SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein eS21 superfamily (Ribosomal_eS21_sf)
Type: Homologous_superfamily

A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts .

This entry represents the ribosomal protein eS21 (RpS21). It bounds to native 40S ribosomal subunits in a salt-labile association and is absent from polysomes, indicating that it acts as a translation initiation factor rather than as a core ribosomal protein .

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 .
Monellin, A chain superfamily (Monellin_A_sf)
Type: Homologous_superfamily

Monellin is an intensely sweet-tasting protein derived from African berries. The protein has a very high specificity for the sweet receptors, making it ~100,000 times sweeter than sugar on a molar basis and several thousand times sweeter on a weight basis. Like the sweet-tasting protein thaumatin, it neither contains carbohydrates nor modified amino acids. Although there is no sequence similarity between the proteins, antibodies for thaumatin compete for monellin (and other sweet compounds, but not for chemically modified non-sweet monellin) and vice versa . It is thought that native conformations are important for the sweet taste. Monellin is a heterodimer, comprising an A chain of 44 amino acid residues, and a B chain of 50 residues. The individual subunits are not sweet, nor do they block the sweet sensation of sucrose or monellin. However, blocking the single SH of monellin abolishes its sweetness, as does reaction of its methionyl residue with CNBr . The cysteinyl and methionyl residues are adjacent, and it has therefore been suggested that this part of the molecule is essential for its sweetness . The structure of monellin belongs to the α/β class, a 5-stranded β-sheet sequestering a single α-helix. The A chain contributes 3 strands to the sheet.

This entry represents the Monellin chain A.
Ornithine decarboxylase antizyme superfamily (ODC_AZ_sf)
Type: Homologous_superfamily

Ornithine decarboxylase antizyme (ODC-AZ) binds to, and destabilises, ornithine decarboxylase (ODC), a key enzyme in polyamine synthesis. ODC is then rapidly degraded. The expression of ODC-AZ requires programmed, ribosomal frameshifting which is modulated according to the cellular concentration of polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of mRNA for the antizyme leading to the expression of a full-length protein. At least two forms of ODC-AZ in mammals and one homologue in Drosophila (protein Gutfeeling) have been identified.
Small ribosomal subunit protein eS31 eukaryotic-type superfamily (Ribosomal_eS31_euk-type_sf)
Type: Homologous_superfamily

This entry includes the small ribosomal subunit protein eS31 (also known as S27A) from eukaryotes and some archaeal species. In eukaryotes, the 40S ribosomal protein S27a is synthesized as a C-terminal extension of ubiquitin, and this fusion protein is known as UBS27 . The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis . The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins .

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 .
L-arabinose isomerase, N-terminal domain superfamily (AraA_N_sf)
Type: Homologous_superfamily

This entry includes L-arabinose isomerases, AraA, (

). These enzymes catalyse the reaction: L-arabinose => L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme .
Large ribosomal subunit protein bL33 superfamily (Ribosomal_bL33_sf)
Type: Homologous_superfamily

Ribosomal protein bL33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, bL33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:

Eubacterial bL33.

Algal and plant chloroplast bL33c.

Cyanelle bL33.

Animal bL33m.

Fungal bL33m (also known as MRPL39).

bL33 is a small protein of 49 to 66 amino-acid residues.

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 .
Tctex-1-like superfamily (Tctex-1-like_sf)
Type: Homologous_superfamily

Tctex-1 is a dynein light chain. Dynein translocates rhodopsin-bearing vesicles along microtubules and it has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin for retrograde or apical transport . An efficient vectorial transport system must be required to deliver large numbers of newly synthesised rhodopsin molecules (~10
7
molecules per day per photoreceptor) to the base of the outer segment of the photoreceptor, Tctex-1 may well play a role in this process. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit the interaction between Tctex-1 and rhodopsin, which may be the molecular basis of retinitis pigmentosa .

In the mouse, the chromosomal location and pattern of expression of Tctex-1 make it a candidate for involvement in male sterility .

This entry also includes Topoisomerase I damage affected protein 2 (TDA2) whose crystal structure revealed that it belongs to the dynein light chain family. It is part of the endocytic machinery and required for normal internalisation of native cargo in yeast .
Large ribosomal subunit protein eL40 superfamily (Ribosomal_eL40_sf)
Type: Homologous_superfamily

This entry includes the large ribosomal subunit protein eL40 from both archaea and eukaryotes (also known as L40). In eukaryotes, L40 is fused to ubiquitin moieties, and this fusion protein is known as UBL40 . Specific endopeptidases cleave these precursor molecules to release ubiquitin moieties . UBL40 plays important roles in gametogenesis . This fusion may also have a pre-cleavage function in ribosome assembly .

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 .
XS domain superfamily (XS_domain_sf)
Type: Homologous_superfamily

This XS (named after rice gene X and SGS3) domain is a single-stranded RNA-binding domain (RBD) and possesses a unique version of a RNA recognition motif (RRM) fold . It is conserved in a family of plant proteins including gene X and SGS3. Although its function is still unknown, the plant SGS3 proteins are thought to be involved in post-transcriptional gene silencing (PTGS) pathways . In addition, they contain a conserved aspartate residue that may be functionally important.
Archaeal transcription elongation factor Spt4 superfamily (Spt4_dom_sf)
Type: Homologous_superfamily

This entry represents Spt4 from Sulfolobus acidocaldarius (also known as RpoE2) and similar sequences mainly found in archaea. Spt4, of about 64 amino acids, forms a heterodimer with Spt5. The Spt4/5 heterodimer is considered a transcription elongation factor, responsible for making the archaeal DNA-directed RNA polymerase (RNAP) processive .

DNA-directed RNA polymerases, also known as DNA-dependent RNA polymerases, are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. Eukaryotes have three different DNA-directed RNA polymerases (RNAPs), Pol I, II, and III, whereas Archaea and Bacteria have single enzymes.

RNAPs are multisubunit enzymes. Archaeal RNAP is closely related to eukaryotic RNAP II , which consists of 12 subunits. Archaeal RNAP has an additional subunit, Rpo13, with no orthologue in the eukaryotic enzyme .
YaeQ superfamily (YaeQ_sf)
Type: Homologous_superfamily

Structural studies indicate that YaeQ contains a variation of the PD-(D/E)XK nuclease motif found in various endonucleases and enzymes involved in DNA replication, repair, and recombination . This structure, and the high degree of sequence conservation amongst YaeQ and its homologues, suggest that it may be involved in the remodeling or modification of nucleic acid DNA or RNA structures. YaeQ has an α-β roll fold.
NolW-like superfamily (NolW-like_sf)
Type: Homologous_superfamily

This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (

). NolW proteins have putative membrane-spanning regions .
CheD-like superfamily (CheD-like_sf)
Type: Homologous_superfamily

CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase . CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs .
RNA polymerase Rpb1, domain 7 superfamily (RNA_pol_Rpb1_7_sf)
Type: Homologous_superfamily

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (

) .
SepF-like superfamily (SepF-like_sf)
Type: Homologous_superfamily

This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation . This protein uses an amphipathic helix for membrane binding and polymerises into large rings that bundle FtsZ filaments . Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins, such as SepF from Haloferax volcanii .
LURP-one-related superfamily (LOR_sf)
Type: Homologous_superfamily

The structure of protein LURP-one-related 15 (At5g01750) has been solved. It comprises a 12-stranded β-barrel with a central C-terminal α-helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein . In plants LURP1 plays a role in defense against pathogens .
Janus superfamily (Janus_sf)
Type: Homologous_superfamily

This superfamily is comprised of the 14kDa phosphohistidine phosphatase from mammals and Janus-A/Janus-B proteins from Drosophila melanogaster. Janus-A and Janus-B regulate somatic sex differentiation and have been found to be testes specific . 14kDa phosphohistidine phosphatase is a histidine phosphatase that may play a role of reversible histidine phosphorylation in neuronal functions .

The 14kDa phosphohistidine phosphatase is of a novel topology, and the structure reveals a positively charged active site defined by conserved residues that provide a suitable environment for binding phosphohistidine-containing substrates .
GGGP/HepGP synthase superfamily (GGGP/HepGP_synthase_sf)
Type: Homologous_superfamily

This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase and Heptaprenylglyceryl phosphate (HepGP) synthase.

GGGP synthase is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) .
LAP1C-like, C-terminal domain superfamily (LAP1C-like_C_sf)
Type: Homologous_superfamily

This entry represents Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1), which are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane . These proteins interact with and activate Torsin A, an AAA+ ATPase localized to the endoplasmic reticulum (ER), through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity . A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease .

This is the conserved C-terminal domain of LAP1, the AAA Activator domain .
CRISPR-associated protein Csn2 superfamily (Csn2_sf)
Type: Homologous_superfamily

This entry represents the Csn2 superfamily of Cas proteins, which are found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas loci. The species range so far for this subtype is animal pathogens and commensals only. This protein is present in some but not all NMENI CRISPR/Cas loci .
The structure of Csn2 contains two domains: an α/β domain and an α-helical domain with significant hinge motion between these two domains . Sn2 is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions .
MttB-like superfamily (MttB-like_sf)
Type: Homologous_superfamily

This superfamily consists of several trimethylamine methyltransferase (MTTB) proteins. This enzyme, which catalyses the transfer of a methyl group from trimethylamine to a trimethylamine-specific corrinoid protein (MttC), is involved in methanogenesis from trimethylamine . This superfamily also includes MtgB, a glycine betaine methyltransferase .
Mite allergen, group-7 superfamily (Mite_allergen_7_sf)
Type: Homologous_superfamily

This entry contains proteins that cause an allergic reaction in humans. Common symptoms of mite allergy are bronchial asthma, allergic rhinitis and conjunctivitis .

The structure of the dust mite allergen Der f 7 from Dermatophagoides farinae is an elongated and curved molecule consisting of two anti-parallel β-sheets (one 4-stranded and the other 5-stranded) that wrap around a long C-terminal helix . Its homologue Der p 7 from Dermatophagoides pteronyssinus has a similar structure , but it differs slightly in the beta1-beta2 loop region, which is proximal to the IgE epitope and responsible of the thermal stability .
FCS-type zinc finger superfamily (Znf_FCS_sf)
Type: Homologous_superfamily

The FCS-type zinc finger, named after the signature FCS residues associated with the third cysteine, is present in several polycomb group proteins. The FCS zinc finger is expected to adopt a Zn-ribbon like fold. Molecular data suggest that this domain can bind RNA in a non-sequence-specific manner .
Type III effector HopJ superfamily (HopJ_sf)
Type: Homologous_superfamily

Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins are called HopJ after the original member HopPmaJ .
Proteasome chaperone 1 superfamily (Pba1_sf)
Type: Homologous_superfamily

This entry represents fungal proteosome chaperone 1, a chaperone of the 20S proteasome which functions in early 20S proteasome assembly .
Takeout superfamily (To_sf)
Type: Homologous_superfamily

Takeout (To) proteins are found in insects and have important roles in various aspects of their physiology and behavior. To was discovered in Drosophila melanogaster as a clock-regulated gene, acting as a molecular link between circadian rhythms and feeding behavior . In addition, To is secreted in the hemolymph of adult males and affects male courtship behavior . To proteins have an unusual α/β-wrap fold, the so-called TULIP fold , seen also in juvenile hormone-binding proteins (JHBPs), with which they share limited sequence similarity. This fold is thought to constitute a scaffold for the binding and/or transport of hydrophobic ligands .