SII-SWORD/CoKE huggingface dataset:
Pfam PF07117: Protein of unknown function (DUF1373) (family)
This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 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 PF18514: Ubiquitin-like protein MDY2, C-terminal domain (domain)
This entry represents the C-terminal domain of Ubiquitin-like protein MDY2 from S. cerevisiae (also known as Get5) and related proteins found in Saccharomycetes. It is an homodimerisation helical domain that adopts a four helical bundle configuration to form an heterotetrameric Get4/Get5 complex. The proteins Get4 and Get5 form an obligate complex that catalyses the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3.
Pfam PF24988: NEW1 helical bundle domain (domain)
This is the helical bundle (HB) domain found in NEW1 from S. cerevisiae, a translation termination and ribosome biogenesis factor. It is an ATP binding cassette protein that cosediments with polysomes and is required for biogenesis of the small ribosomal subunit.
Pfam PF23064: M02D8_5-like, fifth CUB domain (domain)
This entry represents the fifth occurrence of the CUB domain in a family of uncharacterised proteins present in nematodes. Consecutive repetitions of this domain are common in this protein family. The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found predominantly in extracellular and plasma membrane-associated proteins, many of which undergo developmental regulation. CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding  partners.
Pfam PF00832: Ribosomal L39 protein (family)
A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. This entry represents the large ribosomal subunit protein eL39, of about 50 residues long, being the smallest protein of eukaryotic-type ribosomes. In mammals, eL39 has been described as the RNA-binding component of the large ribosomal subunit .
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 PF16627: Unstructured region between BRX_N and BRX domain (disordered)
BRX_assoc is a short stretch of plant transcription regulator proteins carrying the BRX domain that is natively unstructured. It connects the BRX_N and BRX domains in plant transcription regulators. The function is not known.
Pfam PF04149: Domain of unknown function (DUF397) (domain)
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 PF20035: Family of unknown function (DUF6439) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are typically between 87 and 98 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 PF07479: NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus (domain)
NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain.
Wikipedia: Glycerol-3-phosphate dehydrogenase (GPDH) is an enzyme that catalyzes the reversible redox conversion of dihydroxyacetone phosphate to sn-glycerol 3-phosphate.
Pfam PF20025: Family of unknown function (DUF6433) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in phages. Proteins in this family are typically between 144 and 156 amino acids in length. Proteins in this family contain the conserved motifs NFD and LEGL.
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 PF21476: PF0610-like, N-terminal (domain)
This domain is found in PF0610 from Pyrococcus furiosus. This protein has a Zn ribbon-embedded wHTH fold. This entry represents the N-terminal domain, which is composed of three helices.
Pfam PF11079: Bacterial protein YqhG of unknown function (family)
This family of putative proteins is conserved in the Bacillaceae family of the Firmicutes. The function is not known.
Pfam PF17262: Cas6b C-terminal domain (domain)
Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense. This is the C-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF03250: Tropomodulin (family)
Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two domains. The amino terminal domain contains the tropomyosin binding function.
Pfam PF09008: Head binding (domain)
The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively antiparallel. The tailspike protein trimerises through this domain, and the direction of the strands with respect to the molecular triad is almost parallel for beta-sheet A, whereas beta-sheet B is perpendicular to the triad, forming a dome-like structure. This domain is dispensable for thermostability and SDS resistance of the intact protein, and its deletion has only minor effects on tailspike folding kinetics.
Pfam PF11418: Phi29 scaffolding protein (family)
This protein is also referred to as gp7. The protein contains a DNA-binding function and may halve a role in mediating the structural transition from prohead to mature virus and also scaffold release.Gp7 is arranged within the capsid as a series of concentric shells.
Pfam PF14024: Protein of unknown function (DUF4240) (domain)
This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 169 and 263 amino acids in length. This domain is often associated with the WGR domain [pfam:PF05406].
Pfam PF13989: YejG-like protein (family)
The YejG protein family is a group of functionally uncharacterised proteins related to [swissprot:P0AD21]. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Pfam PF09381: Outer membrane protein G (OmpG) (domain)
Porins are channel proteins in the outer membrane of gram negative bacteria which mediate the uptake of molecules required for growth and survival.  Escherichia coli OmpG forms a 14 stranded beta-barrel and in contrast to most porins, appears to function as a monomer. The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the transport of larger oligosaccharides.
Wikipedia: Outer membrane protein G (OmpG)  is a porin, a channel proteins in the outer membrane of Gram-negative bacteria.
Pfam PF22936: Pol polyprotein, beta-barrel domain (domain)
This domain is found in Retrovirus-related Pol polyproteins from transposon TNT 1-94. It is predicted to adopt a beta-barrel fold with significant similarity to retroviral acid proteases.
Pfam PF10150: Ribonuclease E/G family (family)
Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs.
Pfam PF21716: Probable addiction module antidote protein (domain)
This entry represents a helix-turn-helix domain that is found in the HI1420 protein.  Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted helix-turn-helix DNA-binding protein. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Pfam PF18086: Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain (domain)
This is the N-terminal domain found in the Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (PPIP5K2), [ec:2.7.4.24]. Structure analysis of human PPIP5K2 indicate that this region forms alpha-beta-alpha domain.PPIP5K2 is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis.
Pfam PF10706: Aminoglycoside-2''-adenylyltransferase (family)
This family is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents.
Pfam PF10820: Protein of unknown function (DUF2543) (family)
This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. The family has a highly conserved sequence.
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 PF06448: Domain of Unknown Function (DUF1081) (family)
This region is found in Apolipophorin 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 PF20226: Family of unknown function (DUF6585) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 246 and 268 amino acids in length. There are seven highly conserved Gly residues.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10046: Biogenesis of lysosome-related organelles complex-1 subunit 2 (coiled_coil)
Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.
Pfam PF14247: Putative metallopeptidase (family)
This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 247 and 291 amino acids in length.  There is a conserved EED sequence motif. This is a putative metallopeptidase.
Pfam PF20208: ARG and Rhodanese-Phosphatase-superfamily-associated Protein domain (domain)
ARPP-1 shows a distinguishing group of absolutely conserved residues, including a cysteine and a glutamine, suggestive of enzymatic activity. Structural predictions reveal a core beta-sheet comprised of a duplicated four-stranded beta-meander with a beta-barrel domain bearing the absolutely conserved residues inserted into the first repeat. The unifying biochemical theme across its conserved contextual genome linkages is the presence of molecules with sugar moieties (ADPr, nucleotides, and polysaccharides). In genome contexts linking ARPP-1 with ARG and other counter viral ribosylation domains, ARPP is predicted to act on ribose moieties coming from ADPr. The presence of the conserved cysteine suggests that it could function analogous to the recently characterized SRAP domain by forming covalent cross-links with sugars.
Pfam PF19807: Family of unknown function (DUF6290) (family)
This family of proteins is functionally uncharacterised, they are predominantly found in bacteria but also in viruses. Proteins in this family are approximately 80 amino acids in length and presumably contain a ribbon-helix-helix DNA-binding 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 PF00464: Serine hydroxymethyltransferase (domain)
Proteins containing this domain include serine hydroxymethyltransferase, alpha-methylserine aldolase and fluorothreonine transaldolase.
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and methylenetetrahydrofolate . This reaction generates single carbon units for purine, thymidine, and methionine biosynthesis. It belongs to the aspartate aminotransferase superfamily (fold type I) . The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme . SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer .
Fluorothreonine transaldolase catalyzes the final step in 4-fluorothreonine biosynthesis. It mediates a L-threonine/fluoroaceldehyde to 4-fluoro-L-threonine/acetaldehyde crossover reaction. It shares protein sequence similarity with SHMT .
Alpha-methylserine aldolase catalyses the reversible interconversion of alpha-methyl-L-serine to L-alanine and formaldehyde . This enzyme also catalysed alanine racemization.
Pfam PF07810: TMC domain (domain)
These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 ([swissprot:Q7TN63]) and EVIN2 ([swissprot:Q8IU68]) - this region is termed the TMC domain.  Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters.
Pfam PF04498: Poxvirus nucleic acid binding protein VP8/L4R (family)
The 25 kDa product of Vaccinia virus gene L4R is also known as VP8.  VP8 is found in the cores of Vaccinia virions and is essential for the formation of transcriptionally competent viral particles.  It binds both single stranded and double stranded DNA and RNA with similar affinities.  Binding is thought to involve cooperative interactions between protein subunits. The protein is proteolytically cleaved during viral assembly at an Ala-Gly-Ala site. Possible roles for VP8 include packaging and maintaining the DNA genome in a transcribable configuration; binding ssDNA during transcription initiation; and cooperation with I8R protein to unwind early promoter regions.  VP8 may also function in either transcription elongation or release of mRNA molecules from viral particles.
Pfam PF13379: NMT1-like family (family)
This family is closely related to the [pfam:PF09084] family.
Pfam PF19974: Ternary complex associated domain 9 (domain)
Novel uncharacterised protein domain found associated with the vWA-MoxR-VMAP ternary systems. This domain is likely a phosphotransferase enzyme.
Pfam PF17626: Inclusion membrane protein F (family)
The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) are exposed to the cytosol and share a common structural feature of a long, bi-lobed hydrophobic domain but little or no primary amino acid sequence similarity. This family has members such as the IncF proteins found in Chlamydia trachomatis. IncF, is enriched at the point of contact of RBs (reticulate bodies) with the inclusion membrane. It is expressed early in the developmental cycle and interacts with many other Inc proteins, like Ct058 or Ct850, which are expressed later during the cycle. Thus, IncF could act as an interaction node for Inc proteins. IncF consists of 104 amino acids of which 38 N-terminal amino acids encoding the signal sequence for the type III system and 12 C-terminal amino acids may be localized in the host cell cytoplasm. Suggesting that IncF or other small Incs interact with other Inc proteins by their trans-membrane domain. It has been identified to be capable of homo-oligomerization and also displayed self-interacting properties.
Pfam PF03894: D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase (family)
Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P [ec:4.1.2.9], [ec:4.1.2.22]. This family is distantly related to transketolases e.g. [pfam:PF02779].
Pfam PF24672: Domain of unknown function (DUF7654) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to adopt a globular alpha/beta structure.
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 PF05043: Mga helix-turn-helix domain (domain)
M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins.  This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci.  These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Wikipedia: Mga is a DNA-binding protein that activates the expression of several important virulence genes in Streptococcus pyogenes in response to changing environmental conditions. The family also contains VirR like proteins which match only at the C-terminus.