SII-SWORD/CoKE huggingface dataset:
Toxofilin domain superfamily (Toxofilin_sf)
Type: Homologous_superfamily

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 (

).
Outer membrane-associated lipoprotein TP0453 (TP0453)
Type: Domain

This domain is found in TP0453 (

), a lipoprotein associated with the inner leaflet of the outer membrane of Treponema pallidum. This domain consists of an α/β/α-fold and includes five stably folded amphipathic α-helices and may function as a carrier of lipids, glycolipids, and/or derivatives during the biogenesis of the outer membrane (

) .
TRADD-like N-terminal domain (TRADD-like_N)
Type: Domain

This is the RRM fold domain prototyped by the version at the N-terminal of the TRADD protein. The TRADD-N domain is widely present in bacterial conflict systems and in a spectacular diversity of counter-invader systems in metazoa, especially in aggregating marine invertebrates. The domain is predicted to function as a signalling bridge linking invader sensing and effector deployment in multidomain proteins. Metazoans have two broad families of TRADD-N domains, the NCOA6 and the TRADD/DEDD-2 families respectively that are named after the prototypic vertebrate proteins in which they are found .
TRAF1-6, MATH domain (TRAF1-6_MATH_dom)
Type: Domain

Intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain which adopts a β-sandwich structure. This is the MATH domain of TNF receptor-associated factors 1-6 (TRAF1-6). In TRAFS, this domain is essential for self-association and receptor interaction .
Transposase protein (Transposase_29)
Type: Family

This entry represents a family of transposase proteins whose structure prediction shows closest similarity to the TN5 transposase protein .
Potential transfer protein TraK-like (TraK-like)
Type: Family

This entry represents the TraK protein (

) found in the pIP501 Type IV Secretion System operon. The protein localised to the cell envelope, facing towards the cell exterior, and behaves as a monomer under the tested conditions . It adopts a mixed α/β fold with seven α-helices and nine β-strands (

).
Immune protein Tsi1 (Tsi1)
Type: Family

This protein family includes Immune protein Tsi1 (

) from Pseudomonas aeruginosa and similar proteins from bacteria. Tsi1 plays a role in preventing early activation of toxin Tse1. Tsi1 binds to a large surface of Tse1 and thereby occludes the active site to specifically inhibits enzyme activity by forming a hydrogen bond with the catalytic diad. It adopts an all-β fold consisting of 14 β-strands, which constitute three antiparallel blade-shaped β-sheets (

) .
Immune protein Tsi1-like superfamily (Tsi1-like_sf)
Type: Homologous_superfamily

This protein family includes Immune protein Tsi1 (

) from Pseudomonas aeruginosa and similar proteins from bacteria. Tsi1 plays a role in preventing early activation of toxin Tse1. Tsi1 binds to a large surface of Tse1 and thereby occludes the active site to specifically inhibits enzyme activity by forming a hydrogen bond with the catalytic diad. It adopts an all-β fold consisting of 14 β-strands, which constitute three antiparallel blade-shaped β-sheets (

) .
Antitoxin TsiV3 (TsiV3)
Type: Family

Antitoxin TsiV3, also known as TsaB, is a immunity protein from Vibrio cholerae that inhibits the activity of toxin VgrG3, a protein found in the spike of the type VI secretion system (T6SS) syringe- like complex. TsiV3 folds into a three-helical bundle and adopts a dimeric assembly to bind the deep active-site groove of the catalytic domain in the C-terminal region of VgrG3, modifying the conformation and preventing substrate binding (PDBe:

) .
Antitoxin TsiV3 superfamily (TsiV3_sf)
Type: Homologous_superfamily

Antitoxin TsiV3, also known as TsaB, is a immunity protein from Vibrio cholerae that inhibits the activity of toxin VgrG3, a protein found in the spike of the type VI secretion system (T6SS) syringe- like complex. TsiV3 folds into a three-helical bundle and adopts a dimeric assembly to bind the deep active-site groove of the catalytic domain in the C-terminal region of VgrG3, modifying the conformation and preventing substrate binding (PDBe:

) .
DUF2264, N-terminal domain (DUF2264_N)
Type: Domain

This entry represents a N-terminal domain found in the DUF2264 family of uncharacterised proteins found mainly in bacteria and eukaryotes.
Tailspike protein-like, Ig-like domain (TSP_Ig-like)
Type: Domain

This domain is found in Tail spike proteins (TSP) from tailed bacteriophages (such as enterobacteria phages) and bacterial prophages. It forms a β-sandwich consisting of two antiparallel, three stranded β-sheets. A short α-helix is included in the connecting loop between the third and fourth strand. This domain is structurally homologous to viral coat proteins . In bacterial sequences, this domain appears to be inserted in the pectin lyase fold domain.
Immunoglobulin delta heavy chain-like, delta linker region (IgD_del_linker)
Type: Domain

This entry represents the linker region of human Immunoglobulin delta heavy chain (IgD) and similar sequences from primates. This region is the longest hinge sequence of any immunoglobulin, which connects the Fab and Fc fragments. It has up to seven O-linked oligosaccharide sites, and is thought to be related to the flexible T-shape of IgD .
Rolling stone (Rost)
Type: Family

This entry includes protein rolling stone (Rost) from fruit fly (

) and related eukaryotic proteins. It is a transmembrane protein involved in myoblast fusion .
DNA gyrase subunit B, hook (GyrB_hook)
Type: Domain

This entry represents the N-terminal section of the 'Toprim hook' as described in , which is localised between the Toprim (

) and the insert (

) domains . The C-terminal section of the hook is included in (

). The hook is flexible towards the Toprim domain. Proteins in this group are found mainly in proteobacteria.
Baseplate hub protein gp44-like, N-terminal (GpP-like_N)
Type: Domain

This domain is found at the N-terminal end of Baseplate hub protein gp44 from Escherichia phage Mu (GpP,

) and similar proteins predominantly found in tailed bacteriophages and proteobacterial prophages.
Methionyl-tRNA formyltransferase-like, C-terminal domain (Formyl_trans-like_C)
Type: Domain

This domain is found at the C-terminal end of Methionyl-tRNA formyltransferase from Acetivibrio thermocellus (

) and similar bacterial sequences. This domain is usually found associated with

.
Small heat shock protein p36, N-terminal domain (Tsp36_N)
Type: Domain

This domain is found at the N-terminal end of Small heat shock protein p36 from the parasitic flatworm Taenia saginata (Tsp36) and similar proteins from flatworms. Tsp36 is organised into two α-crystallin domains, two repeat segments on the N-terminal side, a linker region, and a long N-terminal segment of about 80 residues (this entry). This domain consists of a series of helices with sharp turns between them marked by prolines .
Small heat shock protein p36, N-terminal domain superfamily (Tsp36_N_sf)
Type: Homologous_superfamily

This domain is found at the N-terminal end of Small heat shock protein p36 from the parasitic flatworm Taenia saginata (Tsp36) and similar proteins from flatworms. Tsp36 is organised into two α-crystallin domains, two repeat segments on the N-terminal side, a linker region, and a long N-terminal segment of about 80 residues (this entry). This domain consists of a series of helices with sharp turns between them marked by prolines .
Type VI secretion system TssR-like, C-terminal domain (T6SS_TssR-like_C)
Type: Domain

This entry represents the C-terminal domain from the TssR protein. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex .
Type VI secretion system TssR-like, second domain (T6SS_TssR-like_dom_2)
Type: Domain

This entry represents the second domain of TssR which adopts a small β-barrel structure. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex .
Type VI secretion system TssR-like, VWA domain (T6SS_TssR-like_VWA)
Type: Domain

This entry represents the VWA-like domain from the TssR protein. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex .
Zinc finger protein ZFPM1/2, PR domain (ZFPM1/2_PR)
Type: Domain

This entry represents a domain found in Zinc finger protein ZFPM1/2 from humans and similar proteins from vertebrates. ZFPM1, also known as FOG1, is a transcriptional regulator involved in the coordination of the differentiation of platelets and erythrocytes . ZFPM2 plays a central role in heart morphogenesis and development of coronary vessels from epicardium, by regulating genes that are essential during cardiogenesis . This domain shares close structural similarity with SET domains, showing substantial β-sheet secondary structure. Its specific function remains unknown .
TELO2-interacting protein 1, middle region repeats (TTI1_rpt)
Type: Repeat

This entry includes TELO2-interacting protein 1 from yeast and its homologues from mammals. Human TTI1 is a regulator of the DNA damage response (DDR). It is part of the TTT complex that is required to stabilize protein levels of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family proteins. The TTT complex is involved in the cellular resistance to DNA damage stresses . Together with the TTT complex and HSP90, participates in the proper folding of newly synthesized PIKKs . Members of this entry are entirely composed of HEAT repeats .
RMI1, N-terminal domain (RMI1_N)
Type: Domain

The N-terminal domain of RecQ-mediated genome instability protein 1 carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha . At the very N-terminal, it has a three α-helical bundle, represented in this entry, which protrudes to one side of the structure and makes extensive hydrophobic contacts with the convex side of the β-barrel .
Tubulin-like protein TubZ, C-terminal domain (TubZ_C)
Type: Domain

Tubulin-like protein TubZ (

) is a tubulin-like, filament forming GTPase, the motor component of the type III plasmid partition system which ensures correct segregation of the pXO1 plasmid. This entry represents the C-terminal GTPase-activating domain of TubZ (

).
Flagellin, barrel domain (FLIC_barrel)
Type: Domain

This entry represents a barrel domain of flagellins FliC and FljB from enterobacterales, which have a boomerang-shape with one arm composed of domain D1 and the other formed by D2 and D3 . This entry corresponds to to subdomain D2b described in .
Rhamnogalacturonan lyase family 11, C-terminal domain (RGL11_C)
Type: Domain

This is the eight-bladed β-propeller domain found at the C-terminal of Rhamnogalacturonan endolyase YesW and Rhamnogalacturonan exolyase YesX from Bacillus subtilis and other bacterial polysaccharide lyases from family 11 (RGL11). These proteins are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Additionally to this domain, they have a β-sheet domain at the N-terminal

.
Testis-expressed protein 13C/D, MVPLGDSxSHS repeat (TX13C/D_rpt)
Type: Repeat

This entry represents a repeat found in TEX13C and TEX13D (Testis-expressed proteins) from human and similar proteins from mammals. These repeats have the conserved pattern MVPLGDSxSHS.
Chorismatase FkbO/Hyg5-like, N-terminal (FkbO_Hyg5-like_N)
Type: Domain

This domain is found at the N-terminal region of Chorismatase (FkbO) (SwissProt:

) and 3-hydroxybenzoate synthase (Hyg5) (SwissProt:

) from Streptomyces hygroscopicus and in similar bacterial proteins. These enzymes catalyse the hydrolysis of chorismate into pyruvate and (dihydro)benzoic acid derivatives and are involved in the biosynthetic pathways forming polyketidic immunosuppressants such as ascomycin (FK520) and tacrolimus (FK506), which prevent T-cell proliferation through initial binding to the immunophilin FKBP12. FkbO is organised into three domains: N-terminal, central and C-terminal. This entry represents the N-terminal and central domains of FkbO, which show two β-sheets and three α-helices. This fold is also found in Hyg5, which employ a fundamentally different reaction mechanism than the typical hydrolysis seen in FkbO
BF1531-like, N-terminal domain (BF1531-like_N)
Type: Domain

This domain is found at the N-terminal end of a group of bacterial predicted enzymes, including BF1531 from Bacteroides fragilis (

). It shows an α/β structure.
Fimbrium tip subunit Fim1C-like, C-terminal domain (Fim1C-like_C)
Type: Domain

This domain is found at the C-terminal end of the putative fimbrium tip subunit Fim1C from Parabacteroides distasonis (SwissProt:

), and similar proteins from bacteroidetes. Fim1C is thought to be a component of the fimbrium tip that plays a role on the mediation of cell adhesion and biofilm formation. This domain shows a transthyretin-like fold that contains seven core β-strands arranged in two β-sheets .
GspD-like, N0 domain (GspD-like_N0)
Type: Domain

GspD is a type II general secretion pathway protein involved in protein export. This entry represents the N0 domain found at the N-terminal of GspD type II secretins and its close homologues . These proteins form a dodecameric ring, in which the N0 domain mediate extensive contacts suggesting that dodecameric N0 ring is an important feature of T2SS secretins . This domain is also found in virion export proteins, proteins thought to form a channel across the host outer membrane for the purposes of extruding the bacteriophage.
Protein phosphatase 1 regulatory subunit 21, C-terminal (PPP1R21_C)
Type: Domain

This entry represents the C-terminal coiled-coil which contains the characteristic TTKRSYEDQ sequence-motif .

Protein phosphatase 1 regulatory subunit 21 (PPP1R21) belong to a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. PPP1R21 is a regulator of protein phosphatase 1 (PP1) activity and may play a role in the endosomal sorting process or in endosome maturation pathway . These proteins also contain an N-terminal domain with a KLRAQ motif (

). Protein phosphatase 1 regulatory subunit 21 is likely a regulator of protein phosphatase 1 (PP1) activity . It may play a role in the endosomal sorting process or in endosome maturation pathway
L-tyrosine decarboxylase, C-terminal (TyrDC_C)
Type: Domain

This is the C-terminal (small) domain of tyrosine decarboxylase from Enterococcus faecalis (

) and related species . These are PLP-dependent decarboxylases that catalyse tyrosine decarboxylation to produce tyramine. This domain may play a regulatory role.
Adenovirus fiber, head domain (Fiber_head_adenovirus)
Type: Domain

This domain is found at the C-terminal end of proteins from adenovirus, including Fiber from Bovine adenovirus 4 (BAdV-4), which is essential for host cell interaction. This domain shows a β-sandwich with two four-stranded β-sheets and an α-helix in a loop .
Fibroin heavy chain, N-terminal domain (Fib-H_N)
Type: Domain

This domain is found at the N-terminal end of Fibroin heavy chain (Fib-H) from Bombyx mori (

) and similar proteins mainly from insects. This hydrophilic region plays an important role in the assembly of silk by changing its conformation in response to pH decreases: it transitions from random coil to β-sheets and form micelle-like oligomers at around pH 6.0 .
Fibroin heavy chain, N-terminal domain superfamily (Fib-H_N_sf)
Type: Homologous_superfamily

This domain is found at the N-terminal end of Fibroin heavy chain (Fib-H) from Bombyx mori (

) and similar proteins mainly from insects. This hydrophilic region plays an important role in the assembly of silk by changing its conformation in response to pH decreases: it transitions from random coil to β-sheets and form micelle-like oligomers at around pH 6.0 .
Factor H binding protein, N-terminal (FHBP_N)
Type: Domain

Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease . The structure of the N-terminal domain consists of a more unusual taco-shaped β-barrel fold characterised by higher intrinsic flexibility than the C-terminal one . Members of this group of proteins are mainly found in betaproteobacteria.
Factor H binding protein (FHBP)
Type: Family

This entry represents a family of proteins from betaproteobacteria, including Factor H binding protein from Neisseria meningitidis (FHBP) (

). FHBP is a surface exposed lipoprotein that is a potent antigen and a potential candidate for a vaccine against meningococcal disease .
Factor H binding protein B domain (FhbB_dom)
Type: Domain

Treponema denticola, a human pathogen that contributes to periodontitis, survives by binding factor H (FH) to its surface through its Factor H binding protein B (FhbB). The structure of this protein is highly ordered consisting of an α-β fold. This highly thermostable protein forms a weak dimer with an interface occurring along one α-helix from each subunit in an anti-parallel alignment with no direct hydrogen bonding between the subunits . This domain covers most of the protein length in some sequences, including FhbB from Treponema denticola (

).
Factor H binding protein B domain superfamily (FhbB_dom_sf)
Type: Homologous_superfamily

Treponema denticola, a human pathogen that contributes to periodontitis, survives by binding factor H (FH) to its surface through its Factor H binding protein B (FhbB). The structure of this protein is highly ordered consisting of an α-β fold. This highly thermostable protein forms a weak dimer with an interface occurring along one α-helix from each subunit in an anti-parallel alignment with no direct hydrogen bonding between the subunits . This domain covers most of the protein length in some sequences, including FhbB from Treponema denticola (

).
3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, C-terminal domain (UbiD-like_C)
Type: Domain

This domain is found C-terminal in 3-octaprenyl-4-hydroxybenzoate carboxy-lyase from Escherichia coli (UbiD) and similar sequences from cellular organisms. This enzyme catalyses the third reaction in ubiquinone biosynthesis and requires Mn2+ for optimal activity .

This domain is also found in a number of decarboxylase enzymes such as bacterial Gallate decarboxylase , Pyrrole-2-carboxylic acid decarboxylase and Phenolic acid decarboxylase ; and yeast Ferulic acid decarboxylase 1 .
Carbohydrate kinase FGGY, C-terminal domain (FGGY_C_2)
Type: Domain

This domain is found at the C-terminal end of Carbohydrate kinase, FGGY from Novosphingobium aromaticivorans (

) and similar proteins mainly found in proteobacteria and bacteroidetes. This protein may catalyse the transfer of a phosphate group from ATP to their carbohydrate substrates. It contain two large domains, which are separated by a deep cleft. This domain, thought to be responsible for ATP binding, shows an α-β configuration.
3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, N-terminal domain (UbiD-like_N)
Type: Domain

This domain is found N-terminal in 3-octaprenyl-4-hydroxybenzoate carboxy-lyase from Escherichia coli (UbiD) and similar sequences from cellular organisms. This enzyme catalyses the third reaction in ubiquinone biosynthesis and requires Mn2+ for optimal activity .

This domain is also found in a number of decarboxylase enzymes such as bacterial Gallate decarboxylase , Pyrrole-2-carboxylic acid decarboxylase and Phenolic acid decarboxylase ; and yeast Ferulic acid decarboxylase 1 .
P56 (P56)
Type: Family

This entry represents a small family of proteins from tailed bacteriophages, including Protein p56 from Bacillus subtilis phage phi29. P56 inhibits the host uracil-DNA glycosylase (UDG) activity, preventing its binding to DNA and therefore viral replication from being compromised. p56 adopts a dimeric fold, with three anti-parallel β-sheets and a helical region linked by three short loops in each polypeptide chain (

). The highly anionic region of the protein plays a key role in the inhibition, which occurs by mimicking the DNA substrate (

) .
FAK1-like, FERM domain C-lobe (FAK1-like_FERM_C)
Type: Domain

FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localises to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lobe, FERM_M or B-lobe and FERM_C or C-lobe. This entry represents the C-lobe, which is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites . This domain is also present in protein-tyrosine kinase 2-beta (also known as PYK2), a cytoplasmic, non-receptor tyrosine kinase which is a close paralogue to FAK in vertebrates. FRMPD1/3/4 also contain this domain; FRMPD1 regulates the subcellular location of activator of G-protein signalling 3 and its interaction with G-proteins. FRMPD4 has been shown to regulate dendritic spine morphogenesis and the function of FRMPD3 is not clear.
Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central (FCSD_central)
Type: Domain

This domain is located centrally in Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain from the proteobacteria Allochromatium vinosum (

) , a component of the enzyme that catalyses the reversible conversion of sulphide to elemental sulfur in vitro. This domain is C-terminal to

and N-terminal to

. It shows a five-stranded parallel β-sheet flanked on one side by three α-helices and on the other side by a three-stranded anti parallel β-sheet .
Ubiquitin-fold modifier 1 specific protease 2-like, N-terminal (UfSP2-like_N)
Type: Domain

This domain is found at the N-terminal of the eukaryotic protein Ubiquitin-fold modifier 1 (Ufm1), specific protease 2 (UfSP2) and similar proteins. UfSP2 is a cysteine protease which recognises and hydrolyses the peptide bond at the C-terminal Gly residue of the protein Ufm1, a ubiquitin- like modifier. This protein is organised into two domains: the catalytic C-terminal (

) and a N-terminal showing a six-stranded β-sheet with five α-helices

.
Fibrillin, first EGF domain (FBN_EGF_N)
Type: Domain

Fibrillins are the primary constituents of the microfibrills in the extracellular matrix of many elastic and non-elastic connective tissues. They consist of an N-terminal fibrillin unique domain (FUN) (

) and several calcium-binding epidermal growth factor-like (cbEGF-like) domains . This entry represents the first EGF-like domain which together with FUN, contributes to the binding to cbEGFs . Members of this group are found in mammals, fish and birds.
TTHA0281-like (TTHA0281-like)
Type: Family

This entry represents a family of prokaryotic uncharacterised proteins that adopt an α-β-β-β-α fold and are structurally similar to HicB-like antitoxin, including TTHA0281 from Thermus thermophilus (

). TTHA0281, which belongs to the uncharacterised protein family UPF0150, is speculated to be involved in RNA metabolism, including RNA binding and cleavage .