SII-SWORD/CoKE huggingface dataset:
Hfq-related (Hfq_1)
Type: Domain

Hfq proteins participate in RNA folding and translational regulation through pairing of small RNAs and messenger RNAs. Hfq proteins share the distinctive Sm fold, and form ring-shaped structures similar to those of the Sm/Lsm proteins regulating mRNA turnover in eukaryotes.

This entry represents Hfq-related proteins found mainly in Cyano- and Acidobacteria. Although these proteins share low sequence similarity with the bacterial Hfq proteins, they retain the common structural features and fold . These proteins bind very weakly to known Hfq target RNAs and have altered RNA-binding properties.
Condensin complex protein MksE (MksE)
Type: Family

This entry represents a small family of MksE proteins. These proteins are part of MksBEF complex, which primarily function in structural chromosome maintenance . The N-terminal part of MksE is remotely related to the chromosome partition protein MukE and most likely adopts the same structure that consists of two winged helix domains (WHD) .
Mobilization protein NikA-like (NikA-like)
Type: Family

This family includes homologues of mobilisation protein NikA, such as protein TraJ as well as MobC, MobB and MobA. These proteins are involved in mobilisation and replication functions of plasmids. They are distantly related to accessory factor PcfF and likely adopt similar homo-dimeric structure consisting of N-terminal DNA-binding ribbon-helix-helix (RHH) domain and a C-terminal stalk domain.
DnaD, N-terminal domain (DnaD_N)
Type: Domain

DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. The DnaD N-terminal domain has a scaffold-forming activity. This domain adopts a classical winged helix fold decorated with extensions at both termini .
Allophanate hydrolase, C-terminal domain (AH_C)
Type: Domain

Allophanate hydrolase (AH) converts allophanate to ammonium and carbon dioxide. The AH structure is composed of N- and C-terminal domains. These domains catalyse sequential reactions: the N-terminal domain converts allophanate to N-carboxycarbamate, whereas the C-terminal domain converts it to carbon dioxide and ammonium . The C-terminal domain folds into α/β structure in which some of the β-strands form a barrel-like shape. This entry represents the C-terminal domain.

This domain is also found in Urea amidolyase that is involved in hydrolysis of urea to ammonia and CO2.
Domain of unknown function DUF6927 (DUF6927)
Type: Domain

This domain is found at the C-terminal of uncharacterised bacterial proteins. It is probably remotely related to PemK-like, MazF-like toxins and is predicted to adopt SH3-like fold.
Histidyl-tRNA synthetase HisZ, C-terminal domain (HisZ-C)
Type: Domain

This entry represents the C-terminal domain of HisZ mainly found in Bacillales. This is the anticodon binding domain, which consists of three-stranded parallel β-sheet flanked on each side with α-helices.

HisZ is a regulatory subunit of the heteromeric ATP phosphoribosyl transferase that regulates reactions initiating histidine biosynthesis. HisZ is composed of two domains for the catalytic reaction and for anticodon binding. In contrast to other class-II aminoacyl-tRNA synthetases, it lacks the essential editing domain.
Protein of unknown function DUF6928 (DUF6928)
Type: Family

This is a family of uncharacterised bacterial proteins. They are predicted to adopt an α/β structure with a central nine-stranded antiparallel β-sheet with α-helices packed on both sides. The predicted structure has some partial structural similarity to bacterial S-adenosylmethionine decarboxylases.
DNA polymerase IV/DNA polymerase iota-like, thumb domain (IMS_HHH_1)
Type: Domain

This entry represents the thumb domain found in DNA polymerase iota and related proteins such as members of the eukaryotic Y-family DNA polymerases, like DNA repair protein REV1, as well as bacterial Pol IV. This domain makes contacts with the minor groove of DNA .

Y-family polymerases are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases . Y-family that include polymerase eta, kappa, iota and REV1. They exhibit different specificity and fidelity in the lesion bypass owing to the differences in their active site architectures. The Y-family polymerases share similar organisation consisting of an N-terminal catalytic core followed by a flexible intrinsically disordered region and a set of regulatory protein-protein interaction modules toward the C terminus. Architecturally, the catalytic core is reminiscent to the classical polymerases in which the palm domain harbours the residues crucial for catalysis, whereas the thumb and finger domains grasp the DNA and make contacts with the primer and the template, respectively.

DNA polymerase IV is a poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. It copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. It exhibits no 3'-5' exonuclease (proofreading) activity and may be involved in translesional synthesis .
DUF5817, C-terminal domain (DUF5817_C)
Type: Domain

This entry represents a helix-turn-helix (HTH) domain found in a group of functionally uncharacterised archaeal proteins, typically associated with the DUF5817 (

).
Glycoside hydrolase 123, N-terminal domain (Glyco_hydro_123_N_2)
Type: Domain

This entry represents the N-terminal domain of a group of glycoside hydrolases 123, from bacteria , including N-acetylgalactosaminidase from Clostridium perfringens. This enzyme removes specific terminal N-D-acetylgalactosamine from glycosphingolipids. This domain folds into a twisted β-sandwich that consists of two 5-stranded β-sheets, two small β-strands and four small α-helices .
Protein of unknown function DUF6929 (DUF6929)
Type: Family

This is a family of uncharacterised bacterial proteins. They are predicted to fold into five-bladed β-propeller that has similarity to apyrase but it is circularly permuted. The C-terminal two β-strands of this domain occupy the position of the two N-terminal β-strands in apyrase.
Protein of unknown function DUF6910 (DUF6910)
Type: Family

The function of this family of proteins is unknown. They are predicted to adopt a five-bladed β-propeller and are probably distantly related to apyrase.
Antitoxin FitA-like, ribbon-helix-helix (FitA-like_RHH)
Type: Domain

This is the ribbon-helix-helix (RHH) motif found in antitoxin FitA from Neisseria gonorrhoeae and similar bacterial sequences, such as the putative antitoxin VapB12/VapB14 and VapB1 from Mycobacterium tuberculosis . FitA is the antitoxin component of a type II toxin-antitoxin (TA) system. It binds DNA through its ribbon-helix-helix motif .
Domain of unknown function DUF7018 (DUF7018)
Type: Domain

This entry represents a domain of unknown function predominantly found in protein sequences from Bacillus. Many members of this group show this domain at the N-terminal and DUF3994 (

) at the C-terminal. According to structure predictions, this domain consists of α-helices, suggesting it is the membrane spanning region of these sequences.
Protein of unknown function DUF6931 (DUF6931)
Type: Family

This is a family of uncharacterised bacterial proteins. They share significant sequence similarity with immunity protein Imm5 (

) and are predicted to adopt similar α-helical structure.
Cytokine receptor-like factor 2-like, domain 1 (TSLPR_D1)
Type: Domain

Cytokine receptor-like factor 2 also known as TSLPR is a receptor for thymic stromal lymphopoietin. It contains two ectodomains with Ig-like topology. This family represents the first of these domains.

This entry also includes cytokine receptor common subunit gamma, also known as IL2RG, that is known to bind with low affinity to interleukin-2, interleukin-4, interleukin-15, interleukin-21 while in complex with their high affinity cytokine receptors
CRISPR system endoribonuclease Csx1, CARF domain (Csx1_CARF)
Type: Domain

CRISPR system endoribonuclease Csx1 is a metal-independent, endoribonuclease that acts selectively on ssRNA and cleaves specifically after adenosines, as part of the type III-B CRISP-Cas system, and is homologous to Csm6 , sharing the same domain domain architecture consisting of a CARF domain at the N-terminal that is relatively well conserved, and a HEPN nuclease domain at the C-terminal. This entry represents the CARF (CRISPR-associated Rossmann fold) domain, which binds and cleaves the cyclic oligoadenylate molecule (cA) that then activates the HEPN domain.
Arb2 domain (Arb2_dom)
Type: Domain

This entry represents Arb2 domain that was first described in Argonaute-binding protein 2 from S. pombe, from which it gets the name. Arb2 protein is the orthologue of FAM172 from animals, including FAM12A from human, a protein associated with CHARGE syndrome, a severe multi-organ developmental disorder mainly affecting derivatives of cranial and cardiac neural crest cells (NCCs). A general pathological mechanism for CHARGE syndrome has been suggested to be a spliceosomopathy, the perturbation of chromatin-mediated alternative splicing . FAM172A and its homologues contain a large ARB2 domain split into two halves by a classical bipartite NLS that helps to stabilize the chromatin-spliceosome interface as part of a complex that includes CHD7 and AGO2 . It has been suggested that FAM172A can connect the alternative splicing machinery to specific transcribed chromatin regions . Arb2 from S.pombe is a member of the argonaute siRNA chaperone (ARC) complex which is required for histone H3K9 methylation, heterochromatin assembly and siRNA generation . This domain has clear homology to α/β-hydrolases but it lacks the catalytic triad of these enzymes.
Diphosphomevalonate decarboxylase-like N-terminal domain (MVD-like_N)
Type: Domain

This entry represents the N-terminal domain of Diphosphomevalonate decarboxylases which catalyse the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Members of this entry function in the mevalonate pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis.

Diphosphomevalonate decarboxylases are structurally related members of the GHMP superfamily , but do not possess kinase activity.

This entry also includes domains from Mevalonate-3-kinase which catalyses the phosphorylation of mevalonate to mevalonate-3-phosphate. This enzyme functions in an alternative mevalonate pathway, which passes through mevalonate 3-phosphate rather than mevalonate 5-phosphate .
Protein of unknown function DUF6932 (DUF6932)
Type: Family

This is a family of uncharacterised bacterial proteins. They are remotely related to nucleotidyltransferases (

) and share similar active site architecture.
Bacteriophage Mu Gp45, N-terminal (Phage_Mu_Gp45_N)
Type: Domain

This entry represents the N-terminal domain of Gp45 and similar sequences. This domain may adopt a OB-like β-barrel fold.

This entry includes Gp45 from bacteriophage Mu. Gp45 is a component of the baseplate that forms a central needlelike spike used to puncture the host cell membrane for tube insertion during virus entry. It serves as the distal plug of tail tube channel and might regulate the process of the phage DNA and protein ejection into the host cell . The characteristics of the protein distribution suggest prophage matches.
Glyoxalase/Bleomycin resistance-like, N-terminal (Glyoxy/Ble-like_N)
Type: Domain

This entry represents the N-terminal glyoxalase-like domain found in a group of proteins from bacteria, archaea and fungi, related to glyoxalase and bleomycin resistance proteins.
Domain of unknown function DUF6933 (DUF6933)
Type: Domain

This domain is found mainly in bacterial uncharacterised proteins. It is typically between 150 and 160 amino acids in length. It is remotely related to ribonuclease H-like nucleases but it is unlikely to possess any enzymatic activity.
Protein of unknown function DUF6934 (DUF6934)
Type: Family

This is a family of uncharacterised bacterial proteins. They are predicted to adopt an α/β structure consisting of a central mixed β-sheet packed on both sides with α-helices that is reminiscent to the common structural core of N-acetyltransferases (NAT).
PhyR, sigma2 domain (PhyR_sigma2)
Type: Domain

This entry represents the N-terminal domain of the signal transduction response regulator PhyR and related bacterial proteins. It consists of three α-helices and together with sigma4 domain (

), it constitutes the PhyR N-terminal sigma-like (SL) domain . This domain was shown to bind to anti-sigma factor NepR .
PhyR, sigma4 domain (PhyR_sigma4)
Type: Domain

This entry represents a domain of PhyR, a signal transduction response regulator, and related proteins found mainly in Alphaproteobacteria. PhyR contains a C-terminal receiver domain (

) and extracytoplasmic function (ECF) σ-like (SL) domain at the N terminus. The SL domain consists of sigma2 and sigma4 subdomains with the latter represented by this entry . PhyR is the regulator of the two-component signal transduction system which controls transcription in response to general stress.
Pel9A-like, right handed beta-helix region (Pel9A-like_beta_helix)
Type: Domain

This region is found in Pectate lyase L from Erwinia chrysanthemi (Pel9A) and similar bacterial and fungal proteins. Pel9A shows endo-cleaving activity on polygalacturonate or partially methylated pectin and has an important role in soft-rot disease. This region forms a parallel β-helix domain .
C5a peptidase, third Fn3 domain (ScpA_Fn3_3rd)
Type: Domain

This is the third Fn3 domain found at C5a peptidase from Streptococcus pyogenes (ScpA) and similar sequences from firmicutes. ScpA is a multidomain cell-envelope subtilase that cleaves complement component C5a. This protein consists of a catalytic domain (

) with an inserted PA domain (

) and and three tandemly arranged fibronectin type III domains (Fn1-Fn3) .
TiaS-like, TCKD domain (TiaS-like_TCKD)
Type: Domain

This is the TCKD domain found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS and related proteins. TiaS is an ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) . It consists of four domains, the TCKD domain at the N-terminal followed by the FLD domain, an OB fold domain and a zinc ribbon domain (ZRD) domain at the C-terminal . This domain is responsible for ATP binding .
CATSPERG, beta-propeller domain (CATSPERG_beta-prop)
Type: Domain

This entry represents the β-propeller domain of the gamma subunit (CATSPERG) .

The CatSper (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4 that functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation . This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly . These are multidomain proteins which share a similar domain organisation.
CATSPERG, N-terminal domain (CATSPERG_N)
Type: Domain

This entry represents the N-terminal domain of the gamma subunit (CATSPERG) .

The CatSper (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4 that functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation . This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly . These are multidomain proteins which share a similar domain organisation.
CATSPERG, C-terminal domain (CATSPERG_C)
Type: Domain

This entry represents the C-terminal domain of the gamma subunit (CATSPERG), which covers the Stem domain and the transmembrane helix, involved in the association with the channel domain .

The CatSper (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4 that functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation . This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly . These are multidomain proteins which share a similar domain organisation.
CATSPERG, Ig-like domain (CATSPERG_Ig-like)
Type: Domain

This entry represents the Ig-like domain of of the gamma subunit (CATSPERG).

The CatSper (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4 that functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation . This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly . These are multidomain proteins which share a similar domain organisation.
Cytochrome c-type protein NrfB-like domain (Cytochrom_c_NrfB-like_dom)
Type: Domain

This entry includes Cytochrome c-type protein NrfB and similar proteins, which plays a role in nitrite reduction. These proteins contain several copies of the CXXCH haem-binding motif .
Phage integrase, central domain (Phage_int_M)
Type: Domain

This is the central domain of phage integrases and similar sequences from tailed bacteriophages and bacterial prophages. This domain is known to mediate DNA binding and binds to the major groove adjacent to the site of DNA cleavage . It consists of two pairs of antiparallel helices that pack together at nearly a right angle and form a four-helix bundle.
Anti-sigma-K factor RskA, N-terminal domain (RskA_N)
Type: Domain

This domain is found at the N-terminal of the anti-sigma-K factor from Mycobacterium tuberculosis (RskA) and similar proteins mainly found in actinomycetes.

RskA (regulator of sigma K) represses the extra-cytoplasmic function (ECF) sigma factor K (sigK) by binding to it and inhibiting its activity . This leads to a decreased expression of SigK-regulated genes, such as MPB70 and MPT83. RskA from Mycobacterium bovis is however probably dysfunctional, due to at least one of the two natural occurring polymorphisms in its encoding gene, when compared to M. tuberculosis . This leads to an increased expression of SigK-regulated genes.
Major fimbrium subunit FimA, C-terminal domain (FimA_C)
Type: Domain

This entry represents the C-terminal domain of Major fimbrium subunit FimA from Porphyromonas gingivalis and similar sequences from Bacteroidales. It folds into a Ig-like β-sandwich having the characteristic features of the FimA superfamily.

FimA is the structural subunit of the fimbriae, which are filamentous appendages on the cell surface. Fimbriae of P.gingivalis are recognised as a major virulence factor as they mediate cell adhesion and play an important role in invasion of periodontal tissues .
HYDIN/VesB/CFA65-like, Ig-like domain (HYDIN_VesB_CFA65-like_Ig)
Type: Domain

VesB is a serine protease that is secreted by the type II secretion system (T2S) in Vibrio cholerae (

). It efficiently cleaves a trypsin substrate, but not chymotrypsin and elastase substrates . It has been suggested to contribute to intestinal growth or pathogenesis, although is not the only factor required for intestinal survival. VesB can cleave the A subunit of cholera toxin, a process important for cholera toxin activation . It consists of a protease domain (

) followed by a Ig-like domain, represented in this entry, which may be involved in one or more different functions such as stabilizing the protease domain, co-defining substrate specificity, binding to the bacterial surface and being part of a yet undefined secretion motif of the T2S system . This protein belongs to the chymotrypsin subfamily A (which includes mostly eukaryotic proteases), having a structure and specificity profile resembling that of eukaryotic trypsin-like proteases. This domain is also found in some eukaryotic protein, such as HYDIN and CFA65 from human (which contain repeated Ig-like domains).
GPR180-like, N-terminal domain (GPR180-like_N)
Type: Domain

This entry represents the N-terminal domain of GPR180 and TMEM145.

This entry includes GPR180 (also known as intimal thickness-related receptor, ITR) and TMEM145 . In vivo analyses of this gene revealed that expression of GPR180 protein increased with intimal thickening induced by cuff placement around murine femoral artery. Furthermore, GPR180-knockout mice were found to be resistant to this experimental intimal thickening . GPR180 was first thought to be an orphan Rhodopsin-like GPCR (G protein-coupled receptor) given structural similarities to GPCR transmembrane region, however, it was then confirmed not to signal as a a GPCR . This protein is associated with TGF-beta signalling as it regulates the activity of the TGF-beta receptor complex through SMAD3 phosphorylation. Furthermore, GPR180 is also required for the action of Collagen triple helix repeat containing 1 (CTHRC1) to regulate brown and beige adipocyte activity and glucose homeostasis .

GPR180 and TMEME145 are homologous to TMEM181 and Wntless (WLS), which have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) together with TMEM87A/B, GPR107, and GPR108, given they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain .
Utp8, C-terminal (Utp8_C)
Type: Domain

This domain is found at the C-terminal of U3 small nucleolar RNA-associated protein 8 (Utp8) from Saccharomyces cerevisiae and similar proteins from fungi. Utp8 is an essential component of the nuclear tRNA export machinery in S. cerevisiae. It is a tRNA binding protein that acts at a step between tRNA maturation /aminoacylation, and translocation of the tRNA across the nuclear pore complex . It is also co-purified with the U3 snoRNA containing complex, the small subunit (SSU) processome, which is required for the biogenesis of the 18S rRNA . This entry also includes the C1565.05 protein from Schizosaccharomyces pombe. Its function is not clear. This domain shows an all-α structure.
Nlrc4-like, winged helix domain (Nlrc4-like_WHD)
Type: Domain

This entry represents the winged helix domain (WHD) of NLR family CARD domain-containing protein 4 from mouse (Nlrc4) and similar sequences from vertebrates. Nlrc4 is a component of the inflammasome activated as part of the innate immune response .

This domain is also found in human Baculoviral IAP repeat-containing protein 1 (NAIP, Neuronal apoptosis inhibitory protein), which prevents motor-neuron apoptosis induced by a variety of signals and acts as a sensor component of the NLRC4 inflammasome .
DUF3097, N-terminal domain (DUF3097_N)
Type: Domain

This entry represents a domain found at the N-terminal of a group of uncharacterised proteins mainly found in Actinomycetes. Members of this group are thought to have a nuclease function . This domain is predicted to show high structural similarity with a Tudor domain.
DUF4026, middle domain (DUF4026_middle)
Type: Domain

This entry represents a domain found in uncharacterised bacterial proteins. It is usually associated with

and

that flank this domain from N- and C-terminal ends, respectively. This domain is distantly related to SUFU-like domains.