SII-SWORD/CoKE huggingface dataset:
Pfam PF03677: Uncharacterised protein family (UPF0137) (family)
This family includes GP6-D a virulence plasmid encoded protein.
Pfam PF24674: SNTX, MACPF/CDC-like domain (domain)
This MACPF/CDC-like domain is found N-terminal in a number of toxins including Stonustoxin (SNTX), Neoverrucotoxin (NeoVTX), Verrucotoxin (VTX), Sp-CTx and related proteins. This domain is a pore-forming domain and is involved in the formation of large ring-shaped pores in rat erythrocyte membranes. The formation of MACPF/CDC-like pores is probably central to the toxin's hemolytic activity, and cell lysis could explain physiological effects, including edema, increased vascular permeability, and muscle damage.
Pfam PF19514: MobC-like protein (domain)
This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region.
Pfam PF04615: Utp14 protein (family)
This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome.
Pfam PF19371: Family of unknown function (DUF5946) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001707) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF13608: Protein P3 of Potyviral polyprotein (family)
This is the P3 protein section of the Potyviridae polyproteins. The function is not known except that the protein is essential to viral survival.
Pfam PF22116: Family of unknown function (DUF6944) (family)
This is a family of uncharacterised proteins found mainly in Gram-positive bacteria. They are predicted to be associated with the membrane and to adopt structure that has topological similarity to the common structural core of Succinate-acetate permease (SatP) superfamily 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 PF18839: Large polyvalent protein associated domain 24 (domain)
This is an all-beta domain that is mostly seen in polyvalent proteins of conjugative elements.
Pfam PF11456: Protein of unknown function (DUF3019) (family)
This is a bacterial family of uncharacterised 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 PF19546: Family of unknown function (DUF6070) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 388 and 427 amino acids in length. There are two conserved sequence motifs: PEV and DGT.
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 PF16715: Cyclodipeptide synthase (domain)
This family of proteins includes enzymes involved in the synthesis of cyclodipeptides using aminoacyl-tRNAs as substrates, including cyclo(L-leucyl-L-leucyl) synthase, cyclo(L-tyrosyl-L-tyrosyl) synthase and cyclo(L-leucyl-L-phenylalanyl) synthase. They are structurally similar to class Ic aminoacyl-tRNA synthetases (aaRSs).
Pfam PF19280: Ceramide kinase C-terminal domain (domain)
This domain is found at the C-terminus of ceramide kinase enzymes. It is related to the beta sandwich domain of NAD kinases. Along with the N-terminal domain it catalyzes specifically the phosphorylation of ceramide to form ceramide 1-phosphate. This family contains ceramide kinase like proteins that lack the ceramide kinase activity.  It also contains ore distantly related proteins this may have different functions.
Pfam PF03637: Mob1/phocein family (family)
Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein [swissprot:Q9QYW3], a rat protein that by yeast two hybrid interacts with striatin.
Pfam PF16459: Phage tail assembly chaperone, TAC (family)
This family represents the phage-tail assembly chaperone proteins from a small set of Siphoviridae from Gammaproteobacteria. TACs are required for the morphogenesis of all long-tailed phages. The proposed function for the TAC is to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated.
Pfam PF15732: Domain of unknown function (DUF4681) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 101 and 127 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 PF21615: Carbohydrate binding module-like (domain)
This domain is found in a a group of bacterial proteins, including the uncharacterised Fibronectin type-III domain-containing protein from Agathobacter rectalis ([swissprot:C4ZEB7]). It adopts a jelly roll structure.
Pfam PF11819: Cytohesin Ubiquitin Protein Inducing Domain (domain)
C1ORF106 also known as INAVA (Innate Immune Activator), is identified as a risk factor for the chronic inflammatory bowel diseases (IBD). Mice lacking the protein show defects in intestinal barrier integrity at steady state and greater susceptibility to mucosal infection. INAVA carries CUPID (Cytohesin Ubiquitin Protein Inducing Domain). Three other human proteins contain CUPID: FRMD4A, FRMD4B, and CCDC120- proteins implicated in neurite outgrowth, and in human cancer, Alzheimer's, celiac, and heart disease. All appear to bind the ARF-GEF (guanine nucleotide-exchange factors) cytohesin family members, such as proteins (ARF 1-4), which regulate cell membrane and F-actin dynamics. INAVA-CUPID binds cytohesin 2 (also known as ARNO), targets the molecule to lateral membranes of epithelial monolayers, and enables ARNO to affect F-actin assembly that underlies cell-cell junctions and barrier function. In the case of inflammatory signalling, ARNO can coordinate CUPID function by binding and inhibiting CUPID activity of acting as an enhancer of TRAF6 dependent polyubiquitination. In other words, ARNO acts as a negative-regulator of inflammatory responses. In summary, INAVA-CUPID exhibits dual functions, coordinated directly by ARNO, that bridge epithelial barrier function with extracellular signals and inflammation.
Pfam PF17954: Quercetinase C-terminal cupin domain (domain)
Experiments on the YhhW protein show that is has quercetinase activity.  This entry represents the C-terminal cupin domain from the two cupin domains that make up the protein. This domain is usually associated with [pfam:PF02678].
Pfam PF00183: Hsp90 protein (family)
Molecular chaperones, or heat shock proteins (Hsps) are ubiquitous proteins that act to maintain proper protein folding within the cell . They assist in the folding of nascent polypeptide chains, and are also involved in the refolding of denatured proteins following proteotoxic stress. As their name implies, the heat shock proteins were first identified as proteins that were up-regulated under conditions of elevated temperature. However, subsequent studies have shown that increased Hsp expression is induced by a variety of cellular stresses, including oxidative stress and inflammation. Five major Hsp families have been determined, and are categorized according to their molecular size (Hsp100, Hsp90, Hsp70, Hsp60, and the small Hsps). Hsps are involved in a variety of cellular processes that are ATP-dependent. These include: prevention of protein aggregation, protein degradation, protein trafficking, and maintenance of signalling proteins in a conformation that permits activation.

Hsp90 chaperones are unique in their ability to regulate a specific subset of cellular signalling proteins that have been implicated in disease processes, including intracellular protein kinases, steroid hormone receptors, and growth factor receptors .
Wikipedia: Hsp90 is a chaperone protein that assists other proteins to fold properly, stabilizes proteins against heat stress, and aids in protein degradation. It also stabilizes a number of proteins required for tumor growth, which is why Hsp90 inhibitors are investigated as anti-cancer drugs.
Pfam PF17528: Histidine decarboxylase maturation protein HdcB (family)
This family represents histidine decarboxylase maturation protein HdcB, mainly found in Lactobacillus. HdcB performs a cleavage and modification of the pyruvoyl-dependent histidine decarboxylase HdcA, generating the pyruvoyl prosthetic group.
Pfam PF15316: MyoD family inhibitor (family)
Members of this family inhibits the transactivation activity of the MyoD family of myogenic factors. They affect axin-mediated regulation of the Wnt and JNK signaling pathways, and regulate expression from viral promoters.
Pfam PF12280: Brain specific membrane anchored protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein.
Pfam PF12725: Protein of unknown function (DUF3810) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 333 and 377 amino acids in length. There is a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
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 PF14060: Domain of unknown function (DUF4252) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 182 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 PF14747: Domain of unknown function (DUF4473) (family)
This short family is largely confined to Caenorhabditis proteins. The function is not known. There are two well-conserved aspartate residues.
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 PF19478: TrbL/VirB6 plasmid conjugal transfer like protein (family)
Although members of this family are uncharacterised it appears to be related to [pfam:PF04610] which is a conjugal transfer protein TrbL/VirB6 found in proteobacteria. This protein family is found in Firmicute bacteria, and is approximately 170 amino acids in length.
Pfam PF19244: Poly(A) polymerase catalytic subunit (family)
This family represents the Poly(A) polymerase catalytic subunit found in viruses.
Pfam PF02813: Retroviral M domain (family)
Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.
Wikipedia: Retroviral matrix proteins are components of envelope-associated capsids of retroviruses. These proteins line the inner surface of viral envelopes and are associated with viral membranes.
Pfam PF14397: Sugar-transfer associated ATP-grasp (family)
A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides.
Pfam PF13423: Ubiquitin carboxyl-terminal hydrolase (domain)
This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 and PAN3), involved in the initial trimming of poly(A) tails.
Pfam PF21061: Reovirus core-spike protein lambda-2 (L2), 7th domain (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the seventh domain which, together with the sixth ([pfam:PF21060]) and eighth ([pfam:PF06016]) domains forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA. This domain has a Ig-like fold, resembling the C region of an antibody light chain.
Pfam PF14234: Domain of unknown function (DUF4336) (family)
The function of these proteins 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 PF19526: S-layer protein Slr4 (family)
This family represents a novel S-layer protein widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio, and are found exclusively in marine metagenomes. These proteins assemble into paracrystalline sheets with a unique square lattice symmetry.
Pfam PF00866: Ring hydroxylating beta subunit (domain)
This subunit has a similar structure to NTF-2 and scytalone dehydratase.
Pfam PF17135: Ribosomal protein 60S L18 and 50S L18e (family)
This is a family of ribosomal proteins, 60S L18 from eukaryotes and 50S L18e from Archaea.
Pfam PF01106: NifU-like domain (family)
This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Pfam PF15923: Domain of unknown function (DUF4745) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 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 PF00997: Kappa casein (family)
Kappa-casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para kappa-casein) and a soluble hydrophilic glycopeptide (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens.
Pfam PF12731: Mating-type protein beta 1 (family)
This domain is found in some fungi and is the C-terminus of a homeodomain-containing transcription factor protein involved in mating.
Pfam PF22636: Fluoroacetyl-CoA-specific thioesterase (domain)
This entry includes fluoroacetyl-CoA-specific thioesterases (FlK), which catalyses the hydrolysis of fluoroacetyl-coenzyme A and provides an effective self-defense mechanism, preventing any fluoroacetyl-coenzyme A formed from being further metabolised to 4-hydroxy-trans-aconitate, an inhibitor of TCA cycle.
Pfam PF18337: RapA N-terminal Tudor like domain (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 PF12657: Transcription factor IIIC subunit delta bet-propeller domain (repeat)
In humans there are six subunits of transcription factor IIIC, and this one is the 90 kDa subunit; whereas in fungi the complex resolves into nine different subunits and this is No. 9 in yeasts. The whole subunit is involved in RNA polymerase III-mediated transcription. It is possible that this N-terminal domain interacts with TFIIIC subunit 8.
Pfam PF15906: Zinc-finger of nitric oxide synthase-interacting protein (domain)
This entry represents a zinc-finger in nitric oxide synthase-interacting protein (NOSIP) . NOSIP may modulate nitric oxide homeostasis in physiological and pathological pain conditions .
Pfam PF20362: Family of unknown function (DUF6657) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 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 PF22560: GMT-like wHTH domain (domain)
This entry represents a rapidly-evolving wHTH domain C-terminally fused to Rossmann fold methylase specifically related to the guanine methylase. Often co-occurs on the genome across a broad range of bacterial phylogenies with a further gene encoding a RADICAL SAM enzyme (DUF5131 [pfam:PF07505]). This two-gene island is predicted to catalyse a DNA/RNA guanine modification comparable to the precursors of Wybutosine. This wHTH domain could be a sensor that recognises a rapidly-evolving nucleic acid sequence, implicating the gene pair in a conflict response to an invasive genic element.
Pfam PF18601: EZH2 N-terminal domain (domain)
Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. This is the N-terminal domain of EZH2.