SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF6182 (DUF6182)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the spicamycin biosynthetic gene cluster from Streptomyces fimbriatus . This family appears to be predominantly found in Actinobacteria.
Bacteriodetes cell division protein FtsL-like (FtsL-like)
Type: Family

This family of proteins share similarity with cell division protein FtsL, suggesting they may be cell division proteins. Proteins in this family are primarily found in Bacteroidetes.
Protein of unknown function DUF6183 (DUF6183)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001726) is described by MIBiG as an example of the NRP (non-ribosomal peptide) and polyketide biosynthetic classes. It includes a member from the pactamides biosynthetic gene cluster from Streptomyces pactum . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6184 (DUF6184)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000990) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the epothilone biosynthetic gene cluster from Sorangium cellulosum . This family appears to be predominantly found in Proteobacteria.
Solute-binding protein AdeT 1/2 (AdeT1/2)
Type: Family

This entry represents the Probable solute-binding protein AdeT1/2 from Acinetobacter baumannii. These proteins are involved in resistance to antibiotics by active efflux . Members of this protein family are found mostly in Proteobacteria.
Ap4A phosphorylase 1/2, N-terminal domain (Ap4A_phos1/2_N)
Type: Domain

This entry represents the N-terminal HIT-like domain from the Ap4A phosphorylase enzyme .

This entry represents a group of ATP adenylyltransferases found in bacteria and lower eukaryotes which catalyse the interconversion of Ap4A to ATP and ADP . While these enzymes are thought to act primarily to break down Ap4A, there is evidence to suggest that in some circumstances they may also act in a biosynthetic role. Some variability in substrate range is apparent (e.g., the cyanobacterial enzyme can also utilise Ap3A as a substrate, while the Saccharomyces enzymes apparently cannot).

Proteins in this entry include Apa1 and Apa2 from budding yeasts. Apa1 is a bifunctional Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase and ADP sulfurylase involved in catabolism of bis(5'-nucleosidyl) tetraphosphates . Apa2 is a Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase II .
2,4-diaminopentanoate dehydrogenase, C-terminal domain (DAP_DH_C)
Type: Domain

This entry represents the C-terminal presumed domain found in 2,4-diaminopentanoate dehydrogenase (DAPDH, also known as ORD) from Acetoanaerobium sticklandii (formerly known as Clostridium sticklandii) . This enzyme is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate (DAP) to yield 2-amino-4-ketopentanoate (AKP) . The N-terminal domain has a Rossmann fold.
ODP domain (ODP_dom)
Type: Domain

The ODP (Oxygen-binding Di-iron Protein) domain containing proteins belong to a subfamily of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors. ODP was shown to act as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable peroxo adduct .
ADNP, zinc finger domain (ADNP_Znf)
Type: Domain

This is a domain found towards the N terminus of ADNP and ADNP2 which contains zinc finger motifs .

This entry includes a group of homeobox proteins, including ADNP and ADNP2 . ADNP regulates the expression of >400 genes during embryonic development, vital for mammalian brain formation . It has been linked to neurodegenerative diseases and has been shown to play an important roles in autophagy. ADNP has also been associated with the pathophysiology of schizophrenia . ADNP de novo mutations in humans result in a syndromic form of autism-like spectrum disorder (ASD), including cognitive and motor deficits, the ADNP syndrome (Helsmoortel-Van Der Aa) .
BTB/POZ domain-containing protein KCTD11/21, C-terminal domain (KCTD11/21_C)
Type: Domain

This entry represents the C-terminal region of BTB/POZ domain-containing protein KCTD11 (the KCASH1 protein, also known as REN: EGF-, NGF- and retinoic acid-responsive gene) and its homologue, KCTD21 (the KCASH2 protein).

These members of the KCASH family (KCTD containing, Cullin3 adaptor, suppressor of Hedgehog) share high similarity and a BTB domain responsible for oligomerization and formation of a Cullin3 ubiquitin ligase complex. They are specifically expressed in brain and cerebellum where they have a role in neuronal differentiation, and suppressor activity on acetylation-dependent Hedgehog/Gli signalling through ubiquitination and degradation of histone deacetylase 1 (HDAC1). These proteins have been described as tumor suppressors that inhibit medulloblastoma growth by antagonizing Hedgehog signalling .
Protein of unknown function DUF6132 (DUF6132)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 74 amino acids in length.
Protein of unknown function DUF6133 (DUF6133)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Firmicutes. Proteins in this family are typically between 73 and 87 amino acids in length. There are two conserved sequence motifs: KIL and LLLAGLY.
MCAfunc domain (MCAfunc)
Type: Domain

MCAfunc domain (MCAfunc) is located in the N-terminal region of a mechanosensitive channel protein MID1-COMPLEMENTING ACTIVITY (MCA). MCAfunc represents the provisionally advocated ARPK domain (Amino-terminal domain of Rice putative Protein Kinases), overlapping with the EF hand-like region at the N terminus . In MCA proteins, MCAfunc has Ca2 influx activity and is proposed to be a functional domain of MCAs . MCAfunc is exclusively observed in streptophytes and exists not only in MCA but also in E3 ubiquitin ligase-like proteins, ARO3-like proteins and and protein kinases. In the most basal plant lineage, charophytes, MCAfunc is only found in E3 ubiquitin ligase-like proteins and protein of presently unknown function, while MCA proteins are exclusively found in land plants, from bryophytes to angiosperms.
Protein of unknown function DUF6134 (DUF6134)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found predominantly in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 210 and 241 amino acids in length.
Stage II sporulation protein E, N-terminal (SpoIIE_N)
Type: Domain

This is the N-terminal domain of Stage II sporulation protein E (SpoIIE), which includes the 10 transmembrane domains and the regulatory domain, the latter located adjacent the PP2C phosphatase domain. The regulatory domain mediates the formation of dimers between SpoIIE molecules, required for phosphatase activation . An N-terminal 45-residue long α-helix makes intramolecular contacts with the switch helices (alpha1 and alpha2) of the phosphatase domain .
Delta and Notch-like epidermal growth factor-related receptor, C-terminal (DNER_C)
Type: Domain

This entry represents the C-terminal region of the Delta and Notch-like epidermal growth factor-related receptor (DNER) containing the transmembrane domain and the short cytoplasmic region, including the AP-1-binding site required for its somatodendritic distribution.

This receptor is highly expressed in Purkinje cells taking part in the differentiation and maturation of Bergmann glia via physical contact with Purkinje cells and granular cells . Recently, it has been demonstrated that DNER is induced in lung recruited macrophages after chronic inflammation, in which it induces IFN-gamma expression via a non-canonical Notch NF-kappaB pathway . This receptor has also been related to breast cancer .
Protein of unknown function DUF6223 (DUF6223)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001848) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the diazaquinomycin H biosynthetic gene cluster from Micromonospora sp. B006 . This family appears to be predominantly found in bacteria.
Protein of unknown function DUF6224 (DUF6224)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000084) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the laidlomycin biosynthetic gene cluster from Streptomyces sp. CS684 .
Protein of unknown function DUF6225 (DUF6225)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000896) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the cycloserine biosynthetic gene cluster from Streptomyces lavendulae subsp. lavendulae .
Protein of unknown function DUF6226 (DUF6226)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850 . This family appears to be predominantly found in Actinobacteria.
Methylcrotonoyl-CoA carboxylase subunit alpha, BT domain (MCCA_BT_dom)
Type: Domain

This entry represents the BT domain from plant Methylcrotonoyl-CoA carboxylase subunit alpha (MCCA), located between the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains. This domain mediates crucial interactions between the BC domain in the the alpha subunit and the carboxyltransferase (CT) domain in the beta subunit of this enzyme which are based on ion-pair, hydrogen-bonding and hydrophobic interactions. This domain has a backbone fold with a long helix surrounded by an eight-stranded anti-parallel β barrel. There is a hook comprising the C-terminal part of the helix and the loop connecting it to the first strand of the β barrel, which appears to have a central role in alpha and beta subunits interactions .

In Arabidopsis, methylcrotonoyl-CoA carboxylase is involved in the catabolism of leucine, associated with reproductive growth. It may also participate in the catabolism of isoprenoids .
Protein of unknown function DUF6207 (DUF6207)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001709) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the nystatin biosynthetic gene cluster from Streptomyces albulus . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6202 (DUF6202)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000877) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the polyoxin A biosynthetic gene cluster from Streptomyces cacaoi subsp. asoensis .
Protein of unknown function DUF6203 (DUF6203)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001944) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the funisamine biosynthetic gene cluster from Streptosporangium sp. .
Protein of unknown function DUF6204 (DUF6204)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001070) is described by MIBiG as an example of the NRP (non-ribosomal peptide) and polyketide biosynthetic classes. It includes a member from the kirromycin biosynthetic gene cluster from Streptomyces collinus Tu 365 . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6205 (DUF6205)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000078) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the incednine biosynthetic gene cluster from Streptomyces sp. ML694-90F3 .
Protein of unknown function DUF6206 (DUF6206)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001063) is described by MIBiG as an example of the polyketide and NRP (non-ribosomal peptide) biosynthetic classes. It includes a member from the undecylprodigiosin biosynthetic gene cluster from Streptomyces coelicolor A3(2) . This family appears to be predominantly present in bacteria.
Saxitoxin biosynthesis operon protein SxtJ (SxtJ)
Type: Family

This family of integral membrane proteins is functionally uncharacterised. It is found in cyanobacterial Saxitoxin biosynthesis operon . This family of proteins is found in bacteria.
TrbL/VirB6 plasmid conjugal transfer like protein (TrbL_3)
Type: Family

This family of proteins is related to the Type IV secretion system protein TrbL. This family of proteins is found in archaea.
Radical SAM domain-containing protein, N-terminal (Radical_SAM_N2)
Type: Domain

This presumed domain is found at the N terminus of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyse diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation . The function of this domain is unknown.
Dipeptidyl peptidase 8 /9 ,N-terminal (Dpp_8/9_N)
Type: Domain

Dipeptidyl peptidase (DPP) family members 8 and 9 are similar to DPP4, consisting of one N-terminal β-propeller and a C-terminal α/β hydrolase domain, which form a functional homodimer. This entry represents the N-terminal β-propeller of DPP8 and 9 which consists of eight blades and enlaces a central round pore. It provides the key arginine residue fundamental for substrate fixation which is located in the R-segment, at the interconnecting loop between blades 1 and 2. Ligand binding to DPP8/9 induces a rearrangement at the active site through a disorder-order transition in a loop segment which includes the key arginine residue and partially folds in an α-helix (R-helix) . DPP8 and DPP9 play a role in the immune system and in preadipocyte differentiation. DPP9 is also essential for neonatal survival and plays a role in antigen maturation, cell migration, and cell adhesion.
Rho GTPase-activating protein, pG1 and pG2 domain (RhoGAP_pG1_pG2)
Type: Domain

The RhoGAPs (GTPase-activating proteins) regulates Rho GTP hydrolysis and are important for proper Rho signalling. This entry represents a domain found in p190RhoGAP-A (ARHGAP35) and p190RhoGAP-B (ARHGAP5). 190RhoGAP-A/B contain a GTP-binding GTPase domain, four FF domains, two GTPase-like folds (pG1 and pG2) in the middle domain and a C-terminal GAP domain. This entry represents pG1 and pG2 which are important for GAP activity toward RhoA. 190RhoGAP-A/B were classified as pseudoGTPases as they lack nucleotide-binding activity. Crystal structures revealed a small GTPase fold in both cases with a central 6-stranded β-sheet surrounded by four α-helices .
Mesoderm induction early response protein 1/3, C-terminal (MIER1/3_C)
Type: Domain

This domain is found at the C terminus of Mesoderm induction early response proteins 1 and 3 (MIER1/3). MIER1 is a transcriptional repressor that regulates the expression of a number of genes including SP1 target genes, recruiting histone deacetylase 1 (HDAC1) through its ELM2 domain. It has two isoforms, alpha and beta, which differ in their C-terminal domains, both of them being able to interact with HDAC1. The gene encoding MIER3 has been identified as a candidate cancer susceptibility gene . MIER1 and 3 share two regions of high homology, one at the N terminus and the second at the C terminus, represented in this entry, which consists of a short region located immediately downstream of the SANT extension that is 84% identical .
MobC-like protein (MobC_2)
Type: Family

This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region.
Protein inscuteable homologue, C-terminal domain (Insc_C)
Type: Domain

This entry represents the C-terminal region of protein Inscuteable (Insc) containing four putative armadillo repeats and the conserved extreme C-terminal tetrapeptide Glu-Ser-Phe-Val which is in agreement with the class I PDZ-binding motif X-Ser/Thr-X-/ (X and / are unspecified and hydrophobic residues, respectively). Insc functions as an adaptor protein that binds simultaneously with Partner of Insc (Pins, consisting of alpha subunit (Ga) of heterotrimeric G proteins and its guanine nucleotide dissociation inhibitor) and Par3 (PDZ-containing proteins) to regulate their apical localisation in neuroblasts, which is required for the correct execution of the asymmetric division .
E3 ubiquitin-protein ligase RNF180, C-terminal domain (RNF180_C)
Type: Domain

This entry represents the C-terminal domain of the E3 ubiquitin-protein ligase RNF180. This region is predicted to be a transmembrane domain .

RNF180 (also known as Rines: RING finger protein in neural stem cells) is an integral membrane protein located mainly on the cytoplasmic side of the endoplasmic reticulum. It promotes polyubiquitination and degradation by the proteasome pathway of ZIC2. It is thought that it is involved in modulation of neuronal function, such as regulation of synaptic structure and synaptic plasticity due to its high expression in mature brain. It has been related to neurodegenerative diseases and to disorders associated with emotion . Methylation of RNF180 has been linked to gastric cancer .
Semaphorin 4F, C-terminal (Sema4F_C)
Type: Domain

Semaphorins are a large and diverse family of proteins, widely expressed across divergent animal phyla, divided into eight classes (1-7 and V) which are structurally and functionally conserved. These proteins are critical in neural development and adult brain plasticity being involved in axon guidance, neural connectivity, angiogenesis, immunoregulation, and also in cancer .

This entry represents the C-terminal domain of the transmembrane Semaphorin 4F (Sema4F, also known as Semaphorin-W), which plays a role in visual system development and in oligodendrocyte precursor migration and differentiation. Like other Semaphorin 4 members, it includes a Ig-like domain, adjacent the PSI domain (plexin-semaphorin-integrin domain, conserved across all semaphorins) , a transmembrane region and a short intracellular tail. The latter is rich in proline residues similar to other transmembrane semaphorins suggesting that it may interact with cytoskeletal or signalling proteins. It also contains a cyclic nucleotide-dependent protein kinase phosphorylation site, involved in signal transduction into the cell. Sema4F is found in glutamatergic synapses, preferentially in postsynaptic dendrites, attached to SAP90/PSD-95-scaffolding protein. Sema4F interacts with SAP90/PSD-95 PDZ domains through the critical last three C-terminal amino acids .
Domain of unknown function DUF6036 (DUF6036)
Type: Domain

Proteins containing this domain belong to the nucleotidyltransferase superfamily.
PcRGLX/YetA-like (PcRGLX/YetA-like)
Type: Family

This entry includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) and YetA from B. subtilis. YetA is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Members of this family share a 3 domain architecture .
Trypsin-co-occurring domain 1 (Trypco1)
Type: Domain

Trypsin-like peptidase effector in the classical NTP-dependent ternary system (vWA-MoxR-VMAP) frequently co-occurs with one of two proteins (Trypco1 or Trypco2) which are mostly mutually exclusively . This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus .
Transglycosylase, SLT domain (SLT_4)
Type: Domain

This entry represents a set of SLT-like domains found in proteobacteria. SLT domains containing proteins are enzymes that degrade murein.
Failed axon connections homolog, N-terminal domain (FAXC_N)
Type: Domain

This entry represents the N-terminal domain of the Failed axon connections homolog (FAXC) from animals. It is likely that this region anchors this protein to the plasma membrane.

FACX is thought to play a role in axonal development, being involved in cell-cell interactions .
Evasins Class A (EVA_Class_A)
Type: Family

Evasins are secreted glycoproteins from ticks, that enhance host blood flow and have anti-inflammatory activity. They bind to chemokines and prevent leukocyte recruitment . Based on the chemokine selectivity they can be divided in two classes: Class A binds CC chemokines and includes Evasin-1 (EVA-1) and Evasin-4, being EVA-1 more selective; Class B Evasins include Evasin-3 which binds and inhibits several CXC chemokines but not CC chemokines.

This family represents class A evasins, which contain eight conserved Cys residues that define four intramolecular disulfide bonds. The N- and C-terminal regions are flexible, extend from either side of the core and form a concave surface with the first β-sheet suitable for binding another EVA-1 molecule or to a chemokine. There are two Gly residues strictly conserved. Predicted glycosylation sites were identified on the exterior surface of the structure. Due to its anti-inflammatory activity, these proteins are interesting therapeutic agents .
TrbL/VirB6 plasmid conjugal transfer like protein, Firmicutes (TrbL_Firmicutes)
Type: Family

Although members of this family are uncharacterised, it appears to be related to

which is a conjugal transfer protein TrbL/VirB6 found in proteobacteria. This protein family is found mainly in Firmicute bacteria, and is approximately 170 amino acids in length.
TBC1 domain family member 23, C-terminal domain (TBC1D23_C)
Type: Domain

This entry represents the C-terminal domain of TBC1D23 which contains the residues for specific FAM21 binding and for the cargo of endosome-derived carriers. It adopts a fold similar to the Pleckstrin homology (PH) domain. Mutations in this protein, and particularly in this domain, are linked with Pontocerebellar hypoplasia (PCH) , suggesting that the TBC1D23 C-terminal domain is required for neuronal growth and brain development.

TBC1 domain family member 23 (TBC1D23) is a catalytically inactive member of a family of Rab GTPase-activating proteins (GAPs) which plays a role in endosome-to-Golgi trafficking and is important for normal brain development, especially in axonal and dendritic growth. It functions as a bridging factor between golgin-97/245 and the FAM21 subunit of the WASH (Wiskott-Aldrich syndrome protein and SCAR homologue) complex on endosomal vesicles . Mutations of the TBC1D23 gene cause pontocerebellar hypoplasia and alter cortical development .
Heavy metal binding domain (HMBD)
Type: Domain

This entry represents a metal-binding domain found in single or multiple copies at the N-terminal region of a wide variety of copper or other heavy metal binding transporters and other proteins predominantly found in bacteria.

Some members of this entry are:

Cation efflux system protein CusB from Escherichia coli, which mediates resistance to copper and silver .

Copper-exporting P-type ATPase from Legionella pneumophila, which couples the hydrolysis of ATP with the export of copper .

Silver exporting P-type ATPase SilB/P from Salmonella typhimurium, a component of the silver cation-efflux system that confers resistance to silver .