SII-SWORD/CoKE huggingface dataset:
Pfam PF01019: Gamma-glutamyltranspeptidase (domain)
Wikipedia: Gamma-glutamyltransferase is a transferase that catalyzes the transfer of gamma-glutamyl functional groups from molecules such as glutathione to an acceptor that may be an amino acid, a peptide or water. GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione as well as drug and xenobiotic detoxification. Other lines of evidence indicate that GGT can also exert a pro-oxidant role, with regulatory effects at various levels in cellular signal transduction and cellular pathophysiology. This transferase is found in many tissues, the most notable one being the liver, and has significance in medicine as a diagnostic marker.
Pfam PF23206: PCDH15-like domain (domain)
This domain is found in human Protocadherin-15 (PCDH15), a calcium-dependent cell-adhesion protein that is essential for maintenance of normal retinal and cochlear function. This domain is predicted to adopt an alpha-beta configuration. It is found C-terminal to several copies of [pfam:PF00028].
Pfam PF05294: Scorpion short toxin (domain)
This family contains various secreted scorpion short toxins and seems to be unrelated to [pfam:PF00451].
Pfam PF11300: Protein of unknown function (DUF3102) (family)
This family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01532: Glycosyl hydrolase family 47 (repeat)
Members of this family are alpha-mannosidases that catalyse the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).
Wikipedia: In molecular biology, glycoside hydrolase family 47 is a family of glycoside hydrolases.
Pfam PF20402: Domain of unknown function (DUF6692) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in Alphaproteobacteria. Proteins in this family are typically between 161 and 194 amino acids in length. This family is related to [pfam:PF03713] and is therefore part of the ferritin superfamily.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16033: Domain of unknown function (DUF4789) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 87 and 100 amino acids in length. There is a conserved GPC sequence motif. There are two completely conserved C residues that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06090: Inositol-pentakisphosphate 2-kinase (family)
This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation.
Pfam PF25050: TARBP1 domain (domain)
This domain is found in the human probable methyltransferase TARBP1 and similar animal proteins. TARBP1 methylates RNA molecules such as tRNAs. This domain is often found associated with [pfam:PF00588].
Pfam PF11587: Major prion protein bPrPp - N terminal (family)
This family represents the N-terminal domain (1-30) of the bovine prion protein (bPrPp). The proteins structure consists of mainly alpha helices. BPrPp forms a stable helix which inserts in a transmembrane location in the bilayer, with the N -terminal (1-30) functioning as a cell-penetrating peptide.
Pfam PF08548: Peptidase M10 serralysin C terminal (repeat)
Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs). The peptidase unit is found at the N terminal while this domain at the C terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the calcium ion binding domain [pfam:PF00353].
Pfam PF14996: Retinal Maintenance (family)
RMP is encoded for by a gene, C8orf37. Mutations in the gene cause two types of retinal dystrophies: cone-rod dystrophy type 16 (CORD16) and retinitis pigmentosa type 64 (RP64). CORD16 affects the cone receptors which detect red, green or blue wavelengths of light and RP64 affects the cone receptors first and then the rod receptors. Both of these affect the photo-receptors in the eye leading to colour blindness or blindness respectively.
Pfam PF19412: Domain of unknown function (DUF5982) (domain)
This short domain of unknown function is found at the N-terminus of [pfam:PF01103].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09239: Topoisomerase VI B subunit, transducer (domain)
Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme.
Pfam PF19423: E3 ubiquitin-protein ligase UBR4 N-terminal (domain)
This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. These are extraordinarily large proteins that recognise and bind to proteins with N-terminal destabilising residues according to the N-end rule leading them to their ubiquitination and degradation. These proteins share a UBR box ([pfam:PF02207]) with others E3-ligases UBR box proteins but UBR4 lacks the ubiquitylation domain, suggesting that it may interact with other catalytic proteins.
Pfam PF19960: Effector-associated domain 7 (domain)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the EAD-EAD coupling approximates the advantages of collinear transcription requirements. Profile-profile searches unify EAD7 with the Death superfamily of domains.
Pfam PF07669: Eco57I restriction-modification methylase (domain)
Homologues of the Escherichia coli Eco57I restriction-modification methylase are found in several phylogenetically diverse bacteria. The structure of TaqI has been solved.
Pfam PF17511: Mobilization protein B (family)
This is a family of unknown function found in Bacteria. Family members include Mobilization protein B (MobB). MobB contains a putative membrane-spanning domain, and might be involved in anchoring or presenting MobA, and the covalently-linked plasmid DNA, to the conjugative pore for subsequent export. In agreement with this, MobB has been shown to be associated with the membrane. Deletion of the membrane-spanning domain disrupts this association and decreases the frequency of both type IV transport and plasmid mobilization. MobB is one out of three proteins encoded by RSF1010 that are required for its mobilization along with MobA and MobC. MobB encoded by the broad-host-range plasmid R1162 is required for its efficient transfer by conjugation. The C-terminal half of the protein contains a membrane domain essential for transfer, while the other, functionally active region of MobB, identified by mutagenesis, is at the N-terminal end. One mutation affecting this region inhibits replication, suggesting that this part of the protein is contacting and sequestering the relaxase-linked primase. A model that represents MobB molecules as anchored in the membrane at one end and engaging the relaxase at the other. This arrangement is suggested to increase the transfer frequency by raising the probability of contact between the relaxase and the membrane-embedded, coupling protein for type IV secretion.
Pfam PF18322: Serine protease Clip domain PPAF-2 (domain)
This domain is found in Prophenoloxidase-activating factor (PPAF)-II present in the beetle Holotrichia diomphalia. PPAF-II is indispensable for the generation of the active phenoloxidase leading to melanization, a major defense mechanism of insects. This domain is the clip domain and it is thought to tightly associate with regions I-III of the serine protease-like (SPL) domain. The clip domain is a protein-interaction module that plays an essential role in the binding and activation of PO76s via its central cleft.
Pfam PF22222: CRISPR-associated endonuclease Cpf1 PI domain (domain)
The CRISPR-Cpf1 system is a class 2 CRISPR-Cas system that mediates robust DNA interference. Cpf1 differ from Cas9 in many aspects including the guide RNAs and substrate specificity. The Cpf1-crRNA complex cleaves a target double-stranded DNA containing a short T-rich PAM motif on the 5' end of the non-target strand. This PAM motif is recognized by the Cpf1 PI (PAM-interacting) domain. This domain folds into array of four helices and along with the helix-loop-helix motif in the REC1 domain, channel the PAM strand into a cavity leading to the nuclease site.
Pfam PF10513: Enhancer of polycomb-like (family)
This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
Pfam PF02809: Ubiquitin interaction motif (conserved_site)
This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome. This motif has a pattern of conservation characteristic of an alpha helix.
Wikipedia: In molecular biology, the Ubiquitin-Interacting Motif (UIM), or 'LALAL-motif', is a sequence motif of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA, UBX, ENTH domain, EH, VHS, SH3 domain, HECT, VWFA, EF-hand calcium-binding, WD-40, F-box, LIM, protein kinase, ankyrin, PX, phosphatidylinositol 3- and 4-kinase, C2 domain, OTU, DnaJ domain, RING-finger or FYVE-finger. UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs.
Pfam PF11273: Protein of unknown function (DUF3073) (family)
This family of proteins with unknown function appears to be restricted to Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11801: Tom37 C-terminal domain (domain)
The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intra-membrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex.
Pfam PF13861: FlgD Tudor-like domain (domain)
This domain has a tudor domain-like beta barrel fold. It is found in the FlgD protein the flagellar hook capping protein. The structure for this domain shows that it contains a nested Ig-like domain within it.  However in some firmicute proteins this inserted domain is absent such as Q67K21.
Pfam PF08717: Coronavirus replicase NSP8 (domain)
Viral NSP8 (non structural protein 8) forms a hexadecameric supercomplex with NSP7 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase. NSP7 and NSP8 heterodimers play a role in the stabilisation of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex. It has been demonstrated that NSP8 acts as an oligo(U)-templated polyadenylyltransferase but also has robust (mono/oligo) adenylate transferase activities. NSP8 has N- and C-terminal D/ExD/E conserved motifs, being the N-terminal motif critical for RNA polymerase activity as these residues are part of the Mg2-binding active site.
Pfam PF13713: Transcription factor BRX N-terminal domain (domain)
The BREVIS RADIX (BRX) domain was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root.  BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway.  BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot. This family features a short region, also alpha-helical, N-terminal to the repeated alpha-helices of family BRX, [pfam:PF08381]. BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action.
Pfam PF21440: Archaeal selenocysteine-specific elongation factor, domain III (domain)
Selenocysteine-specific elongation factor (SelB) is a transcription factor necessary for the incorporation of selenocysteine into proteins. This entry represents domain III of archaeal SelB, which adopts a beta-barrel fold and is homologous to domain III of EF-Tu.
Pfam PF02725: Non-structural protein C (family)
This family consists of the polymerase accessory protein C from members of the paramyxoviridae.
Pfam PF16931: Putative phage holin (family)
This entry includes a group of putative holins found in bacteriophages from the Caudovirales order. However, proteins in this entry are mostly from Proteobacteria. Their function is not clear.
Pfam PF22634: DNA polymerase epsilon catalytic subunit A, thumb domain (domain)
This entry represents the thumb domain of DNA polymerase epsilon catalytic subunit A from Saccharomyces cerevisiae (POL2), the catalytic component of this complex involved in chromosomal DNA replication. This domain, which makes contacts in the DNA minor groove, shows a mainly alpha-helical structure.
Pfam PF08076: Tetracycline resistance determinant leader peptide (family)
This family consists of the tetracycline resistance  determinant tet(M) leader peptides. A short open  reading frame corresponding to a 28 amino acid peptide  which contain a number of inverted repeat sequences was  found immediately upstream of the tet(M). Transcriptional  analyses has found that expression of tet(M) resulted from an  extension of a small transcript representing the upstream  leader region into the resistance determinant. Thus this  leader sequence is responsible for transcriptional attenuation  and thus regulation of the transcription of tet(M).
Pfam PF23376: VIN3-like, fibronectin type-III domain (domain)
This entry represents the from Protein Vernalization Insensitive 3 from Arabidopsis thaliana (VIN3) and similar plant sequences. VIN3 plays a central role in vernalization by mediating the initial transcriptional repression of the homeotic gene FLC, a floral repressor, after a cold treatment.
Pfam PF10332: Protein of unknown function (DUF2418) (family)
This is a conserved 100 residue central region of a family of proteins found in fungi. It carries a characteristic EYD sequence motif. The function is not known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11067: Protein of unknown function (DUF2868) (family)
Some members in this family of proteins with unknown function are annotated as putative membrane proteins. However, this cannot be confirmed.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23452: Hydroxyproline O-arabinosyltransferase family (domain)
The Hydroxyproline O-arabinosyltransferase family is comprised of glycosyltransferases involved in the post-translational modification of plant proteins. Members of this family catalyze the transfer of L-arabinose to the hydroxyl group of hydroxyproline (Hyp) residues in target proteins, such as extensins and small signaling peptides. This modification is crucial for the proper function of these proteins, which play roles in plant structure and signaling. In legumes, some family members are also implicated in the autoregulation of nodulation (AON), a process that controls the number of root nodules formed in response to nitrogen availability and rhizobial colonization. They function upstream of receptor kinases like SUNN and through CLE peptides to regulate long-distance signaling events between the root and shoot.
Pfam PF03312: Protein of unknown function (DUF272) (family)
This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23890: Family of unknown function (DUF7242) (family)
This entry represents a family of uncharacterised phage proteins. AlphaFold multimer suggests this protein may form a dimeric ring arrangement.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01204: Trehalase (repeat)
Trehalase ([ec:3.2.1.28]) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with [pfam:PF07492] in fungi.
Wikipedia: In molecular biology, glycoside hydrolase family 37 is a family of glycoside hydrolases.
Pfam PF20054: Trypanosoma Tc-38 (p38) protein (domain)
Domain found in multiple copies in kinetoplastid-specific minicircle binding proteins that evolved from a prokaryotic ArdCN domain
Pfam PF20219: Family of unknown function (DUF6579) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Fungi. Proteins in this family are approximately 300 amino acids in length. There are some conserved motifs, HxFF, HPD and FHLLI.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13505: Outer membrane protein beta-barrel domain (domain)
This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.
Pfam PF05696: Protein of unknown function (DUF826) (family)
This family consists of several enterobacterial and siphoviral sequences of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23961: Phage neck terminator protein (domain)
This entry represents the neck terminator protein gp12 from cyanophage Pam3. Six gp12 subunits form a hexameric ring that terminates neck assembly and links to the tail tube/sheath. Each subunit has an N-terminal loop, a conserved globular domain, and a protruding beta-sheet domain.