SII-SWORD/CoKE huggingface dataset:
Pfam PF00024: PAN domain (domain)
The PAN domain contains a conserved core of three disulphide bridges.  In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.
Wikipedia: PAN domains have significant functional versatility fulfilling diverse biological roles by mediating protein-protein and protein-carbohydrate interactions. These domains contain a hair-pin loop like structure, similar to that found in knottins but with a different pattern of disulfide bonds.
Pfam PF11579: Protein of unknown function (DUF3238) (family)
This family of proteins with unknown function appears to be restricted to Bacillus cereus.
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 PF18157: MID domain of pPIWI_RE (domain)
MID domain of the pPIWI_RE PIWI/Argonaute module. pPIWI_RE is found in a conserved three-gene island that also contains a DinG-type helicase and an REase nuclease. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication.
Pfam PF00125: Core histone H2A/H2B/H3/H4 (domain)
Five major families of histones exist: H1/H5, H2A, H2B, H3, and H4 . Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known as the linker histones. The core histones together with some other DNA binding proteins form a superfamily defined by a common fold and distant sequence similarities . Some proteins contain local homology domains related to the histone fold .

This entry represents a domain found in histones H2A, H2B and H3. This domain can also be found in transcription factors, such as OsNF-YC2 from rice .
Wikipedia: In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 9 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.
Pfam PF21548: CATSPER subunit beta protein 2nd domain (repeat)
This entry represents the beta-propeller domain from the Cation channel sperm-associated protein subunit beta protein. The cation channel of sperm (CatSper) is essential for sperm motility and fertility. The auxiliary subunit beta contains a single transmembrane segment and a large extracellular region.
Pfam PF01133: Enhancer of rudimentary (family)
Enhancer of rudimentary is a protein of unknown function that is highly conserved in plants and animals. This protein is found to be an enhancer of the rudimentary gene [swissprot:P05990].
Wikipedia: In molecular biology, Enhancer of rudimentary homolog is a protein that in humans is encoded by the ERH gene.
Pfam PF19382: Family of unknown function (DUF5957) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001062) 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 PF04445: Putative SAM-dependent methyltransferase (family)
This is a family of putative SAM-dependent methyltransferases.
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 PF08642: Histone deacetylation protein Rxt3 (family)
Rxt3 has been shown in yeast to be required for histone deacetylation.
Pfam PF24465: Tri-helical domain (domain)
This domain is found in a group of uncharacterised fungal proteins, including [swissprot:A2QTR8] from Aspergillus niger. This domain, which is often found C-terminal to [pfam:PF14420], is predicted to adopt a tri helical configuration.
Pfam PF03534: Salmonella virulence plasmid 65kDa B protein (family)
Salmonella typhimurium contains a 90kb plasmid that is associated with virulence . This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the 70kDa mkaA protein , a recognised virulence factor, and more recently described, four spv genes under the control of a regulator . The spv genes are induced under carbon-poor conditions at a stationary phase of growth, and their expression is under the control of both the spvR regulator, and the katF locus in Salmonella. It has been proposed that individual spv proteins may be required at different time points during infection .

SpvB is a 65kDa protein that has been localised to the bacterial cytoplasm . Its expression peaks during early stationary phase, but declines as the latent phase of the infection is reached, suggesting a role in initiating virulence.
Pfam PF15310: Vitamin A-deficiency (VAD) rat model signalling (family)
VAD1-2 is a family of proteins found in eukaryotes. The family is expressed in testes and is involved in signalling during spermatogenesis.
Pfam PF18774: APOBEC4-like -AID/APOBEC-deaminase (family)
Cnidarian and Algal homologs of the APOBEC4-like AID/APOBEC-like deaminases characterised by a distinct Zn chelating site involving residues from the conserved loops 1 and 3.
Pfam PF13621: Cupin-like domain (domain)
This cupin like domain shares similarity to the JmjC domain.
Pfam PF02113: D-Ala-D-Ala carboxypeptidase 3 (S13) family (family)
This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The active site residues occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components. There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins. Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity.
Pfam PF22743: PspA-Associated protein (domain)
This entry represents a trihelical domain (alpha+beta) with absolutely conserved R and D, which occurs as a two-gene cluster with PspA. This domain, mostly occurs as a solo, but is occasionally found fused to an N-terminal PspA in actinobacteria and chloroflexi.
Pfam PF14172: Domain of unknown function (DUF4309) (family)
This family includes the B. subtilis YjgB protein [swissprot:O34960], which is functionally uncharacterised. This is not a homologue of E. coli YjgB, Swiss: P27250. Expression of B. subtilis YjgB is regulated by the alternative transcription factor sigma-B. This family is found in bacteria, and is approximately 140 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 PF23541: Corticotropin-releasing factor binding protein C-terminal domain (domain)
This entry corresponds to the C-terminal domain of the eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development.
Wikipedia: Corticotropin-releasing hormone binding protein (CRH-BP) binds corticotropin-releasing hormone (CRH) and several related peptide hormones. It is an ancient, highly conserved protein whose origin predates the divergence of protostomes and deuterostomes.
Pfam PF23811: Domain of unknown function (DUF7183) (domain)
This entry represents an uncharacterized protein domain found in various mycobacteriophages. The domain averages around 150 amino acids in length. It is found as a single domain in the phage proteins. The function of this domain is currently unknown.  One protein in this family [swissprot:G8I4J4] contains an N-terminal associated domain [pfam:PF18909].
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 PF03781: Sulfatase-modifying factor enzyme 1 (domain)
This domain is found in eukaryotic proteins required for post-translational sulfatase modification (SUMF1).  These proteins are associated with the rare disorder multiple sulfatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase.  Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidised cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases. In Mycobacteria and Treponema denticola this enzyme functions as an iron(II)-dependent oxidoreductase.
Wikipedia: Formylglycine-generating enzyme (FGE), located at 3p26.1 in humans, is the name for an enzyme present in the endoplasmic reticulum that catalyzes the conversion of cysteine to formylglycine (fGly). There are two main classes of FGE, aerobic and anaerobic. FGE activates sulfatases, which are essential for the degradation of sulfate esters. The catalytic activity of sulfatases is dependent upon a formylglycine residue in the active site.
Pfam PF24138: Transportin-3/Importin-13 second TPR domain (repeat)
This entry represents the second TPR domain found in Transportin-3 (TNPO3) from animals, as well as orthologues MTR10 and uncharacterised protein YNR7 from yeast and MOS14 from plant. This entry also includes Importin-13 (IPO3) from animals. These proteins are involved in transport of target proteins into the nucleus. TNPO3 mediates the nuclear import of splicing factor serine/arginine (SR) proteins, such as RBM4, SFRS1 and SFRS2, by recognizing phosphorylated SR domains. This domain is involved in the binding to the globular Ran protein in TNOP3. In IPO13, this domain is involved in the protein interaction with Ubc9 for nuclear import and with eIF1A for nuclear import.
Pfam PF16352: Domain of unknown function (DUF4980) (family)
This family consists of uncharacterized proteins around 610 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF21710: Spt6, S1/OB domain (domain)
This entry represents the S1/OB-fold domain of Spt6. This domain has structural similarity to S1 domain but lacks the typical S1 binding cleft residues  involved in nucleic acid binding, therefore, this domain in Spt6 may be involved in interactions with other partners.
Pfam PF24222: Fimbrial adhesin MrpH N-terminal domain (domain)
This entry represents the N-terminal domain of fimbrial adhesin MrpH protein from bacteria. This protein is associated to strain virulence and is involved in surface adherence, biofilm formation and autoaggregation, essential for bladder and kidney colonization. This domain binds to surface receptor and coordinates one Zn cation necessary for attachment and biofilm formation.
Pfam PF23393: WDR90/POC16, second beta-propeller (repeat)
This entry represents the second WD40 beta-propeller found in WD repeat-containing protein 90, identified in animals, and the homologue protein POC16 found in Chlamydomonas reinhardtii. WDR90 is proposed to be localised in the centriole and required for ciliogenesis. The similarities between WDR90 and the flagellar inner B-microtubule protein FAP52/WDR16 lead to the proposal that the WD40 domains of WDR90 might be located within the B-microtubule of the centriole triplet.
Wikipedia: The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Pfam PF13988: Protein of unknown function (DUF4225) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 182 and 282 amino acids in length.
Pfam PF24728: Domain of unknown function (DUF7680) (domain)
This entry represents a group of uncharacterised prokaryotic proteins. These proteins share a common semi-conserved EExxWY sequence motif which is predicted as a solvent-exposed in a alpha/beta structure consisting of a four-stranded antiparallel beta-sheet and alpha-helices packed on one side of it.
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 PF20729: PE-PGRS C-terminal aspartyl peptidase-like domain (domain)
This domain is found at the C-terminus of some PE-PGRS proteins from Mycobacteria. The domain is related to aspartyl peptidases.
Pfam PF05795: Plasmodium vivax Vir protein (family)
This family consists of several Vir proteins specific to Plasmodium vivax. The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation.
Pfam PF19790: Family of unknown function (DUF6274) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000119) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the 7-deoxypactamycin biosynthetic gene cluster from  Streptomyces pactum. This family appears to be  predominantly found in 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 PF06185: YecM protein (family)
This family consists of several bacterial YecM proteins of unknown function.
Wikipedia: In molecular biology, YecM refers to a protein domain found in Escherichia coli. It is a conserved, hypothetical protein with sequence homologues found exclusively in bacteria. Several bacterial YecM proteins in this particular family are of unknown function.
Pfam PF14208: Domain of unknown function (DUF4320) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 131 amino acids in length. There are two completely conserved residues (G and Y) that may be functionally important.
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 PF11003: Protein of unknown function (DUF2842) (family)
This bacterial family of proteins have 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 PF17505: Family of unknown function (DUF5437) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF12380: Gill-associated viral 3C-like peptidase (family)
a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad.
Pfam PF12525: Protein of unknown function (DUF3726) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length. There is a single completely conserved residue E that may be functionally important.
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 PF11201: Protein of unknown function (DUF2982) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF12788: YmaF family (family)
This family of proteins contain 6 HXH motifs and is named after the B. subtilis YmaF protein.      It seems likely that these are involved in metal binding. The function of this protein is unknown.
Pfam PF13595: Domain of unknown function (DUF4138) (family)
Based on Bacteroides thetaiotaomicron gene BT_4780, a putative uncharacterized 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 PF12112: Protein of unknown function (DUF3579) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif.
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 PF05035: 2-keto-3-deoxy-galactonokinase (family)
2-keto-3-deoxy-galactonokinase [ec:2.7.1.58] catalyses the second step in D-galactonate degradation.
Pfam PF14036: YlaH-like protein (family)
The YlaH-like protein family includes the B. subtilis YlaH protein [swissprot:O07632], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved LGFA sequence motif.