SII-SWORD/CoKE huggingface dataset:
Pfam PF05084: Granule antigen protein (GRA6) (family)
This family contains the granule antigen protein GRA6 which is found in the parasitic protozoa Toxoplasma gondii and Neospora caninum. GRA6 protein plays an important role in the antigenicity and pathogenicity in these organisms.
Pfam PF18084: ARTD15 N-terminal domain (domain)
This is the N-terminal domain of poly ADP-ribose polymerase (PARP16 also known as ARTD15) present in homo sapiens. ARTDs catalyse the formation of branched or unbranched chains of ADP-ribose units on protein side chains. The N-terminal domain of ARTD15 does not share any obvious sequence similarity with the regulatory domains of ARTD1-4. The N-terminal domain arrangement in both ARTD15 and ARTD1-3 suggests a regulatory role through different mechanisms.
Pfam PF13755: Sensor N-terminal transmembrane domain (family)
This domain is found at the N-terminus of the sensor component of the two-component regulatory system. It includes a transmembrane region and part of the periplasmic region, which is likely to be involved in stimulus sensing.
Pfam PF22954: Domain of unknown function (DUF7027) (domain)
This is a domain of unknown function found in a group of uncharacterised proteins mainly found in worms. This is likely a transmembrane segment.
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 PF12391: Protocatechuate 3,4-dioxygenase beta subunit N terminal (family)
This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00775].  There are two completely conserved residues (Y and R) that may be functionally important. This family is the N terminal region of the beta subunit of protocatechuate 3,4-dioxidase. This enzyme utilizes a mononuclear, non-heme Fe3+ centre to catalyse metabolic cellular reactions.
Pfam PF07205: Domain of unknown function (DUF1413) (domain)
This family consists of several hypothetical bacterial proteins which seem to be specific to firmicute species. Members of this family are typically around 100 residues in length. The function of this family 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 PF19751: Family of unknown function (DUF6238) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces  kanamyceticus. This family appears to be predominantly 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 PF21489: Fimbrium tip subunit Fim1C-like, C-terminal domain (domain)
This domain is found at the C-terminal end of the putative fimbrium tip subunit Fim1C from Parabacteroides distasonis, and similar proteins from bacteroidetes. Fim1C is thought to be a component of the fimbrium tip that plays a role on the mediation of cell adhesion and biofilm formation. This domain shows transthyretin-like fold that contains seven core beta- strands arranged in two beta-sheets.
Pfam PF04361: Protein of unknown function (DUF494) (family)
Members of this family of uncharacterised proteins are often named Smg.
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 PF10776: Protein of unknown function (DUF2600) (family)
This is a bacterial family of proteins. Some members in the family are annotated as YtpB 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 PF20059: Domain of unknown function (DUF6458) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is primarily found in actinobacteria. Proteins in this family are typically between 74 and 95 amino acids in length. This domain is related to [pfam:PF18969].
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 PF12705: PD-(D/E)XK nuclease superfamily (domain)
Members of this family belong to the PD-(D/E)XK nuclease superfamily
Pfam PF18512: Benzylsuccinate synthase beta subunit (domain)
Members of this family include benzylsuccinate synthase beta subunit found in bacteria. BssB acts as a regulator of activation and may additionally be involved in regulating access to the enzyme's active site. It adopts a fold similar to that of a high potential iron-sulfur protein (HiPIP) and resembles the single small subunit of HPAD, which is known as the HpdC or HPADgamma in that system.
Pfam PF20691: TET-Associated Glycosyltransferase (domain)
This entry represents a Family 2/fringe-like glycosyltransferase domain that is found in DNA-modifying proteins of phages and eukaryotes. The name TAGT is derived from phage versions that are operonic with TET/JBP-dioxygenases. In kinetoplastids, the TAGT enzyme catalyses the second step in forming the hypermodified base J. The vertebrate GREB1 protein appears to catalyse the O-GlcNAcylation of ERalpha, protecting it from ubiquitination-based degradation.
Pfam PF18855: Bacterial archaeo-eukaryotic release factor family 11 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pfam PF17748: VID27 N-terminal region (family)
This region may contain a PH domain.
Pfam PF18849: Bacterial archaeo-eukaryotic release factor family 7 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. Consistent with this, many members of the family associate on the genome with HPF-like ribosome hibernation factor.
Pfam PF05395: Protein phosphatase inhibitor 1/DARPP-32 (family)
This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers.
Pfam PF01899: Na+/H+ ion antiporter subunit (family)
Subunit of a Na+/H+ Prokaryotic antiporter complex (,).
Pfam PF20780: TssR second domain (domain)
This entry represents the second domain of TssR which adopts small beta barrel structure.  T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex.
Pfam PF09160: FimH, mannose binding (domain)
Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology. They are predominantly found in bacterial mannose-specific adhesins, since they are capable of binding to D-mannose.
Pfam PF07328: T-DNA border endonuclease VirD1 (family)
This family consists of several T-DNA border endonuclease VirD1 proteins which appear to be found exclusively in Agrobacterium species. Agrobacterium, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialised bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. VirD1 is thought to interact with VirD2 in this process.
Pfam PF00312: Ribosomal protein S15 (domain)
Small ribosomal subunit protein uS15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF17597: Family of unknown function (DUF5493) (family)
This is a family of unknown function found in viruses.
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 PF06958: S-type Pyocin (family)
This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity.
Pfam PF23420: DUF7108, C-terminal domain (domain)
This domain is found at the C-terminal end of the uncharacterised protein HVO_0731 from Haloferax volcanii ([swissprot:D4GTA0]) and similar proteins from halobacteria. It is predicted to adopt an all-alpha structure. The function of this domain 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 PF09291: Domain of unknown function (DUF1968) (domain)
Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.
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 PF20649: Conserved oligomeric Golgi complex subunit 5, C-terminal (repeat)
This entry represents the C-terminal domain of Cog5, a component of the conserved oligomeric Golgi (COG) complex which is involved in intra-Golgi protein trafficking and consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is a member of the complexes associated with tethering containing helical rods (CATCHR) fold family, which is homologous to subunits of other multisubunit tethering complexes (MTCs) such as Dsl1, exocyst and Golgi-associated retrograde protein (GARP) complexes. COG5 is located in the smaller B lobe together with subunits 6-8, and interacts with subunits 1 and 7. This domain represents the alpha-helical bundle found at the C-terminal of COG5.
Pfam PF13603: Leucyl-tRNA synthetase, editing domain (domain)
This entry represents the editing domain in Leucine-tRNA ligase or Leucyl-tRNA synthetase, [ec:6.1.1.4].
Pfam PF23105: Integrin EGF domain (domain)
This entry represents an EGF that is found in several integrin proteins.
Pfam PF03652: Holliday junction resolvase (family)
The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR). This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR.
Pfam PF09960: Uncharacterised protein conserved in bacteria (DUF2194) (family)
This domain, found in various hypothetical bacterial proteins, has no known 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 PF03842: Silicon transporter (family)
Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na+symport mechanism . The system is found in marine diatoms, which make their "glass houses" out of silicon.
Pfam PF13202: EF hand (domain)
Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue Î±-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Ca2 binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers .
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF20158: Cas5fv helical domain (domain)
This entry represents the Cas5fv helical domain.
Pfam PF11551: Outer membrane protein Omp28 (family)
Omp28 is a 28-kDa outer membrane protein from Porphyromonas gingivalis. Omp28 is thought to be a surface adhesion/receptor protein. Omp28 is expressed in a wide distribution of P.gingivalis strains.
Pfam PF19373: Family of unknown function (DUF5948) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001281) is described by MIBiG as an example of the following biosynthetic class, polyketide.
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 PF07617: Protein of unknown function (DUF1579) (domain)
A family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Sinorhizobium meliloti and Agrobacterium tumefaciens.
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 PF01828: Peptidase A4 family (family)
The peptidases in family G1 form a subset of what were formerly termed 'pepstatin-insensitive carboxyl proteinases'. After its discovery in about 1970, the pentapeptide pepstatin soon came to be thought of as a very general inhibitor of the endopeptidases that are active at acidic pH. But more recently several acid-acting endopeptidases from bacteria and fungi had been found to be resistant to pepstatin. The unusual active sites of the 'pepstatin-insensitive carboxyl peptidases' proved difficult to characterise, but it has now been established that the enzymes from bacteria are acid-acting serine peptidases in family S53 (clan SB), IPR000209, whereas the fungal enzymes are in family G1 (formerly A4) . The importance of glutamate ('E') and glutamine ('Q') residues in the active sites of the family G1 enzymes led to the family name, Eqolisin .

This group of glutamate/glutamine peptidases belong to MEROPS peptidase family G1 (eqolisin family, clan GA). An example of this group is scytalidoglutamic peptidase. The proteins are thermostable, pepstatin insensitive and are active at low pH ranges . The enzyme has a unique heterodimeric structure, with a 39-residue light chain and a 173-residue heavy chain bound to each other non-covalently . The tertiary structure of the active site of scytalidoglutamic peptidase (MEROPS G01.001) with a bound tripeptide product has been interpreted as showing that Glu136 is the primary catalytic residue. The most likely mechanism is suggested to be nucleophilic attack by a water molecule activated by the Glu136 side chain on the si-face of the scissile peptide bond carbon atom to form the tetrahedral intermediate. Electrophilic assistance, and oxyanion stabilisation, are provided by the side-chain amide of Gln53.

Both scytalidoglutamic peptidase (MEROPS G01.001) and aspergilloglutamic peptidase (MEROPS G01.002) cleave the Tyr26 Thr27 bond in the B chain of oxidized insulin; a bond not cleaved by other acid-acting endopeptidases. Scytalidoglutamic peptidase is most active on casein at pH 2 and is inhibited by 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), a compound that also inhibits pepsin.
Pfam PF21903: Hypothetical protein BDI_0842 (domain)
This entry contains the BDI_0842 protein from Parabacteroides distasonis, for which there is a known structure. The structure entry states that the protein has an alpha-lytic protease prodomain-like fold. Proteins in this family have an N-terminal lipoprotein attachment motif. The function of these proteins is unknown.
Pfam PF05596: Taeniidae antigen (family)
This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.