SII-SWORD/CoKE huggingface dataset:
Carbohydrate binding domain 30 (CBM30)
Type: Domain

This carbohydrate binding domain is found at the N-terminal of a Glycoside hydrolase family 9 (GH9) member from Acetivibrio thermocellus (

). This protein consists of GH9 and GH44 as catalytic modules (

and

, respectively), and a family 30 carbohydrate binding domain (CBM30), represented in this entry, which displays affinity for beta-1,4-glucopolymers and plays a pivotal role in the function of of GH9, a typical processive endoglucanase. This domain adopts a β-sandwich fold with two five-stranded β-sheets .
Carbohydrate binding module-like (CBM-like_2)
Type: Domain

This domain is found in a a group of bacterial proteins, including the uncharacterised Fibronectin type-III domain-containing protein from Agathobacter rectalis (

). It adopts a jelly-roll structure.
Histidine kinase VP0354-like, sensor domain (VP0354-like_sensor_dom)
Type: Domain

This entry represents the sensor domain found in the histidine kinase VP0354 from Vibrio parahaemolyticus (

) and similar sequences mainly found in gammaproteobacteria. This domain adopts an α/β structure . It is found associated with

and

.
Helicase SMUBP-2/HCS1, 1B domain (SMUBP-2_HCS1_1B)
Type: Domain

Proteins in this entry belong to the DNA2/NAM7 helicase family and includes SMUBP-2 (also known as IGHMBP2) from mammals and HCS1 (also known as DNA polymerase alpha-associated DNA helicase A) from yeasts.

This entry represents the 1B domain consisting of a short α-helix and a β-barrel. This domain forms the RNA-binding channel together with 1A, 2A and 1C domains . Domains 1B and 1C directly interact with the 3'-end of RNA.
Sortin nexin 17/31, FERM domain, F1 lobe (SNX17-31_FERM_F1)
Type: Domain

Sorting nexin 17 and 31 are known as PX-FERM proteins, a sub-group of the PX superfamily that contain a defining PtdInsP-binding PX domain, and a C-terminal 4.1, ezrin, radixin, moesin (FERM) domain . They are modular peripheral membrane proteins that act as central scaffolds mediating protein-lipid interactions, cargo binding, and regulatory protein recruitment .

The FERM domain comprises three lobes termed F1, F2, and F3: F1 adopts a ubiquitin-like fold, F2 is a helical structure similar to acyl-CoA binding protein (

), and F3 is similar to the phosphotyrosine binding (PTB)/pleckstrin homology domain and referred to as atypical FERM domain (

) . This entry represents the F1 lobe that folds as a prototypical ubiquitin/Ras association (RA) domain .
PylC, N-terminal domain (PylC_N)
Type: Domain

This domain is found at the N-terminal of archaeal PylC (3-methyl-D-ornithine--L-lysine ligase) and similar sequences from prokaryotes. PylC, an ATP-grasp enzyme composed of three domains, is required for the biosynthesis of pyrrolysine. This domain is composed of a central four-stranded β-sheet that is faced on both sides by two helices. It shows an adenine binding pocket that has not been observed in any homologous structure determined before .
PWWP domain-containing DNA repair factor 3A/3B/4, N-terminal (PWP3A_3B_4_N)
Type: Domain

This entry represents the N-terminal domain from PWWP domain-containing DNA repair factors 3A/3B/4 and similar animal proteins. It shows similarities to chromodomains and may function as a histone reader.

PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage . MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organisation of chromatin structure .
Sortin nexin 17/31, FERM domain, F2 lobe (SNX17-31_FERM_F2)
Type: Domain

Sortin nexin 17/31 are known as PX-FERM proteins, a sub-group of the PX superfamily that contain a defining PtdInsP-binding PX domain, and a C-terminal 4.1, ezrin, radixin, moesin (FERM) domain . They are modular peripheral membrane proteins that act as central scaffolds mediating protein-lipid interactions, cargo binding, and regulatory protein recruitment .

The FERM domain comprises three lobes termed F1, F2, and F3: F1 adopts a ubiquitin-like fold, F2 is a helical structure similar to acyl-CoA binding protein, and F3 is similar to the phosphotyrosine binding (PTB)/pleckstrin homology domain and referred to as atypical FERM domain (

) . This entry represents the F2 lobe .
RNA helicase Hera-like, dimerization domain (Hera-like_DD)
Type: Domain

This domain is found at the C-terminal region of Heat resistant RNA dependent ATPase from Thermus thermophilus (also known as Hera, (

) the first DEAD box helicase that forms a stable dimer in the absence of ligands. This dimerization domain (DD) folds into a single turn of a left-handed super-helix .
HepT-like domain (HepT-like_dom)
Type: Domain

This entry represents a group of proteins that are related to the HepT toxin-antitoxin system proteins

. This suggests that these proteins might be ribonuclease toxins.
Adenylyltransferase SoFic-like, C-terminal domain (SoFic-like_C)
Type: Domain

This domain is found at the C-terminal adenylyltransferase SoFic from Shewanella oneidensis and similar bacterial sequences. SoFic mediates the addition of adenosine 5'-monophosphate (AMP) to specific residues of target proteins. This is a winged-helix DNA-binding domain often found associated with (

) .
Glycoside phosphorylase, super sandwich domain (SOGP_2nd)
Type: Domain

Glycoside phosphorylases catalyse the phosphorolysis of oligosaccharides into sugar phosphates . This domain is the second of four domains (nDom2) found in the L. phytofermentans SOGP (sophoro-oligosaccharide beta-1,2-gluco-phosphorylase) (

) and similar bacterial proteins. This domain shows structural similarity to the first domain nDom1, suggesting a possible duplication event . The third domain is the catalytic GH94 domain .
ATP-dependent DNA helicase Hel308-like, domain 4 (Hel308-like_dom4)
Type: Domain

This entry represents a conserved region located towards the C-terminal of ATP-dependent DNA helicase Hel308 and similar archaeal helicases. This domain, named domain 4 in , folds into a seven α-helix bundle structure and seems to be unique within this helicase family. The central helix acts as a ratchet and mediates stacking interactions on base moieties of the DNA .
Glycoside phosphorylase, C-terminal domain (SOGP_C)
Type: Domain

Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates . This domain is the C-terminal domain found in the L. phytofermentans SOGP (sophoro-oligosaccharide beta-1,2-gluco-phosphorylase) (

) and similar bacterial proteins .
Bacteriophage T7 DNA helicase/primase, N-terminal (Helic-prim_T7_N)
Type: Domain

Bacteriophage T7 DNA helicase/primase (also known as Gp4) is an ATP-dependent DNA helicase and primase that is essential for viral DNA replication and recombination . Primase activity synthesises short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present. It consists of an N-terminal zinc ribbon (

) followed by a RNA Polymerase Domain that can be subdivided in an N-terminal α β structure, represented in this entry and a C-terminal TOPRIM fold (

) . At the C-terminal end of the protein there is a DNA helicase domain (

).
CbiG-like, linker domain (CbiG-like_linker)
Type: Domain

This domain is found once in the putative Cobalamin biosynthesis protein G homologue from the archaea Saccharolobus solfataricus (CbiG-like), which links CbiG N-terminal (

) and CbiG C-terminal domains (

).
Histone acetyltransferase type B catalytic subunit, C-terminal (HAT1_C)
Type: Domain

This entry represernts the C-terminal domain of human HAT1 and similar proteins from animals. This domain is highly variable and not required for HAT activity . It consists of a bundle of helices and a short β-strand.

Histone acetyltransferase type B catalytic subunit (HAT1) is the catalytic subunit of the histone acetylase B (HAT-B) complex (composed on HAT1 and HAT2 at least) . It is involved in different biological processes including cell progression, glucose metabolism, histone production or DNA damage repair. HAT1 acetylates histone H4 at Lys-5 and Lys-12, and to a lesser extend, Lys-5 in histone H2A .
Ciliogenesis-associated TTC17-interacting protein, N-terminal domain (CATIP_N)
Type: Domain

This is the N-terminal domain of Ciliogenesis-associated TTC17-interacting protein from humans (CATIP) and similar animal sequences. CATIP plays a role in primary ciliogenesis by modulating actin polymerisation . According to structure predictions, this domain folds into a structure mainly consisting of β-sheets.
NE1300-like (NE1300-like)
Type: Family

This entry represents a group of proteins from Nitrosomonadales, including NE1300 from Nitrosomonas europaea (

), which seems to be a binding partner of Hydroxylamine oxidoreductase (HAO) in vivo that may play a structural role in the ternary complex with cytochrome c554, the physiological electron acceptor of HAO. HAO is responsible for the conversion of hydroxylamine to nitrite in nitrifying bacteria. The exact function of NE1300 is not clear .
Receptor binding protein, neck domain (Caudo_bapla_RBP_neck)
Type: Domain

This domain is centrally located in the receptor binding protein from Lactococcus phage p2 (RBP, also known as Gp18) and similar proteins from closely related lactococcal phages. RBP shows three domains that form the phage tail base-plate: the N-terminal shoulder domain (

), which is attached to the phage, the neck domain and the C-terminal receptor-recognition head domain (

).

This entry represents the central neck domain, which folds into four β-strands, which interlace with the β-strands of two other subunits to form an equilateral triangular prism around the three-fold axis of a triple-stranded β-helix .
Receptor-binding protein, N-terminal shoulder domain (Caudo_bapla_N)
Type: Domain

Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. RBP shows three domains that form the phage tail base-plate: the N-terminal shoulder domain which is attached to the phage, the neck domain (

) and the C-terminal receptor-recognition head domain (

).

This entry represents the shoulder domain, found at the N-terminal of RBP. This domain contains a β-sandwich fold .
Kinetochore protein Sos7, coiled-coil domain (Sos7_CC)
Type: Domain

This entry represents the central coiled-coil domain of fission yeast Kinetochore protein Sos7 (

, also known as Outer kinetochore KNL1 complex subunit sos7) and related fungal proteins.

Attachment of sister chromatids to microtubules in the fission yeast Schizosaccharomyces pombe is mediated by the kinetochore complex NMS (Ndc80-MIND-Spc7). Sos7 is a component of the MIND complex and is required for kinetochore targeting of Spc7 . This fungal kinetochore family represented by Sos7 is not present in yeasts belonging to the Saccharomyces. Instead, these organisms have proteins homologous to the S. cerevisiae Spc105 interaction partner Kre28.
Phage tail base-plate attachment protein, C-terminal barrel domain (Caud_bapl16_4th)
Type: Domain

Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames. This entry represents the C-terminal RIFT barrel domain .
Phage tail base-plate attachment protein, C-terminal insertion domain (Caud_bapl16_3rd)
Type: Domain

Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames. This entry represents the insertion domain found within the C-terminal RIFT barrel domain .
Phage tail base-plate attachment protein, N0 domain (Caud_bapl16_2nd)
Type: Domain

Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames. This entry represents the N0 domain .
NE1300-like superfamily (NE1300-like_sf)
Type: Homologous_superfamily

This entry represents a group of proteins from Nitrosomonadales, including NE1300 from Nitrosomonas europaea (

), which seems to be a binding partner of Hydroxylamine oxidoreductase (HAO) in vivo that may play a structural role in the ternary complex with cytochrome c554, the physiological electron acceptor of HAO. HAO is responsible for the conversion of hydroxylamine to nitrite in nitrifying bacteria. The exact function of NE1300 is not clear .
Cation channel sperm-associated auxiliary subunit beta, N-terminal domain (CATSPERB_N)
Type: Domain

This entry represents the N-terminal domain from the Cation channel sperm-associated protein subunit beta .

CatSper (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility . The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore.

In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits, beta, gamma, delta and epsilon (CATSPERB/G/D/E) , CATSPERB is included in this entry, which mediates extensive contacts with other subunits and thus, it is involved in stabilising the channel complex.
SP_0191-like, C-terminal (SP_0191-like_C)
Type: Domain

This entry represents a domain predominantly found in streptococcus. Members include a lipoprotein from Streptococcus pneumoniae (

), whose structure is known and consists of six-stranded antiparallel β-sheet packed on one side with helices (

). The function of this domain is unknown.

This domain is always found C-terminal to a lipoprotein lipid attachment site suggesting that it may be associated with the membrane.
Cation channel sperm-associated auxiliary subunit beta, 2nd domain (CATSPERB_2nd)
Type: Domain

This entry represents the β-propeller domain from the Cation channel sperm-associated protein subunit beta protein (CASTPERB). The cation channel of sperm (CatSper) is essential for sperm motility and fertility. The auxiliary subunit beta contains a single transmembrane segment and a large extracellular region.

CatSper (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility . The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore.

In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits, beta, gamma, delta and epsilon (CATSPERB/G/D/E) , CATSPERB is included in this entry, which mediates extensive contacts with other subunits and thus, it is involved in stabilising the channel complex.
Cation channel sperm-associated protein subunit beta, C-terminal domain (CATSPERB_C)
Type: Domain

This entry represents the C-terminal segment of CASTPERB.

CatSper (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility . The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore.

In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits, beta, gamma, delta and epsilon (CATSPERB/G/D/E) , CATSPERB is included in this entry, which mediates extensive contacts with other subunits and thus, it is involved in stabilising the channel complex.
Glycoprotein Gn, base, hantavirus (Gn-B_hanta)
Type: Domain

The medium (M) genome segment of Hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins, Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor . Gn and Gc forms homotetramers (spikes) at the surface of the virion which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalisation predominantly through clathrin-dependent endocytosis . This entry represents the C-terminal region of the Gn ectodomain denoted as Gn base (Gn-B) which contributes the most to the intra-spike tetrameric contacts .
Glycoprotein Gc, C-terminal, bunyavirales (Gc_C_bunya)
Type: Domain

The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor. Gn and Gc forms homotetramers at the surface of the virion, which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalisation, predominantly through clathrin-dependent endocytosis . This protein has a typical class II fusion protein fold consisting of a central β-sandwich domain (termed domain I) made of eight β-strands arranged in two antiparallel β-sheets; domain II which has an elongated shape with two subdomains (a central, opened β-barrel proximal to domain I and a distal β-sandwich 'tip') and the C-terminal domain III, represented in this entry, which has a Ig-like fold . This domain is also found in similar proteins from bunyavirales.
CarD, C-terminal domain (CarD_C)
Type: Domain

This entry represents the C-terminal helical domain of CarD from Mycobacterium tuberculosis and similar sequences. CarD is a RNAP-binding protein that regulates transcription and essential processes . This domain binds DNA in a non-specific manner .
CapR homology domain (CapR_dom)
Type: Domain

This entry represents a domain that is found in CapR proteins of PLE phage satellites . Proteins in this entry are DNA-binding proteins.
Structural protein 2, C-terminal domain (SP2_C)
Type: Domain

This entry represents the third domain, also known as P-domain, of structural protein 2 (PORF2) of the hepatitis E virus. This domain adopts a β-barrel structure (

). The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation .
PWWP domain-containing DNA repair factor 3A/3B/4, C-terminal (PWP3A_3B_4_C)
Type: Domain

This entry represents the C-terminal α-helical domain from PWWP domain-containing DNA repair factor 3A/B/4 and similar animal proteins.

PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage . MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organisation of chromatin structure .
Non-Structural protein M domain, nairovirus (NSm_dom_nairovirus)
Type: Domain

This entry represents a domain found in the glycoprotein precursor complex (GPC) encoded in the M segment of nairovirus genome whose function is not yet known . It is located N-terminal to

.
Restriction endonuclease PvuRts1 I-like, N-terminal (PvuRts1I-like_N)
Type: Domain

This domain is found at the N-terminal end of Restriction endonuclease PvuRts1 I from Proteus vulgaris (

) and similar bacterial sequences. PvuRts1I a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine, an epigenetic marker that is crucial for multiple biological processes, over 5-methylcytosine and cytosine. This protein is organised into a nuclease domain (this entry) and a C-terminal SRA (SET and RING associated) domain (

). This domain adopts a typical three-layered α-β-α sandwich configuration, with a central five-stranded β-sheet surrounded by three α-helices on one side and one α-helix on the other side .
PutA, RHH domain (PutA_RHH)
Type: Domain

This domain is found in the Bifunctional protein PutA from Escherichia coli and similar sequences mainly found in proteobacteria. PutA is both a bifunctional proline catabolic enzyme that oxidises proline to glutamate for use as a carbon and nitrogen source and an autogenous transcriptional repressor of the put operon. This entry represents the N-terminal ribbon-helix-helix (RHH) domain, which consists of a β-strand and two α-helices. This domain has a Lys at the end of the β-strand that interacts directly with DNA bases through the major groove, contributing to transcriptional regulation .
P68 RBP/TagC-like, beta-propeller (P68_RBP_TagC-like_beta-prop)
Type: Domain

This entry represents the β-propeller receptor binding domain of a variety of bacteriophages, including the Staphylococcus aureus phage P68 . The cell wall of S. aureus typically contains poly-ribitol phosphate type wall teichoic acid (WTA), which is modified with D-alanine and N-acetyl-glucosamine (GlcNAc). It has been shown that phage psi11 requires GlcNAc residues on WTA for adsorption . Gp45 of phage psi11 was identified and characterised as the receptor-binding protein (RBP) . This domain has been suggested to bind to the GlcNAc substrate .

This domain can also be found within a group of bacterial proteins that have been associated with the synthesis of teichoic acid, including TagC from Bacillus subtilis (

), although its involvement in this process is not clear .

Some uncharacterised proteins from lower eukaryotes are also included in this entry.
Chromatin assembly factor 1 subunit Cac1-like, C-terminal domain (Cac1-like_C)
Type: Domain

Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during nucleosome assembly. CAF-1 complex is composed of several subunits. This entry represents the C-terminal domain of subunit Cac1 from yeast (also known as Chromatin assembly factor 1 subunit p90 or RLF2) and similar proteins from fungi and plants. This domain adopts a winged helix fold and binds to DNA in a sequence-independent manner . This domain was also found to mediate the (H3-H4)2 tetramerization .
Structural glycoprotein Gn, nairovirus (Gn_nairovirus)
Type: Domain

This entry represents the structural glycoprotein Gn from Nairovirus including CCHFV and Dugbe virus . Gn and Gc (at the C-terminal of M segment) form spikes on the viral surface and mediate virus entry into target cells . The C-terminal cytoplasmic tail contains a pair of tightly arranged dual β-β-α zinc fingers .
Structural protein 2, second domain (SP2_M)
Type: Domain

This entry represents the second domain, also known as domain M, of structural protein 2 (PORF2) of the hepatitis E virus. This domain folds into a β-barrel structure that has structural similarity to domains of RIFT-like fold (

). The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation . This domain is found in related proteins from Hepeviridae and Astroviridae.
Chaperone protein gp12 (Gp12)
Type: Family

This entry represents a group of proteins from tailed bacteriophages and prophages from firmicutes, including Chaperone protein gp12 from Lactococcus phage p2 (also known as ORF12), which is thought to be a chaperone for the tape measure protein that might help to maintain the tape measure protein in solution during tail assembly. This late-expressed protein shows an all-α structure with five α-helices oriented to form a hydrophobic cleft on the inner surface of the protein. It adopts a trimeric assembly, forming long spirals .
Decoration protein, N-terminal domain (DECO_N)
Type: Domain

Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. Decoration protein of phage T5 (also known as pb10) binds at the centre of the 120 hexamers formed by the major capsid protein . This protein consists of an N-terminal α-helical capsid-binding domain (this entry) and an Ig-like domain (

) .