SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein eL15, conserved site (Ribosomal_eL15_CS)
Type: Conserved_site

This entry represents a short conserved sequence region located in the central section of the members of the large ribosomal subunit protein eL15 family.

A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities . One of these families consists of:

Mammalian eL15.

Insect eL15.

Plant eL15.

Yeast YL10 (L13) (Rp15r).

Archaebacterial eL15 (known as L15e).

These proteins have about 200 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 .
Large ribosomal subunit protein eL15, archaeal (Ribosomal_eL15_arc)
Type: Family

This entry represents the archaeal eL15 proteins found in archaea.

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 .
Large ribosomal subunit protein uL5, conserved site (Ribosomal_uL5_CS)
Type: Conserved_site

This entry represents a short conserved sequence found in the N-terminal region of the members of the large ribosomal subunit protein uL5 family.

Large ribosomal subunit protein uL5, previously known as Ribosomal protein L5, is ~180 amino acids in length. In Escherichia coli, uL5 is known to be involved in binding 5S RNA to 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 .
Large ribosomal subunit protein uL5, bacterial-type (Ribosomal_uL5_bac-type)
Type: Family

This entry represents uL5 proteins mainly found in bacteria and chloroplasts.

Large ribosomal subunit protein uL5, previously known as Ribosomal protein L5, is ~180 amino acids in length. In Escherichia coli, uL5 is known to be involved in binding 5S RNA to 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 .
Decarboxylase MfnA, archaea (MfnA)
Type: Family

Members of this protein family are the archaeal form of decarboxylases. This entry includes TK1814 from Thermococcus kodakarensis. TK1814 functions as an aspartate 1-decarboxylase (ADC) and may be responsible for beta-alanine biosynthesis .
Phosphodiesterase YfcE, conserved site (PdiEstase_YfcE_CS)
Type: Conserved_site

This entry represents a short conserved sequence region found in a family of short, hydrophilic proteins that are all known or suspected phosphodiestreases. The best characterised of these is YfcE from Escherichia coli . The physiological substrate for this protein is not known, though it is capable of hydrolysing phosphodiesters bonds in the artificial chromogenic substrate bis-p-nitrophenyl phosphate. YfcE is a tetrameric, managanese-binding protein where each monomer forms a β-sandwich fold similar to other metallophosphatases. The member MJ0936 from Methanocaldococcus jannaschii (Methanococcus jannaschii), was shown to act on model phosphodiesterase substrates; a divalent cation was required.
tRNA uridine(34) hydroxylase (TrhO)
Type: Family

TrhO (also known as YceA in E. coli) catalyses oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs, the first step in 5-carboxymethoxyuridine (cmo5U) biosynthesis . This entry also includes uncharacterised proteins from archaea and plants.
SecA conserved site (SecA_CS)
Type: Conserved_site

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .

SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologues of secA are also encoded in the chloroplast genome of some algae as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.

The signature pattern of this entry is located in the C-terminal region of the RecA-like domain.
Large ribosomal subunit protein bL34, conserved site (Ribosomal_bL34_CS)
Type: Conserved_site

This entry represents a conserved site from ribosomal protein L34 (also known as Large ribosomal subunit protein bL34), one of the proteins from the large subunit of the ribosome from bacteria. It is a small basic protein of 44 to 51 amino-acid residues . L34 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Eubacterial L34, Red algal chloroplast L34 and Cyanelle L34.

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 .
Thymidylate synthase, active site (Thymidylate_synthase_AS)
Type: Active_site

Thymidylate synthase (

) catalyzes the reductive methylation of dUMP to dTMP with concomitant conversion of 5,10-methylenetetrahydrofolate to dihydrofolate:
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
This provides the sole
de novo
pathway for production of dTMP and is the only enzyme in folate metabolism in which the 5,10-methylenetetrahydrofolate is oxidised during one-carbon transfer . The enzyme is essential for regulating the balanced supply of the 4 DNA precursors in normal DNA replication: defects in the enzyme activity affecting the regulation process cause various biological and genetic abnormalities, such as thymineless death . The enzyme is an important target for certain chemotherapeutic drugs. Thymidylate synthase is an enzyme of about 30 to 35 Kd in most species except in protozoan and plants where it exists as a bifunctional enzyme that includes a dihydrofolate reductase domain . A cysteine residue is involved in the catalytic mechanism (it covalently binds the 5,6-dihydro-dUMP intermediate) . The sequence around the active site of this enzyme is conserved from phages to vertebrates.

Thymidylate synthase also acts as a regulator of its own expression by binding and inactivating its own RNA. Due to its key role in the de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is one of the most conserved enzymes across species and phyla . Thymidylate synthase is a well-recognized target for anticancer chemotherapy, as well as a valuable new target against infectious diseases . Interestingly, in several protozoa, a single polypeptide chain codes for both dihydrofolate reductase (DHFR) and thymidylate synthase (TS), forming a bifunctional enzyme (DHFR-TS), possibly through gene fusion at a single evolutionary point. DHFR-TS is also active as a dimer .
Suppressor of fused-like domain (SUFU-like_domain)
Type: Domain

Sufu, encoding the human ortholog of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signalling . It is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade , and functions by binding these proteins and preventing their translocation to the nucleus. Sufu has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signalling pathway . Homologues of Sufu have been found in bacteria, though their function is not currently known.

This entry represents a domain found in Sufu and its homologues. It is also found in other proteins that are functionally uncharacterised. In eukaryotic Sufu, an additional domain (

) is found at the C terminus of the protein. This domain binds to the C-terminal domain of the Gli/Ci transcription factors, inhibiting their activity .

This domain is also found in Immunity protein YqcF from B. subtilis, a component of one of 6 LXG toxin-immunity modules. It neutralizes the toxic activity of cognate toxin YqcG .
Class III cytochrome C (Cyt_c_III_dom)
Type: Domain

Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes .

Ambler recognised four classes of cytC.

Class III comprises the low redox potential multiple haem cytochromes: C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV . The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 α-helices and 2 β-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved .
Nodulation protein S (NodS)
Type: Family

This entry consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors .

This entry represents Nodulation protein S found exclusively in bacteria
DMSO/Nitrate reductase chaperone (DMSO/NO3_reduct_chaperone)
Type: Family

This entry represents a family of proteins which are involved in enzymes assembly and/or maturation:

The TorD protein is involved in the maturation of the the trimethylamine N-oxide reductase TorA (a DMSO reductase family member) in Escherichia coli . TorA is a molybdenum-containing enzyme which requires the the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. TorD acts as a chaperone, binding to apoTorA and promoting efficient incorporation of the cofactor into the protein.

Nitrate reductase delta subunit (NarJ). This subunit is not part of the nitrate reductase enzyme but is a chaperone required for proper molybdenum cofactor insertion and final assembly of the nitrate reductase . NarJ exhibits sequence homology to chaperones involved in maturation and cofactor insertion of E. coli redox enzymes that are mediated by twin-arginine translocase (Tat) dependent translocation . The archetypal Tat proofreading chaperones belong to the TorD family .

Twin-arginine leader-binding protein DmsD, which could be required for the biogenesis of DMSO reductase rather than for the targeting of DmsA to the inner membrane .

Dimethyl sulphide dehydrogenase protein DdhD. This protein is thought to function as chaperone protein in the assembly of an active dimethyl sulphide dehydrogenase DdhABC .
Flavin monooxygenase-like (Flavin_mOase-like)
Type: Family

Flavin-containing monooxygenases (FMOs) constitute a family of xenobiotic-metabolising enzymes . Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorus and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In man, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5 . This is a recent nomenclature based on comparison of amino acid sequences, and has been introduced in an attempt to eliminate confusion inherent in multiple, laboratory-specific designations and tissue-based classifications . Following the determination of the complete nucleotide sequence of Saccharomyces cerevisiae (Baker's yeast) , a novel gene was found to encode a protein with similarity to mammalian monooxygenases. In Aspergillus, flavin-containing monooxygenases ustF1 and ustF2 are components in the biosynthesis of the antimitotic tetrapeptide ustiloxin B, a secondary metabolite. The monooxygenases modify the side chain of the intermediate S-deoxyustiloxin H .
Phosphate-starvation-induced PsiE-like (P_starv_induced_PsiE-like)
Type: Family

This entry represents the phosphate-starvation-inducible protein (PsiE) and similar proteins. This entry is sometimes found in proteins that contain other domains such as the protoglobin domain.

Phosphate-starvation-inducible E (PsiE) expression is under direct positive and negative control by PhoB and cAMP-CRP, respectively . PsiE is an integral membrane protein with four transmembrane helices. The second α helix contains a conserved glutamic acid residue and the third helix contains a conserved arginine residue. The function of PsiE remains to be determined.