SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein uL6, bacterial-type (Ribosomal_uL6_bac-type)
Type: Family

Large ribosomal subunit protein uL6 was previously known as L6. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites .

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 uL6, archaea (Ribosomal_uL6_arc)
Type: Family

This protein family represents the archaeal ribosomal protein uL6.

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 .
Endodeoxyribonuclease toxin RalR (Toxin_RalR)
Type: Family

RalR was originally thought to inhibit restriction modification but instead is part of a toxin/antitoxin system and functions as a non-specific DNase . Toxin RalR functions as a non-specific endonuclease that cleaves methylated and unmethylated DNA. The adjacent gene product, RalA (for RalR antitoxin), functions as an antitoxin for RalR.
Haem uptake protein IsdC (Haem_uptake_protein_IsdC)
Type: Family

Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for haem scavenging from hemoproteins . The IsdB protein is only observed in Staphylococcus and consists of an N-terminal hydrophobic signal sequence, a pair of tandem NEAT (NEAr Transporter,

) domains which confers the ability to bind haem and a C-terminal sortase processing signal which targets the protein to the cell wall. IsdB is believed to make a direct contact with methaemoglobin facilitating transfer of haem to IsdB . The haem is then transferred to other cell wall-bound NEAT domain proteins such as IsdA and IsdC.
Luciferase-like, F420-dependent oxidoreductase, MSMEG4879, predicted (Lucif-like_OxRdtase_MSMEG_4879)
Type: Family

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (β/α)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .

Coenzyme F420 is produced by methanogenic archaea, a number of the Actinomycetes (including Mycobacterium tuberculosis), and rare members of other lineages. The resulting information-rich phylogenetic profile identifies candidate F420-dependent oxidoreductases within the family of luciferase-like enzymes, where the species range for the subfamily encompasses many F420-positive genomes without straying beyond.
Alkanesulphonate monooxygenase, FMN-dependent (Alkanesulphonate_mOase_FMN-dep)
Type: Family

This entry represents a distinct group of proteins within the wider luciferase-like family of monooxygenases, including SsuD from E.coli and MsuD from P.fluorescens which are closely related . They catalyse the desulphonation of aliphatic sulfonates in an FMN-dependent fashion . SsuD converts alkanesulfonates to the corresponding aldehyde and sulfite in which it catalyses the C-S bond cleavage of C2-C10 alkyl-substituted sulfonates, in addition to alkyl chains with bulkier chemical groups and larger buffer molecules, whereas MsuD is most active with a C1 sulfonate in the conversion of methanesulfonate to sulfite, completing the sulfur assimilation process during sulfate starvation .
FMN reductase, MsuE-like (FMN_Rdtase_MsuE-like)
Type: Family

This entry represents a protein family that uses NAD(P)H to reduce FMN and regenerate FMNH2. Family members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulphonate monooxygenase.
Pyrimidine utilisation protein RutD (Pyrimidine_utilisation_RutD)
Type: Family

RutD is encoded within the Rut operon which allows growth on pyrimidines as sole nitrogen source . The function of this protein is not known, but it is necessary for growth on pyrimidines, and cells lacking RutD produce much less of the Rut pathway intermediate malonic semialdehyde than normal . It is thought that RutD increases the rate of spontaneous hydrolysis of the toxic intermediate aminoacrylate to malonic semialdehyde.
Pyrimidine monooxygenase RutA (Pyrimidine_monooxygenase_RutA)
Type: Family

Pyrimidine monooxygenase RutA catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid . It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduced to ureidoacrylate .
Transcription regulator, pyrimidine utilisation, RutR (Tscrpt_reg_pyr_util_RutR)
Type: Family

This entry represents a subset of the TetR family of transcriptional regulators. These proteins are encoded in operons responsible for the import and catabolism of pyrimidines, primarily uracil .
Ureidoacrylate amidohydrolase RutB (RutB)
Type: Family

This entry represents the RutB subfamily of isochorismatases, which are peroxyureidoacrylate/ureidoacrylate amidohydrolases. They are encoded in operons responsible for the import and catabolism of pyrimidines, particularly uracil .
FMN reductase (NADH) RutF (RutF)
Type: Family

The Rut pathway allows cells to use pyrimidines as sole nitrogen source. The function of RutF in this pathway is to reduce FMN, producing FMNH2 which is subsequently used by RutA in opening the pyrimidine ring .
Pyrimidine permease RutG, predicted (Pyrimidine_permease_RutG_pred)
Type: Family

This entry represents a set of proteins that are part of the wider uracil-xanthine permease family. They are encoded in operons responsible for the import and catabolism of pyrimidines, primarily uracil, and are predicted to function as pyrimidine permeases .
Luciferase-like, F420-dependent oxidoreductase, MSMEG2256, predicted (Lucif-like_OxRdtase_MSMEG_2256)
Type: Family

F420 is a flavin derivative that functions as a redox coenzyme in methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. A number of luciferase-like protein subfamilies appear only in F420-positive genomes and are likely to be F420-dependent oxidoreductases. This entry represents one such subfamily, exemplified by MSMEG_2256 from Mycobacterium smegmatis.

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (β/α)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .
F420-binding domain, putative (F420-binding_dom_put)
Type: Domain

It has been estimated that just over ten percent of all genome-sequenced prokaryotes, including most actinomycetes, use F420 as a redox coenzyme. This entry represents a set of predicted F420-binding enzymes. The Rv1155 protein from Mycobacterium tuberculosis has been crystallised and its structure shown to broadly resemble that of FMN-binding proteins, though it contains an empty cleft corresponding to, yet differing to the FMN-binding site of pyridoxine 5'-phosphate oxidase .
Luciferase-like, F420-dependent oxidoreductase, Rv2161c, predicted (Lucif-like_OxRdtase_Rv2161c)
Type: Domain

F420 is a flavin derivative that functions as a redox coenzyme in methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. A number of luciferase-like protein subfamilies appear only in F420-positive genomes and are likely to be F420-dependent oxidoreductases. This entry represents one such subfamily found only in F420-positive actinobacteria.

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (β/α)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .
Luciferase-like, F420-dependent oxidoreductase, MSMEG4141, predicted (Lucif-like_OxRdatse_MSMEG_4141)
Type: Family

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (β/α)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .

This entry represents a group of predicted F420-dependent oxidoreductases that are part of the wider luciferase-like family of proteins. Most proteins are in this entry are from actinobacteria, but there are also a small number from the alphaproteobacteria.
Luciferase-like, F420-dependent oxidoreductase, MSMEG2516, predicted (Lucif-like_OxRdtase_MSMEG_2516)
Type: Family

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (β/α)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .

F420 is a flavin derivative that functions as a redox coenzyme in methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. A number of luciferase-like protein subfamilies appear only in F420-positive genomes and are likely to be F420-dependent oxidoreductases. This entry represents one such subfamily, exemplified by MSMEG_2516 from Mycobacterium smegmatis.
ABC transporter, urea permease protein UrtB, archaeal (ABC_UrtB_arc)
Type: Family

This entry represents a small group of ABC transporter permease subunits found in archaea. Several lines of evidence suggest they are functionally analogous, as well as homologous, to the UrtB subunit of the Corynebacterium glutamicum urea transporter. All members of the operons in which they are encoded show sequence similarity to urea transport subunits, their genes are located near the urease structural subunits in two out of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilization.
DNA repair protein, predicted (DNA_repair_protein_predicted)
Type: Family

This entry represents a family of bacterial proteins which are about 900 amino acids in length. They are homologous to the AddB protein (

), which repairs double-strand DNA breaks via homologous recombination, and are predicted to function in DNA repair.
Large ribosomal subunit protein uL3, conserved site (Ribosomal_uL3_CS)
Type: Conserved_site

This entry represents a short conserved region located in the central section of ribosomal uL3 proteins.

Ribosomal protein L3 (also known as uL3) is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui HmaL3 (HL1), and yeast mitochondrial YmL9 .

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 uL3, bacterial/organelle-type (Ribosomal_uL3_bac/org-type)
Type: Family

This entry represents bacterial, mitochondrial and chloroplast uL3 proteins. The organelle proteins typically contain a transit peptide sequence located N-terminal to the region covered by this entry.

Ribosomal protein L3 (also known as uL3) is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui HmaL3 (HL1), and yeast mitochondrial YmL9 .

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 .