SII-SWORD/CoKE huggingface dataset:
Putative RING-H2 finger protein ATL71-like (ATL71-like)
Type: Family

This entry represents a group RING-type zinc finger-containing proteins found predominantly in plants, including ATL71 from Arabidopsis thaliana, which is likely to be involved in protein ubiquitination .
Peroxisomal adenine nucleotide carrier 1/2 (Peroxisomal_Ade_carrier)
Type: Family

This entry represents a group of peroxisomal adenine nucleotide transporters, including the Peroxisomal adenine nucleotide carrier 1/2 from Arabidopsis thaliana (AtPNC1/2) and the Peroxisomal adenine nucleotide transporter 1 from Saccharomyces cerevisiae (ANT1). Members of this family are found in plants and some fungal species.

AtPNC1/2 catalyses the counter exchange of ATP with ADP or AMP. It is required for the beta-oxidation reactions involved in auxin biosynthesis and for the conversion of seed-reserved triacylglycerols into sucrose that is necessary for growth before the onset of photosynthesis .
SANBR-like (SANBR-like)
Type: Family

Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes in the inmune response process. This entry includes the SANT and BTB domain regulator of class switch recombination (SANBR, previously known as KIAA1841), a negative regulator of CSR . This entry also includes some uncharacterised eukaryotic proteins.
E3 ubiquitin-protein ligase ZNRF3, zinc finger, RING-type (ZNRF3_Znf_RING)
Type: Domain

This entry represents the RING-type zinc finger domain of E3 ubiquitin-protein ligase ZNRF3 (Zinc/RING finger protein 3), a transmembrane enzyme (

) homologue of Ring finger protein 43 (RNF43). It is predominantly found in vertebrates.

In humans, ZNRF3 acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components Frizzled and LRP6 . ZNRF3 also functions as a tumour suppressor in the intestinal stem cell zone by restricting the size of the intestinal stem cell zone .

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
KCTD15, tetramerisation-type BTB domain (KCTD15_T1-type_BTB)
Type: Domain

This entry represents the BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain, also known as tetramerization (T1) domain, found in KCTD15 proteins from vertebrates. It is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. The BTB domains from KCTD family members can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD1 BTB domains, closely related to KCTD15, form pentamers .

BTB/POZ domain-containing protein KCTD15 (potassium channel tetramerization domain-containing protein 15) plays a role in the regulation of neural crest (NC) formation and other steps in embryonic development. It inhibits AP2 transcriptional activity by interacting with its activation domain .
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 (R-PTP-delta_cat)
Type: Domain

Receptor-type tyrosine-protein phosphatase delta (R-PTP-delta, also known as PTPRD), belongs to the LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (

) catalyze the dephosphorylation of phosphotyrosine peptides. LAR-RPTPs are synaptic adhesion molecules that play roles in various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function . PTPRD is involved in pre-synaptic differentiation through interaction with SLITRK2 . It contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2) .

This entry represents the catalytic PTP domain (repeat 1) found in the protein PTPRD from chordates.
Serine/threonine-protein kinase ULK4 (ULK4)
Type: Family

This entry represents the Serine/threonine-protein kinase ULK4 (also known as Unc-51-like kinase 4,

), found in animals. This enzyme may be involved in the remodeling of cytoskeletal components, such as alpha-tubulin, and in this way regulates neurite branching and elongation, as well as cell motility. In humans, ULK4 gene has been proposed to be a rare susceptibility risk factor for a range of psychiatric diseases including schizophrenia .
E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type (RNF43_Znf_RING)
Type: Domain

This entry represents the RING-type zinc finger domain of E3 ubiquitin-protein ligase RNF43. Proteins containing this domain are found in vertebrates.

RNF43 acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components Frizzled and LRP6 . RNF43 also interacts with NEDD-4-like ubiquitin-protein ligase-1 (NEDL1) and regulates p53-mediated transcription . It may also be involved in cell growth control potentially through the interaction with, a chromatin-associated protein interfacing the nuclear envelope . Mutations of RNF43 have been identified in various tumours, including colorectal cancer (CRC), endometrial cancer, mucinous ovarian tumours, gastric adenocarcinoma, pancreatic ductal adenocarcinoma, liver fluke-associated cholangiocarcinoma, hepatocellular carcinoma, and glioma . RNF43 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C3H2C3-type RING-H2 finger domain followed by a long C-terminal region .

In frogs (Xenopus), ZNRF3 and RNF43 were seen to play a key role in limb specification, constituting a master switch along with RSPO2, which may have implications for regenerative medicine .
Mitochondrial dynamics protein MID49/MID51 (MID49/MID51)
Type: Family

This entry represents the mitochondrial dynamics protein MID49/MID51. Most members of this protein family contain a Mab-21 domain and are found in chordates.

In humans, MID49 and MID51 are outer membrane proteins involved in the regulation of mitochondrial organisation and required for mitochondrial fission by promoting the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface independently of the mitochondrial fission FIS1 and MFF proteins. They also regulate DNM1L GTPase activity . Deregulation of these proteins has been linked to human diseases such as pulmonary arterial hypertension .
Long-chain primary alcohol dehydrogenase AdhA-like (AdhA-like)
Type: Family

This entry represents the long-chain primary alcohol dehydrogenase AdhA (ADHA) from Thermoanaerobacter ethanolicus (formerly known as Clostridium thermohydrosulfuricum). This enzyme is an alcohol dehydrogenase active against primary long-chain alcohols that catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor . The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols, preferentially from C2 to C8, but is also active towards methanol and glycerol, and is stereospecific for monoterpenes. . Members of this protein family are mainly found in bacteria and archaea.
Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 (R-PTP-mu_cat_rpt1)
Type: Domain

Receptor-type tyrosine-protein phosphatase mu (R-PTP-mu) belongs to the type 2B subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs catalyze the dephosphorylation of phosphotyrosine peptides . R-PTP-mu is a homophilic cell adhesion molecule expressed in cells which display a cellular network such as neurons and glia in the central nervous system . It is required for neurite outgrowth . Loss of this protein contributes to tumor cell migration and dispersal of human glioblastomas . It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains .
Forkhead box protein J2/3-like (FOXJ2/3-like)
Type: Family

This entry represents a group of fork-head domain-containing proteins, including the transcriptional activators FOXJ2/3 from humans.

In humans FOXJ2 has two isoforms, FHX.L and FHX.S. FHX. L can bind to two different type of DNA binding sites. The levels of FOXJ2 expression have been linked to a variety of cancers . The expression of FOXJ3 is associated with cancers and rheumatoid arthritis .

In mice FOXJ2 is involved in the regulation of meiosis during spermatogenesis .
GTPase-activating protein TBC20/Gyp8-like (TBC20/Gyp8-like)
Type: Family

This entry represents a group of Rab GTPase-activating proteins (RabGAPs), including TBC20 from humans and Gyp8 from Saccharomyces cerevisiae. They contain the TBC/rab GTPase-activating protein (GAP) domain.

TBC20 can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude for Rab1 and Rab2 small GTPase families . This protein have been related to numerous diseases due to its critical role in cellular processes . It was also seen to be essential for the replication and assembly of hepatitis C virus (HCV) .

Gyp8 is involved in the regulation of ER to Golgi vesicle transport in yeast mainly by activating the Ypt/Rab-GTPase Ypt1 .
Zinc finger protein 532-like (Zn532-like)
Type: Family

This entry represents Zinc finger protein 532 and related proteins from animals. Most members of this family contain several Zinc-finger C2H2-type domains. ZN532 is thought to be involved in transcriptional regulation.
Solute carrier family 22 members 4/5 (S22A4/5)
Type: Family

This entry represents Solute carrier family 22 members 4/5 (SLC22A4/5) and similar proteins from chordates. This protein family belong to the organic cation transporter family and to the major facilitator superfamily (MFS) of membrane transport proteins. MSF proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement .

SLC22A4/5 are sodium-ion dependent transporters. SLC22A4 is a low affinity carnitine transporter, highly specific for the uptake of ergothioneine (ET), a thiolated derivative of histidine with antioxidant properties. ET is a natural compound produced only by certain fungi and bacteria and must be absorbed from the diet by humans and other vertebrates . SLC22A5 (also known as Organic cation/carnitine transporter 2) is a high affinity carnitine transporter involved in the active cellular uptake of carnitine .
Domain of unknown function DUF5777 (DUF5777)
Type: Domain

This entry represents a domain that contains integral membrane β-barrel proteins. Proteins in this entry are mostly found in bacteria.
Outer capsid protein VP3-like (VP3-like)
Type: Family

This entry represents a group of Reoviridae proteins, including outer capsid protein VP3 from Cryphonectria parasitica mycoreovirus 1 .
Protein of unknown function DUF6337 (DUF6337)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000791) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the O-antigen biosynthetic gene cluster from Cronobacter sakazakii .
Protein of unknown function DUF6338 (DUF6338)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001593) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the ficellomycin biosynthetic gene cluster from Streptomyces ficellus .
Protein of unknown function DUF6339 (DUF6339)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 247 and 267 amino acids in length.
Protein of unknown function DUF6340 (DUF6340)
Type: Family

This family of proteins is mainly found in bacteria and it is functionally uncharacterised. Members in this family are about 350 amino acids in length and are likely to contain tetratricopeptide (TRP) repeats.
Protein of unknown function DUF6341 (DUF6341)
Type: Family

This family of uncharacterised proteins is found mainly in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two conserved sequence motifs, WIF and YW. Most members are though to be Uracil phosphoribosyltransferases.
Protein of unknown function DUF6342 (DUF6342)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001877) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cyphomycin biosynthetic gene cluster from Streptomyces sp. ISID311 .
Protein of unknown function DUF6343 (DUF6343)
Type: Family

This entry represents a member of a bacterial biosynthetic gene cluster (BGC). This BGC (BGC0001558) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cosmomycin C biosynthetic gene cluster from Streptomyces sp. CNT302 . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6344 (DUF6344)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000843) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the alanylclavam biosynthetic gene cluster from Streptomyces clavuligerus ATCC 27064 . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6345 (DUF6345)
Type: Family

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 . This family appears to be predominantly found in bacteria and archaea.
Protein of unknown function DUF6346 (DUF6346)
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 following biosynthetic class, polyketide, rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850 . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6347 (DUF6347)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001130) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the fabclavine Ia biosynthetic gene cluster from Xenorhabdus budapestensis .
Protein of unknown function DUF6348 (DUF6348)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002011) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ansacarbamitocin A biosynthetic gene cluster from Amycolatopsis alba DSM 44262. This family appears to be predominantly found in bacteria.
Protein of unknown function DUF6349 (DUF6349)
Type: Family

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 .
Protein of unknown function DUF6350 (DUF6350)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Actinobacteria.
Protein of unknown function DUF6352 (DUF6352)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Proteobacteria.
Protein of unknown function DUF6353 (DUF6353)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses.
Protein of unknown function DUF6354 (DUF6354)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001735) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the pentostatine biosynthetic gene cluster from Streptomyces antibioticus .
Protein of unknown function DUF6355 (DUF6355)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001807) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the totopotensamide A biosynthetic gene cluster from Streptomyces pactum . This family appears to be predominantly present in Actinobacteria.
Protein of unknown function DUF6356 (DUF6356)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found mostly in bacteria. Proteins in this family are typically between 71 and 88 amino acids in length. There are two conserved sequence motifs: KTGS and RMV.
Protein of unknown function DUF6357 (DUF6357)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000368) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the streptobactin biosynthetic gene cluster from Streptomyces sp. ATCC 700974 .
Protein of unknown function DUF6358 (DUF6358)
Type: Family

This family of integral membrane proteins is functionally uncharacterised. This family of proteins is predominantly found in Bacteroidetes. There are two conserved sequence motifs: FILN and VVLIYLK. This family is related to PF17259.
Endonuclease YhcR, N-terminal domain (YhcR_N)
Type: Domain

This entry represents the N-terminal domain of Bacillus subtilis YhcR endonuclease and related bacterial proteins. YhcR is a Bacillus subtilis sugar-nonspecific endonuclease. It cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to Staphylococcus aureus micrococcal nuclease. YhcR appears to be located in the cell wall, and is thought to be a substrate for a Bacillus subtilis sortase. YhcR is the major calcium-activated nuclease of B. subtilis . The N-terminal domain includes the NYD domain .
Protein of unknown function DUF6360 (DUF6360)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is predominantly found in archaea.
Protein of unknown function DUF6361 (DUF6361)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found mainly in bacteria.
Domain of unknown function DUF6362 (DUF6362)
Type: Domain

This domain of unknown function is found in uncharacterised proteins predominantly from Proteobacteria. It has a conserved WP motif and it may contain a helix-turn-helix motif as it overlaps with members in the Pfam clan CL0123.
Domain of unknown function DUF6363 (DUF6363)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is found at the C-terminal of patatin-like proteins from bacteria. There is a conserved tyrosine residue and a conserved FxxxPP sequence motif.
Protein of unknown function DUF6364 (DUF6364)
Type: Family

This family of uncharacterised proteins is found mainly in bacteria. Proteins in this family seem to belong to the toxin-antitoxin system. They are likely to contain a ribbon-helix-helix DNA-binding motif.
Protein of unknown function DUF6365 (DUF6365)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001960) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the hiroshidine biosynthetic gene cluster from Streptomyces hiroshimensis .
Protein of unknown function DUF6366 (DUF6366)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found predominantly in Firmicutes and contain the RE/K and GW conserved motifs.
Protein of unknown function DUF6367 (DUF6367)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001053) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the tubulysin A biosynthetic gene cluster from Archangium disciforme .
Protein of unknown function DUF6368 (DUF6368)
Type: Family

This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis .
Protein of unknown function DUF6369 (DUF6369)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000728) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the capsular polysaccharide biosynthetic gene cluster from Klebsiella pneumoniae subsp. ozaenae .
Protein of unknown function DUF6370 (DUF6370)
Type: Family

This entry represents a family of proteins mainly found in bacteria and functionally uncharacterised. Some of the members included in this family are thought to be glutaminyl-tRNA synthetases. There are some conserved sequence motifs: CGxC, YFVD/EG and GDAH.
Domain of unknown function DUF6371 (DUF6371)
Type: Domain

This domain of unknown function is predominantly found in uncharacterised proteins from Bacteroidetes. This domain is about 150 amino acids in length.

This domain has a remote similarity to DNA primase core domain (

). It is usually preceded by

that resembles the zinc-ribbon domain of DNA primase found also in a similar location.
Protein of unknown function DUF6372 (DUF6372)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis .
Protein of unknown function DUF6373 (DUF6373)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001517) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the asperphenamate biosynthetic gene cluster from Aspergillus terreus NIH2624 .