SII-SWORD/CoKE huggingface dataset:
Pfam PF00047: Immunoglobulin domain (domain)
Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.
Wikipedia: The immunoglobulin domain, also known as the immunoglobulin fold, is a type of protein domain that consists of a 2-layer sandwich of 7-9 antiparallel β-strands arranged in two β-sheets with a Greek key topology, consisting of about 125 amino acids.
Pfam PF14688: Domain of unknown function (DUF4461) (family)
This domain family is found in eukaryotes, and is approximately 310 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 PF19453: Family of unknown function (DUF5991) (family)
This entry represents a member of a biosynthetic gene cluster (BGC).  This BGC (BGC0001890) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). The exemplar is the amphi-enterobactin 1 biosynthetic gene cluster from Vibrio campbellii.
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 PF02634: FdhD/NarQ family (family)
A pan-bacterial lineage of proteins. Nitrate assimilation protein,  NarQ, and FdhD ([swissprot:P32177]) are required for formate  dehydrogenase activity. Structurally, they possess a deaminase fold with a characteristic binding pocket, suggesting that they  might bind a nucleotide or related molecule allosterically to  regulate the formate dehydrogenase catalytic subunit.
Pfam PF12236: Bacteriophage head to tail connecting protein (family)
This family of head-tail connector proteins is found in bacteria and viruses. Proteins in this family are typically between 516 and 555 amino acids in length.  This protein is found in Phage T7 and T3 among others.
Pfam PF24875: Domain of unknown function (DUF7736) (domain)
This entry represents a small family of bacterial and phage proteins that are uncharacterised. The domain is composed of three alpha helices, which dimerise to create a larger structure. Some members of the families contain two copies of this domain, most appear to homodimerise.
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 PF10368: Putative cell-wall binding lipoprotein (family)
YkyA is a family of proteins containing a lipoprotein signal and a hydrolase domain. It is similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely to belong to pathways important for pathogenicity.
Pfam PF14811: Protein of unknown function TPD sequence-motif (family)
This is a family of eukaryotic proteins of unknown function.  A few members have an associated zinc-finger domain. All members carry a highly conserved TPD sequence-motif.
Pfam PF10044: Retinal tissue protein (family)
LIN52 is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification.  A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. LIN52 is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification).  It is likely to be a house-keeping protein. LIN52 forms a complex (LINC) required for transcriptional activation of G2/M genes. The LINC core complex consists of at least five subunits including the chromatin-associated LIN-9 and RbAp48 proteins. LINC associates with a large number of E2F-regulated promoters in quiescent cells. Family members are required for spermatogenesis by repressing testis-specific gene expression.
Pfam PF19635: Family of unknown function (DUF6138) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000452) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the tyrocidine biosynthetic gene cluster from Brevibacillus brevis NBRC 100599 and 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 PF12154: Glycoprotein B N-terminal antigenic domain of HCMV (disordered)
This domain is found in viruses, and is approximately 40 amino acids in length. The domain is found in association with [pfam:PF00606]. There are two conserved sequence motifs: SVS and TSS. This family is the amino-terminal antigenic domain of glycoprotein B of human cytomegalovirus.
Pfam PF11532: HnRNP M nuclear localisation signal (conserved_site)
This entry represents the nuclear localisation signal of HnRNP M a splicing regulatory factor.
Pfam PF05488: PAAR motif (conserved_site)
This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.
Pfam PF20403: Family of unknown function (DUF6693) (repeat)
This family of small integral membrane proteins is functionally uncharacterised. This family may be distantly related to [pfam:PF05987]. This family of proteins is found in proteobacteria. Proteins in this family are typically between 104 and 121 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 PF04721: PNGase C-terminal domain, mannose-binding module PAW (domain)
The PAW domain is found at the C-terminus of PGNase, or peptide-N-glycanase, enzymes. It was named for 'domain present in PNGases and other worm proteins'. PNGase catalyses the deglycosylation of several misfolded N-linked glycoproteins by cleaving off the bulky glycan chain before these proteins are degraded by the proteasome. PNGase specifically acts on the unfolded form of high-mannose type N-glycosylated proteins, and this domain appears to be the mannose-binding domain, which contributes to the oligosaccharide-binding specificity of PNGase.
Pfam PF19273: Exportin-5 family (repeat)
Exportin-5 mediates the nuclear export of proteins bearing a double-stranded RNA binding domain (dsRBD) and double-stranded RNAs (cargos). Exportin-5 yeast homologue, also known as Msn5, is involved in nuclear import of replication protein A and export of Far1 and transcription factors Swi5, Swi6, Msn2, and Pho4. Its Arabidopsis homologue, HASTY 1, is involved in the nuclear export of microRNAs (miRNAs).
Pfam PF00181: Ribosomal Proteins L2, RNA binding domain (domain)
This entry represents the N-terminal RNA-binding domain of the large ribosomal subunit protein uL2.
Ribosomal protein uL2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, uL2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:


 * Eubacterial uL2 (old name L2).
 * Algal and plant chloroplast uL2 (old name L2).
 * Cyanelle uL2 (old name L2).
 * Archaebacterial uL2 (old name L2).
 * Plant uL2 (old name L2).
 * Slime mold uL2 (old name L2).
 * Marchantia polymorpha mitochondrial uL2m (old name L2).
 * Paramecium tetraurelia mitochondrial uL2m (old name L2).
 * Fission yeast K5, K37 and KD4.
 * Yeast YL6.
 * Vertebrate uL2 (old name L8).

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 PF20284: C-terminal domain 8 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF23132: Domain of unknown function (DUF7049) (domain)
This domain is found in a group of uncharacterised proteins mainly from plants. This domain is predicted to fold into a globular structure that adopts a ferredoxin-like fold.
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 PF17582: Cytomegalovirus UL20 (family)
This family has members such as the human cytomegalovirus glycoprotein UL20. UL20 is a type I trans-membrane glycoprotein with an immunoglobulin-like ectodomain that is highly polymorphic among HCMV strains.
Pfam PF19769: CPxCG-related zinc finger (family)
This family includes small CPxCG-related zinc finger archaeal proteins, which are typically between 200 and 221 amino acids in length. They are likely to bind DNA and to be potential transcriptional regulators. These zinc fingers are characterised by the specific CPxCG pattern (variants CPxCx and CxxCG) and a second Cys/His pattern potentially more general, being 7-40 residues apart, forming a zinc finger motif. This family contains the specific CxxCG motif and the Cys motif (CPxCx) at the N-terminal. A member of this family, the Nif-regulating protein A [swissprot:Q8PW88], contains the patterns CxxCG and HxxxH (the latter unique to this protein, located 24 residues away from the CxxCG pattern) to form the zinc finger motif. It is a DNA-binding protein that enhances the transcription of the nitrogen fixation (nif) operon under nitrogen-limited conditions.
Pfam PF22760: Baseplate component gp38 (family)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. This entry represents the homologs of E217 baseplate cap component gp38. Gp38 forms a heterodimeric complex with gp37. These proteins adopt a similar fold, consisting of two orthogonally packed beta-sheets that coil into a barrel shape.
Pfam PF17647: Family of unknown function (DUF5518) (family)
This is a family of unknown function found in Archaea. Family members have multiple predicted trans-membrane regions.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF21836: Domain of unknown function (DUF6895) (repeat)
This entry contains a set of proteins that have a predicted 6-helical hairpin fold found in a wide range of glycosyl hydrolase enzymes, suggesting a potential function for these proteins. These proteins are largely found in actinobacteria and Alphaproteobacteria.
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 PF06661: VirE3 (family)
This family represents a conserved region within Agrobacterium tumefaciens VirE3. Agrobacterium tumefaciens (a plant pathogen) has a tumour-inducing (Ti) plasmid of which part, the transfer (T)-region, is transferred to plant cells during the infection process. Vir proteins mediate the processing of the T-region and the transfer of a single-stranded (ss) DNA copy of this region, the T-strand, into the recipient cells. VirE3 is a translocated effector protein, but its specific role has not been established.
Pfam PF23648: Domain of unknown function (DUF7147) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to fold into an alpha/beta globular structure with topology similar to NADH-quinone oxidoreductase subunit 16.
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 PF21834: Domain of unknown function (DUF6894) (domain)
This entry represents a small protein domain found in alpha proteobacteria. Its structure is composed of a four stranded sheet packed on one side by an alpha helix. The function of these proteins 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 PF03065: Glycosyl hydrolase family 57 (domain)
This family includes alpha-amylase ([ec:3.2.1.1]), 4--glucanotransferase ([ec:2.4.1.-]) and amylopullulanase enzymes.
Wikipedia: In molecular biology, glycoside hydrolase family 57 is a family of glycoside hydrolases.
Pfam PF19003: Family of unknown function (DUF5732) (family)
This family is found in various Platyhelminthes, with many of the sequences annotated as being the STARP-like antigen. This highly conserved domain is located next to the basic helix-loop-helix motif found in this antigen. The function of this family is currently 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 PF05712: MRG (family)
This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation.  It contains 2 chromo domains and a leucine zipper motif.
Pfam PF04532: Protein of unknown function (DUF587) (family)
This family consists of the N termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N terminal to the Pfam family UL87 ([pfam:PF03043]), which 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 PF07822: Neurotoxin B-IV-like protein (domain)
The members of this family resemble neurotoxin B-IV ([swissprot:P01525]), which is a crustacean-selective neurotoxin produced by the marine worm Cerebratulus lacteus. This highly cationic peptide is approximately 55 residues and is arranged to form two antiparallel helices connected by a well-defined loop in a hairpin structure. The branches of the hairpin are linked by four disulphide bonds. Three residues identified as being important for activity, namely Arg-17, -25 and -34, are found on the same face of the molecule, while another residue important for activity, Trp30, is on the opposite side. The protein's mode of action is not entirely understood, but it may act on voltage-gated sodium channels, possibly by binding to an as yet uncharacterised site on these proteins. Its site of interaction may also be less specific, for example it may interact with negatively charged membrane lipids.
Pfam PF16800: IseA DL-endopeptidase inhibitor (domain)
This domain functions as a DL-endopeptidase inhibitor.
Pfam PF16814: Read-through domain (domain)
The Enterobacteria phage minor coat protein A1 is a C-terminally extended version of the coat protein formed when ribosomes read-through a leaky stop codon. This is the C-terminal read-through domain of A1.
Pfam PF00731: AIR carboxylase (domain)
Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain.
Pfam PF05835: Synaphin protein (family)
This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion.
Wikipedia: Complexin (also known as synaphin) refers to a one of a small set of eukaryotic cytoplasmic neuronal proteins which binds to the SNARE protein complex (SNAREpin) with a high affinity. These are called synaphin 1 and 2. In the presence of Ca2+, the transport vesicle protein synaptotagmin displaces complexin, allowing the SNARE protein complex to bind the transport vesicle to the presynaptic membrane.
Pfam PF04032: RNAse P Rpr2/Rpp21/SNM1 subunit domain (family)
This family contains a ribonuclease P subunit of humans and yeast.  Other members of the family include the probable archaeal homologues. This family includes SNM1.  It is a subunit of RNase MRP (mitochondrial RNA processing), a ribonucleoprotein endoribonuclease that has roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing. SNM1 is an RNA binding protein that binds the MRP RNA specifically. This subunit possibly binds the precursor tRNA.
Pfam PF10316: Serpentine type 7TM GPCR chemoreceptor Srbc (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srbc is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.