SII-SWORD/CoKE huggingface dataset:
Small VCP/p97-interacting protein, metazoa (SVIP_metazoa)
Type: Family

This entry includes mammalian SVIP (small VCP/p97-interacting protein) SVIP and its homologues from animals. It was identified by yeast two-hybrid screening to be an interactive partner of VCP/p97. Mammalian VCP/p97 and its yeast counterpart Cdc48 participate in the formation of organelles, including the endoplasmic reticulum (ER), Golgi apparatus, and nuclear envelope. SVIP has been identified as an endogenous inhibitor of endoplasmic reticulum-associated degradation . Over-expression of SVIP caused the formation of large vacuoles that seemed to be derived from the ER . Proteins in this family have two putative coiled-coil regions and are approximately 80 amino acids in length.
Large helicase-related protein, winged-helix domain 4 (WH4_Lhr)
Type: Domain

This entry represents WH4 of Lhr. It shows three α-helices followed by two loops or 'wings' and two β-strands forming an antiparallel β-sheet .

This is a winged-helix (WH) domain is found in Large helicase-related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis (

) and similar bacterial sequences. These proteins have a C-terminal domain composed of a series of five WH modules (named WH2 to WH6) and a β-barrel module.
Large helicase-related protein, winged-helix domain 3 (WH3_Lhr)
Type: Domain

This entry represents WH3 of Lhr. It shows three α-helices followed by two loops or 'wings' and two β-strands forming an antiparallel β-sheet .

This is a winged-helix (WH) domain is found in Large helicase-related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis (

) and similar bacterial sequences. These proteins have a C-terminal domain composed of a series of five WH modules (named WH2 to WH6) and a β-barrel module.
Large helicase-related protein, winged-helix domain 2 (WH2_Lhr)
Type: Domain

This entry represents WH2 of Lhr. It shows three α-helices followed by two loops or 'wings' and two β-strands forming an antiparallel β-sheet .

This is a winged-helix (WH) domain is found in Large helicase-related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis (

) and similar bacterial sequences. These proteins have a C-terminal domain composed of a series of five WH modules (named WH2 to WH6) and a β-barrel module.
Lsr2, DNA-binding domain (Lsr2_DNA-bd)
Type: Domain

This entry represents the DNA-binding domain found at the C-terminal of Lsr2. It binds AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates . This domain is also found in protein Ku from Mycobacterium phage Omega and Type II methyltransferase M.SalI.

This domain folds into a helix-extended loop-helix (HeH) structure known to engage in nucleic acids interactions.

Lsr2 is a small, basic DNA-binding protein present in Mycobacterium and related actinomycetes that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). It is a functional homologue of the H-NS-like proteins . H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression .

The Lsr2 protein is composed of two domains. The N-terminal domain mediates the dimerization of Lsr2 . The C-terminal DNA-binding domain of Lsr2 interacts with the minor groove of DNA, and shares similarity to other bacterial nucleoid-associated DNA-binding domains . The C-terminal domain is found associated with a variety of other protein domains (such as Ku and Ribonuclease T) where it presumably provides a DNA-binding activity.
SpaA-like, prealbumin fold domain subgroup 4 (SpaA_PFL_dom_4)
Type: Domain

This entry represents a domain found in uncharacterised bacterial proteins. Some members are likely to contain an isopeptide bond.
Carbohydrate-binding module family 96 (CBM96)
Type: Domain

This entry represents a CBM domain, a member of the

family, found in functionally diverse multi-domain proteins including tRNA nuclease WapA, alginate lyase from Defluviitalea phaphyphila, chondroitinase from Dysgonomonas sp. The CBM96 domain from the latter proteins, has been structurally characterised. It folds into a β-sandwich with a significant structural similarity to nucleoplasmin (

,

).
Ribophorin II, N-terminal domain (Ribophorin_II_N)
Type: Domain

This entry represents the N-terminal domain of eukaryotic Ribophorin II (RPN2, also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2) proteins, which forms an α/α6 structure.

The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3 .
Ribophorin II, third domain (Ribophorin_II_3rd)
Type: Domain

This entry represents the third domain of Ribophorin II (RPN2, also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2) proteins, which may adopt a β-sandwich fold.

The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3 .
Ribophorin II, second domain (Ribophorin_II_2nd)
Type: Domain

This entry represents the second domain of Ribophorin II (RPN2, also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2) proteins, which adopts a β-sandwich fold.

The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3 .
GH3, middle domain (GH3_M)
Type: Domain

This entry represents the middle domain of the GH3 IAA-amido conjugating enzyme family, which consists of a β-barrel .

This entry includes GH3 IAA-amido conjugating enzyme family, which consists of proteins that catalyse the synthesis of amino acid conjugates with indole-3-acetic acid (IAA) or jasmonate (JA), which are plant hormones. These enzymes play a crucial role in regulating plant hormone levels by conjugating excess IAA and JA to amino acids, thus providing a mechanism for plants to maintain hormonal homeostasis. The conjugation process is ATP-dependent and involves the adenylation of the hormone followed by the transfer to an amino acid. This group of proteins is involved in various plant physiological processes including disease resistance, stamen and carpel differentiation, floret fertility, and response to environmental stresses such as wounding and pathogen attack. Some members also exhibit activity towards synthetic auxins and may confer resistance to herbicides. Its broad substrate specificity includes various amino acids and analogues of IAA, contributing to the complexity of hormone regulation in plants .
GH3, C-terminal domain (GH3_C)
Type: Domain

This entry represents the C-terminal domain of the GH3 IAA-amido conjugating enzyme family, which consists of a single four-stranded β-sheet bracketed by two α-helices on each side .

This entry includes GH3 IAA-amido conjugating enzyme family, which consists of proteins that catalyse the synthesis of amino acid conjugates with indole-3-acetic acid (IAA) or jasmonate (JA), which are plant hormones. These enzymes play a crucial role in regulating plant hormone levels by conjugating excess IAA and JA to amino acids, thus providing a mechanism for plants to maintain hormonal homeostasis. The conjugation process is ATP-dependent and involves the adenylation of the hormone followed by the transfer to an amino acid. This group of proteins is involved in various plant physiological processes including disease resistance, stamen and carpel differentiation, floret fertility, and response to environmental stresses such as wounding and pathogen attack. Some members also exhibit activity towards synthetic auxins and may confer resistance to herbicides. Its broad substrate specificity includes various amino acids and analogues of IAA, contributing to the complexity of hormone regulation in plants .
BBS2, platform domain (BBS2_pf_dom)
Type: Domain

This entry represents the platform domain of BBS2.

BBSome complex member BBS2 (BBS2) is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. The BBSome complex is required for ciliogenesis, as well as the assembly and movement of intraflagellar transport proteins along the ciliary membrane.

Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. The BBSome is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction .

BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus , and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia .
BBS2, hairpin domain (BBS2_hp_dom)
Type: Domain

This entry represents the hairpin domain of BBS2. This domain connects to the C-terminal region of BBS9 .

BBSome complex member BBS2 (BBS2) is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. The BBSome complex is required for ciliogenesis, as well as the assembly and movement of intraflagellar transport proteins along the ciliary membrane.

Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. The BBSome is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction .

BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus , and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia .
BBS2, C-terminal helix bundle domain (BBS2_CtH_dom)
Type: Domain

This entry represents the C-terminal helix bundle domain of BBS2.

BBSome complex member BBS2 (BBS2) is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. The BBSome complex is required for ciliogenesis, as well as the assembly and movement of intraflagellar transport proteins along the ciliary membrane.

Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. The BBSome is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction .

BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus , and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia .
Domain of unknown function DUF7601 (DUF7601)
Type: Domain

This domain is found in tandem in a number of bacterial proteins which are likely associated with the bacterial cell surface. It is predicted to fold into a β-sandwich. Some members of this entry are likely to contain an intramolecular isopeptide bond connecting their N- and C-terminal strands. This family is closely related to

.
Tip attachment protein J, Fn3-1 domain (FN3-1_GpJ)
Type: Domain

This entry represents the first Fibronectin type III (Fn3) of Tip attachment protein J from Escherichia phage lambda (GpJ) and similar bacterial and viral proteins. It is often found in association with

and

.

The Tip attachment protein J (GpJ) from Escherichia phage lambda is a crucial tail fibre protein responsible for recognising and binding the host cell's LamB receptor, thereby initiating infection. Structurally, GpJ forms the central tail fibre at the phage tip and undergoes conformational changes upon receptor engagement, which are essential for triggering DNA injection into the host . It interacts with other tail proteins during assembly, serving as a scaffold for tail tube formation and coordinating with the tape measure protein to regulate genome delivery . Mutations in GpJ can alter host specificity and affect phage stability, while its exposed position makes it a target for neutralising antibodies .
Domain of unknown function DUF7604 (DUF7604)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is usually associated with von Willebrand factor type A domain (

), which is inserted into the domain core. Members of this entry are likely to contain an intramolecular isopeptide bond. The domain represented by this entry is predicted to fold into a β-sandwich. This entry does not include the two N-terminal strands that precede the von Willebrand factor type A domain and are segregated from the remaining part of the core domain.
Tip attachment protein J, HDII-ins2 domain (GpJ_HDII-ins2)
Type: Domain

This domain is found at the N-terminal of Tip attachment protein J from the bacteriophage lambda (GpJ) and similar sequences from tailed bacteriophages and bacterial prophages . This domain, which shows an Ig-like structure, undergoes rotation and determines the narrowest diameter within the hub domains (HDs) region in the final DNA channel .

The Tip attachment protein J (GpJ) from Escherichia phage lambda is a crucial tail fibre protein responsible for recognising and binding the host cell's LamB receptor, thereby initiating infection. Structurally, GpJ forms the central tail fibre at the phage tip and undergoes conformational changes upon receptor engagement, which are essential for triggering DNA injection into the host . It interacts with other tail proteins during assembly, serving as a scaffold for tail tube formation and coordinating with the tape measure protein to regulate genome delivery . Mutations in GpJ can alter host specificity and affect phage stability, while its exposed position makes it a target for neutralising antibodies .
Fanconi anaemia group A protein, helical domain (FANCA_helical)
Type: Domain

This entry represents the helical domain of Fanconi anaemia group A protein (FANCA), found in the central region of the protein, which is packed against the arcC half of the C-terminal domain .

Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
Fanconi anaemia group A protein, arcN subdomain (FANCA_arcN)
Type: Domain

This entry represents the N-terminal half of the arc-shaped C-terminal domain of Fanconi anaemia group A protein (FANCA), named arcN, which interacts with the C-terminal half of a second FANCA molecule in a head-to-tail manner to form a pseudo-symmetric dimeric interface . The C-terminal domain of FANCA (arcN and arcC halves) consists of HEAT repeats .

Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
Domain of unknown function DUF7617 (DUF7617)
Type: Domain

This domain is found in multiple copies in a number of bacterial proteins mainly from Actinomycetes. It is closely related to domains represented by

and

. Similarly to them, this domain contains a conserved N-terminal lysine and a C-terminal asparagine with central aspartate/glutamate residues suggesting that some members may contain an isopeptide bond. This domain is sometimes found in combination with

,

or

.
L-arabinose isomerase, N-terminal domain (AraA_N)
Type: Domain

This entry represents the N-terminal domain of L-arabinose isomerases, AraA, which is composed of a central parallel β-sheet packed with α-helices on both sides and with topology similar to the topology of the middle domain .

This entry includes L-arabinose isomerases, AraA, (

). These enzymes catalyse the reaction: L-arabinose => L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme .
L-arabinose isomerase, central domain (AraA_central)
Type: Domain

This entry represents a domain found central in L-arabinose isomerases, AraA. The domain represented by this entry is composed of a central parallel β-sheet packed with α-helices on both sides and with topology similar to the topology of the N-terminal domain .

This entry includes L-arabinose isomerases, AraA, (

). These enzymes catalyse the reaction: L-arabinose => L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme .
BROMI, N-terminal domain (BROMI_N)
Type: Domain

This entry represents the N-terminal domain of BROMI.

The Broad-minded family of proteins is essential for the proper response to Sonic hedgehog (Shh) signalling during neural tube development. Members of the Broad-minded family collaborate with cyclin-dependent kinase 20 (CDK20) to regulate the structure of the primary cilium. They are involved in the coordination of the ciliary membrane and axoneme assembly, which is crucial for the activation of the GLI2 transcription factor in response to Shh signalling . It interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in this protein in humans cause ciliopathies .
BROMI, C-terminal Rab TBC-like domain (BROMI_C)
Type: Domain

This entry represents the C-terminal Rab TBC-like domain .

The Broad-minded family of proteins is essential for the proper response to Sonic hedgehog (Shh) signalling during neural tube development. Members of the Broad-minded family collaborate with cyclin-dependent kinase 20 (CDK20) to regulate the structure of the primary cilium. They are involved in the coordination of the ciliary membrane and axoneme assembly, which is crucial for the activation of the GLI2 transcription factor in response to Shh signalling . It interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in this protein in humans cause ciliopathies .
EDC4-like protein pdc1, beta-propeller domain (Beta-prop_EDC4L)
Type: Domain

This entry represents the β-propeller domain of the enhancer of mRNA-decapping protein 4-like protein pdc1 from yeast. This protein is required for the assembly of processing bodies (P-bodies), cytoplasmic RNA granules where mRNA decay occurs . While evidence suggests pdc1 interacts with proteins Edc3 and Dcp2 through its terminal domains to achieve functional P-bodies, the function of this domain remains unknown . This entry also includes the β-propeller domain of pdc1's paralogue, the uncharacterised protein YAG9 (or eti1) from yeast, which localises to P-bodies and interacts with exonuclease Exo2 but whose function remains unknown .
TiaS, C-terminal zinc ribbon domain (Zn_ribbon_TiaS)
Type: Domain

This entry represents the zinc ribbon domain (ZRD) found at the the C-terminal of tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1-3]. This modified base specifically recognises AUA codons. TiaS consists of four domains, the TCKD domain (

) at the N-terminal followed by the FLD domain (

), an OB fold domain and a C-terminal ZRD. The ZRD domain is responsible for the recognition of the acceptor arm of tRNA(Ile2) .