SII-SWORD/CoKE huggingface dataset:
Multidrug resistance protein MdtB (Multidrug-R_MdtB)
Type: Family

This entry represents the multidrug resistance protein MdtB. MdtA is one subunit of the MdtABC tripartate complex which is a RND-type drug exporter. The complex consists of MdtB/C, which form a transmembrane heteromultimer and MdtA which is a membrane fusion protein .
Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF (Flippase_ArnF)
Type: Family

This entry represents ArnF, which is a an integral membrane component of the ArnE/ArnF (heterodimer) undecaprenyl-phosphate-alpha-L-Ara4N flippase. This flippase translocates 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol (alpha-L-Ara4N-phosphoundecaprenol) from the cytoplasmic to the periplasmic side of the inner membrane during lipopolysaccharide biosynthesis .

ArnE and ArnF are membrane proteins with 4 transmembrane helices and belong to the drug/metabolite transporter (DMT) superfamily . Deletion of arnE or arnF results in restoration of polymyxin sensitivity in a polymyxin-resitant pmrAc strain and are defective for transfer of undecaprenyl-phosphate-alpha-L-Ara4N from the cytoplasmic face of the inner membrane to the periplasmic face and for attachment of L-Ara4N to lipid A. Both ArnE and ArnF are required for polymyxin resistance as expression from a plasmid of one cannot replace a deletion of the other .
Uncharacterised protein family UPF0757, YmgG (UPF0757_YmgG)
Type: Family

This entry contains proteins of unknown function, which include YmgG from Escherichia coli.
8-amino-7-oxononanoate synthase, Proteobacteria (AONS_Proteobacteria)
Type: Family

8-amino-7-oxononanoate synthase (AONS) is a pyridoxal 5'-phosphate-dependent enzyme, which catalyses the decarboxylative condensation of L-alanine with pimeloyl-CoA to form 8(S)-amino-7-oxononanoate. This is the first committed step in biotin biosynthesis :
6-carboxyhexanoyl-CoA + L-alanine = 8-amino-7-oxononanoate + CoA + CO2

The enzyme is a symmetrical homodimer with a tertiary structure and active site organisation similar to, but distinct from, those of other PLP-dependent enzymes with known structures. AONS is a critical PLP-binding lysine at the end of a deep cleft that allows access to the pantothenate arm of pimeloyl-CoA. There is a cluster of positively charged residues at the entrance to this cleft, which forms a putative diphosphate binding site for CoA . Trifluoroalanine irreversibly inhibits this enzyme .

This entry represents 8-amino-7-oxononanoate synthases from Proteobacteria.
Chaperone modulatory protein CbpM (CbpM)
Type: Family

This entry represents Chaperone modulatory protein CbpM from Escherichia coli and similar proteins from Gammaproteobacteria. CbpM (named after "CbpA modulator", ) interacts with the N-terminal J-domain of CbpA, forms a stable complex and specifically inhibits its activity . Together with CbpA, it modulates the activity of the DnaK chaperone system . It does not inhibit the co-chaperone activity of DnaJ. The crystal structure of CbpM shows similarity to members of the MerR family of transcriptional regulators .
Protein-methionine-sulfoxide reductase subunit MsrQ-like (MsrQ-like)
Type: Family

MsrPQ is an enzymatic system that repairs proteins containing methionine sulfoxide in the bacterial cell envelope. MsrP, a molybdo-enzyme, and MsrQ, a haem-binding membrane protein, are widely conserved throughout Gram-negative bacteria. MsrPQ uses electrons from the respiratory chain, which represents a novel mechanism to import reducing equivalents into the bacterial cell envelope. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing periplasmic proteins from methionine oxidation, including the primary periplasmic chaperone SurA .

This family represents MsrQ.

This family also includes magnetosome protein MamZ, which despite its similarity of sequence to MsrQ, has been shown not to genetically interact with MsrP. Rather it has been proposed to be involved in balancing the redox state of iron within the magnetosome compartment .
GTP cyclohydrolase FolE2 (GTP_cyclohydrolase_FolE2)
Type: Family

This entry contains proteins belonging to the GTP cyclohydrolase IV family. GTP cyclohydrolase FolE2 converts GTP to 7,8-dihydroneopterin triphosphate .
ArnT (ArnT)
Type: Family

This entry represents the bacterial undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferases. This family of proteins are a subset of the glycosyltransferase 39 family and are responsible for the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides .
GTP cyclohydrolase MptA (GTP_cyclohydrolase_MptA)
Type: Family

This entry represents GTP cyclohydrolases belonging to family IV.

In archaea, GTP cyclohydrolase MptA converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate, the first intermediate in the biosynthesis of coenzyme methanopterin .
5-dehydro-2-deoxygluconokinase, Firmicutes (DKG_kinase_firmi)
Type: Family

Bacterial 5-dehydro-2-deoxygluconokinase is responsible for catalysing the phosphorylation of 5-dehydro-2-deoxy-D-gluconate (2-deoxy-5-keto-D-gluconate or DKG) to 6-phospho-5-dehydro-2-deoxy-D-gluconate (DKGP), the fifth step in the inositol catabolic pathway . This entry consists of Gram-positive (Firmicutes) enzymes.
DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 (RNAP_Rpo3/Rpb3/RPAC1)
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 includes the Rpo3 subunit (also known as subunit D) from archaeal RNAP, Rpb3 subunit from eukaryotic RNAPII and RPAC1 (also known as AC40) subunit from RNAPI/III . These subunits are involved in the assembly of RNAPs.
Formamidase (Formamidase)
Type: Family

This entry represents formamidase. Formamidase is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide .
Glycogen debranching enzyme, bacterial (Glycogen_debranch_bac)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This entry represents the glycogen debranching enzyme GlgX found in Escherichia coli, as well as its equivalogs in other prokaryotic species. This enzyme encodes an isoamylase-type debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues, and is classed as family 13 of glycosyl hydrolases . GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This entry distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages .

This entry only includes proteins predominantly from the Enterobacteriaceae family.
Small ribosomal subunit protein eS31, archaea (Ribosomal_eS31_arc)
Type: Family

This entry represents the archaeal Small ribosomal subunit protein eS31 (S27ae), which is a component of the 30S 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 .
Xaa-Pro dipeptidase (X_Pro_dipept)
Type: Family

This entry represents Xaa-Pro dipeptidase, also known as proline dipeptidase. This enzyme splits dipeptides with a prolyl residue in the C-terminal position.
Translation elongation factor IF5A, archaeal (Transl_elong_IF5A_arc)
Type: Family

Eukaryotic eIF-5A was initially thought to function as a translation initiation factor, based on its ability to stimulate methionyl-puromycin synthesis. However, subsequent work revealed a role for eIF5A in translation elongation . Depletion or inactivation of eIF-5A in the yeast Saccharomyces cerevisiae (Baker's yeast) resulted in the accumulation of polysomes and an increase in ribosomal transit times. Addition of recombinant eIF-5A from yeast, but not a derivative lacking hypusine, enhanced the rate of tripeptide synthesis in vitro. Moreover, inactivation of eIF-5A mimicked the effects of the eEF2 inhibitor sordarin, indicating that eIF-5A might function together with eEF2 to promote ribosomal translocation. Finally, it was shown that eIF5A is specifically required to promote peptide-bond formation between consecutive proline residues. It has been proposed to stimulate the peptidyl-transferase activity of the ribosome and facilitate the reactivity of poor substrates like proline .

eIF-5A is a cofactor for the Rev and Rex transactivator proteins of human immunodeficiency virus-1 and T-cell leukaemia virus I, respectively . IF-5A is the sole protein in eukaryotes and archaea to contain the unusual amino acid hypusine (Ne-(4-amino-2-hydroxybutyl)lysine) that is an absolute functional requirement. The first step in the post-translational modification of lysine to hypusine is catalyzed by the enzyme deoxyhypusine synthase, the structure of which has been reported .

This entry represents the archaeal IF-5A proteins.
Small heat shock protein IbpB (HSP20_IbpB)
Type: Family

This entry represents IbpB, which belongs to the small heat shock protein (HSP20) family. IbpB associates with aggregated proteins, together with IbpA, to stabilise and protect them from irreversible denaturation and extensive proteolysis during heat shock and oxidative stress. Aggregated proteins bound to the IbpAB complex are more efficiently refolded and reactivated by the ATP-dependent chaperone systems ClpB and DnaK/DnaJ/GrpE. Its activity is ATP-independent.
Peptidase S12, YfeW/YbbE-like (Pept_S12_YfeW/YbbE-like)
Type: Family

This entry represents unassigned peptidases that belong to MEROPS peptidase family S12 (D-Ala-D-Ala carboxypeptidase B family, clan SE).

Proteins in this entry include Bacillus subtilis YbbE, also known as AmiE, an amidase that hydrolyzes the N-acetylmuramyl-L-Ala bond of MurNAc peptides . This entry also includes YfeW (also known as pbp4B) from E. coli. YfeW has penicillin-binding capacity and a low DD-carboxypeptidase activity .
UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB (ArnB_NH2Trfase)
Type: Family

This entry represents ArnB, which catalyzes the conversion of UDP-4-keto-arabinose (UDP-Ara4O) to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides.
Translation factor SUI1 homolog, archaea (SUI1_arc)
Type: Family

This entry represents protein translation factor SUI1 homolog, involved in translation regulation.
Carnitinyl-CoA dehydratase (Carnitinyl_CoA_dehydratase)
Type: Family

The CaiD protein is a carnitinyl-CoA dehydratase enzyme which, together with carnitine-CoA transferase enzyme CaiB, is responsible for the transfomation of L-carnitine to crotonobetaine .

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.
Flotillin-like protein FloA (FloA)
Type: Family

This entry represents flotillin-like protein FloA from bacteria.

Bacterial flotillin-like proteins are found in membrane microdomains that may be equivalent to eukaryotic membrane rafts . Similarly to eukaryotic flotillin proteins, flotillins in bacteria play an essential role in organizing and maintaining the correct architecture of the functional membrane microdomains . Bacillus subtilis has two flotillin paralogs, FloT and FloA. The absence of one of the flotillins has only minor effects, but the absence of both proteins has very severe effects: loss of proper cell shape, a defect in cell division .
Transcriptional regulator GfcR (GfcR-like)
Type: Family

This entry represents Transcriptional regulator GfcR and related proteins from archaea. They share protein sequence similarity to the PyrE protein (Orotate phosphoribosyltransferase) from Salmonella typhimurium .

GfcR is a DNA-binding transcriptional regulator that functions as a regulator of central sugar catabolic pathways. It acts by binding directly to the promoter region of the regulated genes. In the presence of D-glucose, activates expression of the gene encoding the gluconate dehydratase (gad), which is involved in D-glucose catabolism while In the presence of D-fructose, activates expression of the genes encoding the PTS system EIIC component (ptfC) and the fructose-1,6-bisphosphate aldolase (fba), which are involved in D-fructose uptake and degradation
Multidrug resistance protein MdtH (Multidrug-R_MdtH)
Type: Family

Multidrug resistance protein MdtH confers resistance to norfloxacin and enoxacin .
Large ribosomal subunit protein eL21, archaeal (Ribosomal_eL21_arc)
Type: Family

This entry represents the archaeal 50S ribosomal eL21 family of proteins.

The eL21 family contains proteins from a number of eukaryotic and archaebacterial organisms which include mammalian eL21, Entamoeba histolytica eL21, Caenorhabditis elegans eL21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) eL21 (URP1) and Haloarcula marismortui eL21 (HL31).

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 .
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (ArnC_tfrase)
Type: Family

This entry represents the bacterial undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase family. This enzymes catalyse the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides .
Metallothiol transferase FosB (Metallothiol_Trafse_FosB)
Type: Family

FosB is a metallothiol transferase which confers resistance to the antiobiotic fosfomycin by catalyzing the addition of a thiol cofactor to fosfomycin . L-cysteine is thought to be the physiological thiol donor.
Alginate lyase (Alginate_lyase)
Type: Family

This entry represents alginate lyase or poly (beta-D-mannuronate) lyase. It depolymerises alginate by cleaving the beta-1,4 glycosidic bond.

Alginate is a family of 1-4-linked copolymers of beta-D-mannuronic acid (M) and alpha-L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyse the depolymerisation of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end . Two subfamilies of alginate lyase exist: the poly(beta-D-mannuronate) lyase,

, and the poly(alpha-L-guluronate) lyase,

.
Glutamine-tRNA ligase, bacterial (Gln_tRNA_ligase_bac)
Type: Family

This entry represents bacterial glutamine-tRNA ligases.

Glutamine-tRNA ligase (

) is a class Ic aminoacyl-tRNA ligase and shows several similarities with glutamine-tRNA ligase concerning structure and catalytic properties. It is an alpha2 dimer.
Glutamine-tRNA ligase is a relatively rare ligase, found in the cytosolic compartment of eukaryotes, in Escherichia coli and a number of other Gram-negative bacteria, and in Deinococcus radiodurans. In contrast, the pathway to Gln-tRNA in mitochondria, Archaea, Gram-positive bacteria, and a number of other lineages is by misacylation with Glu followed by transamidation to correct the aminoacylation to Gln.

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 .
Ribosomal protein uS12, archaea (Ribosomal_uS12_arc)
Type: Family

This entry represents archaeal 30S subunit ribosomal protein uS12. With S4 and S5, uS12 plays an important role in translational accuracy. It is located at the interface of the 30S and 50S subunits.

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 .