SII-SWORD/CoKE huggingface dataset:
Pfam PF04929: Herpes DNA replication accessory factor (family)
Replicative DNA polymerases are capable of polymerising tens of thousands of nucleotides without dissociating from their DNA templates. The high processivity of these polymerases is dependent upon accessory proteins that bind to the catalytic subunit of the polymerase or to the substrate.  The Epstein-Barr virus (EBV) BMRF1 protein is an essential component of the viral DNA polymerase and is absolutely required for lytic virus replication. BMRF1 is also a transactivator.  This family is predicted to have a UL42 like structure.
Pfam PF02451: Nodulin (family)
Nodulin is a plant protein of unknown function. It is induced during nodulation in legume roots after rhizobium infection.
Pfam PF18027: Cytosolic carboxypeptidase N-terminal domain (domain)
This entry corresponds to the N-terminal domain of cytosolic carboxypeptidases. The N-terminal domain folds into a nine-stranded antiparallel beta sandwich. This domain is specific to CCP proteins and is absent in other carboxypeptidases. It has been hypothesised that the N-terminal domain might contribute to folding, might have a regulatory function and/or might be involved in binding other proteins.
Pfam PF23657: Domain of unknown function (DUF7151) (repeat)
This entry represents a domain of unknown function found in bacterial proteins. Some of the members of this family might contain an EF-hand calcium binding site. The predicted structure of this domain consists of three beta sheets.
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 PF22000: Family of unknown function (DUF6929) (repeat)
This is a family of uncharacterised bacterial proteins. They are predicted to fold into five-bladed beta-propeller that has similarity to apyrase but it is circularly permuted. The C-terminal two beta-strands of this domain occupy the position of the two N-terminal beta-strands in apyrase.
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 PF13995: YebF-like protein (domain)
The YebF-like protein family appears to be a group of colicin immunity proteins. As well as YebF the family includes cmi, the colicin M immunity protein. This domain family is found in bacteria, and is approximately 80 amino acids in length. The alignment contains two conserved cysteine residues that form a disulphide bond in the solved structure.
Pfam PF18990: Family of unknown function (DUF5723) (family)
This is a family of unknown function mainly found in bacteria.
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 PF05467: Herpesvirus glycoprotein U47 (family)
This is a family of U47 herpesvirus proteins . U47 protein is also known as 120kDa glycoprotein O (or 130kDa glycoprotein O from human herpesvirus 6A). U47 proteins are modified with N-linked oligosaccharides and co-immunoprecipitated with glycoprotein H. They may have a role in cell-cell fusion in virus infection .
Pfam PF17965: Mucin binding domain (domain)
This domain is found in bacterial cell surface proteins that interact with mucins.  The archetypal member of this family is the Mub-R5 B1 domain.  This domain has a beta-grasp fold.
Pfam PF14465: NFRKB Winged Helix-like (domain)
This domain covers regions 370-495 of human nuclear factor related  to kappaB binding (NFRKB) protein.
Pfam PF11222: Protein of unknown function (DUF3017) (family)
This bacterial family of proteins with unknown function appear to be restricted to Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23867: Mmc1 N-terminal domain (domain)
This domain is found N-terminal in Mmc1 from Schizosaccharomyces pombe and related proteins. Mmc1 functions in concert with the mitochondrial contact site and cristae organizing system (MICOS) complex to promote normal mitochondrial morphology and respiratory function. This domain is predicted to adopt a globular structure with significant similarity to dynamin-like GTPases, in particular, to mitofusin 1. However, Mmc1 lacks key residues required for GTP binding and hydrolysis. It was proposed that Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane.
Pfam PF07506: RepB plasmid partitioning protein (family)
This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Pfam PF09439: Signal recognition particle receptor beta subunit (domain)
The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.
Pfam PF21655: L544, nucleotidyltransferase domain (domain)
This is the nucleotidyltransferase domain found in uncharacterised proteins from virus, such as L544 from Acanthamoeba polyphaga mimivirus.
Pfam PF08805: PilS N terminal (domain)
Type IV pili are bacterial virulence-associated adhesins that promote bacterial attachment to host cells.  In Salmonella typhi, the structural pilin protein PilS interacts with the cystic fibrosis transmembrane conductance regulator. Mutagenesis studies suggest that residues on an alpha-beta loop and the C terminal disulphide-bonded region of PilS might be involved in binding specificity of the pilus.
Pfam PF08964: Beta/Gamma crystallin (domain)
This family of beta/gamma crystallins includes the N-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1 ([swissprot:P54657]), which mediates cell-cell adhesion through homophilic interactions.
Pfam PF12137: RNA polymerase recycling family C-terminal (domain)
This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with [pfam:PF00271], [pfam:PF00176]. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement.
Pfam PF21840: Domain of unknown function (DUF6899) (domain)
This entry represents a bacterial protein of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15287: KRBA1 family repeat (repeat)
KRBA1 is a short repeating motif found in mammalian proteins. It is characterised by a highly conserved sequence of residues, SSPLxxLxxCLK.  The function of the repeat, which can be present in up to seven copies, is unknown as is the function of the full length proteins.
Pfam PF25128: C16C10.3-like, N-terminal domain (domain)
This domain is found at the N-terminal end of the uncharacterised protein C16C10.3 from Caenorhabditis elegans and similar proteins from worms. This domain is predicted to adopt an alpha-beta configuration.
Pfam PF23415: Microtubule-associated protein 1B N-terminal (domain)
This entry represents the N-terminal domain of Microtubule-associated protein 1B (MAP1B) which, when phosphorylated is required for proper microtubule dynamics and plays a role in the cytoskeletal changes that accompany neuronal differentiation and neurite extension. According to structure predictions and comparisons, this domain may adopt a P-loop fold closely similar to that found in small GTPases, such as Arf6.
Pfam PF13494: Domain of unknown function, B. Theta Gene description (DUF4119) (family)
Based on Bacteroides thetaiotaomicron gene BT_0594, a putative uncharacterised protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture
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 PF05823: Nematode fatty acid retinoid binding protein (Gp-FAR-1) (family)
Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems.
Pfam PF19924: Family of unknown function (DUF6387) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene  cluster from Escherichia coli. This family appears to be  predominantly 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 PF16896: Phosphogluconate dehydrogenase (decarboxylating) C-term (domain)
PGDH_C is the C-terminal domain of putative bacterial phosphogluconate dehydrogenase proteins.
Pfam PF11054: Sporozoite surface antigen (SAG) protein domain (domain)
This entry represents the SAG protein domain family. The SAG family plays a pivotal role in host interactions during infections caused by apicomplexan parasites such as Plasmodium, Toxoplasma gondii, and Eimeria. These interactions are mediated by a diverse array of proteins, including two prominent groups: membrane-anchored cysteine-rich surface antigens (SAGs) and SAG-related sequences (SRS). Structure comparisons confirmed that the fold of the Eimeria SAGs is related to that of the CAP superfamily that include a range of toxins from insects, reptiles and plants suggesting some functional conservation of this domain across these disparate groups of proteins.
Pfam PF13360: PQQ-like domain (repeat)
This domain contains several repeats of the PQQ repeat.
Pfam PF03976: Polyphosphate kinase 2 (PPK2) (domain)
Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world.  In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases.
Pfam PF15979: Glycosyl hydrolase family 115 (family)
Glyco_hydro_115 is a family of glycoside hydrolases likely to have the activity of xylan a-1,2-glucuronidase, [ec:3.2.1.131], or a-(4-O-methyl)-glucuronidase [ec:3.2.1.-].
Pfam PF00033: Cytochrome b/b6/petB (domain)
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (1.10.2.2) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (1.10.99.1), also known as the b6f complex.

Cytochrome b/b6  is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two haem groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two haem groups.

Apart from regions around some of the histidine haem ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry represents the N-terminal region of these proteins.
Wikipedia: Cytochrome b is a protein found in the membranes of aerobic cells. In eukaryotic mitochondria and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III — also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a homologous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase, also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.
Pfam PF10863: Nucleolar protein 19 (family)
Nucleolar protein 19 plays an essential role in 40S ribosomal subunit biogenesis.
Pfam PF06025: Domain of Unknown Function (DUF913) (family)
Members of this family are found in various ubiquitin protein ligases.
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 PF15713: Protein tyrosine phosphatase receptor type C-associated (family)
This group represents protein tyrosine phosphatase receptor type C (PTPRC)-associated protein, also known as CD45-associated protein . It is a positive regulator of PTPRC (CD45), which activates Src family kinases implicated in tumorigenesis .
Wikipedia: Protein tyrosine phosphatase receptor type C-associated protein is an enzyme that in humans is encoded by the PTPRCAP gene.
Pfam PF16503: Zinc-ribbon (family)
This is a family of zinc-ribbons largely from eukaryotes that lie at the C-terminus of cytoplasmic tRNA adenylyltransferase 1 proteins.  Most of these proteins carry an ATP-binding domain towards the N-terminus.
Pfam PF19101: Family of unknown function (DUF5788) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
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 PF09950: Major capsid protein (family)
This entry represents a group of proteins from tailed bacteriophages, bacterial prophages and some lower eukaryotes, including Major capsid protein from Pseudomonas phage KPP22. This family was previously known as DUF2184.
Pfam PF22072: FAP42 domain B3 (domain)
FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection of the ciliary central apparatus (CA). This protein forms a complex with FAP413 and FAP246, which is essential for a stable assembly of the C1b, C1f and C2b projections, and loss of these proteins leads to ciliary motility defects. FAP42 structure has been determined along with other components of the Chlamydomonas reinhardtii ciliary central apparatus. FAP42 contains cysteine peptidase domain, adenylate kinase domain, five guanylate kinase domains and three beta-sandwich domains. The latter adopt a jelly-roll topology and have a significant sequence and structural similarity to domain III in calpains and the predicted beta-sandwich domains in androglobin. This entry represents the third FAP42 beta-sandwich domain B3.
Pfam PF14159: CAAD domains of cyanobacterial aminoacyl-tRNA synthetase (domain)
This domain is present in aminoacyl-tRNA synthetases (aaRSs), enzymes that couple tRNAs to their cognate amino acids. aaRSs from cyanobacteria containing the CAAD (for cyanobacterial aminoacyl-tRNA synthetases appended domain) protein domains are localised in the thylakoid membrane. The domain bears two putative transmembrane helices and is present in glutamyl-, isoleucyl-, leucyl-, and valyl-tRNA synthetases, the latter of which has probably recruited the domain more than once during evolution.
Pfam PF18399: Clip-domain serine protease homolog Scarface (domain)
The clip domain is a structural/regulatory unit in many arthropod serine proteases. The clip domain super-family also includes serine protease homologs (SPHs). This entry describes clip domains in the SPHs (CLIP subfamily A), which belong to group-3. SPHs usually carry between 1 to 5 clip domains. The most prominent family member of carrying this clip domain is Scarface proteins in drosophila, which bear an inactive catalytic site, representing a subgroup of serine protease homologues (SPH). Loss-of-function induces defects in JNK-controlled morphogenetic events such as embryonic dorsal closure and adult male terminalia rotation.
Pfam PF05171: Haemin-degrading HemS.ChuX domain (domain)
The Yersinia enterocolitica O:8 periplasmic binding-protein- dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS (this family). The structure for HemS has been solved and consists of a tandem repeat of this domain.
Pfam PF09539: Protein of unknown function (DUF2385) (family)
Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function 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 PF03830: PTS system sorbose subfamily IIB component (family)
Bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains . The Man family is unique in several respects among PTS permease families:


 * It is the only PTS family in which members possess a IID protein.
 * It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
 * Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.


The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate . This entry is specific for the IIB components of this family of PTS transporters .
Pfam PF13616: PPIC-type PPIASE domain (domain)
Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.
Wikipedia: Prolyl isomerase is an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the amino acid proline. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain bonded to its secondary amine nitrogen. Most amino acids have a strong energetic preference for the trans peptide bond conformation due to steric hindrance, but proline's unusual structure stabilizes the cis form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity include cyclophilin, FKBPs, and parvulin, although larger proteins can also contain prolyl isomerase domains.