SII-SWORD/CoKE huggingface dataset:
Pfam PF13085: 2Fe-2S iron-sulfur cluster binding domain (domain)
The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.
Wikipedia: Succinate dehydrogenase (SDH) or succinate-coenzyme Q reductase (SQR) or respiratory complex II is an enzyme complex, found in many bacterial cells and in the inner mitochondrial membrane of eukaryotes. It is the only enzyme that participates in both the citric acid cycle and oxidative phosphorylation. Histochemical analysis showing high succinate dehydrogenase in muscle demonstrates high mitochondrial content and high oxidative potential.
Pfam PF17814: LisH-like dimerisation domain (domain)
TOPLESS (TPL) proteins have a highly conserved N-terminal domain containing a lissencephaly homologous (LisH) dimerization motif.
Pfam PF18889: Beta helix repeat (repeat)
This entry contains a 30 residue repeat found in a variety of bacterial cell surface proteins. This repeat is related to [pfam:PF14262], meaning that it has a beta-helix structure. The sequence repeat is quite glycine rich.
Pfam PF12290: Protein of unknown function (DUF3802) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif.
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 PF15847: Major keratinocyte cell envelope protein (family)
Loricrin is a family of major keratinocyte cell envelope proteins found in primates. It acts as an important epidermal barrier, and is initially expressed in the granular layer comprising 70% of the total protein mass of the cornified layer. Expression of Loricrin is regulated by TNF-alpha via a c-Jun N-terminal kinase-dependent pathway.
Pfam PF21724: Family of unknown function (DUF6861) (domain)
This domain is a likely integral membrane domain that contains a glycine-zipper motif. This domain is found associated with toxin domains.
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 PF22145: GtfA extended beta-sheet domain (domain)
This entry represents the extended beta-sheet domain (EBD, also known as DUF1975) of UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit. GtfA is the core enzyme of the OGT complex, which also includes the co-activator GtfB, to glycosylate the serine-rich repeat (SRR) of adhesin PsrP in Streptococcus pneumoniae, a protein involved in the infection and pathogenesis. The function of this domain is not clear.
Pfam PF10952: Protein of unknown function (DUF2753) (repeat)
This bacterial 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 PF18496: Collagenase G catalytic helper subdomain (domain)
This is the catalytic helper subdomain found in collagenase G from Clostridium histolyticum. This domain is indispensable for proper folding and full peptidase activity.
Pfam PF11991: Tryptophan dimethylallyltransferase (family)
This family of proteins represents tryptophan dimethylallyltransferase ([ec:2.5.1.34]), which catalyses the first step of ergot alkaloid biosynthesis. Ergot alkaloids, which are produced by endophyte fungi, can enhance plant host fitness, but also cause livestock toxicosis to host plants. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 390 to 465 amino acids in length.
Pfam PF09625: VP9 protein (domain)
VP9 is a protein containing a ferredoxin fold. Two dimers come together to form one asymmetric unit which possesses a DNA recognition fold and specific metal binding sites possibly for zinc. It is postulated that being a non-structural protein VP9 is involved in the transcriptional regulation of the White spot syndrome virus, WSSV, from which it comes. WSSV is the major viral pathogen in shrimp aquaculture. VP9 is found N-terminal to the [pfam:PF07056] domain.
Pfam PF02630: SCO1/SenC (family)
This family is involved in  biogenesis of respiratory and photosynthetic systems. SCO1 ([swissprot:P23833]) is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC ([swissprot:Q52720]) is required for optimal  cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.
Pfam PF07815: Abl-interactor HHR (family)
The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact  with Abl-family tyrosine kinases. More specifically,  it is termed the homeo-domain homologous region (HHR), as it  is similar to the DNA-binding region of homeo-domain  proteins. Other homeo-domain proteins have been  implicated in specifying positional information during embryonic development, and in the regulation of the expression of  cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved  in cytoskeletal reorganisation, but their precise role remains  unclear.
Pfam PF21740: Family of unknown function (DUF6866) C-terminal domain (domain)
This entry represents the C-terminal alpha-helical domain found in DUF6866 family proteins. The function of these proteins is unknown. Proteins in this family are primarily found in Proteobacteria.
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 PF12624: VPS13-like family N-terminal region (repeat)
VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites. It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on  the carbon source and metabolic state. VPS13A, VPS13C and VPS13D from mammals localise at contacts at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localise to endosome-endosome contacts. Mutations in human VPS13 proteins cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia.
Pfam PF19089: Membrane bound beta barrel domain (DUF5777) (domain)
This entry contains integral membrane beta barrel proteins.
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 PF18000: Type 2 DNA topoisomerase 6 subunit B C-terminal domain (domain)
This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B ([ec:5.99.1.3]). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. Mutation analysis of this C-terminal domain showed that the overall activity of the mutant mesophilic methanogen M. mazei Top6B (MmT6) is modestly reduced but its relative activity on different substrates is not affected. Due to the similarity of the B subunit's CTD to known protein- and carbohydrate-binding modules, it has been suggested that it could regulate topo VI spatially, perhaps by localizing the enzyme to a specific subcellular region or functional partner.
Pfam PF10670: Domain of unknown function (DUF4198) (family)
This family was previously missannotated in Pfam as NikM.
Pfam PF00311: Phosphoenolpyruvate carboxylase (family)
Phosphoenolpyruvate carboxylase (PEPCase), an enzyme found in all multicellular plants, catalyses the formation of oxaloacetate from phosphoenolpyruvate (PEP) and a hydrocarbonate ion . This reaction is harnessed by C4 plants to capture and concentrate carbon dioxide into the photosynthetic bundle sheath cells. It also plays a key role in the nitrogen fixation pathway in legume root nodules: here it functions in concert with glutamine, glutamate and asparagine synthetases and aspartate amido transferase, to synthesise aspartate and asparagine, the major nitrogen transport compounds in various amine-transporting plant species .
Wikipedia: Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:PEP + HCO3− → oxaloacetate + Pi
Pfam PF04709: Anti-Mullerian hormone, N terminal region (family)
Anti-Mullerian hormone, AMH is a signalling molecule involved in male and female sexual differentiation.  Defects in synthesis or action of AMH cause persistent Mullerian duct syndrome (PMDS), a rare form of male pseudohermaphroditism. This family represents the N terminal part of the protein, which is not thought to be essential for activity.      AMH contains a TGF-beta domain ([pfam:PF00019]), at the C terminus.
Pfam PF02443: Circovirus capsid protein (domain)
Circoviruses are small circular single stranded viruses.  This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus [swissprot:Q9YUC8]. These proteins are about 220 amino acids long.
Pfam PF23661: SHMOOSE (family)
This protein family includes human Protein SHMOOSE, a 58-residues long micropeptide that increases neural cell metabolic activity and mitochondrial oxygen consumption rate rate. It shows increased expression in Alzheimer disease patient brains.
Pfam PF24759: ASCIZ third C2HC zinc finger domain (domain)
This domain is found in the human ATM interactor (also known as ATM/ATR-substrate CHK2-interacting zinc finger protein (ASCIZ)) and related proteins from animals. These proteins are transcription factors that are essential for cell survival and the formation of RAD51 foci, a response to methylating DNA damage. They are also involved in the regulation of ATM (ataxia telangiectasia mutated) kinase activity, particularly in the absence of DNA damage, potentially by stabilising ATM. ASCIZ is predicted to contain four zinc finger domains. This entry represents the third zinc finger domain, which is a variant of the classical C2H2 zinc fingers bearing cysteine residue instead of histidine in the fourth zinc ligand position.
Pfam PF14000: DNA packaging protein FI (family)
This family includes the lambda phage DNA-packaging protein FI. Proteins in this family are typically between 124 and 140 amino acids in length.  There is a conserved EEE sequence motif.
Pfam PF00894: Luteovirus coat protein (family)
Barley yellow dwarf virus (BYDV) can be separated into two groups based on serological relationships, presumably governed by the viral capsid structure . Coding regions of coat proteins have been identified for the MAV-PS1, P-PAV (group 1) and NY-RPV (group 2) isolates of BYDV. Group 1 proteins show 71% sequence similarity to each other, 51% similarity to those of group 2, and a high degree of similarity to those from other luteoviruses (including coat proteins from Beet western yellows virus (BWYV)  and Potato leafroll virus (PLrV) ).

Among luteovirus coat protein sequences in general, several highly conserved domains can be identified, while other domains differentiate group 1 isolates from group 2 and other luteoviruses. Sequence comparisons between the genomes of PLrV, BWYV and BYDV have revealed ~65% protein sequence similarity between the capsid proteins of BWYV and PLrV and ~45% similarity between BYDV and PLrV . The N-terminal regions of these sequences, like those of many plant virus capsid proteins, is highly basic. These regions may be involved in protein-RNA interaction.
Pfam PF05501: Domain of unknown function (DUF755) (family)
This family is predominated by ORFs from Circoviridae. The function of this family remains to be determined.
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 PF23719: Antitoxin VapB-like (family)
This protein family includes a group of uncharacterised short sequences from actinobacteria, including the predicted Antitoxin VapB from Streptomyces cyaneogriseus. Members of this family are predicted to adopt an alpha-beta structure.
Pfam PF09313: Domain of unknown function (DUF1971) (domain)
Members of this family of functionally uncharacterised domains are predominantly found in bacterial Tellurite resistance protein.
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 PF21585: Archaeal A-ATP synthase, subunit H, N-terminal (domain)
This domain is found at the N-terminal end of MJ0223 from Methanocaldococcus jannaschii ([swissprot:Q57676]), the subunit H of an archaeal A-ATP synthase. This entry represents the region that is involved in subunit H and E assembly. It folds into a continuous alpha-helix with a small kink in the centre of the molecule.
Pfam PF18971: CagA protein (family)
The Helicobacter pylori type IV secretion effector CagA is a major  bacterial virulence determinant and critical for gastric carcinogenesis. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain  II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA.
Pfam PF04005: Hus1-like protein (family)
Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast. These proteins are known to form a stable complex in vivo. Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, and could function as a sliding clamp during checkpoint control.
Pfam PF04411: PD-(D/E)XK nuclease superfamily (domain)
This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches.  The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix.  It has been speculated that it could function as s methylation-dependent restriction. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme.
Pfam PF19600: Family of unknown function (DUF6105) (family)
This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
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 PF25141: GPI inositol-deacylase beta-sandwich domain (domain)
This domain is found in GPI inositol-deacylase (BST1 also known as PGAP1) and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body. This entry represents a beta-sandwich domain which is located next to the PGAP1 alpha/beta domain. The function of this domain is unclear but it is not necessary for the deacylase activity.
Pfam PF01433: Peptidase family M1 domain (domain)
Members of this family are aminopeptidases.  The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues.  This family includes leukotriene-A4 hydrolase [swissprot:P09960], this enzyme also has an aminopeptidase activity.
Wikipedia: Aminopeptidases are enzymes that catalyze the cleavage of amino acids from the N-terminus (beginning), of proteins or peptides. They are found in many organisms; in the cell, they are found in many organelles, in the cytosol, and as membrane proteins. Aminopeptidases are used in essential cellular functions, and are often zinc metalloenzymes, containing a zinc cofactor.
Pfam PF11778: Septation initiation (family)
This family is required for activation of the spg1 GTPase signalling cascade which leads to the initiation of septation and the subsequent termination of mitosis. It may act as a scaffold at the spindle pole body to which other components of the spg1 signalling cascade attach in pombe. In S.cerevisiae it is both required for the proper formation of the spindle pole body outer plaque and may also connect the outer plaque to the central plaque embedded in the nuclear envelope.
Pfam PF04136: Conserved oligomeric Golgi complex subunit 3, N-terminal (repeat)
This entry includes the Conserved oligomeric Golgi complex subunit 3 (COG3, also known as Sec34) which is a component of the peripheral membrane COG complex, involved in intra-Golgi protein trafficking.. COG is a member of the complexes associated with tethering containing helical rods (CATCHR) family which also includes the exocyst, GARP and DSL1 complexes, which are evolutionarily related and share structural features consisting of alpha-helical bundles towards the C-terminal and an N-terminal coiled-coil region.
Pfam PF06684: Amino acid synthesis (family)
This family of proteins is structurally similar to proteins with the Bacillus chorismate mutase-like (BCM-like) fold. This structure, combined with its genomic context, suggest that it has a role in amino acid synthesis.
Pfam PF23529: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AW97] from the parasite Babesia bovis.
Pfam PF22060: Cep192 domain 1 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the first domain found in the metazoan Cep192 homologs.
Pfam PF21258: Glycoside hydrolase 120, insertion domain (domain)
This insertion domain is found in a group of bacterial glycoside hydrolases from the CAZy family 120, including Parallel beta-helix repeat protein from Thermoanaerobacterium saccharolyticum (also known as xylosidase). It is often found associated to [pfam:PF13229].
Pfam PF22554: TY-Chap C-terminal domain (domain)
This entry represents a domain observed in host systems predicted to counter the action of viral ribosylating toxins. It is found C-terminal to the TY-Chap1 ([pfam:PF22551]) and TY-Chap3 ([pfam:PF22552]) domains.
Pfam PF12469: CRISPR-associated protein Cmr2, N-terminal (domain)
This domain family is typically between 101 and 138 amino acids in length and it is found in subunit Crm2 of the CRISPR RNA-Cas protein complex (Cmr complex).
Pfam PF21312: Origin recognition complex subunit 1 C-terminal winged HTH domain (domain)
This entry represents the C-terminal winged helix-turn-helix domain found in the Origin recognition complex subunit 1 protein.
Pfam PF21224: Small RNA 2'-O-methyltransferase-like, La-motif-containing domain (domain)
This domain is found in Small RNA 2'-O-methyltransferase from Arabidopsis thaliana (Hen1) and similar proteins from plants. Hen1 is a methyltransferase for miRNAs and all types of siRNAs, which protects these molecules from 3'-end uridylation and 3'-to-5' exonuclease-mediated degradation. This protein shows five structural domains, four of which directly interact with the RNA substrate. This entry represents one of these four domains: the La-motif-containing domain (LCD).
Pfam PF18124: Kindlin-2 N-terminal domain (domain)
This is the N-terminal domain (K2-N) of Kindlin-2 protein present in Homo sapiens. Kindlin-2 is a regulator for heterodimeric integrin adhesion receptors promotes integrin activation. Activation depends on binding of the N-terminal domain to the integrin beta cytoplasmic tail (CT), which disrupts the receptors association with alpha-CT and triggers the conformational transitions in the receptor. K2-N contains a conserved positively charged surface that binds to membrane enriched with negatively charged phosphatidylinositol-(4,5)-bisphosphate (PIP2). K2-N is also very similar to the homologous kindlin-1 F0.