamily
    1. Anemone pore-forming cytolysin [63725] (2)
      Pfam 06369
    2. Fungal fruit body lectin [117119] (2)
      Pfam 07367
45. Putative glucosidase YicI, C-terminal domain [117124] (1)
  sandwich; 10 strands in two sheets
  1. Putative glucosidase YicI, C-terminal domain [117125] (1)
    uperfamily
    1. Putative glucosidase YicI, C-terminal domain [117126] (1)
46. CsrA-like [117129] (1)
  sandwich; 10 strands in 2 sheets; intertwined dimer (segment-swapped, 5-stranded greek-key sandwich?)
  1. CsrA-like [117130] (1)
    uperfamily
    1. CsrA-like [117131] (1)
      Pfam 02599
47. Osmotin, thaumatin-like protein [49869] (1)
  sandwich; 11 strands in 2 sheets
  1. Osmotin, thaumatin-like protein [49870] (1)
    has two smaller insertion domains
    uperfamily
    1. Osmotin, thaumatin-like protein [49871] (4)
48. SMAD/FHA domain [49878] (1)
  sandwich; 11 strands in 2 sheets; greek-key
  1. SMAD/FHA domain [49879] (4)
    has a few short helices inserted in loops
    uperfamily
    1. SMAD domain [49880] (4)
    2. FHA domain [49885] (12)
    3. Interferon regulatory factor 3 (IRF3), transactivation domain [101630] (1)
      weak sequence similarity to SMAD domain
    4. EssC N-terminal domain-like [141143] (1)
      PfamB 051221 covers two consecutive domains; the first one is of canonical topology, whereas the second domain has a cirular permutation, beginnig at strand 2 and ending at strand 1 of the canonical fold
49. Soluble secreted chemokine inhibitor, VCCI [49888] (1)
  sandwich; 11 strands in 2 sheets; greek-key
  1. Soluble secreted chemokine inhibitor, VCCI [49889] (1)
    uperfamily
    1. Soluble secreted chemokine inhibitor, VCCI [49890] (1)
50. Baculovirus p35 protein [49893] (1)
  sandwich; 14 strands in 2 sheets; greek-key
  1. Baculovirus p35 protein [49894] (1)
    has a few helices inserted in loops
    uperfamily
    1. Baculovirus p35 protein [49895] (1)
51. Concanavalin A-like lectins/glucanases [49898] (1)
  sandwich; 12-14 strands in 2 sheets; complex topology
  1. Concanavalin A-like lectins/glucanases [49899] (25)
    uperfamily
    1. Legume lectins [49900] (28)
    2. Lectin leg-like [74904] (3)
      mammalian protein related to legume lectins
    3. Glycosyl hydrolases family 16 [49925] (8)
      Pfam 00722
      beta-Glucanase-like
    4. Galectin (animal S-lectin) [49932] (11)
    5. Laminin G-like module [49944] (7)
    6. Thrombospondin C-terminal domain [101643] (1)
      Pfam 05735
    7. Pentraxin (pentaxin) [49951] (2)
    8. Calnexin/calreticulin [69236] (1)
    9. vp4 sialic acid binding domain [74907] (1)
    10. Hypothetical protein YesU [101646] (1)
    11. Alginate lyase [101649] (3)
      members have same function and similar structures but low sequence similarity
    12. Clostridium neurotoxins, the second last domain [49956] (3)
    13. Exotoxin A, N-terminal domain [49962] (1)
    14. Vibrio cholerae sialidase, N-terminal and insertion domains [49965] (1)
    15. Leech intramolecular trans-sialidase, N-terminal domain [49968] (1)
    16. Trypanosoma sialidase, C-terminal domain [82038] (2)
    17. Glycosyl hydrolase family 7 catalytic core [49971] (6)
      contains many insertions in the common fold
    18. Glycosyl hydrolases family 32 C-terminal domain [101652] (2)
      Pfam 08244
      flat sheet beta-sandwich lacking the characteristic beta-bulge in the C-terminal strand
    19. Xylanase/endoglucanase 11/12 [49978] (24)
    20. Peptidase A4 [101656] (2)
      circular permutation of the canonical fold
    21. Alpha-L-arabinofuranosidase B, N-terminal domain [110143] (1)
    22. SPRY domain [141154] (5)
      Pfam 00622
    23. Beta-D-xylosidase C-terminal domain-like [141161] (4)
    24. SO2946-like [141167] (1)
    25. MAM domain [141170] (1)
      Pfam 00629
52. Supersandwich [49993] (3)
  sandwich; 18 strands in 2 sheets
  1. Galactose mutarotase-like [74650] (11)
    probable carbohydrate-binding domain in enzymes acting on sugars
    uperfamily
    1. Aldose 1-epimerase (mutarotase) [74911] (4)
    2. Hypothetical protein HI1317 [89279] (1)
    3. beta-Galactosidase, domain 5 [49995] (2)
    4. Hyaluronate lyase-like, central domain [50006] (6)
    5. Glycosyltransferase family 36 N-terminal domain [63733] (2)
      overall domain organization is similar to Bacterial glucoamylase
    6. Bacterial glucoamylase N-terminal domain-like [82042] (2)
      overall domain organization is similar to Lactobacillus maltose phosphorylase
    7. 4-alpha-glucanotransferase, C-terminal domain [89286] (1)
      family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
    8. alpha-mannosidase, C-terminal domain [88656] (2)
      family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
      the supersandwich domain is elaborated with additional beta-strands and beta-sandwich subdomains
    9. MdoG-like [110148] (1)
      Pfam 04349; Pfam coverage extends to the C-terminal immunoglobulin-like domain
    10. Rhamnogalacturonase B, RhgB, N-terminal domain [110151] (1)
    11. YicI N-terminal domain-like [117139] (2)
  2. V-region of surface antigen I/II (SA I/II, PAC) [74914] (1)
    uperfamily
    1. V-region of surface antigen I/II (SA I/II, PAC) [74915] (1)
  3. Amine oxidase catalytic domain [49998] (1)
    uperfamily
    1. Amine oxidase catalytic domain [49999] (5)
53. Leukotriene A4 hydrolase N-terminal domain [63736] (1)
  duplication: two beta-sandwiches of similar topologies are fused together in a single three beta-sheet domain
  1. Leukotriene A4 hydrolase N-terminal domain [63737] (1)
    uperfamily
    1. Leukotriene A4 hydrolase N-terminal domain [63738] (1)
54. EV matrix protein [50011] (1)
  consists of two beta-sandwich domains of similar topologies
  1. EV matrix protein [50012] (1)
    uperfamily
    1. EV matrix protein [50013] (1)
55. Viral chemokine binding protein m3 [82045] (1)
  consists of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds
  1. Viral chemokine binding protein m3 [82046] (1)
    uperfamily
    1. Viral chemokine binding protein m3 [82047] (1)
56. gp9 [50016] (1)
  consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
  1. gp9 [50017] (1)
    uperfamily
    1. gp9 [50018] (1)
57. Flagellar hook protein flgE [117142] (1)
  consists of two different domains; d1: [complex fold made of bifurcated beta-sheets]; d2 (inserted into d1): [beta-sandwich; 8 strands in 2 sheets]
  1. Flagellar hook protein flgE [117143] (1)
    uperfamily
    1. Flagellar hook protein flgE [117144] (1)
58. ISP domain [50021] (1)
  consists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich of two 3-stranded sheets or closed barrel (n=6; S=8)
  1. ISP domain [50022] (3)
    uperfamily
    1. Rieske iron-sulfur protein (ISP) [50023] (11)
    2. Ring hydroxylating alpha subunit ISP domain [50033] (7)
    3. NirD-like [158991] (3)
      retains the common fold but lacks the Fe-S cluster
59. Trm112p-like [158996] (1)
  similar to the small domain of the ISP (scop_cf 50021)
  1. Trm112p-like [158997] (1)
    possibly have evolved from a metal ion (or cofactor)-binding protein of a rubredoxin-like fold; in the known members, from one to three of the four metal-binding positions are occupied by cysteine residues
    1. Trm112p-like [158998] (3)
      Pfam 03966; previously DUF343
60. YopX-like [159005] (1)
  consists of two domains: the N-terminal dimerisation domain of variable structure and the C-terminal domain with similarity to the SH3-like fold
  1. YopX-like [159006] (1)
    conmrises proteins of plasmid and phage origins
    1. YopX-like [159007] (3)
      Pfam 09643
61. Obg-fold [82050] (1)
  this fold is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich
  these regions form six left-handed collagen-like helices packed and H-bonded together
  1. Obg GTP-binding protein N-terminal domain [82051] (1)
    uperfamily
    1. Obg GTP-binding protein N-terminal domain [82052] (2)
62. SH3-like barrel [50036] (21)
  barrel, partly opened; n*=4, S*=8; meander
  the last strand is interrupted by a turn of 3-10 helix
  1. C-terminal domain of transcriptional repressors [50037] (3)
    the N-terminal domains of these repressors bind DNA
    uperfamily
    1. Biotin repressor (BirA) [50038] (2)
    2. FeoA-like [50041] (4)
    3. Transcriptional repressor protein KorB [69242] (1)
  2. SH3-domain [50044] (1)
    uperfamily
    1. SH3-domain [50045] (48)
  3. Prokaryotic SH3-related domain [82057] (4)
    uperfamily
    1. GW domain [82058] (1)
    2. PhnA-like [141190] (2)
      Pfam 03831
    3. Spr N-terminal domain-like [141195] (1)
    4. Ply C-terminal domain-like [141198] (1)
      duplication: tandem repeat of two SH3-like domains swapped with the N-terminal strands; non-overlapping parts of sequence are covered by PfamB 062324 and PfamB 020199
  4. Myosin S1 fragment, N-terminal domain [50084] (1)
    uperfamily
    1. Myosin S1 fragment, N-terminal domain [50085] (4)
  5. Tudor/PWWP/MBT [63748] (4)
    uperfamily
    1. Tudor domain [63749] (7)
      Pfam 00567
    2. PWWP domain [69250] (6)
      includes the C-terminal all-alpha subdomain
    3. MBT repeat [89299] (4)
      Pfam 02820
      contains extended 'arm', N-terminal to the common fold core
    4. CPH domain [159021] (1)
  6. Chromo domain-like [54160] (3)
    SH3-like barrel is capped by a C-terminal helix
    uperfamily
    1. "Histone-like" proteins from archaea [54161] (2)
    2. Chromo domain [54165] (10)
      lacks the SH3-like barrel first strand that can be complemented by bound peptide ligand; in shadow chromo domain the corresponding site is altered by insertion; similarity to the IL8-like fold
    3. Chromo barrel domain [117157] (3)
      typical SH3-like barrel fold; similar sequence motif to the canonical chromo domain
  7. BAH domain [82061] (1)
    uperfamily
    1. BAH domain [82062] (1)
  8. PAZ domain [101690] (1)
    uperfamily
    1. PAZ domain [101691] (5)
  9. Cap-Gly domain [74924] (1)
    uperfamily
    1. Cap-Gly domain [74925] (12)
      Pfam 01302
  10. Electron transport accessory proteins [50090] (4)
    uperfamily
    1. R67 dihydrofolate reductase [50091] (1)
    2. Photosystem I accessory protein E (PsaE) [50094] (4)
    3. Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain [50098] (1)
    4. Nitrile hydratase beta chain [50101] (3)
      contains irregular array of helices in the N-terminal extension
  11. Translation proteins SH3-like domain [50104] (7)
    many known members contain KOW motif
    uperfamily
    1. Ribosomal proteins L24p and L21e [50105] (5)
    2. eIF5a N-terminal domain-like [50110] (7)
    3. C-terminal domain of ribosomal protein L2 [50114] (5)
    4. N-utilization substance G protein NusG, C-terminal domain [82072] (2)
    5. SPT5 KOW domain-like [141242] (1)
      part of Pfam 00467
    6. Ribosomal protein L19 [141245] (3)
      Pfam 01245
    7. Ribosomal protein L14e [159031] (1)
      PfamB 032577
  12. Cell growth inhibitor/plasmid maintenance toxic component [50118] (3)
    contains insert beta-sheet subdomain and C-terminal helix
    uperfamily
    1. CcdB [50119] (1)
    2. Kid/PemK [82075] (3)
    3. Rv2302-like [141248] (1)
      different orientation for the extra C-terminal helix relative the SH3-like barrel
  13. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63433] (1)
    uperfamily
    1. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63434] (1)
      contains 5 short helices in the loop between the third and fourth strands
  14. DNA-binding domain of retroviral integrase [50122] (1)
    uperfamily
    1. DNA-binding domain of retroviral integrase [50123] (3)
  15. Hypothetical protein YfhH [101697] (1)
    contains extra N-terminal all-alpha subdomain
    uperfamily
    1. Hypothetical protein YfhH [101698] (1)
  16. Kinase-associated protein B-like [141251] (1)
    contains extra C-terminal alpha-hairpin
    uperfamily
    1. Kinase-associated protein B-like [141252] (1)
  17. YccV-like [141255] (1)
    contains extra C-terminal helix packed against barrel
    uperfamily
    1. YccV-like [141256] (1)
  18. CarD-like [141259] (1)
    uperfamily
    1. CarD-like [141260] (1)
      Pfam 02559
  19. Mib/herc2 domain-like [159034] (1)
    1. Mib/herc2 domain [159035] (1)
      Pfam 06701
  20. YorP-like [159038] (1)
    1. YorP-like [159039] (1)
      Pfam 09629
  21. Plus3-like [159042] (1)
    1. Plus3 [159043] (1)
      Pfam 03126
63. GroES-like [50128] (2)
  contains barrel, partly opened; n*=4, S*=8; meander
  1. GroES-like [50129] (2)
    uperfamily
    1. GroES [50130] (5)
    2. Alcohol dehydrogenase-like, N-terminal domain [50136] (27)
      C-terminal domain is alpha/beta (classical Rossmann-fold)
  2. SacY-like RNA-binding domain [50151] (1)
    uperfamily
    1. BglG-like antiterminator proteins [50152] (2)
64. PDZ domain-like [50155] (1)
  contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
  1. PDZ domain-like [50156] (6)
    peptide-binding domain
    uperfamily
    1. PDZ domain [50157] (55)
      Pfam 00595
    2. Tail specific protease PDZ domain [68933] (2)
    3. HtrA-like serine proteases [74933] (4)
    4. Interleukin 16 [50172] (1)
    5. EpsC C-terminal domain-like [159046] (1)
      PfamB 005596
    6. MTH1368 C-terminal domain-like [159049] (1)
      middle part of Pfam 02163
65. N-terminal domains of the minor coat protein g3p [50175] (1)
  core: barrel, in some members open; n*=4, S*=8; meander
  1. N-terminal domains of the minor coat protein g3p [50176] (1)
    uperfamily
    1. N-terminal domains of the minor coat protein g3p [50177] (2)
66. Sm-like fold [50181] (5)
  core: barrel, open; n*=4, S*=8; meander; SH3-like topology
  1. Sm-like ribonucleoproteins [50182] (6)
    uperfamily
    1. Sm motif of small nuclear ribonucleoproteins, SNRNP [50183] (13)
      forms homo and heteroheptameric ring structures
    2. Pleiotropic translational regulator Hfq [74939] (3)
      forms homohexameric ring structures
    3. Mechanosensitive channel protein MscS (YggB), middle domain [82090] (1)
    4. PF1955-like [141294] (1)
      homohexadecameric assembly: two stacked octameric rings
    5. LSM14 N-terminal domain-like [141297] (1)
    6. YgdI/YgdR-like [159052] (6)
      Pfam 06004; DUF903, putative lipoprotein; both homohexameric and homoheptameric ring assemblies are observed in the crystals
  2. YhbC-like, C-terminal domain [74942] (1)
    uperfamily
    1. YhbC-like, C-terminal domain [74943] (1)
  3. GatD N-terminal domain-like [141300] (1)
    uperfamily
    1. GatD N-terminal domain-like [141301] (2)
      PfamB 010580
  4. Dom34/Pelota N-terminal domain-like [159065] (1)
    1. Dom34/Pelota N-terminal domain-like [159066] (2)
      Warning: Pfam incorrectly assigns this domain to the same family as the structurally unrelated N-terminal domain of eRF1 (Pfam 03463)
  5. TrmB C-terminal domain-like [159071] (1)
    sugar-binding domain; permuted OB-fold?
    1. TrmB C-terminal domain-like [159072] (1)
      C-terminal part of PfamB 004822
67. SspB-like [101737] (1)
  core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
  1. SspB-like [101738] (2)
    uperfamily
    1. Stringent starvation protein B, SspB [101739] (2)
    2. AGR_C_3712p-like [159075] (1)
      Pfam 07031; DUF1321
68. Rof/RNase P subunit-like [101743] (1)
  core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
  1. Rof/RNase P subunit-like [101744] (2)
    uperfamily
    1. RNase P subunit p29-like [101745] (3)
      two available NMR structures display similar topologies but different barrel shapes
      the barrel shape of the full-length X-ray structures of AF1917 differs from both earlier NMR structures
    2. Rof-like [141305] (1)
      Pfam 07073; ROF
69. Hydrophobin II, HfbII [101750] (1)
  core: barrel, closed; n=4, S=8; complex topology; helix-containing crossover connection
  1. Hydrophobin II, HfbII [101751] (1)
    uperfamily
    1. Hydrophobin II, HfbII [101752] (1)
      a self-assembling amphiphile
70. Ribosomal protein L14 [50192] (1)
  barrel, closed; n=5, S=8, meander
  1. Ribosomal protein L14 [50193] (1)
    uperfamily
    1. Ribosomal protein L14 [50194] (5)
71. OB-fold [50198] (16)
  barrel, closed or partly opened n=5, S=10 or S=8; greek-key
  1. Staphylococcal nuclease [50199] (1)
    uperfamily
    1. Staphylococcal nuclease [50200] (1)
      barrel, closed; n=5, S=10
  2. Bacterial enterotoxins [50203] (2)
    uperfamily
    1. Bacterial AB5 toxins, B-subunits [50204] (9)
    2. Superantigen toxins, N-terminal domain [50219] (15)
  3. TIMP-like [50242] (3)
    uperfamily
    1. Tissue inhibitor of metalloproteinases, TIMP [50243] (3)
      contains an irregular alpha+beta subdomain in the C-terminal extension
    2. Netrin-like domain (NTR/C345C module) [89320] (2)
      Pfam 01759
    3. The laminin-binding domain of agrin [63767] (1)
  4. Heme chaperone CcmE [82093] (1)
    uperfamily
    1. Heme chaperone CcmE [82094] (2)
  5. gp5 N-terminal domain-like [69255] (1)
    uperfamily
    1. gp4 N-terminal domain-like [69256] (2)
  6. Hypothetical protein YgiW [101756] (1)
    uperfamily
    1. Hypothetical protein YgiW [101757] (1)
      Pfam 04076, Domain of unknown function DUF388
  7. Nucleic acid-binding proteins [50249] (16)
    uperfamily
    1. Anticodon-binding domain [50250] (7)
      barrel, closed; n=5, S=10
    2. RecG "wedge" domain [69259] (1)
    3. DNA helicase RuvA subunit, N-terminal domain [50259] (3)
      barrel, closed; n=5, S=10
    4. Single strand DNA-binding domain, SSB [50263] (17)
      barrel, closed; n=5, S=10
    5. Myf domain [50277] (7)
    6. Cold shock DNA-binding domain-like [50282] (56)
      barrel, closed; n=5, S=8
    7. TRAM domain [101768] (3)
      Pfam 01938
    8. Hypothetical protein MTH1 (MT0001), insert domain [74955] (1)
    9. DNA ligase/mRNA capping enzyme postcatalytic domain [50307] (6)
    10. Phage ssDNA-binding proteins [50315] (5)
      barrel, open; n*=5, S*=8; the members' structures vary greater that those from cellular organisms
    11. DNA replication initiator (cdc21/cdc54) N-terminal domain [89332] (1)
    12. RNA polymerase subunit RBP8 [50321] (1)
      duplication; contains tandem repeat of two incomplete OB-folds; forms a single barrel; n=8, S=10
    13. RecO N-terminal domain-like [117204] (1)
      N-terminal part of Pfam 02565
    14. TIP49 domain [141315] (1)
      N-terminal part of Pfam 06068; the RuvA-like OB-fold domain in RuvB-like eukaryotic proteins
    15. SSO2064-like [159109] (1)
      Pfam 01796; DUF35; contains extra N-terminal zinc finger subdomain of the rubredoxin-like fold
    16. RNB domain-like [159112] (3)
      Pfam 00773; RNase II catalytic domain; decorated OB-fold domain with extra C-terminal structures forming the active site
  8. Inorganic pyrophosphatase [50324] (1)
    uperfamily
    1. Inorganic pyrophosphatase [50325] (6)
      barrel, closed; n=5, S=8
  9. MOP-like [50331] (3)
    uperfamily
    1. Molybdate/tungstate binding protein MOP [50332] (2)
    2. BiMOP, duplicated molybdate-binding domain [50335] (2)
      duplication: tandem repeat of two OB-fold domains with swapped C-terminal strands
    3. ABC-transporter additional domain [50338] (5)
      probably stems out from the biMOP domain
  10. CheW-like [50341] (1)
    uperfamily
    1. CheW-like [50342] (2)
      duplication: tandem repeat of two swapped domains, one with a canonical OB-fold topology and one with a circular permutation
  11. TM0957-like [141318] (1)
    extra N-terminal region and large insertion after strand 3 together form an alpha-helical subdomain
    uperfamily
    1. TM0957-like [141319] (1)
  12. NfeD domain-like [141322] (1)
    close structural similarity to some members of the Nucleic acid-binding OB-fold proteins, possibly related to this superfamily
    uperfamily
    1. NfeD domain-like [141323] (1)
      C-terminal part of Pfam 01957
  13. BC4932-like [159121] (1)
    1. BC4932-like [159122] (2)
      Pfam 06486; DUF1093
  14. HupF/HypC-like [159127] (1)
    contains extra C-terminal helix packed against the beta-barrel side
    1. HupF/HypC-like [159128] (3)
      Pfam 01455
  15. EutN/CcmL-like [159133] (1)
    homohexameric unit
    1. EutN/CcmL-like [159134] (3)
      Pfam 03319
  16. HIN-2000 domain-like [159141] (1)
    duplication: tandem repeat of two OB-fold domains
    1. HIN-200/IF120x domain [159142] (1)
      Pfam 02760
72. PRC-barrel domain [50345] (1)
  core: barrel, partly opened; n*=5, S*=8; meander
  1. PRC-barrel domain [50346] (4)
    uperfamily
    1. MTH1895 [101773] (1)
      homodimeric protein; subunits are composed of a stand-alone copy of this domain
    2. Photosynthetic reaction centre, H-chain, cytoplasmic domain [50347] (3)
    3. RIKEN cDNA 2310057j16 protein (KIAA1543) [110202] (1)
      contains an N-terminal alpha-haipin and other fold decorations
    4. RimM C-terminal domain-like [141326] (1)
73. beta-Trefoil [50352] (8)
  barrel, closed; n=6, S=12; and a hairpin triplet; meander
  duplication: has internal pseudo threefold symmetry
  1. Cytokine [50353] (2)
    uperfamily
    1. Fibroblast growth factors (FGF) [50354] (11)
    2. Interleukin-1 (IL-1) [50362] (6)
  2. MIR domain [82109] (1)
    uperfamily
    1. MIR domain [82110] (2)
      Pfam 02815
  3. Ricin B-like lectins [50370] (3)
    uperfamily
    1. Ricin B-like [50371] (18)
    2. Cysteine rich domain [50379] (1)
    3. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [117212] (1)
  4. Agglutinin [50382] (1)
    this superfamily is distinct from the ricin B-like lectin superfamily
    uperfamily
    1. Agglutinin [50383] (1)
  5. STI-like [50386] (2)
    uperfamily
    1. Kunitz (STI) inhibitors [50387] (7)
    2. Clostridium neurotoxins, C-terminal domain [50399] (3)
      overall fold is very similar to that of the STI family
  6. Actin-crosslinking proteins [50405] (2)
    uperfamily
    1. Fascin [50406] (1)
    2. Histidine-rich actin-binding protein (hisactophilin) [50409] (1)
  7. DNA-binding protein LAG-1 (CSL) [110217] (1)
    contains rudiment hairpin triplet lacking one hairpin
    uperfamily
    1. DNA-binding protein LAG-1 (CSL) [110218] (1)
  8. AbfB domain [110221] (1)
    uperfamily
    1. AbfB domain [110222] (1)
      Pfam 05270
74. Reductase/isomerase/elongation factor common domain [50412] (4)
  barrel, closed; n=6, S=10; greek-key
  1. Riboflavin synthase domain-like [63380] (3)
    uperfamily
    1. Riboflavin synthase [63783] (2)
      duplication: consists of two homologous domains
    2. Ferredoxin reductase FAD-binding domain-like [63381] (19)
      coupled with a NADP-binding domain of alpha/beta class
    3. NADPH-cytochrome p450 reductase FAD-binding domain-like [50438] (3)
      there is an alpha-helical subdomain inserted in this domain
  2. Riboflavin kinase-like [82114] (2)
    uperfamily
    1. ATP-dependent riboflavin kinase-like [82115] (3)
    2. CTP-dependent riboflavin kinase-like [159154] (2)
      Pfam 01982; newly characterized archaeal family (formerly DUF120)
  3. FucI/AraA C-terminal domain-like [50443] (2)
    uperfamily
    1. L-fucose isomerase, C-terminal domain [50444] (1)
    2. AraA C-terminal domain-like [141331] (1)
      C-terminal part of Pfam 02610
  4. Translation proteins [50447] (6)
    uperfamily
    1. Elongation factors [50448] (18)
    2. Ribosomal protein L3 [50461] (4)
    3. Ribosomal protein L35ae [117220] (1)
      Pfam 01247
    4. RimM N-terminal domain-like [141338] (1)
      Pfam 01782
    5. Gar1-like SnoRNP [141341] (1)
      stand alone proteins, which are similar structurally but not sequentially to the elongation factor domains, unlike PF0907
    6. AlaX-M N-terminal domain-like [159161] (1)
      Does NOT belong to Pfam 01411
75. Elongation factor/aminomethyltransferase common domain [50464] (2)
  barrel, closed; n=6, S=10; greek-key
  1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50465] (1)
    probably related to the second domain and its superfamiy by a circular permutation
    uperfamily
    1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50466] (12)
  2. Aminomethyltransferase beta-barrel domain [101790] (1)
    uperfamily
    1. Aminomethyltransferase beta-barrel domain [101791] (5)
76. Split barrel-like [50474] (3)
  barrel; n=6, S=10; greek-key
  1. FMN-binding split barrel [50475] (4)
    related to the ferredoxin reductase-like FAD-binding domain
    uperfamily
    1. PNP-oxidase like [50476] (21)
    2. NADH:FMN oxidoreductase-like [50482] (5)
      different dimerization mode than in the PNP-oxidase like family
    3. UbiD middle domain-like [141368] (1)
      N terminal part of Pfam 01977; overall structural similarity to one subunit of the NADH:FMN oxidoreductase-like family (scop_fa 50482); not known to bind a flavin cofactor; also includes the N-terminal alpha+beta subdomain (~110 residues)
    4. MTH863-like [159164] (3)
      Pfam 04289; DUF447; a new dimerisation mode involving (included) all-alpha subdomain of the spectrin-like fold (scop_cf 46965)
  2. PilZ domain-like [141371] (2)
    uperfamily
    1. PilZ domain [141372] (3)
      Pfam 07238
    2. PilZ domain-associated domain [141377] (2)
      this domain preceeds PilZ domain in some proteins
  3. YkvR-like [159173] (1)
    provisional classification, pending better resolution structures
    1. YkvR-like [159174] (1)
      PfamB 102647
77. Phage tail proteins [69278] (1)
  core: barrel; n=6, S=10; greek-key; topologically similar to the FMN-binding split barrel
  1. Phage tail proteins [69279] (3)
    uperfamily
    1. Baseplate protein-like [69280] (5)
      duplication: consists of two similar barrel domains that differ by the first strand directions; the barrels are differently decorated by alpha+beta insertions
    2. gpFII-like [74966] (2)
      similar to the N-terminal barrel of T4 gp27
    3. XkdM-like [159185] (1)
      Pfam 09393; DUF2001
78. Surface presentation of antigens (SPOA) [101800] (1)
  segment-swapped dimer forming two identical conjoint barrels (n=6, S=10) topologically similar to the FMN-binding split barrel
  1. Surface presentation of antigens (SPOA) [101801] (1)
    uperfamily
    1. Surface presentation of antigens (SPOA) [101802] (2)
79. FMT C-terminal domain-like [50485] (1)
  barrel, open; n*=6, S*=10; greek-key
  1. FMT C-terminal domain-like [50486] (2)
    uperfamily
    1. Post formyltransferase domain [50487] (5)
    2. 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) [50490] (1)
80. Trypsin-like serine proteases [50493] (1)
  barrel, closed; n=6, S=8; greek-key
  duplication: consists of two domains of the same fold
  1. Trypsin-like serine proteases [50494] (4)
    uperfamily
    1. Prokaryotic proteases [50495] (16)
    2. Eukaryotic proteases [50514] (68)
    3. Viral proteases [50596] (9)
      beta sheet in the first domain is opened rather than forms a barrel
    4. Viral cysteine protease of trypsin fold [50603] (8)
81. Replicase NSP9 [101815] (1)
  barrel; n=6, S=8, greek-key; similar to one trypsin-like protease barrel
  1. Replicase NSP9 [101816] (1)
    uperfamily
    1. Replicase NSP9 [101817] (1)
82. mu transposase, C-terminal domain [50609] (1)
  barrel; n=6, S=8, greek-key
  1. mu transposase, C-terminal domain [50610] (1)
    uperfamily
    1. mu transposase, C-terminal domain [50611] (1)
83. Domain of alpha and beta subunits of F1 ATP synthase-like [50614] (3)
  barrel, closed; n=6, S=8; greek-key
  1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50615] (1)
    uperfamily
    1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50616] (8)
      6 domains form a ring structure which contains a barrel, closed; n=24, S=24(?)
  2. Alanine racemase C-terminal domain-like [50621] (2)
    the barrel is decorated with additional structures
    uperfamily
    1. Alanine racemase [88682] (3)
    2. Eukaryotic ODC-like [88683] (6)
      barrel is open with strands 4 and 5 having swapped their positions, compared to the alanine racemase barrel
  3. Aminopeptidase/glucanase lid domain [101821] (1)
    uperfamily
    1. Aminopeptidase/glucanase lid domain [101822] (7)
84. Small protein B (SmpB) [74981] (1)
  barrel, closed; n=6, S=8, greek-key, partial similarity to the OB-fold
  1. Small protein B (SmpB) [74982] (1)
    uperfamily
    1. Small protein B (SmpB) [74983] (2)
85. Acid proteases [50629] (1)
  barrel, closed; n=6, S=10, complex topology
  1. Acid proteases [50630] (3)
    uperfamily
    1. Retroviral protease (retropepsin) [50631] (8)
      dimer of identical mono-domain chains, each containing (6,10) barrel
    2. Pepsin-like [50646] (26)
      duplication: consists of two similar barrel domains
      N-terminal: barrel, partly opened; n*=6, S*=10
    3. LPG0085-like [159190] (1)
      Pfam 05618; DUF785; single-domain protein similar to one pepsin domain with the conserved catalytic Asp motif (not in a few archaeal members of this Pfam family)
86. ValRS/IleRS/LeuRS editing domain [50676] (1)
  core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
  1. ValRS/IleRS/LeuRS editing domain [50677] (1)
    uperfamily
    1. ValRS/IleRS/LeuRS editing domain [50678] (4)
      inserted into the catalytic domain
87. Urease metallochaperone UreE, N-terminal domain [69286] (1)
  barrel, closed; n=6, S=8; a crossover loop topology
  1. Urease metallochaperone UreE, N-terminal domain [69287] (1)
    uperfamily
    1. Urease metallochaperone UreE, N-terminal domain [69288] (2)
88. Double psi beta-barrel [50684] (2)
  barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
  1. Barwin-like endoglucanases [50685] (4)
    uperfamily
    1. Eng V-like [50686] (3)
    2. Pollen allergen PHL P 1 N-terminal domain [82135] (1)
      conserved Eng V active site residues and disulfides; better structural similarity to the ADC-like superfamily
    3. Barwin [50689] (1)
    4. MLTA-like [159195] (3)
      Pfam 03562 and Pfam 06725 cover the middle and C-terminal parts, respectively; contains large insert domain of the L25-like fold (scop_cf 50714)
  2. ADC-like [50692] (3)
    uperfamily
    1. Pyruvoyl dependent aspartate decarboxylase, ADC [50693] (2)
    2. Formate dehydrogenase/DMSO reductase, C-terminal domain [50696] (12)
      molybdopterine enzyme
    3. Cdc48 N-terminal domain-like [50708] (5)
89. Ribosomal protein L25-like [50714] (1)
  barrel, closed; n=6, S=10; complex topology
  1. Ribosomal protein L25-like [50715] (2)
    uperfamily
    1. Ribosomal protein L25-like [50716] (3)
    2. Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [50719] (2)
90. Core binding factor beta, CBF [50722] (1)
  barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
  1. Core binding factor beta, CBF [50723] (1)
    uperfamily
    1. Core binding factor beta, CBF [50724] (2)
91. NifT/FixU barrel-like [159202] (1)
  barrel, closed, n=6, S=10; meander
  1. NifT/FixU-like [159203] (1)
    1. NifT/FixU [159204] (1)
      Pfam 06988
92. PH domain-like barrel [50728] (2)
  barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
  1. PH domain-like [50729] (13)
    uperfamily
    1. Pleckstrin-homology domain (PH domain) [50730] (51)
      Pfam 00169
    2. Phosphotyrosine-binding domain (PTB) [50755] (14)
      Pfam 00640
    3. Ran-binding domain [50764] (4)
    4. Enabled/VASP homology 1 domain (EVH1 domain) [50767] (8)
    5. Dcp1 [101836] (1)
      close structural similarity to EVH1 domain
    6. Third domain of FERM [50776] (9)
    7. PreBEACH PH-like domain [82146] (2)
    8. GRAM domain [101839] (1)
    9. TFIIH domain [110272] (2)
    10. SSRP1-like [141436] (1)
      Pfam 03531; Structure-specific recognition protein family; duplication: comprises tandem repeat of two domains of this fold
    11. Necap1 N-terminal domain-like [141439] (1)
      Pfam 07933; DUF1681
    12. VPS36 N-terminal domain-like [141442] (3)
      PfamB 030385
    13. BPHL domain [159216] (2)
      Pfam 08000; DUF1696, bacterial proteins with PH-like domain
  2. PA2021-like [141447] (1)
    prokaryotiic proteins of PH domain-like fold lacking the N-terminal strand
    uperfamily
    1. PA2021-like [141448] (1)
      small family specific to Pseudomonas
93. Transcription factor IIA (TFIIA), beta-barrel domain [50783] (1)
  barrel, closed; n=6, S=12; mixed beta-sheet
  1. Transcription factor IIA (TFIIA), beta-barrel domain [50784] (1)
    dimer of non-identical beta-sheet domains
    uperfamily
    1. Transcription factor IIA (TFIIA), beta-barrel domain [50785] (4)
      heterodimer of two homologous chains
94. Hcp1-like [141451] (1)
  barrel, closed; n=6, S=12; contains extra, non-barrel strand 7 at the C-terminus
  1. Hcp1-like [141452] (1)
    probable biological unit is a ring-like hexamer containing a 24-stranded beta-barrel made of the subunit beta-sheets
    uperfamily
    1. Hcp1-like [141453] (1)
      Pfam 05638; DUF796
95. YopT-like [159221] (1)
  beta-sheet barrel, closed, n=6, S=12, capped at both ends by helices; intertwined dimer of beta-alpha-beta(2) subinits;
  1. YopT-like [159222] (1)
    1. YopT-like [159223] (1)
      Pfam 09467
96. Herpes virus serine proteinase, assemblin [50788] (1)
  core: barrel, closed; n=7, S=8; complex topology
  1. Herpes virus serine proteinase, assemblin [50789] (1)
    uperfamily
    1. Herpes virus serine proteinase, assemblin [50790] (5)
97. PK beta-barrel domain-like [50799] (1)
  barrel, closed; n=7, S=10; complex topology
  1. PK beta-barrel domain-like [50800] (2)
    uperfamily
    1. Pyruvate kinase beta-barrel domain [50801] (6)
      this domain interrupts beta/alpha-barrel domain
      C-terminal domain is alpha/beta
    2. MOSC (MOCO sulphurase C-terminal) domain [101844] (2)
      Pfam 03473
98. XRCC4, N-terminal domain [50808] (1)
  barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
  1. XRCC4, N-terminal domain [50809] (1)
    an HTH motif connects strands 4 and 5
    uperfamily
    1. XRCC4, N-terminal domain [50810] (1)
99. HesB-like domain [89359] (1)
  barrel, closed; n=7, S=10; complex topology
  1. HesB-like domain [89360] (1)
    uperfamily
    1. HesB-like domain [89361] (3)
      Pfam 01521; Iron-sulfur cluster scaffold domain
100. Bacterial fluorinating enzyme, C-terminal domain [101851] (1)
  barrel, closed; n=7, S=10; greek-key topology; one overside connection
  1. Bacterial fluorinating enzyme, C-terminal domain [101852] (1)
    uperfamily
    1. Bacterial fluorinating enzyme, C-terminal domain [101853] (1)
101. SPOC domain-like [100938] (1)
  barrel, closed; n=7, S=10; complex topology
  1. SPOC domain-like [100939] (3)
    uperfamily
    1. SPOC domain [101856] (1)
    2. Ku70 subunit middle domain [100940] (1)
      includes C-terminal alpha-helical arm and DNA encircling insertion
    3. Ku80 subunit middle domain [100943] (1)
      includes C-terminal alpha-helical arm and DNA encircling insertion
102. BH3618-like [141456] (1)
  barrel, closed; n=7, S=10; meander
  1. BH3618-like [141457] (1)
    uperfamily
    1. BH3618-like [141458] (1)
      Pfam 02623; DUF180
103. FAS1 domain [82152] (1)
  core: barrel, closed; n=7, S=12; meander
  1. FAS1 domain [82153] (1)
    uperfamily
    1. FAS1 domain [82154] (2)
104. Lipocalins [50813] (1)
  barrel, closed or opened; n=8, S=12; meander
  1. Lipocalins [50814] (9)
    bind hydrophobic ligands in their interior
    uperfamily
    1. Retinol binding protein-like [50815] (30)
      barrel, closed; n=8, S=12, meander
    2. Fatty acid binding protein-like [50847] (28)
      ten-stranded meander beta-sheet folded upon itself
      relates to the common fold by opening the barrel and insertion of beta-hairpin
    3. Thrombin inhibitor [50872] (1)
      topology permutation: strands 2 and 3 swapped their positions in the barrel
    4. Hypothetical protein YodA [101863] (1)
      bacterial metal-binding, lipocalin-like protein
    5. Hypothetical protein YwiB [101866] (1)
      bacterial proteins with a fatty acid binding protein-like fold
    6. Phenolic acid decarboxylase (PAD) [141469] (1)
      Pfam 05870; dimeric enzyme made of lipocalin-like subunits
    7. Dinoflagellate luciferase repeat [141472] (1)
      PfamB 017809; comprises a fatty acid binding protein-like fold, wrapped into the extra N- and C-terminal 'tails'
    8. Rv2717c-like [141475] (2)
      bacterial and plant proteins with a fatty acid binding protein-like fold
    9. All1756-like [159230] (1)
      cyanobacterial proteins with duplicated fatty acid binding protein-like domains; N-terminal and C-terminal domains correspond to PfamB 40396 and PfamB 60468, respectively
105. Streptavidin-like [50875] (8)
  barrel, closed; n=8, S=10; meander
  1. Avidin/streptavidin [50876] (1)
    uperfamily
    1. Avidin/streptavidin [50877] (2)
  2. beta-Barrel protease inhibitors [50882] (2)
    uperfamily
    1. Metalloprotease inhibitor [50883] (2)
    2. Staphostatin [101869] (2)
      cysteine protease inhibitor; topology permutation: strand 3 is replaced with the N-terminal extra strand
  3. D-aminopeptidase, middle and C-terminal domains [50886] (1)
    uperfamily
    1. D-aminopeptidase, middle and C-terminal domains [50887] (1)
  4. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69298] (1)
    uperfamily
    1. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69299] (2)
  5. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75001] (1)
    uperfamily
    1. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75002] (2)
  6. YceI-like [101874] (1)
    uperfamily
    1. YceI-like [101875] (2)
      Pfam 04264
  7. Extracellular hemoglobin linker subunit, receptor domain [141480] (1)
    uperfamily
    1. Extracellular hemoglobin linker subunit, receptor domain [141481] (3)
  8. YdhA-like [141488] (1)
    uperfamily
    1. YdhA-like [141489] (1)
106. FomD barrel-like [159233] (1)
  barrel, closed; n=8, S=12; meander; similar topology to the AOC barrel-like fold (reversed to the lipocalin barrel topology)
  1. FomD-like [159234] (1)
    1. FomD-like [159235] (1)
      Pfam 04167; DUF402
107. AOC barrel-like [141492] (2)
  barrel, closed; n=8, S=10; meander; mirrored (reversed) topology to the Spreptavidin-like and Lipocalin-like folds
  1. Allene oxide cyclase-like [141493] (1)
    uperfamily
    1. Allene oxide cyclase-like [141494] (2)
      Pfam 06351
  2. SO1590-like [159238] (1)
    1. SO1590-like [159239] (2)
108. AttH-like [159244] (1)
  duplication: two flattened beta-barrels of lipocalin-like topology are orthogonally packed with a pseudo twofold symmetry
  1. AttH-like [159245] (1)
    1. AttH-like [159246] (1)
      Pfam 09410; DUF2006
109. Cyclophilin-like [50890] (1)
  barrel, closed; n=8, S=10; complex topology
  1. Cyclophilin-like [50891] (4)
    uperfamily
    1. Cyclophilin (peptidylprolyl isomerase) [50892] (25)
    2. Outer surface protein, C-terminal domain [110278] (1)
      lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 05913
    3. TM1367-like [141519] (1)
      Pfam 04126; DUF369
    4. PH0987 C-terminal domain-like [159249] (1)
      lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
110. Oncogene products [50903] (1)
  barrel, closed; n=8, S=10; one overside connection
  1. Oncogene products [50904] (1)
    duplication: N- and C-terminal halves are related by pseudo dyad
    uperfamily
    1. Oncogene products [50905] (3)
111. L,D-transpeptidase catalytic domain-like [141522] (1)
  barrel, closed; n=8, S=10; one overside connection
  1. L,D-transpeptidase catalytic domain-like [141523] (1)
    uperfamily
    1. L,D-transpeptidase catalytic domain-like [141524] (2)
      Pfam 03734; ErfK/YbiS/YcfS/YnhG
112. Sortase [63816] (1)
  barrel, closed; n=8, S=10; mixed sheet; two overside connections
  1. Sortase [63817] (1)
    uperfamily
    1. Sortase [63818] (3)
113. PTSIIA/GutA-like [141529] (1)
  barrel, closed; n=8, S=12; mixed sheet; two overside connections; duplication: consists of two intertwinned structural repeats
  1. PTSIIA/GutA-like [141530] (1)
    uperfamily
    1. PTSIIA/GutA-like [141531] (1)
      Pfam 03829
114. Mannose 6-phosphate receptor domain [50910] (1)
  barrel, partly open; n*=8, S*=10; one psi loop
  1. Mannose 6-phosphate receptor domain [50911] (1)
    uperfamily
    1. Mannose 6-phosphate receptor domain [50912] (3)
115. triple barrel [50915] (1)
  dimer of two non-identical subunits; forms two similar barrels, n=8, S=10 each, that are fused together with the formation of third barrel, n=6, S=8
  1. Rap30/74 interaction domains [50916] (1)
    uperfamily
    1. Rap30/74 interaction domains [50917] (2)
116. 4-bladed beta-propeller [50922] (1)
  consists of four 4-stranded beta-sheet motifs; meander
  1. Hemopexin-like domain [50923] (1)
    uperfamily
    1. Hemopexin-like domain [50924] (6)
117. 5-bladed beta-propeller [50933] (3)
  consists of five 4-stranded beta-sheet motifs; meander
  1. Tachylectin-2 [50934] (1)
    uperfamily
    1. Tachylectin-2 [50935] (1)
  2. Arabinanase/levansucrase/invertase [75005] (5)
    uperfamily
    1. alpha-L-arabinanase-like [75006] (7)
    2. Levansucrase [101881] (1)
    3. Glycosyl hydrolases family 32 N-terminal domain [101884] (2)
      Pfam 00251; Glycosyl hydrolase family 32
    4. TM1225-like predicted glycosylases [110284] (1)
      Pfam 04041 DUF377
    5. LmjF10.1260-like [141543] (1)
  3. Apyrase [101887] (1)
    distorted propeller with an alpha helix inserted between the second and third blades
    uperfamily
    1. Apyrase [101888] (1)
      Pfam 06079
118. 6-bladed beta-propeller [50938] (11)
  consists of six 4-stranded beta-sheet motifs; meander
  1. Sialidases [50939] (2)
    uperfamily
    1. Sialidases (neuraminidases) [50940] (11)
    2. Endo-alpha-sialidase [117276] (1)
      possibly related by the other family by circular permutation; includes extra N-terminal domain [dN: alpha/beta ] and insert domain [dI: beta-barrel, similar to the Reductase/isomerase/elongation factor common domain (scop_cf 50412)]
  2. Soluble quinoprotein glucose dehydrogenase [50952] (1)
    uperfamily
    1. Soluble quinoprotein glucose dehydrogenase [50953] (1)
  3. Thermostable phytase (3-phytase) [50956] (1)
    uperfamily
    1. Thermostable phytase (3-phytase) [50957] (1)
  4. TolB, C-terminal domain [50960] (1)
    uperfamily
    1. TolB, C-terminal domain [50961] (1)
  5. YWTD domain [63825] (1)
    uperfamily
    1. YWTD domain [63826] (2)
  6. Calcium-dependent phosphotriesterase [63829] (3)
    uperfamily
    1. SGL-like [63830] (3)
    2. Serum paraoxonase/arylesterase 1, PON1 [101895] (1)
    3. All0351-like [159252] (1)
      N-terminal half is PfamB 89298 and C-terminal half is PfamB 80276; includes recent entry 2qe8 (Ava4197)
  7. Tricorn protease N-terminal domain [69304] (1)
    possibly related to the second domain of tricorn protease (a distorted 7-bladed beta-propeller)
    uperfamily
    1. Tricorn protease N-terminal domain [69305] (1)
  8. Fucose-specific lectin [89372] (1)
    uperfamily
    1. Fucose-specific lectin [89373] (1)
  9. NHL repeat [101898] (1)
    uperfamily
    1. NHL repeat [101899] (2)
      Pfam 01436
  10. GyrA/ParC C-terminal domain-like [101904] (1)
    beta-pinwheel, a variant of beta-propeller fold; unlike an canonical beta-propeller, strands 1 and 4 of each four-strand repeat unit are in one blade whereas strands 2 and 3 are in the next blade
    uperfamily
    1. GyrA/ParC C-terminal domain-like [101905] (2)
      Pfam 03989; functional conformational changes result in breaking the interface between the N- and C-terminal blades
  11. Kelch motif [117281] (1)
    uperfamily
    1. Kelch motif [117282] (2)
      Pfam 01344; sequence motif corresponding to one beta-sheet blade; similar sequences are found in the Galactose oxidase 7-bladed beta-propeller domain (scop_pr 50967)
119. 7-bladed beta-propeller [50964] (14)
  consists of seven 4-stranded beta-sheet motifs; meander
  1. Galactose oxidase, central domain [50965] (1)
    uperfamily
    1. Galactose oxidase, central domain [50966] (3)
  2. YVTN repeat-like/Quinoprotein amine dehydrogenase [50969] (3)
    uperfamily
    1. YVTN repeat [82166] (1)
      more regular propeller with clear sequence repeats
    2. Quinohemoprotein amine dehydrogenase B chain [69309] (2)
      less regular propeller with imperfect sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
    3. Methylamine dehydrogenase, H-chain [50970] (2)
      less regular propeller without notable sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
  3. Nitrous oxide reductase, N-terminal domain [50974] (1)
    uperfamily
    1. Nitrous oxide reductase, N-terminal domain [50975] (2)
  4. WD40 repeat-like [50978] (2)
    also contains 8-bladed propellers
    uperfamily
    1. WD40-repeat [50979] (12)
    2. Cell cycle arrest protein BUB3 [110289] (1)
      possibly related to the WD-repeat family; both sequence similarity between the blades and the WD40 repeat signature are very weak
  5. RCC1/BLIP-II [50985] (2)
    two families are clearly related but differ by the number of strands per blade
    uperfamily
    1. Regulator of chromosome condensation RCC1 [50986] (1)
    2. beta-lactamase inhibitor protein-II, BLIP-II [69315] (1)
      lacks the outer strands
  6. Clathrin heavy-chain terminal domain [50989] (1)
    uperfamily
    1. Clathrin heavy-chain terminal domain [50990] (1)
  7. Integrin alpha N-terminal domain [69318] (1)
    uperfamily
    1. Integrin alpha N-terminal domain [69319] (2)
  8. Peptidase/esterase 'gauge' domain [50993] (2)
    uperfamily
    1. Prolyl oligopeptidase, N-terminal domain [50994] (1)
    2. Acylamino-acid-releasing enzyme, N-terminal donain [117286] (1)
  9. Tricorn protease domain 2 [69322] (1)
    distorted 7-bladed beta-propeller fold; possibly related to the N-terminal domain of tricorn protease (a 6-bladed beta-propeller)
    uperfamily
    1. Tricorn protease domain 2 [69323] (1)
  10. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75011] (1)
    uperfamily
    1. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75012] (1)
  11. Putative isomerase YbhE [101908] (1)
    uperfamily
    1. Putative isomerase YbhE [101909] (1)
  12. Sema domain [101912] (1)
    irregular 7-bladed beta-propeller with a large insertion in the fifth blade
    uperfamily
    1. Sema domain [101913] (3)
      Pfam 01403
  13. Oligoxyloglucan reducing end-specific cellobiohydrolase [110296] (1)
    duplication: # two beta-propeller domains are swapped with the N-terminal strands; similar domain arrangment to the Actin interacting protein 1 (scop_pr 89378)
    uperfamily
    1. Oligoxyloglucan reducing end-specific cellobiohydrolase [110297] (1)
      contains at least 9 BNR/Asp-box repeats (Pfam 02012) usually associated with the 6-bladed propeller Neuraminidases (scop_sf 50939)
  14. Nucleoporin domain [117289] (1)
    uperfamily
    1. Nucleoporin domain [117290] (2)
120. 8-bladed beta-propeller [50997] (3)
  consists of eight 4-stranded beta-sheet motifs; meander
  also found in some members of the WD40-repeat superfamily
  1. Quinoprotein alcohol dehydrogenase-like [50998] (1)
    uperfamily
    1. Quinoprotein alcohol dehydrogenase-like [50999] (6)
  2. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51004] (1)
    uperfamily
    1. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51005] (3)
  3. DPP6 N-terminal domain-like [82171] (1)
    uperfamily
    1. DPP6 N-terminal domain-like [82172] (3)
      Pfam 00930
121. Glycosyl hydrolase domain [51010] (1)
  folded sheet; greek-key
  1. Glycosyl hydrolase domain [51011] (5)
    this domain is C-terminal to the catalytic beta/alpha barrel domain
    uperfamily
    1. alpha-Amylases, C-terminal beta-sheet domain [51012] (46)
      this domain follows the catalytic beta/alpha barrel domain
    2. Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 [89388] (6)
      interrupted by the catalytic domain; the C-terminal core is similar to the alpha-amylase domain
    3. Putative alpha-L-fucosidase C-terminal domain [101928] (1)
      glycosyl hydrolase family 29; beta-sheet forms a closed beta-barrel (n=8, S=10)
    4. Putative glucosidase YicI, domain 3 [117298] (1)
    5. Beta-galactosidase LacA, domain 2 [117301] (1)
      contains extra C-terminal beta-sandwich subdomain [greek-key; partial topological similarity to the immunoglobulin-like fold]
122. WW domain-like [51044] (3)
  core: 3-stranded meander beta-sheet
  1. WW domain [51045] (1)
    uperfamily
    1. WW domain [51046] (13)
  2. Carbohydrate binding domain [51055] (1)
    uperfamily
    1. Carbohydrate binding domain [51056] (3)
  3. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101931] (1)
    uperfamily
    1. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101932] (1)
123. Head domain of nucleotide exchange factor GrpE [51063] (1)
  small mixed beta-sheet, 4 "generalized" strands
  1. Head domain of nucleotide exchange factor GrpE [51064] (1)
    uperfamily
    1. Head domain of nucleotide exchange factor GrpE [51065] (1)
124. Coronavirus RNA-binding domain [110303] (1)
  coiled antiparallel beta-sheet of 5 strands, order 51324; complex topology, crossing loops
  1. Coronavirus RNA-binding domain [110304] (1)
    uperfamily
    1. Coronavirus RNA-binding domain [110305] (2)
      N-terminal part of Pfam 00937
125. Ribonuclease domain of colicin E3 [63839] (1)
  twisted meander beta-sheet of 6 strands
  1. Ribonuclease domain of colicin E3 [63840] (1)
    uperfamily
    1. Ribonuclease domain of colicin E3 [63841] (1)
126. NAC domain [101940] (1)
  core: twisted 7-stranded beta-sheet (half-barrel)
  1. NAC domain [101941] (1)
    uperfamily
    1. NAC domain [101942] (1)
      Pfam 02365, NAM; transcription factor domain
127. At5g01610-like [141561] (1)
  contains large meander beta-sheet bent into a scoop-like shape
  1. At5g01610-like [141562] (1)
    uperfamily
    1. At5g01610-like [141563] (1)
      Pfam 04398; DUF538
128. Carbonic anhydrase [51068] (1)
  single sheet; 10 strands
  1. Carbonic anhydrase [51069] (1)
    uperfamily
    1. Carbonic anhydrase [51070] (10)
129. LolA-like prokaryotic lipoproteins and lipoprotein localization factors [89391] (1)
  11 stranded sheet partly folded in a corner-like structure filled with a few short helices
  1. Prokaryotic lipoproteins and lipoprotein localization factors [89392] (3)
    uperfamily
    1. Outer-membrane lipoproteins carrier protein LolA [89393] (1)
    2. Outer membrane lipoprotein receptor LolB [89396] (1)
    3. LppX-like [141566] (1)
      Pfam 07161; DUF1396; contains a large cavity between the 'flattened' beta-sheet and helix-containing loops
130. YmcC-like [159269] (1)
  12-stranded meander beta-sheet, folded into a deformed beta-barrel; topological similarity to the LolA-like fold (scop_cf 89391)
  1. YmcC-like [159270] (1)
    1. YmcC-like [159271] (1)
      PfamB 007600
131. Spiral beta-roll [159274] (1)
  a large 15-stranded beta-sheet rolled about a single helix core; overlapping edges form a sandwich-like structure; topological similarity to the LolA-like fold (scop_cf 89391)
  1. PA1994-like [159275] (1)
    1. PA1994-like [159276] (1)
      Pfam 06475; DUF1089
132. Bacteriochlorophyll A protein [51080] (1)
  single sheet; 16 strands; meander
  1. Bacteriochlorophyll A protein [51081] (1)
    uperfamily
    1. Bacteriochlorophyll A protein [51082] (2)
133. open-sided beta-meander [51086] (2)
  single sheet formed by beta-hairpin repeats; exposed on both sides in the middle
  1. Outer surface protein [51087] (1)
    21 stranded sheet partly folded upon itself at the ends
    uperfamily
    1. Outer surface protein [51088] (2)
  2. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82185] (1)
    11+ stranded sheet partly folded upon itself at the C-end
    uperfamily
    1. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82186] (1)
134. beta-Prism I [51091] (3)
  consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
  duplication: has internal pseudo threefold symmetry
  1. Vitelline membrane outer protein-I (VMO-I) [51092] (1)
    uperfamily
    1. Vitelline membrane outer protein-I (VMO-I) [51093] (1)
  2. delta-Endotoxin (insectocide), middle domain [51096] (1)
    uperfamily
    1. delta-Endotoxin (insectocide), middle domain [51097] (4)
  3. Mannose-binding lectins [51101] (1)
    uperfamily
    1. Mannose-binding lectins [51102] (8)
135. beta-Prism II [51109] (1)
  consists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axis
  duplication: consists of two domains of this fold
  1. alpha-D-mannose-specific plant lectins [51110] (1)
    uperfamily
    1. alpha-D-mannose-specific plant lectins [51111] (6)
136. Single-stranded right-handed beta-helix [51125] (8)
  superhelix turns are made of parallel beta-strands and (short) turns
  1. beta-Roll [51120] (1)
    superhelix turns are made of two short strands each
    uperfamily
    1. Serralysin-like metalloprotease, C-terminal domain [51121] (4)
      duplication: halfturs of beta-helix are sequence and structural repeats; binds calcium ions between the turns
  2. Pectin lyase-like [51126] (11)
    superhelix turns are made of 3 strands each
    uperfamily
    1. Pectate lyase-like [51127] (6)
    2. Pectin lyase [51133] (2)
    3. Galacturonase [51137] (7)
    4. Chondroitinase B [51144] (1)
    5. iota-carrageenase [69333] (1)
    6. Pectate transeliminase [101951] (1)
    7. Dextranase, catalytic domain [101954] (1)
    8. Pectin methylesterase [51147] (2)
    9. P22 tailspike protein [51150] (1)
    10. Virulence factor P.69 pertactin [51153] (1)
    11. Filamentous hemagglutinin FhaB, secretion domain [101957] (1)
  3. Insect cysteine-rich antifreeze protein [51156] (1)
    superhelix turns are made of two short strands each
    uperfamily
    1. Insect cysteine-rich antifreeze protein [51157] (1)
  4. Cell-division inhibitor MinC, C-terminal domain [63848] (1)
    superhelix turns are made of three short strands each
    uperfamily
    1. Cell-division inhibitor MinC, C-terminal domain [63849] (1)
  5. Alpha subunit of glutamate synthase, C-terminal domain [69336] (1)
    uperfamily
    1. Alpha subunit of glutamate synthase, C-terminal domain [69337] (2)
  6. C-terminal domain of adenylylcyclase associated protein [69340] (1)
    superhelix turns are made of two strands each
    uperfamily
    1. C-terminal domain of adenylylcyclase associated protein [69341] (2)
  7. Stabilizer of iron transporter SufD [101960] (1)
    superhelix turns are made of two very long strands each
    uperfamily
    1. Stabilizer of iron transporter SufD [101961] (1)
  8. Pentapeptide repeat-like [141571] (1)
    superhelix turns are made of four short strands each; duplication: the sequence pentapeptide repeats correspond to individual strands
    uperfamily
    1. Pentapeptide repeats [141572] (3)
      Pfam 00805 (covers eight repeats or two full superhelical turns)
137. Single-stranded left-handed beta-helix [51160] (4)
  superhelix turns are made of parallel beta-strands and (short) turns
  1. Trimeric LpxA-like enzymes [51161] (8)
    superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands
    uperfamily
    1. UDP N-acetylglucosamine acyltransferase [51162] (2)
    2. Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [51165] (1)
      contains extra N-terminal 3-helical domain
    3. Galactoside acetyltransferase-like [51168] (4)
    4. GlmU C-terminal domain-like [51171] (4)
    5. gamma-carbonic anhydrase-like [51174] (3)
      archaeal hexapeptide repeat proteins
    6. Serine acetyltransferase [110309] (2)
    7. YdcK-like [141583] (1)
      part of Pfam 00132
    8. PglD-like [159280] (1)
      contains extra N-terminal alpha/beta subdomain
  2. An insect antifreeze protein [51177] (1)
    superhelical turns are made of three short strands
    uperfamily
    1. An insect antifreeze protein [51178] (2)
  3. Adhesin YadA, collagen-binding domain [101967] (1)
    superhelical turns are made of two short strands
    uperfamily
    1. Adhesin YadA, collagen-binding domain [101968] (1)
  4. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159283] (1)
    probable rudiment form of the LpxA-like hexapeptide domain
    1. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159284] (1)
      corresponds to the N-terminal part of Pfam 01050, but does not extend to the conserved functional motif; the predicted cupin fold may reside in the rest of the Pfam domain
138. Double-stranded beta-helix [51181] (7)
  one turn of helix is made by two pairs of antiparallel strands linked with short turns
  has appearance of a sandwich of distinct architecture and jelly-roll topology
  1. RmlC-like cupins [51182] (24)
    uperfamily
    1. dTDP-sugar isomerase [51183] (9)
    2. Glucose-6-phosphate isomerase, GPI [89403] (2)
    3. Hypothetical protein TM1112 [89406] (1)
    4. TM1287-like [89409] (4)
    5. TM1459-like [101976] (2)
    6. Germin/Seed storage 7S protein [51187] (9)
    7. YlbA-like [101979] (4)
      Pfam 05899; formerly pfam06038; duplication: consists of two germin-like domains
    8. Pirin-like [101984] (2)
      Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    9. Quercetin 2,3-dioxygenase-like [75035] (2)
      Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    10. Type I phosphomannose isomerase [51191] (3)
      Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    11. Homogentisate dioxygenase [51194] (1)
      Share a common two-domain fold with the 7S protein; there is a metal-binding site in the C-terminal domain similar to the metal-binding site of germin
    12. Acireductone dioxygenase [82191] (2)
    13. KduI-like [110318] (2)
      Pfam 04962: duplication: consists of two germin-like domains
    14. Ureidoglycolate hydrolase AllA [117312] (3)
      Pfam 04115; beta-hairpin-swapped dimeric protein of the germin-like fold
    15. Probable transcriptional regulator VC1968, C-terminal domain [117315] (1)
    16. YML079-like [117318] (3)
      Pfam 06172; DUF985
    17. PA5104-like [141609] (1)
      Pfam 05962; DUF886; duplication: consists of two germin-like domains; overall structural similarity to the YlbA-like family (scop_fa 101979) except a deletion in the interdomain linker region
    18. MJ0764-like [141612] (1)
    19. Cysteine dioxygenase type I [141615] (4)
      Pfam 05995, CDO_I
    20. 3-hydroxyanthranilic acid dioxygenase-like [141618] (2)
      Pfam 06052; 3-HAO
    21. Acetylacetone-cleaving enzyme-like [159293] (1)
      PfamB 026844
    22. VPA0057-like [159296] (1)
      Pfam 06865; DUF1255; non-canonical dimerisation mode
    23. Gentisate 1,2-dioxygenase-like [159299] (3)
      Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin; homotetramer
    24. EutQ-like [159304] (1)
      Pfam 06249
  2. Clavaminate synthase-like [51197] (13)
    Iron and ketoglutarate-dependent enzymes; elaborated version of this common fold
    uperfamily
    1. Penicillin synthase-like [51198] (4)
      common fold is rather distorted
    2. Clavaminate synthase [51203] (1)
    3. Gab protein (hypothetical protein YgaT) [63855] (1)
    4. YhcH-like [89413] (1)
    5. Type II Proline 3-hydroxylase (proline oxidase) [63858] (1)
    6. TauD/TfdA-like [75038] (2)
    7. gamma-Butyrobetaine hydroxylase [89416] (2)
      Pfam 03322
    8. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82194] (1)
    9. PhyH-like [141623] (2)
      Pfam 05721
    10. AlkB-like [141628] (2)
    11. Asparaginyl hydroxylase-like [141633] (1)
      Pfam 08007
    12. YbiU-like [141636] (1)
      Pfam 07350; DUF1479
    13. TehB-like [159307] (2)
      Pfam 09313; DUF1971
  3. cAMP-binding domain-like [51206] (3)
    uperfamily
    1. CO-sensing protein CooA, N-terminal domain [51207] (1)
      heme-binding domain
    2. Listeriolysin regulatory protein PrfA, N-terminal domain [89419] (1)
    3. cAMP-binding domain [51210] (14)
      Pfam 00027
  4. Regulatory protein AraC [51215] (1)
    uperfamily
    1. Regulatory protein AraC [51216] (1)
  5. Thiamin pyrophosphokinase, substrate-binding domain [63862] (1)
    uperfamily
    1. Thiamin pyrophosphokinase, substrate-binding domain [63863] (2)
  6. Calcium ATPase, transduction domain A [81653] (1)
    a distorted variant of double-helix
    uperfamily
    1. Calcium ATPase, transduction domain A [81652] (1)
  7. TRAP-like [51219] (2)
    shorter variant of double-helix; assembles in large ring-like structures containing from 9 to 11 domains
    uperfamily
    1. Trp RNA-binding attenuation protein (TRAP) [51220] (2)
      oligomeric ring consists of 11 single-domain subunits
    2. PA3696/SPS0176-like [101995] (2)
      duplication: there are three structural repeats per subunit; nine domains per ring-like trimer
139. Triple-stranded beta-helix [69348] (1)
  (homo)trimer; each chain donates 3 beta-strands per turn of the helix
  1. Phage fibre proteins [69349] (5)
    uperfamily
    1. Middle part of short tail fibre protein gp12 [69350] (1)
    2. Tail-associated lysozyme gp5, C-terminal domain [69353] (1)
    3. Endo-alpha-sialidase [117325] (1)
    4. Lactophage receptor-binding protein domain [141647] (2)
    5. HylP-like [159317] (1)
      Pfam 07212
140. Triple beta-spiral [51224] (1)
  trimer formed by the interlocking beta-hairpin repeat units
  1. Fibre shaft of virus attachment proteins [51225] (2)
    uperfamily
    1. Adenovirus [51226] (1)
    2. Reovirus attachment protein sigma 1 [69356] (1)
141. Trimeric adhesin [101998] (1)
  trimer; contains two different beta-prism-like domains connected by an linker subdomain of less regular structure
  1. Trimeric adhesin [101999] (1)
    uperfamily
    1. Trimeric adhesin [102000] (1)
142. beta-hairpin stack [69359] (1)
  Trp-rich beta-hairpin repeat units form helical structures of 3 units per turn
  1. Cell wall binding repeat [69360] (1)
    uperfamily
    1. Cell wall binding repeat [69361] (3)
143. Barrel-sandwich hybrid [51229] (4)
  sandwich of half-barrel shaped beta-sheets
  1. Single hybrid motif [51230] (1)
    7 to 8 strands in 2 beta-sheets
    uperfamily
    1. Biotinyl/lipoyl-carrier proteins and domains [51231] (13)
  2. Rudiment single hybrid motif [51246] (2)
    uperfamily
    1. BC C-terminal domain-like [51247] (7)
      probable rudiment form of the biotinyl-carrier domain
    2. Cytochrome f, small domain [51256] (5)
  3. Duplicated hybrid motif [51261] (2)
    half-barrel sheet of 8 strands sandwiched with two 3-stranded sheets
    uperfamily
    1. Glucose permease-like [51262] (3)
    2. Peptidoglycan hydrolase LytM [102006] (1)
      Peptidase family M23; contains extra N-terminal, non-conserved beta-sheet subdomain
  4. Ribosomal L27 protein-like [110324] (2)
    rudiment single hybrid fold with a permuted topology
    uperfamily
    1. Ribosomal L27 protein [110325] (3)
      Pfam 01016
    2. ECR1 N-terminal domain-like [159324] (5)
      ECR1 - Exosome complex RNA-binding protein 1
144. beta-clip [51268] (7)
  double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
  1. AFP III-like domain [51269] (1)
    duplication: consists of two structural repeats related by pseudo dyad
    uperfamily
    1. AFP III-like domain [51270] (5)
      Pfam 01354
  2. SET domain [82199] (3)
    duplication: the core is composed of two structural repeats similar to (circularly permuted) repeats of AFPIII
    also contains a substrate-binding alpha+beta subdomain inserted in the core
    uperfamily
    1. Histone lysine methyltransferases [82200] (3)
      contains metal-binding preSET and postSET domains
    2. Viral histone H3 Lysine 27 Methyltransferase [82207] (1)
      consists of SET domain only; dimeric
    3. RuBisCo LSMT catalytic domain [82210] (1)
  3. Head decoration protein D (gpD, major capsid protein D) [51274] (1)
    uperfamily
    1. Head decoration protein D (gpD, major capsid protein D) [51275] (2)
  4. Urease, beta-subunit [51278] (1)
    uperfamily
    1. Urease, beta-subunit [51279] (3)
  5. MoeA C-terminal domain-like [63867] (1)
    uperfamily
    1. MoeA C-terminal domain-like [63868] (5)
  6. dUTPase-like [51283] (1)
    forms tight trimer through an additional beta-sheet in each subunit
    subunit beta-sheets are orthogonally packed around the three-fold axis
    uperfamily
    1. dUTPase-like [51284] (9)
  7. Tlp20, baculovirus telokin-like protein [51289] (1)
    similar to dUTPase in fold and trimeric assembly
    uperfamily
    1. Tlp20, baculovirus telokin-like protein [51290] (1)
145. PheT/TilS domain [56036] (1)
  core: 3 layers; contains beta-sandwich of unusual topology
  1. PheT/TilS domain [56037] (2)
    contains putative tRNA-binding structural motif
    uperfamily
    1. tRNA-Ile-lysidine synthetase, TilS, C-terminal domain [116720] (1)
      PfamB 001050
    2. B3/B4 domain of PheRS, PheT [56038] (1)
      Pfam 03483; decorated with additional structures
146. C-terminal autoproteolytic domain of nucleoporin nup98 [82214] (1)
  multisheet protein with a mixture of beta-sandwich and beta-prism features
  1. C-terminal autoproteolytic domain of nucleoporin nup98 [82215] (1)
    uperfamily
    1. C-terminal autoproteolytic domain of nucleoporin nup98 [82216] (1)
147. Pseudo beta-prism [141657] (1)
  beta-sandwich with one regular beta-sheet and the other beta-sheet bent in the middle with a set of aligned beta-bulges
  1. Bacteriophage trimeric proteins domain [141658] (2)
    found in phage proteins that form trimers, but is not involved in the trimerisation
    uperfamily
    1. Mtd domain-like [141659] (1)
    2. Lactophage receptor-binding protein N-terminal domain [141662] (1)
148. SARS ORF9b-like [141665] (1)
  complex dimeric fold with three intersubunit beta-sheets packed around a single core
  1. 'SARS ORF9b-like [141666] (1)
    uperfamily
    1. SARS ORF9b-like [141667] (1)
      PfamB 005852
149. Adsorption protein p2 [89427] (1)
  multisheet protein containing partial beta-propeller and beta-sandwich regions
  1. Adsorption protein p2 [89428] (1)
    uperfamily
    1. Adsorption protein p2 [89429] (1)
150. Baseplate structural protein gp8 [89432] (1)
  multisheet protein with a mixture of beta-sandwich and beta-barrel features
  1. Baseplate structural protein gp8 [89433] (1)
    uperfamily
    1. Baseplate structural protein gp8 [89434] (1)
151. Hedgehog/intein (Hint) domain [51293] (1)
  complex fold made of five beta-hairpin units and a b-ribbon arc
  1. Hedgehog/intein (Hint) domain [51294] (2)
    duplication: contains two intertwined structural repeats
    uperfamily
    1. Hedgehog C-terminal (Hog) autoprocessing domain [51295] (1)
    2. Intein (protein splicing domain) [51298] (4)
152. LexA/Signal peptidase [51305] (1)
  complex fold made of several coiled beta-sheets; contains an SH3-like barrel
  1. LexA/Signal peptidase [51306] (2)
    uperfamily
    1. LexA-related [51307] (3)
    2. Type 1 signal peptidase [51312] (1)
      contains additional all-beta subdomain inserted in the superfamily fold
153. Cloacin translocation domain [69368] (1)
  complex fold made of several coiled beta-sheets
  1. Cloacin translocation domain [69369] (1)
    uperfamily
    1. Cloacin translocation domain [69370] (2)
      Pfam 03515
154. Mss4-like [51315] (1)
  complex fold made of several coiled beta-sheets
  1. Mss4-like [51316] (4)
    duplication: tandem repeat of two similar structural motifs
    uperfamily
    1. RabGEF Mss4 [51317] (2)
      contains zinc-binding site
    2. Translationally controlled tumor protein TCTP (histamine-releasing factor) [63873] (3)
      contains an insertion of alpha helical hairpin; lacks zinc-binding site
    3. SelR domain [75041] (2)
    4. Glutathione-dependent formaldehyde-activating enzyme, Gfa [117338] (1)
      Pfam 04828; DUF636
155. Cyanovirin-N [51321] (1)
  complex fold
  1. Cyanovirin-N [51322] (1)
    duplication: tandem repeat of two homologous motifs made three stranded beta-sheet and beta-hairpins
    uperfamily
    1. Cyanovirin-N [51323] (1)
156. Tp47 lipoprotein, N-terminal domain [82219] (1)
  complex fold; consists of two intertwined subdomains
  1. Tp47 lipoprotein, N-terminal domain [82220] (1)
    uperfamily
    1. Tp47 lipoprotein, N-terminal domain [82221] (1)
157. Methuselah ectodomain [63876] (1)
  complex fold
  1. Methuselah ectodomain [63877] (1)
    duplication: contains two similar sub domains connected by a structured linker
    uperfamily
    1. Methuselah ectodomain [63878] (1)
158. Head-binding domain of phage P22 tailspike protein [51326] (1)
  complex fold made of bifurcated and partly folded beta-sheet
  1. Head-binding domain of phage P22 tailspike protein [51327] (1)
    uperfamily
    1. Head-binding domain of phage P22 tailspike protein [51328] (1)
159. E2 regulatory, transactivation domain [51331] (1)
  complex fold made of bifurcated and coiled beta-sheets
  1. E2 regulatory, transactivation domain [51332] (1)
    uperfamily
    1. E2 regulatory, transactivation domain [51333] (3)
160. MoeA N-terminal region -like [63881] (1)
  complex fold made of bifurcated and coiled b-sheets
  1. MoeA N-terminal region -like [63882] (1)
    uperfamily
    1. MoeA N-terminal region -like [63883] (5)
161. MOSC N-terminal domain-like [141672] (1)
  complex fold; comprises a beta-hairpin and a meander 3-stranded sheet packed against beta-barrel: closed, n=5, S=8; contains three short helices
  1. MOSC N-terminal domain-like [141673] (1)
    uperfamily
    1. MOSC N-terminal domain-like [141674] (1)
      Pfam 03476
162. MAL13P1.257-like [141677] (1)
  complex fold; duplication: consists of two intertwinned structural repeats related by pseudo dyad
  1. MAL13P1.257-like [141678] (1)
    uperfamily
    1. MAL13P1.257-like [141679] (1)
      PANTHER 12857; DUF866_euk
163. Composite domain of metallo-dependent hydrolases [51337] (1)
  pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
  1. Composite domain of metallo-dependent hydrolases [51338] (11)
    this domain is interrupted by the catalytic beta/alpha barrel domain
    uperfamily
    1. Cytosine deaminase [69373] (1)
    2. alpha-Subunit of urease [51339] (3)
    3. Hydantoinase (dihydropyrimidinase) [75044] (9)
    4. SAH/MTA deaminase-like [82224] (5)
    5. Isoaspartyl dipeptidase [89438] (1)
    6. N-acetylglucosamine-6-phosphate deacetylase, NagA [82227] (3)
    7. D-aminoacylase [82230] (1)
    8. Adenine deaminase [141689] (1)
    9. Zn-dependent arginine carboxypeptidase-like [159340] (3)
    10. Imidazolonepropionase-like [159347] (4)
    11. DR0824-like [159355] (1)
164. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51343] (1)
  pseudobarrel: sandwich of two sheets packed at a positive interstrand angle and interconnected with many short turns
  1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51344] (1)
    uperfamily
    1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51345] (2)
165. N-terminal domain of MutM-like DNA repair proteins [81625] (1)
  pseudobarrel; capped on both ends by alpha-helices
  1. N-terminal domain of MutM-like DNA repair proteins [81624] (1)
    uperfamily
    1. N-terminal domain of MutM-like DNA repair proteins [81623] (6)
166. Hypothetical protein YojF [89441] (1)
  pseudobarrel; capped at one end by an alpha-helix
  1. Hypothetical protein YojF [89442] (1)
    uperfamily
    1. Hypothetical protein YojF [89443] (1)
167. DNA-binding pseudobarrel domain [101935] (1)
  core: barrel, open; n=7, S*=10; capped with helices at both ends; partial similarity to the AbrB/MazE/MraZ-like fold (scop_cf 89446)
  1. DNA-binding pseudobarrel domain [101936] (2)
    uperfamily
    1. Type II restriction endonuclease effector domain [101937] (1)
    2. B3 DNA binding domain [117343] (2)
      Pfam 02362
168. Double-split beta-barrel [89446] (2)
  pseudobarrel; capped on both ends by alpha-helices
  1. AbrB/MazE/MraZ-like [89447] (3)
    members of this superfamily are known or predicted to have DNA-binding function
    uperfamily
    1. Kis/PemI addiction antidote [89448] (1)
      forms intertwined homodimer
    2. AbrB N-terminal domain-like [54743] (2)
      dimeric fold similar to MazE; the DNA-binding site is similar to the conserved surface site of MraZ
    3. Hypothetical protein MraZ [102020] (1)
      duplication: contains two interlocking repeats of similar sequence arranged as subunits in the MazE homodimer
  2. AF2212/PG0164-like [141694] (2)
    six-stranded barrel, topologically similar to the Reductase/isomerase/elongation factor domain fold (scop_cf 50412)
    uperfamily
    1. PG0164-like [141695] (1)
      duplication: comprises two intertwinned beta(2)-alpha-beta structural repeats
    2. AF2212-like [159360] (1)
      Pfam 01954; DUF104; intertwinned homodimer of beta(2)-loop-beta subunits; the capping helices are replaced with extended loops
169. PUA domain-like [88696] (1)
  pseudobarrel; mixed folded sheet of 5 strands; order 13452; strand 1 and 3 are parallel to each other
  1. PUA domain-like [88697] (13)
    uperfamily
    1. PUA domain [88698] (10)
      RNA-binding domain
    2. ATP sulfurylase N-terminal domain [63801] (5)
      contains extra structures; some similarity to the PK beta-barrel domain
    3. YggJ N-terminal domain-like [89451] (3)
    4. Hypothetical protein EF3133 [110339] (1)
      Pfam 06171; DUF984
    5. Hypothetical protein TTHA0113 [117348] (1)
      Pfam 04266; DUF437
    6. ProFAR isomerase associated domain [117351] (2)
      Pfam 07060; DUF1530
    7. yqfB-like [117356] (1)
      Pfam 06164; DUF978
    8. Atu2648/PH1033-like [141703] (6)
      Pfam 01878; DUF55
    9. Hypothetical RNA methyltransferase domain (HRMD) [141716] (3)
      N-terminal part of Pfam 03602, structurally similar to PUA domain family
    10. LON domain-like [141723] (2)
      Pfam 02190
    11. PrgU-like [159365] (1)
      Pfam 09627
    12. SRA domain-like [159368] (2)
      Pfam 02182; recognizes the modified cytosine base (m5C) by flipping it out of DNA
    13. YtmB-like [159372] (1)
      PfamB 020780
170. AXH domain [102030] (1)
  pseudobarrel; some similarity to OB-fold
  1. AXH domain [102031] (1)
    uperfamily
    1. AXH domain [102032] (1)
171. FimD N-terminal domain-like [141728] (1)
  pseudo barrel, capped by an alpha-helix; some topological similarity to the PRC-barrel domain (scop_sf 50346) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
  1. FimD N-terminal domain-like [141729] (1)
    uperfamily
    1. Usher N-domain [141730] (1)
      N-terminal part of Pfam 00577
172. HisI-like [141733] (1)
  pseudo barrel, capped by an alpha-helix; contains a beta-triangle structure on one side; some topological similarity to the Ribosomal protein L25-like fold (scop_cf 50714) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
  1. HisI-like [141734] (1)
    uperfamily
    1. HisI-like [141735] (1)
      Pfam 01502; PRA-CH; metalloenzyme, probable biological unit is dimeric
173. MFPT repeat-like [141738] (1)
  consists of two similar pseudo barrel subdomains with structural similarity to a circularly permuted SAND domain (scop_fa 63764)
  1. MFPT repeat-like [141739] (1)
    uperfamily
    1. MFPT repeat [141740] (2)
      PfamB 008194
174. P-domain of calnexin/calreticulin [63886] (1)
  non-globular proline-rich hairpin
  1. P-domain of calnexin/calreticulin [63887] (1)
    uperfamily
    1. P-domain of calnexin/calreticulin [63888] (2)
Alpha and beta proteins (a/b) [51349] (147)
Mainly parallel beta sheets (beta-alpha-beta units)
1. TIM beta/alpha-barrel [51350] (33)
  contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
  the first seven superfamilies have similar phosphate-binding sites
  1. Triosephosphate isomerase (TIM) [51351] (1)
    uperfamily
    1. Triosephosphate isomerase (TIM) [51352] (18)
  2. Ribulose-phoshate binding barrel [51366] (6)
    uperfamily
    1. Histidine biosynthesis enzymes [51367] (6)
      structural evidence for the gene duplication within the barrel fold
    2. D-ribulose-5-phosphate 3-epimerase [51372] (5)
    3. Decarboxylase [51375] (13)
    4. Tryptophan biosynthesis enzymes [51381] (12)
    5. NanE-like [117362] (2)
      Pfam 04131
    6. PdxS-like [141755] (1)
      Pfam 01680; SOR/SNZ
  3. Thiamin phosphate synthase [51391] (1)
    uperfamily
    1. Thiamin phosphate synthase [51392] (2)
  4. Pyridoxine 5'-phosphate synthase [63892] (1)
    uperfamily
    1. Pyridoxine 5'-phosphate synthase [63893] (1)
  5. FMN-linked oxidoreductases [51395] (1)
    uperfamily
    1. FMN-linked oxidoreductases [51396] (30)
  6. Inosine monophosphate dehydrogenase (IMPDH) [51412] (1)
    The phosphate moiety of substrate binds in the 'common' phosphate-binding site
    uperfamily
    1. Inosine monophosphate dehydrogenase (IMPDH) [51413] (8)
  7. PLP-binding barrel [51419] (2)
    circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
    uperfamily
    1. Alanine racemase-like, N-terminal domain [51420] (9)
    2. "Hypothetical" protein ybl036c [51427] (1)
  8. NAD(P)-linked oxidoreductase [51430] (1)
    uperfamily
    1. Aldo-keto reductases (NADP) [51431] (20)
      Common fold covers whole protein structure
  9. (Trans)glycosidases [51445] (14)
    uperfamily
    1. Amylase, catalytic domain [51446] (54)
      members of the family may contain various insert subdomains
      in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain
    2. beta-glycanases [51487] (54)
      consist of a number of sequence families
    3. Putative alpha-L-fucosidase, catalytic domain [102079] (1)
      glycosyl hydrolase family 29; contains additional beta-barrel with a topological similarity to the C-terminal domain of alpha amylases
    4. Family 1 of glycosyl hydrolase [51521] (15)
    5. Type II chitinase [51534] (22)
      glycosylase family 18
    6. 1,4-beta-N-acetylmuraminidase [63912] (3)
      Glycosyl hydrolase family 25; probably have evolved from a type II chitinase ancestor
      permutation of the common fold; strand 8 is antiparallel to the rest of the barrel
    7. beta-N-acetylhexosaminidase catalytic domain [51550] (5)
      Glycosyl hydrolase family 20, GH20
    8. alpha-D-glucuronidase/Hyaluronidase catalytic domain [82253] (4)
      Glycosyl hydrolase family 67, GH67; structurally related to GH20; contains extra C-terminal alpha-helical subdomain
    9. NagZ-like [51553] (2)
      Pfam 00933; Glycosyl hydrolase family 3 domain
    10. Bee venom hyaluronidase [69387] (1)
      distorted barrel lacks the second strand
    11. Outer surface protein, N-terminal domain [110354] (1)
      corresponds to the N-terminal part of Pfam 05913
    12. YicI catalytic domain-like [117372] (2)
    13. Glycosyl hydrolases family 35 catalytic domain [117375] (1)
      Pfam 01301
    14. TM1410-like [141796] (1)
      Pfam 03537
  10. Metallo-dependent hydrolases [51556] (18)
    the beta-sheet barrel is similarly distorted and capped by a C-terminal helix
    has transition metal ions bound inside the barrel
    uperfamily
    1. Adenosine/AMP deaminase [51557] (4)
    2. Dihydroorotase [63917] (1)
    3. Cytosine deaminase catalytic domain [69390] (1)
    4. alpha-subunit of urease, catalytic domain [51560] (3)
    5. Hydantoinase (dihydropyrimidinase), catalytic domain [75073] (9)
    6. SAH/MTA deaminase-like [82258] (5)
    7. Isoaspartyl dipeptidase, catalytic domain [89489] (1)
    8. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82261] (3)
    9. D-aminoacylase, catalytic domain [82264] (1)
    10. TatD Mg-dependent DNase-like [82267] (4)
    11. Phosphotriesterase-like [51564] (4)
    12. Renal dipeptidase [75079] (1)
    13. Uronate isomerase-like [75082] (2)
      contains all-alpha subdomain inserted after the first strand
    14. Adenine deaminase-like [141816] (1)
    15. PP1699/LP2961-like [141819] (5)
      Pfam 04909; Amidohydrolase; stand-alone domain
    16. DR0824-like [159397] (1)
    17. Imidazolonepropionase-like [159400] (4)
    18. Zn-dependent arginine carboxypeptidase-like [159408] (3)
  11. Aldolase [51569] (8)
    Common fold covers whole protein structure
    uperfamily
    1. Class I aldolase [51570] (37)
      the catalytic lysine forms schiff-base intermediate with substrate
      possible link between the aldolase superfamily and the phosphate-binding beta/alpha barrels
    2. Class II FBP aldolase [51591] (3)
      metal-dependent
    3. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51594] (5)
      hybrid of classes I and II aldolase
    4. Class I DAHP synthetase [51599] (6)
    5. HMGL-like [89494] (3)
      Pfam 00682
    6. NeuB-like [110368] (2)
      Pfam 03102
    7. GatZ-like [141837] (1)
      Pfam 08013
    8. Class-II DAHP synthetase [141840] (1)
      Pfam 01474
  12. Enolase C-terminal domain-like [51604] (2)
    binds metal ion (magnesium or manganese) in conserved site inside barrel
    N-terminal alpha+beta domain is common to this superfamily
    uperfamily
    1. Enolase [51605] (8)
    2. D-glucarate dehydratase-like [51609] (20)
  13. Phosphoenolpyruvate/pyruvate domain [51621] (7)
    uperfamily
    1. Pyruvate kinase [51622] (6)
    2. Pyruvate phosphate dikinase, C-terminal domain [51629] (3)
    3. Phosphoenolpyruvate carboxylase [51632] (1)
    4. Phosphoenolpyruvate mutase/Isocitrate lyase-like [88704] (6)
      forms a swapped dimer
    5. HpcH/HpaI aldolase [51638] (4)
      forms a swapped dimer; contains a PK-type metal-binding site
    6. Ketopantoate hydroxymethyltransferase PanB [89503] (3)
    7. Mll9387-like [159416] (1)
      Pfam 09370; TIM-barrel signal transduction protein; forms a swapped dimer similar to the Phosphoenolpyruvate mutase/Isocitrate lyase-like and HpcH/HpaI aldolase families
  14. Malate synthase G [51645] (1)
    uperfamily
    1. Malate synthase G [51646] (2)
  15. RuBisCo, C-terminal domain [51649] (1)
    uperfamily
    1. RuBisCo, large subunit, C-terminal domain [51650] (12)
      N-terminal domain is alpha+beta
  16. Xylose isomerase-like [51658] (7)
    different families share similar but non-identical metal-binding sites
    uperfamily
    1. Endonuclease IV [51659] (2)
    2. IolI-like [75090] (3)
    3. Hypothetical protein YgbM (EC1530) [75093] (1)
    4. L-rhamnose isomerase [51662] (1)
    5. Xylose isomerase [51665] (12)
    6. UxuA-like [110377] (1)
      Pfam 03786
    7. KguE-like [141854] (1)
      part of Pfam 01261
  17. Bacterial luciferase-like [51679] (4)
    consists of clearly related families of somewhat different folds
    uperfamily
    1. Bacterial luciferase (alkanal monooxygenase) [51680] (2)
      typical (beta/alpha)8-barrel fold
      heterodimer of two similar chains
    2. Non-fluorescent flavoprotein (luxF, FP390) [51683] (2)
      incomplete beta/alpha barrel with mixed beta-sheet of 7 strands
    3. F420 dependent oxidoreductases [51687] (3)
    4. Ssud-like monoxygenases [82275] (2)
  18. Nicotinate/Quinolinate PRTase C-terminal domain-like [51690] (2)
    incomplete beta/alpha barrel with parallel beta-sheet of 7 strands
    uperfamily
    1. NadC C-terminal domain-like [51691] (6)
    2. Monomeric nicotinate phosphoribosyltransferase C-terminal domain [110910] (3)
  19. PLC-like phosphodiesterases [51695] (3)
    uperfamily
    1. Mammalian PLC [51696] (2)
    2. Bacterial PLC [51699] (2)
    3. Glycerophosphoryl diester phosphodiesterase [89508] (4)
      Pfam 03009
  20. Cobalamin (vitamin B12)-dependent enzymes [51703] (4)
    uperfamily
    1. Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [51704] (2)
      the subunits are clearly related but only one (alpha) is active
    2. Glutamate mutase, large subunit [51707] (1)
    3. Diol dehydratase, alpha subunit [51710] (2)
    4. D-lysine 5,6-aminomutase alpha subunit, KamD [117392] (1)
      most similar to the glutamate mutase subunit; contains second cofactor, PLP
  21. tRNA-guanine transglycosylase [51713] (1)
    uperfamily
    1. tRNA-guanine transglycosylase [51714] (2)
  22. Dihydropteroate synthetase-like [51717] (2)
    uperfamily
    1. Dihydropteroate synthetase [51718] (4)
    2. Methyltetrahydrofolate-utiluzing methyltransferases [51723] (2)
  23. UROD/MetE-like [51726] (2)
    uperfamily
    1. Uroporphyrinogen decarboxylase, UROD [51727] (2)
    2. Cobalamin-independent methionine synthase [110384] (1)
      Pfam 01717; duplication; consists of two related domains
  24. FAD-linked oxidoreductase [51730] (2)
    distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation
    uperfamily
    1. Methylenetetrahydrofolate reductase [51731] (2)
    2. Proline dehydrohenase domain of bifunctional PutA protein [82279] (1)
  25. Monomethylamine methyltransferase MtmB [75098] (1)
    uperfamily
    1. Monomethylamine methyltransferase MtmB [75099] (1)
  26. Homocysteine S-methyltransferase [82282] (1)
    uperfamily
    1. Homocysteine S-methyltransferase [82283] (3)
      Pfam 02574
  27. (2r)-phospho-3-sulfolactate synthase ComA [102110] (1)
    uperfamily
    1. (2r)-phospho-3-sulfolactate synthase ComA [102111] (2)
  28. Radical SAM enzymes [102114] (3)
    common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel
    uperfamily
    1. Biotin synthase [102115] (1)
      regular (beta/alpha)8 barrel
    2. Oxygen-independent coproporphyrinogen III oxidase HemN [102118] (1)
      open beta/alpha barrel decorated with additional structures
    3. MoCo biosynthesis proteins [110388] (1)
      open alpha/beta-barrel with a specific second FeS cluster-binding region corresponding to Pfam 06463
  29. GlpP-like [110391] (1)
    uperfamily
    1. GlpP-like [110392] (1)
      Pfam 04309
  30. CutC-like [110395] (1)
    uperfamily
    1. CutC-like [110396] (1)
      Pfam 03932
  31. ThiG-like [110399] (1)
    shares the common phosphate-binding site with other superfamilies
    uperfamily
    1. ThiG-like [110400] (2)
      Pfam 05690
  32. TM1631-like [117396] (1)
    uperfamily
    1. TM1631-like [117397] (2)
      Pfam 01904; DUF72
  33. EAL domain-like [141868] (1)
    variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest
    uperfamily
    1. EAL domain [141869] (1)
      Pfam 00563
2. NAD(P)-binding Rossmann-fold domains [51734] (1)
  core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
  The nucleotide-binding modes of this and the next two folds/superfamilies are similar
  1. NAD(P)-binding Rossmann-fold domains [51735] (12)
    uperfamily
    1. Alcohol dehydrogenase-like, C-terminal domain [51736] (28)
      N-terminal all-beta domain defines family
    2. Tyrosine-dependent oxidoreductases [51751] (108)
      also known as short-chain dehydrogenases and SDR family
      parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7
    3. Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain [51800] (52)
      family members also share a common alpha+beta fold in C-terminal domain
    4. Formate/glycerate dehydrogenases, NAD-domain [51830] (14)
      this domain interrupts the other domain which defines family
    5. Siroheme synthase N-terminal domain-like [75110] (2)
    6. LDH N-terminal domain-like [51848] (33)
    7. 6-phosphogluconate dehydrogenase-like, N-terminal domain [51868] (26)
      the beta-sheet is extended to 8 strands, order 32145678; strands 7 & 8 are antiparallel to the rest
      C-terminal domains also show some similarity
    8. Aminoacid dehydrogenase-like, C-terminal domain [51883] (24)
      extra N-terminal helix displaces the C-terminal helix (following strand 6) from its usual position creating a family nicotineamide-binding site
    9. Potassium channel NAD-binding domain [63944] (4)
    10. Transcriptional repressor Rex, C-terminal domain [102174] (1)
    11. CoA-binding domain [51900] (7)
    12. Ornithine cyclodeaminase-like [110436] (2)
      Pfam 02423; contains additional alpha+beta dimerisation subdomain mostly formed by the N-terminal meander beta-sheet
3. FAD/NAD(P)-binding domain [51904] (1)
  core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
  1. FAD/NAD(P)-binding domain [51905] (8)
    uperfamily
    1. C-terminal domain of adrenodoxin reductase-like [51906] (5)
    2. FAD-linked reductases, N-terminal domain [51913] (25)
      C-terminal domain is alpha+beta is common for the family
    3. GDI-like N domain [51931] (3)
      Similar to FAD-linked reductases in both domains but does not bind FAD
    4. Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain [51934] (7)
    5. FAD/NAD-linked reductases, N-terminal and central domains [51943] (28)
      duplication: both domains have similar folds and functions
      most members of the family contain common C-terminal alpha+beta domain
    6. Thi4-like [141942] (2)
      Pfam 01946; stand-alone, moderately decorated domain
    7. GidA-like [141946] (1)
      part of Pfam 01266
    8. HI0933 N-terminal domain-like [159436] (2)
      N-terminal part of Pfam 03486
4. Nucleotide-binding domain [51970] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
  1. Nucleotide-binding domain [51971] (3)
    this superfamily shares the common nucleotide-binding site with and provides a link between the Rossmann-fold NAD(P)-binding and FAD/NAD(P)-binding domains
    uperfamily
    1. N-terminal domain of adrenodoxin reductase-like [51972] (5)
    2. D-aminoacid oxidase, N-terminal domain [51979] (2)
      This family is probably related to the FAD-linked reductases and shares with them the C-terminal domain fold
    3. UDP-galactopyranose mutase, N-terminal domain [69427] (2)
      domain structure is similar to that of D-aminoacid oxidase
5. MurCD N-terminal domain [51983] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
  1. MurCD N-terminal domain [51984] (1)
    uperfamily
    1. MurCD N-terminal domain [51985] (3)
6. 7-stranded beta/alpha barrel [51988] (3)
  variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
  1. Glycosyl hydrolases family 6, cellulases [51989] (1)
    uperfamily
    1. Glycosyl hydrolases family 6, cellulases [51990] (5)
      Pfam 01341
  2. PHP domain-like [89550] (2)
    uperfamily
    1. PHP domain [89551] (2)
      putative phosphoesterase domain; contains trinuclear metal-binding site; some similarity to the metallohydrolases of TIM-barrel fold
    2. RNase P subunit p30 [110442] (1)
      Pfam 01876
  3. Glycoside hydrolase/deacetylase [88713] (8)
    in the different families beta-barrels are similarly distorted but may vary in the number of strands
    uperfamily
    1. 4-alpha-glucanotransferase, N-terminal domain [89554] (1)
      family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
    2. alpha-mannosidase [88714] (2)
      family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
    3. AmyC N-terminal domain-like [102189] (2)
    4. NodB-like polysaccharide deacetylase [89559] (6)
      variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=6, S=8; strand order 123456
    5. LamB/YcsF-like [117449] (3)
      Pfam 03746
    6. PA1517-like [141965] (1)
      seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel NodB-like family; member of the same Pfam family (Pfam 01522)
    7. Divergent polysaccharide deacetylase [141968] (1)
      Pfam 04748
    8. YdjC-like [159441] (1)
      Pfam 04794
7. PFL-like glycyl radical enzymes [51997] (1)
  contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
  1. PFL-like glycyl radical enzymes [51998] (5)
    duplication: the N- and C-terminal halves have similar topologies
    uperfamily
    1. PFL-like [51999] (2)
      Pfam 02901; except the C-terminal ~100 residues covered by Pfam 01228
    2. R1 subunit of ribonucleotide reductase, C-terminal domain [52002] (2)
    3. B12-dependent (class II) ribonucleotide reductase [75131] (1)
    4. Class III anaerobic ribonucleotide reductase NRDD subunit [52005] (1)
    5. SP0239-like [159444] (1)
      Pfam 05167; DUF771
8. The "swivelling" beta/beta/alpha domain [52008] (10)
  3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
  this domain is thought to be mobile in most multi-domain proteins known to contain it
  1. Phosphohistidine domain [52009] (2)
    contains barrel, closed, n=7, S=10
    uperfamily
    1. Pyruvate phosphate dikinase, central domain [52010] (3)
    2. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52013] (1)
  2. RraA-like [89562] (1)
    structural similarity and possible distant homology to the phosphohistidine domain of pyruvate phosphate dikinase
    uperfamily
    1. RraA-like [89563] (4)
      aka MenG-like; characterized as regulator of RNase E activity A (RraA) that globally modulates RNA abundance in E. coli
  3. Putative cyclase [102198] (1)
    contains mixed beta-sheet barrel, closed n=7, S=10
    uperfamily
    1. Putative cyclase [102199] (2)
      Pfam 04199; COG1878: predicted metal-dependent hydrolase
  4. LeuD/IlvD-like [52016] (3)
    contains mixed beta-sheet barrel, closed n=7, S=10
    uperfamily
    1. LeuD-like [52017] (5)
      Pfam 00694; permutation of the domain order in the proteins containing this family domain
    2. IlvD/EDD C-terminal domain-like [141976] (1)
      C-terminal part of Pfam 00920
    3. AF0055-like [141979] (1)
      PF01989; DUF126; probable link between the LeuD-like and Phosphohistidine domain superfamilies (sequence similarity crosshits)
  5. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52021] (1)
    uperfamily
    1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52022] (1)
  6. Swiveling domain of dehydratase reactivase alpha subunit [82317] (1)
    uperfamily
    1. Swiveling domain of dehydratase reactivase alpha subunit [82318] (2)
  7. PA domain [52025] (1)
    uperfamily
    1. PA domain [52026] (2)
  8. GroEL apical domain-like [52029] (2)
    uperfamily
    1. GroEL-like chaperone, apical domain [52030] (4)
    2. Group II chaperonin (CCT, TRIC), apical domain [52034] (4)
  9. FumA C-terminal domain-like [117457] (1)
    uperfamily
    1. FumA C-terminal domain-like [117458] (1)
      Pfam 05683
  10. LD-carboxypeptidase A C-terminal domain-like [141986] (1)
    uperfamily
    1. LD-carboxypeptidase A C-terminal domain-like [141987] (1)
      C-terminal half of Pfam 02016
9. Barstar-like [52037] (2)
  2 layers, a/b; parallel beta-sheet of 3 strands, order 123
  1. Barstar-related [52038] (1)
    uperfamily
    1. Barstar-related [52039] (2)
  2. Ribosomal protein L32e [52042] (1)
    uperfamily
    1. Ribosomal protein L32e [52043] (1)
      contains irregular N-terminal extension to the common fold
10. MurF and HprK N-domain-like [63417] (2)
  core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core.
  1. MurE/MurF N-terminal domain [63418] (1)
    binds UDP group
    uperfamily
    1. MurE/MurF N-terminal domain [63419] (2)
  2. HprK N-terminal domain-like [75138] (2)
    probable phosphatase
    uperfamily
    1. HPr kinase/phoshatase HprK N-terminal domain [75139] (2)
    2. DRTGG domain [159447] (1)
      Pfam 07085
11. Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [52046] (3)
  2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies
  1. RNI-like [52047] (3)
    regular structure consisting of similar repeats
    uperfamily
    1. 28-residue LRR [52048] (4)
    2. Rna1p (RanGAP1), N-terminal domain [52052] (1)
    3. Cyclin A/CDK2-associated p19, Skp2 [52055] (1)
  2. L domain-like [52058] (8)
    less regular structure consisting of variable repeats
    uperfamily
    1. Internalin LRR domain [52059] (3)
      capped at the N-end with a truncated EF-hand subdomain
    2. Leucine rich effector protein YopM [69433] (1)
    3. Ngr ectodomain-like [75142] (6)
    4. Polygalacturonase inhibiting protein PGIP [89569] (1)
    5. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52062] (1)
    6. mRNA export factor tap [52065] (1)
    7. U2A'-like [52068] (1)
      duplication: consists of 5-6 partly irregular repeats
    8. L domain [52071] (6)
  3. Outer arm dynein light chain 1 [52075] (1)
    (beta-beta-alpha)n superhelix
    uperfamily
    1. Outer arm dynein light chain 1 [52076] (1)
12. Ribosomal proteins L15p and L18e [52079] (1)
  core: three turns of irregular (beta-beta-alpha)n superhelix
  1. Ribosomal proteins L15p and L18e [52080] (1)
    uperfamily
    1. Ribosomal proteins L15p and L18e [52081] (5)
13. SpoIIaa-like [52086] (2)
  core: 4 turns of a (beta-alpha)n superhelix
  1. CRAL/TRIO domain [52087] (1)
    uperfamily
    1. CRAL/TRIO domain [52088] (3)
      Pfam 00650
  2. SpoIIaa-like [52091] (2)
    uperfamily
    1. Anti-sigma factor antagonist SpoIIaa [52092] (4)
    2. Sfri0576-like [159456] (2)
      significant structural variability despite high sequence similarity
14. ClpP/crotonase [52095] (1)
  core: 4 turns of (beta-beta-alpha)n superhelix
  1. ClpP/crotonase [52096] (4)
    uperfamily
    1. Clp protease, ClpP subunit [52097] (5)
    2. Tail specific protease, catalytic domain [52100] (3)
      includes N-terminal all-alpha subdomain
    3. Crotonase-like [52103] (17)
    4. Biotin dependent carboxylase carboxyltransferase domain [89572] (8)
      Pfam 01039
      the active site is formed by two different homologous subunits or domains of this fold
15. BRCT domain [52112] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. BRCT domain [52113] (5)
    Pfam 00533
    uperfamily
    1. BRCT domain [63955] (2)
    2. 53BP1 [75148] (1)
    3. DNA-repair protein XRCC1 [52114] (1)
    4. DNA ligase [52117] (2)
    5. DNA topoisomerase II binding protein 1, TopBP1 [117468] (1)
16. Lumazine synthase [52120] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. Lumazine synthase [52121] (1)
    uperfamily
    1. Lumazine synthase [52122] (7)
17. Uracil-DNA glycosylase-like [52140] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. Uracil-DNA glycosylase-like [52141] (4)
    uperfamily
    1. Uracil-DNA glycosylase [52142] (5)
    2. Mug-like [52147] (4)
    3. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89579] (1)
    4. AF0587 domain-like [159464] (1)
      a middle domain in the founder protein
18. Creatininase [102214] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. Creatininase [102215] (1)
    uperfamily
    1. Creatininase [102216] (1)
19. DNA polymerase III psi subunit [102219] (1)
  3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
  1. DNA polymerase III psi subunit [102220] (1)
    uperfamily
    1. DNA polymerase III psi subunit [102221] (1)
20. Initiation factor IF2/eIF5b, domain 3 [52155] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. Initiation factor IF2/eIF5b, domain 3 [52156] (1)
    uperfamily
    1. Initiation factor IF2/eIF5b, domain 3 [52157] (1)
21. Aminoacid dehydrogenase-like, N-terminal domain [53222] (1)
  core: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134
  1. Aminoacid dehydrogenase-like, N-terminal domain [53223] (5)
    uperfamily
    1. Aminoacid dehydrogenases [53224] (10)
      dimerisation domain; contains additional structures including two extra N-terminal strands in the beta-sheet
    2. Tetrahydrofolate dehydrogenase/cyclohydrolase [53235] (3)
    3. Methylene-tetrahydromethanopterin dehydrogenase [82333] (1)
    4. Shikimate dehydrogenase-like [82336] (5)
    5. Malic enzyme N-domain [53240] (4)
      Pfam 00390; decorated with additional structures; includes N-terminal additional subdomains and extra N-terminal strand
22. Toprim domain [110454] (1)
  3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
  1. Toprim domain [110455] (1)
    this domain is also present in several multidomain proteins that are not split in scop yet: scop_sf 56712, scop_sf 56719, scop_sf 56726, scop_sf 56731
    uperfamily
    1. Toprim domain [110456] (2)
      Pfam 01751
23. AtpF-like [159467] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
  1. AtpF-like [159468] (1)
    1. AtpF-like [159469] (2)
      Pfam 01990; segment-swapping in some members
24. Ribosomal protein L13 [52160] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
  1. Ribosomal protein L13 [52161] (1)
    uperfamily
    1. Ribosomal protein L13 [52162] (5)
25. Ribosomal protein L4 [52165] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
  1. Ribosomal protein L4 [52166] (1)
    uperfamily
    1. Ribosomal protein L4 [52167] (5)
26. Nqo1 FMN-binding domain-like [142018] (1)
  3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
  1. Nqo1 FMN-binding domain-like [142019] (1)
    uperfamily
    1. Nqo1 FMN-binding domain-like [142020] (1)
      N-terminal part of Pfam 01512
27. Flavodoxin-like [52171] (15)
  3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
  1. CheY-like [52172] (7)
    uperfamily
    1. CheY-related [52173] (32)
    2. Receiver domain of the ethylene receptor [52194] (1)
    3. Positive regulator of the amidase operon AmiR [52197] (1)
    4. Ornithine decarboxylase N-terminal "wing" domain [52252] (1)
    5. N-terminal domain of the circadian clock protein KaiA [82344] (1)
      lacks canonical receiver domains features
    6. RcsC linker domain-like [142037] (1)
      PfamB 016190; probable rudiment CheY-like domain; precedes the C-terminal CheY-related domain of similar structure
    7. AF1403 C-terminal domain-like [142040] (1)
  2. Toll/Interleukin receptor TIR domain [52200] (1)
    uperfamily
    1. Toll/Interleukin receptor TIR domain [52201] (2)
  3. Hypothetical protein MTH538 [52206] (1)
    uperfamily
    1. Hypothetical protein MTH538 [52207] (1)
  4. Succinyl-CoA synthetase domains [52210] (1)
    uperfamily
    1. Succinyl-CoA synthetase domains [52211] (6)
      contain additional N-terminal strand "0", antiparallel to strand 2
  5. Flavoproteins [52218] (8)
    uperfamily
    1. Flavodoxin-related [52219] (13)
      binds FMN
    2. Cytochrome p450 reductase N-terminal domain-like [52231] (4)
    3. Quinone reductase [52235] (6)
      binds FAD
    4. Hypothetical protein SP1951 [102234] (1)
    5. Hypothetical protein YwqN [102237] (1)
    6. NADPH-dependent FMN reductase [89590] (4)
      Pfam 03358
    7. Flavoprotein NrdI [110477] (1)
    8. WrbA-like [117474] (3)
  6. Cobalamin (vitamin B12)-binding domain [52242] (1)
    uperfamily
    1. Cobalamin (vitamin B12)-binding domain [52243] (6)
  7. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52255] (1)
    uperfamily
    1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52256] (4)
  8. SGNH hydrolase [52266] (9)
    uperfamily
    1. Esterase [52267] (1)
    2. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52270] (1)
    3. Acetylhydrolase [52273] (3)
    4. Rhamnogalacturonan acetylesterase [52276] (1)
    5. TAP-like [89594] (2)
    6. Hypothetical protein alr1529 [102240] (1)
    7. Putative acetylxylan esterase-like [142058] (2)
      Pfam 03629 (DUF303); contains a characteristic zinc(less) finger-like insertion after strand 1; lacks the conserved in other families Asn residue
    8. YxiM C-terminal domain-like [159482] (1)
      subfamily of Pfam 00657
    9. BT2961-like [159485] (2)
      PfamB 005894;homotrimeric assembly
  9. Beta-D-glucan exohydrolase, C-terminal domain [52279] (1)
    uperfamily
    1. Beta-D-glucan exohydrolase, C-terminal domain [52280] (1)
  10. Formate/glycerate dehydrogenase catalytic domain-like [52283] (3)
    uperfamily
    1. Formate/glycerate dehydrogenases, substrate-binding domain [52284] (9)
      this domain is interrupted by the Rossmann-fold domain
    2. L-alanine dehydrogenase-like [52297] (2)
    3. S-adenosylhomocystein hydrolase [52300] (3)
  11. Type II 3-dehydroquinate dehydratase [52304] (1)
    uperfamily
    1. Type II 3-dehydroquinate dehydratase [52305] (5)
  12. N-(deoxy)ribosyltransferase-like [52309] (3)
    there are similar active site architectures as well as the catalytic mechanisms of functionally characterised members
    uperfamily
    1. N-deoxyribosyltransferase [52310] (3)
    2. Hypothetical protein PA1492 [110461] (1)
      lacks the last strand; monomer; predicted deoxyribosyltransferase activity
    3. ADP ribosyl cyclase-like [56630] (3)
      contains extra N-terminal all-alpha subdomain
  13. Ribosomal protein S2 [52313] (1)
    fold elaborated with additional structures
    uperfamily
    1. Ribosomal protein S2 [52314] (3)
  14. Precorrin-8X methylmutase CbiC/CobH [63965] (1)
    fold elaborated with additional structures
    uperfamily
    1. Precorrin-8X methylmutase CbiC/CobH [63966] (3)
  15. Class I glutamine amidotransferase-like [52317] (9)
    conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
    uperfamily
    1. Class I glutamine amidotransferases (GAT) [52318] (18)
      contains a catalytic Cys-His-Glu triad
    2. A4 beta-galactosidase middle domain [82351] (1)
      probable non-catalytic branch of the class I GAT family; overall fold is very similar but the active site is not conserved
    3. DJ-1/PfpI [52325] (9)
      contains a catalytic triad or dyad different from the class I GAT triad
    4. Catalase, C-terminal domain [52328] (2)
    5. Aspartyl dipeptidase PepE [52331] (1)
      probable circular permutation in the common core; contains a catalytic Ser-His-Glu triad
    6. ThuA-like [110486] (1)
      Pfam 06283; overall fold is very similar the class I GAT family but the putative active site has a different structure
    7. LD-carboxypeptidase A N-terminal domain-like [142074] (1)
      N-terminal half of Pfam 02016
    8. HTS-like [142077] (1)
      Pfam 04204
    9. STM3548-like [159492] (1)
      Pfam 07090; DUF1355
28. Methylglyoxal synthase-like [52334] (1)
  3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
  1. Methylglyoxal synthase-like [52335] (3)
    contains a common phosphate-binding site
    uperfamily
    1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52336] (1)
    2. Methylglyoxal synthase, MgsA [52339] (3)
    3. Inosicase [63971] (3)
29. Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1)
  3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
  1. Ferredoxin reductase-like, C-terminal NADP-linked domain [52343] (5)
    binds NADP differently than classical Rossmann-fold
    N-terminal FAD-linked domain contains (6,10) barrel
    uperfamily
    1. Reductases [52344] (13)
    2. Aromatic dioxygenase reductase-like [52359] (3)
      contains additional 2Fe-2S ferredoxin domain at one of the termini
    3. Dihydroorotate dehydrogenase B, PyrK subunit [52362] (1)
      contains 2Fe-2S cluster in the C-terminal extension
    4. NADPH-cytochrome p450 reductase-like [52365] (3)
    5. Flavohemoglobin, C-terminal domain [52370] (2)
      contains additional globin domain
30. Adenine nucleotide alpha hydrolase-like [52373] (3)
  core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
  1. Nucleotidylyl transferase [52374] (5)
    uperfamily
    1. Class I aminoacyl-tRNA synthetases (RS), catalytic domain [52375] (22)
      contains a conserved all-alpha subdomain at the C-terminal extension
    2. Cytidylyltransferase [52394] (1)
    3. Adenylyltransferase [52397] (13)
    4. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63976] (3)
      contains C-terminal subdomain similar to one structural repeat of the Creatinase/aminopeptidase family
    5. ATP sulfurylase catalytic domain [63979] (5)
  2. Adenine nucleotide alpha hydrolases-like [52402] (6)
    share similar mode of ligand (Adenosine group) binding
    can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group
    uperfamily
    1. N-type ATP pyrophosphatases [52403] (13)
    2. PP-loop ATPase [82359] (2)
    3. PAPS reductase-like [52410] (2)
    4. ETFP subunits [52432] (6)
      alpha/beta heterodimer of homologous subunits; contains additional strands on both edges of the core sheet
    5. Universal stress protein-like [52436] (7)
      Pfam 00582
    6. ThiI-like [142093] (2)
      Pfam 02568
  3. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52413] (1)
    uperfamily
    1. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52414] (2)
31. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
  1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52418] (1)
    uperfamily
    1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52419] (6)
32. Cryptochrome/photolyase, N-terminal domain [52424] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
  1. Cryptochrome/photolyase, N-terminal domain [52425] (1)
    uperfamily
    1. Cryptochrome/photolyase, N-terminal domain [52426] (5)
33. DsrEFH-like [75168] (1)
  3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215
  1. DsrEFH-like [75169] (2)
    uperfamily
    1. DsrEF-like [75170] (6)
      Pfam 02635
    2. DsrH-like [117489] (3)
      Pfam 04077
34. PIN domain-like [88722] (1)
  3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145
  1. PIN domain-like [88723] (2)
    uperfamily
    1. PIN domain [89619] (7)
      Pfam 01850
    2. 5' to 3' exonuclease catalytic domain [53045] (8)
      contains an alpha-helical arch and additional strand 6 antiparallel to the rest; strand order 321456; similarity to the resolvase-like fold
35. Ribose/Galactose isomerase RpiB/AlsB [89622] (1)
  3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topological similarity to a part of the arginase/deacetylase fold
  1. Ribose/Galactose isomerase RpiB/AlsB [89623] (1)
    uperfamily
    1. Ribose/Galactose isomerase RpiB/AlsB [89624] (3)
36. EreA/ChaN-like [159500] (1)
  Core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order:51423;
  1. EreA/ChaN-like [159501] (3)
    there are four conserved residues in the putative active site: two His and two Glu
    1. ChaN-like [159502] (1)
      Pfam 04187; DUF399; Ferric uptake regulator CjrA
    2. PMT domain-like [159505] (1)
      This is the second from the PMT C-terminus; it retains the superfamily fold and the active site mainchain conformation but lacks the conserved in the other two families His and Glu residues
    3. EreA-like [159508] (2)
      Pfam 05139; Erythromycin esterase-like; the superfamily core is decorated with insertion of a four-helical bundle and a C-terminal alpha+beta extension
37. alpha/beta knot [75216] (1)
  core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot
  1. alpha/beta knot [75217] (8)
    known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
    all known members have dimeric structures
    uperfamily
    1. YbeA-like [82371] (4)
      Pfam 02590
    2. tRNA(m1G37)-methyltransferase TrmD [89629] (3)
      fold and dimerisation mode are similar to those of the YbeA-like family; contains additional C-terminal all-alpha subdomain
    3. SpoU-like RNA 2'-O ribose methyltransferase [75218] (4)
      contains extra strand (3) in the parallel beta-sheet, order 321546
    4. Hypothetical protein MTH1 (MT0001), dimerisation domain [75221] (1)
      contains extra strand (3) in the parallel beta-sheet, order 321546; interrupted by an insert OB-fold domain
    5. YggJ C-terminal domain-like [89632] (3)
      contains extra strand (3) in the parallel beta-sheet, order 321546; similar dimerisation to the MTH1 domain
    6. EMG1/NEP1-like [159513] (2)
      Pfam 03587; structurally most similar to the AF1056-like family, but more decorated
    7. AF1056-like [159518] (2)
      Pfam 04013; DUF358
    8. AF0751-like [159523] (1)
      Pfam 01994; DUF127
38. PreATP-grasp domain [52439] (1)
  3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
  possible rudiment form of Rossmann-fold domain
  1. PreATP-grasp domain [52440] (8)
    precedes the ATP-grasp domain common to all superfamily members, can contain a substrate-binding function
    uperfamily
    1. BC N-terminal domain-like [52441] (8)
    2. D-Alanine ligase N-terminal domain [52452] (3)
    3. Lysine biosynthesis enzyme LysX, N-terminal domain [102284] (1)
    4. Prokaryotic glutathione synthetase, N-terminal domain [52457] (1)
    5. Eukaryotic glutathione synthetase, substrate-binding domain [52460] (2)
      circularly permuted version of prokaryotic enzyme
    6. Synapsin domain [52463] (3)
    7. Glutathionylspermidine synthase substrate-binding domain-like [142119] (1)
      central part of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
    8. PurP N-terminal domain-like [159526] (3)
      Pfam 06849; DUF1246
39. DHS-like NAD/FAD-binding domain [52466] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
  1. DHS-like NAD/FAD-binding domain [52467] (6)
    binds cofactor molecules in the opposite direction than classical Rossmann fold
    uperfamily
    1. Deoxyhypusine synthase, DHS [52468] (1)
    2. C-terminal domain of the electron transfer flavoprotein alpha subunit [52471] (3)
      lacks strand 3; shares the FAD-binding mode with the pyruvate oxidase domain
    3. Pyruvate oxidase and decarboxylase, middle domain [52475] (12)
      N-terminal domain is Pyr module, and C-terminal domain is PP module of thiamin diphosphate-binding fold
    4. Transhydrogenase domain III (dIII) [52484] (3)
      binds NADP, shares with the pyruvate oxidase FAD-binding domain a common ADP-binding mode
    5. Sir2 family of transcriptional regulators [63984] (7)
      silent information regulator 2; contains insertion of a rubredoxin-like zinc finger domain
    6. ACDE2-like [142130] (1)
      Pfam 02552
40. Tubulin nucleotide-binding domain-like [52489] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
  1. Tubulin nucleotide-binding domain-like [52490] (1)
    uperfamily
    1. Tubulin, GTPase domain [52491] (9)
41. Isochorismatase-like hydrolases [52498] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
  1. Isochorismatase-like hydrolases [52499] (1)
    uperfamily
    1. Isochorismatase-like hydrolases [100948] (7)
42. Dipeptide transport protein [63991] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain
  1. Dipeptide transport protein [63992] (1)
    uperfamily
    1. Dipeptide transport protein [63993] (1)
43. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52506] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
  1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52507] (1)
    uperfamily
    1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52508] (5)
      Pfam 02441; formerly DFP, DNA/pantothenate metabolism flavoprotein family
44. HAD-like [56783] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
  1. HAD-like [56784] (25)
    usually contains an insertion (sub)domain after strand 1
    uperfamily
    1. Probable phosphatase YrbI [69467] (1)
      the insertion subdomain is a beta-hairpin involved into tetramerisation
    2. HAD-related [56785] (3)
      the insertion subdomain is a 4-helical bundle
    3. beta-Phosphoglucomutase-like [75173] (9)
      the insertion subdomain is a 4-helical bundle
    4. YihX-like [56789] (3)
      the insertion subdomain is a 4-helical bundle
    5. Phosphonoacetaldehyde hydrolase-like [56792] (2)
      the insertion subdomain is a 4-helical bundle
    6. Phosphoserine phosphatase [64511] (2)
      the insertion subdomain is a 4-helical bundle
    7. 5'(3')-deoxyribonucleotidase (dNT-2) [82382] (1)
      the insertion subdomain is a 4-helical bundle; dephosphorylates dUMP and dTMP
    8. Homoserine kinase ThrH [102304] (1)
      the insertion subdomain is a rudiment 4-helical bundle
    9. Class B acid phosphatase, AphA [102307] (2)
      the insertion subdomain is a helical hairpin
    10. Hypothetical protein MW1667 (SA1546) [102310] (1)
      the insertion subdomain is multi-helical
    11. phosphatase domain of polynucleotide kinase [82385] (2)
      no insertion subdomains
    12. Predicted hydrolases Cof [82388] (13)
      contains an alpha+beta subdomain inserted into a new site after strand 3
    13. NagD-like [102317] (6)
      duplication: consists of two segment-swapped domains of this fold; this results in the insertion of a circularly permuted domain after strand 3, analogously to the Cof family
    14. Meta-cation ATPase, catalytic domain P [81656] (2)
      interrupted by a large insertion, domain N
    15. Trehalose-phosphatase [110506] (1)
      Pfam 02358; contains an insert alpha+beta subdomain; similar overall fold to the Cof family
    16. NLI interacting factor-like phosphatase [110509] (1)
      Pfam 03031; NIF; the insertion subdomain is a 3-stranded beta-sheet;
    17. Magnesium-dependent phosphatase-1, Mdp1 [117509] (1)
      the insertion subdomain is a 3-stranded beta-sheet different from the NIF family
    18. Hypothetical protein VC0232 [117512] (1)
      contains a deletion in the common fold; segment-swapped tetramer
    19. Histidinol phosphatase-like [142177] (3)
      no insertion subdomains
    20. MtnX-like [142180] (1)
      Pfam 06888; the insertion subdomain is a rudiment 4-helical bundle
    21. Pyrimidine 5'-nucleotidase (UMPH-1) [142183] (2)
      Pfam 05822; the insertion subdomain is a rudiment 4-helical bundle
    22. Enolase-phosphatase E1 [142186] (2)
      the insertion subdomain is a 4-helical bundle
    23. 5' nucleotidase-like [142191] (1)
      Pfam 05761; the insertion domain cosists of 3-helical bundle and a pseudo beta-barrel; contains extra C-terminal long alpha hairpin subdomain (scop_cf 46556)
    24. AF1437-like [159537] (1)
      the insertion subdomain is a rudiment 4-helical bundle; extra alpha-hairpin insertion after strand 3
    25. BT0820-like [159540] (1)
      PfamB 073209; deletion in the common fold; segment-swapped dimer
45. NagB/RpiA/CoA transferase-like [100949] (1)
  core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
  1. NagB/RpiA/CoA transferase-like [100950] (8)
    uperfamily
    1. NagB-like [52513] (3)
      share a common phosphate-binding site with the RpiA family
    2. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75176] (4)
      share a common phosphate-binding site with the NagB-like family; part of sheet is folded upon itself and forms a barrel-like structure like the CoA transferase subunits
    3. CoA transferase beta subunit-like [74657] (3)
      catalytic subunit: similar active site structure to the NagB and RpiA families; mixed beta-sheet of 7 strands, order 4321567; strand 3 is antiparallel to the rest
    4. CoA transferase alpha subunit-like [74656] (6)
      parallel beta-sheet of 7 strands, order 4321567
    5. IF2B-like [110513] (5)
      Pfam 01008; contains extra N-terminal alpha+beta domain (1-126); beta(3)-alpha(5); 3 layers: b/a/a
    6. Methenyltetrahydrofolate synthetase [110520] (3)
      Pfam 01812; 5-FTHF cyclo-ligase
    7. YkgG-like [142200] (1)
      Pfam 02589; DUF162
    8. SorC sugar-binding domain-like [159545] (5)
      Pfam 04198
46. Hypothetical protein MTH777 (MT0777) [75180] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
  1. Hypothetical protein MTH777 (MT0777) [75181] (1)
    uperfamily
    1. Hypothetical protein MTH777 (MT0777) [75182] (1)
47. Thiamin pyrophosphokinase, catalytic domain [63998] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156
  1. Thiamin pyrophosphokinase, catalytic domain [63999] (1)
    uperfamily
    1. Thiamin pyrophosphokinase, catalytic domain [64000] (2)
48. Undecaprenyl diphosphate synthase [64004] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156
  1. Undecaprenyl diphosphate synthase [64005] (1)
    the sheet topology is similar to those of the N-terminal domain of phosphoglycerate kinase and carbamate kinase
    uperfamily
    1. Undecaprenyl diphosphate synthase [64006] (2)
49. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102323] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456
  1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102324] (1)
    the sheet topology is similar to those of the Periplasmic binding protein-like I domains
    uperfamily
    1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102325] (1)
50. Thiamin diphosphate-binding fold (THDP-binding) [52517] (1)
  3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
  1. Thiamin diphosphate-binding fold (THDP-binding) [52518] (8)
    there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
    two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
    uperfamily
    1. Pyruvate oxidase and decarboxylase Pyr module [88724] (12)
      the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpha/beta domain of Rossmann-like topology
    2. TK-like Pyr module [88735] (5)
      different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    3. Branched-chain alpha-keto acid dehydrogenase Pyr module [88741] (6)
      parent family to TK and PFOR
      heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    4. PFOR Pyr module [88746] (1)
      domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
    5. Pyruvate oxidase and decarboxylase PP module [88749] (12)
      the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpa/beta domain of Rossmann-like topology
    6. TK-like PP module [88760] (5)
      different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    7. Branched-chain alpha-keto acid dehydrogenase PP module [88766] (5)
      parent family to TK and PFOR
      heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    8. PFOR PP module [88771] (1)
      domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
51. P-loop containing nucleoside triphosphate hydrolases [52539] (1)
  3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
  1. P-loop containing nucleoside triphosphate hydrolases [52540] (24)
    division into families based on beta-sheet topologies
    uperfamily
    1. Nucleotide and nucleoside kinases [52541] (46)
      parallel beta-sheet of 5 strands, order 23145
    2. Shikimate kinase (AroK) [52566] (4)
      similar to the nucleotide/nucleoside kinases but acts on different substrate
    3. Chloramphenicol phosphotransferase [52569] (1)
      similar to the nucleotide/nucleoside kinases but acts on different substrate
    4. Gluconate kinase [75195] (1)
      similar to the nucleotide/nucleoside kinases
    5. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82395] (1)
      similar to the nucleotide/nucleoside kinases; extra N- and C-terminal structures
    6. Adenosine-5'phosphosulfate kinase (APS kinase) [52572] (2)
    7. ATP sulfurylase C-terminal domain [64011] (2)
    8. PAPS sulfotransferase [52575] (15)
      Pfam 00685
      similar to the nucleotide/nucleoside kinases but transfer sulphate group
    9. Phosphoribulokinase/pantothenate kinase [52584] (5)
    10. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52589] (2)
    11. G proteins [52592] (118)
      core: mixed beta-sheet of 6 strands, order 231456; strand 2 is antiparallel to the rest
    12. Motor proteins [52641] (15)
    13. Nitrogenase iron protein-like [52652] (29)
      core: parallel beta-sheet of 7 strands; order 3241567
    14. RecA protein-like (ATPase-domain) [52670] (29)
      core: mixed beta-sheet of 8 strands, order 32451678; strand 7 is antiparallel to the rest
    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
    16. ABC transporter ATPase domain-like [52686] (29)
      there are two additional subdomains inserted into the central core that has a RecA-like topology
    17. Tandem AAA-ATPase domain [81268] (27)
      duplication: tandem repeat of two RecA-like (AAA) domains
    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
    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
    20. Helicase-like "domain" of reverse gyrase [69496] (1)
    21. DNA helicase UvsW [102396] (1)
      contains extra N-terminal alpha+beta subdomain
    22. YjeE-like [75213] (1)
      mixed beta-sheet; order 234156(0), strands 2 and 6 are antiparallel to the rest
    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)
    24. Atu3015-like [142332] (2)
      unknown function; similar to the nucleotide/nucleoside kinases
52. PTS IIb component [52727] (1)
  3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
  1. PTS IIb component [52728] (1)
    uperfamily
    1. PTS IIb component [52729] (2)
53. DNA polymerase III chi subunit [102399] (1)
  3 layers, a/b/a; parallel beta-sheet of 7 strands, order 7165243
  1. DNA polymerase III chi subunit [102400] (1)
    structural similarity and possible evolutionary relationship to the AAA domain; lacks the P-loop motif
    uperfamily
    1. DNA polymerase III chi subunit [102401] (1)
54. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
  1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52733] (1)
    uperfamily
    1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52734] (2)
55. CofD-like [142337] (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (scop_cf 52732)
  1. CofD-like [142338] (1)
    uperfamily
    1. CofD-like [142339] (2)
      Pfam 01933; UPF0052
56. MCP/YpsA-like [102404] (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567
  1. MCP/YpsA-like [102405] (2)
    uperfamily
    1. MoCo carrier protein-like [102406] (6)
      Pfam 03641
    2. YpsA-like [159579] (1)
      Pfam 06908; DUF1273; lacking the last strand 7; different set of conserved residues in the putative active site than in the MoCo carrier protein-like family
57. Methylesterase CheB, C-terminal domain [52737] (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
  1. Methylesterase CheB, C-terminal domain [52738] (1)
    uperfamily
    1. Methylesterase CheB, C-terminal domain [52739] (1)
58. Subtilisin-like [52742] (1)
  3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
  1. Subtilisin-like [52743] (2)
    uperfamily
    1. Subtilases [52744] (18)
    2. Serine-carboxyl proteinase, SCP [52764] (3)
      elaborated with additional structures
59. Indigoidine synthase A-like [110580] (1)
  core: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756
  1. Indigoidine synthase A-like [110581] (1)
    uperfamily
    1. Indigoidine synthase A-like [110582] (1)
      Pfam 04227
60. Arginase/deacetylase [52767] (1)
  3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
  1. Arginase/deacetylase [52768] (2)
    uperfamily
    1. Arginase-like amidino hydrolases [52769] (8)
      Pfam 00491
    2. Histone deacetylase, HDAC [52773] (3)
61. Alpha-2,3/8-sialyltransferase CstII [102413] (1)
  3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678
  1. Alpha-2,3/8-sialyltransferase CstII [102414] (1)
    uperfamily
    1. Alpha-2,3/8-sialyltransferase CstII [102415] (1)
62. Cell-division inhibitor MinC, N-terminal domain [64042] (1)
  beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest
  1. Cell-division inhibitor MinC, N-terminal domain [64043] (1)
    uperfamily
    1. Cell-division inhibitor MinC, N-terminal domain [64044] (1)
63. DTD-like [69499] (1)
  beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC
  1. DTD-like [69500] (1)
    active form is a dimer
    uperfamily
    1. DTD-like [69501] (3)
      Pfam 02580
64. CoA-dependent acyltransferases [52776] (1)
  core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
  1. CoA-dependent acyltransferases [52777] (3)
    uperfamily
    1. CAT-like [52778] (5)
      trimeric enzymes with the active sites being located in between subunits
    2. Choline/Carnitine O-acyltransferase [82424] (4)
      Pfam 00755; monomeric enzyme containing tandem repeat of two CAT subunit-like domains
    3. NRPS condensation domain (amide synthase) [75229] (2)
      Pfam 00668; functional domain of multifunctional enzyme containing tandem repeat of two CAT subunit-like domains
65. Phosphotyrosine protein phosphatases I-like [52787] (2)
  3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
  1. Phosphotyrosine protein phosphatases I [52788] (1)
    share the common active site structure with the family II
    uperfamily
    1. Low-molecular-weight phosphotyrosine protein phosphatases [52789] (7)
  2. PTS system IIB component-like [52794] (2)
    uperfamily
    1. PTS system, Lactose/Cellobiose specific IIB subunit [52795] (2)
      Pfam 02302
    2. PTS system, Fructose specific IIB subunit-like [159584] (2)
      Pfam 02379
66. (Phosphotyrosine protein) phosphatases II [52798] (1)
  core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
  1. (Phosphotyrosine protein) phosphatases II [52799] (5)
    share with the family I the common active site structure with a circularly permuted topology
    uperfamily
    1. Dual specificity phosphatase-like [52800] (10)
    2. Higher-molecular-weight phosphotyrosine protein phosphatases [52805] (12)
      has an extension to the beta-sheet of 3 antiparallel strands before strand 4
    3. Myotubularin-like phosphatases [102422] (1)
      common fold is decorated with additional structures
    4. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117583] (1)
    5. Mycobacterial PtpB-like [142348] (1)
67. Rhodanese/Cell cycle control phosphatase [52820] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
  1. Rhodanese/Cell cycle control phosphatase [52821] (4)
    Pfam 00581
    the active site structure is similar to those of the families I and II protein phosphatases; the topology can be related by a different circular permutation to the family I topology
    uperfamily
    1. Cell cycle control phosphatase, catalytic domain [52822] (4)
    2. Single-domain sulfurtransferase [69509] (3)
    3. Multidomain sulfurtransferase (rhodanese) [52827] (6)
      duplication: consists of two domains of this fold
    4. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117586] (1)
68. Thioredoxin fold [52832] (2)
  core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
  1. Thioredoxin-like [52833] (23)
    uperfamily
    1. Thioltransferase [52834] (31)
    2. PDI-like [52849] (6)
      duplication: contains two tandem repeats of this fold
    3. Calsequestrin [52855] (1)
      duplication: contains three tandem repeats of this fold
    4. DsbA-like [100953] (4)
      contains an all-alpha subdomain insertion
    5. Glutathione S-transferase (GST), N-terminal domain [52862] (44)
    6. Phosducin [52888] (2)
    7. ERP29 N domain-like [52892] (2)
    8. spliceosomal protein U5-15Kd [52895] (1)
    9. SH3BGR (SH3-binding, glutamic acid-rich protein-like) [102446] (1)
      related to glutaredoxin 1 (GRX1) but lacks both conserved cysteine residues
    10. KaiB-like [102449] (2)
      Pfam 07689; contains members with alternative folds
    11. DsbC/DsbG C-terminal domain-like [52898] (3)
      elaborated common fold
    12. Glutathione peroxidase-like [52901] (42)
    13. Thioredoxin-like 2Fe-2S ferredoxin [52918] (1)
    14. ArsC-like [69518] (3)
      Pfam 03960
    15. Txnl5-like [110612] (2)
      Pfam 06110
    16. YuzD-like [117605] (1)
      Pfam 07315
    17. YKR049C-like [142395] (1)
      Pfam 07955; DUF1687; contains an all-alpha insert subdomain
    18. Atu2684-like [142398] (1)
      Pfam 06764; DUF1223; contains extra C-terminal domain of Immunoglobulin-like fold (scop_cf 48725), intimately associated with the N-terminal thioredixin-like domain and contributing to the active site
    19. HyaE-like [142401] (2)
      Pfam 07449; have evolved a different function; contains no conserved cysteine residues
    20. NQO2-like [142405] (1)
      complex I 24 kDa subunit; contains 2Fe-2S cluster in the active site; includes extra N-terminal four-helical bundle
    21. Mitochondrial ribosomal protein L51/S25/CI-B8 domain [142408] (1)
      Pfam 05047; "minimalized" version of the thioredoxin-like fold; variable positions for cysteine residues in the putative active site
    22. Selenoprotein W-related [142411] (3)
      Pfam 05169; "minimalized" version of the thioredoxin-like fold
    23. UAS domain [159589] (1)
      SMART 00594
  2. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52913] (1)
    uperfamily
    1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52914] (1)
69. Peptidyl-tRNA hydrolase II [102461] (1)
  3 layers: a/b/a; mixed beta-sheet of 4 strands, order 2143, strand 4 is antiparallel to the rest
  1. Peptidyl-tRNA hydrolase II [102462] (1)
    uperfamily
    1. Peptidyl-tRNA hydrolase II [102463] (4)
      Pfam 01981; UPF0099
70. TK C-terminal domain-like [52921] (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
  1. TK C-terminal domain-like [52922] (3)
    uperfamily
    1. Transketolase C-terminal domain-like [52923] (5)
    2. Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain [52926] (6)
    3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52931] (1)
71. Pyruvate kinase C-terminal domain-like [52934] (2)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
  1. PK C-terminal domain-like [52935] (2)
    uperfamily
    1. Pyruvate kinase, C-terminal domain [52936] (6)
    2. MTH1675-like [110616] (2)
      PfamB 019040; probable flavoenzyme, binds FMN; the phosphoribityl group binds in the equivalent site to the binding site of the PK allosteric regulator FBP
  2. ATP synthase (F1-ATPase), gamma subunit [52943] (1)
    contains an antiparallel coiled coil formed by N- and C-terminal extensions to the common fold
    uperfamily
    1. ATP synthase (F1-ATPase), gamma subunit [52944] (3)
72. Anticodon-binding domain-like [52953] (6)
  3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
  1. Class II aaRS ABD-related [52954] (2)
    uperfamily
    1. Anticodon-binding domain of Class II aaRS [52955] (13)
    2. Brix domain [142420] (2)
      Pfam 04427; tandem repeat of two ABD-like structural repeats, which are associated together with the formation of single beta-sheet, folded into half-barrel
  2. TolB, N-terminal domain [52964] (1)
    uperfamily
    1. TolB, N-terminal domain [52965] (1)
  3. B12-dependent dehydatase associated subunit [52968] (2)
    uperfamily
    1. Diol dehydratase, beta subunit [52969] (2)
      contains additional structures in the C-terminal extension
    2. Dehydratase-reactivating factor beta subunit [82433] (2)
  4. ITPase-like [52972] (3)
    formerly Maf/Ham1; elaborated with additional structures inserted in the common fold
    uperfamily
    1. ITPase (Ham1) [52973] (5)
      Pfam 01725
    2. Maf-like [52976] (2)
    3. YjjX-like [110621] (3)
      Pfam 01931
  5. CinA-like [142433] (1)
    uperfamily
    1. CinA-like [142434] (1)
      Pfam 02464
  6. XCC0632-like [159594] (2)
    short crossover loop between strands 2 and 3; the antiparallel part of the beta-sheet (strands 3, 4 and 5) and the C-terminal helix are quite long
    1. NLBH-like [159595] (1)
      Pfam 05211; Neuraminyllactose-binding hemagglutinin
    2. XCC0632-like [159598] (1)
      Pfam 03886; DUF330
73. MTH938-like [64075] (1)
  core: 3 layers, b+a/b/a ; the central mixed sheet of 5 strands: order 21534; strand 2 is antiparallel to the rest
  1. MTH938-like [64076] (1)
    uperfamily
    1. MTH938-like [64077] (5)
74. Restriction endonuclease-like [52979] (4)
  core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
  1. Restriction endonuclease-like [52980] (33)
    uperfamily
    1. Restriction endonuclease EcoRI [52981] (1)
    2. Restriction endonuclease EcoRV [52984] (1)
    3. Restriction endonuclease BamHI [52987] (1)
    4. Restriction endonuclease BglI [52990] (1)
    5. Restriction endonuclease BglII [52993] (1)
    6. Restriction endonuclease BstyI [102471] (1)
    7. Restriction endonuclease PvuII [52996] (1)
    8. Cfr10I/Bse634I [52999] (2)
    9. Restriction endonuclease MunI [53002] (1)
    10. Restriction endonuclease NaeI [53005] (1)
    11. Restriction endonuclease NgoIV [53008] (1)
    12. Restriction endonuclease BsobI [53011] (1)
    13. Restriction endonuclease HincII [69525] (1)
    14. Restriction endonuclease FokI, C-terminal (catalytic) domain [53014] (1)
    15. Type II restriction endonuclease catalytic domain [102474] (1)
    16. lambda exonuclease [53017] (1)
    17. DNA mismatch repair protein MutH from [53020] (1)
    18. Very short patch repair (VSR) endonuclease [53023] (1)
    19. TnsA endonuclease, N-terminal domain [53026] (1)
    20. Endonuclease I (Holliday junction resolvase) [53029] (1)
    21. Hjc-like [64080] (3)
      Pfam 01870
    22. XPF/Rad1/Mus81 nuclease [89716] (3)
    23. Restriction endonuclease MspI [110624] (1)
    24. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117619] (1)
      related to the RecC domain
    25. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117622] (1)
      related to the RecB domain
    26. Hypothetical protein VC1899 [117625] (1)
      contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
    27. Hypothetical protein TT1808 (TTHA1514) [117628] (1)
      Pfam 05685; DUF820
    28. RecU-like [117631] (2)
      Pfam 03838
    29. Restriction endonuclease EcoO109IR [117635] (1)
    30. MRR-like [117638] (1)
      Pfam 04471
    31. PA4535-like [142449] (1)
      contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix
    32. XisH-like [159601] (2)
      Pfam 08814
    33. YaeQ-like [159605] (2)
      Pfam 07152; contains extra N- and C-terminal beta-structures forming additional five-stranded beta-sheet; retains the PD motif in the putative active site
  2. tRNA-intron endonuclease catalytic domain-like [53032] (1)
    uperfamily
    1. tRNA-intron endonuclease catalytic domain-like [53033] (3)
  3. Eukaryotic RPB5 N-terminal domain [53036] (1)
    uperfamily
    1. Eukaryotic RPB5 N-terminal domain [53037] (1)
  4. TBP-interacting protein-like [159612] (1)
    contains extra C-terminal alpha+beta domain of complex fold with an embeded C2H2 zinc-finger
    1. TBP-interacting protein-like [159613] (1)
      PfamB 059845 (N-terminal domain) and Pfam B059846 (C-terminal region)
75. Resolvase-like [53040] (2)
  Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
  1. Resolvase-like [53041] (1)
    uperfamily
    1. gamma,delta resolvase, catalytic domain [53042] (1)
  2. beta-carbonic anhydrase, cab [53056] (1)
    uperfamily
    1. beta-carbonic anhydrase, cab [53057] (4)
76. PTS system fructose IIA component-like [53061] (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
  1. PTS system fructose IIA component-like [53062] (2)
    active dimer is formed by strand 5 swapping
    uperfamily
    1. EIIA-man component-like [53063] (2)
    2. DhaM-like [159618] (2)
      probable link between the PTS system fructose IIA component-like superfamily and the DAK1/DegV-like superfamily (scop_sf 82549)
77. Ribonuclease H-like motif [53066] (7)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
  1. Actin-like ATPase domain [53067] (14)
    duplication contains two domains of this fold
    uperfamily
    1. Actin/HSP70 [53068] (14)
    2. BadF/BadG/BcrA/BcrD-like [64089] (5)
    3. Acetokinase-like [53080] (3)
    4. ATPase domain of dehydratase reactivase alpha subunit [82440] (2)
    5. Hexokinase [53083] (5)
    6. Glycerol kinase [53089] (2)
    7. Glucokinase [110627] (1)
      Pfam 02685
    8. Ppx/GppA phosphatase [110630] (2)
      Pfam 02541
    9. YeaZ-like [110633] (2)
      Pfam 00814; ubiquitous cytoplasmic protein; annotated as Glycoprotease (Peptidase_M22 family) on the basis of one member's known extracellular activity
    10. ROK [110636] (8)
      Pfam 00480
    11. Cyto-EpsL domain [117644] (1)
      N-terminal part of Pfam 05134
    12. Ta0583-like [142481] (1)
    13. CoaX-like [142484] (3)
      Pfam 03309; Bordetella pertussis Bvg accessory factor family, Baf
    14. Fumble-like [159623] (3)
      Pfam 03630; type II pantothenate kinase-like
  2. Creatinase/prolidase N-terminal domain [53092] (1)
    uperfamily
    1. Creatinase/prolidase N-terminal domain [53093] (4)
  3. Ribonuclease H-like [53098] (14)
    consists of one domain of this fold
    uperfamily
    1. Ribonuclease H [53099] (11)
    2. Retroviral integrase, catalytic domain [53107] (3)
    3. mu transposase, core domain [53112] (1)
    4. Transposase inhibitor (Tn5 transposase) [53115] (1)
    5. DnaQ-like 3'-5' exonuclease [53118] (26)
      contains Pfam 00929
    6. RuvC resolvase [53134] (1)
    7. Mitochondrial resolvase ydc2 catalytic domain [69533] (1)
    8. Putative Holliday junction resolvase RuvX [102485] (3)
    9. CAF1-like ribonuclease [102492] (2)
    10. PIWI domain [110640] (3)
      Pfam 02171
    11. TM1739-like [142505] (1)
      Pfam 04251; DUF430; particular similarity to the PIWI domain family
    12. Hermes transposase-like [142508] (1)
    13. Tex RuvX-like domain-like [159635] (1)
    14. Prp8 beta-finger domain-like [159638] (2)
  4. Translational machinery components [53137] (2)
    uperfamily
    1. Ribosomal protein L18 and S11 [53138] (7)
    2. ERF1/Dom34 middle domain-like [53143] (3)
  5. Nitrogenase accessory factor-like [53146] (2)
    uperfamily
    1. MTH1175-like [53147] (3)
    2. Nitrogenase accessory factor [102496] (1)
      capable of binding the iron molybdenum cofactor, FeMo-co
  6. DNA repair protein MutS, domain II [53150] (1)
    uperfamily
    1. DNA repair protein MutS, domain II [53151] (2)
  7. Methylated DNA-protein cysteine methyltransferase domain [53155] (1)
    uperfamily
    1. Methylated DNA-protein cysteine methyltransferase domain [53156] (3)
78. Phosphorylase/hydrolase-like [53162] (8)
  core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
  1. HybD-like [53163] (2)
    the HybD fold coincides with the consensus core structure
    uperfamily
    1. Hydrogenase maturating endopeptidase HybD [53164] (1)
    2. Germination protease [64095] (1)
      elaborated with the N-terminal alpha+beta subdomain and the insertion all-alpha dimerisation subdomain
  2. Purine and uridine phosphorylases [53167] (1)
    complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8
    uperfamily
    1. Purine and uridine phosphorylases [53168] (18)
  3. Peptidyl-tRNA hydrolase-like [53178] (1)
    uperfamily
    1. Peptidyl-tRNA hydrolase-like [53179] (2)
  4. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53182] (1)
    uperfamily
    1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53183] (4)
  5. Zn-dependent exopeptidases [53187] (9)
    core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest
    uperfamily
    1. Pancreatic carboxypeptidases [53188] (10)
    2. Carboxypeptidase T [53198] (1)
    3. Leucine aminopeptidase, C-terminal domain [53201] (2)
    4. Bacterial dinuclear zinc exopeptidases [53204] (19)
    5. FolH catalytic domain-like [53210] (2)
    6. N-acetylmuramoyl-L-alanine amidase-like [102517] (2)
    7. AstE/AspA-like [142526] (6)
      Pfam 04952; Succinylglutamate desuccinylase / Aspartoacylase family; contains extra C-terminal domain, new variant of the Barrel-sandwich hybrid fold (scop_cf 51229)
    8. Glutaminyl-peptide cyclotransferase-like [142532] (1)
      part of Pfam 04389
    9. FGase-like [159652] (2)
      Pfam 05013; N-formylglutamate amidohydrolase
  6. LigB-like [53213] (1)
    circular permutation of the common fold, most similar to the PNP fold
    uperfamily
    1. LigB-like [53214] (2)
  7. AF0625-like [142535] (1)
    contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
    uperfamily
    1. AF0625-like [142536] (2)
      Pfam 04414; DUF516, binds magnesium ion and pyrophosphate in the putative active site
  8. Cgl1923-like [159659] (1)
    1. Cgl1923-like [159660] (1)
      Pfam 01908; DUF75
79. Molybdenum cofactor biosynthesis proteins [53217] (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
  1. Molybdenum cofactor biosynthesis proteins [53218] (2)
    uperfamily
    1. MogA-like [53219] (8)
    2. MoeA central domain-like [64103] (5)
80. CobE/GbiG C-terminal domain-like [159663] (1)
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32154; strand 5 is antiparallel to the rest
  1. CobE/GbiG C-terminal domain-like [159664] (1)
    probably involved in deacylation steps in both anaerobic and aerobic pathways of cobalamin biosynthesis
    1. CobE/GbiG C-terminal domain-like [159665] (3)
      C-terminal part of Pfam 01890 (CbiG); corresponds to standalone protein CobE in the aerobic pathway; also includes resent structure 3BY5
81. CbiG N-terminal domain-like [159671] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 213456, strand 5 is antiparallel to the rest
  1. CbiG N-terminal domain-like [159672] (1)
    probable biological unit is a homodimer; putative active site is formed by residues from both subunits
    1. CbiG N-terminal domain-like [159673] (1)
      N-terminal part of Pfam 01890; also includes variable linker domain to CobE-like C-terminal domain; the linker domain may be in a rudimentary form or missing
82. Bacterial fluorinating enzyme, N-terminal domain [102521] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands; order: 213546, strand 5 is antiparallel to the rest; topological similarity to the MogA-like family fold
  1. Bacterial fluorinating enzyme, N-terminal domain [102522] (1)
    uperfamily
    1. Bacterial fluorinating enzyme, N-terminal domain [102523] (1)
83. Caspase-like [52128] (1)
  3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest
  1. Caspase-like [52129] (2)
    mature protein may be composed of two chains folded in a single domain
    uperfamily
    1. Caspase catalytic domain [52130] (7)
    2. Gingipain R (RgpB), N-terminal domain [52137] (1)
      contains extra N-terminal alpha/beta subdomain
84. Macro domain-like [52948] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 is antiparallel to the rest
  1. Macro domain-like [52949] (2)
    uperfamily
    1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52950] (2)
    2. Macro domain [89724] (7)
      found in different proteins, including macro-H2a histone and the Appr-1"-p processing enzyme
85. MurD-like peptide ligases, peptide-binding domain [53243] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
  1. MurD-like peptide ligases, peptide-binding domain [53244] (2)
    uperfamily
    1. MurCDEF C-terminal domain [53245] (5)
    2. Folylpolyglutamate synthetase, C-terminal domain [53250] (2)
86. Phosphoglycerate mutase-like [53253] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
  1. Phosphoglycerate mutase-like [53254] (3)
    uperfamily
    1. Cofactor-dependent phosphoglycerate mutase [53255] (8)
    2. Histidine acid phosphatase [53258] (7)
    3. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53267] (2)
87. PRTase-like [53270] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
  1. PRTase-like [53271] (2)
    uperfamily
    1. Phosphoribosyltransferases (PRTases) [53272] (36)
    2. Phosphoribosylpyrophosphate synthetase-like [53296] (3)
      duplication: consists of two domains of this fold
88. vWA-like [53299] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
  1. vWA-like [53300] (5)
    uperfamily
    1. Integrin A (or I) domain [53301] (12)
    2. Trunk domain of Sec23/24 [82458] (2)
    3. Ku70 subunit N-terminal domain [100959] (1)
    4. Ku80 subunit N-terminal domain [100962] (1)
    5. RoRNP C-terminal domain-like [142565] (1)
89. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53322] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
  1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53323] (1)
    uperfamily
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53324] (1)
90. RbsD-like [102545] (1)
  3 layers: a/b/a; mixed beta-sheet of 6 strands, order 251634; strand 6 is antiparallel to the rest
  1. RbsD-like [102546] (1)
    uperfamily
    1. RbsD-like [102547] (2)
91. FabD/lysophospholipase-like [52150] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
  1. FabD/lysophospholipase-like [52151] (3)
    uperfamily
    1. FabD-like [52152] (2)
      the superfamily common core covers almost all of the family fold
    2. Lysophospholipase [53645] (1)
      common core is decorated with many additional structures; mixed beta-sheet of 9 strands, order 654321798; strands 4, 6 and 8 are antiparallel to the rest
    3. Patatin [89729] (1)
      plant proteins; structurally and functionally related to animal cytosolic phospholipase A2
92. L-sulfolactate dehydrogenase-like [89732] (1)
  core: 3 layers, a/b/a; mixed sheet of 7 strands, order 1237456; strands 1, 6 and 7 are antiparallel to the rest
  1. L-sulfolactate dehydrogenase-like [89733] (1)
    topological similarity to the domain 2 of TM1585
    uperfamily
    1. L-sulfolactate dehydrogenase-like [89734] (3)
      Pfam 02615; type II malate/L-lactate dehydrogenase;
93. Formyltransferase [53327] (1)
  3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
  1. Formyltransferase [53328] (1)
    uperfamily
    1. Formyltransferase [53329] (7)
94. S-adenosyl-L-methionine-dependent methyltransferases [53334] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
  1. S-adenosyl-L-methionine-dependent methyltransferases [53335] (57)
    uperfamily
    1. COMT-like [53336] (3)
    2. Plant O-methyltransferase, C-terminal domain [64111] (5)
    3. RNA methyltransferase FtsJ [53339] (1)
    4. Fibrillarin homologue [53342] (3)
    5. rRNA methyltransferase RlmA [102557] (1)
    6. rRNA methyltransferase AviRa [89738] (1)
    7. rRNA adenine dimethylase-like [88784] (5)
    8. mRNA cap methylase [88785] (3)
    9. mRNA cap (Guanine N-7) methyltransferase [102560] (1)
      mRNA capping enzyme
    10. Hypothetical protein MJ0882 [53345] (1)
    11. Hypothetical protein HI0319 (YecO) [69544] (1)
    12. Glycine N-methyltransferase [53348] (3)
    13. Arylamine N-methyltransferase [69547] (2)
    14. Histamine methyltransferase [75261] (1)
    15. Hypothetical Protein YjhP [82469] (1)
    16. Salicylic acid carboxyl methyltransferase (SAMT) [102563] (1)
    17. Thiopurine S-methyltransferase [102566] (2)
    18. Leucine carboxy methyltransferase Ppm1 [102569] (1)
    19. Precorrin-6Y methyltransferase (CbiT) [82472] (1)
    20. MraW-like putative methyltransferases [82475] (2)
    21. N5-glutamine methyltransferase, HemK [89743] (2)
    22. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89746] (2)
    23. Guanidinoacetate methyltransferase [69550] (2)
    24. Arginine methyltransferase [53351] (4)
      lacks the last two strands of the common fold replaced with a beta-sandwich oligomerisation subdomain
    25. Protein-L-isoaspartyl O-methyltransferase [53354] (5)
      topological variant; strand order 3214567; strand 6 is antiparallel to the rest
    26. Glucose-inhibited division protein B (GidB) [75264] (2)
    27. tRNA(1-methyladenosine) methyltransferase-like [64117] (4)
      contains additional N-terminal beta-sandwich domain
    28. NOL1/NOP2/sun [102575] (3)
      Pfam 01189; contains additional N-terminal 3-helical and ferredoxin-like domains
    29. Ribosomal protein L11 methyltransferase PrmA [102578] (1)
      contains additional N-terminal ferredoxin-like domain
    30. (Uracil-5-)-methyltransferase [102581] (1)
      Pfam 05958
    31. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53357] (1)
      contains additional N-terminal all-alpha domain, res. 11-91
    32. C5 cytosine-specific DNA methylase, DCM [88786] (3)
    33. DNA methylase TaqI, N-terminal domain [88787] (1)
    34. N6 adenine-specific DNA methylase, DAM [88788] (2)
    35. Type II DNA methylase [53377] (3)
      circularly permuted version of the common fold
    36. Spermidine synthase [69557] (7)
      contains additional N-terminal tetramerisation all-beta domain, res. 1-71
    37. Mycolic acid cyclopropane synthase [69560] (6)
    38. Ta1320-like [89751] (2)
    39. UbiE/COQ5-like [110671] (5)
      Pfam 01209
    40. AD-003 protein-like [117685] (2)
      Pfam 05891; DUF858
    41. CAC2371-like [117688] (3)
      similar overall fold to the Glycine N-methyltransferase (scop_fa 53348) and mRNA cap (Guanine N-7) methyltransferase (scop_fa 102560) families
    42. TehB-like [142603] (1)
      Pfam 03848; overall structural similarity to Thiopurine S-methyltransferase (Pfam 05724)
    43. N-6 DNA Methylase-like [142606] (3)
      Pfam 02384; contains C-terminal extension to the canonical fold and extra N-terminal all-alpha domain similar to the insert domain of the DAM family (scop_fa 88788)
    44. YhhF-like [142611] (5)
      Pfam 03602
    45. Met-10+ protein-like [142622] (1)
      Pfam 02475; contains extra N-terminal alpha+beta domain: beta(2)-alpha-beta(2); mixed beta-sheet; order: 1234; cf scop_fold 102740
    46. Nsp15 N-terminal domain-like [142625] (2)
      rudiment methyltransferase fold that probably has lost the enzymatic activity; contains extra N-terminal alpha+beta subdomain
    47. BC2162-like [142629] (1)
      contains extra helical regions inserted after strands 5 and 6 of the canonical fold
    48. CmcI-like [142632] (1)
      Pfam 04989; may have evolved different enzymatic activity
    49. hypothetical RNA methyltransferase [142635] (4)
      C-terminal part of Pfam 03602; similar to (Uracil-5-)-methyltransferase (Pfam 05958)
    50. RPA4359-like [142644] (1)
      Pfam 02636; DUF185
    51. TrmB-like [142647] (2)
      Pfam 02390
    52. Methyltransferase 10 domain [142651] (1)
      Pfam 05971; DUF890
    53. YhiQ-like [159686] (3)
      Pfam 04445; DUF548; contains extra N-terminal alpha+beta subdomain [beta-alpha-beta(4)]
    54. FkbM-like [159691] (1)
      contains extra N-terminal alpha/beta and all-alpha subdomains
    55. ML2640-like [159694] (1)
      Pfam 02409; O-methyltransferase N-terminus (DUF142); most similar structure to the Leucine carboxy methyltransferase Ppm1 family
    56. TRM1-like [159697] (1)
      Pfam 02005; contains extra C-terminal alpha+beta subdomain
    57. LPG1296-like [159700] (1)
      Pfam 04378; DUF519
95. LmbE-like [102587] (1)
  3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest; topological similarity to SAM-dependent methyltransferases
  1. LmbE-like [102588] (1)
    uperfamily
    1. LmbE-like [102589] (2)
      putative deacetylases
96. PLP-dependent transferase-like [53382] (3)
  main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
  1. PLP-dependent transferases [53383] (9)
    uperfamily
    1. AAT-like [53384] (28)
    2. Beta-eliminating lyases [53397] (4)
    3. Pyridoxal-dependent decarboxylase [69565] (3)
    4. Cystathionine synthase-like [53402] (24)
    5. GABA-aminotransferase-like [53417] (27)
      formerly omega-Aminoacid:pyruvate aminotransferase-like
    6. Ornithine decarboxylase major domain [53444] (1)
    7. Glycine dehydrogenase subunits (GDC-P) [142678] (2)
      Pfam 02347
    8. SelA-like [142683] (1)
      Pfam 03841
    9. SepSecS-like [159704] (3)
      Pfam 05889
  2. PhnH-like [159709] (1)
    single domain protein of similar topology to the core domain of PLP-transferases
    1. PhnH-like [159710] (1)
      Pfam 05845; Bacterial phosphonate metabolism protein (PhnH)
  3. Dhaf3308-like [159713] (1)
    not known to bind PLP cofactor; the extra N-terminal subdomain has a enolase N-terminal domain-like fold (scop_cf 54825)
    1. Dhaf3308-like [159714] (1)
      Pfam 04016; DUF364
97. Nucleotide-diphospho-sugar transferases [53447] (1)
  3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
  1. Nucleotide-diphospho-sugar transferases [53448] (19)
    uperfamily
    1. Spore coat polysaccharide biosynthesis protein SpsA [53449] (1)
    2. beta 1,4 galactosyltransferase (b4GalT1) [53452] (1)
    3. Galactosyltransferase LgtC [53458] (1)
    4. Glycogenin [75273] (1)
    5. alpha-1,3-galactosyltransferase-like [64131] (3)
    6. UDP-glucose pyrophosphorylase [53461] (6)
    7. glucose-1-phosphate thymidylyltransferase [53464] (6)
    8. 1,3-glucuronyltransferase [53467] (2)
    9. N-acetylglucosaminyltransferase I [64136] (1)
    10. Exostosin [89760] (1)
    11. Molybdenum cofactor biosynthesis protein MobA [53470] (1)
    12. Cytidylytransferase [68901] (12)
    13. Glycolipid 2-alpha-mannosyltransferase [102609] (1)
    14. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117702] (1)
    15. MGS-like [142691] (1)
      contains extra C-terminal all-alpha subdomain: 5 helices, orthogonal array
    16. TTHA0179-like [159717] (1)
    17. mannose-1-phosphate guanylyl transferase [159720] (1)
    18. MM2497-like [159723] (1)
      Pfam 01983; DUF121
    19. Glycosylating toxin catalytic domain-like [159726] (3)
      contains Glycosyltransferase sugar-binding region containing DXD motif, Pfam 04488
98. RibA-like [142694] (1)
  3 layers: a/b/a; mixed beta-sheet of 7 strands, order 1235467, strands 1 and 3 are antiparallel to the rest; partial topological similarity to some alpha/beta hydrolases (scop_cf 53473)
  1. RibA-like [142695] (1)
    uperfamily
    1. RibA-like [142696] (1)
      Pfam 00925; GTP cyclohydrolase II
99. Activating enzymes of the ubiquitin-like proteins [69571] (1)
  3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
  1. Activating enzymes of the ubiquitin-like proteins [69572] (2)
    transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins
    the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
    uperfamily
    1. Molybdenum cofactor biosynthesis protein MoeB [69573] (1)
    2. Ubiquitin activating enzymes (UBA) [89763] (2)
      the common fold is elaborated with additional (sub)domains
100. alpha/beta-Hydrolases [53473] (1)
  core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
  1. alpha/beta-Hydrolases [53474] (41)
    many members have left-handed crossover connection between strand 8 and additional strand 9
    uperfamily
    1. Acetylcholinesterase-like [53475] (11)
    2. Carboxylesterase [53487] (9)
    3. Mycobacterial antigens [53491] (4)
    4. Hypothetical protein TT1662 [102616] (1)
    5. PepX catalytic domain-like [69581] (4)
    6. Prolyl oligopeptidase, C-terminal domain [53496] (1)
      N-terminal domain is a 7-bladed beta-propeller
    7. DPP6 catalytic domain-like [82497] (3)
      N-terminal domain is a 8-bladed beta-propeller
    8. Serine carboxypeptidase-like [53499] (5)
    9. Gastric lipase [53506] (2)
    10. Proline iminopeptidase-like [53509] (3)
    11. Acetyl xylan esterase-like [82504] (2)
      Pfam 05448; AXE1
    12. Haloalkane dehalogenase [53513] (3)
    13. Dienelactone hydrolase [53518] (2)
    14. Carbon-carbon bond hydrolase [53522] (4)
      closely related to the Proline iminopeptidase-like family
    15. Biotin biosynthesis protein BioH [82509] (1)
    16. Aclacinomycin methylesterase RdmC [102620] (1)
    17. Carboxylesterase/lipase [102623] (1)
    18. Epoxide hydrolase [53525] (4)
    19. Haloperoxidase [53531] (7)
    20. Thioesterases [53542] (3)
    21. Carboxylesterase/thioesterase 1 [53547] (5)
    22. Ccg1/TafII250-interacting factor B (Cib) [75285] (1)
    23. A novel bacterial esterase [53552] (1)
    24. Lipase [53555] (1)
    25. Fungal lipases [53558] (12)
    26. Bacterial lipase [53570] (7)
      lack the first two strands of the common fold
    27. Pancreatic lipase, N-terminal domain [53577] (6)
    28. Hydroxynitrile lyase-like [53585] (3)
    29. Thioesterase domain of polypeptide, polyketide and fatty acid synthases [69584] (4)
      Pfam 00975
    30. Cutinase-like [52260] (3)
      minimal alpha/beta hydrolase lacking peripheral secondary structures; similar to a flavodoxin-like fold
    31. YdeN-like [110699] (1)
      Pfam 06821; DUF1234; lack the first two strands of the common fold
    32. Putative serine hydrolase Ydr428c [110702] (1)
    33. Acylamino-acid-releasing enzyme, C-terminal donain [117711] (1)
      closely related to the prolyl peptidase and DPP6 domains (scop_fa 53496 and 82497)
    34. Hypothetical esterase YJL068C [117714] (1)
      part of Pfam 00756
    35. Hypothetical protein VC1974 [117717] (1)
    36. Atu1826-like [159742] (2)
    37. PHB depolymerase-like [159747] (1)
    38. IroE-like [159750] (1)
    39. TTHA1544-like [159753] (1)
      minimal hydrolase fold (one strand less than the cutinase-like family); there is neither catalytic triad, nor nucleopilic residue in the elbow motif
    40. O-acetyltransferase [159756] (3)
    41. 2,6-dihydropseudooxynicotine hydrolase-like [159762] (1)
      Pfam 06500; DUF1100
101. Nucleoside hydrolase [53589] (1)
  core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
  1. Nucleoside hydrolase [53590] (1)
    uperfamily
    1. Nucleoside hydrolase [53591] (4)
102. Dihydrofolate reductase-like [53596] (1)
  3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
  1. Dihydrofolate reductase-like [53597] (2)
    uperfamily
    1. Dihydrofolate reductases [53598] (12)
    2. RibD C-terminal domain-like [142701] (3)
      Pfam 01872
103. Ribokinase-like [53612] (3)
  core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
  potential superfamily: members of this fold have similar functions but different ATP-binding sites
  1. Ribokinase-like [53613] (5)
    has extra strand located between strands 2 and 3
    uperfamily
    1. Thiamin biosynthesis kinases [53620] (4)
    2. YjeF C-terminal domain-like [75292] (2)
    3. PfkB-like kinase [82515] (2)
      includes a variety of carbohydrate and pyrimidine kinases
    4. Ribokinase-like [53614] (13)
    5. ADP-specific Phosphofructokinase/Glucokinase [64147] (3)
      Pfam 04587
  2. MurD-like peptide ligases, catalytic domain [53623] (2)
    has extra strand located between strands 1 and 2
    uperfamily
    1. MurCDEF [53624] (5)
    2. Folylpolyglutamate synthetase [53629] (2)
  3. CoaB-like [102645] (1)
    combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest
    uperfamily
    1. CoaB-like [102646] (2)
      Pfam 04127
104. YjeF N-terminal domain-like [64152] (1)
  3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest
  1. YjeF N-terminal domain-like [64153] (1)
    possible circular permutation of the ribokinase-like fold (of the YjeF C-terminal domain)
    uperfamily
    1. YjeF N-terminal domain-like [64154] (2)
105. Carbamate kinase-like [53632] (1)
  3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
  1. Carbamate kinase-like [53633] (3)
    the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase
    uperfamily
    1. Carbamate kinase [53634] (2)
    2. N-acetyl-l-glutamate kinase [75297] (4)
    3. PyrH-like [142721] (10)
      part of Pfam 00696
106. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64157] (1)
  core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest
  1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64158] (1)
    uperfamily
    1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64159] (1)
107. Alkaline phosphatase-like [53648] (1)
  core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
  1. Alkaline phosphatase-like [53649] (5)
    uperfamily
    1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64162] (1)
    2. Alkaline phosphatase [53650] (3)
      common fold is decorated with several large insertions
    3. Arylsulfatase [53653] (4)
      includes additional C-terminal alpha+beta (sub)domain
    4. Phosphonoacetate hydrolase [102651] (1)
      contains alpha+beta subdomain inserted near C-terminus
    5. DeoB catalytic domain-like [142735] (1)
      Pfam 08342 in the N-terminal part; Pfam 01676 in the C-terminal part; there is an alpha+beta domain between the two parts, inserted in the same location as the substrate-binding domain of 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
108. TTHA0583/YokD-like [110709] (1)
  3 layers: a/b/a; mixed beta-sheet of 8 strands, order 78612354; strands 3, 4 and 8 are antiparallel to the rest
  1. TTHA0583/YokD-like [110710] (2)
    uperfamily
    1. Hypothetical protein TT1679 [110711] (1)
      Pfam 04260, DUF436
    2. Aminoglycoside 3-N-acetyltransferase-like [159765] (1)
      Pfam 02522; CoA-dependent enzymes
109. Glycerol-3-phosphate (1)-acyltransferase [69592] (1)
  3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8 are antiparallel to the rest
  1. Glycerol-3-phosphate (1)-acyltransferase [69593] (1)
    some topological similarity to the dihydrofolate reductase fold
    uperfamily
    1. Glycerol-3-phosphate (1)-acyltransferase [69594] (1)
110. AraD/HMP-PK domain-like [53638] (1)
  3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
  1. AraD/HMP-PK domain-like [53639] (2)
    uperfamily
    1. AraD-like aldolase/epimerase [53640] (4)
      metal (zinc)-ion dependent
    2. Phosphomethylpyrimidine kinase C-terminal domain-like [159768] (2)
111. SurE-like [64166] (1)
  3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7
  1. SurE-like [64167] (1)
    some topological similarity to the N-terminal domain of Glutaminase/Asparaginase family
    uperfamily
    1. SurE-like [64168] (2)
112. YerB-like [159773] (1)
  3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4
  1. YerB-like [159774] (1)
    1. YerB-like [159775] (1)
      PfamB 028118
113. CdCA1 repeat-like [159778] (1)
  contains two parallel beta-strands of four strands each; the sheets contact each other with edges at a right angle
  1. CdCA1 repeat-like [159779] (1)
    1. CdCA1 repeat-like [159780] (1)
      Pfam 10563
114. Isocitrate/Isopropylmalate dehydrogenase-like [53658] (1)
  consists of two intertwined (sub)domains related by pseudo dyad; duplication
  3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
  1. Isocitrate/Isopropylmalate dehydrogenase-like [53659] (5)
    the constituent families form similar dimers
    uperfamily
    1. Dimeric isocitrate & isopropylmalate dehydrogenases [53660] (13)
      the active site is between the two identical subunits
    2. PdxA-like [102656] (2)
      Pfam 04166; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PlsX-like and phosphotransacetylase families
    3. PlsX-like [102660] (2)
      Pfam 02504; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and phosphotransacetylase families
    4. Phosphotransacetylase [102663] (4)
      Pfam 01515; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and PlsX-like families
    5. Monomeric isocitrate dehydrogenase [82526] (1)
      the active site is contained within one subunit between the canonical ICDH fold and a large insert domain that itself is a probable rudiment form of ICDH fold resulted from duplication, domain swapping and deletion
115. Amidase signature (AS) enzymes [75303] (1)
  possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest
  1. Amidase signature (AS) enzymes [75304] (1)
    uperfamily
    1. Amidase signature (AS) enzymes [75305] (5)
116. ATC-like [53670] (2)
  consists of two similar domains related by pseudo dyad; duplication
  core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
  1. Aspartate/ornithine carbamoyltransferase [53671] (1)
    uperfamily
    1. Aspartate/ornithine carbamoyltransferase [53672] (11)
  2. Aspartate/glutamate racemase [53681] (1)
    uperfamily
    1. Aspartate/glutamate racemase [53682] (3)
      C-terminal extension is added to the N-terminal domain
117. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53685] (1)
  consists of two similar domains related by pseudo dyad; duplication
  core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
  1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53686] (1)
    uperfamily
    1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53687] (22)
118. SIS domain [53696] (1)
  3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
  1. SIS domain [53697] (3)
    uperfamily
    1. mono-SIS domain [69599] (8)
      dimer of mono-domain subunits
    2. double-SIS domain [53698] (4)
      duplication: consists of two SIS domains related by pseudo dyad
    3. Phosphoglucose isomerase, PGI [53701] (6)
      permutation of the double-SIS domain fold
119. Formate dehydrogenase/DMSO reductase, domains 1-3 [53705] (1)
  contains of two similar intertwined domains related by pseudo dyad; duplication
  core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
  1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53706] (1)
    molybdopterine enzyme
    uperfamily
    1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53707] (12)
      domain 1 (residues 1-55) binds Fe4S4 cluster in FDH but not DMSO reductase
120. ALDH-like [53719] (1)
  consists of two similar domains with 3 layers (a/b/a) each; duplication
  core: parallel beta-sheet of 5 strands, order 32145
  1. ALDH-like [53720] (2)
    binds NAD differently from other NAD(P)-dependent oxidoreductases
    uperfamily
    1. ALDH-like [53721] (14)
    2. L-histidinol dehydrogenase HisD [69602] (1)
121. NadA-like [142753] (1)
  duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134
  1. NadA-like [142754] (1)
    uperfamily
    1. NadA-like [142755] (1)
      Pfam 02445
122. Aconitase iron-sulfur domain [53731] (1)
  consists of three similar domains with 3 layers (a/b/a) each; duplication
  core: parallel beta-sheet of 5 strands, order 32145
  1. Aconitase iron-sulfur domain [53732] (1)
    uperfamily
    1. Aconitase iron-sulfur domain [53733] (4)
      duplication: consists of three structurally similar subdomains with subdomains 1 and 3 being related by pseudo twofold symmetry
123. Phosphoglucomutase, first 3 domains [53737] (1)
  consists of three similar domains with 3 layers (a/b/a) each; duplication
  core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
  1. Phosphoglucomutase, first 3 domains [53738] (1)
    uperfamily
    1. Phosphoglucomutase, first 3 domains [53739] (3)
124. FucI/AraA N-terminal and middle domains [53742] (1)
  consists of two domains of similar topology, 3 layers (a/b/a) each
  Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
  Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
  1. FucI/AraA N-terminal and middle domains [53743] (2)
    uperfamily
    1. L-fucose isomerase, N-terminal and second domains [53744] (1)
    2. AraA N-terminal and middle domain-like [142760] (1)
      N-terminal part of Pfam 02610
125. YgbK-like [142763] (1)
  consists of two domains with partial topological similarity to the P-loop kinases but without the P-loop motif; the domain association results in the formation of a single mixed beta-sheet of 15 strands
  1. YgbK-like [142764] (1)
    uperfamily
    1. YgbK-like [142765] (1)
      Pfam 07005; DUF1537; the B-fam model-covered region is non-compact in structure and distributed between the two domains
126. Phosphoglycerate kinase [53747] (1)
  consists of two non-similar domains, 3 layers (a/b/a) each
  Domain 1 has parallel beta-sheet of 6 strands, order 342156
  Domain 2 has parallel beta-sheet of 6 strands, order 321456
  1. Phosphoglycerate kinase [53748] (1)
    uperfamily
    1. Phosphoglycerate kinase [53749] (7)
      Domain 2 binds ATP
127. UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1)
  consists of two non-similar domains with 3 layers (a/b/a) each
  domain 1: parallel beta-sheet of 7 strands, order 3214567
  domain 2: parallel beta-sheet of 6 strands, order 321456
  1. UDP-Glycosyltransferase/glycogen phosphorylase [53756] (11)
    uperfamily
    1. beta-Glucosyltransferase (DNA-modifying) [53757] (1)
    2. Peptidoglycan biosynthesis glycosyltransferase MurG [53760] (1)
    3. UDP-N-acetylglucosamine 2-epimerase [53763] (3)
    4. Gtf glycosyltransferase [64178] (3)
      Glycosyltransferase family 28
    5. ADP-heptose LPS heptosyltransferase II [89784] (1)
    6. Trehalose-6-phosphate synthase, OtsA [82540] (1)
      family 20 glycosyltransferase; good structural similarity in the active site to the Oligosaccharide phosphorylases
    7. Oligosaccharide phosphorylase [53766] (4)
    8. Glycosyl transferases group 1 [110734] (4)
      Pfam 00534
    9. Sialyltransferase-like [142773] (1)
    10. UDPGT-like [159785] (4)
      Pfam 00201
    11. FucT-like [159794] (1)
      Pfam 00852; Glycosyltransferase family 10 (fucosyltransferase)
128. Glutaminase/Asparaginase [53773] (1)
  consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
  Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
  Domain 2 has parallel beta-sheet of 4 strands, order 1234
  1. Glutaminase/Asparaginase [53774] (1)
    uperfamily
    1. Glutaminase/Asparaginase [53775] (8)
129. Phosphofructokinase [53783] (1)
  consists of two non-similar domains, 3 layers (a/b/a) each
  Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
  Domain 2 has parallel sheet of 4 strands, order 2314
  1. Phosphofructokinase [53784] (1)
    uperfamily
    1. Phosphofructokinase [53785] (3)
130. Tetrapyrrole methylase [53789] (1)
  consists of two non-similar domains
  Domain 1 has parallel sheet of 5 strands, order 32415
  Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
  1. Tetrapyrrole methylase [53790] (1)
    uperfamily
    1. Tetrapyrrole methylase [53791] (10)
      Pfam 00590
131. GckA/TtuD-like [82543] (1)
  consists of two non-similar domains
  Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology
  Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2
  1. GckA/TtuD-like [82544] (1)
    uperfamily
    1. GckA/TtuD-like [82545] (1)
132. DAK1/DegV-like [82548] (1)
  2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order: 2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest]
  1. DAK1/DegV-like [82549] (2)
    domain folds and architecture show some similarity to the tubulin-like GTPases; the nucleotide-binding sites of the Dihydroxyacetone kinase and tubulin families are different
    uperfamily
    1. DegV-like [82550] (2)
      Pfam 02645, DUF194
    2. DAK1 [109613] (2)
      Pfam 02733
133. DHH phosphoesterases [64181] (1)
  consists of two non-similar domains
  Domain 1 has parallel sheet of 6 strands, order 321456
  Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest
  1. DHH phosphoesterases [64182] (2)
    constituent families have similar domain organization with variable interdomain linker and spatial arrangement of the domains
    uperfamily
    1. Manganese-dependent inorganic pyrophosphatase (family II) [64183] (3)
    2. Exonuclease RecJ [75323] (1)
134. Glycerate kinase I [110737] (1)
  consists of two different alpha/beta domains; (1) of the Flavodoxin-like fold (scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf 52979), inserted into domain 1
  1. Glycerate kinase I [110738] (1)
    uperfamily
    1. Glycerate kinase I [110739] (1)
      Pfam 02595
135. PEP carboxykinase-like [53794] (1)
  contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
  1. PEP carboxykinase-like [53795] (2)
    uperfamily
    1. PEP carboxykinase C-terminal domain [53796] (4)
    2. HPr kinase HprK C-terminal domain [64186] (3)
136. PEP carboxykinase N-terminal domain [68922] (1)
  contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain
  1. PEP carboxykinase N-terminal domain [68923] (1)
    uperfamily
    1. PEP carboxykinase N-terminal domain [68924] (4)
137. Chelatase-like [53799] (3)
  duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
  1. Chelatase [53800] (3)
    interdomain linker is short; swapping of C-terminal helices between the two domains
    uperfamily
    1. Ferrochelatase [53801] (3)
    2. Cobalt chelatase CbiK [53804] (1)
    3. CbiX-like [110742] (1)
      Pfam 01903; single-domain protein; forms the C-terminal helix-swapped dimer similar to the CbiK subunit
  2. "Helical backbone" metal receptor [53807] (4)
    contains a long alpha helical insertion in the interdomain linker
    uperfamily
    1. Periplasmic ferric siderophore binding protein FhuD [53808] (1)
    2. TroA-like [53811] (5)
    3. Nitrogenase iron-molybdenum protein [53816] (6)
      contains three domains of this fold; "Helical backbone" holds domains 2 and 3
      both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
    4. TM0189-like [142789] (3)
      Part of Pfam 01497 that include some other superfamily members
  3. PrpR receptor domain-like [159800] (1)
    recent PDB entry 2q5c belongs to this superfamily
    1. PrpR receptor domain-like [159801] (1)
      N-terminal domain corresponds to Pfam 06506; C-terminal domain, assigned to Pfam 00158, is distinct from other structures of this Pfam family
138. HemD-like [69617] (1)
  duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345
  1. HemD-like [69618] (1)
    uperfamily
    1. HemD-like [69619] (2)
      Pfam 02602
139. CAC2185-like [142794] (1)
  consists of two non-similar domains, 3 layers (a/b/a) each; d1 has parallel sheet of 4 strands, order 2134; d2 has parallel sheet of 5 strands, order 21345, and antiparallel meander sheet of 3 strands
  1. CAC2185-like [142795] (1)
    uperfamily
    1. CAC2185-like [142796] (1)
140. Periplasmic binding protein-like I [53821] (1)
  consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
  parallel beta-sheet of 6 strands, order 213456
  1. Periplasmic binding protein-like I [53822] (1)
    Similar in architecture to the superfamily II but partly differs in topology
    uperfamily
    1. L-arabinose binding protein-like [53823] (18)
141. Periplasmic binding protein-like II [53849] (1)
  consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
  mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
  1. Periplasmic binding protein-like II [53850] (3)
    Similar in architecture to the superfamily I but partly differs in topology
    uperfamily
    1. Phosphate binding protein-like [53851] (65)
    2. Transferrin [53888] (11)
      further duplication: composed of two two-domain lobes
    3. PG0945 N-terminal domain-like [159818] (1)
      truncated to one domain; extra C-terminal region provides dimerisation interface
142. Thiolase-like [53900] (1)
  consists of two similar domains related by pseudo dyad; duplication
  3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
  1. Thiolase-like [53901] (2)
    uperfamily
    1. Thiolase-related [53902] (12)
    2. Chalcone synthase-like [53914] (10)
143. NIF3 (NGG1p interacting factor 3)-like [102704] (1)
  consist of two intertwined domains; duplication: contains two structural repeats of alpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 is antiparallel to the rest
  1. NIF3 (NGG1p interacting factor 3)-like [102705] (1)
    di-iron binding protein
    uperfamily
    1. NIF3 (NGG1p interacting factor 3)-like [102706] (3)
      Pfam 01784
144. Fe-only hydrogenase [53919] (1)
  consist of two intertwined domains; contains partial duplication
  1. Fe-only hydrogenase [53920] (1)
    uperfamily
    1. Fe-only hydrogenase [53921] (2)
145. ComB-like [142822] (1)
  contains of two similar intertwined domains related by pseudo dyad; duplication; core: 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 1423
  1. ComB-like [142823] (1)
    uperfamily
    1. ComB-like [142824] (1)
      Pfam 04029; 2-phosphosulpholactate phosphatase
146. CoA-transferase family III (CaiB/BaiF) [89795] (1)
  consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit
  1. CoA-transferase family III (CaiB/BaiF) [89796] (1)
    uperfamily
    1. CoA-transferase family III (CaiB/BaiF) [89797] (4)
      forms interlocked homodimer of two ring-like subunits
147. Cytidine deaminase-like [53926] (2)
  core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 1 is antiparallel to the rest
  1. Cytidine deaminase-like [53927] (5)
    contains extra C-terminal strand 5, order 21345
    uperfamily
    1. Cytidine deaminase [53928] (7)
      strand 5 is antiparallel to strand 4
    2. Deoxycytidylate deaminase-like [89800] (10)
      strand 5 is parallel to strand 4
    3. Hypothetical protein TM1506 [110651] (1)
      strand 5 is parallel to strand 4
    4. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64198] (3)
      duplication: consists of two domains of this fold with extra secondary structures within and in between the two core motifs
    5. FdhD/NarQ [159821] (1)
      Pfam 02634; contains extra N-terminal beta-hairpin arm, involved in dimerization, and an alpha+beta subdomain of beta-grasp fold (scop_cf 54235)
  2. JAB1/MPN domain [102712] (1)
    uperfamily
    1. JAB1/MPN domain [102713] (1)
      Pfam 01398; synonyms Mov34, PAD-1;
Alpha and beta proteins (a+b) [53931] (376)
Mainly antiparallel beta sheets (segregated alpha and beta regions)
1. Microbial ribonucleases [53932] (1)
  single helix packs against antiparallel beta-sheet
  1. Microbial ribonucleases [53933] (3)
    uperfamily
    1. Bacterial ribonucleases [81307] (5)
    2. Fungal ribonucleases [81311] (5)
    3. Ribotoxin [81310] (2)
      the fungal cytotoxic ribonucleases with many insertions in the common fold
2. Lysozyme-like [53954] (1)
  common alpha+beta motif for the active site region
  1. Lysozyme-like [53955] (11)
    uperfamily
    1. Family 19 glycosidase [53956] (2)
    2. C-type lysozyme [53960] (20)
    3. Phage lysozyme [53981] (3)
    4. Lambda lysozyme [53984] (1)
    5. G-type lysozyme [53987] (2)
    6. Bacterial muramidase, catalytic domain [53991] (2)
      the large N-terminal domain is all-alpha superhelix
    7. Chitosanase [53996] (2)
    8. RPF-like [159824] (1)
      Pfam 06737; Transglycosylase-like domain
    9. NMB1012-like [159827] (2)
      Pfam 05838; predicted lysozyme (DUF847)
    10. PBP transglycosylase domain-like [159832] (2)
      Pfam 00912; lacking the characteristic beta-sheet; otherwise has a similar fold to the Family 19 glycosidase
    11. PA2222-like [159837] (1)
      PfamB 104465
3. Cysteine proteinases [54000] (1)
  consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
  1. Cysteine proteinases [54001] (22)
    the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet
    uperfamily
    1. Papain-like [54002] (30)
    2. Avirulence protein Avrpph3 [102723] (1)
    3. FMDV leader protease [54037] (1)
    4. Calpain large subunit, catalytic domain (domain II) [54040] (5)
    5. Transglutaminase core [54044] (6)
    6. Arylamine N-acetyltransferase [54047] (4)
      fold similar to that of the factor XIII catalytic domain
    7. Ubiquitin carboxyl-terminal hydrolase UCH-L [54050] (3)
    8. Ubiquitin carboxyl-terminal hydrolase, UCH [82568] (5)
      Pfam 00443
    9. Adenain-like [54054] (5)
      Pfam 02902; Ulp1 protease family
    10. Microbial transglutaminase [75336] (1)
      inverted positions of the catalytic triad Asp and His residues
    11. Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [110773] (1)
      probably the same as Pfam 02338, OTU-like cysteine protease, but 1TFF (SQ Q96DC9) was not detected by the Pfam model
    12. IgG-specific endopeptidase IdeS (Sib38) [117762] (1)
    13. Lpg0564-like [142864] (1)
      Pfam 07313, DUF1460; contains new PDB entry 2p1g, annotated as putative xylanase
    14. Phytochelatin synthase [142867] (1)
      Pfam 05023; assosiated Pfam 09328 (DUF1984) is a part of the same functional unit
    15. CHAP domain [142870] (1)
      Pfam 05257
    16. NlpC/P60 [142873] (1)
      Pfam 00877
    17. PMT C-terminal domain like [159843] (1)
      displays a minimal thiol-protease fold and its catalytic triad; potential redox regulation: the catalytic cysteine can form a disulfide bond with an N-terminal cysteine
    18. MOA C-terminal domain-like [159846] (1)
      PfamB 070855
    19. Atu2299-like [159849] (1)
      Pfam 09641; DUF2026; putative Cys/Ser-His-Asp catalytic triad
    20. M48USP-like [159852] (1)
      Pfam 04843; Herpesvirus tegument protein, N-terminal conserved region
    21. YiiX-like [159855] (1)
      Pfam 06520; DUF1105; circularly permuted active site residues compare to papain
    22. Autophagin-like [159858] (2)
      Pfam 03416
4. His-Me finger endonucleases [54059] (1)
  core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
  1. His-Me finger endonucleases [54060] (6)
    common motif contains conserved histidine residue and metal-binding site
    uperfamily
    1. Endonuclease I [102726] (1)
    2. HNH-motif [54061] (2)
    3. DNA/RNA non-specific endonuclease [54066] (2)
      the core motif is inserted in a six-stranded meander beta-sheet domain
    4. Intron-encoded homing endonucleases [54069] (2)
    5. Recombination endonuclease VII, N-terminal domain [68915] (1)
    6. Caspase-activated DNase, CAD (DffB, DFF40) [110778] (1)
5. RNase A-like [54075] (1)
  contains long curved beta-sheet and 3 helices
  1. RNase A-like [54076] (1)
    can be classified as disulfide-rich
    uperfamily
    1. Ribonuclease A-like [54077] (15)
6. EndoU-like [142876] (1)
  comprises several helices and two three-stranded antiparallel beta-sheets; similar architecture to the RNase A-like fold (scop_cf 54075)
  1. EndoU-like [142877] (2)
    similarity to the RNase A-like superfamily (scop_sf 54076) extends to the active site location and architecture; the two structural cores of the RNase A and EndoU superfamilies are interrelated by a topological permutation - transposition of two pereferial beta-strands, suggesting possible distant homology of the two superfamilies (and their unification in a hyperfamily)
    uperfamily
    1. Eukaryotic EndoU ribonuclease [142878] (1)
      PfamB 010233; common fold decorated with additional structures
    2. Nsp15 C-terminal domain-like [142881] (2)
      PfamB 001946
7. Prion-like [54097] (1)
  beta-alpha-beta-alpha(2); antiparallel beta-ribbon
  1. Prion-like [54098] (1)
    uperfamily
    1. Prion-like [54099] (14)
8. LysM domain [54105] (1)
  beta-alpha(2)-beta; antiparallel strands
  1. LysM domain [54106] (1)
    uperfamily
    1. LysM domain [54107] (2)
9. gpW/XkdW-like [64209] (2)
  alpha-beta(2)-alpha; antiparallel hairpin
  1. Head-to-tail joining protein W, gpW [64210] (1)
    uperfamily
    1. Head-to-tail joining protein W, gpW [64211] (1)
  2. XkdW-like [159865] (1)
    different packing of secondary structures than in gpW
    1. XkdW-like [159866] (1)
      Pfam 09636
10. Hypothetical protein MTH677 [110782] (1)
  alpha-beta(2)-alpha; 2 layers a/b; antiparallel beta-hairpin
  1. Hypothetical protein MTH677 [110783] (1)
    uperfamily
    1. Hypothetical protein MTH677 [110784] (1)
11. GTF2I-like repeat [117772] (1)
  alpha(2)-beta-alpha-beta-alpha; 2 layers: a/b; antiparallel beta-ribbon
  1. GTF2I-like repeat [117773] (1)
    uperfamily
    1. GTF2I-like repeat [117774] (1)
      Pfam 02946
12. Urease, gamma-subunit [54110] (1)
  alpha(3)-beta(2); antiparallel hairpin
  1. Urease, gamma-subunit [54111] (1)
    uperfamily
    1. Urease, gamma-subunit [54112] (3)
13. IL8-like [54116] (2)
  beta(3)-alpha
  1. Interleukin 8-like chemokines [54117] (1)
    form dimers with different dimerisation modes
    uperfamily
    1. Interleukin 8-like chemokines [54118] (29)
  2. PhtA domain-like [142887] (1)
    contains extra N-terminal beta-hairpin, like structurally similar archaeal "histone-like" proteins (scop_fa 54161), but does not adopt its SH3-like barrel fold
    uperfamily
    1. PhtA domain-like [142888] (1)
      Pfam 04270; Streptococcal histidine triad protein
14. DNA-binding domain [54170] (1)
  beta(3)-alpha; 2 layers: alpha/beta
  1. DNA-binding domain [54171] (4)
    uperfamily
    1. DNA-binding domain from tn916 integrase [54172] (1)
    2. lambda integrase N-terminal domain [75344] (1)
    3. GCC-box binding domain [54175] (1)
    4. Methyl-CpG-binding domain, MBD [54178] (3)
15. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54183] (1)
  alpha1-beta3; 2 layers: alpha/beta; order 132
  1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54184] (1)
    duplication: consists of 2 subdomains of this fold
    uperfamily
    1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54185] (1)
16. Dodecin subunit-like [88797] (6)
  beta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132
  1. Dodecin-like [89807] (1)
    uperfamily
    1. Dodecin-like [89808] (2)
      Subunit assembly and a probable biological unit is a dodecamer, hence the name
  2. Amyloid beta a4 protein copper binding domain (domain 2) [89811] (1)
    uperfamily
    1. Amyloid beta a4 protein copper binding domain (domain 2) [89812] (1)
  3. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88798] (1)
    uperfamily
    1. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88799] (3)
  4. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117778] (1)
    uperfamily
    1. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117779] (1)
  5. YbjQ-like [117782] (1)
    pentamer, beta/alpha-propeller; additional short beta-strands promote oligomeric assembly
    uperfamily
    1. YbjQ-like [117783] (2)
      Pfam 01906; DUF 74, UPF0145
  6. YdgH-like [159871] (1)
    extra N-terminal structures: short strand and short helix; topological similarity to the YbjQ-like superfamily
    1. YdgH-like [159872] (2)
      Pfam 07338; DUF1471
17. Ribosomal proteins S24e, L23 and L15e [54188] (1)
  beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
  1. Ribosomal proteins S24e, L23 and L15e [54189] (3)
    uperfamily
    1. L23p [54190] (4)
    2. L15e [54193] (1)
      elaborated with additional structures
    3. Ribosomal protein S24e [117786] (4)
      Pfam 01282
18. Ribosome binding domain-like [100965] (2)
  beta-(2)-alpha(2)-beta(2); 2 layers: beta/alpha; antiparallel beta-sheet: order 1243; topological similarity to the common core of ribosomal proteins L23 and L15e
  1. Trigger factor ribosome-binding domain [102735] (1)
    uperfamily
    1. Trigger factor ribosome-binding domain [102736] (2)
  2. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100966] (1)
    uperfamily
    1. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100967] (2)
19. TFB5-like [142896] (1)
  beta-alpha-beta(2)-alpha; 2 layers, a/b; antiparallel sheet, order: 132; dimerises in solution (PDB 2jnj) via extended N-terminal strand
  1. TFB5-like [142897] (1)
    uperfamily
    1. TFB5-like [142898] (1)
      Pfam 06331
20. Obg GTP-binding protein C-terminal domain [102740] (1)
  beta-(2)-alpha(3)-beta(2); 2 layers: beta/alpha; mixed beta-sheet: order 1234; strands 2 and 3 a parallel to each other
  1. Obg GTP-binding protein C-terminal domain [102741] (1)
    uperfamily
    1. Obg GTP-binding protein C-terminal domain [102742] (1)
21. HIT-like [54196] (2)
  alpha-beta(3)-alpha-beta(2); 3 layers: alpha/beta/alpha
  1. HIT-like [54197] (4)
    uperfamily
    1. HIT (HINT, histidine triad) family of protein kinase-interacting proteins [54198] (7)
      Pfam 01230
      topologically similar to the N-terminal domain of protein kinases
    2. Hexose-1-phosphate uridylyltransferase [54207] (2)
      duplication: consists of 2 HIT-like motifs
      binds zinc and iron ions
    3. mRNA decapping enzyme DcpS C-terminal domain [102745] (2)
    4. CDH-like [159882] (1)
      Pfam 02611; CDP-diacylglycerol pyrophosphatase; duplication: consists of the N-terminal HIT subdomain and C-terminal rudiment HIT-like subdomain
  2. Rotavirus NSP2 fragment, C-terminal domain [75347] (1)
    uperfamily
    1. Rotavirus NSP2 fragment, C-terminal domain [75348] (1)
22. Secretion chaperone-like [69634] (5)
  alpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/beta
  1. Type III secretory system chaperone-like [69635] (2)
    uperfamily
    1. Type III secretory system chaperone [69636] (11)
      the family sequences are very divergent
    2. Tll0839-like [159885] (1)
      Pfam 08851; DUF1821; cyanobacterial family of similar subunit and dimer structures to the Type III secretory system chaperone from proteobacteria
  2. Arp2/3 complex subunits [69645] (1)
    uperfamily
    1. Arp2/3 complex subunits [69646] (2)
  3. YjbR-like [142906] (1)
    overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
    uperfamily
    1. YjbR-like [142907] (2)
      Pfam 04237; DUF419
  4. YdhG-like [159888] (1)
    some similarity to YjbR-like (scop_sf 136320)
    1. YdhG-like [159889] (2)
      Pfam 08818; DUF1801
  5. YgaC/TfoX-N like [159894] (2)
    overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
    1. YgaC-like [159895] (1)
      Pfam 09400; DUF2002
    2. TfoX N-terminal domain-like [159898] (1)
      Pfam 04993
23. DNA-binding domain of intron-encoded endonucleases [64495] (1)
  beta(2)-alpha(2)-beta; 2 layers; 3-stranded antiparallel beta-sheet, order 213; HTH motif; also includes the extra N-terminal, DNA minor groove-binding helix
  1. DNA-binding domain of intron-encoded endonucleases [64496] (1)
    uperfamily
    1. DNA-binding domain of intron-encoded endonucleases [64497] (2)
24. MotA C-terminal domain-like [69651] (1)
  alpha-beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta
  1. DNA-binding C-terminal domain of the transcription factor MotA [69652] (1)
    uperfamily
    1. DNA-binding C-terminal domain of the transcription factor MotA [69653] (1)
25. YktB/PF0168-like [142912] (1)
  alpha-beta(4)-alpha-beta(2)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order: 1234756; half-barrel shape; topological similarity to the MotA C-terminal domain-like fold (scop_cf 69651) and the Secretion chaperone-like fold (scop_cf 69634)
  1. YktB/PF0168-like [142913] (2)
    uperfamily
    1. YktB-like [142914] (1)
      Pfam 06335; DUF1054
    2. PF0168-like [142917] (1)
26. Mago nashi protein [89816] (1)
  beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, order: 651234
  1. Mago nashi protein [89817] (1)
    uperfamily
    1. Mago nashi protein [89818] (2)
27. WGR domain-like [142920] (1)
  beta(4)-alpha-X-beta; 2 layers, a/b; antiparallel beta-sheet, order 51234; the beta-hairpin insetrion in strand 1 results in the formation of a beta-triangle structure
  1. WGR domain-like [142921] (1)
    uperfamily
    1. WGR domain [142922] (1)
      Pfam 05406; the conserved WGR motif maps to the C-end of strand 3, both large sidechains are exposed
28. PH1570-like [159901] (1)
  duplication: two beta(4)-alpha structural repeats, related by pseudo twofold symmetry; two extra helices in the linker region; single 8-standed antiparallel beta-sheet, order: 12348765
  1. PH1570-like [159902] (1)
    1. PH1570-like [159903] (1)
      Pfam 09638
29. Ribosomal protein S5 domain 2-like [54210] (1)
  core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
  1. Ribosomal protein S5 domain 2-like [54211] (12)
    uperfamily
    1. Translational machinery components [54212] (8)
    2. RNase P protein [54220] (3)
    3. DNA gyrase/MutL, second domain [54224] (7)
    4. Hsp90 middle domain [102755] (1)
      related to the DNA gyrase/MutL family; contains extra C-terminal alpha/beta subdomain
    5. Ribonuclease PH domain 1-like [54229] (14)
    6. GHMP Kinase, N-terminal domain [54232] (10)
    7. Early switch protein XOL-1, N-terminal domain [89824] (1)
      diverged from the GHMP Kinase family; lost the ATP-binding site
    8. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89827] (1)
      duplication; there are two structural repeats of this fold; each repeat is elaborated with additional structures forming the active site
    9. Imidazole glycerol phosphate dehydratase [102766] (3)
      duplication; there are two structural repeats of this fold
    10. ATP-dependent protease Lon (La), catalytic domain [102769] (2)
      contains extra C-terminal alpha/beta subdomain
    11. YigZ N-terminal domain-like [102772] (2)
      modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand is inserted between strands 3 and 4
    12. Formaldehyde-activating enzyme, FAE [117795] (1)
      modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand extends beta-sheet antiparallel to strand 3
30. beta-Grasp (ubiquitin-like) [54235] (14)
  core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
  1. Ubiquitin-like [54236] (8)
    uperfamily
    1. Ubiquitin-related [54237] (47)
      Pfam 00240
    2. UBX domain [54250] (5)
      Pfam 00789
    3. GABARAP-like [54253] (5)
      intracellular membrane trafficking and fusion proteins
    4. First domain of FERM [54256] (7)
    5. Ras-binding domain, RBD [54263] (16)
      contains Pfam 00788 and Pfam 02196
    6. BM-002-like [75362] (3)
      Pfam 03671; UPF0185; this family comprises small uncharacterized proteins including human protein BM-002
    7. APG12-like [142972] (1)
      Pfam 04110
    8. DIX domain [159926] (1)
      Pfam 00778
  2. CAD & PB1 domains [54277] (2)
    contain extra helix; similar heterodimerization modes; possibly related to the ubiquitin-like superfamily
    uperfamily
    1. CAD domain [54278] (5)
    2. PB1 domain [64225] (11)
      Pfam 00564
      forms heterodimers, although not all PB1 domain pairs associate.
  3. MoaD/ThiS [54285] (4)
    possible link between the ubiquitin-like and 2Fe-2S ferredoxin-like superfamilies
    uperfamily
    1. MoaD [54286] (3)
    2. ThiS [54289] (5)
    3. C9orf74 homolog [117833] (1)
    4. HI0395-like [159931] (1)
      Pfam 03658; UPF0125
  4. TGS-like [81271] (2)
    possibly related to the ubiquitin-like and MoaD/ThiS superfamilies; some similarity to the alpha-L RNA-binding motif
    uperfamily
    1. TGS domain [81270] (2)
    2. G domain-linked domain [82583] (3)
  5. 2Fe-2S ferredoxin-like [54292] (2)
    uperfamily
    1. 2Fe-2S ferredoxin-related [54293] (19)
    2. 2Fe-2S ferredoxin domains from multidomain proteins [54312] (16)
  6. Staphylokinase/streptokinase [54328] (1)
    uperfamily
    1. Staphylokinase/streptokinase [54329] (2)
  7. Doublecortin (DC) [89837] (1)
    possibly related to the ubiquitin-like superfamily
    uperfamily
    1. Doublecortin (DC) [89838] (2)
  8. Superantigen toxins, C-terminal domain [54334] (1)
    uperfamily
    1. Superantigen toxins, C-terminal domain [54335] (15)
  9. Immunoglobulin-binding domains [54358] (1)
    uperfamily
    1. Immunoglobulin-binding domains [54359] (2)
  10. Translation initiation factor IF3, N-terminal domain [54364] (1)
    uperfamily
    1. Translation initiation factor IF3, N-terminal domain [54365] (1)
  11. Glutamine synthetase, N-terminal domain [54368] (1)
    uperfamily
    1. Glutamine synthetase, N-terminal domain [54369] (2)
  12. TmoB-like [110814] (1)
    possibly related to the ubiquitin-like and/or 2Fe-2S ferredoxin-like superfamilies
    uperfamily
    1. TmoB-like [110815] (1)
      Pfam 06234
  13. Nqo1 middle domain-like [142984] (1)
    possibly evolved from 2Fe-2S ferredoxins; contains no iron-sulfur cluster
    uperfamily
    1. Nqo1 middle domain-like [142985] (1)
      C-terminal part of Pfam 01512
  14. NSP3A-like [159936] (1)
    short helical inserions in the common fold
    1. NSP3A-like [159937] (1)
31. MM3350-like [159940] (1)
  beta(2)-alpha-beta(4); antiparallel beta-sheet; order: 216534; similar to a ubiquitin-like fold with the extra C-terminal strand inserted in the middle of the beta-sheet
  1. MM3350-like [159941] (1)
    1. MM3350-like [159942] (1)
      Pfam07929; plasmid pRiA4b ORF-3-like protein
32. WWE domain [117838] (1)
  beta(2)-alpha-beta(4); antiparallel folded beta-sheet (half-barrel), order 216543
  1. WWE domain [117839] (1)
    uperfamily
    1. WWE domain [117840] (2)
      Pfam 02825
33. FAD-linked reductases, C-terminal domain [54372] (1)
  alpha+beta sandwich
  1. FAD-linked reductases, C-terminal domain [54373] (7)
    N-terminal domain is beta/beta/alpha common fold
    uperfamily
    1. GMC oxidoreductases [54374] (8)
    2. PHBH-like [54378] (5)
    3. D-aminoacid oxidase-like [54384] (4)
    4. UDP-galactopyranose mutase [69670] (2)
    5. L-aminoacid/polyamine oxidase [54394] (9)
    6. GDI-like [54399] (3)
      Similar to FAD-linked reductases in both domains but does not bind FAD
    7. Electron transfer flavoprotein-ubiquinone oxidoreductase-like [142988] (1)
34. Cystatin-like [54402] (7)
  Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
  1. Cystatin/monellin [54403] (6)
    has a additional strand at the N-terminus
    uperfamily
    1. Monellin [54404] (1)
    2. Cystatins [54407] (6)
    3. Cathelicidin motif [82592] (1)
      cathelin-like domain
    4. Staphopain B, prodomain [117846] (1)
    5. Latexin-like [142991] (1)
      Pfam 06907; duplication: consits of two domains of this fold
    6. PepSY-like [159955] (1)
      Pfam 03413; Peptidase propeptide and YPEB domain
  2. Amine oxidase N-terminal region [54416] (1)
    uperfamily
    1. Amine oxidase N-terminal region [54417] (5)
      duplication: contains two domains of this fold
  3. DsbC/DsbG N-terminal domain-like [54423] (1)
    uperfamily
    1. DsbC/DsbG N-terminal domain-like [54424] (3)
  4. NTF2-like [54427] (30)
    has a beta-alpha(2)-beta insertion after the main helix
    uperfamily
    1. Scytalone dehydratase [54428] (1)
    2. NTF2-like [54431] (11)
    3. Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A [89851] (3)
    4. Limonene-1,2-epoxide hydrolase-like [89854] (2)
    5. SnoaL-like polyketide cyclase [102810] (5)
    6. PhzA/PhzB-like [102813] (4)
    7. Ketosteroid isomerase-like [54434] (4)
    8. Ring hydroxylating beta subunit [54438] (7)
      Pfam 00866
    9. Penicillin binding protein 2a (PBP2A), N-terminal domain [82595] (1)
      some sequence similarity to KSI
    10. Orange carotenoid protein, C-terminal domain [82598] (1)
    11. Hypothetical protein egc068 from a soil-derived mobile gene cassette [110826] (1)
    12. PA1314-like [110829] (1)
      COG4460
    13. TIM44-like [143001] (2)
      contains extra N-terminal helices but lacks the beta-hairpin in the superfamily-specific insertion
    14. Sbal0622-like [159985] (1)
      PfamB 002762
    15. CHU142-like [159988] (1)
      single domain covered by PfamB 000743 in the N-terminal part and PfamB 000860 in the C-terminal part
    16. SO0125-like [159991] (2)
      PfamB 003666
    17. SAV4671-like [159996] (1)
      PfamB 000442; uncertain annotation of some members as 3-dehydroquinate dehydratase
    18. BxeB1374-like [159999] (2)
      similar dimer to KSI
    19. Atu0744-like [160004] (1)
      PfamB 003773
    20. Rpa4348-like [160007] (2)
      PfamB 000085
    21. Ava4193-like [160012] (1)
      PfamB 183524
    22. YybH-like [160015] (1)
      PfamB 052627
    23. PFL3262-like [160018] (1)
      Pfam 07080; DUF1348
    24. Exig0174-like [160021] (1)
      PfamB 092483
    25. Rv3472-like [160024] (2)
      similar trimer to Scytalone dehydratase
    26. VirB8-like [160029] (2)
      Pfam 04335
    27. ECA1476-like [160033] (1)
      single domain covered by PfamB 006272 in the N-terminal part and PfamB 005262 in the C-terminal part
    28. BaiE/LinA-like [160036] (5)
      PfamB 000019; includes sequences of characterized enzymes BaiE and LinA
    29. Atu0742-like [160047] (1)
      PfamB 017405
    30. SEC-C associated NTF2-like domain [160050] (1)
      there is a C-terminal SEC-C motif, also there can be an additional SEC-C like motif at the N-terminus (there is only C-terminal motif in the new entry 2JQ5)
  5. Uracil-DNA glycosylase inhibitor protein [54441] (1)
    has an additional strand at the C-terminus and a helix inserted after the first strand
    uperfamily
    1. Uracil-DNA glycosylase inhibitor protein [54442] (2)
  6. Putative dsDNA mimic [102816] (1)
    elaborated with additional structures; some similarity to Uracil-DNA glycosylase (UGI) and Nuclease A (NuiA) inhibitors
    uperfamily
    1. Putative dsDNA mimic [102817] (1)
      Pfam 04269, DUF440
  7. Pre-PUA domain [88802] (5)
    this domain is found in association with the PUA domain in the C-terminal region of Archaeosine tRNA-guanine transglycosylase and related stand-alone proteins
    uperfamily
    1. Archaeosine tRNA-guanine transglycosylase, C2 domain [88803] (1)
    2. Hypothetical protein Ta1423, N-terminal domain [102820] (1)
    3. Nip7p homolog, N-terminal domain [110832] (1)
    4. Hypothetical protein APE0525, N-terminal domain [143004] (1)
    5. AF0587 pre C-terminal domain-like [160053] (1)
      PfamB 006016
35. Nuclease A inhibitor (NuiA) [82601] (1)
  alpha-beta-alpha-beta-alpha(2)-beta(3); antiparallel beta-sheet; order: 15432
  1. Nuclease A inhibitor (NuiA) [82602] (1)
    some structural similarity to Uracil-DNA glycosylase inhibitor and putative dsDNA mimic HI1450 of the cystatin-like fold
    uperfamily
    1. Nuclease A inhibitor (NuiA) [82603] (1)
36. Colicin D/E5 nuclease domain [102823] (1)
  alpha(2)-beta(4)-alpha, 2 layers: alpha/beta, antiparallel beta sheet, meander
  1. Colicin D/E5 nuclease domain [102824] (2)
    uperfamily
    1. Colicin D nuclease domain [102825] (1)
    2. Colicin E5 nuclease domain [143007] (1)
37. RelE-like [143010] (1)
  beta-alpha(2)-beta(4), 2 layers; a/b, antiparallel beta-sheet; order 15432
  1. RelE-like [143011] (2)
    Toxin component of plasmid stabilisation system
    uperfamily
    1. YoeB/Txe-like [143012] (1)
      Pfam 06769
    2. RelE-like [143015] (2)
      Pfam 05016
38. Hypothetical protein SAV1430 [110835] (1)
  beta(3)-alpha-beta(2)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet, order: 12543
  1. Hypothetical protein SAV1430 [110836] (1)
    uperfamily
    1. Hypothetical protein SAV1430 [110837] (1)
39. Ns1 effector domain-like [143020] (1)
  beta-X-beta(5)-alpha-beta-alpha; 2 layers: a/b; bifurcated beta-sheet; order 23654[1,7]
  1. Ns1 effector domain-like [143021] (1)
    uperfamily
    1. Ns1 effector domain-like [143022] (1)
      C-terminal part of Pfam 00600
40. YbaB-like [82606] (1)
  core: alpha-beta(3)-alpha, 2 layers:alpha/beta, three-stranded antiparallel beta sheet, strand order 123
  1. YbaB-like [82607] (1)
    forms tight dimer of a 3-layer structure: beta/alpha/beta
    uperfamily
    1. YbaB-like [82608] (2)
      Pfam 02575; DUF149; function unknown
41. Kinetochore globular domain-like [143025] (1)
  core: alpha-beta(3)-alpha; variant: alpha-beta(4)-alpha(2)
  1. Kinetochore globular domain [143026] (2)
    swapped heterodimer with the N-terminal helices; Spc24-like subunits have the core fold, whereas Spc25-like subunits have a variant fold
    uperfamily
    1. Spc25-like [143027] (1)
      Pfam 08234
    2. Spc24-like [143030] (1)
      Pfam 08286
42. L35p-like [143033] (1)
  core: alpha-beta(3)-alpha; 2layers a/b
  1. L35p-like [143034] (1)
    uperfamily
    1. Ribosomal protein L35p [143035] (3)
      Pfam 01632
43. Cell division protein ZapA-like [102828] (1)
  core: beta(2)-alpha(2), 2 layers: alpha/beta; long C-terminal helix forms dimeric parallel and tetrameric antiparallel coiled coils
  1. Cell division protein ZapA-like [102829] (1)
    uperfamily
    1. Cell division protein ZapA-like [102830] (1)
      Pfam 05164; ZapA is a Z-ring associated protein first discovered in B. subtilis (formerly hypothetical protein YshA);
44. ssDNA-binding transcriptional regulator domain [54446] (1)
  helix-swapped dimer of beta(4)-alpha motifs
  1. ssDNA-binding transcriptional regulator domain [54447] (4)
    uperfamily
    1. Transcriptional coactivator PC4 C-terminal domain [54448] (1)
      dimer of two separate motifs
    2. Plant transcriptional regulator PBF-2 [75375] (1)
      single-chain domain formed by a tandem repeat of two motifs
    3. PMN2A0962/syc2379c-like [143038] (2)
      Pfam 08848; DUF1818; specific to cyanobacteria; single-chain domain made of two repeats of this structural motif
    4. Guide RNA binding protein gBP [143043] (2)
      includes PfamB 080318 and PB073991; forms heterooligomers; similar subunit and oligomeric structures to the Plant transcriptional regulator family
45. Photosystem I subunit PsaD [64233] (1)
  beta-BETA(2)-beta-alpha-beta(2); antiparallel sheet: order 2134 packed against helix and BETA-hairpin on the same side; irregular C-terminal tail
  1. Photosystem I subunit PsaD [64234] (1)
    uperfamily
    1. Photosystem I subunit PsaD [64235] (1)
46. GINS/PriA/YqbF domain [160058] (1)
  beta(4)-alpha-beta; 3-stranded antiparallel beta-sheet (strands 4,1 and 5) are covered on the same side by the helix and beta hairpin of strands 2 and 3; similarity to the L9 N-domain-like fold (scop_cf 55657) and the PsaD fold (scop_sf 64243)
  1. PriA/YqbF domain [160059] (4)
    associated with known or presumed DNA-binding domains; this superfamily also includes the C-terminal domain of PriA (PDB entry 1zt2)
    1. YqbF N-terminal domain-like [160060] (2)
    2. PSF2 N-terminal domain-like [160065] (1)
      N-terminal part of Pfam 04128
    3. SLD5 C-terminal domain-like [160068] (1)
      C-terminal part of Pfam 05916
    4. PSF3 N-terminal domain-like [160071] (1)
      N-terminal part of Pfam 06425
47. MHC antigen-recognition domain [54451] (1)
  dimeric
  1. MHC antigen-recognition domain [54452] (1)
    uperfamily
    1. MHC antigen-recognition domain [54453] (73)
48. UBC-like [54494] (1)
  alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
  1. UBC-like [54495] (4)
    uperfamily
    1. UBC-related [54496] (38)
    2. UEV domain [75383] (2)
    3. RWD domain [110843] (4)
      Pfam 05773
    4. UFC1-like [143072] (1)
49. SAND domain-like [63762] (1)
  core: three short helices packed against a barrel-like beta-sheet; some similarity to the SH3-like fold
  1. SAND domain-like [63763] (2)
    uperfamily
    1. SAND domain [63764] (3)
    2. SMAD4-binding domain of oncoprotein Ski [82611] (1)
50. NRDP1 C-terminal domain-like [160087] (1)
  alpha-beta-alpha(3)-beta(3); a pseudo barrel beta-sheet of an SH3-like topology, surrounded by helices
  1. NRDP1 C-terminal domain-like [160088] (1)
    1. USP8 interacting domain [160089] (1)
      Pfam 08941
51. Coronavirus NSP8-like [143075] (1)
  core: alpha-beta(2)-alpha-beta(4)-alpha-beta; bifurcated barrel-like beta-sheet
  1. Coronavirus NSP8-like [143076] (1)
    uperfamily
    1. Coronavirus NSP8-like [143077] (1)
52. ParB/Sulfiredoxin [110848] (1)
  beta*-alpha-beta(2)-alpha-beta-alpha; mixed beta sheet forms a partly open barrel: (n*=4, S*=8)
  1. ParB/Sulfiredoxin [110849] (4)
    uperfamily
    1. ParB-like nuclease domain [110850] (1)
      Pfam 02195
    2. Hypothetical protein PF0380 [110853] (1)
      contains insert domain (101-200) of an unusual alpha+beta fold beta-alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order 516342; possibly related to Pfam 06245
    3. Atu1540-like [160092] (1)
      Pfam 08857; ParBc_2; contains extra C-terminal all-alpha subdomain
    4. Sulfiredoxin-like [160095] (1)
      PfamB 015736
53. Gamma-glutamyl cyclotransferase-like [110856] (1)
  beta-alpha-beta(4)-alpha-beta(2); contains beta-sheet barrel (n=5, S=8)
  1. Gamma-glutamyl cyclotransferase-like [110857] (1)
    uperfamily
    1. Gamma-glutamyl cyclotransferase-like [110858] (3)
      Pfam 03674
54. BB1717-like [143080] (1)
  complex fold with a bifurcated beta-sheet structure surrounded by helices; contains beta-sheet barrel, closed (n=5, S=8)
  1. BB1717-like [143081] (1)
    uperfamily
    1. BB1717-like [143082] (4)
      Pfam 02586; DUF159, COG2135
55. SARS Nsp1-like [160098] (1)
  complex alpha+beta fold; contains mixed beta-sheet barrel, n=6, S=10
  1. SARS Nsp1-like [160099] (1)
    1. SARS Nsp1-like [160100] (1)
56. Acetoacetate decarboxylase-like [160103] (1)
  complex fold: contains a 3-layer beta-sheet structure, which is folded in two conjoint barrels capped by helices; one rounded barrel has 7 strands, the other flattened barrel has 9 strands
  1. Acetoacetate decarboxylase-like [160104] (1)
    1. Acetoacetate decarboxylase-like [160105] (2)
      Pfam 06314
57. AF0104/ALDC/Ptd012-like [117855] (1)
  duplication: consists of two similar beta-alpha-beta(4) motifs
  1. AF0104/ALDC/Ptd012-like [117856] (3)
    characteristic metal ion (zinc)-binding motif in the putative active site
    uperfamily
    1. Alpha-acetolactate decarboxylase-like [117857] (1)
      Pfam 03306
    2. PTD012-like [143091] (1)
    3. AF0104-like [143094] (2)
      Pfam 03479; DUF296; PD1 domain; plant- and prokaryote conserved (PPC; see new PDB 2DT4)
58. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102847] (1)
  beta(3)-alpha(2)-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other
  1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102848] (1)
    uperfamily
    1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102849] (2)
59. TTHA1013/TTHA0281-like [143099] (1)
  beta(3)-alpha-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other; topological similarity to the SEP domain fold (scop_cf 102847); dimerises via the long C-terminal strand with the formation of a single beta-sheet
  1. TTHA1013/TTHA0281-like [143100] (2)
    uperfamily
    1. TTHA1013-like [143101] (1)
    2. TTHA0281-like [160109] (1)
      Pfam 03681; UPF0150; alpha-beta(3)-alpha-X
60. YegP-like [160112] (1)
  comprises two subunits or tandem repeats of beta(3)-alpha-beta motifs; these assemble with the formation of a single beta-sheet and swapping of the C-terminal strands
  1. YegP-like [160113] (1)
    1. YegP-like [160114] (4)
      Pfam 07411; DUF1508
61. Diaminopimelate epimerase-like [54505] (1)
  mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
  1. Diaminopimelate epimerase-like [54506] (4)
    duplication: consists of two similar domain swapped with C-terminal strands
    uperfamily
    1. Diaminopimelate epimerase [54507] (1)
    2. PhzC/PhzF-like [89863] (4)
      Pfam 02567
    3. Proline racemase [110863] (1)
      Pfam 05544
    4. PA0793-like [160123] (1)
      Pfam 04303; DUF453
62. GFP-like [54510] (1)
  beta-sheet folds into a barrel (n=11, S=14) around the central helix
  1. GFP-like [54511] (2)
    uperfamily
    1. Fluorescent proteins [54512] (6)
    2. Domain G2 of nidogen-1 [64244] (1)
63. Tubby C-terminal domain-like [54517] (1)
  beta-sheet folds into a barrel (n=12, S=12) around the central helix
  1. Tubby C-terminal domain-like [54518] (2)
    uperfamily
    1. Transcriptional factor tubby, C-terminal domain [54519] (1)
    2. At5g01750-like [143104] (1)
      Pfam 04525; DUF567
64. Pili subunits [54522] (1)
  contains very long N-terminal helix, which end is packed against beta-sheet
  1. Pili subunits [54523] (7)
    bacterial filament proteins
    uperfamily
    1. Pilin [54524] (4)
    2. TcpA-like pilin [89868] (1)
      common fold is decorated with additional structures
    3. Pseudopilin [117865] (1)
    4. YadA C-terminal domain-like [143107] (1)
      Pfam 03895; trimerizes with the formation of closed beta-barrel (n=12, S=12), wrapped around triple parallel coiled coil
    5. EpsJ-like [160127] (2)
    6. GspK pilin-like domain [160132] (1)
      N-terminal and C-terminal regions of Pfam 03934
    7. GSPII I/J protein-like [160135] (2)
      Pfam 02501
65. Mitochondrial glycoprotein MAM33-like [54528] (1)
  core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
  1. Mitochondrial glycoprotein MAM33-like [54529] (1)
    uperfamily
    1. Mitochondrial glycoprotein MAM33-like [54530] (2)
66. NAP-like [143112] (1)
  core: central meander 4-stranded beta-sheet (order: 1234) transversed by a C-terminal helix
  1. NAP-like [143113] (1)
    uperfamily
    1. NAP-like [143114] (2)
      Pfam 00956
67. Polo-box domain [82614] (1)
  beta(6)-alpha; antiparallel beta-sheet, meander
  1. Polo-box domain [82615] (2)
    Serine/threonine protein kinase-associated motif embedded in two distinct folds
    uperfamily
    1. Polo-box duplicated region [102856] (1)
      duplication: consists of two polo-box domains; binds phosphothreonine peptide
    2. Swapped Polo-box domain [82616] (1)
      beta(5)-alpha-beta; forms swapped dimer with two 6-stranded antiparallel beta sheets; order [6]123[4][5]
68. mRNA decapping enzyme DcpS N-terminal domain [102859] (1)
  beta(3)-alpha-beta(3)-alpha; 3 layers a/b/a
  1. mRNA decapping enzyme DcpS N-terminal domain [102860] (1)
    forms swapped dimer with two 6-stranded antiparallel beta sheets; order 1236[5][4]
    uperfamily
    1. mRNA decapping enzyme DcpS N-terminal domain [102861] (2)
69. Inhibitor of vertebrate lysozyme, Ivy [89871] (1)
  alpha(2)-beta(5)-alpha(2); 3 layers a/b/a; meander beta-sheet
  1. Inhibitor of vertebrate lysozyme, Ivy [89872] (1)
    uperfamily
    1. Inhibitor of vertebrate lysozyme, Ivy [89873] (2)
70. FKBP-like [54533] (3)
  core: beta(2)-alpha-beta(2); antiparallel beta-sheet
  1. FKBP-like [54534] (3)
    uperfamily
    1. FKBP immunophilin/proline isomerase [54535] (24)
    2. GreA transcript cleavage factor, C-terminal domain [54549] (3)
    3. 3-mercaptopyruvate sulfurtransferase, C-terminal domain [102868] (1)
  2. Colicin E3 immunity protein [54552] (1)
    uperfamily
    1. Colicin E3 immunity protein [54553] (1)
  3. Chitinase insertion domain [54556] (1)
    uperfamily
    1. Chitinase insertion domain [54557] (15)
71. Ribosomal protein S16 [54564] (1)
  beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
  1. Ribosomal protein S16 [54565] (1)
    uperfamily
    1. Ribosomal protein S16 [54566] (3)
72. Ribosomal protein S19 [54569] (1)
  alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
  1. Ribosomal protein S19 [54570] (1)
    uperfamily
    1. Ribosomal protein S19 [54571] (2)
73. YefM-like [143119] (1)
  core: beta-alpha(2)-beta(2)-alpha; mixed beta-sheet, order:123, strands 1 and 2 are parallel; forms compact dimer with a single beta-sheet;
  1. YefM-like [143120] (1)
    uperfamily
    1. YefM-like [143121] (2)
      antitoxin component of the YefM/YoeB-like system; binds to the toxin component wia extra C-terminal tail, unstructured in the free state, but adopting a RelB-like conformation in the bound state
74. Ribosomal protein L31e [54574] (1)
  beta-alpha-beta-(alpha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
  1. Ribosomal protein L31e [54575] (1)
    uperfamily
    1. Ribosomal protein L31e [54576] (1)
75. Allophycocyanin linker chain (domain) [54579] (1)
  beta(2)-alpha-beta; 2 layers: alpha/beta
  1. Allophycocyanin linker chain (domain) [54580] (1)
    uperfamily
    1. Allophycocyanin linker chain (domain) [54581] (1)
76. Cdc48 domain 2-like [54584] (1)
  beta-alpha-beta(3); 2 layers: alpha/beta
  1. Cdc48 domain 2-like [54585] (1)
    uperfamily
    1. Cdc48 domain 2-like [54586] (5)
77. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54592] (1)
  beta-alpha-beta(3); 2 layers: alpha/beta
  1. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54593] (10)
    uperfamily
    1. Glyoxalase I (lactoylglutathione lyase) [54594] (3)
      duplication: consists of two clear structural repeats each having this fold
    2. Antibiotic resistance proteins [54598] (10)
      duplication: consists of two clear structural repeats each having this fold
      subunit fold and dimeric assembly are similar to those of glyoxalase
    3. Methylmalonyl-CoA epimerase [64257] (1)
      Different association of repeats but a similar dimeric structure to the glyoxalase dimer
    4. Hypothetical protein YecM (EC4020) [75396] (1)
      Similar subunit fold is to methylmalonyl-CoA epimerase
    5. Extradiol dioxygenases [54602] (10)
      duplication: consists of 2 similar domains with 2 repeats in each
      Similar to the Methylmalonyl-CoA epimerase dimer
    6. Hypothetical protein BC1747 [110880] (1)
      subunit fold and dimeric assembly are similar to those of glyoxalase
    7. 3-demethylubiquinone-9 3-methyltransferase [110883] (4)
      Pfam 06983; both variants of dimeric assembly are observed in the family (domain swapping)
    8. Hypothetical protein YycE [110888] (1)
      subunit fold and dimeric assembly are similar to those of glyoxalase
    9. Hypothetical protein At5g48480 [117876] (1)
      subunit fold and dimeric assembly are similar to those of glyoxalase
    10. BC1024-like [143129] (1)
      duplication: consists of 2 similar domains with 2 repeats in each; similar to the glyoxalase dimer
78. Chromosomal protein MC1 [102874] (1)
  beta(2)-alpha-beta(3); 2 layers: alpha/beta
  1. Chromosomal protein MC1 [102875] (1)
    uperfamily
    1. Chromosomal protein MC1 [102876] (1)
79. CPE0013-like [160147] (1)
  beta(2)-alpha-beta(3); mixed, mostly antiparallel beta-sheet, folded in a half-barrel; order:31254; strand 3 is parallel to strand 1 and is shorter than the rest
  1. CPE0013-like [160148] (1)
    1. CPE0013-like [160149] (1)
      Pfam 07892; DUF1667; the founding protein lacks the predicted metal-binding motif, found at the N-termini of other members of the Pfam family
80. beta-hairpin-alpha-hairpin repeat [74651] (2)
  multiple repeats of beta(2)-alpha(2) motif
  1. Ankyrin repeat [48403] (1)
    repeats organized in elongated structures
    uperfamily
    1. Ankyrin repeat [48404] (20)
  2. Plakin repeat [75399] (1)
    repeats associate forming globular subdomains
    uperfamily
    1. Plakin repeat [75400] (1)
81. Proguanylin [89889] (1)
  beta(2)-alpha(3)-beta; two layers: alpha/beta; antiparallel sheet: order 213
  1. Proguanylin [89890] (1)
    uperfamily
    1. Proguanylin [89891] (1)
82. SecB-like [54610] (1)
  beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
  1. SecB-like [54611] (2)
    uperfamily
    1. Bacterial protein-export protein SecB [54612] (2)
    2. SP1558-like [160154] (2)
      Pfam 06619; DUF1149
83. MesJ substrate recognition domain-like [82828] (1)
  beta-alpha(2)-beta(3); 2 layers: a/b; antiparallel beta-sheet, order:1432
  1. MesJ substrate recognition domain-like [82829] (1)
    uperfamily
    1. MesJ substrate recognition domain-like [82830] (2)
84. FYSH domain [89894] (1)
  beta(2)-alpha(2)-beta(2)-alpha-beta; two layers: alpha/beta; antiparallel sheet: order 51234
  1. FYSH domain [89895] (2)
    uperfamily
    1. Hypothetical protein Yhr087W [89896] (1)
    2. Hypothetical protein AF0491, N-terminal domain [110893] (1)
85. VSV matrix protein [75403] (1)
  beta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiled beta-sheet: order of the first 5 strands: 23154
  1. VSV matrix protein [75404] (1)
    uperfamily
    1. VSV matrix protein [75405] (1)
86. DNA-binding domain of Mlu1-box binding protein MBP1 [54615] (1)
  beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
  1. DNA-binding domain of Mlu1-box binding protein MBP1 [54616] (1)
    has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain
    uperfamily
    1. DNA-binding domain of Mlu1-box binding protein MBP1 [54617] (1)
87. Heme-binding protein A (HasA) [54620] (1)
  beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
  1. Heme-binding protein A (HasA) [54621] (1)
    uperfamily
    1. Heme-binding protein A (HasA) [54622] (1)
88. Chalcone isomerase [54625] (1)
  beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
  1. Chalcone isomerase [54626] (1)
    uperfamily
    1. Chalcone isomerase [54627] (1)
89. Coproporphyrinogen III oxidase [102885] (1)
  alpha-beta(6)-alpha(2)-beta-alpha(n); 3 layers alpha/beta/alpha; antiparallel sheet: order 1234567
  1. Coproporphyrinogen III oxidase [102886] (1)
    uperfamily
    1. Coproporphyrinogen III oxidase [102887] (2)
      Pfam 01218
90. Hypothetical protein Ta1206 [102890] (1)
  beta(4)-alpha-beta(2)-alpha(2); mixed, predominately antiparallel beta-sheet, order: 123465, strands 4 and 5 are parallel to each other
  1. Hypothetical protein Ta1206 [102891] (1)
    can be divided into an N-terminal, tetramerisation all-beta subdomain and a C-terminal alpha+beta subdomain related by a circular permutation to the Y-family DNA-polymerase 'fingers' subdomain
    uperfamily
    1. Hypothetical protein Ta1206 [102892] (1)
91. CBS-domain pair [54630] (1)
  duplication: tandem repeat of two beta-X-beta-alpha-beta(2)-alpha motifs of similar sequences; 4 layers: a/b/b/a
  1. CBS-domain pair [54631] (1)
    uperfamily
    1. CBS-domain pair [54632] (24)
      Pfam 00571; pairs of CBS domains dimerize to form a stable globular domain, a.k.a. Bateman domain
92. Thioesterase/thiol ester dehydrase-isomerase [54636] (1)
  core: beta-alpha-beta(4); 2 layers: alpha/beta
  1. Thioesterase/thiol ester dehydrase-isomerase [54637] (8)
    uperfamily
    1. 4HBT-like [54638] (18)
      Pfam 03061
    2. beta-Hydroxydecanol thiol ester dehydrase [54641] (1)
      contains two additional beta-strands in the N-terminal extension
    3. Acyl-CoA thioesterase [54644] (2)
      duplication: consists of two domains of this fold
    4. MaoC-like [82636] (7)
    5. PaaI/YdiI-like [89902] (16)
    6. FabZ-like [110902] (2)
    7. TTHA0967-like [143187] (2)
      contains extra C-terminal helix
    8. Acyl-ACP thioesterase-like [143190] (2)
      Pfam 01643; duplication: consists of two 4HBT-like domains
93. DLC [54647] (1)
  core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
  1. DLC [54648] (1)
    uperfamily
    1. DLC [54649] (4)
      8 kDa dynein light chain, DLC8
94. CI-2 family of serine protease inhibitors [54653] (1)
  alpha+beta sandwich; loop across free side of beta-sheet
  1. CI-2 family of serine protease inhibitors [54654] (1)
    uperfamily
    1. CI-2 family of serine protease inhibitors [54655] (4)
95. Integrin beta tail domain [69686] (1)
  alpha-beta-loop-beta(3); loop across free side of beta-sheet
  1. Integrin beta tail domain [69687] (1)
    uperfamily
    1. Integrin beta tail domain [69688] (1)
96. YcgL-like [160190] (1)
  beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order:3124
  1. YcgL-like [160191] (1)
    1. YcgL-like [160192] (1)
      Pfam 05166
97. alpha/beta-Hammerhead [54664] (5)
  core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
  1. CO dehydrogenase molybdoprotein N-domain-like [54665] (1)
    uperfamily
    1. CO dehydrogenase molybdoprotein N-domain-like [54666] (8)
  2. Nicotinate/Quinolinate PRTase N-terminal domain-like [54675] (2)
    uperfamily
    1. NadC N-terminal domain-like [54676] (6)
    2. Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like [110907] (3)
  3. Pyrimidine nucleoside phosphorylase C-terminal domain [54680] (1)
    uperfamily
    1. Pyrimidine nucleoside phosphorylase C-terminal domain [54681] (3)
  4. Ribosomal protein L16p/L10e [54686] (2)
    uperfamily
    1. Ribosomal protein L10e [54687] (2)
    2. Ribosomal protein L16p [117888] (4)
      Pfam 00252
  5. Molybdopterin synthase subunit MoaE [54690] (1)
    uperfamily
    1. Molybdopterin synthase subunit MoaE [54691] (1)
98. POZ domain [54694] (1)
  core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
  1. POZ domain [54695] (2)
    uperfamily
    1. BTB/POZ domain [54696] (6)
    2. Tetramerization domain of potassium channels [54701] (6)
99. EF-Ts domain-like [54712] (2)
  beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
  1. Elongation factor Ts (EF-Ts), dimerisation domain [54713] (1)
    comprises two structural repeats of this fold
    uperfamily
    1. Elongation factor Ts (EF-Ts), dimerisation domain [54714] (3)
  2. Band 7/SPFH domain [117892] (1)
    beta(2)-alpha(3)-beta
    uperfamily
    1. Band 7/SPFH domain [117893] (1)
      Pfam 01145
100. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54718] (1)
  alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
  1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54719] (1)
    uperfamily
    1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54720] (19)
101. ClpS-like [54735] (1)
  beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
  1. ClpS-like [54736] (2)
    uperfamily
    1. Ribosomal protein L7/12, C-terminal domain [54737] (3)
    2. Adaptor protein ClpS (YljA) [82641] (1)
102. Hypothetical protein MTH1880 [75411] (1)
  beta-alpha-beta(2)-alpha(2); 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
  1. Hypothetical protein MTH1880 [75412] (1)
    uperfamily
    1. Hypothetical protein MTH1880 [75413] (1)
103. Ribosomal L11/L12e N-terminal domain [54746] (1)
  beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
  1. Ribosomal L11/L12e N-terminal domain [54747] (1)
    uperfamily
    1. Ribosomal L11/L12e N-terminal domain [54748] (5)
      Pfam 03946
104. Anti-LPS factor/recA domain [54751] (2)
  alpha-beta(3)-alpha(2); 2 layers, alpha/beta
  1. RecA protein, C-terminal domain [54752] (1)
    uperfamily
    1. RecA protein, C-terminal domain [54753] (4)
  2. Anti-lipopolysaccharide factor [54757] (1)
    uperfamily
    1. Anti-lipopolysaccharide factor [54758] (1)
105. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54761] (1)
  (beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
  1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54762] (1)
    uperfamily
    1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54763] (4)
106. dsRBD-like [54767] (5)
  alpha-beta(3)-alpha; 2 layers: alpha/beta
  1. dsRNA-binding domain-like [54768] (3)
    uperfamily
    1. Double-stranded RNA-binding domain (dsRBD) [54769] (15)
      Pfam 00035
    2. The homologous-pairing domain of Rad52 recombinase [82645] (1)
      contains N- and C-terminal extensions to the common fold involved in the oligomerization
    3. Ribosomal S5 protein, N-terminal domain [54778] (3)
  2. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54782] (1)
    uperfamily
    1. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54783] (1)
  3. YcfA/nrd intein domain [54786] (3)
    uperfamily
    1. PI-Pfui intein middle domain [54787] (1)
    2. YcfA-like [117905] (1)
      Pfam 07927
    3. YkfF-like [160203] (1)
      Pfam 06006; DUF905
  4. Peptidyl-tRNA hydrolase domain-like [110916] (1)
    uperfamily
    1. Peptidyl-tRNA hydrolase domain [110917] (1)
      Pfam 00472; related to domain 3 of the Polypeptide chain release factors RF1 and RF2 (scop_fa 75621)
  5. Rv2632c-like [143212] (1)
    lacks the N-terminal helix; dimerises via the N-terminal strand and the C-terminal helix with the formation of a single beta-sheet wrapped around an antiparallel coiled coil
    uperfamily
    1. Rv2632c-like [143213] (1)
107. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110920] (1)
  duplication: consists of two beta(3)-alpha repeats; 3 layers, beta/alpha/beta
  1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110921] (1)
    uperfamily
    1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110922] (1)
108. NMB0488-like [160206] (1)
  duplication: two beta(3)-alpha motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456, shaped into a half-barrel; helical linker region
  1. NMB0488-like [160207] (1)
    1. NMB0488-like [160208] (1)
      Pfam 07262; DUF1436
109. SRP19 [69694] (1)
  beta-alpha-beta(2)-alpha; 2 layers: alpha/beta
  1. SRP19 [69695] (1)
    uperfamily
    1. SRP19 [69696] (3)
110. SufE/NifU [82648] (1)
  alpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
  1. SufE/NifU [82649] (3)
    iron-sulfur cluster assembly proteins
    uperfamily
    1. SufE-like [82650] (2)
      Fe-S metabolism associated domain
    2. NifU/IscU domain [102928] (4)
    3. SP1160 C-terminal domain-like [143216] (2)
111. FlaG-like [160213] (1)
  alpha(2)-beta(3)-alpha; 2 layers: a/b; antiparallel beta-sheet, order: 123; partial similatity to the dsRBD-like fold(sop_cf 54767)
  1. FlaG-like [160214] (1)
    1. FlaG-like [160215] (1)
      Pfam 03646
112. AMPKBI-like [160218] (1)
  comprises 3 short helices and 3-stranded meander beta-sheet; makes extensive intermolecular interactions
  1. AMPKBI-like [160219] (1)
    1. AMPKBI-like [160220] (3)
      Pfam 04739; 5'-AMP-activated protein kinase, beta subunit, complex-interacting region
113. DNA-binding protein Tfx [89914] (1)
  alpha(3)-beta-alpha(2)-beta(2); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
  1. DNA-binding protein Tfx [89915] (1)
    uperfamily
    1. DNA-binding protein Tfx [89916] (1)
114. Eukaryotic type KH-domain (KH-domain type I) [54790] (1)
  beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
  1. Eukaryotic type KH-domain (KH-domain type I) [54791] (1)
    Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
    uperfamily
    1. Eukaryotic type KH-domain (KH-domain type I) [54792] (20)
      an RNA-binding domain
115. Alpha-lytic protease prodomain-like [54805] (10)
  core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
  1. Alpha-lytic protease prodomain [54806] (1)
    uperfamily
    1. Alpha-lytic protease prodomain [54807] (1)
  2. GMP synthetase C-terminal dimerisation domain [54810] (1)
    uperfamily
    1. GMP synthetase C-terminal dimerisation domain [54811] (1)
  3. Prokaryotic type KH domain (KH-domain type II) [54814] (1)
    Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
    uperfamily
    1. Prokaryotic type KH domain (KH-domain type II) [54815] (9)
  4. Probable GTPase Der, C-terminal domain [82653] (1)
    possible distant relative of the Era C-terminal domain lacking the KH motif
    uperfamily
    1. Probable GTPase Der, C-terminal domain [82654] (1)
  5. Ribosome-binding factor A, RbfA [89919] (1)
    possible distant homologue of the type I KH domain lacking the KH motif
    uperfamily
    1. Ribosome-binding factor A, RbfA [89920] (5)
  6. YhbC-like, N-terminal domain [75420] (1)
    uperfamily
    1. YhbC-like, N-terminal domain [75421] (1)
  7. BolA-like [82657] (1)
    uperfamily
    1. BolA-like [82658] (2)
      Pfam 01722
  8. Fe-S cluster assembly (FSCA) domain-like [117916] (2)
    similar putative active site with a conserved cysteine residue
    uperfamily
    1. NifU C-terminal domain-like [117917] (3)
      Pfam 01106
    2. PaaD-like [117922] (2)
      Pfam 01883; DUF59
  9. Cation efflux protein cytoplasmic domain-like [160240] (1)
    1. Cation efflux protein cytoplasmic domain-like [160241] (2)
      C=terminal part of Pfam 01545
  10. EspE N-terminal domain-like [160246] (1)
    contains extra C-terminal helix that packs against shorter N-terminal helix
    1. GSPII protein E N-terminal domain-like [160247] (2)
      Pfam 05157 (also includes PfamB 000210)
116. Nucleotidyltransferase [81302] (1)
  core: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands: 123
  1. Nucleotidyltransferase [81301] (14)
    uperfamily
    1. Catalytic subunit of bi-partite nucleotidyltransferase [102932] (3)
      insert X in the core is an alpha-helix; minimal nucleotidyltransferase fold
    2. Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [56708] (1)
      insert X in the core is a beta-strand ; mixed 4-stranded sheet, order: 1243
    3. Poly(A) polymerase, PAP, N-terminal domain [81589] (2)
      insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543
    4. 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [102937] (1)
      similar overall structure to the first two domains of poly(A) polymerase, PAP
    5. Archaeal tRNA CCA-adding enzyme catalytic domain [102940] (1)
      similar overall structure to poly(A) polymerase, PAP
    6. DNA polymerase beta-like [81300] (5)
      insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543; contains extra C-terminal alpha+beta subdomain
    7. Poly A polymerase head domain-like [82661] (3)
      overlaps with the N-terminal part of Pfam 01743; this family is distinct from eukaryotic PAPs
      insert X in the core is an alpha-beta(2) unit; contains two extra C-terminal strands; mixed 7-stranded sheet, order: 7612543
    8. RelA/SpoT domain [102945] (2)
      Pfam 04607; ppGpp-synthetase
    9. GlnE-like domain [110933] (1)
      Pfam 03710; Pfam coverage excludes the extra N-terminal subdomain but includes a short segment of the next domain 2
    10. RNA editing terminal uridyl transferase 2, RET2, catalytic domain [143236] (1)
      contains insert domain of a ferredoxin-like fold
    11. TM1012-like [143239] (1)
      insert X in the core is an alpha-beta(2) unit; contains extra C-terminal structures; mixed 7-stranded sheet, order: 6712543;
    12. Iojap/YbeB-like [160252] (2)
      Pfam 02410, probably has evolved a different function; closer relationship to the GrpB-like family
    13. AadK N-terminal domain-like [160257] (1)
      N-terminal part of Pfam 04439; Streptomycin adenylyltransferase; insert X is alpha-beta(2) unit; overall domain architecture is similar to Kanamycin nucleotidyltransferase
    14. GrpB-like [160260] (1)
      Pfam 04229, different set of active-site residues
117. Nqo5-like [143242] (1)
  core: alpha-beta(2)-alpha-beta(3); 2 layers, a/b; mixed beta-sheet, order 12534, strands 2 and 5 are parallel
  1. Nqo5-like [143243] (1)
    uperfamily
    1. Nqo5-like [143244] (1)
      Globular region is covered by PfamB 121908 from N-end and then by PfamB 000646; contains extra C-terminal unstructured region, corresponding to Pfam 00329
118. Ribosomal protein S3 C-terminal domain [54820] (1)
  alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
  1. Ribosomal protein S3 C-terminal domain [54821] (1)
    uperfamily
    1. Ribosomal protein S3 C-terminal domain [54822] (2)
119. Transcription factor NusA, N-terminal domain [69704] (1)
  alpha-beta(3)-alpha-beta-alpha; bifurcated coiled beta-sheet
  1. Transcription factor NusA, N-terminal domain [69705] (1)
    uperfamily
    1. Transcription factor NusA, N-terminal domain [69706] (2)
120. Enolase N-terminal domain-like [54825] (1)
  beta(3)-alpha(3); meander and up-and-down bundle
  1. Enolase N-terminal domain-like [54826] (1)
    uperfamily
    1. Enolase N-terminal domain-like [54827] (28)
      C-terminal domain is beta/alpha-barrel
121. Ribosomal protein L22 [54842] (1)
  beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
  1. Ribosomal protein L22 [54843] (1)
    some topological similarity to prokaryotic ribosomal protein L17
    uperfamily
    1. Ribosomal protein L22 [54844] (5)
122. Prokaryotic ribosomal protein L17 [64262] (1)
  alpha-beta-alpha(3)-beta(2); 2 layers: alpha/beta;
  1. Prokaryotic ribosomal protein L17 [64263] (1)
    some topological similarity to ribosomal protein L22
    uperfamily
    1. Prokaryotic ribosomal protein L17 [64264] (4)
123. GroEL-intermediate domain like [54848] (1)
  3-helical bundle packed against 3-stranded mixed beta-sheet
  1. GroEL-intermediate domain like [54849] (2)
    uperfamily
    1. GroEL-like chaperone, intermediate domain [54850] (4)
    2. Group II chaperonin (CCT, TRIC), intermediate domain [54853] (3)
124. PX domain [64267] (1)
  beta(3)-alpha(4); meander beta-sheet packed against array of helices; contains Pro-rich stretch
  1. PX domain [64268] (1)
    uperfamily
    1. PX domain [64269] (5)
      Pfam 00787
125. Shew3726-like [160271] (1)
  beta(3)-alpha(n)-beta; 2 layers, a/b; mixed beta-sheet, order 1234, strands 3 and 4 are parallel with a left-handed crossover connection
  1. Shew3726-like [160272] (1)
    1. Shew3726-like [160273] (1)
      Pfam 07369; DUF1488
126. DsrC, the gamma subunit of dissimilatory sulfite reductase [69720] (1)
  beta(3)-alpha(5); meander beta-sheet packed against array of helices
  1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69721] (1)
    uperfamily
    1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69722] (2)
127. DNA damage-inducible protein DinI [54856] (1)
  beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
  1. DNA damage-inducible protein DinI [54857] (1)
    uperfamily
    1. DNA damage-inducible protein DinI [54858] (1)
128. HSP90 C-terminal domain [110941] (1)
  alpha-beta(3)-alpha(3); 2 layers, a/b; mixed beta-sheet, order:132; crossing loops
  1. HSP90 C-terminal domain [110942] (1)
    uperfamily
    1. HSP90 C-terminal domain [110943] (1)
      C-terminal part of Pfam 00183
129. Ferredoxin-like [54861] (59)
  alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
  1. 4Fe-4S ferredoxins [54862] (6)
    uperfamily
    1. Short-chain ferredoxins [54863] (5)
      contains two 4Fe-4S clusters
    2. 7-Fe ferredoxin [54870] (5)
      has C-terminal extension to the common fold
    3. Archaeal ferredoxins [54874] (1)
    4. Single 4Fe-4S cluster ferredoxin [54877] (5)
      contains only one 4Fe-4S cluster
    5. Ferredoxin domains from multidomain proteins [54884] (15)
      members of this "family" may be more closely related to other ferredoxins than to each other
    6. ETF-QO domain-like [143256] (1)
      Pfam 05187; Electron transfer flavoprotein-ubiquinone oxidoreductase; contains single Fe4-S4 cluster
  2. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1)
    uperfamily
    1. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54894] (2)
  3. Protease propeptides/inhibitors [54897] (3)
    uperfamily
    1. Pancreatic carboxypeptidase, activation domain [54898] (6)
    2. Subtilase propeptides/inhibitors [54905] (4)
      decorated with additional structure
    3. Prohormone convertase 1 pro-domain [75431] (1)
  4. Dimeric alpha+beta barrel [54909] (23)
    dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
    uperfamily
    1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82666] (1)
    2. Plant stress-induced protein [89927] (3)
    3. PG130-like [102959] (5)
      subfamily of Pfam 03992
    4. Hypothetical protein YjcS [102962] (1)
    5. YciI-like [102965] (1)
      structural similarity to MLI extends to the active site cavity location
    6. Muconalactone isomerase, MLI [54910] (1)
      decamer: pentamer of dimers
    7. Lrp/AsnC-like transcriptional regulator C-terminal domain [69733] (4)
      octamer: tetramer of dimers
    8. Polyketide synthesis cyclase [110959] (1)
      Pfam 04673
    9. DGPF domain (Pfam 04946) [110962] (1)
      there is the putative active site cavity in the equivalent location location to the MLI and YciI active sites
    10. Chlorite dismutase-like [110965] (2)
      Pfam 06778; duplication: consists of two similar domains; forms a pentamer similar to the MLI decamer
    11. PA3566-like [110970] (5)
      subfamily of Pfam 03992
    12. Hypothetical protein YdhR [117940] (1)
    13. NIPSNAP [117943] (2)
      Pfam 07978
    14. Dyp-type peroxidase-like [143265] (3)
      Pfam 04261
    15. EthD-like [143272] (1)
      Pfam 07110
    16. Atu0297-like [143275] (1)
      Pfam 07045; DUF1330
    17. SOR-like [143278] (1)
      Pfam 07682; duplication: consists of two similar domains
    18. YbaA-like [160289] (1)
      Pfam 07237; DUF1428
    19. MmlI-like [160292] (1)
      Pfam 09448; Methylmuconolactone methyl-isomerase
    20. Marine metagenome family DABB2 [160295] (1)
    21. YiiL-like [160298] (1)
      Pfam 05336; DUF718
    22. Marine metagenome family DABB1 [160301] (2)
    23. Marine metagenome family DABB3 [160306] (1)
      duplication: consists of two similar domains; forms a pentamer similar to the Chlorite dismutase-like pentamer and the MLI decamer
  5. GlnB-like [54913] (5)
    form timeric structures with the orthogonally packed beta-sheets
    uperfamily
    1. Prokaryotic signal transducing protein [54914] (8)
    2. Divalent ion tolerance proteins CutA (CutA1) [75434] (7)
    3. DUF190/COG1993 [89934] (1)
    4. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [88851] (2)
    5. RPA1041-like [160310] (1)
      PF09413; DUF2007; provisional superfamily assignment based on a single monomeric solution structure
  6. SEA domain [82671] (1)
    uperfamily
    1. SEA domain [82672] (1)
  7. Nucleoside diphosphate kinase, NDK [54919] (1)
    uperfamily
    1. Nucleoside diphosphate kinase, NDK [54920] (20)
  8. RNA-binding domain, RBD [54928] (5)
    uperfamily
    1. Canonical RBD [54929] (71)
    2. Non-canonical RBD domain [54954] (1)
    3. Splicing factor U2AF subunits [64276] (1)
    4. Smg-4/UPF3 [102987] (1)
      Pfam 03467
    5. GUCT domain [160314] (1)
      Pfam 08152
  9. Viral DNA-binding domain [54957] (1)
    uperfamily
    1. Viral DNA-binding domain [54958] (6)
  10. RuBisCO, large subunit, small (N-terminal) domain [54966] (1)
    C-terminal domain is beta/alpha barrel
    uperfamily
    1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54967] (12)
  11. Acylphosphatase/BLUF domain-like [54975] (2)
    uperfamily
    1. Acylphosphatase-like [54976] (6)
    2. BLUF domain [143364] (3)
      Pfam 04940; sensors of blue-light using FAD
  12. EF-G C-terminal domain-like [54980] (3)
    uperfamily
    1. EF-G/eEF-2 domains III and V [54981] (3)
      domain III structure is lacking some of the superfamily characters and is often disordered in crystals
    2. YigZ C-terminal domain-like [102991] (2)
      similar to EF-G domain V; N-terminal domain shares structural similarity with the EF-G domain IV
    3. Hypothetical protein AF0491, C-terminal domain [110976] (1)
  13. eEF-1beta-like [54984] (1)
    uperfamily
    1. eEF-1beta-like [54985] (3)
  14. eEF1-gamma domain [89942] (1)
    elaborated with additional structures
    uperfamily
    1. eEF1-gamma domain [89943] (1)
  15. Anticodon-binding domain of PheRS [54991] (1)
    uperfamily
    1. Anticodon-binding domain of PheRS [54992] (1)
  16. Ribosomal protein S6 [54995] (1)
    uperfamily
    1. Ribosomal protein S6 [54996] (4)
  17. Ribosomal protein S10 [54999] (1)
    uperfamily
    1. Ribosomal protein S10 [55000] (2)
  18. N-utilization substance G protein NusG, N-terminal domain [82679] (1)
    uperfamily
    1. N-utilization substance G protein NusG, N-terminal domain [82680] (2)
  19. PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2)
    uperfamily
    1. Poly(A) polymerase, PAP, C-terminal domain [55004] (2)
    2. Archaeal tRNA CCA-adding enzyme [102995] (1)
      decorated fold with a large insertion
  20. HMA, heavy metal-associated domain [55008] (1)
    uperfamily
    1. HMA, heavy metal-associated domain [55009] (12)
  21. Urease metallochaperone UreE, C-terminal domain [69737] (1)
    uperfamily
    1. Urease metallochaperone UreE, C-terminal domain [69738] (2)
  22. ACT-like [55021] (14)
    regulatory domain linked to a wide range of metabolic enzymes
    uperfamily
    1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55022] (2)
    2. Allosteric threonine deaminase C-terminal domain [55025] (1)
    3. Phenylalanine metabolism regulatory domain [55028] (2)
    4. Nickel responsive regulator NikR, C-terminal domain [102999] (2)
    5. Glycine cleavage system transcriptional repressor [110980] (1)
      tandem repeat of two ACT-like domains; swapped domain dimer
    6. IlvH-like [143376] (3)
      Duplication: tandem repeat of two ACT-like domains; dimer, the N- and C-terminal domains have different dimerisation modes
    7. SP0238-like [143381] (1)
      stand-alone protein; dimer, the dimerization interface is formed by parallel packing of the subunit beta-sheets
    8. Atu0741-like [143384] (1)
      duplication: tandem repeat of two ACT-like domains; contains strand invasion of extra N-terminal strand into the C-terminal domain beta-sheet; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    9. VC0802-like [143387] (1)
      duplication: tandem repeat of two ACT-like domains; contains circular permutation (the C-terminal strand replacement with extra N-terminal strand); dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    10. Aspartokinase allosteric domain-like [143390] (3)
      duplication: tandem repeat of two ACT-like domains; similar subunit and oligomeric structures to the VC0802-like family
    11. BT0572-like [143395] (1)
      duplication: tandem repeat of two ACT-like domains; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    12. AF1403 N-terminal domain-like [143398] (1)
      dimerizes with the formation of a single intersubunit beta-sheet
    13. NIL domain-like [160322] (4)
      Pfam 09383
    14. TM1266-like [160329] (1)
      PfamB 015436; stand-alone tetrameric protein; there are single beta-sheet dimers, whose beta-sheets are packed in parallel fasion in the tetramer
  23. Bacterial exopeptidase dimerisation domain [55031] (1)
    uperfamily
    1. Bacterial exopeptidase dimerisation domain [55032] (9)
  24. NAD-binding domain of HMG-CoA reductase [55035] (1)
    uperfamily
    1. NAD-binding domain of HMG-CoA reductase [55036] (2)
  25. Molybdenum cofactor biosynthesis protein C, MoaC [55040] (1)
    uperfamily
    1. Molybdenum cofactor biosynthesis protein C, MoaC [55041] (1)
  26. TRADD, N-terminal domain [55044] (1)
    uperfamily
    1. TRADD, N-terminal domain [55045] (1)
  27. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1)
    uperfamily
    1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55049] (2)
  28. CheY-binding domain of CheA [55052] (1)
    uperfamily
    1. CheY-binding domain of CheA [55053] (2)
  29. D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1)
    uperfamily
    1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75446] (4)
  30. Killer toxin KP6 alpha-subunit [55056] (1)
    uperfamily
    1. Killer toxin KP6 alpha-subunit [55057] (1)
  31. Hypothetical protein VC0424 [89946] (1)
    uperfamily
    1. Hypothetical protein VC0424 [89947] (1)
  32. Hypothetical protein TT1725 [103007] (1)
    uperfamily
    1. Hypothetical protein TT1725 [103008] (1)
  33. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82689] (1)
    the last strand of the fold is flipped away and involved in oligomerisation
    uperfamily
    1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82690] (1)
  34. GHMP Kinase, C-terminal domain [55060] (7)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Galactokinase [103011] (3)
    2. Homoserine kinase [55061] (1)
    3. Mevalonate kinase [75450] (2)
    4. Phosphomevalonate kinase (PMK) [75454] (1)
    5. Mevalonate 5-diphosphate decarboxylase [64281] (1)
    6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89950] (2)
    7. Early switch protein XOL-1 [89953] (1)
      lost the ATP-binding site
  35. Translational regulator protein regA [55064] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Translational regulator protein regA [55065] (1)
  36. Peptide methionine sulfoxide reductase [55068] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Peptide methionine sulfoxide reductase [55069] (3)
  37. Nucleotide cyclase [55073] (2)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Adenylyl and guanylyl cyclase catalytic domain [55074] (5)
      Pfam 00211
      structurally similar to the "palm" domain of DNA/RNA polymerase superfamily
    2. GGDEF domain [117984] (1)
      Pfam 00990; less decorated than the adenylyl/guanylyl cyclase domain
  38. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55084] (2)
  39. Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69743] (1)
  40. MTH1187/YkoF-like [89957] (2)
    uperfamily
    1. MTH1187-like [89958] (5)
      Pfam 01910; two domains form a single beta-sheet dimer; two dimers pack sheet-to-sheet in a tetramer; contains extra C-terminal helix
    2. Putative thiamin/HMP-binding protein YkoF [110987] (1)
      duplication: one subunit consists of two domains assembled as in the MHT1178-like dimer
  41. Methyl-coenzyme M reductase subunits [55088] (2)
    each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
    uperfamily
    1. Methyl-coenzyme M reductase gamma chain [55089] (3)
    2. Methyl-coenzyme M reductase alpha and beta chain N-terminal domain [55094] (6)
      C-terminal domain is all-alpha
  42. FAD-linked oxidases, C-terminal domain [55103] (4)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Vanillyl-alcohol oxidase-like [55104] (2)
    2. D-lactate dehydrogenase [55109] (1)
    3. Cholesterol oxidase [64284] (1)
    4. Cytokinin dehydrogenase 1 [110990] (1)
  43. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55113] (3)
  44. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55117] (1)
  45. Nitrite/Sulfite reductase N-terminal domain-like [55124] (2)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Duplicated SiR/NiR-like domains 1 and 3 [55125] (3)
    2. DsrA/DsrB N-terminal-domain-like [160336] (4)
      Dissimilatory sulfite reductase is a heterodimer of homologous DsrA and DsrB subunits, the assembly of which is similar to the architecture of duplicated sulfite reductase CysI
  46. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82693] (1)
    duplication: the N- and C-terminal halves of the whole proteins are structurally similar; each half contains two domains of this fold
    uperfamily
    1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82694] (1)
  47. YajQ-like [89963] (1)
    duplication: consists of two domains of this fold swapped with their N-terminal strands
    uperfamily
    1. YajQ-like [89964] (1)
  48. eIF-2-alpha, C-terminal domain [110993] (1)
    uperfamily
    1. eIF-2-alpha, C-terminal domain [110994] (2)
  49. Sporulation related repeat [110997] (1)
    duplication: one domain contains two repeats of similar sequence and structure
    uperfamily
    1. Sporulation related repeat [110998] (1)
      Pfam 05036; SPOR
  50. CRISPR-associated protein [117987] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. CRISPR-associated protein [117988] (1)
  51. YbeD/HP0495-like [117991] (2)
    uperfamily
    1. YbeD-like [117992] (1)
      Pfam 04359; DUF493
    2. HP0495-like [160343] (1)
      PfamB 045675
  52. DOPA-like [143410] (1)
    probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
    uperfamily
    1. DOPA dioxygenase-like [143411] (1)
      Pfam 08883
  53. CcmK-like [143414] (1)
    contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
    uperfamily
    1. CcmK-like [143415] (3)
      Pfam 00936; BMC domain
  54. Transposase IS200-like [143422] (1)
    contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
    uperfamily
    1. Transposase IS200-like [143423] (3)
      Pfam 01797
  55. TTP0101/SSO1404-like [143430] (1)
    contains extra C-terminal beta-strand that integrates into the beta-sheet of the other subunit in the homodimer, a probable biological unit of this superfamily
    uperfamily
    1. TTP0101/SSO1404-like [143431] (3)
      Pfam 02647; DUF196; this family includes recent structure of SSO1404 (PDB entry 2IVY)
  56. Rnp2-like [160350] (1)
    contains extra C-terminal helix
    1. Rpp14/Pop5-like [160351] (2)
      Pfam 01900
  57. Bacterial polysaccharide co-polymerase-like [160355] (1)
    Decorated common fold with extra helical regions, which facilitate oligomerization
    1. FepE-like [160356] (3)
      the ferredoxin-like fold resides mainly on in the N-terminal part that corresponds to Pfam 02706 (Wzz)
  58. MTH889-like [160363] (1)
    assembles into hexameric ring-like structures with the formation of a singe beta-barrel sheet of 24 strands
    1. MTH889-like [160364] (2)
      Pfam 02680; DUF211, COG1888
  59. Ribosomal protein L10-like [160369] (1)
    consists of globular N-terminal domain, structurally similar to NDK, and the L7/L12-binding C-terminal alpha-helical tail
    1. Ribosomal protein L10-like [160370] (1)
      Pfam 00466; covers globular domain only
130. PurS-like [109622] (1)
  consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
  1. PurS-like [82697] (2)
    segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit
    uperfamily
    1. PurS subunit of FGAM synthetase [82698] (3)
    2. FGAM synthase PurL, PurS-like domain [111002] (1)
      duplication: consists of 2 structural repeats of the PurS subunit fold, assembled like the PurS dimer
131. RplX-like [160373] (1)
  beta(2)-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 213; some structural similarity to the PurS subunit/repeat (scop_cf 109622)
  1. RplX-like [160374] (1)
    similar structural motif to the Ribosomal S24e family (scop_fa 117786); possible structural permutation
    1. RplX-like [160375] (1)
      Pfam 01911
132. Dystroglycan, domain 2 [111005] (1)
  beta-alpha-beta-X-beta(2)-alpha(2)-beta; antiparallel beta-sheet, order 24153; topological similarity to the ferredoxin-like fold (scop_cf 54861)
  1. Dystroglycan, domain 2 [111006] (1)
    uperfamily
    1. Dystroglycan, domain 2 [111007] (1)
133. Pseudouridine synthase [100877] (1)
  consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
  1. Pseudouridine synthase [55120] (4)
    the active site is the most conserved structural region of the superfamily and is located between the subdomains
    uperfamily
    1. Pseudouridine synthase I TruA [55121] (1)
    2. Pseudouridine synthase II TruB [69746] (5)
      contains C-terminal PUA domain
    3. Pseudouridine synthase RsuA/RluD [75459] (4)
      contains N-terminal alpha-L RNA-binding motif
    4. tRNA pseudouridine synthase TruD [103021] (1)
      natural circular permutation in the catalytic domain; insertion of the family-specific alpha+beta subdomain
134. SP0830-like [160378] (1)
  duplication: two beta-alpha-beta(2)-alpha-beta-alpha motifs are organized in ferredoxin-like subdomains swapped with the extra C-terminal helices
  1. SP0830-like [160379] (1)
    1. SP0830-like [160380] (1)
      Pfam 08002; DUF1697
135. Folate-binding domain [103024] (1)
  duplication: consists of two beta(2)-alpha-beta(3)-alpha subdomains swapped with the first strands
  1. Folate-binding domain [103025] (2)
    some topological similarity to Formylmethanofuran:tetrahydromethanopterin formyltransferase
    uperfamily
    1. Aminomethyltransferase folate-binding domain [103026] (5)
    2. TrmE formyl-THF-binding domain [117997] (1)
      dimeric biological unit; one subunit domain corresponds to one "unswapped" subdomain of the other family
136. THUMP domain [143436] (1)
  contains mixed 8-stranded beta-sheet, folded into a half-barrel and covered with 4 helices on the outside; order 32148756; strands 5, 6 and 7 are parallel
  1. THUMP domain-like [143437] (3)
    predicted RNA-binding function
    uperfamily
    1. THUMP domain [143438] (2)
      Pfam 02926
    2. PAE0736-like [143443] (1)
      orphan protein; rudiment, disulfide-stabilized form of THUMP domain fold
    3. Minimal THUMP [160383] (1)
      subfamily of Pfam 02926; 4 stranded mixed beta-sheet with 2 helices on one side and a crossover loop on the other side
137. AMMECR1-like [143446] (1)
  duplication; contains two beta(2)-alpha-beta(2) structural repeats, swapped with C-terminal strands; extra N-terminal helix and C-terminal strand
  1. AMMECR1-like [143447] (1)
    uperfamily
    1. AMMECR1-like [143448] (3)
      Pfam 01871
138. NosL/MerB-like [160386] (1)
  unusual fold; comprises two structural repeats of beta(2)-alpha-beta motifs, forming separate beta-sheets; probable duplication
  1. NosL/MerB-like [160387] (2)
    1. NosL-like [160388] (1)
      Pfam 05573
    2. MerB-like [160391] (1)
      Pfam 03243
139. YehU-like [118000] (1)
  beta-alpha(2)-beta(2)-alpha; 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
  1. YehU-like [118001] (1)
    uperfamily
    1. YehU-like [118002] (1)
      Pfam 06794; UPF0270
140. Hypothetical protein YwqG [103031] (1)
  duplication: contains two similar beta-x-beta(4) motifs swapped with the first strands
  1. Hypothetical protein YwqG [103032] (1)
    uperfamily
    1. Hypothetical protein YwqG [103033] (1)
141. VC0467-like [143455] (1)
  complex fold; contains bifurcated beta-sheet structure folded into pseudo barrel
  1. VC0467-like [143456] (1)
    uperfamily
    1. VC0467-like [143457] (5)
      Pfam 02622; DUF179
142. Lesion bypass DNA polymerase (Y-family), little finger domain [100878] (1)
  beta-alpha-beta(2)-alpha-beta; antiparallel beta-sheet: order 1423; "reversed" ferredoxin-like topology
  1. Lesion bypass DNA polymerase (Y-family), little finger domain [100879] (1)
    uperfamily
    1. Lesion bypass DNA polymerase (Y-family), little finger domain [100880] (7)
143. ImmE5-like [143468] (1)
  alpha-beta(2)-alpha-beta; 2 layers, a/b; antiparallel beta-sheet, order 213
  1. ImmE5-like [143469] (1)
    uperfamily
    1. ImmE5-like [143470] (1)
144. Ribosomal protein L30p/L7e [55128] (1)
  core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity to the ferredoxin-like fold
  1. Ribosomal protein L30p/L7e [55129] (1)
    uperfamily
    1. Ribosomal protein L30p/L7e [55130] (4)
145. Chorismate lyase-like [64287] (1)
  duplication of alpha(2)-beta(3) motif; antiparallel beta sheet, order 123654
  1. Chorismate lyase-like [64288] (3)
    uperfamily
    1. Chorismate lyase [64289] (1)
    2. UTRA domain [143473] (10)
      Pfam 07702
    3. AF1396-like [160415] (1)
      Pfam 01947; DUF98
146. YdfO-like [160418] (1)
  duplication: two alpha(2)-beta(3) motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456
  1. YdfO-like [160419] (1)
    1. YdfO-like [160420] (1)
      Pfam 07166; DUF1398
147. TM1622-like [143476] (1)
  alpha-beta(3)-alpha-beta(4)-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 1237654
  1. TM1622-like [143477] (1)
    uperfamily
    1. TM1622-like [143478] (1)
148. BH3703-like [160423] (1)
  alpha-beta(3)-alpha-beta(2)-alpha(2); antiparallel beta-sheet, order:32145; duplication: two alpha-beta(2) structural repeats are arranged with pseudo twofold symmetry
  1. BH3703-like [160424] (1)
    1. BH3703-like [160425] (1)
      Pfam 04634; DUF600
149. Probable bacterial effector-binding domain [55135] (1)
  duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
  1. Probable bacterial effector-binding domain [55136] (4)
    uperfamily
    1. Gyrase inhibitory protein GyrI (SbmC, YeeB) [75462] (1)
    2. Multidrug-binding domain of transcription activator BmrR [55137] (1)
    3. Rob transcription factor, C-terminal domain [55140] (1)
    4. SOUL heme-binding protein [143481] (1)
      Pfam 04832
150. CheC-like [103038] (1)
  duplication: tandem repeat of two intertwined alpha-beta-(X)-beta(2) motifs
  1. CheC-like [103039] (1)
    uperfamily
    1. CheC-like [103040] (2)
      Pfam 04509
151. LigT-like [55143] (1)
  duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
  1. LigT-like [55144] (4)
    uperfamily
    1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [55145] (1)
    2. 2'-5' RNA ligase LigT [89967] (1)
    3. 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [103043] (1)
    4. Atu0111-like [143484] (1)
152. Pepsin inhibitor-3 [55148] (1)
  duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
  1. Pepsin inhibitor-3 [55149] (1)
    uperfamily
    1. Pepsin inhibitor-3 [55150] (1)
153. CYTH-like phosphatases [55153] (1)
  duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
  1. CYTH-like phosphatases [55154] (2)
    uperfamily
    1. mRNA triphosphatase CET1 [55155] (1)
      Pfam 02940
    2. CYTH domain [118007] (4)
      Pfam 01928
154. Antiparallel beta/alpha barrel (PT-barrel) [143491] (1)
  tandem repeat of five alpha(2)-beta(2) motifs; antiparallel beta-sheet barrel, closed; n=10, S=10; order 123456789A; there is a channel along the barrel axis
  1. Prenyltransferase-like [143492] (1)
    the barrel channel harbours the substrate-binding site
    uperfamily
    1. Prenyltransferase-like [143493] (1)
155. eIF1-like [55158] (2)
  beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
  1. eIF1-like [55159] (1)
    uperfamily
    1. eIF1-like [55160] (2)
  2. TM1457-like [118010] (1)
    forms a homodimer via alpha-helical interface
    uperfamily
    1. TM1457-like [118011] (4)
      Pfam 04327; DUF464
156. Hedgehog/DD-peptidase [55165] (1)
  alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
  1. Hedgehog/DD-peptidase [55166] (5)
    zinc-binding motif
    uperfamily
    1. Muramoyl-pentapeptide carboxypeptidase [55167] (1)
    2. MepA-like [111019] (1)
    3. VanX-like [111022] (1)
      Pfam 01427
    4. Hedgehog (development protein), N-terminal signaling domain [55170] (2)
    5. VanY-like [160436] (1)
      Pfam 02557
157. Alpha-L RNA-binding motif [55173] (1)
  alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
  1. Alpha-L RNA-binding motif [55174] (5)
    common motif in otherwise different folds
    uperfamily
    1. Ribosomal protein S4 [55178] (3)
      has a RRF/tRNA synthetase additional domain-like fold
    2. Heat shock protein 15 kD [55182] (1)
      there are additional C-terminal structures
    3. Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [75465] (2)
      there are additional N-terminal structures
    4. YbcJ-like [103046] (1)
      overall topological similarity to the TyrRS C-domain
    5. Pseudouridine synthase RsuA N-terminal domain [75468] (2)
158. RRF/tRNA synthetase additional domain-like [55185] (4)
  core: alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
  1. ThrRS/AlaRS common domain [55186] (2)
    putative editing domain found in the N-terminal part of ThrRS, the C-terminal of AlaRS, and as a stand-alone protein; probable circular permutation of LuxS (d.185.1.2)
    uperfamily
    1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain [55187] (2)
    2. AlaX-like [103051] (2)
  2. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55190] (1)
    uperfamily
    1. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55191] (2)
  3. Ribosome recycling factor, RRF [55194] (1)
    uperfamily
    1. Ribosome recycling factor, RRF [55195] (7)
  4. General secretion pathway protein M, EpsM [103054] (1)
    uperfamily
    1. General secretion pathway protein M, EpsM [103055] (1)
159. LuxS/MPP-like metallohydrolase [63410] (1)
  core: beta-alpha-beta(2)-alpha(2); 2 layers: alpha/beta
  1. LuxS/MPP-like metallohydrolase [63411] (2)
    Share the same "active site motif" HxxEH located in the first core helix, but differ in one of the zinc-binding residues
    uperfamily
    1. Autoinducer-2 production protein LuxS [64294] (4)
      contains additional N-terminal strand; possible relationships to the putative editing domain of ThrRS (d.67.1)
    2. MPP-like [63412] (10)
      Common fold elaborated with many additional structures; duplication: each family member consists of two similar domains of beta(2)-alpha(2)-beta(2)-alpha(5)-beta structure, but only the N-terminal domain of MPP beta chain binds the catalytic metal
160. IF3-like [55199] (8)
  beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
  1. Translation initiation factor IF3, C-terminal domain [55200] (1)
    uperfamily
    1. Translation initiation factor IF3, C-terminal domain [55201] (3)
  2. YhbY-like [75471] (1)
    uperfamily
    1. YhbY-like [75472] (3)
      Pfam 01985
  3. SirA-like [64307] (1)
    uperfamily
    1. SirA-like [88852] (4)
      predicted redox protein, regulator of disulfide bond formation
  4. AlbA-like [82704] (2)
    uperfamily
    1. DNA-binding protein AlbA [82705] (4)
    2. Hypothetical protein At2g34160 [111027] (1)
  5. C-terminal domain of ProRS [64586] (1)
    contains a metal (zinc)-binding site
    uperfamily
    1. C-terminal domain of ProRS [64587] (3)
  6. R3H domain [82708] (1)
    possibly lacks the N-terminal strand of the common fold
    uperfamily
    1. R3H domain [82709] (3)
      Pfam 01424; predicted nucleic acid-binding domain
  7. EPT/RTPC-like [55205] (2)
    uperfamily
    1. RNA 3'-terminal phosphate cyclase, RPTC [55206] (1)
      duplication: 3 repeats of this fold are packed together around the pseudo threefold axis
    2. Enolpyruvate transferase, EPT [55209] (4)
      duplication: 6 repeats of this fold are organized in two RPTC-like domains
  8. SMR domain-like [160443] (1)
    1. Smr domain [160444] (1)
      Pfam 01713
161. PUG domain-like [143502] (1)
  alpha(2)-beta-alpha(2)-beta(2)-alpha; cluster of helices with a small antiparallel beta-sheet on one side; order 132; topological similarity to the fold of an extended R3H domain (PDB 1whr)
  1. PUG domain-like [143503] (1)
    uperfamily
    1. PUG domain [143504] (2)
      SMART 00580; domain in protein kinases, N-glycanases and other nuclear proteins
162. PG1857-like [160447] (1)
  alpha-beta-alpha-beta(2)-alpha(3); 3 layers, a/b/a; antiparallel beta-sheet, order: 132
  1. PG1857-like [160448] (1)
    1. PG1857-like [160449] (1)
      Pfam 09633; DUF2023
163. PB2 C-terminal domain-like [160452] (1)
  alpha-beta-alpha-X-alpha-beta(2); 3 layers, a/b/a; antiparallel beta-sheet, order 132; connection between helices 2 and 3 runs over the edge of the beta-sheet
  1. PB2 C-terminal domain-like [160453] (1)
    1. PB2 C-terminal domain-like [160454] (1)
      C-terminal part of Pfam 00604
164. Ribosome binding protein Y (YfiA homologue) [69753] (1)
  beta-alpha-beta(3)-alpha; 2 layers; mixed sheet 1234, strand 3 is antiparallel to the rest
  1. Ribosome binding protein Y (YfiA homologue) [69754] (1)
    uperfamily
    1. Ribosome binding protein Y (YfiA homologue) [69755] (3)
165. TolA/TonB C-terminal domain [74652] (1)
  beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit in non-swapped monomer
  1. TolA/TonB C-terminal domain [74653] (2)
    uperfamily
    1. TolA [55217] (2)
      contains extra N-terminal helix
    2. TonB [64326] (1)
      isolated domain can form different segment-swapped dimers depending on the fragment length
166. Yeast killer toxins [55220] (1)
  beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
  1. Yeast killer toxins [55221] (2)
    uperfamily
    1. Virally encoded KP4 toxin [55222] (1)
    2. SMK toxin [55225] (1)
167. Cell division protein MinE topological specificity domain [55228] (1)
  dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
  1. Cell division protein MinE topological specificity domain [55229] (1)
    uperfamily
    1. Cell division protein MinE topological specificity domain [55230] (1)
168. Hypothetical protein YoaG [103062] (1)
  dimer of beta(2)-alpha motifs ; 2 layers, alpha/beta; reverse MinE topology
  1. Hypothetical protein YoaG [103063] (1)
    uperfamily
    1. Hypothetical protein YoaG [103064] (1)
169. BLRF2-like [160458] (1)
  homodimer of alpha(2)-beta motif; also includes extra N-terminal helix of variable position
  1. BLRF2-like [160459] (1)
    1. BLRF2-like [160460] (1)
      Pfam 05812; Herpesvirus BLRF2 protein
170. Nucleocapsid protein dimerization domain [103067] (1)
  dimer of alpha-beta(2)-alpha motifs ; 2 layers, alpha/beta
  1. Nucleocapsid protein dimerization domain [103068] (2)
    uperfamily
    1. Arterivirus nucleocapsid protein [103069] (2)
    2. Coronavirus nucleocapsid protein [143508] (2)
      C-terminal part of Pfam 00937
171. Cyanase C-terminal domain [55233] (1)
  intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
  1. Cyanase C-terminal domain [55234] (1)
    uperfamily
    1. Cyanase C-terminal domain [55235] (1)
      active form is a decamer formed by five dimers
172. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82713] (1)
  Intertwined pseudo hexamer of an alpha+beta motif
  1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82714] (1)
    duplication: the N- and C-terminal halves of the whole proteins are structurally similar
    uperfamily
    1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82715] (1)
173. RuBisCO, small subunit [55238] (1)
  alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
  1. RuBisCO, small subunit [55239] (1)
    uperfamily
    1. RuBisCO, small subunit [55240] (8)
174. DCoH-like [55247] (5)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
  1. PCD-like [55248] (1)
    has additional alpha helix at the N-terminus
    uperfamily
    1. PCD-like [55249] (3)
      Pfam 01329
  2. C-terminal domain of arginine repressor [55252] (1)
    forms trimers with three closely packed beta-sheets
    uperfamily
    1. C-terminal domain of arginine repressor [55253] (3)
  3. RBP11-like subunits of RNA polymerase [55257] (2)
    form homo and heterodimers
    uperfamily
    1. RBP11/RpoL [64311] (2)
    2. RNA polymerase alpha subunit dimerisation domain [55258] (4)
  4. GAD domain-like [55261] (2)
    uperfamily
    1. GAD domain [55262] (4)
      has additional structures inserted in the common fold loops
    2. PH0730 C-terminal domain-like [160464] (1)
  5. PH0987 N-terminal domain-like [160467] (1)
    1. PH0987 N-terminal domain-like [160468] (1)
      corresponds to the N-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
175. TRCF domain-like [143516] (1)
  beta-alpha(3)-beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed beta sheet, order 12354, strands 1 and 2 are parallel; some topological similarity to the DCoH-like fold (scop_cf 55247)
  1. TRCF domain-like [143517] (1)
    uperfamily
    1. TRCF domain [143518] (1)
      Pfam 03461
176. NMB0513-like [160471] (1)
  alpha(3)-beta(2)-alpha-beta(2); some similarity to the "winged helix" DNA-binding domain fold
  1. NMB0513-like [160472] (1)
    1. NMB0513-like [160473] (1)
      C-terminal part corresponds to Pfam 04591, DUF596
177. PA1123-like [160476] (1)
  irregular array of short helices and two three-stranded beta-sheets
  1. PA1123-like [160477] (1)
    1. PA1123-like [160478] (1)
      Pfam 09634; DUF2025
178. Hypothetical protein Yml108w [100886] (1)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta; mixed beta-sheet 2143, strands 1 and 4 are parallel
  1. Hypothetical protein Yml108w [89975] (1)
    uperfamily
    1. Hypothetical protein Yml108w [89976] (1)
179. MutS N-terminal domain-like [55266] (2)
  beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
  1. tRNA-intron endonuclease N-terminal domain-like [55267] (1)
    uperfamily
    1. tRNA-intron endonuclease N-terminal domain-like [55268] (2)
  2. DNA repair protein MutS, domain I [55271] (1)
    uperfamily
    1. DNA repair protein MutS, domain I [55272] (2)
180. GYF/BRK domain-like [55276] (2)
  beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
  1. GYF domain [55277] (1)
    uperfamily
    1. GYF domain [55278] (2)
      Pfam 02213
  2. BRK domain-like [160481] (1)
    1. BRK domain-like [160482] (2)
      Pfam 07533; TCH domain
181. GTP cyclohydrolase I feedback regulatory protein, GFRP [69760] (1)
  beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta, antiparallel beta-sheet: order 342165
  1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69761] (1)
    uperfamily
    1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69762] (1)
182. RL5-like [55281] (1)
  beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
  1. RL5-like [55282] (2)
    uperfamily
    1. Ribosomal protein L5 [55283] (5)
    2. SSO1042-like [160489] (4)
      Pfam 01877; DUF54
183. RPB5-like RNA polymerase subunit [55286] (1)
  core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
  1. RPB5-like RNA polymerase subunit [55287] (1)
    uperfamily
    1. RPB5 [55288] (3)
184. Bacillus chorismate mutase-like [55297] (9)
  core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
  1. YjgF-like [55298] (2)
    forms trimers with three closely packed beta-sheets; possibly related to the IspF (d.79.5) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
    uperfamily
    1. YjgF/L-PSP [55299] (15)
      some members possess an endoribonuclease activity inhibiting mRNA translation
    2. Chorismate mutase [55304] (3)
  2. IpsF-like [69765] (1)
    forms trimers with three closely packed beta-sheets; possible link between the YjgF-like (d.79.1) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
    uperfamily
    1. IpsF-like [69766] (5)
  3. Tubulin C-terminal domain-like [55307] (1)
    uperfamily
    1. Tubulin, C-terminal domain [55308] (9)
  4. L30e-like [55315] (3)
    uperfamily
    1. L30e/L7ae ribosomal proteins [55316] (11)
    2. RNA 2'-O ribose methyltransferase substrate binding domain [75480] (2)
    3. ERF1/Dom34 C-terminal domain-like [55323] (4)
  5. PurM N-terminal domain-like [55326] (1)
    uperfamily
    1. PurM N-terminal domain-like [55327] (6)
  6. Holliday junction resolvase RusA [103084] (1)
    uperfamily
    1. Holliday junction resolvase RusA [103085] (1)
  7. OmpA-like [103088] (1)
    uperfamily
    1. OmpA-like [103089] (3)
      Pfam 00691
  8. YueI-like [160515] (1)
    1. YueI-like [160516] (1)
      Pfam 07997; DUF1694
  9. BB2672-like [160519] (1)
    contains extra N-terminal strand and a beta-hairpin insertion between strands 3 and 4 that packs against the main beta-sheet
    1. BB2672-like [160520] (2)
      Pam 06684; DUF1185
185. YjbQ-like [111037] (1)
  beta(2)-alpha-beta(2)-alpha(2)-beta(3); contains a beta-sandwich: 7 strands in 2 sheets; trimerizes with orthogonally packed beta-sheets
  1. YjbQ-like [111038] (1)
    uperfamily
    1. YjbQ-like [111039] (4)
      Pfam 01894
186. Tautomerase/MIF [55330] (1)
  (beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
  generally forms trimers with three closely packed beta-sheets
  1. Tautomerase/MIF [55331] (6)
    uperfamily
    1. 4-oxalocrotonate tautomerase-like [55332] (5)
      dimer of beta-alpha-beta subunits: may assemble further in hexamer (trimer of the dimers)
    2. 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) [55336] (1)
    3. MIF-related [55339] (6)
    4. Hypothetical protein HI1388.1 [103098] (1)
      lacks the N-terminal proline
    5. VC0714-like [111043] (1)
    6. MSAD-like [143532] (1)
187. FwdE/GAPDH domain-like [55346] (4)
  core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
  1. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain [55347] (5)
    N-terminal domain is the classic Rossmann-fold
    uperfamily
    1. GAPDH-like [55348] (29)
      has many additional secondary structures
    2. Homoserine dehydrogenase-like [55363] (2)
    3. Dihydrodipicolinate reductase-like [55368] (12)
    4. Biliverdin reductase [55373] (1)
    5. Glucose 6-phosphate dehydrogenase-like [55376] (8)
      has many additional secondary structures
  2. Serine metabolism enzymes domain [143548] (2)
    contains extra C-terminal beta-hairpin
    uperfamily
    1. Serine dehydratase beta chain-like [143549] (1)
      Pfam 03315
    2. SerA intervening domain-like [143552] (1)
      PfamB 001360; this domain is found in some but not all D-3-phosphoglycerate dehydrogenases (SerA) and related enzymes
  3. FwdE-like [143555] (1)
    contains extra N-terminal and C-terminal structures
    uperfamily
    1. FwdE-like [143556] (2)
      Pfam 02663; Tungsten formylmethanofuran dehydrogenase, subunit E, FwdE, is a stand-alone domain of this fold
  4. V-type ATPase subunit E-like [160527] (1)
    extra N-terminal helix and extra C-terminal helix form dimerisation subdomain
    1. V-type ATPase subunit E [160528] (1)
      Pfam 01991
188. Ava3019-like [160531] (1)
  alpha(2)-beta-alpha-beta(4); 2 layers, a/b; antiparallel beta-sheet, order: 32145; similarity to the insert domain of Glucose 6-phosphate dehydrogenase-like family (sop_fa 55376)
  1. Ava3019-like [160532] (1)
    1. Ava3019-like [160533] (1)
      Pfam 08854; DUF1824
189. Hypothetical protein PF0899 [111056] (1)
  alpha-beta-alpha-beta(4); 2 layers: a/b; mixed beta-sheet, order 23145, strands 1 and 3 are parallel; similar to the GAPDH C-terminal domain-like fold (scop_cf 55346)
  1. Hypothetical protein PF0899 [111057] (1)
    possibly related to Major capsid protein gp5 (scop_sf 56563)63566
    uperfamily
    1. Hypothetical protein PF0899 [111058] (1)
190. Major capsid protein gp5 [56562] (1)
  unusual fold; contains PF0899-like core, decorated with additional structure
  1. Major capsid protein gp5 [56563] (1)
    possibly related to the hypothetical protein PF0899 superfamily (scop_sf 111057)
    uperfamily
    1. Major capsid protein gp5 [56564] (1)
191. MK0786-like [143559] (1)
  alpha(2)-beta(4); 2 layers: a/b; antiparallel beta-sheet, order 1234 (meander)
  1. MK0786-like [143560] (1)
    probable biological unit is a teramer; all subunit interfaces are provided by helices
    uperfamily
    1. MK0786-like [143561] (2)
      single domain; the N-terminal half is covered by Pfam 04036 (DUF372) and the C-terminal half by Pfam 04038 (DUF381)
192. YkuJ-like [143566] (1)
  alpha-beta(4)-alpha; 2 layers a/b; antiparallel beta-sheet, order 1234
  1. YkuJ-like [143567] (1)
    uperfamily
    1. YkuJ-like [143568] (1)
193. N domain of copper amine oxidase-like [55382] (5)
  alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
  1. Copper amine oxidase, domain N [55383] (1)
    uperfamily
    1. Copper amine oxidase, domain N [55384] (1)
  2. Frataxin/Nqo15-like [55387] (2)
    uperfamily
    1. Frataxin-like [55388] (3)
      iron homeostasis proteins
    2. Nqo15-like [143572] (1)
      overall structural similarity to the frataxin-like family
  3. Hypothetical protein c14orf129, hspc210 [103107] (1)
    uperfamily
    1. Hypothetical protein c14orf129, hspc210 [103108] (1)
      Pfam 05303
  4. GAS2 domain-like [143575] (1)
    this superfamily may include the most C-terminal domain of IBP39 (scop_fa 103410); the preceeding (middle) domain of IBP39 may be split and reassigned to the EF-hand superfamily (scop_sf 47473)
    uperfamily
    1. GAS2 domain [143576] (1)
      Pfam 02187
  5. GK1464-like [143579] (1)
    dimer; pseudo barrel; the true dimeric barrel formation requires swapping of the C-ternimal beta-alpha units
    uperfamily
    1. GK1464-like [143580] (1)
194. Aha1/BPI domain-like [55393] (2)
  core: [beta]-alpha-beta(5)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, meander
  1. Activator of Hsp90 ATPase, Aha1 [103111] (1)
    consists of a single domain of this fold
    uperfamily
    1. Activator of Hsp90 ATPase, Aha1 [103112] (1)
  2. Bactericidal permeability-increasing protein, BPI [55394] (1)
    duplication: consists of two clear structural repeats of this fold also containing an extra C-terminal beta-hairpin
    uperfamily
    1. Bactericidal permeability-increasing protein, BPI [55395] (1)
195. SpoVG-like [160536] (1)
  beta(5)-alpha; comprises a coiled antiparallel beta-sheet (order: 12345) packed against the C-terminal helix; the extensions of strands 4 and 5 form an isolated beta-hairpin
  1. SpoVG-like [160537] (1)
    probable biological unit is a hexamer (trimer of dimers)
    1. SpoVG-like [160538] (2)
      Pfam 04026
196. Subtilisin inhibitor [55398] (1)
  alpha+beta sandwich
  1. Subtilisin inhibitor [55399] (1)
    uperfamily
    1. Subtilisin inhibitor [55400] (2)
197. RNA bacteriophage capsid protein [55404] (1)
  6-standed beta-sheet followed with 2 helices; meander
  1. RNA bacteriophage capsid protein [55405] (1)
    uperfamily
    1. RNA bacteriophage capsid protein [55406] (5)
198. eIF4e-like [55417] (1)
  beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
  1. eIF4e-like [55418] (2)
    uperfamily
    1. Translation initiation factor eIF4e [55419] (3)
    2. BLES03-like [143583] (1)
      the N-terminal strand is missing, but there extra C-terminal strands in the beta-sheet
199. CO dehydrogenase flavoprotein C-domain-like [55423] (2)
  core: beta(3,4)-alpha(3); alpha+beta sandwich
  1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55424] (1)
    both first two domains are of same beta/beta/alpha fold
    uperfamily
    1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55425] (22)
  2. CO dehydrogenase flavoprotein C-terminal domain-like [55447] (1)
    uperfamily
    1. CO dehydrogenase flavoprotein C-terminal domain-like [55448] (6)
200. SRF-like [55454] (1)
  alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
  1. SRF-like [55455] (1)
    uperfamily
    1. SRF-like [55456] (4)
201. Origin of replication-binding domain, RBD-like [55463] (1)
  alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel sheet 41325
  1. Origin of replication-binding domain, RBD-like [55464] (5)
    uperfamily
    1. The origin DNA-binding domain of SV40 T-antigen [55465] (1)
    2. DNA-binding domain of REP protein [82728] (1)
    3. Replication initiation protein E1 [64332] (2)
    4. Replication protein Rep, nuclease domain [75492] (1)
    5. Relaxase domain [103120] (2)
      circular permutation of the common fold
202. SARS receptor-binding domain-like [143586] (1)
  core: 3 layers, a/b/a; antiparallel beta-sheet of 5 strands, order 13542
  1. SARS receptor-binding domain-like [143587] (1)
    uperfamily
    1. SARS receptor-binding domain-like [143588] (1)
      part of PfamB 000266
203. Hut operon positive regulatory protein HutP [111063] (1)
  alpha(2)-beta-alpha(2)-beta(3); 3 layers: a/b/a; antiparallel beta-sheet: order 1234
  1. Hut operon positive regulatory protein HutP [111064] (1)
    uperfamily
    1. Hut operon positive regulatory protein HutP [111065] (1)
204. Hypothetical protein yfbM [111068] (1)
  beta-alpha(2)-beta-alpha(2)-beta(2)-alpha(n)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 21543
  1. Hypothetical protein yfbM [111069] (1)
    uperfamily
    1. Hypothetical protein yfbM [111070] (1)
205. TTHA1528-like [143591] (1)
  beta-alpha-beta(3)-alpha-beta-alpha(2)-beta; 3 layers: a/b/a; mixed beta-sheet, order: 143256, parallel strands' pairs are 1-4 and 2-5
  1. TTHA1528-like [143592] (1)
    uperfamily
    1. TTHA1528-like [143593] (1)
206. YojJ-like [143596] (1)
  alpha-beta-X-beta-alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; 7-stranded mixed beta-sheet, order 2431567; strands 1 and 3 are parallel to each other
  1. YojJ-like [143597] (1)
    uperfamily
    1. YojJ-like [143598] (1)
      Pfam 02457; DUF147
207. STIV B116-like [143601] (1)
  subunit fold consists of mixed 5-stranded beta-sheet, order:31452, strand 5 is antiparallel to the rest, with 3 helices on one side; dimerises with the formation of a single 10-stranded beta-sheet; strand 2 is in the dimer interface
  1. STIV B116-like [143602] (1)
    uperfamily
    1. STIV B116-like [143603] (2)
208. Bacillus phage protein [111073] (1)
  alpa-beta(3)-alpha-beta(3)-alpha; 3 layers: b/a/b, 3-helical bundle flanked by two 3-stranded meander beta-sheets
  1. Bacillus phage protein [111074] (1)
    uperfamily
    1. Bacillus phage protein [111075] (1)
209. FMN-dependent nitroreductase-like [55468] (1)
  core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
  1. FMN-dependent nitroreductase-like [55469] (2)
    uperfamily
    1. NADH oxidase/flavin reductase [55470] (11)
    2. Putative nitroreductase TM1586 [111078] (1)
      duplication: consists of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site
210. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55480] (1)
  alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
  1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55481] (1)
    uperfamily
    1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55482] (1)
211. EscU C-terminal domain-like [160543] (1)
  alpha-beta(3)-alpha-beta-alpha(2); 3 layers, a/b/a; mixed beta-sheet, order: 4123, strand 2 is antiparallel to the rest
  1. EscU C-terminal domain-like [160544] (1)
    1. EscU C-terminal domain-like [160545] (3)
      C-terminal part of Pfam 01312; self-cleaving type III secretion protein domain
212. Zincin-like [55485] (2)
  contains mixed beta sheet with connection over free side of the sheet
  1. Metalloproteases ("zincins"), catalytic domain [55486] (17)
    uperfamily
    1. Zinc protease [55487] (1)
      single domain
    2. Fungal zinc peptidase [64335] (2)
      single domain with insertions in the common fold
    3. Thermolysin-like [55490] (4)
      includes alpha-helical C-terminal domain characteristic for the family
    4. Leukotriene A4 hydrolase catalytic domain [64338] (1)
      adopts thermolysin-like fold
    5. Neutral endopeptidase (neprilysin) [55502] (1)
    6. Neurolysin-like [55505] (6)
      combines M2, M3 and M32 families of metalloproteases
      the N-terminal half of the structure is multihelical; the C-terminal half contains the thermolysin-like catalytic domain
    7. Anthrax toxin lethal factor, N- and C-terminal domains [69775] (1)
    8. Leishmanolysin [55499] (1)
    9. Serralysin-like metalloprotease, catalytic (N-terminal) domain [55508] (4)
      characteristic HEXXHXXGXXH motif and Met located near C-terminus
    10. Clostridium neurotoxins, catalytic domain [55512] (4)
    11. Astacin [55516] (1)
    12. Reprolysin-like [55519] (8)
      Pfam 01421
    13. TNF-alpha converting enzyme, TACE, catalytic domain [55525] (1)
    14. Matrix metalloproteases, catalytic domain [55528] (15)
    15. Predicted metal-dependent hydrolase [103132] (3)
      Pfam 02130; UPF0054; COG0319; MMP-like fold with a different sequence motif in the putative active site
    16. Caur0242-like [160552] (1)
      Pfam 10103; DUF2342; there is a characteristic HExxH motif but no metal ion bound to it in the first structure.
    17. TTHA0227-like [160555] (2)
      PF06262; DUF1025; minimal zincin fold that retains 3-stranded mixed beta-sheet and contains HExxH motif in the C-terminal helix; no metal ion bound to this motif is observed in the first determined structures
  2. beta-N-acetylhexosaminidase-like domain [55545] (3)
    contains similar fold but lacks its catalytic centre
    uperfamily
    1. beta-N-acetylhexosaminidase domain [55546] (4)
      family GH20
    2. alpha-D-glucuronidase, N-terminal domain [82737] (2)
      family GH67
    3. Hyaluronidase N-terminal domain-like [143618] (2)
213. SH2-like [55549] (1)
  3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
  1. SH2 domain [55550] (1)
    uperfamily
    1. SH2 domain [55551] (39)
      Pfam 00017
214. HPr-like [55593] (2)
  beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
  1. HPr-like [55594] (1)
    uperfamily
    1. HPr-like [55595] (8)
  2. Putative transcriptional regulator TM1602, C-terminal domain [75500] (1)
    uperfamily
    1. Putative transcriptional regulator TM1602, C-terminal domain [75501] (1)
215. TrkA C-terminal domain-like [116725] (1)
  beta-X-beta(2)-X-beta-alpha; pseudo barrel capped by helix at one end; topological similarity to the HPr-like fold
  1. TrkA C-terminal domain-like [116726] (1)
    uperfamily
    1. TrkA C-terminal domain-like [116727] (2)
      Pfam 02080
216. Hypothetical protein YjiA, C-terminal domain [90001] (1)
  beta-alpha-beta(4)-alpha; 2 layers: a/b; antiparallel sheet 15234; topological similarity to the HPr-like fold
  1. Hypothetical protein YjiA, C-terminal domain [90002] (1)
    uperfamily
    1. Hypothetical protein YjiA, C-terminal domain [90003] (1)
217. YggU-like [69785] (1)
  beta(2)-loop-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243; some similarity to the Homing endonuclease-like fold
  1. YggU-like [69786] (1)
    uperfamily
    1. YggU-like [69787] (2)
218. Homing endonuclease-like [55603] (2)
  alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
  1. Glucose permease domain IIB [55604] (1)
    uperfamily
    1. Glucose permease domain IIB [55605] (1)
  2. Homing endonucleases [55608] (2)
    uperfamily
    1. Group I mobile intron endonuclease [55609] (5)
      contains two extra helices in the C-terminal extension
    2. Intein endonuclease [55614] (2)
      duplication: contains tandem repeat of this fold
219. T-fold [55619] (2)
  beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
  tunnel-shaped: its known members form wide oligomeric barrels different sizes
  1. Tetrahydrobiopterin biosynthesis enzymes-like [55620] (4)
    bind purine or pterin in topologically similar sites between subunits
    uperfamily
    1. GTP cyclohydrolase I [55621] (4)
    2. 6-pyruvoyl tetrahydropterin synthase [55625] (4)
    3. DHN aldolase/epimerase [55628] (4)
      beta-sheets of four subunits form a barrel, closed: n=16, S=16
    4. Urate oxidase (uricase) [55633] (3)
  2. ApbE-like [143631] (2)
    duplication: contains two differently decorated beta(2)-alpha(2)-beta(2) subdomains, similar to other T-fold domains; probably does not form the tunnel-shaped oligomers
    uperfamily
    1. ApbE-like [143632] (1)
      Pfam 02424
    2. DVU1097-like [160566] (1)
      Pfam 04040; DUF375
220. Cell cycle regulatory proteins [55636] (1)
  beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
  can form strand-exchange dimers
  1. Cell cycle regulatory proteins [55637] (1)
    uperfamily
    1. Cell cycle regulatory proteins [55638] (4)
221. YonK-like [160569] (1)
  intertwined dimer of beta(3)-alpha-beta subunits; assembles further in octamer with formation of a wide 16-stranded beta-barrel
  1. YonK-like [160570] (1)
    (Pro)phage and phage-related proteins
    1. Yonk-like [160571] (1)
      Pfam 09642
222. BLIP-like [55647] (2)
  alpha(2)-beta(4); 2 layers: alpha/beta
  1. beta-lactamase-inhibitor protein, BLIP [55648] (1)
    uperfamily
    1. beta-lactamase-inhibitor protein, BLIP [55649] (1)
      duplication: consists of two clear structural repeats each having this fold
  2. BT0923-like [160574] (1)
    Duplication: tandem repeat of two similar structural subdomains, which associate like the BLIP repeats but differ from them by transposition of the helices
    1. BT0923-like [160575] (2)
      after putative calcium-regulated periplasmic protein BT0923 (PDB ID 3DUE; new)
223. Ribosomal protein L9 C-domain [55652] (1)
  alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
  1. Ribosomal protein L9 C-domain [55653] (1)
    uperfamily
    1. Ribosomal protein L9 C-domain [55654] (3)
224. MbtH/L9 domain-like [55657] (2)
  beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
  1. L9 N-domain-like [55658] (2)
    uperfamily
    1. Ribosomal protein L9 N-domain [55659] (3)
    2. N-terminal domain of RNase HI [55662] (1)
  2. MbtH-like [160582] (1)
    the first helix is replaced with an extended loop; contains extra C-terminal helix of variable position
    1. MbtH-like [160583] (1)
      Pfam 03621
225. Tombusvirus P19 core protein, VP19 [103144] (1)
  beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel sheet: order 2134
  1. Tombusvirus P19 core protein, VP19 [103145] (1)
    uperfamily
    1. Tombusvirus P19 core protein, VP19 [103146] (2)
226. Ribonuclease PH domain 2-like [55665] (1)
  beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
  1. Ribonuclease PH domain 2-like [55666] (1)
    uperfamily
    1. Ribonuclease PH domain 2-like [55667] (14)
227. Regulatory factor Nef [55670] (1)
  alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
  1. Regulatory factor Nef [55671] (1)
    uperfamily
    1. Regulatory factor Nef [55672] (1)
228. CytB endotoxin-like [55675] (1)
  core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
  1. CytB endotoxin-like [55676] (1)
    uperfamily
    1. CytB endotoxin-like [55677] (2)
      Pfam 01338
229. Class II aaRS and biotin synthetases [55680] (1)
  contains large mixed beta-sheet
  1. Class II aaRS and biotin synthetases [55681] (4)
    uperfamily
    1. Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain [55682] (28)
    2. Biotin holoenzyme synthetase [55707] (2)
    3. LplA-like [143642] (6)
      part of Pfam 03099
    4. PH0223-like [160611] (1)
      Pfam 04017; DUF366
230. Subdomain of clathrin and coatomer appendage domain [55710] (1)
  beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
  1. Subdomain of clathrin and coatomer appendage domain [55711] (2)
    uperfamily
    1. Clathrin adaptor appendage, alpha and beta chain-specific domain [55712] (2)
    2. Coatomer appendage domain [103159] (2)
231. SCP-like [55717] (1)
  alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
  1. SCP-like [55718] (4)
    uperfamily
    1. Sterol carrier protein, SCP [55719] (5)
      Pfam 02036
    2. Micothiol-dependent maleylpyruvate isomerase C-terminal domain-like [160614] (1)
      lacking the short edge strand 3
    3. Alkylsulfatase C-terminal domain-like [160617] (1)
    4. EF1021 C-terminal domain-like [160620] (3)
232. Ta1353-like [103164] (1)
  core: beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 51423;
  1. Ta1353-like [103165] (1)
    uperfamily
    1. Ta1353-like [103166] (2)
      Pfam 04008
233. Mog1p/PsbP-like [55723] (1)
  (beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
  1. Mog1p/PsbP-like [55724] (4)
    uperfamily
    1. Ran-binding protein mog1p [55725] (1)
    2. PsbP-like [111092] (1)
      Pfam 01789
    3. PA0094-like [111095] (1)
      segment-swapped dimer; some sequence similarity to the PsbP-like family
    4. DIP2269-like [160627] (1)
      Pfam 09449; DUF2020
234. SMI1/KNR4-like [160630] (1)
  alpha(4)-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet, order 1234(meander)
  1. SMI1/KNR4-like [160631] (1)
    1. SMI1/KNR4-like [160632] (3)
      Pfam 09346
235. Acyl-CoA N-acyltransferases (Nat) [55728] (1)
  3 layers: a/b/a; contains mixed beta-sheet
  1. Acyl-CoA N-acyltransferases (Nat) [55729] (10)
    uperfamily
    1. N-acetyl transferase, NAT [55730] (60)
    2. N-myristoyl transferase, NMT [55748] (3)
      duplication: consists of two NAT-like domains swapped with the C-terminal strands
    3. Autoinducer synthetase [75508] (2)
      Pfam 00765
    4. FemXAB nonribosomal peptidyltransferases [82749] (3)
      duplication: consists of two NAT-like domains swapped with the C-terminal strands
    5. Hypothetical protein cg14615-pa [103179] (1)
      duplication: consists of two NAT-like domains swapped with the C-terminal strands
    6. LFTR-like [143711] (1)
      Pfam 03588; closer relative to the nonribosomal peptidyltransferases (scop_fa 82749); deletion of the N-terminal half of the N-terminal NAT-like domain after the domain duplication/swapping events
    7. Ornithine decarboxylase antizyme-like [143714] (1)
      Pfam 02100; may have evolved different function; putative active site maps to the same location in the common fold
    8. AstA-like [143717] (1)
      Pfam 04958; contains extra C-terminal domain, similar to the double psi beta-barrel fold (scop_cf 50684) with missing one strand and untangled psi-loops
    9. Aq_1966-like [143720] (1)
      Pfam 06557; DUF1122; probable biological unit is homotrimeric; may have evolved different function; putative active site maps to the same location in the common fold
    10. EF1021-like [160644] (3)
      duplication: consists of two NAT domains swapped with the C-terminal strands; overall structural similarity to Mycothiol synthase and N-myristoyl transferase (NMT); the similarity to NMT extends to the participation of the protein C-terminus (after the SCP2-like C-terminal domain) in the active site
236. Gelsolin-like [55752] (3)
  3 layers: a/b/a; contains mixed beta-sheet
  1. Actin depolymerizing proteins [55753] (2)
    uperfamily
    1. Gelsolin-like [55754] (5)
    2. Cofilin-like [55762] (11)
  2. C-terminal, gelsolin-like domain of Sec23/24 [82754] (1)
    uperfamily
    1. C-terminal, gelsolin-like domain of Sec23/24 [82755] (2)
  3. FLJ32549 C-terminal domain-like [160651] (1)
    alpha-beta(2)-alpha-beta(3)-alpha; similar to the Roadblock/LC7 domain
    1. FLJ32549 C-terminal domain-like [160652] (1)
      C-terminal part of Pfam 09404; DUF2003
237. PHP14-like [143723] (1)
  beta(3)-alpha-beta(2)-alpha-beta; 3 layers, a/b/a; mixed beta-sheet, half-barrel, order: 132456; strands 2 and 5 are antiparallel to the rest
  1. PHP14-like [143724] (2)
    uperfamily
    1. Janus/Ocnus [143725] (1)
      Pfam 05005
    2. PPK middle domain-like [143728] (2)
      central part of Pfam 02503
238. Profilin-like [55769] (10)
  core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
  1. Profilin (actin-binding protein) [55770] (1)
    alpha-beta(2)-alpha-beta(5)-alpha
    uperfamily
    1. Profilin (actin-binding protein) [55771] (8)
  2. GAF domain-like [55781] (4)
    alpha(2)-beta(3)-alpha-beta(3)-alpha; antiparallel beta-sheet: order 321654
    uperfamily
    1. GAF domain [55782] (8)
    2. IclR ligand-binding domain-like [75513] (3)
      Pfam 01614
    3. HrcA C-terminal domain-like [111115] (1)
      Pfam 01628; contains insert domain (140-229) of the Enolase N-terminal domain-like fold (scop_cf 54825)
    4. Phytochrome-specific domain [160664] (2)
      Pfam 00360
  3. PYP-like sensor domain (PAS domain) [55785] (7)
    alpha-beta(2)-alpha(2)-beta(3)
    uperfamily
    1. PYP-like [55786] (2)
    2. Heme-binding PAS domain [55789] (3)
    3. Flavin-binding PAS domain [88853] (3)
      contains PAC motif
    4. N-terminal PAS domain of Pas kinase [82764] (1)
    5. Hypoxia-inducible factor Hif2a, C-terminal domain [103184] (1)
      contains PAC motif
    6. PAS domain of steroid receptor coactivator 1A, NCo-A1 [103187] (1)
    7. BphP N-terminal domain-like [160669] (4)
      Pfam 08446; PAS_2
  4. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75516] (1)
    alpha(2)-beta(2)-alpha(2)-beta(3)-alpha; possibly related to the PAS domain
    uperfamily
    1. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75517] (1)
  5. Sensory domain-like [103190] (3)
    alpha(2)-beta(2)-alpha(2)-beta(3); possibly related to the PAS domain
    uperfamily
    1. Sensory domain of two-component sensor kinase [103191] (2)
    2. YkuI C-terminal domain-like [143732] (2)
      PfamB 021678
    3. LuxQ-periplasmic domain-like [160679] (1)
      Pfam 09308; two-domain arrangement similar to the YkuI C-terminal domain-like
  6. SNARE-like [64356] (4)
    beta(2)-alpha-beta(3)-alpha(2)
    uperfamily
    1. Synatpobrevin N-terminal domain [64357] (2)
    2. Sedlin (SEDL) [82767] (1)
    3. Clathrin coat assembly domain [75521] (2)
    4. SRP alpha N-terminal domain-like [90019] (2)
  7. Roadblock/LC7 domain [103196] (1)
    alpha-beta(2)-alpha-beta(3)-alpha; structurally most similar to the SNARE-like superfamily with a circular permutation of the terminal helices
    uperfamily
    1. Roadblock/LC7 domain [103197] (6)
      Pfam 03259
  8. YeeU-like [143737] (1)
    beta(2)-alpha-beta(3); 2 layers, a/b; there is an oligomerization interface instead of the 'missing' helical layer
    uperfamily
    1. YagB/YeeU/YfjZ-like [143738] (3)
      Pfam 06154
  9. GlcG-like [143744] (1)
    alpha-beta(2)-alpha(3)-beta(2)-alpha; similar to the Roadblock/LC7 domain
    uperfamily
    1. GlcG-like [143745] (1)
      Pfam 03928; DUF336
  10. YNR034W-A-like [160683] (1)
    1. YNR034W-A-like [160684] (1)
239. Ligand-binding domain in the NO signalling and Golgi transport [111125] (1)
  an N-terminal helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomain enclose a ligand-binding cavity
  1. Ligand-binding domain in the NO signalling and Golgi transport [111126] (3)
    uperfamily
    1. H-NOX domain [111127] (1)
      binds heme between the N-terminal 4-helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomains
    2. TRAPP components [118076] (2)
      Pfam 04051; form homo- and hetero-dimers with the first two helices of one subunit complementing the fold of the other subunit to the H-NOX domain fold
    3. MJ1460-like [160689] (1)
      C-terminal part corresponds to Pfam 02830; V4R (vinyl 4 reductase) domain
240. Phage tail protein-like [143748] (1)
  alpha-beta-X-beta(2)-alpha-beta(2); 2 layers: a/b; mixed beta-sheet: order 12354, strands 1 and 2 are parallel
  1. Phage tail protein-like [143749] (2)
    Can form ring, tube-like oligomers, where the subunit beta-sheets are joined in a single beta-sheet (or barrel)
    uperfamily
    1. Lambda phage gpU-like [143750] (1)
      Pfam 06141
    2. STM4215-like [143753] (1)
241. PR-1-like [55796] (1)
  alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
  1. PR-1-like [55797] (1)
    uperfamily
    1. PR-1-like [55798] (4)
      Pfam 00188; groups mammalian SCP/TPX1; insects AG3/AG5; fungi SC7/SC14 and plant PR-1
242. Phoshotransferase/anion transport protein [55803] (1)
  beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342; loop crossing
  1. Phoshotransferase/anion transport protein [55804] (2)
    uperfamily
    1. IIA domain of mannitol-specific and ntr phosphotransferase EII [55805] (3)
    2. Anion transport protein, cytoplasmic domain [64362] (1)
      elaborated with additional secondary structures
243. Nudix [55810] (1)
  beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
  contains beta-grasp motif
  1. Nudix [55811] (7)
    uperfamily
    1. MutT-like [55812] (20)
    2. MutY C-terminal domain-like [103211] (2)
    3. NADH pyrophosphatase [103214] (1)
      duplication: consists of two structurally similar domains separated by a rubredoxin-like zinc finger; the N-terminal domain has a rudiment Nudix fold, the C-terminal, probably catalytic, domain has the canonical fold
    4. IPP isomerase-like [64369] (4)
    5. GDP-mannose mannosyl hydrolase NudD [111132] (1)
    6. BT0354 N-terminal domain-like [143772] (2)
      accosiated with the C-terminal "winged helix" domain (scop_sf 46785)
    7. mRNA decapping enzyme-like [143777] (1)
      part of Pfam 00293
244. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55815] (1)
  core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
  1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55816] (1)
    uperfamily
    1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55817] (3)
245. YrdC/RibB [55820] (1)
  core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta; 3 layers; mixed twisted sheet of 7 strands; order 7126354; strands 7 and 1 are parallel to each other
  1. YrdC/RibB [55821] (2)
    uperfamily
    1. YrdC-like [55822] (3)
      contains two additional strands in the C-terminal extension
    2. 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [64372] (4)
      contains one additional helix in the C-terminal extension
246. GIY-YIG endonuclease [82770] (1)
  beta(2)-alpha(2)-beta-alpha-(beta); strand 4 is very short; 3 layers; antiparallel (mixed) beta-sheet; order 312(4)
  1. GIY-YIG endonuclease [82771] (1)
    uperfamily
    1. GIY-YIG endonuclease [82772] (1)
247. YbaK/ProRS associated domain [55825] (1)
  core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
  1. YbaK/ProRS associated domain [55826] (1)
    uperfamily
    1. YbaK/ProRS associated domain [55827] (4)
      Pfam 04073
248. Thymidylate synthase/dCMP hydroxymethylase [55830] (1)
  contains large mixed beta-sheet
  1. Thymidylate synthase/dCMP hydroxymethylase [55831] (1)
    uperfamily
    1. Thymidylate synthase/dCMP hydroxymethylase [55832] (10)
249. Thymidylate synthase-complementing protein Thy1 [69795] (1)
  complex alpha+beta fold; contains antiparallel 5-stranded beta-sheet: order 12354
  1. Thymidylate synthase-complementing protein Thy1 [69796] (1)
    uperfamily
    1. Thymidylate synthase-complementing protein Thy1 [69797] (1)
250. N-acetylmuramoyl-L-alanine amidase-like [55845] (1)
  contains mixed beta-sheet
  1. N-acetylmuramoyl-L-alanine amidase-like [55846] (1)
    uperfamily
    1. N-acetylmuramoyl-L-alanine amidase-like [55847] (10)
      Family 2 zinc amidase;
251. Cytochrome b5-like heme/steroid binding domain [55855] (1)
  beta-alpha-beta(2)-alpha(1,2)-(beta)-alpha(2)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 1532(4)
  1. Cytochrome b5-like heme/steroid binding domain [55856] (2)
    uperfamily
    1. Cytochrome b5 [55857] (7)
    2. Steroid-binding domain [103222] (1)
252. BTG domain-like [160695] (1)
  alpha(2)-beta-alpha(2)-beta(3); four-helical bundle, capped at one end by an antiparallel beta-sheet, order:1234
  1. BTG domain-like [160696] (1)
    1. BTG domain-like [160697] (2)
      Pfam 07742
253. DUSP-like [143790] (1)
  alpha-beta-alpha-X-beta-alpha-beta; three-helical bundle capped at one end by antiparallel beta-sheet, order: 213
  1. DUSP-like [143791] (1)
    uperfamily
    1. DUSP, domain in ubiquitin-specific proteases [143792] (1)
      Pfam 06337 (DUF1055); SMART 00695
254. DNA topoisomerase I domain [55868] (1)
  beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
  1. DNA topoisomerase I domain [55869] (1)
    uperfamily
    1. Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment [55870] (1)
255. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55873] (1)
  8-stranded mixed beta-sheet; 2 layers: alpha/beta
  1. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55874] (4)
    uperfamily
    1. Heat shock protein 90, HSP90, N-terminal domain [55875] (3)
    2. DNA gyrase/MutL, N-terminal domain [55879] (7)
    3. Histidine kinase [55884] (7)
    4. alpha-ketoacid dehydrogenase kinase, C-terminal domain [69804] (3)
256. YehR-like [160703] (1)
  beta(3)-alpha-beta(2)-alpha(3)-beta; 2 layers, a/b; antiparallel beta-sheet, order: 612354
  1. YehR-like [160704] (1)
    1. YehR-like [160705] (1)
      Pfam 06998; DUF1307
257. Sporulation response regulatory protein Spo0B [55889] (1)
  core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
  1. Sporulation response regulatory protein Spo0B [55890] (1)
    Histidine kinase-like fold lacking the kinase ATP-binding site
    uperfamily
    1. Sporulation response regulatory protein Spo0B [55891] (1)
258. Ribonuclease Rh-like [55894] (1)
  alpha+beta fold
  1. Ribonuclease Rh-like [55895] (1)
    uperfamily
    1. Ribonuclease Rh-like [55896] (8)
259. YlxR-like [64375] (1)
  alpha+beta fold; could have evolved from a glucocorticoid receptor-like zinc finger domain
  1. YlxR-like [64376] (1)
    uperfamily
    1. YlxR-like [64377] (1)
      some family sequences retain zinc-binding residues
260. YggX-like [111147] (1)
  beta(2)-alpha(3); contains zinc-less 'zinc finger'-like fold (scop_cf 57715; see also scop_cf 64375)
  1. YggX-like [111148] (1)
    uperfamily
    1. YggX-like [111149] (2)
      Pfam 04362
261. L28p-like [143799] (1)
  unusual fold consisting of three beta-hairpins, that form a paper clip-like structure, and two helices; could have evolved from a glucocorticoid receptor-like zinc finger domain (scop_cf 57715)
  1. L28p-like [143800] (2)
    In early ribosomal structures, L28p has been misinterpreted as L31p. in the Ribosomal protein L28p family, there are sequences containing two CxxC pairs. Threading these sequences into this fold brings the four cysteines in a similar site to the zinc-binding site of glucocorticoid receptor-like zinc fingers. In the Ribosomal protein L31p, there are also members with two CxxC pairs. However, these won't form a putative zinc-binding site in this fold. The L31p family are classified here temporarily, until its true fold is known
    uperfamily
    1. Ribosomal protein L28 [143801] (4)
    2. Ribosomal protein L31p [143804] (2)
      Pfam 01197
262. YqaI-like [160712] (1)
  dimeric zinc-less 'zinc finger'-like fold; similar to the C-terminal strand-swapped B-box domain (scop_cf 57844)
  1. YqaI-like [160713] (1)
    1. YqaI-like [160714] (1)
      Pfam 09466
263. Ornithine decarboxylase C-terminal domain [55903] (1)
  complex alpha+beta motif
  1. Ornithine decarboxylase C-terminal domain [55904] (1)
    uperfamily
    1. Ornithine decarboxylase C-terminal domain [55905] (1)
264. Pentein, beta/alpha-propeller [55908] (1)
  duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
  1. Pentein [55909] (7)
    uperfamily
    1. Ribosome anti-association factor eIF6 (aIF6) [55910] (2)
    2. Amidinotransferase [55914] (2)
      common fold is elaborated with many active site-forming insertions
    3. Dimethylarginine dimethylaminohydrolase DDAH [64380] (1)
      functionally related to the amidinotransferase, similar active sites
    4. Arginine deiminase [103232] (2)
      functionally related to the amidinotransferase, similar active sites
    5. Peptidylarginine deiminase Pad4, catalytic C-terminal domain [111152] (1)
      # functionally related to the amidinotransferase, similar active sites
    6. Porphyromonas-type peptidylarginine deiminase [111155] (6)
      Pfam 04371; functionally related to the amidinotransferase, similar active site
    7. Succinylarginine dihydrolase-like [143809] (1)
      Pfam 04996
265. Creatinase/aminopeptidase [55919] (1)
  duplication: composed of two very similar alpha+beta folds
  1. Creatinase/aminopeptidase [55920] (1)
    uperfamily
    1. Creatinase/aminopeptidase [55921] (9)
266. gpW/gp25-like [160718] (1)
  alpha(2)-beta(3); similar to one structural repeat of the Creatinase/aminopeptidase family and the C-terminal subdomain of PanC
  1. gpW/gp25-like [160719] (1)
    Contains phage tail lysozyme
    1. gpW/gp25-like [160720] (1)
      Pfam 04965; T4 gene 25-like lysozyme
267. Glutamine synthetase/guanido kinase [55930] (1)
  duplication: common core consists of two beta-alpha-beta2-alpha repeats
  1. Glutamine synthetase/guanido kinase [55931] (5)
    uperfamily
    1. Glutamine synthetase catalytic domain [55932] (2)
    2. Guanido kinase catalytic domain [55935] (8)
    3. Glutamate-cysteine ligase family 2 (GCS2) [111160] (2)
      Pfam 04107; structural and functional relationships to Glutamine synthetase
    4. Glutamate-cysteine ligase [118090] (1)
      Pfam 04262
    5. GatB/GatE catalytic domain-like [143812] (3)
      N-terminal and C-terminal parts correspond to Pfam 02934 (GatB_N) and Pfam 01162 (GatB), respectively
268. TBP-like [55944] (11)
  beta-alpha-beta(4)-alpha
  1. TATA-box binding protein-like [55945] (2)
    uperfamily
    1. TATA-box binding protein (TBP), C-terminal domain [55946] (5)
      duplication: consists of two clear structural repeats
    2. DNA repair glycosylase, N-terminal domain [55952] (2)
      contains a single copy of this fold
  2. MoaD-related protein, C-terminal domain [103239] (1)
    contains a single copy of this fold
    uperfamily
    1. MoaD-related protein, C-terminal domain [103240] (1)
  3. KA1-like [103243] (2)
    contains a single copy of this fold
    uperfamily
    1. Kinase associated domain 1, KA1 [103244] (1)
      Pfam 02149
    2. Ssp2 C-terminal domain-like [160723] (3)
      PfamB 166430
  4. TT1751-like [103247] (1)
    contains a single copy of this fold decorated with additional structures; forms dimer
    uperfamily
    1. TT1751-like [103248] (2)
      Pfam 03625; DUF302
  5. Cell-division protein ZipA, C-terminal domain [64383] (1)
    contains a single copy of this fold
    uperfamily
    1. Cell-division protein ZipA, C-terminal domain [64384] (1)
  6. Phosphoglucomutase, C-terminal domain [55957] (1)
    contains a single copy of this fold and an extra beta-strand at the C-terminus
    uperfamily
    1. Phosphoglucomutase, C-terminal domain [55958] (4)
      Pfam 00408
  7. Bet v1-like [55961] (10)
    contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix
    uperfamily
    1. Pathogenesis-related protein 10 (PR10)-like [55962] (8)
    2. STAR domain [55966] (4)
    3. Phoshatidylinositol transfer protein, PITP [64388] (4)
    4. Ring hydroxylating alpha subunit catalytic domain [55969] (7)
      Pfam 00848; contains a few insertion and C-terminal extension compared with Bet v1
    5. AHSA1 domain [111168] (11)
      Pfam 05146
    6. oligoketide cyclase/dehydrase-like [118101] (3)
      Pfam 03654
    7. PA1206-like [143839] (1)
    8. Atu1531-like [160742] (2)
      Pfam 10604; Polyketide cyclase/dehydrase and lipid transport
    9. Smu440-like [160747] (1)
      PfamB 094079
    10. CoxG-like [160750] (2)
      Pfam 06240
  8. Rbstp2229 protein [111171] (1)
    forms segment-swapped dimers further organized in hexamers
    uperfamily
    1. Rbstp2229 protein [111172] (1)
  9. RalF, C-terminal domain [118104] (1)
    contains a single copy of this fold decorated with additional structures
    uperfamily
    1. RalF, C-terminal domain [118105] (1)
  10. YwmB-like [143842] (1)
    duplication: tandem repeat of two circularly permuted motifs, alpha-beta-alpha-beta(4), assembled as in the TATA-box binding domain; forms a swapped dimer by exchanging the equivalent parts of the C-terminal motifs
    uperfamily
    1. YwmB-like [143843] (1)
  11. YugN-like [160755] (1)
    1. YugN-like [160756] (1)
      Pfam 08868
269. XisI-like [143846] (1)
  alpha-beta(4)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order 1234, meander; the open side of beta-sheet provides dimerization interface
  1. XisI-like [143847] (1)
    uperfamily
    1. XisI-like [143848] (3)
      Pfam 08869
270. S-adenosylmethionine synthetase [55972] (1)
  duplication: consists of 3 similar intertwined domains
  structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
  1. S-adenosylmethionine synthetase [55973] (1)
    uperfamily
    1. S-adenosylmethionine synthetase [55974] (3)
271. DNA clamp [55978] (1)
  contains two helices and two beta sheets
  duplication: fold has internal pseudo two-fold symmetry
  1. DNA clamp [55979] (2)
    uperfamily
    1. DNA polymerase III, beta subunit [55980] (2)
      duplication: consists of three domains of this fold
    2. DNA polymerase processivity factor [55983] (9)
      duplication: consists of two domains of this fold
272. Hypothetical protein TM0160 [103255] (1)
  duplication: consists of two beta(3)-alpha(2) structural repeats; single barrel-like beta-sheet
  1. Hypothetical protein TM0160 [103256] (1)
    uperfamily
    1. Hypothetical protein TM0160 [103257] (1)
273. TTHC002-like [160760] (1)
  alpha-beta-alpha-beta(3); forms dimer with a single beta-sheet, folded in a barrel-like shape
  1. TTHC002-like [160761] (1)
    1. TTHC002-like [160762] (1)
274. Molybdenum cofactor-binding domain [56002] (1)
  beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
  1. Molybdenum cofactor-binding domain [56003] (1)
    duplication: consists of 4 structural repeats arranged in 2 lobes
    contains one left-hand beta-alpha-beta unit per lobe
    uperfamily
    1. Molybdenum cofactor-binding domain [56004] (8)
275. NE1680-like [160765] (1)
  beta(2)-alpha-beta-alpha-beta; 2 layers, a/b; antiparallel sheet, order 3124
  1. NE1680-like [160766] (1)
    1. NE1680-like [160767] (1)
      Pfam 09630; DUF2024
276. Nitrite and sulphite reductase 4Fe-4S domain-like [56013] (1)
  beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection between strands 1 and 2
  1. Nitrite and sulphite reductase 4Fe-4S domain-like [56014] (1)
    duplication: contains two domains of this fold
    uperfamily
    1. Nitrite and sulphite reductase 4Fe-4S domain-like [56015] (7)
277. DeoB insert domain-like [143855] (1)
  alpha-beta-X-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 2 and 5 are antiparallel to the rest
  1. DeoB insert domain-like [143856] (1)
    uperfamily
    1. DeoB insert domain-like [143857] (1)
278. The spindle assembly checkpoint protein mad2 [56018] (1)
  core: alpha(2)-beta(2)-alpha-beta; mixed sheet: order 213
  1. The spindle assembly checkpoint protein mad2 [56019] (1)
    N- and C-termini undergo large conformational rearrangement upon ligand binding
    uperfamily
    1. The spindle assembly checkpoint protein mad2 [56020] (1)
279. Phospholipase D/nuclease [56023] (1)
  beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
  1. Phospholipase D/nuclease [56024] (5)
    uperfamily
    1. Nuclease [56025] (1)
    2. Phospholipase D [64391] (1)
      duplication: contains two domains of this fold arranged as in the Nuc dimer
    3. Tyrosyl-DNA phosphodiesterase TDP1 [69815] (2)
    4. Polyphosphate kinase C-terminal domain [143860] (2)
      C-terminal part of Pfam 02503; similar to PLD; contains two domains of this fold arranged as in the Nuc dimer
    5. TrmB middle domain-like [160780] (1)
      N-terminal part of PfamB 004822
280. CorA soluble domain-like [143864] (1)
  beta(2)-alpha-beta-alpha(2)-beta(4)-alpha(3); 3 layers: a/b/a; mixed beta-sheet, order 2137654; strands 3 and 7 are parallel
  1. CorA soluble domain-like [143865] (1)
    uperfamily
    1. CorA soluble domain-like [143866] (1)
      N-terminal part of Pfam 01544
281. Monooxygenase (hydroxylase) regulatory protein [56028] (1)
  corner-like structure formed by two sheets and filled in with 2-3 helices
  1. Monooxygenase (hydroxylase) regulatory protein [56029] (1)
    duplication: consists of two beta-alpha-(beta)-beta(2) motifs; some topological similarity to the ferredoxin-like fold
    uperfamily
    1. Monooxygenase (hydroxylase) regulatory protein [56030] (4)
      note: the solution structure determinations disagree in the relative orientations of two motifs
282. PurM C-terminal domain-like [56041] (1)
  3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
  1. PurM C-terminal domain-like [56042] (1)
    uperfamily
    1. PurM C-terminal domain-like [56043] (6)
283. PF0523-like [143869] (1)
  beta-alpha-beta-alpha(3)-beta-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order 4132; some similarity to the PurM C-terminal domain-like fold (scop_cf 56041)
  1. PF0523-like [143870] (1)
    uperfamily
    1. PF0523-like [143871] (1)
      Pfam 04416; DUF509
284. Chorismate synthase, AroC [103262] (1)
  duplication: consists of two DCoH-like beta(2)-alpha-beta(2)-alpha structural repeats; 3 layers, beta/alpha/beta
  1. Chorismate synthase, AroC [103263] (1)
    uperfamily
    1. Chorismate synthase, AroC [103264] (5)
285. Hsp33 domain [64396] (1)
  3 layers: beta/alpha/beta; buried helix
  1. Hsp33 domain [64397] (1)
    uperfamily
    1. Hsp33 domain [64398] (3)
      forms strand-swapped dimer
286. MTH1598-like [69818] (1)
  beta(2)-alpha-beta-alpha-beta(4); 3 layers: beta/alpha/beta; some similarity to the Hsp33 fold
  1. MTH1598-like [69819] (1)
    uperfamily
    1. MTH1598-like [69820] (2)
287. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68929] (1)
  beta-alpha-beta(4)-alpha-beta(2); 3 layers: beta/alpha/beta; buried helix
  1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68930] (1)
    uperfamily
    1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68931] (1)
288. OsmC-like [82783] (1)
  swapped dimer of beta(3)-alpha-beta(2)-alpha(2)-beta subunits; mixed beta-sheet; order: 321[4][5][6]; buried helix
  1. OsmC-like [82784] (2)
    uperfamily
    1. Ohr/OsmC resistance proteins [82785] (9)
    2. YhfA-like [90027] (2)
289. Hypothetical protein HI1480 [103276] (1)
  beta-alpha(4)-beta-alpha-beta; segregated alpha-helical and beta-sheet subdomains; dimeric beta-sheet barrel: n=6, S=10
  1. Hypothetical protein HI1480 [103277] (1)
    uperfamily
    1. Hypothetical protein HI1480 [103278] (1)
290. ERH-like [143874] (1)
  beta(2)-alpha(2)-beta(2)-alpha; antiparallel beta-sheet, order:2134; helices are arranged in a bundle rather than packed agains beta-sheet; dimerises via with the formation of a flattened beta-barel: closed n=8, S=10
  1. ERH-like [143875] (1)
    uperfamily
    1. ERH-like [143876] (1)
      Pfam 01133
291. Ribosomal protein S8 [56046] (1)
  consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
  1. Ribosomal protein S8 [56047] (1)
    uperfamily
    1. Ribosomal protein S8 [56048] (4)
292. Ribosomal protein L6 [56052] (1)
  consists of two beta-sheets and one alpha-helix packed around single core
  1. Ribosomal protein L6 [56053] (1)
    uperfamily
    1. Ribosomal protein L6 [56054] (6)
293. NE0471 N-terminal domain-like [143879] (1)
  beta(3)-alpha(n)-beta(3)-alpha; the two meander beta-sheets and helices are packed against the same core
  1. NE0471 N-terminal domain-like [143880] (1)
    uperfamily
    1. NE0471 N-terminal domain-like [143881] (1)
294. Lp2179-like [160799] (1)
  beta(2)-alpha-beta(4)-alpha-beta; contains two antiparallel beta-sheets (orders: 127 and 3456) packed against the longer C-terminal helix
  1. Lp2179-like [160800] (1)
    1. Lp2179-like [160801] (1)
      Pfam 08866, DUF1831
295. RGC domain-like [143884] (1)
  consists of two beta-sheets and four helices eclosing a cental cavity
  1. RGC domain-like [143885] (1)
    uperfamily
    1. RGC domain [143886] (1)
      Pfam 03836; RasGAP C-terminus
296. Smc hinge domain [75552] (1)
  consists of 2 different alpha+beta subdomains; forms subdomain-swapped dimers
  1. Smc hinge domain [75553] (1)
    uperfamily
    1. Smc hinge domain [75554] (1)
297. DNA mismatch repair protein MutL [118115] (1)
  consists of two different alpha+beta (sub)domains; d1: [beta(3)-alpha-(insert of d2)-alpha(2)-beta; 2 layers, a/b; antiparallel sheet, order: 1234]; d2: [beta-alpha-beta(2)-alpha(2); 2 layers, a/b; antiparallel sheet, order: 132]
  1. DNA mismatch repair protein MutL [118116] (1)
    uperfamily
    1. DNA mismatch repair protein MutL [118117] (1)
298. ATP-grasp [56058] (2)
  Consists of two subdomains with different alpha+beta folds
  shares functional and structural similarities with the PIPK and protein kinase superfamilies
  1. Glutathione synthetase ATP-binding domain-like [56059] (9)
    uperfamily
    1. ATP-binding domain of peptide synthetases [56060] (4)
    2. Lysine biosynthesis enzyme LysX ATP-binding domain [103281] (1)
    3. BC ATP-binding domain-like [56067] (8)
    4. Synapsin C-terminal domain [56078] (3)
    5. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56081] (2)
    6. Pyruvate phosphate dikinase, N-terminal domain [56085] (3)
    7. Eukaryotic glutathione synthetase ATP-binding domain [56088] (2)
      circularly permuted version of prokaryotic enzyme
    8. Glutathionylspermidine synthase ATP-binding domain-like [143890] (1)
      both terminal parts of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
    9. PurP ATP-binding domain-like [160804] (3)
      Pfam 06973; DUF1297
  2. DNA ligase/mRNA capping enzyme, catalytic domain [56091] (4)
    has a circularly permuted topology
    uperfamily
    1. ATP-dependent DNA ligase catalytic domain [56092] (3)
    2. Adenylation domain of NAD+-dependent DNA ligase [56096] (3)
    3. mRNA capping enzyme [56100] (2)
    4. RNA ligase [103286] (2)
299. SAICAR synthase-like [56103] (1)
  consists of two alpha+beta subdomains
  1. SAICAR synthase-like [56104] (3)
    shares functional and structural similarities with the ATP-grasp fold and protein kinase superfamilies
    uperfamily
    1. SAICAR synthase [56105] (2)
    2. Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta [56108] (1)
    3. Inositol polyphosphate kinase (IPK) [111188] (2)
      Pfam 03770
300. Protein kinase-like (PK-like) [56111] (1)
  consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
  1. Protein kinase-like (PK-like) [56112] (7)
    shares functional and structural similarities with the ATP-grasp fold and PIPK
    uperfamily
    1. Protein kinases, catalytic subunit [88854] (74)
      members organized in the groups and subfamiles specified by the comments
    2. Actin-fragmin kinase, catalytic domain [56168] (1)
      Atypical protein kinases
    3. MHCK/EF2 kinase [64408] (1)
      Atypical protein kinases
    4. Phoshoinositide 3-kinase (PI3K), catalytic domain [56171] (2)
    5. Choline kinase [90040] (1)
    6. APH phosphotransferases [64411] (5)
    7. RIO1-like kinases [111204] (1)
      Pfam 01163
301. FAD-binding/transporter-associated domain-like [56175] (1)
  consists of two alpha+beta subdomains
  1. FAD-binding/transporter-associated domain-like [56176] (4)
    uperfamily
    1. FAD-linked oxidases, N-terminal domain [56177] (5)
    2. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain [56184] (2)
    3. CO dehydrogenase flavoprotein N-terminal domain-like [56187] (6)
    4. CorC/HlyC domain-like [160820] (12)
      Pfam 03471; similar to the C-terminal subdomain of FAD-binding domain with transposition of strands 3 and 4; possible adenosine cofactor-binding domain
302. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56193] (1)
  consists of two alpha+beta subdomains
  1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56194] (1)
    uperfamily
    1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56195] (2)
303. Methenyltetrahydromethanopterin cyclohydrolase [56198] (1)
  consists of two alpha+beta subdomains
  1. Methenyltetrahydromethanopterin cyclohydrolase [56199] (1)
    uperfamily
    1. Methenyltetrahydromethanopterin cyclohydrolase [56200] (1)
304. Prim-pol domain [56746] (1)
  consists of two alpha+beta domains
  1. Prim-pol domain [56747] (3)
    uperfamily
    1. PriA-like [56748] (3)
      contains additional insert all-alpha subdomain
    2. Bifunctional DNA primase/polymerase N-terminal domain [103305] (1)
    3. HP0184-like [143897] (1)
      stand-alone domain with the least decorated Prim-pol fold
305. Hect, E3 ligase catalytic domain [56203] (1)
  consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit; conformational flexibility of domain orientation
  1. Hect, E3 ligase catalytic domain [56204] (1)
    uperfamily
    1. Hect, E3 ligase catalytic domain [56205] (2)
306. Nitrile hydratase alpha chain [56208] (1)
  4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
  1. Nitrile hydratase alpha chain [56209] (1)
    duplication: contains two structural repeats
    uperfamily
    1. Nitrile hydratase alpha chain [56210] (3)
307. 4'-phosphopantetheinyl transferase [56213] (1)
  beta-alpha(3)-beta(2) motif
  1. 4'-phosphopantetheinyl transferase [56214] (2)
    possibly related to the IspF (d.79.5) and YjgF-like superfamilies (d.79.1)
    uperfamily
    1. Holo-(acyl carrier protein) synthase ACPS [64418] (2)
      forms trimers with three closely packed beta-sheets similar to the IspF trimers
    2. 4'-Phosphopantetheinyl transferase SFP [56215] (1)
      monomeric; tandem duplication of beta-alpha(3)-beta(2) motif
308. DNase I-like [56218] (1)
  contains beta-sandwich; duplication of alpha+beta motif
  1. DNase I-like [56219] (3)
    uperfamily
    1. DNase I-like [56220] (8)
    2. Inositol polyphosphate 5-phosphatase (IPP5) [64422] (2)
    3. Sphingomyelin phosphodiesterase-like [143902] (2)
      part of Pfam 03372
309. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56227] (1)
  contains sandwich; duplication of alpha+beta motif with single mixed sheet
  motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
  1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56228] (1)
    uperfamily
    1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56229] (2)
310. Ntn hydrolase-like [56234] (2)
  4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
  1. N-terminal nucleophile aminohydrolases (Ntn hydrolases) [56235] (7)
    N-terminal residue provides two catalytic groups, nucleophile and proton donor
    uperfamily
    1. Class II glutamine amidotransferases [56236] (9)
      has slightly different topology than other families do
    2. Penicillin acylase, catalytic domain [56244] (4)
    3. Penicillin V acylase [56248] (1)
    4. Proteasome subunits [56251] (14)
    5. (Glycosyl)asparaginase [56261] (3)
    6. Gamma-glutamyltranspeptidase-like [143906] (4)
      Pfam 01019
    7. SPO2555-like [160846] (1)
      Pfam 06267; DUF1028
  2. Archaeal IMP cyclohydrolase PurO [75569] (1)
    has a putative active site in the same topological location as the Ntn hydrolase but lacks the N-terminal nucleophile
    uperfamily
    1. Archaeal IMP cyclohydrolase PurO [75570] (1)
      Pfam 07826
311. DmpA/ArgJ-like [56265] (1)
  duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
  1. DmpA/ArgJ-like [56266] (2)
    convergent similarity to the Ntn amidohydrolases
    uperfamily
    1. DmpA-like [56267] (1)
      Pfam 03576
    2. ArgJ-like [111219] (1)
      Pfam 01960; contains extra C-terminal alpha+beta domain [beta-alpha(2)-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet, order: 51423, strands 1 and 4 are parallel to each other]
312. Pyruvoyl-dependent histidine and arginine decarboxylases [56270] (1)
  duplication of beta-alpha-beta(2) motif; 4 layers: alpha/beta/beta/alpha; contains "silk" beta-sandwich
  1. Pyruvoyl-dependent histidine and arginine decarboxylases [56271] (2)
    two chains result from self-processing single-chain precursor; form heterohexamer
    uperfamily
    1. Arginine decarboxylase [90046] (1)
    2. Histidine decarboxylase [56272] (1)
313. S-adenosylmethionine decarboxylase [56275] (1)
  duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
  1. S-adenosylmethionine decarboxylase [56276] (2)
    uperfamily
    1. S-adenosylmethionine decarboxylase [56277] (2)
    2. Bacterial S-adenosylmethionine decarboxylase [111222] (1)
      Pfam 02675;homodimer; the subunit fold and assembly are similar to those of the structural repeats of the eukaryotic enzyme
314. Metallo-hydrolase/oxidoreductase [56280] (1)
  duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
  1. Metallo-hydrolase/oxidoreductase [56281] (14)
    uperfamily
    1. Zn metallo-beta-lactamase [56282] (10)
    2. Hypothetical protein TM0207 [103317] (1)
    3. Glyoxalase II (hydroxyacylglutathione hydrolase) [56288] (3)
    4. ROO N-terminal domain-like [56291] (3)
    5. Methyl parathion hydrolase [111227] (1)
    6. Coenzyme PQQ synthesis protein B, PqqB [118146] (1)
    7. RNase Z-like [143916] (3)
      part of Pfam 00753; tRNA 3'-endonuclease; elaborated with additional structures and insert alpha(2)-beta(2) subdomain
    8. Pce catalytic domain-like [143921] (1)
      part of Pfam 00753
    9. YhfI-like [143924] (1)
      part of Pfam 00753
    10. beta-CASP RNA-metabolising hydrolases [143927] (4)
      contains insertion of a single helicase-like alpha/beta domain (from scop_sf 52540) but without the P-loop motif
    11. TM0894-like [143930] (1)
      part of Pfam 00753
    12. Ava3068-like [160858] (1)
    13. Alkylsulfatase-like [160861] (1)
      subfamily of Pfam 00753; includes all-alpha linker subdomain
    14. PqsE-like [160864] (1)
      part of Pfam 00753; extended C-terminal region with extra helices
315. PP2C-like [81607] (1)
  4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
  1. PP2C-like [81606] (1)
    contain binuclear metal (Mn) centre
    uperfamily
    1. PP2C-like [81605] (2)
      Pfam 00481
316. Metallo-dependent phosphatases [56299] (1)
  4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
  1. Metallo-dependent phosphatases [56300] (12)
    different families of this superfamily are groupped in a single Pfam family, Pfam 00149
    uperfamily
    1. Purple acid phosphatase-like [56301] (4)
    2. DNA double-strand break repair nuclease [64427] (1)
      contains C-terminal alpha/beta subdomain
    3. 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [56307] (3)
    4. Protein serine/threonine phosphatase [56310] (9)
    5. Phosphoesterase-related [82803] (1)
    6. TT1561-like [103320] (2)
      similar to purple acid and protein phosphatases
    7. YfcE-like [111233] (6)
    8. Hypothetical protein aq_1666 [118152] (1)
    9. DR1281-like [118155] (2)
    10. TTHA0625-like [143938] (1)
      part of Pfam 00149
    11. GpdQ-like [160875] (2)
      part of Pfam 00149
    12. ADPRibase-Mn-like [160880] (1)
      contains Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase (ADPRibase-Mn); part of Pfam 00149
317. Carbon-nitrogen hydrolase [56316] (1)
  4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
  1. Carbon-nitrogen hydrolase [56317] (2)
    Pfam 00795; some topological similarities to the metallo-dependent phosphatases and DNase I-like nucleases
    uperfamily
    1. Nitrilase [56318] (2)
    2. Carbamilase [64433] (3)
318. CNF1/YfiH-like putative cysteine hydrolases [64437] (1)
  4 layers: alpha/beta/beta/alpha; mixed beta sheets
  1. CNF1/YfiH-like putative cysteine hydrolases [64438] (3)
    uperfamily
    1. Type 1 cytotoxic necrotizing factor, catalytic domain [64439] (1)
    2. YfiH-like [111238] (5)
      Pfam 02578; COG1496
    3. CheD-like [160883] (1)
      Pfam 03975
319. ADC synthase [56321] (1)
  duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
  1. ADC synthase [56322] (1)
    the active site is formed by additional structures inserted into the core structure
    uperfamily
    1. ADC synthase [56323] (7)
320. Sulfolobus fructose-1,6-bisphosphatase-like [111248] (1)
  4 layers: a/b/b/a; antiparallel beta sheets; similarities to ferredoxin-like fold (scop_cf 54861) in the N-terminal part (1-120) and to the Bacterial S-adenosylmethionine decarboxylase subunit (scop_fa 997656) in the C-terminal part (121-340)
  1. Sulfolobus fructose-1,6-bisphosphatase-like [111249] (1)
    uperfamily
    1. Sulfolobus fructose-1,6-bisphosphatase-like [111250] (1)
      Pfam 01950
321. LDH C-terminal domain-like [56326] (1)
  unusual fold, defines family
  1. LDH C-terminal domain-like [56327] (2)
    uperfamily
    1. Lactate & malate dehydrogenases, C-terminal domain [56328] (28)
      N-terminal domain is NAD-binding module (alpha/beta Rossmann-fold domain)
    2. AglA-like glucosidase [90050] (5)
      family 4 glycosyl hydrolase
322. DNA breaking-rejoining enzymes [56348] (1)
  core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
  1. DNA breaking-rejoining enzymes [56349] (2)
    uperfamily
    1. Lambda integrase-like, catalytic core [56350] (5)
    2. Eukaryotic DNA topoisomerase I, catalytic core [56361] (2)
323. Replication modulator SeqA, C-terminal DNA-binding domain [82807] (1)
  consists of seven alpha-helices and three-stranded beta-sheet
  1. Replication modulator SeqA, C-terminal DNA-binding domain [82808] (1)
    uperfamily
    1. Replication modulator SeqA, C-terminal DNA-binding domain [82809] (1)
324. SMAD MH1 domain [56365] (1)
  consists of four alpha-helices and three beta-ribbons
  1. SMAD MH1 domain [56366] (1)
    uperfamily
    1. SMAD MH1 domain [56367] (1)
325. YopH tyrosine phosphatase N-terminal domain [64448] (1)
  consists of four alpha-helices and two beta-hairpins
  1. YopH tyrosine phosphatase N-terminal domain [64449] (1)
    uperfamily
    1. YopH tyrosine phosphatase N-terminal domain [64450] (2)
326. Rotavirus NSP2 fragment, N-terminal domain [75573] (1)
  consists of six alpha-helices and two beta-hairpins
  1. Rotavirus NSP2 fragment, N-terminal domain [75574] (1)
    uperfamily
    1. Rotavirus NSP2 fragment, N-terminal domain [75575] (1)
327. Rv2827c C-terminal domain-like [160886] (1)
  multihelical array flanked by two three-stranded mixed beta-sheets
  1. Rv2827c C-terminal domain-like [160887] (1)
    1. Rv2827c C-terminal domain-like [160888] (1)
      the C-terminal part (~210 residues) of Pfam 09407; DUF2005
328. Phosphoprotein oligomerization domain-like [160891] (1)
  intertwinned homodimer of beta(2)-alpha-beta(2) motifs; 3 layers: b/a/b; each antiparallel beta-sheet is formed by the N-terminal beta-hairpin of one subunit and the C-terminal beta-hairpin of the other subunit; order 1243
  1. Phosphoprotein oligomerization domain-like [160892] (1)
    1. Phosphoprotein oligomerization domain-like [160893] (1)
      middle part of Pfam 00922
329. Taf5 N-terminal domain-like [160896] (1)
  multihelical cluster with a C-terminal beta-alpha(2)-beta motif; one central buried helix; parallel beta-ribbon
  1. Taf5 N-terminal domain-like [160897] (1)
    1. Taf5 N-terminal domain-like [160898] (3)
      Pfam 04494
330. Jann2411-like [160903] (1)
  unusual fold; consists of seven alpha-helices and three beta-hairpins
  1. Jann2411-like [160904] (1)
    1. Jann2411-like [160905] (1)
      Pfam 07336; DUF1470
331. ATP12-like [160908] (1)
  contains an N-terminal beta-sheet that forms a beta-triangle structure; the remainder is a multihelical array of long and short helices
  1. ATP12-like [160909] (1)
    1. ATP12-like [160910] (2)
      Pfam 07542; F1-ATPase chaperone
332. Ribosome inactivating proteins (RIP) [56370] (1)
  contains mixed beta-sheet
  1. Ribosome inactivating proteins (RIP) [56371] (2)
    uperfamily
    1. Plant cytotoxins [56372] (17)
    2. Shiga toxin, A-chain [56395] (2)
333. ADP-ribosylation [56398] (1)
  unusual fold
  1. ADP-ribosylation [56399] (7)
    uperfamily
    1. ADP-ribosylating toxins [56400] (12)
    2. Ecto-ART [82814] (1)
      the two disulfide bridges and N-terminal alpha helices are characteristic for all ecto-ARTs
    3. Poly(ADP-ribose) polymerase, C-terminal domain [56416] (3)
    4. AvrPphF ORF2, a type III effector [111257] (1)
      shares the common structural core with other families; unknown function
    5. Tpt1/KptA [118162] (1)
      Pfam 01885; contains extra N-terminal domain similar to the "winged helix" DNA-binding domain (scop_sf 46785)
    6. BC2332-like [143947] (1)
      minimized common structural core with two large, mainly helical insertions on one side forming dimerization "domain"
    7. CC0527-like [143950] (1)
      Pfam 06108; DUF952
334. Peptide deformylase [56419] (1)
  alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
  1. Peptide deformylase [56420] (1)
    nickel-dependent enzyme
    uperfamily
    1. Peptide deformylase [56421] (9)
335. LCCL domain [69847] (1)
  unusual fold
  1. LCCL domain [69848] (1)
    uperfamily
    1. LCCL domain [69849] (1)
336. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56424] (1)
  unusual fold
  1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56425] (1)
    uperfamily
    1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56426] (7)
337. C-type lectin-like [56435] (1)
  unusual fold
  1. C-type lectin-like [56436] (8)
    uperfamily
    1. C-type lectin domain [56437] (51)
      Pfam 00059
    2. Aerolysin/Pertussis toxin (APT) domain [56467] (2)
    3. Invasin/intimin cell-adhesion fragment, C-terminal domain [56472] (2)
    4. Link domain [56477] (2)
    5. Endostatin [56480] (3)
      decorated with many insertions in the common fold
    6. Noncollagenous (NC1) domain of collagen IV [75585] (2)
      duplication: consists of two subdomains of this fold; segment swapping within and between individual domains
    7. Sulfatase-modifying factor-like [143959] (2)
      Pfam 03781 (DUF323); fold decorated with many additional structures; C-alpha-formyglycine-generating enzyme
    8. Mtd variable domain [143964] (1)
      fold decorated with many additional structures; overall similarity to the Sulfatase modifying factor family; lacks the characteristic disulfide
338. Hemolytic lectin CEL-III, C-terminal domain [111264] (1)
  unusual fold
  1. Hemolytic lectin CEL-III, C-terminal domain [111265] (1)
    uperfamily
    1. Hemolytic lectin CEL-III, C-terminal domain [111266] (1)
339. SRCR-like [56486] (2)
  unusual fold; disulfide-rich; core: beta-x-alpha-beta-loop-beta
  1. SRCR-like [56487] (2)
    uperfamily
    1. Scavenger receptor cysteine-rich (SRCR) domain [56488] (1)
      has some structural similarity to the long-chain scorpion toxins
    2. Hepsin, N-terminal domain [103355] (1)
  2. A heparin-binding domain [56491] (1)
    uperfamily
    1. A heparin-binding domain [56492] (1)
340. Fibrinogen C-terminal domain-like [56495] (1)
  unusual fold
  1. Fibrinogen C-terminal domain-like [56496] (1)
    uperfamily
    1. Fibrinogen C-terminal domain-like [56497] (8)
341. gp120 core [56501] (1)
  unusual fold
  1. gp120 core [56502] (1)
    uperfamily
    1. gp120 core [56503] (1)
342. Methionine synthase activation domain-like [56506] (1)
  unusual fold; core: beta-alpha(2)-beta(2)-alpha(2)-beta-alpha-beta; antiparallel beta-sheet: order 12354
  1. Methionine synthase activation domain-like [56507] (2)
    uperfamily
    1. Methionine synthase SAM-binding domain [56508] (1)
    2. Hypothetical protein TM0269 [75590] (1)
343. UbiD C-terminal domain-like [143967] (1)
  alpha-beta(2)-alpha-beta-alpha-beta(2); 3 layers, a/b/a; mixed beta-sheet, order: 12354, strands 2,3 and 5 are parallel to each other
  1. UbiD C-terminal domain-like [143968] (1)
    uperfamily
    1. UbiD C-terminal domain-like [143969] (1)
      C-terminal part of Pfam 01977; hexamerisation domain
344. Hypothetical protein TM0875 [90063] (1)
  unusual fold; core: beta(2)-loop-beta(2)-alpha-beta; mixed beta-sheet: order 51243; parallel strands 2 and 4
  1. Hypothetical protein TM0875 [90064] (1)
    uperfamily
    1. Hypothetical protein TM0875 [90065] (1)
345. Metal cation-transporting ATPase, ATP-binding domain N [81661] (1)
  unusual fold; core: beta-alpha(2)-beta(3)-alpha(2)-beta(2); 6-stranded antiparallel beta-sheet, order: 165432
  1. Metal cation-transporting ATPase, ATP-binding domain N [81660] (1)
    uperfamily
    1. Metal cation-transporting ATPase, ATP-binding domain N [81659] (5)
346. Suppressor of Fused, N-terminal domain [103358] (1)
  unusual fold; bifurcated beta-sheet; left-handed beta-alpha-beta unit
  1. Suppressor of Fused, N-terminal domain [103359] (1)
    uperfamily
    1. Suppressor of Fused, N-terminal domain [103360] (1)
347. Nitric oxide (NO) synthase oxygenase domain [56511] (1)
  unusual fold
  1. Nitric oxide (NO) synthase oxygenase domain [56512] (1)
    uperfamily
    1. Nitric oxide (NO) synthase oxygenase domain [56513] (6)
348. Penicillin binding protein dimerisation domain [56518] (1)
  unusual fold
  1. Penicillin binding protein dimerisation domain [56519] (1)
    uperfamily
    1. Penicillin binding protein dimerisation domain [56520] (2)
      contains an insert subdomain of ClpS-like fold
349. Oxidoreductase molybdopterin-binding domain [56523] (1)
  unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
  1. Oxidoreductase molybdopterin-binding domain [56524] (1)
    uperfamily
    1. Oxidoreductase molybdopterin-binding domain [56525] (3)
      Pfam 00174
350. FAH [56528] (1)
  unusual fold; contains 3 layers of beta-sheet structure
  1. FAH [56529] (1)
    uperfamily
    1. FAH [56530] (6)
351. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56533] (1)
  unusual fold
  1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56534] (1)
    uperfamily
    1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56535] (5)
352. Substrate-binding domain of HMG-CoA reductase [56541] (1)
  unusual fold
  1. Substrate-binding domain of HMG-CoA reductase [56542] (1)
    uperfamily
    1. Substrate-binding domain of HMG-CoA reductase [56543] (2)
353. Argininosuccinate synthetase, C-terminal domain [69863] (1)
  unusual fold
  1. Argininosuccinate synthetase, C-terminal domain [69864] (1)
    uperfamily
    1. Argininosuccinate synthetase, C-terminal domain [69865] (3)
354. Hypothetical protein PH1602 [103364] (1)
  complex alpha+beta fold; contains a region of similarity to the ferredoxin-like fold
  1. Hypothetical protein PH1602 [103365] (1)
    uperfamily
    1. Hypothetical protein PH1602 [103366] (1)
355. IlvD/EDD N-terminal domain-like [143974] (1)
  contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
  1. IlvD/EDD N-terminal domain-like [143975] (1)
    uperfamily
    1. lvD/EDD N-terminal domain-like [143976] (1)
      N-terminal part of Pfam 00920
356. DNA methylase specificity domain [116733] (1)
  comprises the N-terminal, double beta-helix like structure and C-terminal alpha-hairpin
  1. DNA methylase specificity domain [116734] (2)
    uperfamily
    1. TaqI C-terminal domain-like [116735] (1)
    2. Type I restriction modification DNA specificity domain [143979] (2)
      Pfam 01420
357. GCM domain [90072] (1)
  consists of two different alpha+beta subdomains; 2 zinc-binding sites
  1. GCM domain [90073] (1)
    DNA-binding domain
    uperfamily
    1. GCM domain [90074] (1)
358. Conserved core of transcriptional regulatory protein vp16 [56547] (1)
  unusual fold
  1. Conserved core of transcriptional regulatory protein vp16 [56548] (1)
    uperfamily
    1. Conserved core of transcriptional regulatory protein vp16 [56549] (1)
359. Insert subdomain of RNA polymerase alpha subunit [56552] (1)
  unusual fold; contains a left-handed beta-alpha-beta unit
  1. Insert subdomain of RNA polymerase alpha subunit [56553] (1)
    uperfamily
    1. Insert subdomain of RNA polymerase alpha subunit [56554] (4)
360. Baseplate structural protein gp11 [56557] (1)
  unusual fold; trimer
  1. Baseplate structural protein gp11 [56558] (1)
    uperfamily
    1. Baseplate structural protein gp11 [56559] (1)
361. Receptor-binding domain of short tail fibre protein gp12 [88873] (1)
  unusual fold; trimer
  1. Receptor-binding domain of short tail fibre protein gp12 [88874] (1)
    uperfamily
    1. Receptor-binding domain of short tail fibre protein gp12 [88875] (1)
362. Outer capsid protein sigma 3 [64464] (1)
  unusual fold
  1. Outer capsid protein sigma 3 [64465] (1)
    uperfamily
    1. Outer capsid protein sigma 3 [64466] (1)
363. Phosphoprotein M1, C-terminal domain [118172] (1)
  consists of 6 helices and one beta-hairpin
  1. Phosphoprotein M1, C-terminal domain [118173] (1)
    uperfamily
    1. Phosphoprotein M1, C-terminal domain [118174] (1)
      C-terminal part of Pfam 03012
364. L,D-transpeptidase pre-catalytic domain-like [143984] (1)
  unusual fold, made of four helices and four 2-3 stranded beta-sheets
  1. L,D-transpeptidase pre-catalytic domain-like [143985] (1)
    uperfamily
    1. L,D-transpeptidase pre-catalytic domain-like [143986] (1)
365. YbiA-like [143989] (1)
  consists of six alpha-helices and two two-stranded beta-sheets
  1. YbiA-like [143990] (1)
    uperfamily
    1. YbiA-like [143991] (1)
366. NinB [103369] (1)
  unusual fold; intertwined dimer; consists of two different structural domains
  1. NinB [103370] (1)
    uperfamily
    1. NinB [103371] (1)
367. AF2331-like [143994] (1)
  interlocked dimer of beta-alpha-beta(2)-alpha-beta-(alpha) subunits; 3 layers: b/b/a
  1. AF2331-like [143995] (1)
    uperfamily
    1. AF2331-like [143996] (1)
368. SSo0622-like [111277] (1)
  alpha(2)-beta(2)-alpha-beta-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel beta-sheet: order 21354; strands 1,3 and 5 and the C-terminal helix are longer than other secondary structures
  1. SSo0622-like [111278] (1)
    the dimer, formed in the crystals, is a probable biological unit
    uperfamily
    1. SSo0622-like [111279] (1)
      Pfam 02676
369. Putative modulator of DNA gyrase, PmbA/TldD [111282] (1)
  consists of two different alpha+beta domains; d1: [duplication of alpha-beta(3)-alpha motif; 2 layers: a/b; antiparallel beta-sheet, order: 321456; strands 1, 2, 4 and 5 are twice longer than other secondary structures]; d2 [ complex fold; contains beta-barrel (n=5, S=10)]
  1. Putative modulator of DNA gyrase, PmbA/TldD [111283] (1)
    uperfamily
    1. Putative modulator of DNA gyrase, PmbA/TldD [111284] (2)
      Pfam 01523
370. PSTPO5379-like [160919] (1)
  complex fold; consists of two alpha+beta subdomains, one is inserted in the other
  1. PSTPO5379-like [160920] (1)
    1. PSTPO5379-like [160921] (1)
      Pfam 07286; DUF1445
371. PG1388-like [160924] (1)
  consists of 2 alpha+beta subdomains, each having a meander beta-sheet; d1: alpha(2)-beta(7); d2: alpha(2)-beta(2)-alpha(2)-beta(2)
  1. PG1388-like [160925] (1)
    1. PG1388-like [160926] (1)
      PfamB 104512
372. Oxysterol-binding protein-like [143999] (1)
  core: large meander beta-sheet of 12 strands wrapped around the N-terminal (distorted) alpha-hairpin; some similarity to transmembrane beta-barrel proteins
  1. Oxysterol-binding protein-like [144000] (1)
    uperfamily
    1. Oxysterol-binding protein [144001] (1)
      Pfam 01237
373. ORC1-binding domain [144004] (1)
  complex fold, composed of an alpha hairpin, meander beta-sheet and a five-stranded barrel of unusual topology
  1. ORC1-binding domain [144005] (1)
    uperfamily
    1. ORC1-binding domain [144006] (1)
374. CofE-like [144009] (1)
  consists of two different domains; d1: beta-alpha-beta-alpha-beta(2)-alpha-beta, mixed sheet of 5 strands, order:15234, strands 2 and 3 are parralel; d2 is inserted in d1 after strand 2 and comprises a helix-turn-helix motif and two 3-stranded sheets
  1. CofE-like [144010] (1)
    uperfamily
    1. CofE-like [144011] (1)
      Pfam 01996; DUF129; contains known activity
375. Peptidoglycan deacetylase N-terminal noncatalytic region [144014] (1)
  consists of two different domains, d1: [alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; mixed beta-sheet, order 12345, strands 2 and 3 are parallel to each other with a left-handed crossover connection], d2: alpha-beta(3)-alpha; 2 layers; antiparallel beta-sheet, order 123]
  1. Peptidoglycan deacetylase N-terminal noncatalytic region [144015] (1)
    uperfamily
    1. Peptidoglycan deacetylase N-terminal noncatalytic region [144016] (1)
376. Non-globular alpha+beta subunits of globular proteins [56567] (1)
  not a true fold
  1. Non-globular alpha+beta subunits of globular proteins [56568] (3)
    not a true superfamily
    uperfamily
    1. Phycoerythrin 545 alpha-subunits [56569] (1)
      consists of a long beta-hairpin and a single alpha-helix
    2. Virulence effector SptP domain [69868] (1)
    3. Ubiquinol-cytochrome c reductase 8 kDa protein [90077] (1)
      beta-hairpin and a short alpha-helix bound to the core subunits
Multi-domain proteins (alpha and beta) [56572] (66)
Folds consisting of two or more domains belonging to different classes
1. Serpins [56573] (1)
  contains a cluster of helices and a beta-sandwich
  1. Serpins [56574] (1)
    uperfamily
    1. Serpins [56575] (17)
2. 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
3. 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
4. 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)
5. 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
6. 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)
7. 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)
8. 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
9. 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
10. 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
11. 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)
12. 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)
    2. Allene oxide synthase [118183] (1)
13. 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)
    2. acyl-CoA oxidase N-terminal domains [75600] (2)
14. 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)
    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
15. 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)
    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)
    3. Reverse transcriptase [56686] (3)
    4. T7 RNA polymerase [56691] (1)
    5. RNA-dependent RNA-polymerase [56694] (11)
    6. dsRNA phage RNA-dependent RNA-polymerase [64480] (1)
16. 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)
    2. RNA-polymerase beta-prime [64490] (3)
17. 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
18. 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
19. 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
20. 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
21. 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
22. 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)
    2. Primase fragment of primase-helicase protein [90090] (1)
23. 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
24. 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)
25. 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)
26. 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)
    2. Nqo4-like [144028] (1)
      Pfam 00346; Respiratory-chain NADH dehydrogenase, 49 Kd subunit
27. 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)
    2. Nq06-like [144031] (1)
      Pfam 01058
28. 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)
    2. Iron-containing alcohol dehydrogenase [69892] (6)
      Pfam 00465
29. 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)
30. 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)
31. 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)
32. 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
33. 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
34. 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
35. 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)
36. 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)
37. 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)
38. 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)
    2. Hybrid cluster protein (prismane protein) [56822] (2)
      contains extra N-terminal 3-helical bundle domain
    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
39. 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)
    2. Capz beta-1 subunit [90100] (1)
40. 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)
    2. Glutaminase [90084] (2)
      Pfam 04960
    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
41. 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)
42. 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
43. 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)
44. 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)
45. 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
46. 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
47. 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
48. 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
    2. Diacylglycerol kinase-like [160984] (3)
      N-terminal, catalytic domain is covered by Pfam 00781
49. 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
50. 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
51. 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
52. 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
53. 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
54. 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
55. 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
56. 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
    2. ChuX-like [144070] (1)
      Pfam 06228; DUF1008; single-domain subunits form a dimer similar to the HemS/ChuS subunits
57. 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
58. 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)
59. 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
    2. E2F dimerization segment [144078] (1)
      PfamB 001971
60. 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)
61. 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
62. 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
    2. Spike glycoprotein-like [161012] (1)
      Pfam 00974; Rhabdovirus spike glycoprotein
63. 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)
    2. Phytoreovirus core [103413] (1)
64. 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)
65. 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)
66. 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
Membrane and cell surface proteins and peptides [56835] (58)
Does not include proteins in the immune system
1. Toxins' membrane translocation domains [56836] (5)
  multi-helical domains of various folds which is thought to unfold in the membrane
  1. Colicin [56837] (1)
    uperfamily
    1. Colicin [56838] (4)
      contains "globin-like fold" with additional N-terminal and C-terminal helices
  2. Diphtheria toxin, middle domain [56845] (1)
    uperfamily
    1. Diphtheria toxin, middle domain [56846] (1)
  3. delta-Endotoxin (insectocide), N-terminal domain [56849] (1)
    uperfamily
    1. delta-Endotoxin (insectocide), N-terminal domain [56850] (4)
      seven-helical bundle with central helix surrounded by six others
  4. Bcl-2 inhibitors of programmed cell death [56854] (1)
    PROVISIONAL CLASSIFICATION, based on structural similarity to the diphtheria toxin domain
    uperfamily
    1. Bcl-2 inhibitors of programmed cell death [56855] (13)
      Pfam 00452
  5. Exotoxin A, middle domain [56864] (1)
    uperfamily
    1. Exotoxin A, middle domain [56865] (1)
2. Family A G protein-coupled receptor-like [81322] (1)
  core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane
  1. Family A G protein-coupled receptor-like [81321] (2)
    uperfamily
    1. Bacteriorhodopsin-like [81319] (6)
    2. Rhodopsin-like [81320] (1)
      Individual TM segments have a number of kinks and distortions
3. Single transmembrane helix [81407] (38)
  not a true fold
  1. Photosystem II reaction centre subunit H, transmembrane region [81490] (1)
    uperfamily
    1. Photosystem II reaction centre subunit H, transmembrane region [81489] (3)
  2. Mitochondrial cytochrome c oxidase subunit IV [81406] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit IV [81405] (1)
  3. Mitochondrial cytochrome c oxidase subunit VIa [81411] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIa [81410] (1)
  4. Mitochondrial cytochrome c oxidase subunit VIc [81415] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIc [81414] (1)
  5. Mitochondrial cytochrome c oxidase subunit VIIa [81419] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIIa [81418] (1)
  6. Mitochondrial cytochrome c oxidase subunit VIIb [81423] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIIb [81422] (1)
  7. Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) [81427] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) [81426] (1)
  8. Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) [81431] (1)
    uperfamily
    1. Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) [81430] (1)
  9. Bacterial aa3 type cytochrome c oxidase subunit IV [81469] (1)
    uperfamily
    1. Bacterial aa3 type cytochrome c oxidase subunit IV [81468] (2)
  10. Bacterial ba3 type cytochrome c oxidase subunit IIa [81473] (1)
    uperfamily
    1. Bacterial ba3 type cytochrome c oxidase subunit IIa [81472] (1)
  11. F1F0 ATP synthase subunit B, membrane domain [81573] (1)
    uperfamily
    1. F1F0 ATP synthase subunit B, membrane domain [81572] (1)
  12. Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81496] (1)
    uperfamily
    1. Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81495] (3)
  13. ISP transmembrane anchor [81502] (1)
    uperfamily
    1. ISP transmembrane anchor [81501] (5)
  14. Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81508] (1)
    uperfamily
    1. Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81507] (3)
  15. Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81514] (1)
    uperfamily
    1. Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81513] (3)
  16. Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81518] (1)
    uperfamily
    1. Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81517] (1)
  17. Subunit III of photosystem I reaction centre, PsaF [81536] (1)
    uperfamily
    1. Subunit III of photosystem I reaction centre, PsaF [81535] (1)
  18. Subunit VIII of photosystem I reaction centre, PsaI [81540] (1)
    uperfamily
    1. Subunit VIII of photosystem I reaction centre, PsaI [81539] (1)
  19. Subunit IX of photosystem I reaction centre, PsaJ [81544] (1)
    uperfamily
    1. Subunit IX of photosystem I reaction centre, PsaJ [81543] (1)
  20. Subunit XII of photosystem I reaction centre, PsaM [81548] (1)
    uperfamily
    1. Subunit XII of photosystem I reaction centre, PsaM [81547] (1)
  21. Subunit PsaX of photosystem I reaction centre [81552] (1)
    uperfamily
    1. Subunit PsaX of photosystem I reaction centre [81551] (1)
  22. Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor [81597] (1)
    uperfamily
    1. Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor [81596] (1)
  23. Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103431] (1)
    uperfamily
    1. Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103432] (2)
  24. PetL subunit of the cytochrome b6f complex [103436] (1)
    uperfamily
    1. PetL subunit of the cytochrome b6f complex [103437] (2)
  25. PetM subunit of the cytochrome b6f complex [103441] (1)
    uperfamily
    1. PetM subunit of the cytochrome b6f complex [103442] (2)
  26. PetG subunit of the cytochrome b6f complex [103446] (1)
    uperfamily
    1. PetG subunit of the cytochrome b6f complex [103447] (2)
  27. PetN subunit of the cytochrome b6f complex [103451] (1)
    uperfamily
    1. PetN subunit of the cytochrome b6f complex [103452] (2)
  28. Preprotein translocase SecE subunit [103456] (1)
    uperfamily
    1. Preprotein translocase SecE subunit [103457] (2)
  29. Sec-beta subunit [103460] (1)
    uperfamily
    1. Sec-beta subunit [103461] (2)
  30. Oligosaccharyltransferase subunit ost4p [103464] (1)
    uperfamily
    1. Oligosaccharyltransferase subunit ost4p [103465] (1)
  31. Photosystem II reaction center protein L, PsbL [161017] (1)
    1. PsbL-like [161018] (1)
      Pfam 02419
  32. Photosystem II reaction center protein J, PsbJ [161021] (1)
    1. PsbJ-like [161022] (1)
      Pfam 01788
  33. Photosystem II 10 kDa phosphoprotein PsbH [161025] (1)
    1. PsbH-like [161026] (1)
      Pfam 00737
  34. Photosystem II reaction center protein T, PsbT [161029] (1)
    1. PsbT-like [161030] (1)
      Pfam 01405
  35. Photosystem II reaction center protein M, PsbM [161033] (1)
    1. PsbM-like [161034] (1)
      Pfam 05151
  36. Photosystem II reaction center protein K, PsbK [161037] (1)
    1. PsbK-like [161038] (1)
      Pfam 02533
  37. Photosystem II reaction center protein I, PsbI [161041] (1)
    1. PsbI-like [161042] (1)
      Pfam 02532
  38. Cytochrome b559 subunits [161045] (1)
    1. Cytochrome b559 subunits [161046] (2)
      Pfam 00283 comprises PsbF beta subunit (PsbF) and the transmembrane helix of alpha subunit (PsbE) that bind one heme group between them; the lumenal region of the alpha subunit is covered by Pfam 00284
4. Bacterial photosystem II reaction centre, L and M subunits [81484] (1)
  five transmembrane helices forming a sheet-like structure
  1. Bacterial photosystem II reaction centre, L and M subunits [81483] (1)
    uperfamily
    1. Bacterial photosystem II reaction centre, L and M subunits [81482] (8)
      L and M are probably related to each other
5. Cytochrome c oxidase subunit I-like [81443] (1)
  12 transmembrane helices in an approximate threefold rotational symmetric arrangement
  1. Cytochrome c oxidase subunit I-like [81442] (1)
    uperfamily
    1. Cytochrome c oxidase subunit I-like [81441] (5)
      the largest and best conserved subunit, contains two heme groups, low spin heme a and high spin heme a3
6. Cytochrome c oxidase subunit III-like [81453] (1)
  core: 7 transmembrane helices organized into two bundles, one formed by the first two helices and the other by the rest
  1. Cytochrome c oxidase subunit III-like [81452] (1)
    uperfamily
    1. Cytochrome c oxidase subunit III-like [81451] (4)
      function unknown, possibly involved in the assembly or form the entrance to "oxygen" channel
7. Transmembrane helix hairpin [81334] (5)
  two antiparallel transmembrane helices
  1. Cytochrome c oxidase subunit II-like, transmembrane region [81464] (1)
    uperfamily
    1. Cytochrome c oxidase subunit II-like, transmembrane region [81463] (5)
  2. F1F0 ATP synthase subunit C [81333] (1)
    uperfamily
    1. F1F0 ATP synthase subunit C [81332] (1)
  3. Magnesium transport protein CorA, transmembrane region [144083] (1)
    forms homopentameric channel
    uperfamily
    1. Magnesium transport protein CorA, transmembrane region [144084] (1)
      C-terminal part of Pfam 01544
  4. Htr2 transmembrane domain-like [158212] (1)
    1. Htr2 transmembrane domain-like [158213] (1)
  5. PsbZ-like [161055] (1)
    1. PsbZ-like [161056] (1)
      Pfam 01737; Ycf9
8. F1F0 ATP synthase subunit A [81337] (1)
  core: up-and-down bundle of four transmembrane helices
  1. F1F0 ATP synthase subunit A [81336] (1)
    uperfamily
    1. F1F0 ATP synthase subunit A [81335] (1)
9. ATP synthase B chain-like [161059] (1)
  long single helix, part of the stator subcomplex
  1. ATP synthase B chain-like [161060] (1)
    1. ATP synthase B chain-like [161061] (1)
      Pfam 05405
10. ATP synthase D chain-like [161064] (1)
  non-globular, mostly helical component of the stator subcomplex
  1. ATP synthase D chain-like [161065] (1)
    1. ATP synthase D chain-like [161066] (1)
      Pfam 05873
11. Aquaporin-like [81339] (1)
  core: 8 helices, 2 short helices are surrounded by 6 long transmembrane helices
  1. Aquaporin-like [81338] (1)
    uperfamily
    1. Aquaporin-like [56895] (6)
      duplication: consist of two similar structural parts
12. Ammonium transporter [111351] (1)
  11 transmembrane helices; duplication: consist of 2 structural repeats of five helices each plus extra C-terminal helix
  1. Ammonium transporter [111352] (1)
    uperfamily
    1. Ammonium transporter [111353] (1)
      Pfam 00909
13. MFS general substrate transporter [103472] (1)
  12 transmembrane helices; duplication: the N- and C-terminal halves are structurally similar
  1. MFS general substrate transporter [103473] (2)
    uperfamily
    1. Glycerol-3-phosphate transporter [103474] (1)
    2. LacY-like proton/sugar symporter [103477] (1)
14. SNF-like [161069] (1)
  12 transmembrane helices; duplication: consists of two structurally similar halves
  1. SNF-like [161070] (1)
    1. SNF-like [161071] (1)
      Pfam 00209; Sodium:neurotransmitter symporter
15. Proton glutamate symport protein [118214] (1)
  multihelical membrane protein; partial structural duplication in the C-terminal region; oligomeric state: trimer
  1. Proton glutamate symport protein [118215] (1)
    uperfamily
    1. Proton glutamate symport protein [118216] (1)
16. Clc chloride channel [81341] (1)
  core: 18 transmembrane helices
  1. Clc chloride channel [81340] (1)
    uperfamily
    1. Clc chloride channel [69912] (2)
      duplication: consist of two similar structural parts
17. Voltage-gated potassium channels [81325] (1)
  oligomeric transmembrane alpha-helical proteins
  1. Voltage-gated potassium channels [81324] (1)
    uperfamily
    1. Voltage-gated potassium channels [81323] (6)
18. Small-conductance potassium channel [81328] (1)
  oligomeric transmembrane alpha-helical protein
  1. Small-conductance potassium channel [81327] (1)
    uperfamily
    1. Small-conductance potassium channel [81326] (1)
19. Gated mechanosensitive channel [81331] (1)
  oligomeric transmembrane alpha-helical protein
  1. Gated mechanosensitive channel [81330] (1)
    uperfamily
    1. Gated mechanosensitive channel [81329] (1)
20. Neurotransmitter-gated ion-channel transmembrane pore [90111] (1)
  heteropentameric transmembrane alpha-helical protein; 4 transmembrane helices per subunit
  1. Neurotransmitter-gated ion-channel transmembrane pore [90112] (1)
    uperfamily
    1. Neurotransmitter-gated ion-channel transmembrane pore [90113] (4)
21. Mechanosensitive channel protein MscS (YggB), transmembrane region [82860] (1)
  oligomeric fold; 3 transmembrane helices per subunit
  1. Mechanosensitive channel protein MscS (YggB), transmembrane region [82861] (1)
    uperfamily
    1. Mechanosensitive channel protein MscS (YggB), transmembrane region [82862] (1)
22. Multidrug resistance efflux transporter EmrE [103480] (1)
  oligomeric fold; 3 transmembrane helices per subunit
  1. Multidrug resistance efflux transporter EmrE [103481] (1)
    uperfamily
    1. Multidrug resistance efflux transporter EmrE [103482] (1)
23. V-type ATP synthase subunit C [103485] (1)
  9 transmembrane helices
  1. V-type ATP synthase subunit C [103486] (1)
    duplication: consists of three similar structural parts
    uperfamily
    1. V-type ATP synthase subunit C [103487] (1)
24. Preprotein translocase SecY subunit [103490] (1)
  10 transmembrane helices forming of a gated channel
  1. Preprotein translocase SecY subunit [103491] (1)
    duplication: consists of two similar structural parts
    uperfamily
    1. Preprotein translocase SecY subunit [103492] (1)
25. Photosystem I subunits PsaA/PsaB [81559] (1)
  core:11 transmembrane helices
  1. Photosystem I subunits PsaA/PsaB [81558] (1)
    uperfamily
    1. Photosystem I subunits PsaA/PsaB [81557] (2)
      Photosystem I p700 chlorophyll a apoprotein a1/a2
26. Photosystem I reaction center subunit X, PsaK [81564] (1)
  core: hairpin of two transmembrane helices
  1. Photosystem I reaction center subunit X, PsaK [81563] (1)
    uperfamily
    1. Photosystem I reaction center subunit X, PsaK [81562] (1)
27. Photosystem I reaction center subunit XI, PsaL [81569] (1)
  core: three transmembrane helices, bundle
  1. Photosystem I reaction center subunit XI, PsaL [81568] (1)
    uperfamily
    1. Photosystem I reaction center subunit XI, PsaL [81567] (1)
28. ABC transporter involved in vitamin B12 uptake, BtuC [81346] (1)
  multihelical; complex architecture with several transmembrane helices
  1. ABC transporter involved in vitamin B12 uptake, BtuC [81345] (1)
    uperfamily
    1. ABC transporter involved in vitamin B12 uptake, BtuC [75648] (1)
29. ABC transporter transmembrane region [90122] (1)
  multihelical; complex architecture with several transmembrane helices
  1. ABC transporter transmembrane region [90123] (1)
    uperfamily
    1. ABC transporter transmembrane region [90124] (3)
30. Multidrug efflux transporter AcrB transmembrane domain [82865] (1)
  12 transmembrane helices; duplication: the N- and C-terminal halves of the whole proteins are structurally similar
  1. Multidrug efflux transporter AcrB transmembrane domain [82866] (1)
    uperfamily
    1. Multidrug efflux transporter AcrB transmembrane domain [82867] (1)
31. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81649] (1)
  core: three transmembrane helices, up-and-down bundle
  1. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81648] (1)
    uperfamily
    1. a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81647] (5)
      a part (domain) of mitochondrial cytochrome b subunit, separate subunit in plants and cyanobacteria
32. Heme-binding four-helical bundle [81344] (3)
  core: four transmembrane helices, up-and-down bundle, binds one or two heme groups in between the helices
  1. Transmembrane di-heme cytochromes [81342] (2)
    Three of the four heme-ligands are conserved between the two families; both heme groups bind similarly but not identically
    uperfamily
    1. Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81642] (5)
      a part (domain) of a larger mitochondrial cytochrome b subunit, separate subunit in plants and cyanobacteria
    2. Formate dehydrogenase N, cytochrome (gamma) subunit [75645] (1)
  2. Respiratory nitrate reductase 1 gamma chain [103501] (1)
    possible link between the two other superfamilies: this subunit corresponds to the gamma subunit of a functionally related Formate dehydrogenase N complex but is structurally closer to the Fumarate reductase subunit FrdC
    uperfamily
    1. Respiratory nitrate reductase 1 gamma chain [103502] (1)
  3. Fumarate reductase respiratory complex transmembrane subunits [81343] (2)
    two distinct families: in one family the common fold is contained in a single-chain subunit, in the other it is formed by two chains
    uperfamily
    1. Fumarate reductase respiratory complex cytochrome b subunit, FrdC [56910] (1)
      duplication: consists of two structural repeats; the heme-binding sites are related by pseudo two fold symmetry
    2. Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) [81373] (4)
      consists of two homologous non-identical subunits that form a heterodimer; may or may not contain heme groups
33. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81525] (1)
  membrane-associated alpha-helical protein; no transmembrane helices
  1. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81524] (1)
    location - matrix side of the bc1 complex
    uperfamily
    1. 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81523] (3)
      probably important for the complex assembly, caps the matrix face of cytochrome b
34. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81532] (1)
  membrane-associated alpha-helical protein; no transmembrane helices
  1. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81531] (1)
    location - intermembrane side of the bc1 complex
    uperfamily
    1. Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) [81530] (3)
      "acidic/hinge protein", essential for the complex formation, interacts with the functional domain of cytochrome c1
35. Mitochondrial ATP synthase coupling factor 6 [111356] (1)
  2 helices, hairpin
  1. Mitochondrial ATP synthase coupling factor 6 [111357] (1)
    uperfamily
    1. Mitochondrial ATP synthase coupling factor 6 [111358] (1)
      Pfam 05511
36. Calcium ATPase, transmembrane domain M [81666] (1)
  core: multihelical; consists of three transmembrane regions of 2, 2 and 6 helices, separated by cytoplasmic domains
  1. Calcium ATPase, transmembrane domain M [81665] (1)
    uperfamily
    1. Calcium ATPase, transmembrane domain M [81664] (1)
37. Light-harvesting complex subunits [56917] (1)
  membrane all-alpha fold
  1. Light-harvesting complex subunits [56918] (1)
    uperfamily
    1. Light-harvesting complex subunits [56919] (5)
38. Photosystem II antenna protein-like [161076] (1)
  6 transmembrane helices arranged in three antiparallel pairs (hairpins), segregated by cofactors; there can be insertions of different small subdomains in different exposed loops
  1. Photosystem II antenna protein-like [161077] (1)
    1. Photosystem II antenna protein-like [161078] (2)
      Pfam 00421
39. Mitochondrial carrier [103505] (1)
  membrane all-alpha fold; 6-helical "barrel" with internal binding cavity
  1. Mitochondrial carrier [103506] (1)
    duplication: consists of three alpha-hairpin repeats
    uperfamily
    1. Mitochondrial carrier [103507] (1)
40. Chlorophyll a-b binding protein [103510] (1)
  membrane all-alpha fold; three transmembrane helices
  1. Chlorophyll a-b binding protein [103511] (1)
    duplication: contains two structural repeats
    uperfamily
    1. Chlorophyll a-b binding protein [103512] (1)
41. MAPEG domain-like [161083] (1)
  4 helices, bundle; left-handed superhelix
  1. MAPEG domain-like [161084] (1)
    1. MAPEG domain [161085] (3)
      Pfam 01124
42. MgtE membrane domain-like [161092] (1)
  5 transmembrane helices; bundle, right-handed twist
  1. MgtE membrane domain-like [161093] (1)
    homodimer, swapped with the N-terminal helices
    1. MgtE membrane domain-like [161094] (1)
      Pfam 01769; Divalent cation transporter
43. MetI-like [161097] (1)
  core: 5 transmembrane helices; flattened bundle
  1. MetI-like [161098] (1)
    1. MetI-like [161099] (5)
      Pfam 00528; Binding-protein-dependent transport system inner membrane component
44. Rhomboid-like [144090] (1)
  6 transmembrane helices
  1. Rhomboid-like [144091] (1)
    uperfamily
    1. Rhomboid-like [144092] (2)
      Pfam 01694; transmembrane serine protease
45. Cation efflux protein transmembrane domain-like [161110] (1)
  6 transmembrane helices, bundle
  1. Cation efflux protein transmembrane domain-like [161111] (1)
    1. Cation efflux protein transmembrane domain-like [161112] (1)
      N-terminal part of Pfam 01545
46. Connexin43 [118219] (1)
  mostly unstructured; 2 helices, hairpin
  1. Connexin43 [118220] (1)
    uperfamily
    1. Connexin43 [118221] (1)
      Pfam 03508
47. Transmembrane beta-barrels [56924] (6)
  not a true fold, gathers together transmembrane barrels of different (n,S)
  1. OMPA-like [56925] (4)
    forms (8,10) barrel
    uperfamily
    1. Outer membrane protein [56926] (3)
    2. Outer membrane enzyme PagP [82874] (1)
    3. GNA1870 immunodominant domain-like [144097] (1)
      related to Pfam 01298; GNA1870 is a bacterial cell surface-exposed lipoprotein
    4. PsbO-like [161115] (1)
      Pfam 01716; MSP
  2. OMPT-like [69917] (2)
    forms (10,12) barrel
    uperfamily
    1. Outer membrane protease OMPT [69918] (1)
    2. Outer membrane adhesin/invasin OpcA [75651] (1)
  3. Autotransporter [103515] (1)
    forms (12,14) barrel; contains a long alpha-helix running along the barrel axis
    uperfamily
    1. Autotransporter [103516] (1)
  4. Outer membrane phospholipase A (OMPLA) [56931] (1)
    forms (12,16) barrel
    uperfamily
    1. Outer membrane phospholipase A (OMPLA) [56932] (1)
  5. Porins [56935] (4)
    uperfamily
    1. Porin [56936] (5)
      trimer, one subunit folds into (16,20) barrel
    2. Maltoporin-like [56942] (3)
      trimer, one subunit folds into (18,22) barrel
    3. Ligand-gated protein channel [56948] (4)
      monomeric (22,24) barrel; ~150 N-terminal residues form a "plug" or "cork" subdomain
    4. Outer membrane protein transport protein [111361] (1)
      Pfam 03349; monomeric (14,16) barrel; plugged by an N-terminal all-alpha subdomain (1-40)
  6. Tsx-like channel [111364] (1)
    forms (12,16) barrel
    uperfamily
    1. Tsx-like channel [111365] (1)
      Pfam 03502
48. Outer membrane efflux proteins (OEP) [56953] (1)
  subunit fold contains tandem repeat of alpha-beta hairpin-alpha(2) motif
  trimeric fold contains barrel (n=12, S=18) formed by beta-hairpins, two from each subunit, and a bundle of helices with a channel running through it
  1. Outer membrane efflux proteins (OEP) [56954] (1)
    uperfamily
    1. Outer membrane efflux proteins (OEP) [56955] (2)
      Pfam 02321
49. HlyD-like secretion proteins [111368] (1)
  consists of three domains: beta-barrel (res. 29-38,170-259; scop_cf 50412); barrel-sandwich hybrid (39-72,135-169; scop_sf 51230) and long alpha-hairpin (73-134; scop_cf 46556)
  1. HlyD-like secretion proteins [111369] (1)
    uperfamily
    1. HlyD-like secretion proteins [111370] (1)
      Pfam 00529
50. Leukocidin-like [56958] (1)
  subunit fold contains beta-sandwich of Ig-like (grerk-key) topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel
  1. Leukocidin-like [56959] (2)
    uperfamily
    1. Leukocidin (pore-forming toxin) [56960] (4)
      heptameric fold contains barrel (n=14, S=14) formed by beta-ribbon arms, one from each subunit
    2. Porin MspA [103519] (1)
      octameric fold contains barrel (n=16, S=16) formed by beta-ribbon arms, one from each subunit
51. Lipovitellin-phosvitin complex; beta-sheet shell regions [56967] (1)
  contains several large open beta-sheets
  1. Lipovitellin-phosvitin complex; beta-sheet shell regions [56968] (1)
    uperfamily
    1. Lipovitellin-phosvitin complex; beta-sheet shell regions [56969] (1)
52. Aerolisin/ETX pore-forming domain [56972] (1)
  3 domains: (1) alpha+beta; (2&3) all-beta
  1. Aerolisin/ETX pore-forming domain [56973] (2)
    uperfamily
    1. (Pro)aerolysin, pore-forming lobe [56974] (1)
    2. ETX/MTX2 [111375] (1)
      Pfam 03318
53. Perfringolysin [56977] (1)
  2 domains: (1) alpha+beta; (2) all-beta, similar to the CalB domain fold but the two last strands are transposed
  1. Perfringolysin [56978] (1)
    uperfamily
    1. Perfringolysin [56979] (1)
54. Viral glycoprotein, central and dimerisation domains [56982] (1)
  2 intertwined domains; all-beta and alpha+beta
  1. Viral glycoprotein, central and dimerisation domains [56983] (1)
    uperfamily
    1. Viral glycoprotein, central and dimerisation domains [56984] (3)
55. VP4 membrane interaction domain [111378] (1)
  2 domains; d1: complexed all-beta fold; d2: coiled-coil (trimeric) helical region
  1. VP4 membrane interaction domain [111379] (1)
    uperfamily
    1. VP4 membrane interaction domain [111380] (1)
56. Head and neck region of the ectodomain of NDV fusion glycoprotein [69921] (1)
  3 intertwined all-beta domains
  1. Head and neck region of the ectodomain of NDV fusion glycoprotein [69922] (1)
    uperfamily
    1. Head and neck region of the ectodomain of NDV fusion glycoprotein [69923] (1)
57. OmpH-like [111383] (1)
  trimer; one subunit consists of an alpha/beta oligomerization subdomain [3-stranded parallel beta-sheet, order 213], and an antiparallel coiled coil
  1. OmpH-like [111384] (1)
    uperfamily
    1. OmpH-like [111385] (1)
      Pfam 03938
58. Anthrax protective antigen [56987] (1)
  4 domains; I (res. 14-225) and II (226-487) are beta-sandwiches of similar gamma-crystallin like topologies; III (488-594) has a beta-grasp like fold; IV (595-735) has an Ig-like fold
  1. Anthrax protective antigen [56988] (1)
    uperfamily
    1. Anthrax protective antigen [56989] (1)
Small proteins [56992] (90)
Usually dominated by metal ligand, heme, and/or disulfide bridges
1. Insulin-like [56993] (1)
  nearly all-alpha
  can be classified as disulfide-rich
  1. Insulin-like [56994] (1)
    uperfamily
    1. Insulin-like [56995] (6)
2. Knottins (small inhibitors, toxins, lectins) [57015] (19)
  disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
  1. Plant lectins/antimicrobial peptides [57016] (2)
    uperfamily
    1. Hevein-like agglutinin (lectin) domain [57017] (6)
    2. Antimicrobial peptide 2, AC-AMP2 [57024] (1)
  2. Plant inhibitors of proteinases and amylases [57027] (1)
    uperfamily
    1. Plant inhibitors of proteinases and amylases [57028] (7)
  3. Cyclotides [57038] (4)
    macrocyclic plant knottins closed with the formation of an Asn-Gly peptide
    uperfamily
    1. Kalata B1 [57039] (1)
    2. Cycloviolacin [57042] (2)
    3. Circulin A [57045] (1)
    4. Palicourein [103526] (1)
  4. Gurmarin-like [57048] (2)
    uperfamily
    1. Gurmarin, a sweet taste-suppressing polypeptide [57049] (1)
    2. Antifungal peptide [57052] (2)
  5. Agouti-related protein [57055] (1)
    uperfamily
    1. Agouti-related protein [57056] (1)
  6. omega toxin-like [57059] (5)
    uperfamily
    1. Conotoxin [57060] (13)
    2. Spider toxins [57072] (25)
    3. Insect toxins [69930] (2)
    4. Albumin 1 [90134] (2)
    5. Vhv1.1, polydnaviral gene product [118237] (1)
  7. Scorpion toxin-like [57095] (5)
    uperfamily
    1. Long-chain scorpion toxins [57096] (22)
    2. Short-chain scorpion toxins [57116] (38)
    3. Defensin MGD-1 [57160] (1)
    4. Insect defensins [57163] (6)
    5. Plant defensins [57170] (10)
  8. Cellulose-binding domain [57180] (1)
    uperfamily
    1. Cellulose-binding domain [57181] (1)
  9. Growth factor receptor domain [57184] (1)
    uperfamily
    1. Growth factor receptor domain [57185] (9)
  10. Colipase-like [57190] (1)
    uperfamily
    1. Colipase-like [57191] (2)
  11. EGF/Laminin [57196] (7)
    uperfamily
    1. EGF-type module [57197] (27)
    2. Integrin beta EGF-like domains [69940] (1)
    3. EGF-like domain of nidogen-1 [64541] (1)
    4. Laminin-type module [57233] (1)
    5. Follistatin (FS) module N-terminal domain, FS-N [57236] (2)
    6. Merozoite surface protein 1 (MSP-1) [57239] (3)
    7. Cripto EGF-like domain-like [144100] (1)
  12. Bromelain inhibitor VI (cysteine protease inhibitor) [57243] (1)
    uperfamily
    1. Bromelain inhibitor VI (cysteine protease inhibitor) [57244] (1)
  13. Bowman-Birk inhibitor, BBI [57247] (1)
    uperfamily
    1. Bowman-Birk inhibitor, BBI [57248] (10)
  14. Elafin-like [57256] (1)
    uperfamily
    1. Elafin-like [57257] (2)
  15. Leech antihemostatic proteins [57262] (2)
    uperfamily
    1. Huristasin-like [57263] (3)
    2. Hirudin-like [57270] (3)
  16. Granulin repeat [57277] (1)
    uperfamily
    1. Granulin repeat [57278] (3)
  17. Satiety factor CART (cocaine and amphetamine regulated transcript) [64546] (1)
    uperfamily
    1. Satiety factor CART (cocaine and amphetamine regulated transcript) [64547] (1)
  18. DPY module [90148] (1)
    uperfamily
    1. DPY module [90149] (1)
  19. Bubble protein [103565] (1)
    uperfamily
    1. Bubble protein [103566] (1)
3. PMP inhibitors [57282] (1)
  disulfide-rich fold; all-beta: 3 antiparallel strands
  1. PMP inhibitors [57283] (1)
    uperfamily
    1. PMP inhibitors [57284] (4)
4. Midkine [57287] (1)
  disulfide-rich fold; all-beta: 3 antiparallel strands
  1. Midkine [57288] (2)
    uperfamily
    1. Midkine, a heparin-binding growth factor, N-terminal domain [57289] (1)
    2. Midkine, a heparin-binding growth factor, C-terminal domain [57292] (1)
5. TSP-1 type 1 repeat [82894] (1)
  disulfide-rich fold; all-beta: 3 antiparallel strands
  1. TSP-1 type 1 repeat [82895] (1)
    uperfamily
    1. TSP-1 type 1 repeat [82896] (1)
6. Amb V allergen [57295] (1)
  disulfide-rich; alpha+beta: 3 antiparallel strands followed by a short alpha helix
  1. Amb V allergen [57296] (1)
    uperfamily
    1. Amb V allergen [57297] (1)
7. Snake toxin-like [57301] (1)
  disulfide-rich fold: nearly all-beta
  1. Snake toxin-like [57302] (3)
    uperfamily
    1. Snake venom toxins [57303] (36)
    2. Dendroaspin [57351] (1)
    3. Extracellular domain of cell surface receptors [57354] (9)
8. BPTI-like [57361] (1)
  disulfide-rich alpha+beta fold
  1. BPTI-like [57362] (3)
    uperfamily
    1. Small Kunitz-type inhibitors & BPTI-like toxins [57363] (12)
    2. Soft tick anticoagulant proteins [57386] (2)
    3. Tick tryptase inhibitor-like [161132] (1)
9. Defensin-like [57391] (1)
  Disulfide-rich fold, nearly all-beta
  1. Defensin-like [57392] (3)
    uperfamily
    1. Defensin [57393] (17)
    2. Myotoxin [90157] (1)
      structurally similar to beta-defensin
    3. Tick carboxypeptidase inhibitor-like [161135] (1)
10. Hairpin loop containing domain-like [57413] (1)
  alpha+beta fold with two crossing loops
  1. Hairpin loop containing domain-like [57414] (3)
    the middle part is structurally similar to some knottins and defensins but differs in the disulfide pattern
    uperfamily
    1. Hairpin loop containing domain [57415] (1)
    2. Anti-platelet protein [64556] (1)
    3. Pan module (APPLE domain) [82901] (1)
      probable carbohydrate-binding function
11. Neurotoxin III (ATX III) [57418] (1)
  disulfide-rich fold
  1. Neurotoxin III (ATX III) [57419] (1)
    uperfamily
    1. Neurotoxin III (ATX III) [57420] (1)
12. LDL receptor-like module [57423] (1)
  disulfide-rich calcium-binding fold
  1. LDL receptor-like module [57424] (1)
    uperfamily
    1. LDL receptor-like module [57425] (6)
13. Crambin-like [57428] (1)
  disulfide-rich alpha+beta fold
  1. Crambin-like [57429] (1)
    uperfamily
    1. Crambin-like [57430] (9)
14. Kringle-like [57439] (1)
  disulfide-rich fold; nearly all-beta
  1. Kringle-like [57440] (2)
    uperfamily
    1. Kringle modules [57441] (9)
    2. Fibronectin type II module [57459] (4)
      shorter two-disulfide version of a kringle module
15. Kazal-type serine protease inhibitors [100894] (1)
  1. Kazal-type serine protease inhibitors [100895] (2)
    conserved core consists of a helix and a loop crosslinked with two disulfides
    uperfamily
    1. Ovomucoid domain III-like [57468] (14)
    2. Serine proteinase inhibitor lekti [69960] (1)
16. Plant proteinase inhibitors [100896] (1)
  disulfide-rich small alpha+beta fold; topological similarity to the Ovomucoid domain III
  1. Plant proteinase inhibitors [100897] (1)
    uperfamily
    1. Plant proteinase inhibitors [57486] (3)
17. Trefoil/Plexin domain-like [57491] (3)
  disulfide-rich fold; common core is alpha+beta with two conserved disulfides
  1. Trefoil [57492] (1)
    uperfamily
    1. Trefoil [57493] (3)
  2. Plexin repeat [103575] (1)
    uperfamily
    1. Plexin repeat [103576] (3)
      Pfam 01437
  3. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118251] (1)
    alpha-beta(2)-alpha; fragment of a larger dimeric protein
    uperfamily
    1. Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain [118252] (1)
18. Necrosis inducing protein 1, NIP1 [103579] (1)
  disulfide-rich fold; all-beta; duplication: contains two structural repeats
  1. Necrosis inducing protein 1, NIP1 [103580] (1)
    uperfamily
    1. Necrosis inducing protein 1, NIP1 [103581] (1)
19. Cystine-knot cytokines [57500] (1)
  disulfide-rich fold; common core is all-beta
  1. Cystine-knot cytokines [57501] (7)
    uperfamily
    1. Platelet-derived growth factor-like [57502] (5)
    2. Transforming growth factor (TGF)-beta [57507] (7)
    3. Noggin [82904] (1)
    4. Neurotrophin [57520] (5)
    5. Gonadodropin/Follitropin [57528] (3)
    6. Interleukin 17F, IL-17F [69955] (1)
    7. Coagulogen [57531] (1)
20. Complement control module/SCR domain [57534] (1)
  disulfide-rich all-beta fold
  1. Complement control module/SCR domain [57535] (1)
    uperfamily
    1. Complement control module/SCR domain [57536] (15)
      Pfam 00084
21. Crisp domain-like [57545] (1)
  disulfide-rich all-alpha fold
  1. Crisp domain-like [57546] (2)
    uperfamily
    1. Sea anemone toxin k [57547] (2)
    2. Crisp domain [118259] (1)
      Pfam 08562; contains extra N-terminal knottin-like subdomain
22. Blood coagulation inhibitor (disintegrin) [57551] (1)
  small disulfide-rich
  1. Blood coagulation inhibitor (disintegrin) [57552] (1)
    uperfamily
    1. Blood coagulation inhibitor (disintegrin) [57553] (6)
23. Methylamine dehydrogenase, L chain [57560] (1)
  disulfide-rich; nearly all-beta
  1. Methylamine dehydrogenase, L chain [57561] (1)
    uperfamily
    1. Methylamine dehydrogenase, L chain [57562] (2)
24. Serine protease inhibitors [57566] (1)
  disulfide-rich; nearly all-beta
  1. Serine protease inhibitors [57567] (2)
    uperfamily
    1. ATI-like [57568] (4)
    2. BSTI [57577] (1)
25. TB module/8-cys domain [57580] (1)
  disulfide-rich; alpha+beta
  1. TB module/8-cys domain [57581] (1)
    uperfamily
    1. TB module/8-cys domain [57582] (2)
      transforming growth factor beta binding protein-like domain
26. TNF receptor-like [57585] (1)
  duplication: consists of three similar disulfide-rich domains
  1. TNF receptor-like [57586] (2)
    uperfamily
    1. TNF receptor-like [57587] (5)
      Pfam 00020; TNFR/NGFR cysteine-rich region
    2. BAFF receptor-like [90174] (3)
      only fragments of the receptor structures are available; no domain division is provided here
27. Heparin-binding domain from vascular endothelial growth factor [57592] (1)
  duplication: consists of two similar disulfide-rich domains, alpha+beta
  1. Heparin-binding domain from vascular endothelial growth factor [57593] (1)
    uperfamily
    1. Heparin-binding domain from vascular endothelial growth factor [57594] (1)
28. Antifungal protein (AGAFP) [57597] (1)
  disulfide-rich; all-beta: open barrel, 5 strands; OB-fold-like
  1. Antifungal protein (AGAFP) [57598] (1)
    uperfamily
    1. Antifungal protein (AGAFP) [57599] (1)
29. FnI-like domain [57602] (1)
  disulfide-rich, all-beta
  1. FnI-like domain [57603] (2)
    uperfamily
    1. Fibronectin type I module [57604] (2)
    2. VWC domain [118264] (1)
      Pfam 00093; similar to FnI domain in the N-terminal part, contains extra C-terminal subdomain
30. Thyroglobulin type-1 domain [57609] (1)
  disulfide-rich, alpha+beta
  1. Thyroglobulin type-1 domain [57610] (1)
    uperfamily
    1. Thyroglobulin type-1 domain [57611] (4)
      Pfam 00086
31. Type X cellulose binding domain, CBDX [57614] (1)
  disulfide-rich, alpha+beta
  1. Type X cellulose binding domain, CBDX [57615] (1)
    uperfamily
    1. Type X cellulose binding domain, CBDX [57616] (1)
32. Cellulose docking domain, dockering [64570] (1)
  disulfide-rich, alpha+beta
  1. Cellulose docking domain, dockering [64571] (1)
    uperfamily
    1. Cellulose docking domain, dockering [64572] (1)
33. Carboxypeptidase inhibitor [57619] (1)
  disulfide-rich, alpha+beta
  1. Carboxypeptidase inhibitor [57620] (1)
    uperfamily
    1. Carboxypeptidase inhibitor [57621] (1)
34. Invertebrate chitin-binding proteins [57624] (1)
  disulfide-rich
  1. Invertebrate chitin-binding proteins [57625] (2)
    shares a putative chitin-binding motif with the plant lectins/antimicrobial peptides superfamily but lacks one of the conserved disulfides of the knottin fold
    uperfamily
    1. Tachycitin [57626] (1)
    2. Antifungal peptide scarabaecin [90179] (1)
35. Pheromone ER-23 [69963] (1)
  disulfide-rich, all-alpha
  1. Pheromone ER-23 [69964] (1)
    uperfamily
    1. Pheromone ER-23 [69965] (1)
36. Mollusk pheromone [90182] (1)
  disulfide-rich; all-alpha
  1. Mollusk pheromone [90183] (1)
    uperfamily
    1. Mollusk pheromone [90184] (1)
37. Apical membrane antigen 1 [82909] (1)
  disulfide-rich, alpha+beta
  1. Apical membrane antigen 1 [82910] (1)
    uperfamily
    1. Apical membrane antigen 1 [82911] (1)
38. Somatomedin B domain [90187] (1)
  disulfide-rich
  1. Somatomedin B domain [90188] (1)
    uperfamily
    1. Somatomedin B domain [90189] (1)
39. Notch domain [90192] (1)
  disulfide-rich; all-alpha; calcium-binding
  1. Notch domain [90193] (1)
    uperfamily
    1. Notch domain [90194] (1)
      also called DSL domain or LNR repeat
40. Mini-collagen I, C-terminal domain [103588] (1)
  disulfide-rich
  1. Mini-collagen I, C-terminal domain [103589] (1)
    uperfamily
    1. Mini-collagen I, C-terminal domain [103590] (1)
41. Hormone receptor domain [111417] (1)
  disulfide-rich all-beta fold; contains beta sandwich of 5 strands
  1. Hormone receptor domain [111418] (1)
    uperfamily
    1. Hormone receptor domain [111419] (2)
      Pfam 02793; HRM
42. Resistin [111422] (1)
  disulfide-rich six-stranded beta-sandwich; jelly-roll
  1. Resistin [111423] (1)
    uperfamily
    1. Resistin [111424] (2)
      Pfam 06954
43. YAP1 redox domain [111429] (1)
  bipartite cysteine-rich all-alpha domain; a single helix in the N-terminal part (chain A) is linked by disulfides to the C-terminal part (chain B) [3-helical bundle of the RuvA C-terminal domain-like fold (scop_cf 46928)
  1. YAP1 redox domain [111430] (1)
    uperfamily
    1. YAP1 redox domain [111431] (1)
44. Toxic hairpin [57006] (4)
  disulfide crosslinked alpha-helical hairpin
  1. Heat-stable enterotoxin B [57007] (1)
    uperfamily
    1. Heat-stable enterotoxin B [57008] (1)
      contains 2 disulfides
  2. Neurotoxin B-IV [57011] (1)
    uperfamily
    1. Neurotoxin B-IV [57012] (1)
      contains 4 disulfides
  3. Pollen allergen ole e 6 [111388] (1)
    contains 3 disulfides
    uperfamily
    1. Pollen allergen ole e 6 [111389] (1)
  4. VhTI-like [161148] (1)
    1. VhTI-like [161149] (1)
45. Tim10-like [144121] (1)
  alpha-hairpin crosslinked by two disulfides; assembles into a heterohexameric ring-like structure
  1. Tim10-like [144122] (1)
    uperfamily
    1. Tim10/DDP [144123] (2)
      Pfam 02953; note: not a zinc finger
46. Cysteine zipper [144128] (1)
  string of helices that contain cysteines at almost every turn; folds upon itself and is crosslnked by multiple disulfides
  1. Vanabin-like [144129] (1)
    uperfamily
    1. Vanabin-like [144130] (1)
47. GLA-domain [57629] (1)
  Calcium ion-bound
  1. GLA-domain [57630] (1)
    gamma-carboxy-glutamic acid-rich domain
    uperfamily
    1. GLA-domain [57631] (9)
48. Cholecystokinin A receptor, N-domain [57641] (1)
  a few helical turns and a disulfide-crosslinked loop
  1. Cholecystokinin A receptor, N-domain [57642] (1)
    uperfamily
    1. Cholecystokinin A receptor, N-domain [57643] (1)
49. HIV-1 VPU cytoplasmic domain [57646] (1)
  a few helical turns assembled without a hydrophobic core?
  1. HIV-1 VPU cytoplasmic domain [57647] (1)
    uperfamily
    1. HIV-1 VPU cytoplasmic domain [57648] (1)
50. HIPIP (high potential iron protein) [57651] (1)
  folds around 4Fe-4S cluster
  1. HIPIP (high potential iron protein) [57652] (1)
    uperfamily
    1. HIPIP (high potential iron protein) [57653] (7)
51. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57661] (1)
  folds around 4Fe-4S cluster
  1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57662] (1)
    uperfamily
    1. Ferredoxin thioredoxin reductase (FTR), catalytic beta chain [57663] (1)
52. beta-beta-alpha zinc fingers [57666] (1)
  simple fold, consisting of the N-terminal beta-hairpin and C-terminal alpha-helical region; each part provides two zinc-coordinating residues with the observed sequences including C2H2, C2HC and CHHC
  1. beta-beta-alpha zinc fingers [57667] (7)
    uperfamily
    1. Classic zinc finger, C2H2 [57668] (30)
    2. Plant C2H2 finger (QALGGH zinc finger) [90198] (1)
    3. C2HC finger [57697] (3)
    4. HkH motif-containing C2H2 finger [111436] (4)
      putative dsRNA-specific zinc finger with a helix-kink-helix (HkH) motif; the kink results from the incompatibility of the cation-coordinating H-x5-H motif with a regular alpha-helix and contributes to RNA recognition
    5. CHHC finger [161158] (1)
    6. variant C2H2 finger [118273] (1)
      contains extra C-terminal, alpha-helical subdomain
    7. BED zinc finger [144157] (1)
      Pfam 02892; contains extra N-terminal and C-terminal helices bundled together with the core helix
53. Zn2/Cys6 DNA-binding domain [57700] (1)
  all-alpha dimetal(zinc)-bound fold
  1. Zn2/Cys6 DNA-binding domain [57701] (1)
    duplication: two structural repeats are related by the pseudo dyad
    uperfamily
    1. Zn2/Cys6 DNA-binding domain [57702] (6)
54. Glucocorticoid receptor-like (DNA-binding domain) [57715] (1)
  alpha+beta metal(zinc)-bound fold
  1. Glucocorticoid receptor-like (DNA-binding domain) [57716] (18)
    uperfamily
    1. Erythroid transcription factor GATA-1 [57717] (3)
      single zinc-binding motif
    2. Nuclear receptor [57721] (12)
      duplication: two zinc-binding motifs
    3. Transcription factor grauzone Cg33133-Pa, zinc finger associated domain [103605] (1)
    4. LIM domain [57736] (21)
      duplication: contains two (sub)domains of this fold
    5. LASP-1 [57743] (1)
    6. DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain [57746] (1)
    7. Ribosomal protein L24e [57749] (1)
    8. Hypothetical zinc finger protein YacG [82914] (1)
      Zn-binding site is particularly similar to that of ribosomal protein L24e
    9. Ribosomal protein S14 [57752] (2)
    10. C-terminal, Zn-finger domain of MutM-like DNA repair proteins [81627] (6)
    11. ClpX chaperone zinc binding domain [103608] (1)
    12. PARP-type zinc finger [111445] (1)
      Pfam 00645
    13. Prokaryotic DksA/TraR C4-type zinc finger [111448] (1)
      Pfam 01258; Pfam coverage extends to the second helix of the upstream alpha-hairpin domain
    14. Type II thymidine kinase zinc finger [118276] (3)
      C-terminal part of Pfam 00265
    15. A20-like zinc finger [144187] (2)
      Pfam 01754
    16. THAP domain [161163] (1)
      Pfam 05485
    17. TRASH domain [161166] (1)
      SMART 00746
    18. FwdE C-terminal domain-like [161169] (1)
      the C-terminus of PF02663; FwdE
55. SBT domain [103611] (1)
  consist of two different zn-binding subdomains, each subdomain resembles a distorted glucocorticoid receptor-like fold
  1. SBT domain [103612] (1)
    uperfamily
    1. SBT domain [103613] (3)
      Pfam 03110
56. Retrovirus zinc finger-like domains [57755] (1)
  metal(zinc)-bound fold
  1. Retrovirus zinc finger-like domains [57756] (1)
    uperfamily
    1. Retrovirus zinc finger-like domains [57757] (6)
57. Rubredoxin-like [57769] (17)
  metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
  1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57770] (1)
    uperfamily
    1. Methionyl-tRNA synthetase (MetRS), Zn-domain [57771] (2)
      in the Pyrococcus abyssi MetRS structure there is a tandem repeat of two such domains swapped with their zinc-binding 'knuckles', this duplicated finger occupies a larger region (124-183) than defined below; there is a structurally equivalent region in the E. coli enzyme lacking the second zinc-binding site
  2. Microbial and mitochondrial ADK, insert "zinc finger" domain [57774] (1)
    uperfamily
    1. Microbial and mitochondrial ADK, insert "zinc finger" domain [57775] (8)
  3. NADH pyrophosphatase intervening domain [116738] (1)
    uperfamily
    1. NADH pyrophosphatase intervening domain [116739] (1)
  4. Zinc beta-ribbon [57783] (5)
    uperfamily
    1. Transcriptional factor domain [57784] (6)
    2. DNA primase zinc finger [57792] (2)
      contains alpha-helices in the N- and C-terminal extensions (linkers?)
    3. Prokaryotic DNA topoisomerase I, a C-terminal fragment [57795] (1)
      Duplication: contains tandem repeats of several domains with zinc-binding sites being lost in some of them
    4. Putative zinc binding domain [118285] (1)
      Pfam 05129; DUF701
    5. PhnA zinc-binding domain [144191] (1)
      Pfam 08274
  5. Casein kinase II beta subunit [57798] (1)
    uperfamily
    1. Casein kinase II beta subunit [57799] (3)
      contains alpha-helices in the N- and C-terminal extensions (linkers?)
  6. Rubredoxin-like [57802] (3)
    uperfamily
    1. Rubredoxin [57803] (10)
    2. Desulforedoxin [57813] (3)
    3. Cytochrome c oxidase Subunit F [57818] (1)
      membrane-anchored rubredoxin-like domain
  7. Zn-finger domain of Sec23/24 [82919] (1)
    uperfamily
    1. Zn-finger domain of Sec23/24 [82920] (2)
  8. Ran binding protein zinc finger-like [90209] (1)
    contains CxxxxC-x(n)-CxxC zinc-binding site; similar to the Sec23/24 zinc finger domain
    uperfamily
    1. Ran binding protein zinc finger-like [90210] (6)
  9. Hypothetical protein Ta0289 C-terminal domain [103623] (1)
    contains CxxC-x(n)-CxxxxC zinc-binding site; sequence similarity to NAD-dependent DNA ligase zinc-finger subdomain
    uperfamily
    1. Hypothetical protein Ta0289 C-terminal domain [103624] (1)
  10. Hypothetical protein MTH1184 [57821] (1)
    contains two CXC motifs
    uperfamily
    1. Hypothetical protein MTH1184 [57822] (1)
      possible metal-binding fold
  11. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57825] (1)
    uperfamily
    1. Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain [57826] (2)
  12. Zn-binding ribosomal proteins [57829] (8)
    uperfamily
    1. Ribosomal protein L37ae [57830] (1)
    2. Ribosomal protein L37e [57833] (1)
    3. Ribosomal protein L44e [57836] (1)
    4. Ribosomal protein S27e [90217] (1)
    5. Ribosomal protein L32p [144200] (3)
      Pfam 01783; metal ion-binding site is lost in some members; includes the N-terminal, mainly helical tail
    6. Ribosomal protein L33p [144203] (3)
      Pfam 00471; corresponds structurally and functionally to the ribosomal L44e from eukaryota and archaea; metal ion-binding site is lost in most members
    7. Ribosomal protein L40e [161181] (1)
      Pfam 01020
    8. Ribosomal protein S27a [161184] (1)
      Pfam 01599
  13. RNA polymerase subunits [63393] (2)
    uperfamily
    1. RBP12 subunit of RNA polymerase II [64576] (1)
    2. RpoE2-like [111454] (1)
      Pfam 04035
  14. NOB1 zinc finger-like [144206] (1)
    uperfamily
    1. NOB1 zinc finger-like [144207] (1)
  15. Nop10-like SnoRNP [144210] (1)
    uperfamily
    1. Nucleolar RNA-binding protein Nop10-like [144211] (3)
      Pfam 04135; contains N-terminal zinc-finger domain similar to the insert finger of the Initiation factor eIF2 gamma subunit (scop_pr 75204)
  16. CSL zinc finger [144217] (1)
    uperfamily
    1. CSL zinc finger [144218] (2)
      Pfam 05207
  17. YfgJ-like [161187] (1)
    duplication: consists of two rubredoxin-like (sub)domains, interlocked together
    1. YfgJ-like [161188] (1)
      Pfam 07191, DUF1407
58. Ribosomal protein L36 [57839] (1)
  zinc-bound beta-ribbon motif
  1. Ribosomal protein L36 [57840] (1)
    uperfamily
    1. Ribosomal protein L36 [57841] (3)
59. Zinc-binding domain of translation initiation factor 2 beta [75688] (1)
  zinc-bound beta-ribbon motif
  1. Zinc-binding domain of translation initiation factor 2 beta [75689] (1)
    uperfamily
    1. Zinc-binding domain of translation initiation factor 2 beta [75690] (2)
60. WRKY DNA-binding domain [118289] (1)
  zinc-bound 4-stranded meander beta-sheet, distinct from the beta-ribbon motifs
  1. WRKY DNA-binding domain [118290] (1)
    uperfamily
    1. WRKY DNA-binding domain [118291] (1)
      Pfam 03106
61. B-box zinc-binding domain [57844] (1)
  zinc-bound alpha+beta motif
  1. B-box zinc-binding domain [57845] (1)
    uperfamily
    1. B-box zinc-binding domain [57846] (7)
62. RING/U-box [57849] (1)
  dimetal(zinc)-bound alpha+beta motif; structurally diverse
  1. RING/U-box [57850] (6)
    uperfamily
    1. RING finger domain, C3HC4 [57851] (14)
    2. U-box [90222] (4)
      Associated with multi-ubiquitination; lacks the RING-domain metal ion-binding residues
    3. Variant RING domain [118300] (2)
    4. IBR domain [144228] (1)
      Smart 00647; RING-associated domain
    5. Zf-UBP [161204] (3)
      Pfam 02148
    6. ZZ domain [161211] (3)
      Pfam 00569
63. ArfGap/RecO-like zinc finger [57862] (1)
  zinc-bound alpha+beta motif
  1. ArfGap/RecO-like zinc finger [57863] (2)
    uperfamily
    1. Pyk2-associated protein beta ARF-GAP domain [57864] (1)
    2. RecO C-terminal domain-like [118303] (1)
      C-terminal part of Pfam 02565
64. Metallothionein [57867] (1)
  metal(iron)-bound fold
  duplication: consists of clear structural/sequence repeats
  1. Metallothionein [57868] (1)
    uperfamily
    1. Metallothionein [57869] (11)
65. Zinc domain conserved in yeast copper-regulated transcription factors [57878] (1)
  metal(zinc)-bound alpha+beta fold
  1. Zinc domain conserved in yeast copper-regulated transcription factors [57879] (1)
    uperfamily
    1. Zinc domain conserved in yeast copper-regulated transcription factors [57880] (1)
66. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57883] (1)
  metal(zinc)-bound alpha+beta fold
  1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57884] (1)
    uperfamily
    1. Ada DNA repair protein, N-terminal domain (N-Ada 10) [57885] (1)
67. Cysteine-rich domain [57888] (1)
  dimetal(zinc)-bound alpha+beta fold
  1. Cysteine-rich domain [57889] (3)
    uperfamily
    1. Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) [57890] (6)
      Pfam 00130
    2. TFIIH p44 subunit cysteine-rich domain [57899] (1)
    3. C1-like domain [111463] (1)
      contains Pfam 03107 (C1_2) and Pfam 07649 (C1_3)
68. AN1-like Zinc finger [118309] (1)
  dimetal(zinc)-bound alpha+beta fold; partial similarity to the Cysteine-rich domain fold (scop_cf 57888)
  1. AN1-like Zinc finger [118310] (1)
    uperfamily
    1. AN1-like Zinc finger [118311] (6)
      Pfam 01428
69. HIT/MYND zinc finger-like [144231] (1)
  dimetal(zinc)-bound alpha+beta fold; structural similarity to members of the Cysteine-rich domain fold (scop_cf 57888)
  1. HIT/MYND zinc finger-like [144232] (2)
    uperfamily
    1. MYND zinc finger [144233] (3)
      Pfam 01753
    2. HIT zinc finger [144240] (1)
      Pfam 04438
70. CHY zinc finger-like [161218] (1)
  trimetal-bound fold; integration of HIT/MYND-like and rubredoxin-like fingers
  1. CHY zinc finger-like [161219] (1)
    1. CHY zinc finger [161220] (1)
      Pfam 05495
71. FYVE/PHD zinc finger [57902] (1)
  dimetal(zinc)-bound alpha+beta fold
  1. FYVE/PHD zinc finger [57903] (3)
    uperfamily
    1. FYVE, a phosphatidylinositol-3-phosphate binding domain [57904] (6)
    2. PHD domain [57911] (14)
    3. variant PHD-like domain [118346] (1)
72. Zn-binding domains of ADDBP [57916] (1)
  metal(zinc)-bound alpha+beta fold
  1. Zn-binding domains of ADDBP [57917] (1)
    duplication: contains two Zn-binding domains of similar fold
    uperfamily
    1. Zn-binding domains of ADDBP [57918] (2)
73. Inhibitor of apoptosis (IAP) repeat [57923] (1)
  metal(zinc)-bound alpha+beta fold
  1. Inhibitor of apoptosis (IAP) repeat [57924] (1)
    uperfamily
    1. Inhibitor of apoptosis (IAP) repeat [57925] (7)
74. CCCH zinc finger [90228] (1)
  metal(zinc)-bound alpha+beta fold
  1. CCCH zinc finger [90229] (1)
    uperfamily
    1. CCCH zinc finger [90230] (4)
      C-x8-C-x5-C-x3-H type and similar
75. E6 C-terminal domain-like [161228] (1)
  alpha+beta zinc-binding fold with topological similarity to the fold of lambda cro protein
  1. E6 C-terminal domain-like [161229] (1)
    1. E6 C-terminal domain-like [161230] (1)
      C-terminal part of Pfam 00518
76. E7 C-terminal domain-like [161233] (1)
  alpha+beta zinc-binding domain; beta(2)-alpha(2)
  1. E7 C-terminal domain-like [161234] (1)
    1. E7 C-terminal domain-like [161235] (2)
      C-terminal part of Pfam 00527
77. Zinc finger domain of DNA polymerase-alpha [90233] (1)
  Zn-binding, all-alpha fold
  1. Zinc finger domain of DNA polymerase-alpha [90234] (1)
    some sequence similarity to the TAZ domain Zn-binding sites
    uperfamily
    1. Zinc finger domain of DNA polymerase-alpha [90235] (1)
78. TAZ domain [57932] (1)
  all-alpha fold; Zn-binding sites are in the loops connecting helices
  1. TAZ domain [57933] (1)
    uperfamily
    1. TAZ domain [57934] (2)
79. T-antigen specific domain-like [161239] (1)
  all-alpha zinc-binding domain; there are two zinc ion-binding sites with a common CxCxxC motif but different fourth ligands
  1. T-antigen specific domain-like [161240] (1)
    1. T-antigen specific domain-like [161241] (1)
      Pfam 02380
80. Cysteine-rich DNA binding domain, (DM domain) [82926] (1)
  alpha-helical fold with two Zn-binding sites
  1. Cysteine-rich DNA binding domain, (DM domain) [82927] (1)
    uperfamily
    1. Cysteine-rich DNA binding domain, (DM domain) [82928] (1)
81. Coronavirus NSP10-like [144245] (1)
  binds two zinc ion per subunit; forms a dodecameric shell
  1. Coronavirus NSP10-like [144246] (1)
    uperfamily
    1. Coronavirus NSP10-like [144247] (1)
      partly covered by PfamB 001266
82. Zinc hairpin stack [161244] (1)
  stack of beta-hairpins; in the middle hairpins, there is HCxxCxxC motif, the first and the last residues of which contribute to the zinc-binding site on one side of hairpin, whereas the middle residues contribute to the zinc-binding site on the other side
  1. Zinc hairpin stack [161245] (1)
    1. Zinc hairpin stack [161246] (1)
      PfamB 004087
83. DnaJ/Hsp40 cysteine-rich domain [57937] (1)
  metal(zinc)-bound extended beta-hairpin fold
  1. DnaJ/Hsp40 cysteine-rich domain [57938] (1)
    uperfamily
    1. DnaJ/Hsp40 cysteine-rich domain [57939] (2)
84. HSP33 redox switch-like [118351] (1)
  alpha+beta zinc-binding domain; alpha(2)-beta(2)-alpha
  1. HSP33 redox switch-like [118352] (1)
    uperfamily
    1. HSP33 redox switch-like [118353] (3)
85. CCHHC domain [103636] (1)
  metal(zinc)-bound fold
  1. CCHHC domain [103637] (1)
    uperfamily
    1. CCHHC domain [103638] (1)
86. Sec-C motif [103641] (1)
  metal(zinc)-bound fold
  1. Sec-C motif [103642] (1)
    uperfamily
    1. Sec-C motif [103643] (3)
87. Viral leader polypeptide zinc finger [144250] (1)
  consists of small beta-hairpin with CxH motif and short helix with CxxC motif
  1. Viral leader polypeptide zinc finger [144251] (1)
    uperfamily
    1. Viral leader polypeptide zinc finger [144252] (1)
88. TSP type-3 repeat [103646] (1)
  metal(calcium)-bound fold
  1. TSP type-3 repeat [103647] (1)
    uperfamily
    1. TSP type-3 repeat [103648] (1)
89. Expressed protein At2g23090/F21P24.15 [118358] (1)
  not assigned; partly disordered
  1. Expressed protein At2g23090/F21P24.15 [118359] (1)
    putative zinc-finger protein
    uperfamily
    1. Expressed protein At2g23090/F21P24.15 [118360] (1)
90. Intrinsically disordered proteins [144255] (1)
  not a true fold
  1. TSP9-like [144256] (1)
    uperfamily
    1. TSP9-like [144257] (1)
Coiled coil proteins [57942] (7)
Not a true class
1. Parallel coiled-coil [57943] (34)
  this is not a true fold; includes oligomers of shorter identical helices
  1. Triple coiled coil domain of C-type lectins [57944] (1)
    uperfamily
    1. Triple coiled coil domain of C-type lectins [57945] (5)
  2. Trimerization domain of TRAF [57953] (1)
    uperfamily
    1. Trimerization domain of TRAF [57954] (2)
  3. Leucine zipper domain [57959] (1)
    uperfamily
    1. Leucine zipper domain [57960] (18)
  4. Inovirus (filamentous phage) major coat protein [57987] (1)
    uperfamily
    1. Inovirus (filamentous phage) major coat protein [57988] (8)
  5. Tropomyosin [57997] (1)
    uperfamily
    1. Tropomyosin [57998] (5)
  6. Chicken cartilage matrix protein [58002] (1)
    uperfamily
    1. Chicken cartilage matrix protein [58003] (1)
  7. Assembly domain of cartilage oligomeric matrix protein [58006] (1)
    uperfamily
    1. Assembly domain of cartilage oligomeric matrix protein [58007] (1)
  8. Fibrinogen coiled-coil and central regions [58010] (1)
    uperfamily
    1. Fibrinogen coiled-coil and central regions [58011] (12)
      in the central region two triple coiled-coils are stacked end-to-end and interlock with N-terminal tails
  9. Coiled-coil domain of nucleotide exchange factor GrpE [58014] (1)
    uperfamily
    1. Coiled-coil domain of nucleotide exchange factor GrpE [58015] (1)
  10. Coiled-coil dimerization domain from cortexillin I [58018] (1)
    uperfamily
    1. Coiled-coil dimerization domain from cortexillin I [58019] (1)
  11. XRCC4, C-terminal oligomerization domain [58022] (1)
    uperfamily
    1. XRCC4, C-terminal oligomerization domain [58023] (1)
  12. Intermediate filament protein, coiled coil region [64593] (1)
    uperfamily
    1. Intermediate filament protein, coiled coil region [64594] (2)
      C-terminal part of Pfam 00038
  13. Delta-sleep-inducing peptide immunoreactive peptide [58026] (1)
    uperfamily
    1. Delta-sleep-inducing peptide immunoreactive peptide [58027] (1)
  14. Rotavirus nonstructural proteins [58030] (2)
    not a true superfamily
    uperfamily
    1. NSP4 oligomerization domain [58031] (1)
    2. NSP3 C-terminal domain, NS34 [75699] (1)
  15. Multimerization domain of the phosphoprotein from sendai virus [58034] (1)
    uperfamily
    1. Multimerization domain of the phosphoprotein from sendai virus [58035] (1)
  16. SNARE fusion complex [58038] (1)
    tetrameric parallel coiled coil
    uperfamily
    1. SNARE fusion complex [58039] (18)
  17. Outer membrane lipoprotein [58042] (1)
    uperfamily
    1. Outer membrane lipoprotein [58043] (1)
  18. Fibritin [58046] (1)
    uperfamily
    1. Fibritin [58047] (1)
  19. N-terminal coiled coil domain from apc [58050] (1)
    uperfamily
    1. N-terminal coiled coil domain from apc [58051] (1)
  20. Tetrabrachion [58054] (1)
    uperfamily
    1. Tetrabrachion [58055] (1)
  21. Eea1 homodimerisation domain [69979] (1)
    uperfamily
    1. Eea1 homodimerisation domain [69980] (1)
  22. Mitotic arrest deficient-like 1, Mad1 [75704] (1)
    uperfamily
    1. Mitotic arrest deficient-like 1, Mad1 [75705] (1)
  23. Dimerization motif of sir4 [90242] (1)
    uperfamily
    1. Dimerization motif of sir4 [90243] (1)
  24. Head morphogenesis protein gp7 [90246] (1)
    uperfamily
    1. Head morphogenesis protein gp7 [90247] (1)
  25. Troponin coil-coiled subunits [90250] (2)
    form heterodimeric coiled coil
    uperfamily
    1. Troponin T [90251] (2)
    2. Troponin I [90254] (2)
  26. Myosin rod fragments [90257] (1)
    uperfamily
    1. Myosin rod fragments [90258] (2)
  27. G protein-binding domain [103652] (2)
    uperfamily
    1. RhoA-binding domain [103653] (2)
    2. Rabaptin-5 [118367] (1)
  28. Geminin coiled-coil domain [111469] (1)
    uperfamily
    1. Geminin coiled-coil domain [111470] (2)
  29. Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain [118370] (1)
    tetrameric parallel coiled coil with a right-handed twist
    uperfamily
    1. Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain [118371] (1)
  30. MPN010-like [144266] (1)
    segmented trimeric coiled coil
    uperfamily
    1. MPN010-like [144267] (1)
      Pfam 01519; DUF16
  31. Eferin C-derminal domain-like [144270] (1)
    uperfamily
    1. Eferin C-derminal domain-like [144271] (2)
      contains PfamB 042332, PfamB 026102
  32. Heterotrimerisation domain of extracellular hemoglobin linker subunits [144276] (1)
    uperfamily
    1. Heterotrimerisation domain of extracellular hemoglobin linker subunits [144277] (3)
  33. Sec2 N-terminal region [144284] (1)
    dimeric coiled coil
    uperfamily
    1. Sec2 N-terminal region [144285] (1)
  34. RILP dimerisation region [161256] (1)
    1. RILP dimerisation region [161257] (1)
2. Tetramerization domain of the Mnt repressor [58058] (1)
  1. Tetramerization domain of the Mnt repressor [58059] (1)
    tetrameric antiparallel bundle with a right-handed twist
    uperfamily
    1. Tetramerization domain of the Mnt repressor [58060] (1)
3. Stalk segment of viral fusion proteins [58063] (3)
  core: trimeric coiled coil
  1. Influenza hemagglutinin (stalk) [58064] (1)
    uperfamily
    1. Influenza hemagglutinin (stalk) [58065] (2)
  2. Virus ectodomain [58069] (1)
    uperfamily
    1. Virus ectodomain [58070] (12)
  3. Coronavirus S2 glycoprotein [111474] (1)
    uperfamily
    1. Coronavirus S2 glycoprotein [111475] (2)
      Pfam 01601
4. Antiparallel coiled-coil [58086] (17)
  this is not a true fold; contains at least two very long antiparallel helices
  1. Variant surface glycoprotein (N-terminal domain) [58087] (1)
    uperfamily
    1. Variant surface glycoprotein (N-terminal domain) [58088] (1)
  2. Clostridium neurotoxins, "coiled-coil" domain [58091] (1)
    uperfamily
    1. Clostridium neurotoxins, "coiled-coil" domain [58092] (2)
  3. Colicin Ia, N-terminal domain [58096] (1)
    uperfamily
    1. Colicin Ia, N-terminal domain [58097] (1)
  4. Colicin E3 receptor domain [69985] (1)
    uperfamily
    1. Colicin E3 receptor domain [69986] (1)
  5. Bacterial hemolysins [58100] (2)
    uperfamily
    1. Hemolysin E (HlyE, ClyA, SheA) [58101] (1)
    2. HBL-like [161263] (1)
      Pfam 05791; Bacillus haemolytic enterotoxin
  6. Methyl-accepting chemotaxis protein (MCP) signaling domain [58104] (1)
    uperfamily
    1. Methyl-accepting chemotaxis protein (MCP) signaling domain [58105] (2)
  7. Oligomerization domain of hepatitis delta antigen [58108] (1)
    uperfamily
    1. Oligomerization domain of hepatitis delta antigen [58109] (1)
  8. F1 ATPase inhibitor, IF1, C-terminal domain [64602] (1)
    uperfamily
    1. F1 ATPase inhibitor, IF1, C-terminal domain [64603] (1)
  9. Chemotaxis phosphatase CheZ [75708] (1)
    dimerizes with the formation of a 4-helical bundle
    uperfamily
    1. Chemotaxis phosphatase CheZ [75709] (1)
  10. Rad50 coiled-coil Zn hook [75712] (1)
    dimerizes via a CxxC motif in the loop, zinc-hook
    uperfamily
    1. Rad50 coiled-coil Zn hook [75713] (1)
  11. C-terminal domain of PLC-beta [69989] (1)
    left-handed antiparallel coiled-coil; dimerizes with the formation of a 4-helical bundle
    uperfamily
    1. C-terminal domain of PLC-beta [69990] (1)
  12. Tumor suppressor gene product Apc [82931] (1)
    uperfamily
    1. Tumor suppressor gene product Apc [82932] (1)
  13. Proline/betaine transporter ProP, C-terminal cytoplasmic domain [103661] (1)
    uperfamily
    1. Proline/betaine transporter ProP, C-terminal cytoplasmic domain [103662] (1)
  14. Fzo-like conserved region [111479] (1)
    antiparallel coiled-coil in the crystals
    uperfamily
    1. Fzo-like conserved region [111480] (1)
      Pfam 04799
  15. occludin/ELL-like [144292] (1)
    antiparallel hairpin with a kinked second helix; similar to the N-terminal structure of the thermostable carboxypeptidase 1 (scop_pr 82731)
    uperfamily
    1. Occludin/ELL domain [144293] (1)
      Pfam 07303
  16. Gam-like [161266] (1)
    homodimeric fold with a ring-like structure formed by kinked coiled-coil and a beta-ribboon, interrupted by small helical insertions
    1. Gam-like [161267] (1)
      Pfam 07352; Bacteriophage Mu Gam-like protein
  17. PspA lactotransferrin-binding region [161270] (1)
    3 helices, the middle one is longer than the two others
    1. PspA lactotransferrin-binding region [161271] (1)
5. Apolipoprotein A-I [58112] (1)
  tetrameric antiparallel coiled coil, closed in a circuit
  1. Apolipoprotein A-I [58113] (1)
    uperfamily
    1. Apolipoprotein A-I [58114] (1)
6. Apolipoprotein A-II [82935] (1)
  segmented tetrameric parallel coiled coil
  1. Apolipoprotein A-II [82936] (1)
    uperfamily
    1. Apolipoprotein A-II [82937] (1)
7. Synuclein [118374] (1)
  1. Synuclein [118375] (1)
    uperfamily
    1. Synuclein [118376] (1)
      Pfam 01387
Low resolution protein structures [58117] (26)
Not a true class
1. Ribosome and ribosomal fragments [58118] (1)
  1. Ribosome and ribosomal fragments [58119] (3)
    uperfamily
    1. Ribosome complexes [58120] (9)
    2. Large subunit [58124] (6)
    3. Small subunit [58132] (1)
2. Collagen fibre [144296] (1)
  1. Collagen fibre [144297] (1)
    uperfamily
    1. Collagen fibre [144298] (1)
3. Fatty acid synthase [144301] (1)
  1. Fatty acid synthase [144302] (1)
    uperfamily
    1. Fatty acid syntase [144303] (2)
4. Helicase [58135] (1)
  1. Helicase [58136] (1)
    uperfamily
    1. Helicase [58137] (1)
5. ATP synthase [58140] (1)
  1. ATP synthase [58141] (1)
    uperfamily
    1. ATP synthase [58142] (3)
6. Membrane ion ATPase [82940] (1)
  1. Membrane ion ATPase [82941] (1)
    uperfamily
    1. Membrane ion ATPase [82942] (1)
7. Multidrug resistance ABC transporter [64606] (1)
  1. Multidrug resistance ABC transporter [64607] (1)
    uperfamily
    1. Multidrug resistance ABC transporter [64608] (1)
8. Electron transport chains [58146] (1)
  1. Electron transport chains [58147] (1)
    uperfamily
    1. Electron transport chains [58148] (4)
      not a true family
9. Photosystems [58155] (1)
  1. Photosystems [58156] (1)
    uperfamily
    1. Photosystems [58157] (6)
      not a true family
10. Viruses and virus-receptor complexes [58162] (1)
  1. Viruses and virus-receptor complexes [58163] (1)
    uperfamily
    1. Viruses and virus-receptor complexes [58164] (12)
11. Reovirus components [58175] (1)
  1. Reovirus components [58176] (1)
    uperfamily
    1. Reovirus components [58177] (3)
12. Virus envelope proteins [75718] (1)
  1. Virus envelope proteins [75719] (1)
    uperfamily
    1. Virus envelope proteins [75720] (2)
13. Bacteriophage HK97 procapsid (prohead II) [64611] (1)
  1. Bacteriophage HK97 procapsid (prohead II) [64612] (1)
    uperfamily
    1. Bacteriophage HK97 procapsid (prohead II) [64613] (1)
14. Bacteriophage T4 3D cryo-EM reconstruction [103674] (1)
  1. Bacteriophage T4 3D cryo-EM reconstruction [103675] (1)
    uperfamily
    1. Bacteriophage T4 3D cryo-EM reconstruction [103676] (1)
15. RNA polymerase [58180] (1)
  1. RNA polymerase [58181] (1)
    uperfamily
    1. RNA polymerase [58182] (3)
16. Blood clotting [58187] (1)
  1. Blood clotting [58188] (1)
    uperfamily
    1. Blood clotting [58189] (2)
17. Microtubule complexes [58193] (1)
  1. Microtubule complexes [58194] (1)
    uperfamily
    1. Microtubule complexes [58195] (3)
18. Muscle protein complexes [64616] (1)
  1. Muscle protein complexes [64617] (1)
    uperfamily
    1. Muscle protein complexes [64618] (3)
19. Ep-cadherin [103681] (1)
  1. Ep-cadherin [103682] (1)
    uperfamily
    1. Ep-cadherin [103683] (1)
20. Transferrin receptor-transferrin complex [103686] (1)
  1. Transferrin receptor-transferrin complex [103687] (1)
    uperfamily
    1. Transferrin receptor-transferrin complex [103688] (1)
21. Signal recognition particle (SRP) complex [103691] (1)
  1. Signal recognition particle (SRP) complex [103692] (1)
    uperfamily
    1. Signal recognition particle (SRP) complex [103693] (1)
22. GroE chaperon [69998] (1)
  1. GroE chaperon [69999] (1)
    uperfamily
    1. GroE chaperon [70000] (1)
23. clathrin assemblies [111484] (1)
  1. clathrin assemblies [111485] (1)
    uperfamily
    1. clathrin assemblies [111486] (3)
24. anthrax toxin protective antigen-receptor complex [111489] (1)
  1. anthrax toxin protective antigen-receptor complex [111490] (1)
    uperfamily
    1. anthrax toxin protective antigen-receptor complex [111491] (1)
25. Computational models partly based on experimental data [58198] (1)
  1. Computational models partly based on experimental data [58199] (1)
    uperfamily
    1. Computational models partly based on experimental data [58200] (6)
      this is not a true family
26. Proteins of incorrect, partial and unknown sequence [58207] (1)
  1. Proteins of incorrect, partial and unknown sequence [58208] (1)
    uperfamily
    1. Proteins of incorrect, partial and unknown sequence [58209] (12)
Peptides [58231] (121)
Peptides and fragments. Not a true class
1. Membrane ion channel-forming peptide antibiotics containing D-aminoacids [58232] (1)
  1. Membrane ion channel-forming peptide antibiotics containing D-aminoacids [58233] (2)
    uperfamily
    1. Gramicidin [58234] (1)
    2. Peptaibol [58237] (8)
2. Lantibiotic peptides [58243] (1)
  peptide antibiotic
  1. Lantibiotic peptides [58244] (3)
    uperfamily
    1. Actagardine [58245] (1)
    2. Mersacidin [58248] (1)
    3. Nisin [111494] (1)
3. Leucocin-like bacteriocin [100898] (1)
  consists of a conserved, disulfide-containing N-terminal region (forming a beta-sheet) and a C-terminal helix
  1. Leucocin-like bacteriocin [100899] (1)
    uperfamily
    1. Leucocin-like bacteriocin [100900] (3)
4. Antimicrobial beta-hairpin [58251] (1)
  contains beta-hairpin crosslinked by disulfide bridge(s)
  1. Antimicrobial beta-hairpin [58252] (8)
    not a true superfamily
    uperfamily
    1. Insect defense peptide thanatin [58256] (1)
    2. Androctonin [58259] (1)
    3. Gomesin [75725] (1)
    4. Tachyplesin I [82958] (2)
    5. theta defensin-like [58262] (2)
    6. Lactoferricin B (lfcinb) [58265] (1)
    7. Hepcidin [82961] (2)
    8. Cyclic trypsin inhibitor STFI-1 [90265] (1)
5. Antimicrobial helix [58268] (1)
  antibiotic peptide
  1. Antimicrobial helix [58269] (5)
    not a true superfamily
    uperfamily
    1. Magainin [58270] (2)
    2. Moricin [75728] (2)
    3. Tachykinin peptides [82964] (3)
    4. Cytotoxic linear peptide IsCT [118386] (1)
    5. Distinctin [144312] (2)
6. Macrocyclic bacteriocins [58278] (1)
  macrocyclic antimicrobial peptide; bacteriocin
  1. Macrocyclic bacteriocins [58279] (2)
    uperfamily
    1. Microcin J25 [58280] (1)
    2. Subtilosin A [111498] (1)
      unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons
7. Peptide hormones [58283] (1)
  contains one alpha-helix
  1. Peptide hormones [58284] (1)
    this is not a true superfamily
    uperfamily
    1. Peptide hormones [58285] (27)
8. Angiotensin [90269] (1)
  1. Angiotensin [90270] (1)
    uperfamily
    1. Angiotensin [90271] (2)
9. delta toxin-like [58307] (3)
  single alpha helix
  1. delta-Toxin [58308] (1)
    uperfamily
    1. delta-Toxin [58309] (1)
  2. Antimicrobial peptide HP(2-20) [90276] (1)
    uperfamily
    1. Antimicrobial peptide HP(2-20) [90277] (1)
  3. Anticancer peptides [118391] (1)
    uperfamily
    1. Anticancer peptides [118392] (1)
10. PSP1-like [58312] (1)
  1. PSP1-like [58313] (1)
    uperfamily
    1. PSP1-like [58314] (8)
11. Arg-rich RNA binding peptides [58321] (7)
  1. 30S ribosomal protein THX [58322] (1)
    uperfamily
    1. 30S ribosomal protein THX [58323] (1)
  2. HIV-1 REV fragments [58326] (1)
    uperfamily
    1. HIV-1 REV fragments [58327] (1)
  3. RSG-1.2 peptide [58330] (1)
    uperfamily
    1. RSG-1.2 peptide [58331] (1)
  4. TAT peptides [58334] (1)
    uperfamily
    1. TAT peptides [58335] (2)
  5. Box B RNA-binding N peptide [58339] (1)
    uperfamily
    1. Box B RNA-binding N peptide [58340] (4)
  6. HTLV-1 peptide [58344] (1)
    uperfamily
    1. HTLV-1 peptide [58345] (1)
  7. Ilarvirus coat protein N-terminal fragment [118396] (1)
    uperfamily
    1. Ilarvirus coat protein N-terminal fragment [118397] (1)
      N-terminal part of Pfam 01787; RNA-binding helix
12. DNA-binding domains of HMG-I(Y) [58348] (1)
  1. DNA-binding domains of HMG-I(Y) [58349] (1)
    uperfamily
    1. DNA-binding domains of HMG-I(Y) [58350] (1)
13. VPR protein fragments [58353] (1)
  1. VPR protein fragments [58354] (1)
    uperfamily
    1. VPR protein fragments [58355] (1)
14. Inactivation gate of potassium and sodium channels [58358] (1)
  1. Inactivation gate of potassium and sodium channels [58359] (1)
    uperfamily
    1. Inactivation gate of potassium and sodium channels [58360] (5)
      it is not a true family
15. Coagulation factor VIII, membrane-binding peptide [58368] (1)
  1. Coagulation factor VIII, membrane-binding peptide [58369] (1)
    uperfamily
    1. Coagulation factor VIII, membrane-binding peptide [58370] (1)
16. Phosphocholine cytidylyltransferase membrane-binding peptides [58373] (1)
  1. Phosphocholine cytidylyltransferase membrane-binding peptides [58374] (1)
    uperfamily
    1. Phosphocholine cytidylyltransferase membrane-binding peptides [58375] (1)
17. Parathyroid hormone fragments (residues between 1 and 39) [58378] (1)
  1. Parathyroid hormone fragments (residues between 1 and 39) [58379] (1)
    uperfamily
    1. Parathyroid hormone fragments (residues between 1 and 39) [58380] (3)
18. Corticotropin releasing hormone [58384] (1)
  1. Corticotropin releasing hormone [58385] (1)
    uperfamily
    1. Corticotropin releasing hormone [58386] (3)
19. Liposaccharide-binding protein CAP18 (residues 106-137) [58389] (1)
  1. Liposaccharide-binding protein CAP18 (residues 106-137) [58390] (1)
    uperfamily
    1. Liposaccharide-binding protein CAP18 (residues 106-137) [58391] (1)
20. Polymorphic antigen SPAM-H1 (residues 90-127) [58394] (1)
  1. Polymorphic antigen SPAM-H1 (residues 90-127) [58395] (1)
    uperfamily
    1. Polymorphic antigen SPAM-H1 (residues 90-127) [58396] (1)
21. Insect toxins [58399] (1)
  1. Insect toxins [58400] (2)
    uperfamily
    1. Mellitin-like toxins [58401] (2)
    2. Poneratoxin (Pac-Tx) [103712] (1)
22. Tertiapin [58404] (1)
  small disulfide-rich peptide
  1. Tertiapin [58405] (1)
    uperfamily
    1. Tertiapin [58406] (1)
23. Antifreeze polypeptide HPLC-6 [58409] (1)
  1. Antifreeze polypeptide HPLC-6 [58410] (1)
    uperfamily
    1. Antifreeze polypeptide HPLC-6 [58411] (1)
24. Troponin I fragments [58414] (1)
  1. Troponin I fragments [58415] (1)
    uperfamily
    1. Troponin I fragments [58416] (3)
25. Pilin fragments [58420] (1)
  1. Pilin fragments [58421] (1)
    uperfamily
    1. Pilin fragments [58422] (3)
26. RP71935 [58427] (1)
  1. RP71935 [58428] (1)
    uperfamily
    1. RP71935 [58429] (1)
27. Atrial natriuretic peptide [58432] (1)
  1. Atrial natriuretic peptide [58433] (1)
    uperfamily
    1. Atrial natriuretic peptide [58434] (1)
28. Compstatin [58437] (1)
  1. Compstatin [58438] (1)
    uperfamily
    1. Compstatin [58439] (1)
29. Membrane-bound antimicrobial peptides [58442] (1)
  1. Membrane-bound antimicrobial peptides [58443] (1)
    uperfamily
    1. Membrane-bound antimicrobial peptides [58444] (2)
      no or little secondary structure
30. Endothelin-like [58449] (1)
  small disulfide-rich
  1. Endothelin-like [58450] (1)
    uperfamily
    1. Endothelin-like [58451] (3)
31. Heat-stable enterotoxin (HSE) [58457] (1)
  1. Heat-stable enterotoxin (HSE) [58458] (1)
    uperfamily
    1. Heat-stable enterotoxin (HSE) [58459] (2)
      short disulfide-bound peptide
32. Conotoxins [58464] (1)
  disulfide-rich fold
  1. Conotoxins [58465] (7)
    all apart omega class; it is not a true superfamily
    uperfamily
    1. mu-conotoxin [58466] (4)
    2. alpha-conotoxin [58471] (11)
      13-16 residue peptide with 2 disulfides
    3. Alpha-a-conotoxin [58488] (2)
    4. psi-conotoxin [58491] (2)
    5. Conotoxin tiA [75733] (1)
    6. Conotoxin mrIB [75736] (1)
    7. Delta-conotoxin [103723] (1)
33. Conantokin [58494] (1)
  1. Conantokin [58495] (2)
    gamma-carboxyglutamic acid (GLA)-rich peptide; active conformation may be stabilized by metal ions
    uperfamily
    1. Conantokin G (conatoxin G) [58496] (1)
    2. Conantokin-T [58499] (1)
34. Contryphan-R [58502] (1)
  1. Contryphan-R [58503] (1)
    uperfamily
    1. Contryphan-R [58504] (1)
35. Kappa-hefutoxin-like [58507] (2)
  hairpin of two short helices crosslinked with two disulfides
  1. Immunodominant region of protein G of BRSV [58508] (1)
    uperfamily
    1. Immunodominant region of protein G of BRSV [58509] (2)
  2. Potassium channel toxins [75739] (1)
    uperfamily
    1. Potassium channel toxins [75740] (1)
36. Penaeidin-3a [103726] (1)
  1. Penaeidin-3a [103727] (1)
    uperfamily
    1. Penaeidin-3a [103728] (1)
37. Bradykinin [58512] (1)
  1. Bradykinin [58513] (1)
    uperfamily
    1. Bradykinin [58514] (2)
38. Transmembrane helical fragments [58517] (1)
  1. Transmembrane helical fragments [58518] (1)
    uperfamily
    1. Transmembrane helical fragments [58519] (32)
      the member of this family may be not related
39. Topogenic peptides [58555] (4)
  1. Ferredoxin chloroplastic transit peptide [58556] (1)
    uperfamily
    1. Ferredoxin chloroplastic transit peptide [58557] (1)
  2. Vacuolar targeting peptide from NA-PROPI (residues 29-54) [58560] (1)
    uperfamily
    1. Vacuolar targeting peptide from NA-PROPI (residues 29-54) [58561] (1)
  3. Microcin leader peptide [58564] (1)
    uperfamily
    1. Microcin leader peptide [58565] (1)
  4. ATP synthase beta chain, mitochondrial prepeptide [103737] (1)
    uperfamily
    1. ATP synthase beta chain, mitochondrial prepeptide [103738] (1)
40. Phospholamban fragments [58568] (1)
  1. Phospholamban fragments [58569] (1)
    uperfamily
    1. Phospholamban fragments [58570] (3)
41. Influenza hemagglutinin fragments [64631] (1)
  1. Influenza hemagglutinin fragments [64632] (1)
    uperfamily
    1. Influenza hemagglutinin fragments [64633] (2)
42. Fragments of bowman-birk inhibitor [58574] (1)
  1. Fragments of bowman-birk inhibitor [58575] (1)
    uperfamily
    1. Fragments of bowman-birk inhibitor [58576] (1)
43. Fragments of apolipoproteins [58579] (1)
  1. Fragments of apolipoproteins [58580] (1)
    uperfamily
    1. Fragments of apolipoproteins [58581] (10)
44. Transactivation protein TAT [58593] (1)
  1. Transactivation protein TAT [58594] (1)
    uperfamily
    1. Transactivation protein TAT [58595] (2)
45. Proline pipe [58599] (1)
  1. Proline pipe [58600] (1)
    uperfamily
    1. Proline pipe [58601] (1)
46. Amyloid peptides [58604] (1)
  1. Amyloid peptides [58605] (1)
    uperfamily
    1. Amyloid peptides [58606] (5)
47. Gelsolin fragment (residues 150-169) [58609] (1)
  1. Gelsolin fragment (residues 150-169) [58610] (1)
    uperfamily
    1. Gelsolin fragment (residues 150-169) [58611] (1)
48. Acetylcholine receptor fragment (residues alpha 67-76) [58614] (1)
  1. Acetylcholine receptor fragment (residues alpha 67-76) [58615] (1)
    uperfamily
    1. Acetylcholine receptor fragment (residues alpha 67-76) [58616] (1)
49. Thrombomodulin EGF domain fragment (residues 409-426) [58619] (1)
  1. Thrombomodulin EGF domain fragment (residues 409-426) [58620] (1)
    uperfamily
    1. Thrombomodulin EGF domain fragment (residues 409-426) [58621] (1)
50. C-terminal fragment of thermolysin [63387] (1)
  1. C-terminal fragment of thermolysin [63388] (1)
    uperfamily
    1. C-terminal fragment of thermolysin [63389] (1)
51. Capsid protein major homology region peptide analog [58629] (1)
  1. Capsid protein major homology region peptide analog [58630] (1)
    uperfamily
    1. Capsid protein major homology region peptide analog [58631] (2)
52. CD4 and CD8 receptor regions [58635] (1)
  1. CD4 and CD8 receptor regions [58636] (1)
    uperfamily
    1. CD4 and CD8 receptor regions [58637] (2)
      interact with proto-oncogene tyrosine-protein kinase lck
53. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103748] (1)
  1. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103749] (1)
    uperfamily
    1. Proto-oncogene tyrosine-protein kinase lck CD4/CD8 interacting region [103750] (1)
54. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58640] (1)
  1. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58641] (1)
    uperfamily
    1. Heparin binding site of non collagenous domain I (nc1) of collagen facit xiv [58642] (1)
55. GroES fragments [58645] (1)
  1. GroES fragments [58646] (1)
    uperfamily
    1. GroES fragments [58647] (2)
56. cAMP and cGMP phosphodiesterase (PDE) fragments [58650] (1)
  1. cAMP and cGMP phosphodiesterase (PDE) fragments [58651] (1)
    uperfamily
    1. cAMP and cGMP phosphodiesterase (PDE) fragments [58652] (2)
      not a true family
57. HIV-1 Nef protein fragments [58657] (1)
  1. HIV-1 Nef protein fragments [58658] (1)
    uperfamily
    1. HIV-1 Nef protein fragments [58659] (1)
58. HIV-1 envelope gp120 protein fragments [58662] (1)
  1. HIV-1 envelope gp120 protein fragments [58663] (1)
    uperfamily
    1. HIV-1 envelope gp120 protein fragments [58664] (2)
59. HIV-1 gp41 fragments [70010] (1)
  1. HIV-1 gp41 fragments [70011] (1)
    uperfamily
    1. HIV-1 gp41 fragments [70012] (4)
60. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58667] (1)
  1. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58668] (1)
    uperfamily
    1. Hepatitis C virus N-terminal capsid protein fragment 2-45 [58669] (1)
61. P27(KIP1) fragment 22-106 [58672] (1)
  1. P27(KIP1) fragment 22-106 [58673] (1)
    uperfamily
    1. P27(KIP1) fragment 22-106 [58674] (1)
62. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58677] (1)
  1. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58678] (1)
    uperfamily
    1. Transducin alpha-1 subunit rhodopsin binding domain (res. 340-350) [58679] (1)
63. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90290] (1)
  1. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90291] (1)
    uperfamily
    1. Transducin gamma-t1 subunit rhodopsin bound fragment (res. 60-71) [90292] (1)
64. alpha-lactalbumin peptide model [58682] (1)
  1. alpha-lactalbumin peptide model [58683] (1)
    uperfamily
    1. alpha-lactalbumin peptide model [58684] (1)
65. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58687] (1)
  1. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58688] (1)
    uperfamily
    1. Coat protein-binding domain of bacteriophage P22 scaffolding protein [58689] (1)
66. Immunoreceptor tyrosine kinase activation motif, ITAM [58692] (1)
  1. Immunoreceptor tyrosine kinase activation motif, ITAM [58693] (1)
    uperfamily
    1. Immunoreceptor tyrosine kinase activation motif, ITAM [58694] (1)
67. Integrin fragments [58697] (1)
  1. Integrin fragments [58698] (1)
    uperfamily
    1. Integrin fragments [58699] (3)
68. Human glutathione reductase (HGR) inhibitor [58702] (1)
  1. Human glutathione reductase (HGR) inhibitor [58703] (1)
    uperfamily
    1. Human glutathione reductase (HGR) inhibitor [58704] (1)
69. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58707] (1)
  1. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58708] (1)
    uperfamily
    1. Small subunit C-terminal inhibitory peptide of ribonucleotide reductase [58709] (1)
70. Histone H3 C-terminal fragment 130-135 [58712] (1)
  1. Histone H3 C-terminal fragment 130-135 [58713] (1)
    uperfamily
    1. Histone H3 C-terminal fragment 130-135 [58714] (1)
71. Smad-binding domain of Sara [58717] (1)
  1. Smad-binding domain of Sara [58718] (1)
    uperfamily
    1. Smad-binding domain of Sara [58719] (1)
72. Transactivation domain [81275] (1)
  1. Transactivation domain [74800] (1)
    uperfamily
    1. Transactivation domain [74801] (2)
73. Nuclear receptor coactivator Src-1 [100901] (1)
  1. Nuclear receptor coactivator Src-1 [48682] (1)
    uperfamily
    1. Nuclear receptor coactivator Src-1 [48683] (1)
74. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90297] (1)
  1. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90298] (1)
    uperfamily
    1. TBP-binding domain of the transcription factor IIIb Brf1 subunit [90299] (1)
75. BRCA2 BRC4 repeat [82985] (1)
  1. BRCA2 BRC4 repeat [82986] (1)
    uperfamily
    1. BRCA2 BRC4 repeat [82987] (1)
76. Peptide derived from p-21 activated kinase [58722] (1)
  1. Peptide derived from p-21 activated kinase [58723] (1)
    uperfamily
    1. Peptide derived from p-21 activated kinase [58724] (2)
77. pak1 autoregulatory domain [58728] (1)
  1. pak1 autoregulatory domain [58729] (1)
    uperfamily
    1. pak1 autoregulatory domain [58730] (1)
78. Translocated intimin receptor (tir) intimin-binding domain [58733] (1)
  1. Translocated intimin receptor (tir) intimin-binding domain [58734] (1)
    uperfamily
    1. Translocated intimin receptor (tir) intimin-binding domain [58735] (1)
79. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58738] (1)
  1. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58739] (1)
    uperfamily
    1. Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor) [58740] (4)
80. Tumor suppressor p53 fragments [58743] (1)
  1. Tumor suppressor p53 fragments [58744] (1)
    uperfamily
    1. Tumor suppressor p53 fragments [58745] (2)
81. FxFG nucleoporin repeats [58748] (1)
  1. FxFG nucleoporin repeats [58749] (1)
    uperfamily
    1. FxFG nucleoporin repeats [58750] (1)
82. beta-Catenine bound non-globular protein regions [58753] (1)
  1. beta-Catenine bound non-globular protein regions [58754] (1)
    uperfamily
    1. beta-Catenine bound non-globular protein regions [58755] (3)
83. Synaptobrevin-II fragments [58758] (1)
  1. Synaptobrevin-II fragments [58759] (1)
    uperfamily
    1. Synaptobrevin-II fragments [58760] (1)
84. VMIP-II fragment [58763] (1)
  1. VMIP-II fragment [58764] (1)
    uperfamily
    1. VMIP-II fragment [58765] (1)
85. Papillomavirus e6-interacting peptide of e6ap [58768] (1)
  1. Papillomavirus e6-interacting peptide of e6ap [58769] (1)
    uperfamily
    1. Papillomavirus e6-interacting peptide of e6ap [58770] (1)
86. Isolated insulin B-chain [58773] (1)
  1. Isolated insulin B-chain [58774] (1)
    uperfamily
    1. Isolated insulin B-chain [58775] (3)
87. N-terminal hairpin of ubiquitin (residues 1-17) [58778] (1)
  1. N-terminal hairpin of ubiquitin (residues 1-17) [58779] (1)
    uperfamily
    1. N-terminal hairpin of ubiquitin (residues 1-17) [58780] (1)
88. alpha-helical hairpin of p8mtcp1 [58783] (1)
  1. alpha-helical hairpin of p8mtcp1 [58784] (1)
    uperfamily
    1. alpha-helical hairpin of p8mtcp1 [58785] (1)
89. Syndecan-4 cytoplasmic domain [64638] (1)
  1. Syndecan-4 cytoplasmic domain [64639] (1)
    uperfamily
    1. Syndecan-4 cytoplasmic domain [64640] (1)
90. Actin-binding peptides [70017] (1)
  1. Actin-binding peptides [70018] (1)
    uperfamily
    1. Actin-binding peptides [70019] (2)
91. Pituitary adenylate cyclase activating polypeptide, pacap21 [64643] (1)
  1. Pituitary adenylate cyclase activating polypeptide, pacap21 [64644] (1)
    uperfamily
    1. Pituitary adenylate cyclase activating polypeptide, pacap21 [64645] (1)
92. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70022] (1)
  1. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70023] (1)
    uperfamily
    1. Rack1 interaction site of the CAMP-specific phosphodiesterase pde4d5. [70024] (1)
93. Prepeptide of 5-ALAS [70027] (1)
  1. Prepeptide of 5-ALAS [70028] (1)
    uperfamily
    1. Prepeptide of 5-ALAS [70029] (1)
94. Cholecystokinin receptor fragments [64648] (1)
  1. Cholecystokinin receptor fragments [64649] (1)
    uperfamily
    1. Cholecystokinin receptor fragments [64650] (2)
95. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70032] (1)
  1. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70033] (1)
    uperfamily
    1. the cytoplasmic N-terminus of the bk beta-subunit kcnmb2 [70034] (1)
96. Trypsin inhibitor SFTIf-1 [64653] (1)
  1. Trypsin inhibitor SFTIf-1 [64654] (1)
    uperfamily
    1. Trypsin inhibitor SFTIf-1 [64655] (1)
97. Prion protein fragments [70037] (1)
  1. Prion protein fragments [70038] (1)
    uperfamily
    1. Prion protein fragments [70039] (3)
98. Tumor suppressor protein p19-ARF fragment [70042] (1)
  1. Tumor suppressor protein p19-ARF fragment [70043] (1)
    uperfamily
    1. Tumor suppressor protein p19-ARF fragment [70044] (1)
99. Antennapedia homeodomain fragments [70047] (1)
  1. Antennapedia homeodomain fragments [70048] (1)
    uperfamily
    1. Antennapedia homeodomain fragments [70049] (1)
100. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75751] (1)
  1. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75752] (1)
    uperfamily
    1. Sheep myeloid antimicrobial peptide SMAP29 based peptides [75753] (1)
101. alpha-2a adrenergic receptor pepride t3-i2 [75756] (1)
  1. alpha-2a adrenergic receptor pepride t3-i2 [75757] (1)
    uperfamily
    1. alpha-2a adrenergic receptor pepride t3-i2 [75758] (1)
102. Catestatin fragment from chromogranin A [75761] (1)
  1. Catestatin fragment from chromogranin A [75762] (1)
    uperfamily
    1. Catestatin fragment from chromogranin A [75763] (1)
103. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82992] (1)
  1. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82993] (1)
    uperfamily
    1. Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide [82994] (1)
104. N-terminal fragment of gastric H/K-ATPase [82997] (1)
  1. N-terminal fragment of gastric H/K-ATPase [82998] (1)
    uperfamily
    1. N-terminal fragment of gastric H/K-ATPase [82999] (1)
105. Barstar fragment [83002] (1)
  1. Barstar fragment [83003] (1)
    uperfamily
    1. Barstar fragment [83004] (1)
106. Cannabinoid receptor 1 (CB1) fragment [83007] (1)
  1. Cannabinoid receptor 1 (CB1) fragment [83008] (1)
    uperfamily
    1. Cannabinoid receptor 1 (CB1) fragment [83009] (1)
107. Ribosomal protein L10 [64658] (1)
  1. Ribosomal protein L10 [64659] (1)
    uperfamily
    1. Ribosomal protein L10 [64660] (1)
108. Ubiquitin interacting motif (UIM) [90302] (1)
  1. Ubiquitin interacting motif (UIM) [90303] (1)
    uperfamily
    1. Ubiquitin interacting motif (UIM) [90304] (2)
      amphipathic helix
109. Metal-binding peptide from MerP [103758] (1)
  1. Metal-binding peptide from MerP [103759] (1)
    uperfamily
    1. Metal-binding peptide from MerP [103760] (1)
110. Marinostatin, MstI [103763] (1)
  1. Marinostatin, MstI [103764] (1)
    uperfamily
    1. Marinostatin, MstI [103765] (1)
111. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103768] (1)
  1. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103769] (1)
    uperfamily
    1. Cross-reactive peptides from 60S acidic ribosomal protein p2 [103770] (2)
112. NTR, cyclotide processing element [111516] (1)
  1. NTR, cyclotide processing element [111517] (1)
    uperfamily
    1. NTR, cyclotide processing element [111518] (2)
113. HMG-box transcription factor 1 fragments [111523] (1)
  1. HMG-box transcription factor 1 fragments [111524] (1)
    uperfamily
    1. HMG-box transcription factor 1 fragments [111525] (1)
114. MAD protein fragments [111528] (1)
  1. MAD protein fragments [111529] (1)
    uperfamily
    1. MAD protein fragments [111530] (1)
115. Fragments of TNF receptors [111533] (1)
  1. Fragments of TNF receptors [111534] (1)
    uperfamily
    1. Fragments of TNF receptors [111535] (1)
116. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111538] (1)
  1. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111539] (1)
    uperfamily
    1. Ezrin-radixin-moesin binding phosphoprotein 50 (ebp50) fragments [111540] (1)
117. Ribosomal protein L34p [144320] (1)
  non-globular, mainly alpha-helical
  1. Ribosomal protein L34p [144321] (1)
    uperfamily
    1. Ribosomal protein L34p [144322] (3)
      Pfam 00468
118. Ribosomal protein S21p [161307] (1)
  non-globular, mainly alpha-helical
  1. Ribosomal protein S21p [161308] (1)
    1. Ribosomal protein S21p [161309] (1)
      Pfam 01165
119. Retinoblastoma-associated protein RB1 fragments [144325] (1)
  1. Retinoblastoma-associated protein RB1 fragments [144326] (1)
    uperfamily
    1. Retinoblastoma-associated protein RB1 fragments [144327] (1)
120. Genome linked protein vpg [144330] (1)
  1. Genome linked protein vpg [144331] (1)
    uperfamily
    1. Genome linked protein vpg [144332] (1)
      PfamB 000297
121. Programmed cell death protein 5 fragments [144335] (1)
  1. Programmed cell death protein 5 fragments [144336] (1)
    uperfamily
    1. Programmed cell death protein 5 fragments [144337] (1)
Designed proteins [58788] (44)
Experimental structures of proteins with essentially non-natural sequences. Not a true class
1. New fold designs [103774] (1)
  1. New fold designs [103775] (1)
    uperfamily
    1. alpha+beta folds [103776] (2)
2. In vitro evolution products [103779] (1)
  1. In vitro evolution products [103780] (1)
    uperfamily
    1. Function-directed selections [103781] (1)
3. Hybrid and chimeric proteins [58789] (1)
  1. Hybrid and chimeric proteins [58790] (1)
    uperfamily
    1. Hybrid and chimeric proteins [58791] (3)
4. Amphiphilic (amphipathic) alpha helix [58798] (1)
  1. Amphiphilic (amphipathic) alpha helix [58799] (1)
    uperfamily
    1. Amphiphilic (amphipathic) alpha helix [58800] (3)
5. Collagen-like peptides [58805] (1)
  1. Collagen-like peptides [58806] (1)
    uperfamily
    1. Collagen-like peptides [58807] (8)
6. Coiled serine [58812] (1)
  1. Coiled serine [58813] (1)
    uperfamily
    1. Coiled serine [58814] (2)
7. Designed trimeric coiled-coil [100903] (1)
  1. Designed trimeric coiled-coil [100904] (1)
    uperfamily
    1. Designed trimeric coiled-coil [100905] (4)
      not a true family
8. Designed heterodimeric coiled-coil [58822] (1)
  1. Designed heterodimeric coiled-coil [58823] (1)
    uperfamily
    1. Designed heterodimeric coiled-coil [58824] (2)
9. Thermostable heterotrimeric coiled coil [58827] (1)
  1. Thermostable heterotrimeric coiled coil [58828] (1)
    uperfamily
    1. Thermostable heterotrimeric coiled coil [58829] (1)
10. Designed four-helix bundle protein [58832] (1)
  1. Designed four-helix bundle protein [58833] (1)
    uperfamily
    1. Designed four-helix bundle protein [58834] (5)
      this is not a true family
11. Designed single chain three-helix bundle [58839] (1)
  not a true fold: both possible topologies are created
  1. Designed single chain three-helix bundle [58840] (1)
    uperfamily
    1. Designed single chain three-helix bundle [58841] (3)
12. Peptide f (amphiphilic octadecapeptide) [58846] (1)
  1. Peptide f (amphiphilic octadecapeptide) [58847] (1)
    uperfamily
    1. Peptide f (amphiphilic octadecapeptide) [58848] (1)
13. Retro-GCN4 leucine zipper [58851] (1)
  1. Retro-GCN4 leucine zipper [58852] (1)
    uperfamily
    1. Retro-GCN4 leucine zipper [58853] (1)
14. Glytm1bzip [70053] (1)
  1. Glytm1bzip [70054] (1)
    uperfamily
    1. Glytm1bzip [70055] (1)
15. Zinc finger design [58856] (1)
  1. Zinc finger design [58857] (1)
    uperfamily
    1. Zinc finger design [58858] (11)
16. Protein A Ig(Fc)-binding domain mimics [58863] (1)
  1. Protein A Ig(Fc)-binding domain mimics [58864] (1)
    uperfamily
    1. Protein A Ig(Fc)-binding domain mimics [58865] (1)
17. Zinc finger based beta-beta-alpha motif [58868] (1)
  1. Zinc finger based beta-beta-alpha motif [58869] (1)
    uperfamily
    1. Zinc finger based beta-beta-alpha motif [58870] (5)
18. helix-turn-helix motif [58877] (1)
  1. helix-turn-helix motif [58878] (1)
    uperfamily
    1. helix-turn-helix motif [58879] (2)
19. alpha2d [58882] (1)
  1. alpha2d [58883] (1)
    uperfamily
    1. alpha2d [58884] (1)
20. Right-handed coiled coil [58887] (1)
  1. Right-handed coiled coil [58888] (1)
    uperfamily
    1. Right-handed coiled coil [58889] (3)
21. TPR domain-based design [90307] (1)
  1. TPR domain-based design [90308] (1)
    uperfamily
    1. TPR domain-based design [90309] (6)
      alpha-helical arrays from an idealized TPR motif
22. Erythropoietin (EPO) mimetic peptides [58892] (1)
  1. Erythropoietin (EPO) mimetic peptides [58893] (1)
    uperfamily
    1. Erythropoietin (EPO) mimetic peptides [58894] (1)
23. IL-1 receptor type 1 antagonist peptide AF10847 [58897] (1)
  1. IL-1 receptor type 1 antagonist peptide AF10847 [58898] (1)
    uperfamily
    1. IL-1 receptor type 1 antagonist peptide AF10847 [58899] (1)
24. Octreotide (Sandostatine), a somatostatine analogue [58902] (1)
  1. Octreotide (Sandostatine), a somatostatine analogue [58903] (1)
    uperfamily
    1. Octreotide (Sandostatine), a somatostatine analogue [58904] (1)
25. Calmodulin [58907] (1)
  1. Calmodulin [58908] (1)
    uperfamily
    1. Calmodulin [58909] (1)
26. WW domain-based designs [58912] (1)
  1. WW domain-based designs [58913] (1)
    uperfamily
    1. WW domain-based designs [58914] (4)
27. Artificial ankyrin repeat proteins [83017] (1)
  1. Artificial ankyrin repeat proteins [83018] (1)
    uperfamily
    1. Artificial ankyrin repeat proteins [83019] (9)
28. Carboxypeptidase A prodomain-based design [103789] (1)
  1. Carboxypeptidase A prodomain-based design [103790] (1)
    uperfamily
    1. Carboxypeptidase A prodomain-based design [103791] (1)
29. Ubiquitin [144344] (1)
  1. Ubiquitin [144345] (1)
    uperfamily
    1. Ubiquitin [144346] (4)
30. Cro lambda fold design [144349] (1)
  1. Cro lambda fold design [144350] (1)
    uperfamily
    1. Cro lambda fold design [144351] (1)
31. Scorpion toxin-based designs [58917] (1)
  1. Scorpion toxin-based designs [58918] (2)
    uperfamily
    1. Potassium channel toxin hstx1 [58919] (1)
    2. Mini-protein reproducing the core of the CD4 surface [58922] (1)
32. TH (toxin hand)-motif beta-sheet mini-protein designs [64673] (1)
  1. TH (toxin hand)-motif beta-sheet mini-protein designs [64674] (1)
    uperfamily
    1. TH (toxin hand)-motif beta-sheet mini-protein designs [64675] (3)
33. Inhibitor of mammalian ribonucleotide reductase [58925] (1)
  1. Inhibitor of mammalian ribonucleotide reductase [58926] (1)
    uperfamily
    1. Inhibitor of mammalian ribonucleotide reductase [58927] (1)
34. Integrin-binding RGD peptide [64682] (1)
  1. Integrin-binding RGD peptide [64683] (1)
    uperfamily
    1. Integrin-binding RGD peptide [64684] (1)
35. Peptide antagonists of IGF-1 [64687] (1)
  1. Peptide antagonists of IGF-1 [64688] (1)
    uperfamily
    1. Peptide antagonists of IGF-1 [64689] (1)
36. beta-hairpin design [64692] (1)
  1. beta-hairpin design [64693] (1)
    uperfamily
    1. beta-hairpin design [64694] (9)
37. Trp-cage miniprotein [75769] (1)
  1. Trp-cage miniprotein [75770] (1)
    uperfamily
    1. Trp-cage miniprotein [75771] (1)
38. Synthetic high affinity IgE receptor antagonists [64703] (1)
  1. Synthetic high affinity IgE receptor antagonists [64704] (2)
    not a true superfamily
    uperfamily
    1. Hairpin peptide [64705] (1)
    2. Zeta peptides [75774] (2)
39. IFN mimetic syr6 [75779] (1)
  1. IFN mimetic syr6 [75780] (1)
    uperfamily
    1. IFN mimetic syr6 [75781] (1)
40. TAZ (CH) Zn-binding domain based design [75784] (1)
  1. TAZ (CH) Zn-binding domain based design [75785] (1)
    uperfamily
    1. TAZ (CH) Zn-binding domain based design [75786] (1)
41. Beta-sheet designs [75789] (1)
  1. Beta-sheet designs [75790] (1)
    uperfamily
    1. Beta-sheet designs [75791] (2)
42. PW2, a tryptophan-rich anticocidial peptide [75796] (1)
  1. PW2, a tryptophan-rich anticocidial peptide [75797] (1)
    uperfamily
    1. PW2, a tryptophan-rich anticocidial peptide [75798] (1)
43. Designed EF-hand type cation-binding loop [111554] (1)
  1. Designed EF-hand type cation-binding loop [111555] (1)
    uperfamily
    1. Designed EF-hand type cation-binding loop [111556] (1)
44. Metalloporphyrin-binding designed peptides [90314] (1)
  1. Metalloporphyrin-binding designed peptides [90315] (1)
    uperfamily
    1. Metalloporphyrin-binding designed peptides [90316] (2)