SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein uS15, archaea/eukaryotes (Ribosomal_uS15_arc_euk)
Type: Family

This entry contains the small ribosomal subunit protein uS15 from archaea and eukaryotes (also known as 30S ribosomal protein S15P/S13e and 40S ribosomal protein S13, respectively).

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 .
Bifunctional protein HldE (Bifunc_HldE)
Type: Family

This entry represents the bifunctional protein HldE. It comprises D-beta-D-heptose 7-phosphate kinase [ec:2.7.1.-] and D-beta-D-heptose 1-phosphate adenosyltransferase [ec:2.7.7.-] activities.
Orotate phosphoribosyltransferase (OPRT)
Type: Family

Orotate phosphoribosyltransferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. In the pyrimidine synthesis pathway, OPRT catalyses the reversible phosphoribosyl transfer from 5'-phospho-alpha-D-ribose 1'-diphosphate (PRPP) to orotic acid (OA), forming pyrophosphate and orotidine 5'-monophosphate (OMP) . The structures and properties of the OPRTases from different species have been described in several publications .
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC (tRNA_MAMT_biosynth_bifunc_MnmC)
Type: Family

This entry represents the tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC. It has FAD-dependent oxidoreductase and methytransferase activity ([ec:1.5.-.-] and [ec:2.1.1.-] respectively).
Alanine-tRNA ligase, eukaryota/bacteria (Ala_tRNA_ligase_euk/bac)
Type: Family

Alanine-tRNA ligase (also known as alanyl-tRNA synthetase) (

) is an alpha4 tetramer that belongs to class IIc.

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Peptidyl-prolyl isomerase SurA (PPIase_SurA)
Type: Family

SurA in Escherichia coli is a periplasmic peptidyl-prolyl isomerase which is necessary for the proper folding of outer membrane proteins (OMP) including OmpA, OmpF and LamB. There are at least two pathways for periplasmic chaperone activity, one involving Skp and DegP, and another involving SurA. It has been proposed that the SurA pathway is the primary pathway for assembly of OMPs, while the DegP/Skp pathway is important for rescuing proteins that fall off of the SurA pathway. However recent proteonomic studies show that only 8 of 23 identified β-barrel proteins were negatively affected in a surA knockout mutant . The decreased OMP included FadL, FecA, LptD, FhuA, OmpX as well as the major OMP OmpA, OmpF and LamB.
Small ribosomal subunit protein uS9, bacterial/plastid (Ribosomal_uS9_bac/plastid)
Type: Family

This entry represents bacterial, plastid and mitochondrial ribosomal uS9 proteins. Small ribosomal subunit protein uS9, previously known as S9, is required for central cell maturation and endosperm development in
Arabidopsis thaliana
.

uS9 proteins adopt a β/α/β fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family .

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 .
Small ribosomal subunit protein uS14, bacteria/plastid (Ribosomal_uS14_bac/plastid)
Type: Family

This entry includes bacterial and plastid small ribosomal subunit protein uS14.

uS14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, uS14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins that include bacterial, algal and plant chloroplast uS14, cyanelle uS14, archaebacteria Methanococcus vannielii uS14, as well as yeast mitochondrial MRP2, yeast RPS29A/B, and mammalian RPS29.

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 .
Glucose receptor Git3-like, N-terminal (Glucose_rcpt_Git3-like_N)
Type: Domain

This entry contains the conserved N-terminal uncharacterised region belonging to the G-protein coupled receptors Git3, GPR1, GPR2, and GPR3 that are involved in glucose sensing and signaling pathways.

Git3, found in Schizosaccharomyces pombe, is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail .

GPR1 is present in Saccharomyces cerevisiae (budding yeast) and Candida albicans. Git3 and GPR1 are part of the glucose/cAMP pathway and are considered functionally related. GPR1 interacts with glucose and sucrose as agonists, while mannose acts as an antagonist . It forms part of a GPCR system with Gpa2 and Rgs2 for glucose sensing .

GPR2 and GPR3 from the Nematode-trapping fungus Arthrobotrys oligospora are G protein-coupled receptors that sense nematode ascaroside pheromones and signals via adenylate cyclase to positively regulate trap formation for nematode capture .
Peptidase M17, leucine aminopeptidase (Peptidase_M17_leu_NH2_pept)
Type: Family

The majority of members of this family are zinc-dependent exopeptidases belonging to MEROPS peptidase family M17 (leucyl aminopeptidase, clan MF).

This family excludes pepB aminopeptidases, which are also members of MEROPS family M17 (see

).
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid (NAD(P)H_OxRDtase_bac/plastid)
Type: Family

This family represents the subunit 3 of complex I.
Molybdenum cofactor biosynthesis C (MoaC)
Type: Family

The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism .

This entry represents the molybdenum cofactor biosynthesis protein MoaC from prokaryotes and eukaryotes, also known as cyclic pyranopterin monophosphate synthase.
Probable cyclic pyranopterin monophosphate synthase accessory protein, archaea (Mo_CF_biosynth-C_arc)
Type: Family

This entry contains probable cyclic pyranopterin monophosphate synthase accessory protein (also known as molybdenum cofactor biosynthesis protein C, or MoaC) from archaea. Members of this entry seem to be an outgroup of the eukaryotic and bacterial branch.

Members of this MoaC family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis .
NADH:quinone oxidoreductase, FMN-dependent (NADH:quinone_OxRdtase_FMN_depd)
Type: Family

This entry represents FMN-dependent NADH:quinone oxidoreductases (also known as FMN-dependent NADH-azoreductases) which function as quinone reductases that provides resistance to thiol-specific stress caused by electrophilic quinones . These enzymes also exhibit azoreductase activity, catalysing the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines . They require NADH, as an electron donor for its activity. These enzymes are homodimers that binds one FMN molecule per subunit.
Glucose-1-phosphate adenylyltransferase GlgC, bacterial (GlgC_bac)
Type: Family

This entry represent glucose-1-phosphate adenylyltransferase, also called ADP-glucose pyrophosphorylase . In bacteria, both homomeric forms of GlgC and more active heterodimers of GlgC and GlgD have been described. This entry describes the GlgC subunit only.
Bifunctional protein PyrR (PyrR)
Type: Family

The PyrR protein from Bacillus subtilis and many other bacteria is a bifunctional protein. Its primary function is the regulation of expression of pyrimidine biosynthetic (pyr) genes by binding to specific sites on pyr mRNA in a uridine nucleotide-dependent manner and altering the folding of downstream RNA to promote termination of transcription. PyrR also catalyzes the uracil phosphoribosyltransferase (UPRTase) reaction (

) even though it bears little amino acid sequence similarity to other bacterial UPRTases .
Low affinity potassium transport system protein Kup (Kup)
Type: Family

This entry represents potassium transport Kup system proteins. These proteins are involved in the uptake of K+ ions under hyper-osmotic stress and likely operate as K+:H+ symporters. Kup proteins are composed of two domains--an integral membrane domain that has 12 putative trans-membrane sections and a hydrophilic C-terminal domain.
Cell division protein SepF (Cell_div_SepF)
Type: Family

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 . Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology.
Small ribosomal subunit protein uS14, bacteria (Ribosomal_uS14_bact)
Type: Family

This entry includes bacterial small ribosomal subunit protein uS14. In bacteria the gene coding for ribosomal protein S14 has been subject to horizontal gene transfer, subsequent differential gene loss and insertions/deletions near the N terminus. Different groups have been described according to this . This family represents the type Z, or zinc-binding S14 proteins.

uS14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, uS14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins that include bacterial, algal and plant chloroplast uS14, cyanelle uS14, archaebacteria Methanococcus vannielii uS14, as well as yeast mitochondrial MRP2, yeast RPS29A/B, and mammalian RPS29.

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 .
Sporulation regulator WhiA, C-terminal (Sporulation_regulator_WhiA_C)
Type: Domain

This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure .
Putative competence-damage inducible protein, Archaea (CinA_Arc)
Type: Family

This entry represents a putative competence-damage inducible protein from Archaea, related to CinA from bacteria (

).
Bifunctional glutamine synthetase adenylyltransferase/adenylyl-removing enzyme (GlnE)
Type: Family

This entry represents GlnE family proteins. These proteins adenylate and deadenylate glutamate-ammonia ligases:
ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}

The two activities are functionally the reverse of one another and must be controlled by the organism to prevent futile cycling .
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site (PPIase_PpiC_CS)
Type: Conserved_site

Peptidylprolyl isomerase (

) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides . It has been reported in bacteria and eukayotes.

Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.
Foldase protein PrsA (Foldase_PrsA)
Type: Family

The PrsA protein of Bacillus subtilis is an essential membrane-bound lipoprotein that is assumed to assist post-translocational folding of exported proteins and stabilise them in the compartment between the cytoplasmic membrane and cell wall. This folding activity is consistent with the homology of a segment of PrsA with parvulin-type peptidyl-prolyl cis/trans isomerases (PPIase). PrsA is a PPIase, but the essential role in vivo seems to depend on some non-PPIase activity of both the parvulin-like and flanking domains .
Membrane insertase YidC/YidC1/YidC2, Firmicutes (YidC/YidC1/YidC2_Firmicutes)
Type: Family

This family includes membrane insertase YidC, YidC1 (also called MisCB), and YidC2 (also called MisCA). Members in this family are required for the insertion of integral membrane proteins into the membrane. They may also be involved in protein secretion processes.

Besides having the membrane insertase function, Bacillus MisCA is essential for sporulation by activating sigma factor SpoIIIG/SigG after engulfment is completed in the prespore, maybe by acting on SpoIIIAE. It has an overlapping, although partly distinct, function compared to YqjG(MisCB) .
Selenophosphate synthetase, class I (SelD_I)
Type: Family

The UGA (TGA) codon is normally a termination codon, however it is also used as a selenocysteine (Sec) codon by numerous organisms . Sec is the 21st amino acid that is inserted into selenoproteins (protein that includes a selenocysteine (Se-Cys) amino acid residue). The synthesis of Sec and its incorporation into proteins requires the activity of a number of proteins, one of which is selenophosphate synthetase (SPS), also known as the SelD gene product . SPS catalyses the production of the selenium donor compound monoselenophosphate (MSP) from selenide and ATP. MSP is then used to synthesize Sec from seryl-tRNAs .

SPS was initially identified in E. coli as the product of the gene selD, one of four essential selenoprotein synthesis genes (selA-D) . SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
NADH dehydrogenase, subunit CD (NADH_DH_suCD)
Type: Family

This entry represents the NADH-quinone oxidoreductase subunit C and D fusion protein found in the Alpha-, Beta-, Gamma-and some Deltaproteobacteria. The CD subunit fusion protein found in the Aquificae, Bacteroidetes, some other Delta-and Epsilon proteobacteria is different enough that it seems to be another subfamily (see

).
D-ribose pyranase (D-ribose_pyranase)
Type: Family

D-ribose pyranase catalyses the interconversion of beta-pyran and beta-furan forms of D-ribose.
Uncharacterised protein family ApaG (Uncharacterised_ApaG)
Type: Family

This entry represents the bacterial protein ApaG that contains a single ApaG domain, which is ~125 amino acids in length. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several β-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity .