SII-SWORD/CoKE huggingface dataset:
Tubulin-like protein TubZ-like, C-terminal domain (TubZ-like_C)
Type: Domain

This entry represents the C-terminal domain of TubZ from Bacillus thuringiensis and similar proteins from firmicutes. The structure of TubZ consists of an N-terminal GTPase domain and a C-terminal domain. TubZ is part of the polymerising cytomotive filament, a complex that drives newly replicated plasmids to opposite ends of the dividing cell .
HpiC1 cyclase (HpiC1)
Type: Family

This entry represents HpiC1, a Stig cyclase that catalyses the formation of 12-epi-hapalindole U. This enzyme folds into a β-sandwich with jelly-roll topology that is distantly related to galactose-binding domains. HpiC1 has two integral Ca2 ions, each with octahedral coordination geometry. Ca2 ions are required for catalytic activity .
GEO12453p1-like (GEO12453p1-like)
Type: Family

This protein family includes GEO12453p1 from Drosophila melanogaster (

, also known as CG13067) and similar sequences from insects. CG13067 is the product of a small open reading frame (small ORFs) contained in a long noncoding RNA (lncRNA) .
Retrovirus-related Pol polyprotein from transposon TNT 1-94-like, beta-barrel domain (PolX-like_BBD)
Type: Domain

This domain is found in retrovirus-related Pol polyproteins from transposon TNT 1-94 (PolX) from Nicotiana tabacum and similar retrovirus-related Pol polyprotein from transposons found in eukaryotes, mainly plant, fungi and arthropods. It is predicted to adopt a β-barrel fold with significant similarity to retroviral acid proteases.
Alpha-mannosidase Ams1-like, N-terminal (Ams1-like_N)
Type: Domain

This domain is found at the N-terminal of Alpha-mannosidase from Schizosaccharomyces pombe (Ams1) and its orthologues from eukaryotes including alpha-mannosidase 2C1 from vertebrates and alpha-mannosidase G from Dictyostelium discoideum. Ams1 hydrolyses terminal alpha-linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid-linked oligosaccharide donors. This entry represents the jelly-roll domain .
DNA (cytosine-5)-methyltransferase, N-terminal (DNM3A_N)
Type: Domain

This entry represents the N-terminal region of DNA (cytosine-5)-methyltransferase 3A (DNMT3A) from mouse and its homologues, a protein that is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. The dimethylation of lysine 44 (K44) in this region, contained in the conserved TARK tetrapeptide sequence, represents a molecular link between the mechanisms that establish DNA methylation and H3K9 methylation .
Minor extracellular protease Epr, GA-like domain (Epr_GA-like)
Type: Domain

This entry represents a small domain found in bacterial cell surface proteins such as the minor extracellular protease Epr from Bacillus subtilis. It adopts a three helical bundle structure and is often found in several tandem copies. This domain was identified in potential periscope proteins .

Epr is a serine protease involved in the production of the competence and sporulation stimulating factor CSF but not essential for growth or sporulation . In addition, is essential for swarming motility .
DUF569 associated ubiquitin-like domain (Ubiq_DUF569-assoc)
Type: Domain

This entry represents a small domain with a ubiquitin like fold found in plants, that is often associated with

. The function of this domain is not known.
Protein bicaudal C homolog 1, KH-like domain (BICC1_KH)
Type: Domain

This domain is found in human protein bicaudal C homolog 1 (Bicc1) and its homologues. Bicc1 is an RNA-binding protein composed of three KH and two KH-like domains that are linked by an intervening sequence to a C-terminal SAM domain. Bicc1 acts as a negative regulator of Wnt signalling . It is also involved in regulating gene expression during embryonic development. Bicc1 binds the 3' UTRs of the target mRNAs via KH domains, whereas self-polymerisation of its SAM domain mediates recruitment to large cytoplasmic foci for translational silencing . This entry represents the Bicc1 KH-like domains.
Ribosomal RNA small subunit methyltransferase B-like, ferredoxin-like domain (RsmB-like_ferredoxin)
Type: Domain

This entry represents a central ferredoxin-like domain found in SAM-dependent methyltransferases RsmB and related sequences (

, ).
Telomere ends associated, middle domain (Tea_mid)
Type: Domain

This entry represents a presumed domain, mostly α-helical, found near the middle region of protein telomere ends associated (Tea) found in Drosophila species and related fly sequences.

Tea protects telomeres from fusion and it likely functions as a component of the MTV complex along with moi and ver. The complex binds single-stranded DNA in a sequence-independent manner and can protect it from DNA degradation .
Telomere ends associated, C-terminal domain (Tea_C)
Type: Domain

This entry represents the C-terminal domain of protein telomere ends associated (Tea) found in Drosophila species and related fly sequences. The function of this domain is still unknown. According to structure predictions, it adopts and α/β structure consisting of 7 β-strands and 3 α-helices.

Tea protects telomeres from fusion and it likely functions as a component of the MTV complex along with moi and ver. The complex binds single-stranded DNA in a sequence-independent manner and can protect it from DNA degradation .
Histidine Kinase domain observed in conflict contexts (HisKin-conflict)
Type: Domain

This histidine kinase domain is predicted to function in signal transduction during effector activation in at least a subset of (TOTE TPR, OB, TBP, Effector) biological conflict systems .
NACHT C-terminal Alpha/Beta 2 (NCAB2)
Type: Domain

This is a domain containing α-helices and β-strands, found at the C-terminal of certain bacterial NACHT conflict systems .
Coenzyme PQQ synthesis protein F, C-terminal lobe, domain 3 (PqqF_C_3)
Type: Domain

This entry represents domain 3 from the C-terminal lobe of Coenzyme PQQ synthesis protein F (PqqF), a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented by

and domain 2) and C-terminal (domain 3 represented by this entry and domain 4 by

) lobes . Members of this group are mainly found in Pseudomonadales.
Coenzyme PQQ synthesis protein F-like, C-terminal lobe, domain 4 (PqqF-like_C_4)
Type: Domain

This entry represents domain 4 from the C-terminal lobe of Coenzyme PQQ synthesis protein F (PqqF,) a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented by

and domain 2) and C-terminal (domain 3 represented by

and domain 4 by this entry) lobes . This domain is also found in other Peptidase M16 members, such as insulin degrading enzymes from human .
NACHT C-terminal Helical domain 1 (NCH1)
Type: Domain

This is an helical domain found at the C-terminal of bacterial NACHT conflict systems .
NACHT C-terminal Helical domain 3 (NCH3)
Type: Domain

This entry represents an helical domain found at the C-terminal of bacterial NACHT conflict systems .
NACHT N-terminal Helical domain 6 (NNH6)
Type: Domain

This is the helical domain found at the N-terminal of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain .
Siphovirus-type tail component, C-terminal domain (Siphovirus-type_tail_C)
Type: Domain

This entry consists of several phage tail component proteins, including bacteriophage SPP1 distal tail protein Dit (also known as Gp19.1 or Gp19) , as well as some bacterial proteins of unknown function. This entry represents the C-terminal domain.
Coenzyme PQQ synthesis protein F, N-terminal lobe, domain 2 (PqqF_N_2)
Type: Domain

This entry represents domain 2 from the N-terminal lobe of Coenzyme PQQ synthesis protein F (PqqF), a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented by

and domain 2) and C-terminal (domain 3 and domain 4) lobes . Members of this group are mainly found in enterobacterales.
DNA double-strand break repair protein Mre11, second domain (Mre11_dom)
Type: Domain

This entry represents the second calcineurin-like nuclease domain of DNA double-strand break repair protein Mre11 from Pyrococcus furiosus and similar archaeal proteins. Mre11, also known as Mre11 nuclease, is part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. This domain consists of a β-sheet and two α-helices .
Autotransporter adhesin NhhA, Trp-ring domain (NhhA_Tpr-ring_dom)
Type: Domain

This domain is found in autotransporter adhesin NhhA from Haemophilus influenzae (also known as Hia) and similar proteins predominantly from proteobacteria. Hia is a trimeric autotransporter that mediates bacterial adherence to the respiratory epithelium. This protein shows a modular architecture with repeats of structurally distinct domains. This entry represents one of the Trp-ring domains .
PA2794-like, C-terminal (PA2794-like_C)
Type: Domain

This domain is found at the C-terminal of Exo-alpha-sialidase from Pseudomonas aeruginosa (PA2794,

), which adopts a trimeric structure, partly held together by an immunoglobulin-like trimerisation domain, represented in this entry, that is C-terminal to the sialidase domain

.
DNA double-strand break repair protein Mre11, thermococcales (Mre11_thermococcales)
Type: Family

This entry represents DNA double-strand break repair protein Mre11 from Pyrococcus furiosus and similar proteins mainly found in thermococcales. Mre11, also known as Mre11 nuclease, is part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair .
GLMA-like, second domain (GLMA-like_second)
Type: Domain

This entry represents the second domain of exo-beta-D-glucosaminidase (GLMA) from Thermococcus kodakarensis and similar archaeal and bacterial proteins, just before the C-terminal domain (

). It is an exo-type enzyme that specifically cleaves the non-reducing terminal glycosidic bond of chitooligosaccharides, being involved in chitin degradation . This is an α/β fold domain with central β-sheets and α-helices .

This domain is also found in the beta-1,2-glucosyltransferase which acts on the beta-1,2-glucooligosaccharides and has a very broad specificity for the acceptor by acting on various aryl- and alkyl-glucosides . It catalyses the transfer of a glucosyl residue from the non-reducing end of a 1,2-beta-D-glucan to a glucose residue of an acceptor molecule, forming a beta-1,2-glucosidic bond .
GLMA-like, C-terminal (GLMA-like_C)
Type: Domain

This entry represents a β-sandwich domain found at the C-terminal of exo-beta-D-glucosaminidase from Thermococcus kodakarensis (GLMA) and similar archaeal proteins. It is an exo-type enzyme that specifically cleaves the non-reducing terminal glycosidic bond of chitooligosaccharides, being involved in chitin degradation .
NAD(P)H:rubredoxin oxidoreductase, C-terminal domain (NROR-like_C)
Type: Domain

This domain is found at the C-terminal end of NAD(P)H:rubredoxin oxidoreductase from Pyrococcus furiosus (NROR) and similar sequences mainly found in archaea. NROR catalyses the NADH -dependent reduction of rubredoxin (Rd), a small iron-containing redox protein . This domain, likely to be involved in dimerisation, is often found associated with

.
PF0095-like, C-terminal domain (PF0095-like_C)
Type: Domain

This domain is found at the C-terminal end of the transcription factor PF0095 from Pyrococcus furiosus (

) and similar archaeal sequences.
DNA polymerase II small subunit, N-terminal domain (PolB_N)
Type: Domain

This domain is found at the N-terminal of DNA polymerase II small subunit from Pyrococcus horikoshii (PolB) and similar sequences from thermococcales. PolB possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. This domain folds into a four α-helix bundle that includes a short parallel β-sheet .
NBAS subunit of NRZ tethering complex, C-terminal (NBAS_C)
Type: Domain

This domain is found towards the C-terminal of human NBAS subunit of NRZ tethering complex (NBAS) and similar sequences mainly found in vertebrates. NBAS (also known as Neuroblastoma-amplified sequence) is involved in Golgi-to-endoplasmic reticulum (ER) retrograde transport . This domain is predicted to adopt an all-α structure.
Interferon-gamma receptor, N-terminal domain (CR4_N)
Type: Domain

This domain is found at the N-terminal of Interferon-gamma receptor from Ectromelia virus (C4R,

) and similar viral sequences. CR4 consists of two fibronectin type III domains (FBNIII) containing seven conserved β-strands each: this entry and

.
E3 SUMO-protein ligase MMS21, N-terminal domain (MMS21_N)
Type: Domain

This domain is found at the N-terminal of E3 SUMO-protein ligase MMS21 from Saccharomyces cerevisiae and similar proteins specific to Saccharomycetales. MMS21 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. This domain forms an helix bundle with a coiled-coil structure. It is required for the binding to Smc5, which is essential for cell growth and resistance to DNA damage .
U8 snoRNA-decapping enzyme NudT16 (NudT16)
Type: Family

This entry represents a group of proteins mainly found in animals that contain the NUDIX hydrolase domain, including U8 snoRNA -decapping enzyme NudT16 . NudT16 was initially described as an RNA-binding and decapping enzyme but it was later reported to be specialised in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. It adopts a canonical NUDIX fold, an α-β-α sandwich constituted by two β-sheets whose strands interact in a way that could also be described as a single extended β-sheet .
Sas-6-like, oligomerization domain (Sas-6-like_oligomerization)
Type: Domain

This entry represents the coiled-coil region of Sas-6 from Chlamydomonas reinhardtii (

), which mediates oligomerisation . In human, Sas-6 is essential for the onset of procentriole formation and accumulates on the torus where Plk4 has focused. This entry is specific to Chlorophyta.
Tubulin-like protein TubZ, C-terminal domain, clostridia-type (TubZ_C_clostridia)
Type: Domain

This domain is found at the C-terminal end of Tubulin-like protein TubZ from Clostridium botulinum C phage and similar sequences found in tailed bacteriophages and prophages from Clostridium species. TubZ is a tubulin-like, filament forming GTPase. This protein adopts a tubulin/FtsZ protein family fold organised into two domains, a canonical N-terminal GTP-binding domain, and a C-terminal GTPase domain (this entry) .
Type II secretion system protein E, N1E domain (GSPE_N1E)
Type: Domain

Type II secretion system protein E (GSPE) is an ATPase component of the type II secretion system required for the energy-dependent secretion of extracellular factors such as proteases and toxins from the periplasm. This entry represents its N-terminal N1E domain, which associates with the cytoplasmic domain of the inner membrane protein GspL .
Putative surface anchored protein-like, helical insertion domain (Lrp-like_ins_dom)
Type: Domain

This entry represents the helical insertion domain found in surface proteins in certain pathogens, such as Putative surface anchored protein from Streptococcus pneumoniae (Lrp,

, ).
RickCE-like, catalytic domain (RickCE_cat)
Type: Domain

This entry represents the catalytic domain of a subset of ubiquitin-like proteases from the CE clan, including RickCE from Rickettsia bellii (

, ).
Transcriptional regulator DIP2311-like, C-terminal domain (DIP2311-like_C)
Type: Domain

This domain is found at the C-terminal of transcriptional regulator DIP2311 from Corynebacterium diphtheriae (

) and similar bacterial sequences. This domain, which shows a winged helix fold, is normally found associated to

.
Glutathione S-transferase, C-terminal domain, proteobacteria (GST_C_proteobact)
Type: Domain

This domain is found at the C-terminal of Glutathione S-transferase from Agrobacterium fabrum (Atu5508,

) and similar sequences mainly found in proteobacteria. This domain adopts an α-helical configuration .
Terminase, large subunit, ribonuclease H-like domain (Gp19_RNaseH-like)
Type: Domain

This entry represents the C-terminal ribonuclease (RNase) H-like domain in the terminase, large subunit from Escherichia phage T7 (Gp19), which functions as an ATP-powered molecular motor essential for the translocation of viral DNA into empty capsids. It also acts as an endonuclease, cleaving the viral genome at a specific and precise double-stranded DNA sequence to initiate and conclude the packaging process . Members of this group are found in tailed bacteriophages and bacterial prophages.
Argonaute, middle domain (Ago_mid)
Type: Domain

This domain is found in protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domains: N (

), PAZ (

), Mid (this entry) and PIWI (

). This domain contains residues that have been reported to be critical for cleavage activity. It folds into an α-β three layered sandwich . This group of proteins is specific to Thermus species.
Argonaute, N-terminal domain, thermus (Ago_N_thermus)
Type: Domain

This domain is found at the N-terminal of protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N (this entry), PAZ (

), Mid (

) and PIWI (

). This domain shows a mixed α-β structure . This group of proteins is specific to Thermus species.
SLBB domain (SLBB_dom)
Type: Domain

This entry represents a set of soluble ligand-binding β-grasp domain (SLBB) domains from bacterial and eukaryotic NADH:ubiquinone oxidoreductases, including human NDUFV1 , and bacterial polysaccharide export proteins, such as Wza from Escherichia coli . This domain has been proposed to bind soluble cofactors .
Initiator protein NS1-like, N-terminal domain, Bocavirus (BoV_NS1-like_N)
Type: Domain

This entry represents the N-terminal domain of the Human bocavirus 1 (HBoV1) nonstructural protein 1 (NS1) and similar sequences specific to bocavirus. HBoV-NS1 is a member of the histidine-hydrophobic-histidine (HUH) superfamily of endonucleases .
Cas10/Cmr2, second palm domain (Cas10-Cmr2_palm2)
Type: Domain

This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems . This domain contains a conserved GGDD motif that is important for DNA polymerase activity .
Phage tubulin-like protein, C-terminal domain (PhuZ_C)
Type: Domain

This domain is found at the C-terminal of phage tubulin-like protein from the Pseudomonas phage phiKZ (PhuZ, also known as TubZ) and similar viral sequences. TubZ is a tubulin-like GTPase that forms filaments, which are required for positioning viral DNA and capsids in the middle of the host cell for optimal replication. This protein adopts a tubulin/FtsZ protein family fold organised into two domains, a canonical N-terminal GTP-binding domain, and a C-terminal GTPase activation domain (this entry). This domain shows an α-β structure .
Internalin J, EF-hand domain (InlJ_EF-hand)
Type: Domain

This entry represents the N-terminal EF-hand domain present in Internalin J proteins from Listeria species . InlJ is involved in several steps of L.monocytogenes infection by both intravenous and oral infection .
SgrA-like, Ig-like domain (SgrA-like_Ig-like)
Type: Domain

This entry represents a Immunoglobulin-like (Ig-like) domain present in the Serine-glutamate repeat protein A (SgrA,

), also known as LPXTG family cell surface protein Fms2 .
Minor fimbrium tip subunit MfA4, C-terminal (MfA4_C)
Type: Domain

This domain is found at the C-terminal of Minor fimbrium tip subunit MfA4 from Porphyromonas gingivalis and similar sequences mainly found in bacteroidales. MfA4 is involved in biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome. This domain adopts a transthyretin-like fold that contains seven core β-strands arranged in two β-sheets .
Lmo2445-like, C-terminal domain (Lmo2445-like_C)
Type: Domain

This domain is found at the C-terminal of the Lmo2445 protein from Listeria monocytogenes (

). This domain shows a immunoglobulin-like fold.
Protein P1-like, N-terminal domain (P1-like_N)
Type: Domain

This domain is found at the N-terminal of Protein P1 from Acyrthosiphon pisum virus (

) and similar proteins from arthropod-infecting viruses. This region has been named 'Widespread, Intriguing, Versatile' (WIV) domain. This region is likely to play a role in viral infection of arthropods. It is often found associated with
2-Component system ADP-ribose glycohydrolase domain (2CompARG)
Type: Domain

This entry represents the 2CompARG domain, which coupled with its partner 2CompART (represented by

), forms a two-domain T-A-like association in the duplex-forming systems likely functioning as the principal effector of these systems in bacteroidetes. One is likely to function as the antitoxin, regulating the toxin activity of the other .
2-Component system ADP-ribosyltransferase domain (2CompART)
Type: Domain

This entry represents the 2CompART domain, which coupled with its partner 2CompARG (represented by

), forms a two-domain T-A-like association in the duplex-forming systems likely functioning as the principal effector of these systems in bacteroidetes. One is likely to function as the antitoxin, regulating the toxin activity of the other .
Virilizer, yeast (VIR1_yeast)
Type: Family

This entry includes virilizer (VIR1), the yeast homologue of human virilizer (VIRMA) . VIR1 is a component of the MIS complex, a complex that mediates N6-methyladenosine (m6A) methylation of meiotic mRNAs and is required for initiation of meiosis, progression through the meiotic divisions and sporulation. In the complex, it plays a scaffolding role, stabilising the other complex members .
BARF1, second Ig-like domain (BARF1_Ig_2)
Type: Domain

This entry represents the second immunoglobulin-like domain present in the BARF1 protein from Epstein-Barr virus and similar proteins from Herpesvirales. BARF1 plays diverse functions in immunomodulation and oncogenicity, maybe by acting as a functional receptor for human CSF1. It may also inhibit interferon secretion from mononuclear cells .
Regulatory protein SIR3, C-terminal domain (SIR3_C)
Type: Domain

This domain is found at the C-terminal of Regulatory protein SIR3 from Saccharomyces cerevisiae and similar fungal proteins. SIR3 is essential for gene silencing. It is organised into a highly conserved N-terminal BAH domain (

), a C-terminal AAA+ ATPase-like domain (

), plus an extreme C-terminal domain (this entry). This domain form a winged helix-turn-helix (HTH) variant with a strong homodimerization function but without the ability to bind DNA .
Cysteine peptidase, putative, mycoplasmatota (Cys_pept_put_mycoplasmatota)
Type: Domain

This entry represents a region about 240 amino acids long with local similarity to C39 and C10 families of cysteine peptidases, including the region of the active site Cys. Members of this group occur in Mycoplasmatota.
Cytochrome c550, firmicutes (Cytochro_C550_firm)
Type: Family

C-type cytochrome c550 (also known as CccA) differs from its close homologue cytochrome c551 (also known as CccB) in having a regular rather than lipoprotein signal peptide . Cytochrome c550 is dispensable for growth and sporulation, however, it may play an important role for initiation of sporulation . Members of this protein family are specific to Bacillales.
Asp23-related (Asp23-rel)
Type: Family

This family, restricted to the phylum Mycoplasmatota, shows evidence of homology to some members of the Asp23 family (

), which was named for a Staphylococcus aureus stress protein called alkaline shock protein 23.