SII-SWORD/CoKE huggingface dataset:
Pfam PF19289: PmbA/TldA metallopeptidase C-terminal domain (domain)
This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation.
Pfam PF17547: Family of unknown function (DUF5462) (family)
This is a family of unknown function found in Gammaproteobacteria.
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 PF18587: PTX/LNS-Like (PLL) domain (domain)
Adhesion G protein-coupled receptors (aGPCRs) play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. The aGPCR GPR56/ADGRG1 regulates both oligodendrocyte and cortical development. The N-terminal domain of GPR56 has low sequence identity and a fold that likely diverged from the PTX and LNS domains. It also has a conserved motif (HphiC91xxWxxxxG) that was identified among canonical PTX domains.  Thus, it is termed the Pentraxin/Laminin/neurexin/sex-hormone-binding-globulin-Like (PLL) domain. Truncation-based analyses suggest that the regions of GPR56 responsible for binding TG2 and collagen III are within the PLL domain, most likely in the surface-exposed conserved patch.  Furthermore, it is suggested that the conserved patch of the PLL domain mediates an essential function in CNS myelination.
Pfam PF08509: Adenylate cyclase G-alpha binding domain (domain)
This fungal domain is found in adenylate cyclase and interacts with the alpha subunit of heterotrimeric G proteins.
Pfam PF17216: Rrp44-like cold shock domain (domain)
Rrp44 (also known as Dis3) constitutes the only active nuclease of the yeast exosome core . The structure of Rrp44 consists of CSD1, CSD2, RNB, and S1 domains. The two N-terminal cold shock domains (CSD1 and CSD2) and the C-terminal S1 domain all display characteristic OB folds . This entry represents CSD1.
Pfam PF22408: PsV, capsid protein, C-terminal domain (domain)
This domain is found at the C-terminal end of the putative capsid protein from Penicillium stoloniferum virus F (CP, [swissprot:Q4G3H1]). This protein has a disordered N-terminal end that interacts with the dsRNA genome and probably participates in its packaging or transcription, and a C-terminal domain (this entry) that shows a helix-loop-helix motif involved in the formation flexible channels thought to be involved in RNA synthesis activity.
Pfam PF00270: DEAD/DEAH box helicase (domain)
Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Wikipedia: DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids. They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not all. Many organisms, including humans, contain DEAD-box (SF2) helicases, which are involved in RNA metabolism.
Pfam PF20266: Mab-21 protein HhH/H2TH-like domain (domain)
This family contains Mab-21 and Mab-21 like proteins.  In C. elegans these proteins are required for several aspects of embryonic development.
Pfam PF14046: Nuclear receptor repeat (family)
This is a repeat domain involved in dimerisation of nuclear receptors proteins and in transcriptional regulation in general. It contains a  Leu-Xaa-Xaa-Leu-Leu motif which has been characterized for the orphan  nuclear receptor Dax-1, which represses the constitutively expressed  protein Ad4BP/SF-1. The LXXLL motif plays in important role in binding of Dax-1 to Ad4BP/SF-1. The domain is subject to structure determination by the Joint Center of Structural Genomics.
Pfam PF06450: Bacterial Na+/H+ antiporter B (NhaB) (family)
This family consists of several bacterial Na+/H+ antiporter B (NhaB) proteins. The exact function of this family is unknown.
Pfam PF15516: BpuSI N-terminal domain (domain)
This is the N-terminal (nuclease) domain of the BpuSI restriction endonuclease.
Pfam PF06174: Protein of unknown function (DUF987) (family)
Family of bacterial proteins that are related to the hypothetical  protein yeeT.
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 PF23636: Domain of unknown function (DUF7144) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to fold into a four-helical up-and-down bundle and it is likely transmembrane.
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 PF24296: SrfA protein (family)
This entry represents the Stress Response Facilitator A SrfA. SrfA was shown to play a positive role in the sigma(22)-dependent activation of the algD promoter under stress in both sessile and planktonic conditions. This protein folds into an alpha-helical hairpin.
Pfam PF16106: Domain of unknown function (DUF4824) (family)
This family consists of several hypothetical lipoproteins around 270 residues in length and is mainly found in Pseudomonas species. The function of this family is unknown.
Pfam PF14588: YjgF/chorismate_mutase-like, putative endoribonuclease (domain)
YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes.
Pfam PF20817: Type III effector Xcv3220, C-terminal domain (domain)
This domain is found at the C-terminal end of the type III effector Xcv3220 (XopL) from the plant pathogen Xanthomonas campestris and similar proteins from Xanthomonadales. XopL induces plant cell death, subverts plant immunity and shows E3 ubiquitin ligase activity, which is associated with this domain. This domain interacts with plant E2 ubiquitin conjugating enzymes and folds into a four-helix bundle, which can be subdivided into two uneven lobes almost perpendicular to each other giving the molecule an 'L' shape. A large cleft with a net negative charge is formed at the intersection of the two lobes.
Pfam PF07231: Hs1pro-1 N-terminus (family)
This family represents the N-terminus (approximately 180 residues) of plant Hs1pro-1, which is believed to confer resistance to nematodes.
Pfam PF18177: La HTH in kinetoplastid DICER domain (domain)
Winged HTH domain family observed in kinetoplastid DICER-like (DCL) enzymes, situated N-terminal to the KptA_kDCL domain [pfam:PF18176].
Pfam PF23620: KIAA0319 C-terminal domain (domain)
This domain is found in human Dyslexia-associated protein KIAA0319 and related proteins. KIAA0319 is involved in neuronal migration during development of the cerebral neocortex. This protein probably function in a cell autonomous and a non-cell autonomous manner and play a role in appropriate adhesion between migrating neurons and radial glial fibers. This domain is found C-terminal and it is predicted to adopt an alpha/beta structure with some similarity to NOTCH heterodimerisation domain.
Pfam PF21021: Fas-associated factor 1 (domain)
This entry represents the UAS domain from the Fas-associated factor 1 protein.
Pfam PF15383: Transmembrane protein 237 (family)
This protein family is found in eukaryotes. The function of this protein is to aid the production of new cilia in ciliogenesis. Mutations in the protein cause a disease, named Joubert syndrome type 14 (JBTS14) and also affect cell signalling using the Wnt pathway. Proteins in this family are typically between 203 and 512 amino acids in length. There are two completely conserved G residues that may be functionally important.
Pfam PF05138: Phenylacetic acid catabolic protein (domain)
This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid. These proteins may form part of a dioxygenase complex.
Pfam PF00221: Aromatic amino acid lyase (family)
This family includes proteins with phenylalanine ammonia-lyase, [ec:4.3.1.24], histidine ammonia-lyase, [ec:4.3.1.3], and tyrosine aminomutase, [ec:5.4.3.6], activities.
Pfam PF11691: Protein of unknown function (DUF3288) (family)
This family of proteins with unknown function appears to be restricted to Cyanobacteria.
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 PF20127: Family of unknown function (DUF6517) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 210 and 252 amino acids in length. These proteins contain an N-terminal TAT signal.
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 PF02752: Arrestin (or S-antigen), C-terminal domain (domain)
Ig-like beta-sandwich fold.  Scop reports duplication with N-terminal domain.
Wikipedia: Arrestins are a small family of proteins important for regulating signal transduction at G protein-coupled receptors.
Arrestins were first discovered as a part of a conserved two-step mechanism for regulating the activity of G protein-coupled receptors (GPCRs) in the visual rhodopsin system by Hermann Kühn, Scott Hall, and Ursula Wilden and in the β-adrenergic system by Martin J. Lohse and co-workers.
Pfam PF17615: Family of unknown function (family)
Family members found in Fuselloviridae are predicted to play a role in virus function.
Pfam PF07982: Herpes UL74 glycoproteins (family)
Members of this family are viral glycoproteins that form part of an  envelope complex.
Pfam PF18493: Domain of unknown function (DUF5617) (domain)
This domain of unknown function is found at the C-terminal end of proteins mainly from Legionella, including lpg0944 from Legionella pneumophila ([swissprot:Q5ZWY9]), which is thought to be an effector of the Icm/Dot translocation system from this bacteria. This domain folds into an all-alpha structure.
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 PF13684: Fatty acid kinase subunit A-like, C-terminal (domain)
This domain is found at the C-terminal of FakA (fatty acid subunit A) proteins, which is part of the fatty acid kinase machinery. In the human pathogens Staphylococcus and Streptococcus, this system is used to scavenge host fatty acids. FakA is an ATP-binding subunit which interacts with varied FakB (fatty acid-binding protein) isoforms and synthesises acyl-phosphate from extracellular fatty acids. FakA comprises three domains (FakA_N, FakA_M and FakA_C) and resembles an evolutionary mimic of the DhaK-DhaL kinase system. This entry represents FakA_C, which acts as a recipient of fatty acids transferred from FakB in the context of Fak activity.
Pfam PF24389: ORC-CDC6-like (family)
This entry represents a group of sequences that belong to the ORC-CDC6-family of AAA+ ATPases associated with prokaryotic antiviral immunity and is commonly found with double CARF, methylase and protein containing variable effector domains.
Pfam PF18131: KN17 SH3-like domain (domain)
This domain can be found at the C terminus of the human KIN17 protein and its homologues. In human cells, over-expression of KIN17 modifies the nuclear morphology and inhibits S-phase progression, thus  blocking cell growth as part of the response to genotoxic stress. The  C-terminal domain exhibits an all-beta structure consisting of two  tightly packed SH3-like subdomains, the first one represented in this entry. This domain has structural similarity with various  SH3-like domains, although it lacks similarities in both primary  sequence and charge distribution.
Pfam PF16893: Fibronectin type III domain (domain)
This fibronectin type III domain is found in fungal chitin biosynthesis protein CHS5 where, together with the neighbouring BRCT domain ([pfam:PF00533]), it binds to the Arf1 GTPase.
Pfam PF23368: Domain of unknown function (DUF7092) (domain)
This domain represents a small beta barrel domain that is found at the N-terminus of some bacterial peptidase M48 proteins. It has a PH-domain like structure. It likely acts as a chaperone for membrane protein complexes. May interact with [pfam:PF05987] members based on AlphaFold predictions.
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 PF10104: Di-sulfide bridge nucleocytoplasmic transport domain (family)
Brr6_like_C_C is the highly conserved C-terminal region of a group of proteins found in fungi. It carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulfide bridges to form a complex which is involved in nucleocytoplasmic transport. Brr6 in yeast is an essential integral membrane protein of the NE-ER, wit two predicted transmembrane domains, and is a dosage suppressor of Apq12, [pfam:PF12716].
Pfam PF00408: Phosphoglucomutase/phosphomannomutase, C-terminal domain (domain)
This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (5.4.2.2) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (5.4.2.2; 5.4.2.8) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (5.4.2.3) and PAGM (5.4.2.10) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Pfam PF19794: Family of unknown function (DUF6278) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  formicamycins A-M biosynthetic gene cluster from Streptomyces  sp. KY5. 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 PF01648: 4'-phosphopantetheinyl transferase superfamily (domain)
Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of [pfam:PF00550]. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP. This superfamily consists of two subtypes: The ACPS type such as [swissprot:P24224] and the Sfp type such as [swissprot:P39135]. The structure of the Sfp type is known, which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion.
Wikipedia: In enzymology and molecular biology, a holo-[acyl-carrier-protein] synthase is an enzyme that catalyzes the chemical reaction:CoA-[4'-phosphopantetheine] + apo-acyl carrier protein  adenosine 3',5'-bisphosphate + holo-acyl carrier protein
Pfam PF00665: Integrase core domain (domain)
Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  The amino-terminal domain is a zinc binding domain [pfam:PF02022].  This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain [pfam:PF00552]. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.
Wikipedia: Retroviral integrase (IN) is an enzyme produced by a retrovirus that integrates its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases (recombinases) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination.
Pfam PF11950: Protein of unknown function (DUF3467) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 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 PF15224: Scrapie-responsive protein 1 (family)
This protein family has an important function in acting against the prion protein, Scrapie.This family of proteins is found in eukaryotes. Proteins in this family are approximately 98 amino acids in length.
Wikipedia: Scrapie is a fatal, degenerative disease affecting the nervous systems of sheep and goats. It is one of several transmissible spongiform encephalopathies (TSEs), and as such it is thought to be caused by a prion. Scrapie has been known since at least 1732 and does not appear to be transmissible to humans. However, it has been found to be experimentally transmissible to humanised transgenic mice and non-human primates.
Pfam PF08191: LRR adjacent (family)
These are small, all beta strand domains, structurally described for the protein Internalin (InlA) and related proteins InlB, InlE, InlH from the pathogenic bacterium Listeria monocytogenes. Their function appears to be mainly structural: They are fused to the C-terminal end of leucine-rich repeats (LRR), significantly stabilising the LRR, and forming a common rigid entity with the LRR.  They are themselves not involved in protein-protein-interactions but help to present the adjacent LRR-domain for this purpose.  These domains belong to the family of Ig-like domains in that they consist of two sandwiched beta sheets that follow the classical connectivity of Ig-domains. The beta strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier,.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF03343: SART-1 family (family)
SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing.  It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae.  SART-1 is a known tumour antigen in a range of cancers recognised by T cells.
Pfam PF11496: Class II histone deacetylase complex subunits 2 and 3 (domain)
This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in [swissprot:Q10432]. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus.