SII-SWORD/CoKE huggingface dataset:
Gp22-like (Gp22-like)
Type: Family

This entry includes Gp22 from Bacillus phage SPP1 (

), a protein that shows a significant structural similarity with the N-terminal shoulder domain (

) of Receptor binding protein from Lactococcus phage p2 (RBP). It folds into two small three-stranded antiparallel β-sheets and one large five-stranded mixed β-sheet forming a pseudo-β-sandwich . Members of this protein family are found in tailed bacteriophages and prophages from firmicutes.
Thioredoxin 2, N-terminal domain (Thio2_N)
Type: Domain

This entry represents the N-terminal domain of thioredoxin 2, which is a zinc finger domain, unusual in thioredoxin proteins . Thio2 reduces disulfide bonds and is an efficient electron donor for the essential enzyme ribonucleotide reductase. This domain may mediate protein-protein interactions .

Proteins containing this domain are found predominantly in proteobacteria. This domain is structurally similar to Rubredoxin-like zinc-fingers (

) .
Gp22-like superfamily (Gp22-like_sf)
Type: Homologous_superfamily

This entry includes Gp22 from Bacillus phage SPP1 (

), a protein that shows a significant structural similarity with the N-terminal shoulder domain (

) of Receptor binding protein from Lactococcus phage p2 (RBP). It folds into two small three-stranded antiparallel β-sheets and one large five-stranded mixed β-sheet forming a pseudo-β-sandwich . Members of this protein family are found in tailed bacteriophages and prophages from firmicutes.
Capsid Gp10A/Gp10B-like domain (Capsid_Gp10A/Gp10B-like_dom)
Type: Domain

This entry describes a domain found in capsid proteins, such as Gp10A (also known as Major capsid protein,

) and Gp10B (also known as Minor capsid protein,

) from bacteriophage T7 and T3. Gp10A subunits adopt an HK97-like conformation to form the viral shell . This domain is also found in other tailed bacteriophages and bacterial prophages.
Major coat protein-like (Gp10-like)
Type: Family

This protein family includes Major coat protein from Salmonella phage epsilon15 (Gp10) and similar sequences from tailed bacteriophages and from bacterial prophages. Gp10 binds to the outer surface of the virus capsid. It adopts a jellyroll viral protein fold with two sheets consisting of four β-strands each .
Glycosyl hydrolase 109, C-terminal domain (Glyco_hydro_109_C)
Type: Domain

This domain is found at the C-terminal end of the group of bacterial glycosyl hydrolases 109, including Alpha-N-acetylgalactosaminidase from Elizabethkingia meningoseptica. This domain shows a large open-faced, seven-stranded, anti-parallel β-sheet, adjacent to nine α-helices and an α-helical bundle covering the dinucleotide-binding tunnel .
Glycine-rich domain (Gly_rich_dom)
Type: Domain

This glycine rich region forms a compact hexagonal lattice of polyglycine helices in a variety of bacterial and phage surface proteins, including Collagen-like protein 4 from Acanthamoeba polyphaga mimivirus (

) and Gene 32 protein from Mycobacterium phage D29 (

).
GlxA-like, beta barrel domain (GlxA-like_b-barrel)
Type: Domain

This entry represents the second domain of the GlxA protein from Streptomyces lividans (

). GlxA contains a β-propeller domain and this β-barrel domain is inserted within it . This domain is often found associated with

.
Golven 1/2-like (GLV1-2)
Type: Family

This entry represents a group of plant proteins, including GLV1 and GLV2 (also known as RGF9) from Arabidopsis. GLV2 is a signalling peptide (root growth factor) that regulates the pattern of root growth and lateral root development by modulating the length and the number of cortical cells in the root apical meristem (RAM), and the anticlinal asymmetric cell divisions in lateral root initiation cells . It is also involved in the regulation of hypocotyl bending and root gravitropism, probably by influencing the formation of auxin gradients . In general, RGFs are required for maintenance of the root stem cell niche and transit amplifying cell proliferation in Arabidopsis .
OspI-like (OspI-like)
Type: Family

This entry represents a protein family that includes OspI (

), a Shigella flexneri effector encoded by ORF169b that suppresses the TNF-receptor-associated factor 6 (TRAF6)-mediated signalling pathway and inhibits acute inflammatory responses in the initial stage of infection. This is a glutamine deamidase essential for the deamidation of UBC13 .
OspI-like superfamily (OspI-like_sf)
Type: Homologous_superfamily

This entry represents a protein superfamily that includes OspI (

), a Shigella flexneri effector encoded by ORF169b that suppresses the TNF-receptor-associated factor 6 (TRAF6)-mediated signalling pathway and inhibits acute inflammatory responses in the initial stage of infection. This is a glutamine deamidase essential for the deamidation of UBC13 .
Defective in germ line development protein 3, KH3 domain (GLD-3_KH3)
Type: Domain

This entry represents the third KH3 domain of Defective in germ line development protein 3 (GLD-3) from C. elegans, the second of the KH domains organised into a globular structural unit .

GLD-3 is required maternally for germline survival and embryogenesis. It forms a complex with Gls-1 which promotes the oogenic cell fate by freeing the translational repressor Fbf to repress sperm promoting factors. This protein promotes maturation of primary spermatocytes to mature sperm and is required during hermaphrodite development to promote sperm fate, which is critical for determining the normal number of sperm. It is also required during male development for the continued production of sperm and inhibition of oogenesis. Together with Gld-2, promotes the transition from mitosis to meiosis . GLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The four K homology (KH) domains KH2 to KH5 form a proteolytically stable structure .
Defective in germ line development protein 3, KH4 domain (GLD3_KH4)
Type: Domain

This entry represents the third KH4 domain of Defective in germ line development protein 3 (GLD-3) from C. elegans, the third of the KH domains organised into a globular structural unit .

GLD-3 is required maternally for germline survival and embryogenesis. It forms a complex with Gls-1 which promotes the oogenic cell fate by freeing the translational repressor Fbf to repress sperm promoting factors. This protein promotes maturation of primary spermatocytes to mature sperm and is required during hermaphrodite development to promote sperm fate, which is critical for determining the normal number of sperm. It is also required during male development for the continued production of sperm and inhibition of oogenesis. Together with Gld-2, promotes the transition from mitosis to meiosis . GLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The four K homology (KH) domains KH2 to KH5 form a proteolytically stable structure .
GIY-YIG, catalytic domain (GIY_YIG_cat)
Type: Domain

This entry represents a GIY-YIG-like domain related to homing endonucleases that is found in a group of bacterial proteins, including

from Treponema denticola, in which it covers most of the length of the protein.
tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal, N-terninal subdomain (GIDA_C_N)
Type: Domain

This entry represents the first helices of the GidA associated domain, the C-terminal domain of MnmG (also known as GidA). This domain consists of several helices, the last three being rather short and forming small bundle (covered in

). GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA and, in particular the small bundle, to be responsible for the interaction with protein MnmE (

) . Structures of GidA in complex with either tRNA or MnmE are missing.
Endo-alpha-N-acetylgalactosaminidase, domain 5 (GH101_dom-5)
Type: Domain

Endo-alpha-N-acetylgalactosaminidase is a member of glycoside hydrolase (GH) family 101 and hydrolases the O-glycosidic bonds in mucin-type O-glycan between alpha-GalNAc and Ser/Thr. It is a multidomain protein . It contains a distorted (α/β)8 barrel catalytic domain (referred to as domain 3) flanked by four additional domains, which are mainly made of β-sheets (domains 2, 4, 5 and 6). This entry represents domain 5 which is part of the carbohydrate binding module.
Glycine cleavage system P-protein, N-terminal domain (GDC-P_N)
Type: Domain

This entry represents a domain found at the N-terminal of P proteins from eukaryotes and some from prokaryotes and covers the whole length of the protein in the shorter prokaryotic ones.

The P protein, also known as Glycine dehydrogenase (decarboxylating), is part of the glycine decarboxylase multienzyme complex (GDC), also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T . The P protein (

) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. The reaction catalysed by this protein is:

Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2

The subunit composition of glycine cleavage system P proteins have been classified into two types. Those from eukaryotes and some of the P proteins from prokaryotes (e.g. Escherichia coli) are in the homodimeric form. The rest of those from prokaryotes are heterotetrameric, with two different subunits which, based on sequence similarities, correspond respectively to the N and C-terminal halves of the eukaryotic subunit .
Glycine dehydrogenase, C-terminal domain (GDC-P_C)
Type: Domain

This entry represents a small domain found at the C-terminal end of Glycine dehydrogenases, also known as glycine cleavage system P protein (GDC-P), part of the glycine decarboxylase multienzyme complex (GDC). GDC-P binds the α-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. The monomer consists of two domains, a large domain and a small domain. This domain has a complex α/β structure .
Cyclin-D1-binding protein 1-like, N-terminal (GCIP-like_N)
Type: Domain

This entry represents the N-terminal region of human Cyclin-D1-binding protein 1 (GCIP), which contains an helix-loop-helix domain , and its homologues in eukaryotes.

GCIP, or Grap2 and cyclin-D-interacting protein (also Human homologue of murine maternal Id-like molecule (HHM)), is found in eukaryotes, and in the protein

, residues 149-190 constitute a helix-loop-helix domain, residues 190-240 an acidic region, and 240-261 a leucine zipper domain . GCIP interacts with full-length Grap2 protein and with the COOH-terminal unique and SH3 domains (designated QC domain) of Grap2. It is potentially involved in the regulation of cell differentiation and proliferation through Grap2 and cyclin D-mediated signalling pathways . In mice, it is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumours. In vitro, it acts as an inhibitory HLH protein, for example, blocking transcription of the HNF-4 promoter. In its function as a cyclin D1-binding protein it is able to reduce CDK4-mediated phosphorylation of the retinoblastoma protein and to inhibit E2F-mediated transcriptional activity . GCIP has also been shown to have interact physically with Rad (Ras associated with diabetes), Rad being important in regulating cellular senescence . GCIP adopts a V-shaped conformation, with N and C-terminal five-helix bundles .
Cyclin-D1-binding protein 1-like, C-terminal (GCIP_C)
Type: Domain

This entry represents the C-terminal domain of human Cyclin-D1-binding protein 1 (GCIP) and similar eukaryotic proteins.

GCIP, or Grap2 and cyclin-D-interacting protein (also Human homologue of murine maternal Id-like molecule (HHM)), is found in eukaryotes, and in the protein

, residues 149-190 constitute a helix-loop-helix domain, residues 190-240 an acidic region, and 240-261 a leucine zipper domain . GCIP interacts with full-length Grap2 protein and with the COOH-terminal unique and SH3 domains (designated QC domain) of Grap2. It is potentially involved in the regulation of cell differentiation and proliferation through Grap2 and cyclin D-mediated signalling pathways . In mice, it is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumours. In vitro, it acts as an inhibitory HLH protein, for example, blocking transcription of the HNF-4 promoter. In its function as a cyclin D1-binding protein it is able to reduce CDK4-mediated phosphorylation of the retinoblastoma protein and to inhibit E2F-mediated transcriptional activity . GCIP has also been shown to have interact physically with Rad (Ras associated with diabetes), Rad being important in regulating cellular senescence . GCIP adopts a V-shaped conformation, with N and C-terminal five-helix bundles .
Tip pilin GBS104-like, Ig-like domain (GBS104-like_Ig)
Type: Domain

This domain is found in Streptococcus agalactiae tip pilin GBS104 and similar proteins . It is usually associated with von Willebrand factor type A domain (e.g.

), which inserts into the domain core composed of two sequentially segregated fragments. Members of this entry are likely to contain an intramolecular isopeptide bond. This domain does not include the two N-terminal strands that precede the inserted von Willebrand factor type A domain.
E3 ubiquitin-protein ligase CARP1/2, FYVE/PHD zinc finger (CARP1_2_FYVE)
Type: Domain

This entry represents the FYVE/PHD zinc finger form E3 ubiquitin-protein ligase RNF34 and RFFL, also known as Caspase regulator 1 and 2 (CARP1/2), respectively . This domain is also found in similar proteins from vertebrates.

CARP1 ubiquitinates the caspases CASP8 and CASP10, promoting their proteasomal degradation, to negatively regulate cell death downstream of death domain receptors in the extrinsic pathway of apoptosis . It negatively regulates p53/TP53 through its direct ubiquitination and targeting to proteasomal degradation .

CARP2 is a novel caspase regulator that regulates the p53 signalling pathway through degrading 14-3-3 sigma and stabilising MDM2 .
Tyrosine 3-monooxygenase-like, ACT domain (TH_ACT)
Type: Domain

This domain is found in tyrosine 3-monooxygenase (TH) similar proteins from vertebrates. TH catalyses the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine in the biosynthesis of the catecholamine neurotransmitters.

This entry represents the regulatory domain, which is centrally located between

and

). The ACT domain adopts a four stranded antiparallel β-sheet and two α-helices connected by four loops. This domain self-associates to form a dimer . In humans, TH is associated with several disorders .
E3 ubiquitin-protein ligase CARP2, FYVE/PHD zinc finger (CARP2_FYVE)
Type: Domain

This entry represents the FYVE/PHD zinc finger form E3 ubiquitin-protein ligase RFFL, also known as Caspase regulator 2 (CARP2) . This domain is also found in similar proteins from vertebrates.

CARP2 is a novel caspase regulator that regulates the p53 signalling pathway through degrading 14-3-3 sigma and stabilising MDM2 .
E3 ubiquitin-protein ligase CARP1, FYVE/PHD zinc finger (CARP1_FYVE)
Type: Domain

This entry represents the FYVE/PHD zinc finger form E3 ubiquitin-protein ligase RNF34, also known as Caspase regulator 1 (CARP1) . This domain is also found in similar proteins from vertebrates.

CARP1 ubiquitinates the caspases CASP8 and CASP10, promoting their proteasomal degradation, to negatively regulate cell death downstream of death domain receptors in the extrinsic pathway of apoptosis . It negatively regulates p53/TP53 through its direct ubiquitination and targeting to proteasomal degradation .
Capsid protein, N-terminal domain, fungal virus (P2_N_fungal_virus)
Type: Domain

This domain is found at the N-terminal end of Capsid protein from Penicillium chrysogenum virus (P2,

), which self-assembles to form an icosahedral capsid with a T=1 symmetry. It is organised into two domains with similar α-β morphology .
Thermo-DBP-RP2-like, C-terminal domain (Thermo-DBP2-like_C)
Type: Domain

This domain is found in proteins from archaea, including ThermoDBP-related protein (ThermoDBP-RP) 2 (

) from hyperthermophilic crenarchaea. This protein shows great affinity in vitro for single-stranded DNA and consists of two globular domains. The C-terminal domain, represented in this entry, is composed of a five-stranded, antiparallel β-sheet sandwiched between two α-helices .
Rhodopsin domain, fungi (Rhodopsin_dom_fungi)
Type: Domain

This entry describes the fungal rhodopsin domain, found in a wide range of fungi. This domain typically consists of seven transmembrane helices that form an interior pocket for the all-trans-retinal chromophore, which is covalently bound to a lysine residue in helix-G via a protonated Schiff base . While the core structure of the fungal rhodopsin domain shares similarities with other microbial rhodopsins, there are distinct differences. For instance, some fungal rhodopsins, like those found in Leptosphaeria, have an elongated extracellular loop 1 (ECL1) domain and an N-terminal β-strand, which appear to be signatures of a specific subfamily of fungal rhodopsins .

Fungal rhodopsins are membrane-embedded photoreceptors characterised by seven transmembrane helices and a retinal chromophore. They are widely distributed across fungal species, forming large multigene families . These proteins exhibit diverse functions, including light-driven proton pumping, green light sensing, and involvement in signalling pathways. Fungal rhodopsins are particularly prevalent in plant-associated and phytopathogenic fungi .
Autotransproter heptosyltransferase TibC/BAHTCr-like, N-terminal domain (TibC/BAHTCr-like_N)
Type: Domain

This entry represents the N-terminal domain of autotransproter heptosyltransferases TibC (

) from Escherichia coli, BAHTCr from Citrobacter rodentium and similar bacterial sequences. TibC is an autotransporter adhesin heptosyltransferase (AAH) homologue that catalyses the heptosylation of the autotransporters AIDA-I/TibA and confers AIDA-I-mediated bacterial adhesion to host cells. BAHTCr glycosylates the autotransporter CARC which is involved in the colonization of the mouse host gastrointestinal tract . This domain adopts a β-barrel fold with two four-stranded sheets that pack against each other . This domain is also found in BimC, an inactive autotransporter that lacks heptosyltransferase activity .
Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment (TM_ErbB1)
Type: Domain

Epidermal growth factor receptor (ErbB) family is a class of receptor tyrosine kinases (RTKs) that have a pivotal role in the processes of cell growth, proliferation, and differentiation . They exist on the cell surface as dimers in both active and inactive states, which switch between them through conformational changes upon ligand binding. They suffer a strong lateral dimerization that leads to proper assembly of their extracellular ligand-binding, single-span transmembrane, and cytoplasmic kinase domains which is key for ErbB activation. The transmembrane (TM) and juxtamembrane region of these receptors are essential for dimerization and activation .

This entry represents the TM and juxtamembrane segment of EGFR, ErbB2 and ErbB4 and similar sequences.
Tomato mosaic virus helicase, N-terminal domain (ToMV_Hel_N)
Type: Domain

Tomato mosaic virus (ToMV) generates two large replication proteins in the host cell. The smaller one contains the methyltransferase domain and the helicase domain (Hel). This core helicase domain consists of two RecA domains and an N-terminal accessory domain, represented in this entry, containing a flexible loop, a long α-helix and an antiparallel, six-stranded β-sheet. This N-terminal domain plays a role in the binding of the host factors TOM1 and ARL8 required for viral replication . It is also found in proteins from related viruses.
Topoisomerase I, zinc finger (TOP1_Znf)
Type: Domain

This entry represents a zinc ribbon domain found at the C terminus of topoisomerase I from gammaproteobacteria (it corresponds to D6 described in . Topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. The C-terminal domains bind ssDNA to recognise the accumulation of negative supercoils in duplex DNA .
DNA topoisomerase IB, N-terminal domain (Top1B_N_bact)
Type: Domain

This is the N-terminal of Type I topoisomerase from Deinococcus radiodurans and similar bacterial sequences. This small-sized protein modify DNA topology by cleaving and resealing one strand of duplex DNA. This domain comprises three α-helices plus a five strand antiparallel β-sheet . It is found associated with

.
Formamidopyrimidine-DNA glycosylase-like, C-terminal domain (Fpg-like_C)
Type: Domain

This entry represents the C-terminal domain of Formamidopyrimidine-DNA glycosylase-like from Arabidopsis thaliana (Fpg1) (SwissProt:

) and similar proteins from plants. Fpg is involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. It catalyses the hydrolysis of the N-glycosylic bond between the damaged base and the deoxyribose (glycosylase activity) before cleaving the DNA backbone (lyase activity). This domain, which shows four α-helices, two of them forming the helix-two-turn-helix (H2TH) motif, and two antiparallel β-strands involved in a structural motif mimicking an antiparallel β-hairpin zinc finger .
Type II DNA topoisomerase VI subunit A, all-beta domain (Topo_VI_alpha)
Type: Domain

In all organisms, type II DNA topoisomerases are essential for untangling chromosomal DNA. The archaeal type II protein is termed DNA topoisomerase VI. This entry represents an all-β domain found in these proteins.
Topoisomerase V, second (HhH)2 tandem domain (Topo-V_HhH2_2nd)
Type: Domain

This domain is found in Topoisomerase V from Methanopyrus kandleri (Topo-V), a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities. Topo-V consists of an N-terminal topoisomerase domain followed by 12 tandem (HhH)2 domains, showing four active sites. This entry represents the second of these tandem domains .
Flagellar protein FlgA-like, N-terminal domain (FlgA-like_N)
Type: Domain

This domain is found at the N-terminal end of Flagellar protein FlgA, putative from Thermotoga maritima (SwissProt:

). It adopts α-β structure.
Tyrosine-protein kinase receptor torso, second FN3 domain (Tor_FN3_2nd)
Type: Domain

This domain is found in the Tyrosine-protein kinase receptor torso from Bombyx mori (Tor), which is involved in the initiation of metamorphosis during postembryonic development. This protein is organised into three consecutive fibronectin type III (FN3) domains and a C-terminal Kinase domain . This entry represents the second FN3 domain.
Torsin-1A, C-terminal domain (TOR1A_C)
Type: Domain

This domain is found at the C-terminal of Torsin-1A from humans (TOR1A), an AAA ATPase that resides in the endoplasmic reticulum and the contiguous perinuclear space primarily in nerve cells. TOR1A needs the AAA-like proteins Lamina-associated protein 1 (LAP1) or Luminal domain like LAP1 (LULL1) to catalyse ATP hydrolysis. A single amino acid deletion in the domain represented in this entry is known to be at the root of primary dystonia, probably by weakening these interactions. This small domain forms a three-helical bundle .
Toxofilin domain (Toxofilin_dom)
Type: Domain

This domain is found in a group of proteins from eukaryotic parasites, including Toxofilin (

) from Toxoplasma gondii, an actin-binding protein involved in invasion. This domain interacts with the host mammalian actin. It folds into five α-helices connected by loops (

).