SII-SWORD/CoKE huggingface dataset:
Pfam PF12467: Cucumber mosaic virus 1a protein family (family)
This domain family is found in viruses, and is typically between 156 and 171 amino acids in length. The family is found in association with [pfam:PF01443], [pfam:PF01660]. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein.
Pfam PF18168: Prim-pol family 5 (family)
Family of prim-pol enzymes currently known only in kinetoplastids.
Pfam PF00385: Chromo (CHRromatin Organisation MOdifier) domain (domain)
The CHROMO (CHRromatin Organization MOdifier) domain  is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting.

Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain , eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.

Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro .

The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three Î²-strands packed against an Î±-helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein .
Wikipedia: A chromodomain is a protein structural domain of about 40–50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved among both plants and animals, and is represented in a large number of different proteins in many genomes, such as that of the mouse. Some chromodomain-containing genes have multiple alternative splicing isoforms that omit the chromodomain entirely. In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions. Chromodomain-containing proteins also bind methylated histones and appear in the RNA-induced transcriptional silencing complex. In histone modifications, chromodomains are very conserved. They function by identifying and binding to methylated lysine residues that exist on the surface of chromatin proteins and thereby regulate gene transcription.
Pfam PF07592: Rhodopirellula transposase DDE domain (domain)
These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces.
Pfam PF10836: Protein of unknown function (DUF2574) (family)
This family of proteins appears to be restricted to Enterobacteriaceae. Members of the family are annotated as yehE 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 PF05659: Arabidopsis broad-spectrum mildew resistance protein RPW8 (family)
This family consists of several broad-spectrum mildew resistance proteins from Arabidopsis thaliana. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The Arabidopsis thaliana locus Resistance To Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance.
Pfam PF20656: Malate synthase, N-terminal domain (domain)
Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function. They consist of an N-terminal alpha-helical claps, a central TIM barrel and a C-terminal alpha-helical plug. This entry represents the N-terminal clasp that wraps around one side of the TIM barrel and buttressed it.
Pfam PF09462: Mus7/MMS22 family (family)
This family includes a conserved region from the Mus7 protein. Mus7 is involved in the repair of replication-associated DNA damage in the fission yeast Schizosaccharomyces pombe. Mus7 functions in the same pathway as Mus81, a subunit of the Mus81-Eme1 structure-specific endonuclease, which has been implicated in the repair of the replication-associated DNA damage. The MMS22 proteins are involved in repairing double-stranded DNA breaks created by the cleavage reaction of topoisomerase II.
Pfam PF10507: Transmembrane protein 65 (family)
MEM65 is an intercalated disc protein that interacts  with with connexin 43 (Cx43) and  is required for  correct localization of Cx43 to the intercalated disc. It is essential for cardiac function in zebrafish.
Pfam PF21115: BRSK1/2 UBA domain (domain)
This entry represents a UBA domain found C-terminal to the kinase domain in the brain-specific kinases BRSK1 and BRSK2.
Pfam PF18902: Domain of unknown function (DUF5658) (domain)
This family of proteins is found in bacteria, archaea and viruses.  Proteins in this family are typically between 101 and 135 amino acids in length. There is a completely conserved aspartate and a conserved EXNP motif 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 PF01936: NYN domain (domain)
These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions.  Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.
Pfam PF12778: PXPV repeat (3 copies) (repeat)
This short repeat is found in multiple copies in a variety of Burkholderia proteins. The function of this region is unknown.
Pfam PF02505: Methyl-coenzyme M reductase operon protein D (family)
Methyl coenzyme M reductase (MCR) catalyses the final step in methanogenesis. MCR is composed of three subunits, alpha ([pfam:PF02249]), beta ([pfam:PF02241]) and gamma ([pfam:PF02240]). Genes encoding the beta (mcrB) and gamma (mcrG) subunits are separated by two open reading frames coding for two proteins C and D. The function of proteins C and D (this  family) is unknown.
Pfam PF23988: Domain of unknown function (DUF7309) (domain)
This entry represents a domain of unknown function found in uncharacterised proteins from bacteria, as well as in some plasmid pRiA4b ORF-3 family of 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 PF03301: Tryptophan 2,3-dioxygenase (family)
This is a family of tryptophan 2,3-dioxygenase (1.13.11.11) enzymes involved in tryptophan metabolism, which catalyses the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring .
Pfam PF17362: Family of unknown function (family)
This is a family of unknown function found in Bacilli.
Pfam PF07192: SNURF/RPN4 protein (family)
This family consists of several mammalian SNRPN upstream reading frame (SNURF) proteins. SNURF or RPF4 is a RING-finger protein and a coregulator of androgen receptor-dependent transcription. It has been suggested that  SNURF is involved in the regulation of processes required for late steps of spermatid maturation.
Pfam PF13141: Protein of unknown function (DUF3979) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.
Pfam PF04571: lipin, N-terminal conserved region (family)
Mutations in the lipin gene lead to fatty liver dystrophy in mice.  The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. The conserved region is found at the N-terminus of the member proteins.
Pfam PF08553: VID27 C-terminal WD40-like domain (repeat)
This is a family of fungal and plant proteins and contains many hypothetical proteins.  VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. This region is predicted to contain a WD40 repeat domain.
Pfam PF15848: Odontogenesis associated phosphoprotein (family)
This family is found in mammals. It includes odontogenesis associated phosphoprotein (ODAPH or in human C4orf26) which is expressed in the enamel organ of the tooth and may promote nucleation of  hydroxyapatite.
Pfam PF23787: Domain of unknown function (DUF7172) (domain)
This entry represents a domain found in proteins typically around 200 amino acids in length. It is found in phage that infect Mycobacteria, Gordonia, and Nocardia. The exact function is unknown. The structure of the domain shows an extended beta sandwich fold where one sheet is hinged in the middle to form a kink.
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 PF08815: Nuclear receptor coactivator (domain)
This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.
Pfam PF14379: MYB-CC type transfactor, LHEQLE motif (family)
This family is found towards the C-terminus of Myb-CC type transcription factors, and carries a highly conserved LHEQLE sequence motif.
Pfam PF24908: Integrin beta-like protein A-E, second Ig-like domain (domain)
This entry represents the second Ig-like domain (according to structure predictions) of Integrin beta-like proteins A-E (SIBA-E) from Dictyostelium discoideum and similar sequences. These proteins may be implicated in cellular adhesion to substrate or phagocytic particles.
Pfam PF05351: GMP-PDE, delta subunit (family)
GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)([ec:3.1.4.35]).  The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues.  PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport.
Wikipedia: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta is an enzyme that in humans is encoded by the PDE6D gene. PDE6D was originally identified as a fourth subunit of rod cell-specific cGMP phosphodiesterase (PDE). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport.
Pfam PF22556: Phage DNA Adenine Methylase-like domain 2 (domain)
This domain has been characterised as part of a nucleic acid modifying system in certain phages. This system may modify tRNAs that are encoded adjacent to the system on the genome. These tRNAs are then possibly packaged into the viral head, to render them resistant to host restriction.
Pfam PF08495: FIST N domain (domain)
The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.
Pfam PF05462: Slime mold cyclic AMP receptor (family)
This family consists of cyclic AMP receptor (CAR) proteins from slime molds. CAR proteins are responsible for controlling development in Dictyostelium discoideum.
Wikipedia: Cyclic AMP receptors  from slime molds are a distinct family of 
G-protein coupled receptors. These receptors control development in
Dictyostelium discoideum.
Pfam PF15583: Immunity protein 68 (family)
A predicted immunity protein with an alpha+beta fold and a conserved glutamate residue. The domain is often fused to one or more immunity domains in poly-immunity proteins.
Pfam PF22570: LiaF transmembrane domain (domain)
This entry represents the transmembrane region found at the N-terminal of LiaF ([swissprot:O32199]), which is thought to be a sensory domain (Preprint https://doi.org/10.1101/2020.09.24.301986). LiaF-TM may tie into a two-component system to regulate the membrane integrity and permeability in response to the stress signal.
Pfam PF01902: Diphthamide synthase (domain)
Diphthamide synthase catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2). In some members of this family e.g. [swissprot:Q12429], this domain is associated with [pfam:PF01042]. The enzyme classification is [ec:6.3.1.14].
Pfam PF13228: Domain of unknown function (DUF4037) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. There is a single completely conserved residue P 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 PF15543: Bacterial toxin 5 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system.
Pfam PF16024: Domain of unknown function (DUF4785) N-terminal domain (domain)
This family of proteins is found in bacteria. Proteins in this family are typically between 392 and 442 amino acids in length. This entry represents the N-terminal jelly roll domain.
Pfam PF11220: Protein of unknown function (DUF3015) (family)
This bacterial family of 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 PF13044: Fusion glycoprotein F0, Isavirus (family)
Fusion between viral and cellular membranes is mediated by viral membrane fusion glycoproteins. This entry represents fusion glycoprotein F0 from the infectious salmon anemia  virus (ISAV). The precursor protein F0 is proteolytically  cleaved to F1 and F2, which are held together by disulphide  bridges.
Pfam PF23843: Domain of unknown function (DUF7210) (domain)
This entry represents a small domain found in a variety of uncharacterised phage 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 PF18477: PIN like domain (domain)
This is a domain of unknown function that resembles the PIN like domains. Family members include Ribonuclease VapC9.
Pfam PF18632: Family of unknown function (DUF5630) (domain)
This is a domain of unknown function mostly found in Legionella.
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 PF22364: VirG insertion domain (VID) (domain)
Outer membrane autotransporter VirG/IcsA is a virulence factor from Shigella flexneri that acts as an adhesin and actin-polymerising factor during infection. VirG/IcsA consists of three major domains: an atypical signal peptide at the N-terminal, followed by the passenger domain (presented on the cell surface) and a beta-domain that anchors the protein to the bacterial outer membrane. This entry represents the insertion domain (VID) that appears to be inserted into a continuous sequence of beta-helical coils.
Pfam PF16326: ABC transporter C-terminal domain (coiled_coil)
This domain is found at the C-terminus of ABC transporters. It has a coiled coil structure with an atypical 3(10)-helix in the alpha-hairpin region. It is involved in DNA_binding.
Pfam PF04368: Protein of unknown function (DUF507) (family)
This entry represents a bacterial domain with an unknown function. It folds into a Y-shaped alpha-helical structure, comprising an anti- parallel 4-helix bundle at the base and two helical arms.
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 PF11653: Bacteriophage T7 virion assembly protein (family)
This family of proteins represents the gene product 7.3 from T7 bacteriophage. The protein is localised to the tail and is thought to be important in virion assembly. Particles assembled in the absence of the protein fail to adsorb to cells.
Pfam PF06081: Aromatic acid exporter family member 1 (family)
This family consists of bacterial proteins with three transmembrane regions that are purported to be aromatic acid exporters.
Pfam PF18936: Family of unknown function (DUF5684) (family)
This is a family of unknown function mostly found in bacteria. Some family members can be found at the N-terminal region of [pfam:PF00717].
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 PF21796: Chromatin assembly factor 1 subunit Cac1, C-terminal domain (domain)
Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during nucleosome assembly. CAF-1 complex is composed of several subunits. This entry represents the C-terminal domain of subunit Cac1 that adopts a winged helix fold and binds to DNA in a sequence-independent manner. This domain was also found to mediate the (H3-H4)2 tetramerisation.
Pfam PF02036: SCP-2 sterol transfer family (domain)
This domain is involved in binding sterols. It is found in the SCP2 protein [swissprot:P22307], as well as the C terminus of [swissprot:P51659] the enzyme estradiol 17 beta-dehydrogenase [ec:1.1.1.62]. The UNC-24 protein [swissprot:Q17372] contains an SPFH domain [pfam:PF01145].
Wikipedia: Sterol carrier proteins is a family of proteins that transfer steroids and probably also phospholipids and gangliosides between cellular membranes.