SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein uS9, archaeal (Ribosomal_uS9_archaeal)
Type: Family

This entry represents the archaeal small ribosomal subunit protein uS9.

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 .
T1SS-143 repeat-containing domain (T1SS-143_rpt-cont_dom)
Type: Domain

This entry represents a domain of about 143 amino acids that may occur singly or in up to 23 tandem repeats in very large proteins in the genus Vibrio, and in related species such as Legionella pneumophila, Photobacterium profundum, Rhodopseudomonas palustris, Shewanella pealeana, and Aeromonas hydrophila. Proteins with these domains represent a subset of a broader set of proteins with a particular signal for type 1 secretion, consisting of several glycine-rich repeats modeled by

, followed by a C-terminal domain modeled by

. Proteins with this domain tend to share several properties with the RtxA (Repeats in Toxin) protein of Vibrio cholerae, including a large size often containing tandemly repeated domains and a C-terminal signal for type 1 secretion.
Type I secretion C-terminal target domain, VC_A0849 subclass (T1SS_VCA0849)
Type: Domain

This entry represents a C-terminal domain associated with secretion by type 1 secretion systems (T1SS). Members of this subclass do not include the RtxA toxin of Vibrio cholerae and its homologues, although the two classes of proteins share large size, occurrence in genomes with T1SS, regions with long tandem repeats, and regions with the glycine-rich repeat modeled by

.
Small ribosomal subunit protein uS11, archaeal (Ribosomal_uS11_archaeal)
Type: Family

This entry represents archaeal ribosomal uS11 proteins.

Small ribosomal subunit protein uS11, previously known as Ribosomal protein S11 , plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small 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 .
Conserved hypothetical protein CHP03663 (CHP03663)
Type: Family

This entry represents a protein family found in bacteria and archaea, almost always in the same genomes as members of family

, and frequently as a nearby gene. The few invariant residues in this family, found toward the N terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three members may be found in a genome.

This group of proteins include Dolichyl-phosphate-mannose-protein mannosyltransferase from the extremely halophilic archaea Haloarcula hispanica (Dpm4, also known as Agl23, (

). This protein is involved in both N- and O-glycosylation of S-layer glycoproteins in whole cells, but not in lysates, suggesting a flippase-like or flippase-associated function .
Futalosine hydrolase (FL_hydrolase_MqnB)
Type: Family

This enzyme catalyses the conversion of futalosine to de-hypoxanthine futalosine in a pathway for the biosynthesis of menaquinone distinct from the pathway observed in E. coli .
KH domain protein, archaea (KH_domain_protein_archaea)
Type: Family

This family of proteins is universal among 41 archaeal genomes analysed and is not observed outside of the archaea. The proteins contain a single KH domain, which is likely to confer the ability to bind RNA.
PPOX class F420-dependent enzyme, family Rv2061, putative (PPOX_F420-dep_Rv2061_put)
Type: Family

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN .
F420-dependent enzyme, PPOX class, family Rv3369, probable (F420-dep_enz_PPOX_Rv3369)
Type: Family

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN .
F420-dependent enzyme, PPOX class, family Rv0121, probable (F420-dep_enz_PPOX_Rv0121)
Type: Family

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN .
Urea ABC transporter, substrate-binding protein (Urea_ABC_transptr_substrate-bd)
Type: Family

Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilisation.
DNA-directed RNA polymerase subunit Rpo2 (RNAP_Rpo2)
Type: Family

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 .

This entry represents the archaeal DNA-directed RNA polymerase subunit Rpo2 (previously known as subunit B), it is the homologue of eukaryotic Rpb2 .
Large ribosomal subunit protein uL4, archaea (Ribosomall_uL4-arc)
Type: Family

This entry represents the large ribosomal subunit protein uL4 found in archaea. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Structurally well characterised protein .
Large ribosomal subunit protein uL14, archaeal (Ribosomal_uL14_arc)
Type: Family

This protein is part of the 50S ribosomal subunit. It forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in two inter-subunit bridges .
Large ribosomal subunit protein uL14, conserved site (Ribosomal_uL14_CS)
Type: Conserved_site

This entry represents the large ribosomal subunit protein uL14 (formerly known as L14) from all domains of life. In eubacteria, uL14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins . L14 is a protein of 119 to 137 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 .

This entry represents a conserved region located in the C-terminal half of these proteins.
Flap endonuclease, archaea (Flap_endonuc_arc)
Type: Family

This entry represents an endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment . It has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities and cleaves the junction between single and double-stranded regions of flap DNA.
XPG conserved site (XPG_CS)
Type: Conserved_site

Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms . XPGC cleaves one strand of the duplex at the border with the single-stranded region .

XPG (ERCC-5) belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N-and I-regions are not conserved.

The first pattern,

, corresponds to the central part of the N-region, the second pattern,

, is part of the I-region and includes the putative catalytic core pentapeptide.
Transcription termination factor CPSF1, archaea (aCPSF1)
Type: Family

This entry represents the Factor that terminates transcription in archaea (FttA), also known as archaeal Cleavage and Polyadenylation Specificity Factor 1 (aCPSF1), and similar sequences mainly found in archaea.

FttA is a homologue of eukaryotic CPSF73 (Cleavage and Polyadenylation Specificity Factor 73 kDa subunit) and INTS11 (Integrator Complex Subunit 11) . FttA has been characterised as a ribonuclease essential for transcription termination to ensure programmed transcriptome and optimal growth and physiology. It associates with archaeal RNA polymerase (RNAP) and cleaves the transcript at the 3'-end, downstream of the uridine-rich sequences recognised by its N-terminal KH-domain, a characteristic RNA binding domain . FttA from various archaeal species, including Pyrococcus abyssi and Thermococcus kodakarensis, is included in this family. FttA is a single-stranded endoribonuclease (endoRNase) with a preference for cleavage at CA dinucleotides and 5'-3' exoribonuclease (exoRNase) activity on 5'-monophosphorylated RNA .
Small ribosomal subunit protein uS13, archaeal (Ribosomal_uS13_archaeal)
Type: Family

This entry represents archaeal ribosomal uS13 proteins.

Small ribosomal subunit protein uS13, previously known as Ribosomal protein S13, is one of the proteins from the small ribosomal subunit. In Escherichia coli, it is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a β-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and 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 .
Small ribosomal subunit protein uS17, archaeal (Ribosomal_uS17_archaeal)
Type: Family

This entry represents archaeal ribosomal uS17 proteins.

The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein uS17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence has revealed that uS17 has virtually no groups exposed on the ribosomal surface.
Small ribosomal subunit protein uS13, bacterial-type (Ribosomal_uS13_bac-type)
Type: Family

This entry represents bacterial uS13 and some, but not all instances of chloroplast and mitochondrial uS13 as well.

Small ribosomal subunit protein uS13, previously known as Ribosomal protein S13, is one of the proteins from the small ribosomal subunit. In Escherichia coli, it is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a β-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and 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 .