Coverage for Superfamily Prediction


SuperfamilyDescriptionComments
a.1.1Globin-likecore: 6 helices; folded leaf, partly opened
a.3.1Cytochrome ccore: 3 helices; folded leaf, opened
a.4.1DNA/RNA-binding 3-helical bundlecore: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
a.4.5DNA/RNA-binding 3-helical bundlecore: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
a.4.6DNA/RNA-binding 3-helical bundlecore: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
a.5.2RuvA C-terminal domain-like3 helices; bundle, right-handed twist
a.6.1Putative DNA-binding domaincore: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
a.16.1S15/NS1 RNA-binding domain3 helices; irregular array
a.22.1Histone-foldcore: 3 helices; long middle helix is flanked at each end with shorter ones
a.25.1Ferritin-likecore: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
a.26.14-helical cytokinescore: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
a.35.1lambda repressor-like DNA-binding domainscore: 4 helices; folded leaf, closed
a.39.1EF Hand-likecore: 4 helices; array of 2 hairpins, opened
a.43.1Ribbon-helix-helixcore: 4 helices; array of 2 hairpins, opened
a.52.1Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin4 helices; folded leaf; right-handed superhelix
a.60.1SAM domain-like4-5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins
a.74.1Cyclin-likecore: 5 helices; one helix is surrounded by the others
a.77.1DEATH domain6 helices: closed bundle; greek-key; internal pseudo twofold symmetry
a.93.1Heme-dependent peroxidasesmultihelical; consists of two all-alpha domains
a.100.16-phosphogluconate dehydrogenase C-terminal domain-likemultihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
a.102.4alpha/alpha toroidmultihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
a.118.1alpha-alpha superhelixmultihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
a.129.1GroEL equatorial domain-likemultihelical; 8 helices arranged in 2 parallel layers
a.132.1Heme oxygenase-likemultihelical; bundle
a.138.1Multiheme cytochromesvariable number of helices and little beta structure; not a true fold
b.1.1Immunoglobulin-like beta-sandwichsandwich; 7 strands in 2 sheets; greek-key ! some members of the fold have additional strands
b.1.18Immunoglobulin-like beta-sandwichsandwich; 7 strands in 2 sheets; greek-key ! some members of the fold have additional strands
b.1.11Immunoglobulin-like beta-sandwichsandwich; 7 strands in 2 sheets; greek-key ! some members of the fold have additional strands
b.2.2Common fold of diphtheria toxin/transcription factors/cytochrome fsandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
b.2.3Common fold of diphtheria toxin/transcription factors/cytochrome fsandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
b.2.5Common fold of diphtheria toxin/transcription factors/cytochrome fsandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
b.6.1Cupredoxin-likesandwich; 7 strands in 2 sheets, greek-key ! variations: some members have additional 1-2 strands
b.7.1C2 domain-likesandwich; 8 strands in 2 sheets; greek-key
b.121.4Nucleoplasmin-like/VP (viral coat and capsid proteins)sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands ! characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
b.121.5Nucleoplasmin-like/VP (viral coat and capsid proteins)sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands ! characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
b.12.1Lipase/lipooxygenase domain (PLAT/LH2 domain)sandwich; 8 strands in 2 sheets; complex topology ! duplication: has weak internal pseudo twofold symmetry
b.18.1Galactose-binding domain-likesandwich; 9 strands in 2 sheets; jelly-roll
b.19.1Viral protein domainsandwich; 9 strands in 2 sheets; jelly-roll; form trimers
b.26.1SMAD/FHA domainsandwich; 11 strands in 2 sheets; greek-key
b.29.1Concanavalin A-like lectins/glucanasessandwich; 12-14 strands in 2 sheets; complex topology
b.30.5Supersandwichsandwich; 18 strands in 2 sheets
b.34.9SH3-like barrelbarrel, partly opened; n*=4, S*=8; meander ! the last strand is interrupted by a turn of 3-10 helix
b.35.1GroES-likecontains barrel, partly opened; n*=4, S*=8; meander
b.36.1PDZ domain-likecontains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
b.40.2OB-foldbarrel, closed or partly opened n=5, S=10 or S=8; greek-key
b.40.4OB-foldbarrel, closed or partly opened n=5, S=10 or S=8; greek-key
b.40.6OB-foldbarrel, closed or partly opened n=5, S=10 or S=8; greek-key
b.42.1beta-Trefoilbarrel, closed; n=6, S=12; and a hairpin triplet; meander ! duplication: has internal pseudo threefold symmetry
b.42.4beta-Trefoilbarrel, closed; n=6, S=12; and a hairpin triplet; meander ! duplication: has internal pseudo threefold symmetry
b.43.4Reductase/isomerase/elongation factor common domainbarrel, closed; n=6, S=10; greek-key
b.45.1FMN-binding split barrelbarrel; n=6, S=10; greek-key
b.47.1Trypsin-like serine proteasesbarrel, closed; n=6, S=8; greek-key ! duplication: consists of two domains of the same fold
b.49.2Domain of alpha and beta subunits of F1 ATP synthase-likebarrel, closed; n=6, S=8; greek-key
b.50.1Acid proteasesbarrel, closed; n=6, S=10, complex topology
b.52.2Double psi beta-barrelbarrel, closed; n=6, S=10; complex topology with crossover (psi) loops
b.55.1PH domain-likebarrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
b.60.1Lipocalinsbarrel, closed or opened; n=8, S=12; meander
b.71.1Glycosyl hydrolase domainfolded sheet; greek-key
b.80.1Single-stranded right-handed beta-helixsuperhelix turns are made of parallel beta-strands and (short) turns
b.81.1Single-stranded left-handed beta-helixsuperhelix turns are made of parallel beta-strands and (short) turns
b.82.1Double-stranded beta-helixone turn of helix is made by two pairs of antiparallel strands linked with short turns ! has appearance of a sandwich of distinct architecture and jelly-roll topology
b.84.2Barrel-sandwich hybridsandwich of half-barrel shaped beta-sheets
b.92.1Composite domain of metallo-dependent hydrolasespseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
b.122.1PUA domain-likepseudobarrel; mixed folded sheet of 5 strands; order 13452; strand 1 and 3 are parallel to each other
c.1.2TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.1.8TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.1.9TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.1.10TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.1.11TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.1.12TIM beta/alpha-barrelcontains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
c.2.1NAD(P)-binding Rossmann-fold domainscore: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456 ! The nucleotide-binding modes of this and the next two folds/superfamilies are similar
c.3.1FAD/NAD(P)-binding domaincore: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
c.8.5The "swivelling" beta/beta/alpha domain3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology ! this domain is thought to be mobile in most multi-domain proteins known to contain it
c.10.2Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies
c.14.1ClpP/crotonasecore: 4 turns of (beta-beta-alpha)n superhelix
c.18.1DNA glycosylase3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
c.58.1Aminoacid dehydrogenase-like, N-terminal domaincore: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134
c.23.5Flavodoxin-like3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
c.23.16Flavodoxin-like3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
c.25.1Ferredoxin reductase-like, C-terminal NADP-linked domain3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
c.26.1Adenine nucleotide alpha hydrolase-likecore: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
c.26.2Adenine nucleotide alpha hydrolase-likecore: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
c.116.1alpha/beta knotcore: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot
c.30.1PreATP-grasp domain3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands ! possible rudiment form of Rossmann-fold domain
c.31.1DHS-like NAD/FAD-binding domain3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
c.124.1NagB/RpiA/CoA transferase-likecore: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
c.36.1Thiamin diphosphate-binding fold (THDP-binding)3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
c.37.1P-loop containing nucleoside triphosphate hydrolases3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
c.41.1Subtilisin-like3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
c.43.1CoA-dependent acyltransferasescore: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
c.45.1(Phosphotyrosine protein) phosphatases IIcore: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
c.46.1Rhodanese/Cell cycle control phosphatase3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
c.47.1Thioredoxin foldcore: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
c.48.1TK C-terminal domain-like3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
c.55.1Ribonuclease H-like motif3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
c.55.3Ribonuclease H-like motif3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
c.56.5Phosphorylase/hydrolase-likecore: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
c.57.1Molybdenum cofactor biosynthesis proteins3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
c.60.1Phosphoglycerate mutase-likecore: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
c.66.1S-adenosyl-L-methionine-dependent methyltransferasescore: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
c.67.1PLP-dependent transferasesmain domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
c.68.1Nucleotide-diphospho-sugar transferases3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
c.69.1alpha/beta-Hydrolasescore: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
c.72.1Ribokinase-likecore: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest ! potential superfamily: members of this fold have similar functions but different ATP-binding sites
c.76.1Alkaline phosphatase-likecore:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
c.80.1SIS domain3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
c.87.1UDP-Glycosyltransferase/glycogen phosphorylaseconsists of two non-similar domains with 3 layers (a/b/a) each ! domain 1: parallel beta-sheet of 7 strands, order 3214567 ! domain 2: parallel beta-sheet of 6 strands, order 321456
c.91.1PEP carboxykinase-likecontains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
c.92.2Chelatase-likeduplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
c.94.1Periplasmic binding protein-like IIconsists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
c.95.1Thiolase-likeconsists of two similar domains related by pseudo dyad; duplication ! 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
d.1.1Microbial ribonucleasessingle helix packs against antiparallel beta-sheet
d.2.1Lysozyme-likecommon alpha+beta motif for the active site region
d.3.1Cysteine proteinasesconsists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
d.13.1HIT-likealpha-beta(3)-alpha-beta(2); 3 layers: alpha/beta/alpha
d.14.1Ribosomal protein S5 domain 2-likecore: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
d.15.1beta-Grasp (ubiquitin-like)core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
d.15.2beta-Grasp (ubiquitin-like)core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
d.15.3beta-Grasp (ubiquitin-like)core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
d.15.4beta-Grasp (ubiquitin-like)core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
d.16.1FAD-linked reductases, C-terminal domainalpha+beta sandwich
d.32.1Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenasebeta-alpha-beta(3); 2 layers: alpha/beta
d.38.1Thioesterase/thiol ester dehydrase-isomerasecore: beta-alpha-beta(4); 2 layers: alpha/beta
d.42.1POZ domaincore: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
d.218.1Nucleotidyltransferasecore: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands: 123
d.56.1GroEL-intermediate domain like3-helical bundle packed against 3-stranded mixed beta-sheet
d.58.1Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.58.3Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.58.4Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.58.5Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.58.7Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.58.31Ferredoxin-likealpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
d.265.1Pseudouridine synthaseconsists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
d.185.1LuxS/MPP-like metallohydrolasecore: beta-alpha-beta(2)-alpha(2); 2 layers: alpha/beta
d.79.1Bacillus chorismate mutase-likecore: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
d.79.3Bacillus chorismate mutase-likecore: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
d.80.1Tautomerase/MIF(beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet ! generally forms trimers with three closely packed beta-sheets
d.81.1Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domaincore: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
d.92.1Zincin-likecontains mixed beta sheet with connection over free side of the sheet
d.95.2Homing endonuclease-likealpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
d.96.1T-foldbeta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234 ! tunnel-shaped: its known members form wide oligomeric barrels different sizes
d.108.1Acyl-CoA N-acyltransferases (Nat)3 layers: a/b/a; contains mixed beta-sheet
d.109.1Gelsolin-like3 layers: a/b/a; contains mixed beta-sheet
d.110.2Profilin-likecore: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
d.110.3Profilin-likecore: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
d.113.1Nudixbeta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet ! contains beta-grasp motif
d.115.1YrdC/RibBcore: 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
d.122.1ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase8-stranded mixed beta-sheet; 2 layers: alpha/beta
d.129.3TBP-likebeta-alpha-beta(4)-alpha
d.131.1DNA clampcontains two helices and two beta sheets ! duplication: fold has internal pseudo two-fold symmetry
d.142.1ATP-graspConsists of two subdomains with different alpha+beta folds ! shares functional and structural similarities with the PIPK and protein kinase superfamilies
d.145.1FAD-binding domainconsists of two alpha+beta subdomains
d.153.1Ntn hydrolase-like4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
d.159.1Metallo-dependent phosphatases4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
d.162.1LDH C-terminal domain-likeunusual fold, defines family
d.163.1DNA breaking-rejoining enzymescore: alpha3-beta3-alpha4; one side of beta-sheet is exposed
d.166.1ADP-ribosylationunusual fold
d.169.1C-type lectin-likeunusual fold
e.8.1DNA/RNA polymerasesdivided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
e.29.1beta and beta-prime subunits of DNA dependent RNA-polymeraseMultidomain subunits of complex domain organization
f.4.3Transmembrane beta-barrelsnot a true fold, gathers together transmembrane barrels of different (n,S)
g.3.6Knottins (small inhibitors, toxins, lectins)disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
g.3.7Knottins (small inhibitors, toxins, lectins)disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
g.3.11Knottins (small inhibitors, toxins, lectins)disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
g.3.15Knottins (small inhibitors, toxins, lectins)disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
g.7.1Snake toxin-likedisulfide-rich fold: nearly all-beta
g.8.1BPTI-likedisulfide-rich alpha+beta fold
g.14.1Kringle-likedisulfide-rich fold; nearly all-beta
g.17.1Cystine-knot cytokinesdisulfide-rich fold; common core is all-beta
g.24.1TNF receptor-likeduplication: consists of three similar disulfide-rich domains
g.37.1C2H2 and C2HC zinc fingersalpha+beta metal(zinc)-bound fold: beta-hairpin + alpha-helix
g.39.1Glucocorticoid receptor-like (DNA-binding domain)alpha+beta metal(zinc)-bound fold
g.41.5Rubredoxin-likemetal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
g.50.1FYVE/PHD zinc fingerdimetal(zinc)-bound alpha+beta fold