SII-SWORD/CoKE huggingface dataset:
Coiled-coil domain-containing protein 61, N-terminal head domain (CCDC61_N)
Type: Domain

Coiled-coil domain-containing protein 61 (CCDC61), also known as variable flagellar number 3 (VFL3), is a centrosomal protein required for spindle assembly and precise chromosome alignments in mitosis. It is the human orthologue of proteins required for anchoring distinct sets of cytoskeletal fibers to centrioles in unicellular eukaryotes. CCDC61 monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two homodimerization domains, the N-terminal globular head domains and long extended α-helical coiled-coil regions. These CCDC61 homodimers assembles into linear filaments.

This entry represents the N-terminal head domain of CCDC61, which is structurally related to other XRCC4-superfamily members, XRCC4, XLF, SAS6, and PAXX .
NADH pyrophosphatase-like, C-terminal domain (NudC-like_C)
Type: Domain

NADH pyrophosphatase, also known as NAD-capped RNA hydrolase NudC, is a member of the Nudix hydrolase superfamily. This enzyme catalyses the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP and requires a divalent cation, such as Mg2+ or Mn2+ , for activity. Members of this family are also recognised by the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. A block of 8 conserved amino acids downstream of the Nudix motif is thought to give NADH pyrophosphatase its specificity for NADH .
NovE/LmbU-like transcriptional regulators (NovE/LmbU-like)
Type: Family

This entry represents a family of DNA-binding transcriptional activators for natural product biosynthesis in Streptomyces and related species found mainly in Actinomycetes. Transcriptional regulator NovE has been found to specifically regulate expression of genes involved in the novobiocin biosynthesis pathway . NovE acts as a positive regulator of transcription but does not bind DNA . Besides NovE, this family includes LmbU (lincomycin), CouE (coumermycin A1), CloE (clorobiocin), and HrmB (hormaomycin).
Intermembrane transport lipoprotein PqiC (PqiC)
Type: Family

This entry represents the Intermembrane transport lipoprotein PqiC and related proteins mainly from enterobacterales. PqiC (also known as YmbA), a lipoprotein, has been identified as part of the PqiABC system, a transporter that bridges the inner and outer membranes in species such as Escherichia coli and is important to membrane integrity .
BTB/POZ domain-containing protein 6-A-like, BTB and C-terminal Kelch domain (Btbd6a-like_BACK)
Type: Domain

This entry represents the BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 6-A from Danio rerio (Btbd6a) and similar sequences from animals. Btbd6a is an adapter protein for the cul3 E3 ubiquitin-protein ligase complex. It promotes the export of zbtb16/plzf from the nucleus to the cytoplasm, targets zbtb16/plzf for ubiquitination and degradation and up-regulates neurog1 expression and antagonises zbtb16/plzf, to promote neurogenesis. This protein is required for proper embryogenesis and plays an essential evolutionarily-conserved role during neuronal development
BTB/POZ domain-containing protein 6, BTB/POZ domain (BTB_POZ_BTBD6)
Type: Domain

This entry represents the BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 6 from Xenopus laevis (BTBD6) and similar sequences from vertebrates. BTBD6 is required for proper embryogenesis and plays an essential evolutionary conserved role during late neuronal development and muscle formation . The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids .
YraL-like (YraL-like)
Type: Family

This entry represents the uncharacterised protein YraL (

) from Bacillus subtilis and related proteins mainly from firmicutes. Members of this family contain stretches with sequence similarity to Mor, which is a transcriptional activator from phage Mu, and to other members of

.
Copper chaperone CopZ (CopZ)
Type: Family

This entry represents the Copper chaperone CopZ and related proteins found in firmicutes. CopZ is a small copper chaperone that serves for the intracellular sequestration and transport of Cu+. It delivers Cu+ to the copper-transporting ATPase CopA . A number of longer protein, such as copper-translocating P-type ATPases, contain multiple CopZ-like domains, with its signature invariant CxxC sequence motif .
3',5'-nucleoside bisphosphate phosphatase (35NBP)
Type: Family

This entry represents the 3',5'-nucleoside bisphosphate phosphatase (

) found in Chromobacterium violaceum and related proteins mainly from betaproteobacteria.

This enzyme hydrolyzes 3',5'-bisphosphonucleosides (pGp, pCp, pUp, and pIp) to nucleoside 5'-phosphate and orthophosphate. Also shows activity with ribonucleoside 2'-deoxyribonucleoside 3',5'-bisphosphates .
Intermembrane phospholipid transport system binding protein MlaB (MlaB)
Type: Family

This entry represents the Intermembrane phospholipid transport system binding protein MlaB from Escherichia coli (

) and related proteins from enterobacterales. MlaB belongs to the ABC transporter complex MlaFEDB that maintains asymmetry in the outer membrane of Gram-negative bacteria , with lipopolysaccharides in the outer leaflet and phospholipids in the inner leaflet . MlaB plays critical roles in both the assembly and activity of the complex and may act by modulating MlaF structure and stability .
CC/Se motif containing family (CC/Se_fam)
Type: Family

This entry represents a family of uncharacterised bacterial proteins. Many members of this family have a double-Cys motif. Others, including several from the genus Moorella, have a selenocysteine at a similar location.
N-acetylmuramoyl-L-alanine amidase AmiC (AmiC)
Type: Family

This entry represents N-acetylmuramoyl-L-alanine amidase AmiC from Escherichia coli and similar sequences specific to Enterobacterales. AmiC is a cell-wall hydrolase involved in septum cleavage during cell division. This enzyme hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides .
TcpD-like, C-terminal domain (TcpD-like_C)
Type: Domain

This entry represents a domain found at the C-terminal of the TcpD protein from Clostridium perfringens (A0A0K2Y2J0) and related proteins, primarily from Firmicutes. TcpD localises to the cell envelope fraction independently of the presence of other pCW3-encoded proteins and was shown that TcpD and TcpE were essential for the conjugative transfer of pCW3 . The function of this domain is unknown.
SCO2522-like (SCO2522-like)
Type: Family

This entry represents the family of the uncharacterised protein SCO2522 of Streptomyces coelicolor (

) and related proteins from Actinomycetes. This family of proteins is part of a conserved gene neighbourhood encoding proteins SCO2521-SCO2524.
Plant virulence effector HPE1-like, N-terminal domain (HPE1-like_N_CxxC)
Type: Domain

This entry describes a domain found N-terminal in a family bacterial proteins mainly from order Hyphomicrobiales. Most members of this family have some form of additional C-terminal domain of similar length. However, the best-studied members of this family, such as the virulence effector HPE1 ("hypothetical protein effector 1") from Candidatus Liberibacter solanacearum , are shorter proteins. Members of this family begin with an N-terminal signal peptide, for apparent Sec-mediated secretion, and nearly all share a common CxxC sequence motif.
SCO2521-like (SCO2521-like)
Type: Family

This entry represents the family of uncharacterised protein SCO2521 [

] from Streptomyces coelicolor and related proteins found mainly in Actinomycetes. This family of proteins is part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524.
SGM_5486-like transporter-associated (SGM_5486-like-assoc)
Type: Family

Members of this family, found mainly in the genus Streptomyces, regularly are found encoded next to an MFS transporter gene. These proteins average about 40 amino acids in length, with the last 25 residues extremely hydrophobic.
TraI/MobA conjugative relaxases (TraI/MobA_relaxases)
Type: Family

This entry represents the TraI protein as found in Escherichia coli (including

and

) and related bacterial proteins. The initiation process of transfer DNA synthesis requires the interaction of at least three plasmid-specific components (TraH, I, and J) at the transfer origin resulting in the assembly of a specialised nucleoprotein complex - the relaxosome. The site- and strand-specific cleavage at the transfer origin is dependent on TraI and TraJ. Members of this family of conjugative relaxases are also known as MobA of type P mobilisation systems .
DNA-binding transcriptional regulator YeiE (YeiE)
Type: Family

This entry represents the YeiE protein from Escherichia coli (

) and related proteins from enterobacterales. YeiE is an HTH-type transcriptional regulator modulated by sulfite ion .
Hormogonium polysaccharide biosynthesis protein HpsL-like (EPS_HpsL-like)
Type: Family

This entry represents hormogonium polysaccharide biosynthesis protein HpsL from Nostoc punctiforme and related proteins found in filamentous cyanobacteria. HpsL gene is a member of a gene cluster involved in hormogonium polysaccharide (HPS) production. Deletion of HpsL completely abolish motility in N. punctiforme. HpsL is essential for productive motility but not for earlier stages of hormogonium development .
Selenate/tellurate reductase subunit YnfE (YnfE)
Type: Family

This entry represents the YnfE protein from Escherichia coli (

) and related proteins from enterobacterales. YnfE and YnfF (

) function as catalytic elements within the YnfEFGH complex, playing a role in its capacity as a selenate/tellurate reductase . The ynfEFGHI operon is a paralogue of the Escherichia coli dimethyl sulfoxide reductase dmsABC operon and ynfE and ynfF are paralogues of dmsA .
DNA-binding transcriptional regulators YafC/CrgA (YafC/CrgA)
Type: Family

This entry represents the uncharacterised HTH-type transcriptional regulator YafC found in Escherichia coli (

) and related proteins, such as the Neisseria meningitidis CrgA protein (

). CrgA is a regulatory protein that activates transcription of the NADPH:quinone oxidoreductase MdaB and represses its own transcription . This protein is involved in the regulation of bacterial adhesion to host epithelial cells and may play a central regulatory role in meningococcal adhesion, particularly in switching from initial adhesion to intimate adhesion by downregulating the bacterial surface structures that hinder this adhesion . CrgA is directly responsible for transcriptional repression through specific base contacts, probably in the major DNA groove, resulting in DNA looping. Upon contact with target cells, CrgA is released from the DNA, allowing transcription of the target gene to proceed to elongation and facilitating tight control of the expression of genes regulated by CrgA

].
Phospholipase C-like domain (PlcA-like_dom)
Type: Domain

This entry represents a domain that covers the whole protein in phospholipase C from Legionella pneumophila (PlcA,

) and Pseudomonas fluorescens (PlcC,

), and similar sequences mainly from bacteria and fungi. PlcA and PlcC are secreted phosphatidylcholine-hydrolysing phospholipases. PlcC is involved in the hemolytic activity of P. fluorescens. Its preferred substrates are 1-palmitoyl-2-arachidonoyl-phosphatidylcholine and dipalmitoyl-phosphatidylcholine. The active enzyme is a monomer that requires calcium and zinc ions for activity .

This domain is also found associated with

in some uncharacterised proteins and with

in others.
Type III secretion protein HrpP-like, C-terminal domain (T3SS_HrpP-like_C)
Type: Domain

This entry represents the C-terminal domain of Pseudomonas syringae HrpP (

), a type III secretion system (T3SS) substrate specificity switch-domain protein that has an atypical T3SS translocation signal. HrpP is required for the export of pathogenicity factors into plant cells. This protein contains a C-terminal domain similar to the globular C-terminal substrate-switching (SS) domain, also called the type III secretion substrate specificity switch (T3S4) domain, of Yersinia pestis YscP . Members of this group are found in gammaproteobacteria.
Anti-CRISPR type I subtype E3-like (AcrIE3-like)
Type: Family

This entry represents a group of short sequences mainly found in Pseudomonas tailed bacteriophages and prophages, including Type I-E anti-CRISPR protein from Pseudomonas phage PaMx73 (also known as AcrIE3,

). Members of this family are anti-CRISPR (Acr) proteins. These are small proteins which are the natural inhibitors for CRISPR-Cas systems encoded on bacterial and archaeal viruses to evade host CRISPR-Cas systems. They associate with the Cascade complex to hinder DNA binding, via an unknown mechanism
Immunity protein CdiI-like (CdiI-like)
Type: Family

This entry represents Immunity protein CdiI (

)from Escherichia coli and similar sequences from proteobacteria. Together with the elongation factor Tu (EF-Tu), CdiI exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is an essential and highly conserved translation factor that delivers aminoacyl-tRNAs (aa-tRNA) to the ribosome during protein synthesis. Structure studies suggest the toxin remodels the GTP:EF-Tu:aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site .

CDI toxins, part of a a cellular contact-dependent growth inhibition (CDI) system, are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighbouring cells. CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI bacteria. The CdiI immunity protein binds the CdiA toxin via its C-terminal domain to prevent auto-inhibition. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition .
EF-hand calcium-binding domain-containing protein 10, dimerization/docking domain (DD_EFCAB10)
Type: Domain

This entry represents the N-terminal dimerization/docking (D/D) domain found in human EF-hand calcium-binding domain-containing protein 10 (EFCAB10,

) and similar sequences mainly from animals. This domain has a high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.
Serine/threonine-protein kinase , Mob-binding domain (LATS1-like_MobB)
Type: Domain

This entry represents the Mob-binding domain found in human Serine/threonine-protein kinase LATS1 (also known as large tumor suppressor homolog 1,

) and similar proteins mainly from vertebrates.

LATS1, also called WARTS protein kinase, is a serine/threonine-protein kinase that functions as a tumour suppressor and is implicated in cell cycle regulation. Inactivation of LATS1 in mice results in the development of various tumours, including sarcomas and ovarian cancer. Promoter methylation, loss of heterozygosity, and missense mutations targeting the LATS1 gene have also been found in human sarcomas and ovarian cancers. In addition, decreased expression of LATS1 is associated with an aggressive phenotype and poor prognosis . LATS1 induces G2 arrest and promotes cytokinesis. It may be a component of the mitotic exit network in higher eukaryotes. This protein belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of "Hippo" signalling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. Members of this group contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain (

) that contains an auto-inhibitory sequence .
Polymorphic Nuclease effector domain (PoNe_dom)
Type: Domain

The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This entry contains proteins with PoNe domains that co-occur with varied N-terminal domains such as DUF637 (

), in some instances, predicted to be a hemagglutinin domain .
Rabankyrin-5,BTB and C-terminal Kelch domain (ANKFY1_BACK)
Type: Domain

This entry represents the BACK (BTB and C-terminal Kelch) domain found in human Rabankyrin-5 (ANFY1) and similar animal proteins. This domain is usually found associated with

and

.

Rabankyrin-5, also called ankyrin repeat and FYVE domain-containing protein 1 (ANKFY1), or ankyrin repeats hooked to a zinc finger motif (ANKHZN), a Rab5 effector that regulates and coordinates different endocytic mechanisms . It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, followed by a BACK domain, several ankyrin (ANK) repeats in the middle, and a C-terminal FYVE domain .
Rabankyrin-5, FYVE domain (ANFY1_FYVE)
Type: Domain

This entry represents the FYVE domain found in human Rabankyrin-5 (ANFY1) and similar animal proteins. This domain is usually found associated with

Rabankyrin-5, also called ankyrin repeat and FYVE domain-containing protein 1 (ANKFY1), or ankyrin repeats hooked to a zinc finger motif (ANKHZN), a Rab5 effector that regulates and coordinates different endocytic mechanisms . It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, followed by a BACK domain, several ankyrin (ANK) repeats in the middle, and a C-terminal FYVE domain .
Rabankyrin-5, BTB/POZ domain (ANFY1_BTB_POZ)
Type: Domain

This entry represents the BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in human Rabankyrin-5 (ANFY1) and similar animal proteins. This domain is a common protein-protein interaction motif of about 100 amino acids and usually found associated to

.

Rabankyrin-5, also called ankyrin repeat and FYVE domain-containing protein 1 (ANKFY1), or ankyrin repeats hooked to a zinc finger motif (ANKHZN), a Rab5 effector that regulates and coordinates different endocytic mechanisms . It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, followed by a BACK domain, several ankyrin (ANK) repeats in the middle, and a C-terminal FYVE domain .
Transcriptional regulatory protein CseB (CseB)
Type: Family

This entry represents the CseB family as it is found in Streptomyces coelicolor (

) and related species. CseB is a member of the two-component regulatory system CseB/CseC and is involved in maintaining the stability of the cell envelope. CseB activates the transcription of the RNA polymerase sigma-E factor in response to changes in the cell envelope .
Two-component system response regulator RppA (RppA)
Type: Family

This entry represents the RppA family as it is found in Synechocystis sp. (

) and related cyanobacterial species. RppA is member of two-component regulatory system RppA/RppB, involved in the establishment of the appropriate stoichiometry between the 2 photosystems. It senses changes in the plastoquinone (PQ) redox poise .

It has also been reported that the RppA/RppB two-component pair (also known as NrsR/NrsS) regulates the nickel-dependent expression of the nrsBACD operon . It has been suggested that the photosystem-related activities are a result of the expression of NrsS (formerly RppB) in the absence of its natural substrate NrsR (formerly RppA) .
Ubiquitin thioesterase ZRANB1, ovarian tumor domain (ZRANB1_OTU)
Type: Domain

This entry represents OTU (ovarian tumor) domain of Ubiquitin thioesterase ZRANB1 and similar animal proteins, including the homologue Ubiquitin thioesterase Trabid from Drosophila melanogaster (Trbd).

ZRANB1, also called TRAF-binding domain-containing protein, Trabid, or zinc finger Ran-binding domain-containing protein 1, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically hydrolyses 'Lys-29'-linked and 'Lys-33'-linked diubiquitin and cleaves 'Lys-63'-linked chains with less efficiency. This protein binds, deubiquitinates, and stabilises EZH2, which is the catalytic component of the Polycomb repressive complex 2 (PRC2) that silences gene transcription by methylating histone H3 at lysine 27 and is mutated or highly expressed in many types of cancer, including lymphoma, melanoma, prostate cancer, ovarian cancer, and breast cancer. It belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. ZRANB1 does not contain the conserved aspartate, and uses cysteine and histidine as a catalytic dyad. It is classified as a family C64 cysteine protease by MEROPS .

Drosophila Trabid interacts with TGF-beta Activating Kinase 1 (TAK1), which triggers both immunity and apoptosis, resulting in reduced immune signalling output and K63-linked ubiquitination .
Protein ovarian tumor locus, ovarian tumor domain (OTU_OTU)
Type: Domain

This entry represents the OTU (ovarian tumor) domain of a group of proteins mainly found in arthropods, including Protein ovarian tumor locus from Drosophila melanogaster (OTU) which is essential for female fertility, germ cell division and differentiation .
Protein ovarian tumor locus, Tudor domain (OTU_Tudor)
Type: Domain

This entry represents the Tudor domain of a group of proteins mainly found in arthropods, including Protein ovarian tumor locus from Drosophila melanogaster (OTU), a homologue of OTU domain-containing protein 4 (OTUD4) that is essential for female fertility, germ cell division and differentiation .
OTU domain-containing protein 2-like, ovarian tumor domain (OTU2-like_OTU)
Type: Domain

This entry represents the OTU (ovarian tumor) domain of OTU domain-containing protein 2 from Saccharomyces cerevisiae (OTU2), Ubiquitin thioesterase otu2 from Schizosaccharomyces pombe and similar proteins from ascomycetes. The S. pombe OTU2 is an ubiquitin thioesterase/hydrolase (

) that can remove conjugated ubiquitin from protein substrates and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. The fungal OTU2 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as a catalytic triad .