SII-SWORD/CoKE huggingface dataset:
Pfam PF19982: Family of unknown function (DUF6418) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001589) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the exopolysaccharides biosynthetic gene cluster from Burkholderia  cenocepacia J2315. 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 PF20794: Bacterial PH domain (domain)
This entry represents a group of bacterial PH domains that contain two transmembrane helices. The function of this family is uncertain, but they may act as antitoxins or as chaperones for membrane bound complexes.
Pfam PF24738: Domain of unknown function (DUF7689) (domain)
This entry represents a group of uncharacterised proteins. They are predicted to adopt a fold typical for cysteine proteinases and topology similar to that of NlpC/P60 family proteins. These proteins are likely enzymes as they have similar active site architecture.
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 PF13883: CREG, beta-barrel (domain)
This entry represents the beta-barrel domain found in CREG (cellular repressor of E1A-stimulated genes) proteins from animals and closely homologues from plants, fungi and bacteria. CREG is a secreted glycoprotein that inhibits proliferation and enhances differentiation of human embryonal carcinoma cells. It forms a tight homodimer that, unlike related structural homologues it does not bind flavin mononucleotide as the putative flavin mononucleotide-binding pocket in CREG is sterically blocked by a loop and several key bulky residues. The structure of this domain from bacterial and plant proteins revealed that it is involved in heme binding, such as [swissprot:A0R6E4] and [swissprot:Q8LDU1].
Pfam PF09148: Domain of unknown function (DUF1934) (domain)
Members of this family are found in a set of hypothetical bacterial proteins. Their precise function has not, as yet, been defined.
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 PF19653: Family of unknown function (DUF6156) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 96 and 117 amino acids in length. There are two conserved sequence motifs: RNT and VYGE.
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 PF13566: Domain of unknown function (DUF4130 (domain)
This presumed domain is functionally uncharacterised.
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 PF15289: Regulatory factor X-associated C-terminal binding domain (domain)
This C-terminal domain of Regulatory factor X-associated protein binds to RFXANK, the Ankyrin-repeat regulatory factor X proteins. RFXA is part of the RFX complex, Mutants of either RFXAP or RFXANK protein fail to bind to each other. RFX5 binds only to the RFXANK-RFXAP scaffold and not to either protein alone, and neither the scaffold nor RFX5 alone can bind DNA. The binding of the RFXANK-RFXAP scaffold to RFX5 leads to a conformational change in the latter that exposes the DNA-binding domain of RFX5. The DNA-binding domain of RFX5 anchors the RFX complex to MHC class II X and S promoter boxes.
Pfam PF06429: Flagellar basal body rod FlgEFG protein C-terminal (domain)
This family consists of a number of C-terminal domains of unknown function. This domain seems to be specific to flagellar basal-body rod and flagellar hook proteins in which [pfam:PF00460] is often present at the extreme N terminus.
Pfam PF08257: Sulfakinin family (family)
The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects.  For most species there is the potential for producing two sulfakinin peptides one have a short sulfakinin sequence The function of the sulfakinins is difficult to assess.  For the American cockroach, various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart.  In C. vomitoria the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia.  In adults of P. monodon they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia.
Pfam PF07290: Inner membrane protein YqiJ, OB-fold (domain)
This entry represents the OB-fold domain found in several bacterial proteins, including the inner membrane protein YqiJ from E. coli, whose function is not clear.
Pfam PF04077: DsrH like protein (domain)
DsrH  is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D.
Pfam PF16915: Annelid erythrocruorin linker subunit C-terminus (domain)
This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms.
Pfam PF10925: Protein of unknown function (DUF2680) (family)
Members in this family of proteins are annotated as yckD however currently no function is 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 PF07933: Protein of unknown function (DUF1681) (domain)
This family is composed of sequences derived from a  number of hypothetical eukaryotic proteins 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 PF14714: KH-domain-like of EngA bacterial GTPase enzymes, C-terminal (domain)
The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position.  The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, [pfam:PF01926], pack at either side of the C-terminal domain.  This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2. This family has not been added to the KH clan since SCOP classifies it separately due to its missing the key KH motif/fold.
Pfam PF18154: REase associating with pPIWI_RE (domain)
Restriction endonuclease (REase) domain family, found in a conserved three-gene island that also contains a DinG-type helicase and the pPIWI_RE module. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication.
Pfam PF25028: RECK, fibronectin type I module (domain)
This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar animal proteins. RECK is a membrane-anchored glycoprotein that plays a role in Wnt7-specific responses in the central nervous system angiogenesis and in the blood-brain barrier regulation.
Pfam PF02862: DDHD domain (family)
The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues.  This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family.
Pfam PF22834: Polo box domain (domain)
This entry represents a POLO box-like domain found in DUF4520-containing proteins ([pfam:PF15016]). This domains consist of a six-stranded beta-sheet with an alpha-helix packed against one side.
Pfam PF09264: Vibrio cholerae sialidase, lectin insertion (domain)
Members of this family are predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. They bind to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme.
Pfam PF24265: Family of unknown function (DUF7466) (family)
This entry represents a family of uncharacterised phage proteins. Structurally these are composed of a pair of alpha helices.  Structure prediction suggests these proteins may homodimerise (iPTM=0.89). These proteins are annotated as RDF proteins but the source of this annotation is uncertain.
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 PF13983: YsaB-like lipoprotein (family)
This family of proteins is functionally uncharacterised. These proteins are related to E.coli YsaB [swissprot:Q0TBP2]. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. These proteins are lipoproteins.
Pfam PF18371: Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase (domain)
This is a flavin adenine dinucleotide (FAD) binding domain found in Quiescin sulfhydryl oxidases (QSOX) ([ec:1.8.3.2]). QSOX is a multi-domain disulfide catalyst that is localized primarily to the Golgi apparatus and secreted fluids and has attracted attention due to its over-production in tumors. Structural studies indicate that the closure of the Trx1 domain over the FAD-binding site may enhance the active-site chemistry for disulfide formation.
Pfam PF24557: DExH14 plug domain (domain)
This entry represents the plug domain of DExH-box ATP-dependent RNA helicase DExH14 from Arabidopsis, an RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. This is a smal alpha-helical bundle domain related to the plug domain of BRR2 proteins ([pfam:PF21188]).
Pfam PF19312: NtrY N-terminal region (family)
This entry represents the probable sensor region of the two component regulator protein NtrY. This region includes four probable transmembrane helices.
Pfam PF14754: Papain-like auto-proteinase (domain)
The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase [pfam:PF05579] and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate.
Pfam PF18837: Leucine-rich repeat (repeat)
This Pfam entry includes some LRRs that fail to be detected with the [pfam:PF00560] model. This entry represents one repeat unit.
Pfam PF09508: Lacto-N-biose phosphorylase N-terminal TIM barrel domain (domain)
The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme ([ec:2.4.1.211]), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.
Pfam PF14904: Family of unknown function (family)
Function of this protein family is not known.
Pfam PF09698: Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH) (family)
This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.
Pfam PF13233: Complex1_LYR-like (family)
This is a family of proteins carrying the LYR motif of family Complex1_LYR, [pfam:PF05347], likely to be involved in Fe-S cluster biogenesis in mitochondria.
Pfam PF13581: Histidine kinase-like ATPase domain (domain)
This domain is found in several ATP-binding proteins, including: histidine kinase , DNA gyrase B, topoisomerases , heat shock protein HSP90 , phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, Î±/Î², which contains an 8-stranded mixed Î²-sheet.
Wikipedia: The GHKL domain is an evolutionary conserved protein domain. It is an ATPase domain found in several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins.
Pfam PF22833: C5orf34-like, second domain (domain)
This entry represents a domain located C-terminal to [pfam:PF15025] in a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavourable prognosis of patients from a variety of human malignancies. This domain is predicted to show an alpha-beta structure with high structural similarity to a polo box.
Pfam PF02415: Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat (repeat)
This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterised by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localisation. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown. This family shows some similarity to [pfam:PF05594] and hence is likely to also form a beta-helical structure (personal obs:C Yeats).
Pfam PF20586: Family of unknown function (DUF6788) (family)
This family of proteins is functionally uncharacterised. This family of proteins is mainly found in bacteria and archaea. Proteins in this family are around 100 amino acids in length. There are two conserved sequence motifs, CGxxxCxC containing three conserved Cys residues and HGP.
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 PF16790: Bacteriophage clamp loader A subunit (domain)
This is the A subunit of bacteriophage DNA clamp loader required for loading of sliding clamps onto chromosomal DNA. These clamps are involved in processivity of DNA replication.
Pfam PF18594: Sas6/XLF/XRCC4 coiled-coil domain (coiled_coil)
This is a coiled-coil domain found at the C-terminal of spindle assembly abnormal protein 6 (Sas6). The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis.Structural analysis of Sas6 show that similar to XLF, and XRCC4 it forms a parallel coiled-coil dimer.
Pfam PF21918: CRISPR-associated endonuclease Cpf1 REC2 domain (domain)
This Pfam entry represents the REC2 domain from the Cpf1 protein, an RNA-guided endonuclease of a type V CRISPR-Cas system that has been harnessed for genome editing. The REC2 domain is a part of the REC lobe of the bilobed architecture of Cpf1, which consists of both REC1 and REC2 domains. The REC2 domain comprises 10 alpha helices and 2 beta strands that form a small antiparallel sheet. The crRNA-target DNA heteroduplex is accommodated within the positively charged, central channel formed by the REC1, REC2, and RuvC domains, and is recognized by the protein in a sequence-independent manner.
Pfam PF21317: Beta-galactosidase, first all-beta domain (domain)
Beta-galactosidases belong to glycosyl hydrolase 35 family (GH35) which catalyse the cleaveage of beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans. These proteins consist of a catalytic TIM-barrel and two all-beta domains (ABD1 and ABD2). This entry represents the first all-beta domain ABD1. ABD2 is represented in [pfam:PF13364].
Pfam PF12223: Protein of unknown function (DUF3602) (family)
This domain family is found in eukaryotes, and is typically between 78 and 89 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 PF00813: FliP family (family)
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior . There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia. The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself , type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. It is believed that the family of type III inner membrane proteins are used as structural moieties in a complex with several other subunits , including the ATPase necessary for driving the secretion system.

One such set of inner membrane proteins, termed "P" here for nomenclature purposes, includes the Salmonella and Shigella SpaP, the Yersinia YscR, the Erwinia HrcR, and the Xanthamonas Pro2 genes , as well as several FliP flagellar biosynthesis genes . FliP is an ~30Kd protein containing three or four transmembrane (TM) regions.
Pfam PF17439: Family of unknown function (DUF5418) (family)
This is a family of unknown function found in Methanocaldococcus jannaschii. Family members have three predicted trans-membrane regions.
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 PF13779: Domain of unknown function (DUF4175) (family)
Members of this family are found predominantly in the alphaproteobacteria and bacteroidetes. Each has 2-3 predicted transmembrane helices near the N terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species.
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 PF14317: YcxB-like protein (domain)
The YcxB-like protein family includes the B. subtilis YcxB protein [swissprot:Q08793], which is a functionally uncharacterised transmembrane protein.  This family of proteins is found in bacteria, and is approximately 60 amino acids in length.