SII-SWORD/CoKE huggingface dataset:
Immunity protein 12 (Imm12)
Type: Domain

This entry represents a predicted immunity protein with an α+β fold and several conserved charged and hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family . The protein is also found in heterogeneous polyimmunity loci.
Protein of unknown function DUF4660 (DUF4660)
Type: Family

This entry represents a group of eukaryotic proteins that are typically between 93 and 189 amino acids in length.
Protein of unknown function DUF4659 (DUF4659)
Type: Family

This entry represents a group of eukaryotic proteins that are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.
Chromatin assembly factor 1 subunit p150, N-terminal (CAF1_p150_N)
Type: Domain

Chromatin assembly factor 1 (CAF-1) consists of three evolutionary conserved subunits, p150, p60, and p48 (yeast homologues Cac1, cac2 and cac3 respectively), and mediates the assembly of nucleosomes onto newly replicated DNA. The p150 subunit (CAF-1_p150, also known as subunit A) is the core component of the CAF-1 histone chaperone complex, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair , being essential for cell viability and efficient DNA replication . The p150 subunit contains the interaction regions with proliferating cell nuclear antigen (PCNA), heterochromatin protein 1 (HP1), the CAF-1 p60 subunit among others proteins . It is thought that the DNA association with two histone-bound CAF-1 complexes may promote the formation of the (H3-H4)2 tetramer on DNA .

This entry represents the N-terminal region of the CAF-1 subunit p150 that contains one of the PCNA (proliferating cell nuclear antigen) binding sites, designated PIP1 and the heterochromatin protein 1 (HP1) interacting domain MIR . These domains are dispensable for p150 role in nucleosome assembly and it is thought that this N-terminal region of CAF-1 might act as a regulatory domain contributing to CAF-1-PCNA interaction stability or mediate other functions during DNA repair or heterochromatin maintenance .
ZW10 interactor (Zwint-1)
Type: Family

ZW10 interactor (also known as Zwint-1) is part of the MIS12 complex, which is required for kinetochore formation and spindle checkpoint activity . It recruits ZW10 to unattached kinetochores at prometaphase . It is essential for stable binding of a Mad1-Mad2 complex to unattached kinetochores . It can be phosphoryltated by Aurora B (AurB) kinase .
Testis-expressed protein 19 (TEX19)
Type: Family

This family of proteins is expressed in testis and in undifferentiated embryonic stem cells from humans . Their function is not clear.
Draxin (Draxin)
Type: Family

Draxin is a chemorepulsive axon guidance protein required for the neural development . It acts as a Wnt antagonist that is predominantly expressed in developing neural tissues .
NarX-like, N-terminal (NarX-like_N)
Type: Domain

This domain is found N-terminal in histidine kinase NarX and other sensor proteins, as well as in type IV pilin, PilJ . This domain recognises nitrate and nitrite .
Developmental pluripotency-associated protein 3 (Dppa3)
Type: Family

Dppa3 (developmental pluripotency-associated protein 3), also known as Stella or PGC7, belongs to family known only in placental mammals . The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization . This suggests that it might bind methylated DNA sequences directly . Dppa3 also seems to be involved in the demethylation process during reprogramming of embryonic germ cell precursors . Most placental mammals contain 3-6 paralogues of this family.

The conserved core of Dppa3 includes a positively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion . The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins .
Bacterial toxin 8 (Ntox8)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a domain found in a predicted RNase toxin from bacterial polymorphic toxin systems. The toxin possesses an α+β fold and HxR and HxxxH motifs that is usually exported by the type 2 and type 6 secretion system .
UDP N-acetylglucosamine O-acyltransferase, C-terminal (Acetyltransf_C)
Type: Domain

This is the C-terminal domain of UDP N-acetylglucosamine O-acyltransferase. This enzyme is a zinc-dependent enzyme that catalyses the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate .
Ribose-phosphate pyrophosphokinase, N-terminal domain (Pribosyltran_N)
Type: Domain

This domain is found in N-terminal of ribose-phosphate pyrophosphokinase, frequently N-terminal to

.
Bacterial toxin 50 (Ntox50)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts between related strains. Toxin proteins of these systems are as a rule multi-domain and display a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved histidine, a serine, two lysine, and a threonine residue and a HxVP motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7, and MuF-type secretion system .
Sigma factor regulator, N-terminal (Sigma_reg_N)
Type: Domain

This domain is found near the N terminus of a sigma factor regulator. The N terminus is responsible for interaction with the sigma factor .
Bacterial toxin 4 (Ntox4)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Bacterial toxin 47 (Ntox47)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a two conserved aspartates, a glutamate, a histidine and an arginine residue and an RT motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system .
Retro-transcribing virus envelope glycoprotein (HERV-K_env)
Type: Domain

This entry represents a group of mammalian proteins that have retroviral origin. They are retrovirus K envelope glycoprotein genes that entry into human ancestral genome millions of years ago . These endogenous envelope proteins have lost their original fusogenic properties .
Chromatin assembly factor 1 subunit p150, C-terminal (CAF1-p150_C2)
Type: Domain

Chromatin assembly factor 1 (CAF-1) consists of three evolutionary conserved subunits, p150, p60, and p48 (yeast homologues Cac1, cac2 and cac3 respectively), and mediates the assembly of nucleosomes onto newly replicated DNA. The p150 subunit (CAF-1_p150, also known as subunit A) is the core component of the CAF-1 histone chaperone complex, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair , being essential for cell viability and efficient DNA replication . The p150 subunit contains the interaction regions with proliferating cell nuclear antigen (PCNA), heterochromatin protein 1 (HP1), the CAF-1 p60 subunit among others proteins . It is thought that the DNA association with two histone-bound CAF-1 complexes may promote the formation of the (H3-H4)2 tetramer on DNA .

This entry represents the C-terminal domain of CAF-1 subunit p150, which includes the winged helix domain (WHD), a DNA binding domain that requires the presence of histones, and a p60 subunit binding site. It is proposed that histone binding to CAF-1 triggers the DNA-WHD interaction, promoting the juxtaposition of two CAF-1 complexes bound to H3-H4 dimer and allows the formation of the tetramer on the DNA .
Bacterial toxin 43 (Ntox43)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold with two conserved histidine residues. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 or TcdB/TcaC-type secretion system . A of this, the Pseudomonas RhsT-C has been experimentally characterised.
Bacterial toxin 3 (Ntox3)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-β fold and conserved aspartate, arginine, histidine and cysteine residues that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Bacterial toxin 35 (Ntox35)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a conserved histidine residue and a KH motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 secretion system .
Bacterial toxin 33 (Ntox33)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold and [DN]xHxxK and DxxxD motifs. It is usually exported by the Type 2 secretory system .
Bacterial toxin 30 (Ntox30)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-β fold and two conserved histidines present in an RxH and THIP motif. The domain additionally has a highly conserved arginine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system .
Bacterial toxin 27 (Ntox27)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold and conserved aspartate and glutamate residues, and an RxW motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system .
Bacterial toxin 25 (Ntox25)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-β fold and conserved FGPY motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 5 secretion system .
Bacterial toxin 24 (Ntox24)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts. They are characterised by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-β fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system. Interestingly, the toxin is also found in type-II toxin-antitoxin systems .
Bacterial toxin 23 (Ntox23)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-β fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system .
Bacterial toxin 22 (Ntox22)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly β fold and two conserved histidines, two aspartates and a glutamate residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 5 secretion system .
Novel toxin 17 (Ntox17)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-β fold and a conserved ExD motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or TcdB/TcaC-type secretion system .
Novel toxin 16 (Ntox16)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-α helical fold and conserved (DNE)xxH motif and arginine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or Photorhabdus virulence cassette (PVC)-type secretion system .
Adenine DNA glycosylase, C-terminal (MutY_C)
Type: Domain

This entry represents the C-terminal domain of MutY. Its structure is similar to the NUDIX fold, which is an α/β/α sandwich .

Adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A-oxoG to C-G by removing the inappropriately paired adenine base from the DNA backbone. MutY belongs to a structural superfamily of proteins (the NUDIX hydrolase superfamily) that hydrolyse a wide range of organic pyrophosphates .

Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to oxo-dGMO and inorganic pyrophosphate. The similarity strongly suggests that the two proteins share a common evolutionary origin .
Novel toxin 14 (Ntox14)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Novel toxin 11 (Ntox11)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin contains two structural domains, an N-terminal α/β domain and a C-terminal all-β domain. This domain contains conserved GxR, RxxxoH GxE and GxxH motifs and a conserved histidine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Novel toxin 10 (Ntox10)
Type: Domain

This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold that is usually exported by the type 2 secretion system .
Splicing factor RBM39, linker (RBM39_linker)
Type: Domain

This entry represents a conserved linker between the second and the third RRM domain in human RBM39 (also known as CAPER) protein and other RNA splicing proteins. CAPER is a transcriptional coactivator of activating protein-1 (AP-1) and estrogen receptors (ERs). This linker was implicated in interactions with ERalpha and ERbeta . Preliminary results from JCSG suggest that this is a structured domain with a well defined fold.
RNA-directed RNA polymerase L, N-terminal (L_protein_N)
Type: Domain

This endonuclease domain is found at the N-terminal of many Bunyavirus L proteins , that possess a cap-snatching mechanism that cannibalizes host cellular mRNA cap structures and it is crucial for cap-dependent viral mRNA transcription. L protein is a RNA-dependent RNA polymerase responsible for replication and transcription of the viral RNA genome.
TBP-interacting protein, N-terminal (TIP_N)
Type: Domain

This entry represents the N-terminal restriction endonuclease-like domain found in several archaeal TATA-binding protein (TBP)-interacting proteins. The N-terminal domain forms an α/β structure, in which three α-helices enclose the central β-sheet .
Restriction endonuclease BpuSI, N-terminal domain (BpuSI_N)
Type: Domain

This entry represents the N-terminal (nuclease) domain of the BpuSI restriction endonuclease .
MvaI/BcnI restriction endonuclease (MvaI_BcnI)
Type: Domain

This entry represents a domain found in some restriction endonucleases, such as MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends .
Restriction endonuclease ThaI (ThaI)
Type: Family

This family of restriction endonucleases belongs to the PD-(D/E)XK superfamily . It cuts the recognition site CG^CG leaving blunt ends .
Chromatin assembly factor 1 subunit B, C-terminal (CAF1_p60_C)
Type: Domain

This entry represents the C-terminal domain of the chromatin assembly factor 1 subunit B (also known as CAF-1 subunit p60), which is one of the three subunits of the CAF-1 complex. This domain binds to the C-terminal region of the CAF-1 subunit A (

) . The N-terminal part of the CAF-1 p60 proteins has a WD-repeat (

).
Acid ceramidase, N-terminal (Acid_ceramidase_N)
Type: Domain

This entry represents the N-terminal domain of acid ceramidase (AC), which degrades ceramide into sphingosine and fatty acid , and N-acylethanolamine-hydrolysing acid amidase (NAAA). NAAA is an N-acylethanolamine-hydrolysing enzyme that shows structural and functional similarity to acid ceramidase . AC and NAAA can be cleaved into two chains: alpha and beta . This entry represent the beta subunit (chain).
HAUS augmin-like complex subunit 5 (HAUS5)
Type: Family

This entry represents HAUS augmin-like complex subunit 5 (HAUS5) from eukaryotes. The HAUS augmin-like complex shares similarity with Drosophila Augmin that regulates gamma-tubulin localization in mitotic spindles, but not at the centrosome. It contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis .

Plant and animal augmin complexes have similar functions in microtubule nucleation and organisation in mitotic microtubule arrays. The human augmin complex contains 8 subunits . The Arabidopsis augmin complex contains both conserved and unique subunits compared with its animal counterparts . This entry includes plant AUG5.
Choloylglycine hydrolase/NAAA C-terminal (CBAH/NAAA_C)
Type: Domain

This domain can be found in several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides. These include choloylglycine hydrolase (conjugated bile acid hydrolase, CBAH) (

), penicillin acylase (

) and acid ceramidase (

). This domain is also found at the C terminus of acid ceramidase (AC) and N-acylethanolamine-hydrolysing acid amidase (NAAA) . AC and NAAA can be cleaved into two chains: alpha and beta. This domain represent the alpha subunit (chain).
Overexpressed in colon carcinoma 1 (OCC1)
Type: Family

The human member of this family, overexpressed in colon carcinoma 1 protein (

) has been shown to be overexpressed in several colon carcinomas .
Protein of unknown function DUF4647 (DUF4647)
Type: Family

This entry represent a group of uncharacterised eukaryotic proteins. They are typically between 282 and 480 amino acids in length.
Protein phosphatase 1 regulatory subunit 35, C-terminal (PPP1R35_C)
Type: Domain

This entry represents the C terminus of protein phosphatase 1 regulatory subunit 35. This protein inhibits the serine/threonine-protein phosphatase PPP1CA .
Nuclear protein MDM1 (MDM1)
Type: Family

MDM1 is a microtubule-binding protein that negatively regulates centriole duplication. It binds to and stabilizes microtubules .
Putative RNase-like toxin, toxin1 (Ntox1)
Type: Domain

Prokaryotic polymorphic toxin systems are implicated in intra-specific conflicts between related strains. Toxin proteins of these systems are as a rule multi-domain and display a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. This entry represents a predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold and conserved cysteine, histidine and glutamate residues that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
snRNA-activating protein complex subunit 5 (SNAPC5)
Type: Family

snRNA-activating protein complex subunit 5 (also known as SNAPC5 or SNAPc19) is part of the core components of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes . The RNA polymerase II snRNA promoters consist of a proximal sequence element (PSE), while the RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. SNAPc binds to the PSE in both RNA polymerases and other PSE sequences in other snRNA genes. Therefore, SNAPc is also called the PSE transcription factor (PTF) or PSE-binding protein (PBP).
NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal (QueF_N)
Type: Domain

The QueF (NADPH-dependent 7-cyano-7-deazaguanine reductase) monomer is made up of two ferredoxin-like domains aligned together with their β-sheets that have additional embellishments. This subunit is composed of a three-stranded β-sheet and two α-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets .
Minor fimbrium subunit Mfa1, C-terminal (Mfa1_C)
Type: Domain

This entry represents the C-terminal domain of the Minor fimbrium subunit Mfa1 . It may play an important role in invasion of periodontal tissues and are recognized as major virulence factors .
Major fimbrial subunit protein, N-terminal (FimA_N)
Type: Domain

This entry represents the N-terminal of the major fimbrial subunit protein (FimA). FimA is the structural subunit of the fimbriae, which are filamentous appendages on the cell surface. Fimbriae of P.gingivalis are recognied as a major virulence factor as they mediate cell adhesion and play an important role in invasion of periodontal tissues . FimA proteins have been classified into five types, types I to V, based on nucleotide sequences. It has been found that type II FimA can bind to epithelial cells most efficiently through specific host receptors .