SII-SWORD/CoKE huggingface dataset:
Pfam PF19236: ADAMTS cysteine-rich domain (domain)
This cysteine rich domain is found in a variety of ADAMTS and ADAMTS-like endopeptidases widely spread in animals. It is a well-conserved cysteine-rich sequence containing 10 cysteine residues. ADAM-TS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) is closely related to the ADAM family (A Disintegrin and Metalloproteinase, [pfam:PF08516]) and consists of at least 20 members sharing a high degree of sequence similarity and conserved domain organisation. Members of the ADAMTS family have been implicated in a range of diseases.
Pfam PF07123: Photosystem II reaction centre W protein (PsbW) (family)
This family consists of several plant specific photosystem II reaction centre W (PsbW) proteins. PsbW is a nuclear-encoded protein located in the thylakoid membrane of the chloroplast. PsbW is a core component of photosystem II but not photosystem I. This family does not appear to be related to [pfam:PF03912].
Pfam PF19473: Family of unknown function (DUF6010) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001011) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the meridamycin  biosynthetic gene cluster from Streptomyces sp. NRRL 30748.
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 PF14309: Domain of unknown function (DUF4378) (family)
This domain is found in protein LONGIFOLIA 2. The function of this domain 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 PF22746: SHOCT-like domain (domain)
This is a SHOCT-like domain that occurs as a fusion of ZnR+DUF2089-HTH+SHOCT-like. It is found at the C-terminal of DUF2089 ([pfam:PF09862]).
Pfam PF04308: Ribonuclease H-like (family)
RNaseH_like is a family of uncharacterised eubacterial proteins that are distant homologues of Ribonuclease H-like. The family maintains all the core secondary structure elements of the RNase H-like fold and shares several conserved, presumably active site residues with RNase HI. This finding suggests that it functions as a nuclease.
Pfam PF11895: Fungal peroxidase extension region (family)
This region is found as an extension to a haem peroxidase domain in some fungi. This region is about 80 amino acids in length and forms an extended structure on the surface of the peroxidase domain [pfam:PF00141].
Wikipedia: Haem peroxidases (or heme peroxidases) are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme:Fe3+ + H2O2  [Fe4+=O]R' (Compound I) + H2O[Fe4+=O]R' + substrate --&gt; [Fe4+=O]R (Compound II) + oxidized substrate[Fe4+=O]R + substrate --&gt; Fe3+ + H2O + oxidized substrate
Pfam PF03214: Reversibly glycosylated polypeptide (family)
This family includes UDP-arabinopyranose mutases and putative alpha-1,4-glucan-protein synthase [UDP-forming]. The former catalyses the interconvertion of UDP-L-arabinopyranose (UDP-Arap) and UDP-L-arabinofuranose (UDP-Araf), while the latter catalyses the reaction between UDP-glucose and a protein to produce UDP and alpha-D-glucosyl-protein. UDP-arabinopyranose mutases are essential for cell wall establishment and plant development . This entry also includes uncharacterized prokaryotic proteins.
Pfam PF22206: CRISPR-associated protein Csm6 6H domain (domain)
This entry includes Csm6 from bacteria (i.e Enterococcus italicus), a Cas (CRISPR-associated) protein from type III-A CRISPR-Cas system. It consists of a CARF domain at the N-terminal, a six-helix (6H) domain and a C-terminal HEPN domain at the C-terminal, which has RNase activity. This is the 6H domain.
Pfam PF10295: Uncharacterised protein (DUF2406) (family)
This is a family of small proteins conserved in fungi. 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 PF15353: Headcase N-terminal (domain)
HECA was characterised first in Drosophila where it regulates the proliferation and differentiation of cells during adult morphogenesis. It is involved in dendrite pruning and is a branching inhibitor during tracheal development. It also promotes cell survival and niche maintenance in the Drosophila testis. In humans, HECA affects cell cycle progression and proliferation in head and neck cancer cells. It by slows down cell division of oral squamous cell carcinoma cells and may thereby act as a tumour-suppressor in head and neck cancers. It may be considered as an interesting therapeutic agent against Wnt-dependent tumor progression. This entry represents a domain found towards the N-terminal.
Pfam PF21547: TELO2-interacting protein 1 (repeat)
This entry includes TELO2-interacting protein 1 from yeast and its homologues from mammals. Budding yeast Tti1 is a subunit of the ASTRA complex, which is involved in chromatin remodelling. Human TTI1 is a regulator of the DNA damage response (DDR). It is part of the TTT complex that is required to stabilize protein levels of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family proteins. The TTT complex is involved in the cellular resistance to DNA damage stresses. Together with the TTT complex and HSP90, participates in the proper folding of newly synthesized PIKKs. Members of this entry are entirely composed of HEAT repeats.
Pfam PF03058: Sar8.2 family (family)
Members of this family are found in Solanaceae plants, a taxonomic group (family) that includes pepper and tobacco plant species.  Synthesis of these proteins is induced by tobacco mosaic virus (TMV) and salicylic acid; indeed they are thought to be involved in the development of systemic acquired resistance (SAR) after an initial hypersensitive response to microbial infection. SAR is characterised by long-lasting resistance to infection by a wide range of pathogens, extending to plant tissues distant from the initial infection site.
Pfam PF06588: Muskelin N-terminus (family)
This family represents the N-terminal region of muskelin and is found in conjunction with several [pfam:PF01344] repeats. Muskelin is an intracellular, kelch repeat protein that is needed in cell-spreading responses to the matrix adhesion molecule, thrombospondin-1.
Pfam PF09834: Predicted membrane protein (DUF2061) (family)
This domain, found in various prokaryotic 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 PF12339: DNA-J related protein (family)
This domain family is found in bacteria, and is approximately 130 amino acids in length. The family is found in association with [pfam:PF00226]. There is a conserved YYLD sequence motif. Mostof the sequences in this family are annotated as DNA-J related proteins but there is little publication to back this up.
Pfam PF21659: Flavivirus envelope glycoprotein E, stem/anchor domain (domain)
This entry represents the stem/anchor domain found at the C-terminal of envelope glycoprotein E from Flavivirus. This domain comprises a stem region followed by two transmembrane anchor domains.
Pfam PF06600: Protein of unknown function (DUF1140) (family)
This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown.
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 PF03340: Poxvirus rifampicin resistance protein (family)
This family represents the Poxvirus rifampicin resistance protein (Scaffold protein OPG125), a scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. It is targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of OPG158 N terminus .
Pfam PF06180: Cobalt chelatase (CbiK) (family)
This family consists of several bacterial cobalt chelatase (CbiK) proteins ([ec:4.99.1.-]).
Pfam PF12820: Serine-rich domain associated with BRCT (domain)
This domain is found on BRCA1 proteins.
Pfam PF21732: Domain of unknown function (DUF6864) (domain)
This entry represents a family of bacterial proteins that adopt a beta-sandwich domain. The function of these proteins is currently unknown.
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 PF02711: E4 protein (family)
This is is a family of Papillomavirus proteins, E4, coded for by ORF4. A splice variant, E1--E4, exists but neither the function of E4 or E1--E4 is known.
Pfam PF15844: Transmembrane and coiled-coil domain-containing protein 2 (family)
This family of proteins is found in primates. Proteins in this family are approximately 180 amino acids in length.
Pfam PF19944: Family of unknown function (DUF6406) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lavendiol biosynthetic gene cluster from Streptomyces lavendulae.
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 PF09595: Metaviral_G glycoprotein (domain)
This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated.
Pfam PF19985: Family of unknown function (DUF6421) (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), in particular the polyoxin A biosynthetic gene cluster from Streptomyces cacaoi  subsp. asoensis. This family appears to be predominantly found in 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 PF23166: Alpha-glucan water dikinase 1 Ig-like N-terminal domain (domain)
This domain is found N-terminal in the Alpha-glucan water dikinase 1 (CWD1) from Arabidopsis thaliana and related plant proteins including Alpha-amylase 3 (AMY3). CWD1 is involved in the incorporation of phosphate into starch-like alpha-glucan, with preferred C-6 position of glucose units. It acts as an overall regulator of starch mobilization and it is required for starch degradation. AMY3 is involved in the determination of the final structure of glucans by shortening long linear phospho-oligosaccharides in the chloroplast stroma. Can act on both soluble and insoluble glucan substrates to release small linear and branched malto-oligosaccharides. The domain represented by this entry is predicted to adopt a globular structure with an Ig-like topology. This domain is distantly related to CBM98 carbohydrate-binding family.
Pfam PF24171: Straight fiber protein PB4 third Fn3-like domain (domain)
This entry represents the third Fn3-like domain of the Straight fiber protein PB4 found in T5-like phages. PB4 along with PB3, forms the central straight fiber, bearing the receptor binding protein PB5 at its C terminus. Upon PB5 binding to the host receptor FhuA, the central fiber reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring. The PB4-PB3 interactions are ensured by the proximal loops of the first and the distal loops of the second of the three PB4 Fn3-like domains. These interactions are disrupted upon binding to the host receptor and the string of the three PB4 Fn3-like domains undergoes drastic conformational changes.
Pfam PF18834: Large polyvalent protein associated domain 22 (domain)
This is a predicted enzymatic alpha-helical domain with highly conserved aspartate residues. The domain is found in polyvalent proteins of phage and prophage genes and is often the immediate neighbour of a lysozyme gene.
Pfam PF18174: CCDC81-like prokaryotic HU domain 1 (domain)
First of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope.
Pfam PF01864: CDP-archaeol synthase (family)
CDP-archaeol synthase functions in the archaeal lipid biosynthetic pathway. It catalyses the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached. Bacterial members of this family are uncharacterized.
Pfam PF19465: Family of unknown function (DUF6002) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000833) is described by MIBiG as an example of the following biosynthetic classes, saccharide and other (unspecified). This family includes a protein from the coumermycin A1 biosynthetic  gene cluster from Streptomyces rishiriensis.
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 PF22097: Methyl-accepting chemotaxis protein McpB, first HAMP domain (domain)
This domain is found at the N-terminal end of Methyl-accepting chemotaxis protein McpB from Pseudomonas aeruginosa and similar sequences from gammaproteobacteria. McpB, also known as Aerotaxis transducer Aer2, is a chemoreceptor that plays a critical role in the virulence and pathogenesis of the bacteria in a variety of hosts. This entry represents the first of the five HAMP domains of McpB. This domain consists of a monomeric unit of two parallel alpha-helices joined by an elongated connector of 12-14 residues. The three N-terminal are likely to be required for dimerisation.
Pfam PF10557: Cullin protein neddylation domain (domain)
This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue.
Wikipedia: Cullins are a family of hydrophobic scaffold proteins which provide support for ubiquitin ligases (E3). All eukaryotes appear to have cullins. They combine with RING proteins to form Cullin-RING ubiquitin ligases (CRLs) that are highly diverse and play a role in myriad cellular processes, most notably protein degradation by ubiquitination.
Pfam PF19018: Vanin C-terminal domain (domain)
This domain is found at the C terminus of Vanin 1 and related proteins.
Pfam PF06965: Na+/H+ antiporter 1 (family)
This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyse the exchange of H+ for Na+ in a manner that is highly dependent on the pH.
Wikipedia: Na+/H+ antiporter A (NhaA) family (TC# 2.A.33) contains a number of bacterial sodium-proton antiporter (SPAP) proteins. These are integral membrane proteins that catalyse the exchange of H+ for Na+ in a manner that is highly pH dependent. Homologues have been sequenced from a number of bacteria and archaea. Prokaryotes possess multiple paralogues. A representative list of the proteins that belong to the NhaA family can be found in the Transporter Classification Database.
Pfam PF08237: PE-PPE domain (domain)
This domain is found C terminal to the PE ([pfam:PF00934]) and PPE ([pfam:PF00823]) domains.  The secondary structure of this domain is predicted to be a mixture of alpha helices and beta strands.
Pfam PF18132: Tyrosinase C-terminal domain (domain)
This is the C-terminal domain of Tyrosinase present in Aspergillus oryzae. Tyrosinase is a dinuclear copper monooxygenase/oxidase that plays a crucial role in the melanin pigment biosynthesis. The C-terminal domain is referred to as the shielding domain as it prohibits substrate access to the enzyme-active site and blocks the oxidase/oxygenase activity to avoid undesirable intracellular reactions of highly reactive quinonoid products. This means the domain may play an important role in regulating the enzyme activity. Two of the three cysteines (Cys522, and Cys525) that play a significant role in the copper incorporation process belong to the C-terminal domain.
Pfam PF00165: Bacterial regulatory helix-turn-helix proteins, AraC family (domain)
In the absence of arabinose, the N-terminal arm of AraC  binds to the DNA binding domain ([pfam:PF00165]) and helps to hold the two DNA binding domains in a relative  orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and  hence AraC ceases looping the DNA when arabinose is added.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF09097: Baseplate structural protein, domain 1 (domain)
Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27.
Pfam PF14683: Polysaccharide lyase family 4, domain III (domain)
CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.
Pfam PF03717: Penicillin-binding Protein dimerisation domain (domain)
This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' structure.
Wikipedia: Penicillin-binding proteins (PBPs) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of transpeptidase enzymes called DD-transpeptidases.
Pfam PF18318: Glutamine synthetase C-terminal domain (domain)
This domain is found in type III glutamine synthetase present in Bacteroides fragilis. Glutamine synthetase (GS) are large oligomeric enzymes that catalyze the condensation of ammonium and glutamate to form glutamine, the principal source of nitrogen for protein and nucleic acid synthesis. This domain is located in the C-terminal end of the protein.