SII-SWORD/CoKE huggingface dataset:
Pfam PF15787: Neurobeachin/BDCP, DUF4704 alpha solenoid region (repeat)
This domain of unknown function is found in eukaryotes on neurobeachin and BEACH domain-containing proteins (BDCPs). Mutations in this proteins are associated with Lipopolysaccharide-responsive and beige-like anchor (LRBA) deficiency. According to structure prediction is adopts an alpha-helical solenoid 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 PF24734: Domain of unknown function (DUF7685) (domain)
This domain is found in uncharacterised bacterial proteins. It contains two pairs of conserved cysteine residues and it is predicted to adopt a fold typical for treble clef zinc fingers. It has a detectable similarity to the N-terminal zinc finger domain of the bacterial AAA+ disaggregase ClpG, which confers extreme heat resistance to bacteria. The latter is is crucial for structural integrity and disaggregase functionality of ClpG.
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 PF09721: Transmembrane exosortase (Exosortase_EpsH) (family)
Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distribution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif, IPR013424. Members of this entry are integral membrane proteins with eight predicted transmembrane helices in common. Some members of this family have long trailing sequences past the region described by this model. This model does not include the region of the first predicted transmembrane region. The best characterised member is EpsH of Methylobacillus sp. 12S, where it is part of a locus associated with biosynthesis of the exopolysaccharide methanol-an.
Wikipedia: Exosortase refers to a family of integral membrane proteins that occur in Gram-negative bacteria that recognizes and cleaves the carboxyl-terminal sorting signal PEP-CTERM. The name derives from a predicted role analogous to sortase, despite the lack of any detectable sequence homology, and a strong association of exosortase genes with exopolysaccharide or extracellular polymeric substance biosynthesis loci. Many archaea have an archaeosortase, homologous to exosortases rather than to sortases. Archaeosortase A recognizes the signal PGF-CTERM, found at the C-terminus of some archaeal S-layer proteins. Following processing by archaeosortase A, the PGF-CTERM region is gone, and a prenyl-derived lipid anchor is present at the C-terminus instead.
Pfam PF23498: MgtT (family)
This protein family includes the uncharacterised protein MgtT from Escherichia coli, a 34-residues micropeptide encoded by a small open reading frame (smORF) that lies just downstream of mgtS and is encoded antisense of the mgrR small regulatory RNA gene. Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF23818: Bacteriophage Tail Tube Terminator Protein (domain)
The Tail Tube Terminator Protein family is involved in the assembly of bacteriophage tail structures. Members of this family, such as the Tail Tube Terminator Protein p142, are responsible for capping the tail tube during its polymerization, ensuring that it reaches the correct length. This capping function is crucial for the proper formation of the phage tail, which is essential for the phage's ability to infect host bacteria by facilitating the injection of genetic material.
Pfam PF05222: Alanine dehydrogenase/PNT, N-terminal domain (domain)
This family now also contains the lysine 2-oxoglutarate reductases.
Pfam PF04092: SRS domain (family)
Toxoplasma gondii is a persistent protozoan parasite capable of infecting almost any warm-blooded vertebrate. The surface of Toxoplasma is coated with a family of developmentally regulated glycosylphosphatidylinositol (GPI)-linked proteins (SRSs), of which SAG1 is the prototypic member. SRS proteins mediate attachment to host cells and interface with the host immune response to regulate the virulence of the parasite. SAG1 is composed of two disulphide linked SRS domains. These have 6 cysteines that form 1-6,2-5 and 3-4 pairings. The structure of the immunodominant SAG1 antigen reveals a homodimeric configuration. The SRS domain is found in a single copy in the SAG2 proteins. This family of surface antigens are found in other apicomplexans.
Wikipedia: In molecular biology, the SAG1 protein domain is an example of a group of glycosylphosphatidylinositol (GPI)-linked proteins named SRSs. SAG1 is found on the surface of a protozoan parasite Toxoplasma gondii. This parasite infects almost any warm-blooded vertebrate. The surface of T. gondii is coated with a family of developmentally regulated glycosylphosphatidylinositol (GPI)-linked proteins (SRSs), of which SAG1 is the prototypic member.
Pfam PF24996: N-acetylneuraminate epimerase (repeat)
This entry includes N-acetylneuraminate epimerase (NANM) from Haemophilus influenzae, E. coli and its homologues. It converts alpha-N-acetylneuranimic acid (Neu5Ac) to the beta-anomer, accelerating the equilibrium between the alpha- and beta-anomers.
Pfam PF05480: Phenol-soluble modulin beta protein (family)
This family consists of several different short Staphylococcal proteins known as the phenol-soluble modulin beta proteins. The family contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus. Gonococcal growth inhibitor from Staphylococcus act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death.
Pfam PF01200: Ribosomal protein S28e (family)
A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are:


 * Mammalian S28 
 * Plant S28 
 * Fungi S33 
 * Archaebacterial S28e.


These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28e protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28e might be involved in protein synthesis .
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 PF24712: YxiG-like protein (domain)
This entry represents a family of uncharacterised proteins found in actinobacteria. Although this family does not contain the YxiG protein from B. subtilis [pfam:PF24711] it is clearly highly related from a structural point of view. These proteins like YxiG are also strongly predicted to form homodimers.
Pfam PF18898: Family of unknown function (DUF5654) (family)
This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 79 and 98 amino acids in length. The region contains two predicted transmembrane helices. The Eukaryotic examples are found in the Foraminiferan Reticulomyxa filosa that contains several proteins with this family.s
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 PF19106: Family of unknown function (DUF5793) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
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 PF15971: DolP-mannose mannosyltransferase (family)
This family catalyses the transfer of mannose from DolP-mannose to the N-linked tetrasaccharide bound to the S-layer glycoprotein to form a pentasaccharide.
Pfam PF11236: Protein of unknown function (DUF3037) (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 PF20980: lpg1496 N-terminal domain (domain)
This domain is found at the N terminus of the uncharacterised Lpg1496 (also known as Lem10) protein from Legionella pneumophila. It is also known as KLAMP domain. This domain adopts an alpha/beta structure with two alpha-helices flanked on one side by a five-stranded beta-sheet and a four-stranded on the other. Lpg1496 contains two copies of this domain, known as KLAMP1 and KLAMP2.
Pfam PF15789: Hyphally regulated cell wall GPI-anchored protein 1 (repeat)
Hyr1 family is a repeated domain found up to 39 times in a range of fungal and vertebral proteins.  Hyr1 is a hypha-specific protein.
Pfam PF16898: C-terminal associated domain of TOPRIM (family)
TOPRIM_C is found as the C-terminal extension of the TOPRIM domain, [pfam:PF01751] in metazoa.
Pfam PF14023: Protein of unknown function (DUF4239) (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 254 and 270 amino acids in length.
Pfam PF11966: SSURE domain (domain)
Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins. The structure was predicted to be composed of two subdomains.
Pfam PF01396: Topoisomerase DNA binding C4 zinc finger (domain)
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single-or double-strand breaks, crossing the strands through one another, then resealing the breaks . These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis . DNA topoisomerases are divided into two classes: type I enzymes (5.6.2.2; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.6.2.2; topoisomerases II, IV and VI) break double-strand DNA .
Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB . They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases . The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases .
This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc . This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc.
Pfam PF09987: Uncharacterized protein conserved in archaea (DUF2226) (family)
This domain, found in various hypothetical archaeal 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 PF03556: Cullin binding (family)
This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices.
Pfam PF00226: DnaJ domain (domain)
DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction.  DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature.
Wikipedia: In molecular biology, chaperone DnaJ, also known as Hsp40, is a molecular chaperone protein. It is expressed in a wide variety of organisms from bacteria to humans.
Pfam PF23649: FK506-binding protein 15-like domain (domain)
This domain is found in human FK506-binding protein 15 (FKBP15) and similar animal proteins. FKBP15 is involved in the transport of early endosomes and probably in the cytoskeletal organisation of neuronal growth cones. This domain, predicted to show a long alpha-helix, is often found C-terminal to [pfam:PF00254].
Pfam PF00742: Homoserine dehydrogenase (domain)
This entry represents the catalytic domain of homoserine dehydrogenase.
Homoserine dehydrogenase (1.1.1.3) catalyses the third step in the aspartate pathway; the NAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine . Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain . The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel Î±-Î² mixed sheet.
Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids -lysine, threonine, methionine and isoleucine -in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see .
Wikipedia: In enzymology, a homoserine dehydrogenase (EC 1.1.1.3) is an enzyme that catalyzes the chemical reactionL-homoserine + NAD(P)+  L-aspartate 4-semialdehyde + NAD(P)H + H+
Pfam PF16177: Acetyl-coenzyme A synthetase N-terminus (family)
This domain is found at the N-terminus of many acetyl-coenzyme A synthetase enzymes.
Pfam PF20089: Family of unknown function (DUF6481) (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.
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 PF01135: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) (family)
Wikipedia: Protein L-isoaspartyl methyltransferase , also called S-adenosyl-L-methionine:protein-L-isoaspartate O-methyltransferase, is an enzyme which recognizes and catalyzes the repair of damaged L-isoaspartyl and D-aspartyl groups in proteins. It is a highly conserved enzyme which is present in nearly all eukaryotes, archaebacteria, and Gram-negative eubacteria.
Pfam PF24571: Cohesin subunit SCC3/SA, HEAT-repeats domain (repeat)
This entry includes subunits of the cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes, including SA-1, SA-2 and SA-3 from vertebrates (STAG1-3), the orthologue from S.pombe Psc3 and the homologue from Arabidopsis, SCC3. This entry represents the C-terminal region of these proteins containing HEAT repeats, which may be involved in binding Scc1 subunit and nucleic acids. In STAG3, mutations in this region cause male infertility due to meiotic arrest.
Pfam PF21463: Cry1Ac, domain VII (domain)
This entry includes insecticidal protein Cry1Ac from Bacillus thuringiensis, which contains a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N terminus (domains I-III). The protoxin segment consists of domains IV-VII. This entry represents domain VII, which is a beta-roll that closely resembles carbohydrate-binding modules.
Pfam PF00058: Low-density lipoprotein receptor repeat class B (repeat)
This domain is also known as the YWTD motif after the most conserved region of the repeat.  The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
Wikipedia: The low-density lipoprotein receptor gene family codes for a class of structurally related cell surface receptors that fulfill diverse biological functions in different organs, tissues, and cell types. The role that is most commonly associated with this evolutionarily ancient family is cholesterol homeostasis. In humans, excess cholesterol in the blood is captured by low-density lipoprotein (LDL) and removed by the liver via endocytosis of the LDL receptor. Recent evidence indicates that the members of the LDL receptor gene family are active in the cell signalling pathways between specialized cells in many, if not all, multicellular organisms.
Pfam PF20144: TIG domain (domain)
This entry represents a TIG-like domain found in the suppressor of hairless protein.
Pfam PF19397: Family of unknown function (DUF5972) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001634) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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.