Structural Classification of Proteins

Class: Alpha and beta proteins (a+b)

: Mainly antiparallel beta sheets (segregated alpha and beta regions)

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)

Folds:

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
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
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
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)
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)
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
Prion-like [54097] (1)
beta-alpha-beta-alpha(2); antiparallel beta-ribbon
1. Prion-like [54098] (1)
  uperfamily
  1. Prion-like [54099] (14)
LysM domain [54105] (1)
beta-alpha(2)-beta; antiparallel strands
1. LysM domain [54106] (1)
  uperfamily
  1. LysM domain [54107] (2)
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
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)
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
Urease, gamma-subunit [54110] (1)
alpha(3)-beta(2); antiparallel hairpin
1. Urease, gamma-subunit [54111] (1)
  uperfamily
  1. Urease, gamma-subunit [54112] (3)
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
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)
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)
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
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
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)
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
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)
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)
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
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)
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)
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)
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)
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
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
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
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)
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
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
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)
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
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)
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)
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
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)
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
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
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
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
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);
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
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)
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
MHC antigen-recognition domain [54451] (1)
dimeric
1. MHC antigen-recognition domain [54452] (1)
  uperfamily
  1. MHC antigen-recognition domain [54453] (73)
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)
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)
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
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)
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
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
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
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)
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
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)
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)
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
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
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
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)
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
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
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)
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
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]
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)
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)
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)
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)
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)
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
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)
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)
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)
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
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)
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
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)
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)
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
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)
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)
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)
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)
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)
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)
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
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)
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
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
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
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)
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)
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
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)
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)
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
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)
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)
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)
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
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)
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)
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)
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)
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
SRP19 [69694] (1)
beta-alpha-beta(2)-alpha; 2 layers: alpha/beta
1. SRP19 [69695] (1)
  uperfamily
  1. SRP19 [69696] (3)
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)
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
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
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)
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
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)
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
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
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)
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)
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
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)
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)
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)
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
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
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)
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)
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
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
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
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
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)
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
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
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
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
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
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
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
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)
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
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)
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)
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)
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
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
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)
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
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
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
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)
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)
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
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)
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
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
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)
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)
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
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
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
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
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
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)
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
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)
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)
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)
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
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
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
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)
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)
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)
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
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
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
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)
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)
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
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)
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
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)
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
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
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)
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
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
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)
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)
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)
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)
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)
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)
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
Subtilisin inhibitor [55398] (1)
alpha+beta sandwich
1. Subtilisin inhibitor [55399] (1)
  uperfamily
  1. Subtilisin inhibitor [55400] (2)
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)
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
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)
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)
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
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
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)
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)
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)
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
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)
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)
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
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)
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
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)
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
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)
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
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)
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)
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
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
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)
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
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)
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)
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
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)
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)
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)
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
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
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)
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)
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
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
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
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
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
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
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)
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
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)
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
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
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
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)
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
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)
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
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)
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)
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;
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)
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
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
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)
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)
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
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)
Ribonuclease Rh-like [55894] (1)
alpha+beta fold
1. Ribonuclease Rh-like [55895] (1)
  uperfamily
  1. Ribonuclease Rh-like [55896] (8)
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
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
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
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
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)
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
Creatinase/aminopeptidase [55919] (1)
duplication: composed of two very similar alpha+beta folds
1. Creatinase/aminopeptidase [55920] (1)
  uperfamily
  1. Creatinase/aminopeptidase [55921] (9)
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
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
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
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
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)
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
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)
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)
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)
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
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)
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)
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)
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
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
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
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)
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
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)
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
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)
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)
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)
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)
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
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)
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)
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)
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
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
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)
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)
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)
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
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
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
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)
Methenyltetrahydromethanopterin cyclohydrolase [56198] (1)
consists of two alpha+beta subdomains
1. Methenyltetrahydromethanopterin cyclohydrolase [56199] (1)
  uperfamily
  1. Methenyltetrahydromethanopterin cyclohydrolase [56200] (1)
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
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)
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)
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
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
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)
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
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]
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)
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
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
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
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
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)
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
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)
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
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
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)
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)
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)
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)
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)
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
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
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
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
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
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)
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
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)
LCCL domain [69847] (1)
unusual fold
1. LCCL domain [69848] (1)
  uperfamily
  1. LCCL domain [69849] (1)
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)
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
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)
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)
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)
gp120 core [56501] (1)
unusual fold
1. gp120 core [56502] (1)
  uperfamily
  1. gp120 core [56503] (1)
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)
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
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)
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)
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)
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)
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
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
FAH [56528] (1)
unusual fold; contains 3 layers of beta-sheet structure
1. FAH [56529] (1)
  uperfamily
  1. FAH [56530] (6)
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)
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)
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)
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)
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
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
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)
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)
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)
Baseplate structural protein gp11 [56557] (1)
unusual fold; trimer
1. Baseplate structural protein gp11 [56558] (1)
  uperfamily
  1. Baseplate structural protein gp11 [56559] (1)
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)
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)
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
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)
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)
NinB [103369] (1)
unusual fold; intertwined dimer; consists of two different structural domains
1. NinB [103370] (1)
  uperfamily
  1. NinB [103371] (1)
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)
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
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
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
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
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
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)
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
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)
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