SII-SWORD/CoKE huggingface dataset:
Pfam PF01733: Nucleoside transporter (family)
This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their own de novo synthesis pathways. Also in this family is mouse and human nucleolar protein HNP36 [swissprot:Q14542] a protein of unknown function; although it has been hypothesised to be a plasma membrane nucleoside transporter.
Pfam PF21738: Double jelly roll-like domain (domain)
This entry represents a domain found in a group of proteins mainly from arthropods containing a jelly-roll domain, which has similarity to domains otherwise found in a variety of large dsDNA virus capsid proteins.
Pfam PF18754: Nucleotide modification associated domain 3 (domain)
An alpha+beta fold domain with a high conserved HxD and D motifs suggestive of enzymatic function and predicted to be involved in modifed nucleotide biosynthesis.
Pfam PF09651: CRISPR-associated protein (Cas_APE2256) (family)
This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.
Pfam PF21231: GH141 insertion domain (domain)
This domain is found in proteins that belong to Glycoside hydrolase family 141 (GH141). This domain consists of two subdomains: a beta-sandwich and a partly open beta-barrel that are inserted into the catalytic domain comprising a right-handed parallel beta-helix domain.
Pfam PF02964: Methane monooxygenase, hydrolase gamma chain (domain)
Methane monooxygenases (1.14.13.25) catalyse the oxidation of methane to methanol in the presence of oxygen and NADH in methanotrophs. It has a broad specificity, hydroxylating many alkanes, and converting alkenes into the corresponding epoxides. In additional reactions, CO is oxidized to CO2, ammonia is oxidized to hydroxylamine, and some aromatic compounds and cyclic alkanes can also be hydroxylated, although more slowly. In Methylococcus capsulatus there are two forms of the enzyme, a soluble and a membrane-bound type. The soluble form consists of 3 components, A, B and C. Protein A is made up of 3 chains, alpha, beta and gamma.

This entry represents the gamma chain of methane monooxygenases. Structurally, the gamma chain contains two domains, each consisting of a three helices arranged in an open bundle topology .
Pfam PF21925: XRCC4 C-terminal region (disordered)
This entry represents the C-terminal disordered region from the XRCC4 protein.
Pfam PF16781: Domain of unknown function (DUF5068) (domain)
This family is expressed by Firmicutes. 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 PF08000: Bacterial PH domain (domain)
This family contains many bacterial hypothetical proteins. The structures of [swissprot:A1SD03], PDB:3hsa, and [swissprot:A3QB43], PDB:3dcx, show similarities to the PH or pleckstrin homology domain. First evidence of PH-like domains in bacteria suggests role in  cell envelope stress response.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF06347: Bacterial SH3 domain (domain)
SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues. They are found in a great variety of intracellular or membrane-associated proteins for example, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division.
Pfam PF01846: FF domain (family)
This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.
Pfam PF06534: Repulsive guidance molecule (RGM) C-terminus (family)
This family represents the C-terminal region of repulsive guidance molecule (RGM), although in some sequences it represents the full protein. RGM is a GPI-linked axon guidance molecule of the retinotectal system, and controls cell motility, adhesion, immune cell regulation and systemic iron metabolism. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.  This domain is responsible for neogenin (NEO1) binding.
Pfam PF24076: Family of unknown function (DUF7368) (family)
ThiS entry represents a family of uncharacterised phage 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 PF15003: HAUS augmin-like complex subunit 2 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 203 and 291 amino acids in length. HAUS augmin-like complex subunit 2 is alternatively called centrosomal protein of 27 kDa (CEP27). It localised in the microtubule organising centre, the centrosome. These microtubules are part of the cytoskeleton and give the cell its shape, provides it with a platform for motility and are crucial for mitosis.  This protein is part of the HAUS augmin-like complex. This interacts with the gamma-tubulin ring complex (gamma-TuRC) which is required for spindle generation. HAUS2 may also increase the tension between spindle and kinetochore allowing for chromosome segregation during mitosis. This protein is involved in mitotic spindle assembly, maintenance of centrosome integrity and completion of cytokinesis.
Pfam PF06441: Epoxide hydrolase N terminus (family)
This family represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases ([ec:3.3.2.3]) comprise a group of functionally related enzymes that catalyse the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organisms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarization of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites which arise during the biotransformation of foreign compounds. This family is often found in conjunction with [pfam:PF00561].
Pfam PF21413: SHQ1-like, CS domain (domain)
This domain is found at the N-terminal end of Protein SHQ1 homolog from humans and similar eukaryotic proteins. SHQ1 is a factor required for the biogenesis and assembly of H/ACA small nucleolar ribonucleoparticle (snoRNP), which are essential for ribosomal RNA and telomerase RNA processing and metabolism. This protein contains two domains: an N-terminal CS (named after CHORD-containing proteins and SGT1) or HSP20-like domain (represented by this entry), and a C-terminal region called the Shq1 domain ([pfam:PF04925]). The CS domain folds into a compact anti-parallel beta-sandwich made of two beta-sheets with four and three beta-strands, respectively, and a short alpha-helix.
Pfam PF14846: Domain of unknown function (DUF4485) (family)
This family is found in eukaryotes, and is approximately 90 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 PF09967: VWA-like domain (DUF2201) (domain)
This domain, found in various hypothetical bacterial proteins, has no known function. However, it is clearly related to the VWA domain.
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 PF24535: Domain of unknown function (DUF7598) (domain)
This domain is found in a group of uncharacterised fungal proteins. It is predicted to adopt an all-alpha configuration.
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 PF03212: Pertactin (repeat)
Bordetella pertussis is a Gram-negative, aerobic coccobacillus that causes pertussis (whooping cough), especially in young children . Once present in the lungs, the bacterium attaches to ciliated pulmonary epithelial cells via a collection of outer membrane proteins, all of which are virulence factors.

Pertactin, or P69 protein, is one of these virulence factors. Pertactin and filamentous haemagglutinin have been identified as Bordetella adhesins . Both proteins contain an arg-gly-asp (RGD) motif that promotes binding to integrins, known to be important in cell mobility and development. The production of most Bordetella virulence factors (including pertactin) is controlled by a two-component signal transduction system, comprising the BvgA regulator and the BvgS sensor . Pertactin shares a high level of similarity with other Bordetella adhesins, such as BrkA. The protein is first produced as a 93kDa precursor. Upon secretion into the extracellular environment, a 30kDa domain at the C terminus remains in the outer membrane, while the mature 60.4kDa pertactin molecule is released .

The crystal structure of mature pertactin has been determined to 2.5A resolution by means of X-ray diffraction. The fold is characterised by a 16-stranded parallel Î²-helix, with a V-shaped cross-section. Several between-strand amino-acid repeats form internal and external ladders. The helical structure is interrupted by several protruding loops that contain motifs associated with the activity of the protein. One such sequence -[GGXXP]5 -appears directly after the RGD motif, and may mediate interaction with epithelial cells. The C-terminal region of P.69 pertactin contains a [PQP]5 motif loop, which contains the major immunoprotective epitope .

The superfamily also includes immunoglobulin A1 protease and adhesion penetration protein HAP.
Wikipedia: In molecular biology, pertactin (PRN) is a highly immunogenic virulence factor of Bordetella pertussis, the bacterium that causes pertussis. Specifically, it is an outer membrane protein that promotes adhesion to tracheal epithelial cells. PRN is purified from Bordetella pertussis and is used for the vaccine production as one of the important components of acellular pertussis vaccine.
Pfam PF20056: Family of unknown function (DUF6455) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. This presumed domain contains a conserved histidine and four conserved cysteines suggestive of zinc binding.
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 PF02588: Uncharacterised 5xTM membrane BCR, YitT family COG1284 (family)
This is probably a bacterial ABC transporter permease (personal obs:Yeats C).
Pfam PF15111: TMEM101 protein family (family)
The function of this family of transmembrane proteins, TMEM101, has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 257 amino acids in length.
Pfam PF21379: Baseplate wedge protein gp6-like, helical domain (domain)
This domain is found in Baseplate wedge protein gp6 from Enterobacteria phage T4 and similar sequences predominantly from tailed bacteriophages. Gp6 is a protein involved in tail assembly. This entry represents its N-terminal helical domain.
Pfam PF20210: Laa1/Sip1/HEATR5 HEAT repeat region (repeat)
This entry represents a region consisting of HEAT repeats that is found in a group of eukaryotic proteins, including HEAT repeat-containing protein 5A/B (HEATR5A/B) from vertebrates, Pof6 interactor protein 1 (SIP1), AP-1 accessory protein LAA1 from yeast and SWEETIE from Arabidopsis thaliana.
Pfam PF16816: DotD protein (domain)
The DotD protein is a component of the Dot/Icm type IVB secretion system. It is involved in the outer membrane targeting of DotH.
Pfam PF19068: Family of unknown function (DUF5764) (family)
This is a family of uncharacterised proteins of known function found in viruses, particularly in Conferred and Mummified.
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 PF04259: Small, acid-soluble spore protein, gamma-type (family)
The SASP family is a family of small, glutamine and asparagine-rich  peptides that store amino acids in the spores of Bacillus subtilis  and related bacteria.
Pfam PF12472: Phage related protein (family)
This domain family is found in bacteria and viruses, and is approximately 60 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 PF17664: Cilia- and flagella-associated protein HOATZ-like (family)
This entry represents cilia- and flagella-associated protein, HOATZ, and related proteins, found in metazoa. In mice HOATZ is encoded by the gene designated 4833427G06Rik (C11orf88). Mouse Hoatz mRNA is specifically expressed in tissues with motile cilia and flagella. Hoatz knockout mice developed hydrocephalus and male infertility, and the ependymal cilia frequently showed disorganised axonemes.
Pfam PF18491: SET and RING associated domain (domain)
This is the C-terminal domain found in PvuRts1I, a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA in bacteria. Structural analysis indicates that it has the typical SRA (SET and RING associated) domain fold ([pfam:PF02182]).
Pfam PF07474: G2F domain (domain)
Nidogen, an invariant component of basement membranes, is a multifunctional protein that interacts with most other major basement membrane proteins. The G2 fragment or (G2F domain) contains binding sites for collagen IV and perlecan. The structure is composed of an 11-stranded beta-barrel with a central helix. This domain is structurally related to that of green fluorescent protein [pfam:PF01353]. A large surface patch on the beta-barrel is conserved in all metazoan nidogens.
Pfam PF16850: Peptidase inhibitor I66 (family)
This family of serine protease inhibitors has a beta-trefoil fold and inhibits trypsin and chymotrypsin.
Pfam PF03535: Paxillin family (family)
Paxillin is a multi-domain protein that localises in cultured cells primarily to sites of cell adhesion to the extracellular matrix (ECM) called focal adhesions. The family here represents the N-terminal regions with the proline-rich part as well as the Paxillin part. Focal adhesions form a structural link between the ECM and the actin cytoskeleton and are also important sites of signal transduction; their components propagate signals arising from the activation of integrins following their engagement with ECM proteins, such as fibronectin, collagen and laminin. Importantly, focal adhesion proteins including paxillin also serve as a point of convergence for signals resulting from stimulation of various classes of growth factor receptor.
Pfam PF14262: Carbohydrate-binding domain-containing protein Cthe_2159 (repeat)
Cthe_2159 from Clostridium thermocellum is the first representative of a novel family of cellulose and/or  acid-sugar binding beta-helix proteins that share  structural similarities with polysaccharide lyases.
Pfam PF15029: Transmembrane protein 174 (family)
This family of proteins is found in chordates and  includes the human integral membrane protein TMEM174 protein.
Pfam PF18339: RapA N-terminal Tudor like domain 1 (domain)
This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG , ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP.
Pfam PF19808: Family of unknown function (DUF6291) (family)
This family of proteins, found in bacteria and viruses, is functionally uncharacterised. Proteins in this family are typically between 179 and 275 amino acids in length. There are two conserved residues, a leucine and a tyrosine.
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 PF11835: RRM-like domain (domain)
This domain is related to the RRM domains suggesting it may have an RNA-binding function.
Pfam PF14755: Nsp2, transmembrane domain (domain)
This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2.
Pfam PF13212: Domain of unknown function (DUF4020) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 176 and 195 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 PF08143: CBFNT (NUC161) domain (domain)
This N terminal domain is found in proteins of CARG-binding factor A-like proteins.
Pfam PF20223: Family of unknown function (DUF6582) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically around 100 amino acids in length. It includes two conserved motifs, FA and HVRxA.
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 PF14592: Chondroitinase B (repeat)
This family includes chondroitinases. These enzymes cleave the glycosaminoglycan dermatan sulfate.