SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein eL18, archaea (Ribosomal_eL18_arc)
Type: Family

This entry represents the large ribosomal subunit protein eL18 from the 50S ribosomal subunit of 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 .
Chitooligosaccharide deacetylase ChbG-like, bacteria (COD_ChbG_bac)
Type: Family

This entry represents chitooligosaccharide deacetylase ChbG (YdjC)-like proteins found in bacteria, including carbohydrate deacetylases from Firmicutes and chitooligosaccharide deacetylases from Enterobacteriaceae . ChbG is involved in the degradation of chitin.
Homogentisate 1,2-dioxygenase, bacterial (Homogentis_dOase_bac)
Type: Family

This entry represents bacterial homogentisate 1,2-dioxygenase

. This enzyme mediates the conversion of homogentisate to maleylacetoacetate; a step in the catabolism of both tyrosine and phenylalanine.
Uncharacterised protein family UPF0309 (UPF0309)
Type: Family

The proteins in this entry are functionally uncharacterised, but the majority contain a sugar isomerase (SIS) domain, which is a phosphosugar-binding module found in proteins that have a role in phosphosugar isomerisation or regulation.
Archease, archaea (Archease_arc)
Type: Family

The archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore have been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally.

The function of one of the archeases from the hyperthermophile Pyrococcus abyssi has been determined. The gene encoding the archease (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which encodes a tRNA m5C methyltransferase. The methyl transferase catalyses m5C formation at several cytosine's within tRNAs with preference for C49; the specificity of the methyltransferase reaction being increased by the archease. The archease protects the tRNA (cytosine-5-)-methyltransferase PAB1947 against aggregation and increases its specificity. The archease exists in monomeric and oligomeric states, with only the oligomeric forms able to bind the methyltransferase .

The function of this family of archeases as chaperones is supported by structural analysis of

from Methanobacterium thermoautotrophicum, which shows homology to heat shock protein 33, which is a chaperone protein that inhibits the aggregation of partially denatured proteins .

This entry represents the archaeal form of archeases.
ATP-dependent 6-phosphofructokinase (ATP_PFK)
Type: Family

The enzyme-catalysed transfer of a phosphoryl group from ATP is an important reaction in a wide variety of biological processes . One enzyme that utilises this reaction is phosphofructokinase (PFK), which catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate, a key regulatory step in the glycolytic pathway . PFK exists as a homotetramer in bacteria and mammals (where each monomer possesses 2 similar domains), and as an octomer in yeast (where there are 4 alpha- (PFK1) and 4 beta-chains (PFK2), the latter, like the mammalian monomers, possessing 2 similar domains ). PFK is ~300 amino acids in length, and structural studies of the bacterial enzyme have shown it comprises two similar (α/β) lobes: one involved in ATP binding and the other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme activity). The identical tetramer subunits adopt 2 different conformations: in a 'closed' state, the bound magnesium ion bridges the phosphoryl groups of the enzyme products (ADP and fructose-1,6-bisphosphate); and in an 'open' state, the magnesium ion binds only the ADP , as the 2 products are now further apart. These conformations are thought to be successive stages of a reaction pathway that requires subunit closure to bring the 2 molecules sufficiently close to react .

Deficiency in PFK leads to glycogenosis type VII (Tarui's disease), an autosomal recessive disorder characterised by severe nausea, vomiting, muscle cramps and myoglobinuria in response to bursts of intense or vigorous exercise . Sufferers are usually able to lead a reasonably ordinary life by learning to adjust activity levels .
Uncharacterised protein family UPF0148 (UPF0148)
Type: Family

The proteins in this entry are functionally uncharacterised. However, they show protein sequence similarity with Sjoegren syndrome/scleroderma autoantigen 1 protein (

).
GMP synthase (GMP_synthase)
Type: Family

GMP synthase or glutamine amidotransferase

catalyzes the synthesis of GMP from xantosine monophosphate.
Beta-hexosaminidase, bacterial (Beta_hexosaminidase_bac)
Type: Family

This entry represents bacterial beta-hexosaminidases

that are involved in cell wall biogenesis and peptidoglycan recycling .
Uncharacterised protein family UPF0299 (Uncharacterised_UPF0299)
Type: Family

This family, UPF0299, is represented by YohJ, an inner membrane protein with four predicted transmembrane domains; the C terminus is located in the periplasm . The proteins in this entry are functionally uncharacterised.
Uncharacterised protein family UPF0294 (UPF0294)
Type: Family

The proteins in this entry are functionally uncharacterised, but contain a single endonuclease/exonuclease/phosphatase domain. The family is represented by YafD, which has been reported to be similar to YadD, YjiP, YjiQ and YhgA, , though these are not found in this entry.
Soluble pyridine nucleotide transhydrogenase, gammaproteobacteria (STH_gammaproteobact)
Type: Family

This entry represents soluble pyridine nucleotide transhydrogenases

mainly found in gammaproteobacteria. Its physiological role is the conversion of NADPH generated by peripheral catabolic pathways to NADH, which can be oxidized for energy generation, maintaining the homeostasis of these two redox cofactors .
Galactokinase, bacterial (Galactokinase_bac)
Type: Family

Galactokinase catalyses the first reaction in the galactose metabolism pathway, the ATP-dependent phosphorylation of galactose, yielding galactose-1-phosphate . Deficiency in this enzyme results in the disease galactosemia, which is responsible for the formation of cataracts in newborn babies, and is possibly responsible for presenile cataracts in adults . In yeast, the GAL3 gene product is required for the GAL4-mediated induction of other enzymes involved in galactose metabolism. The induction of GAL1 production then reinforces this process, increasing the expression of other galactose-inducible genes. GAL3 has been shown to be similar to the GAL1 protein .

This entry represents bacterial-type galactokinases.
Translation initiation factor 2, alpha subunit, archaeal (TIF2_asu_arc)
Type: Family

Archaeal transcription initiation factor 2 is, like its eukaryotic homologue, a heterotrimeric protein with alpha, beta and gamma subunits . It is thought play an essential role in the recognition of the correct codon for the start of translation, similar to the role of eukaryotic transcription initiation factor. The eukaryotic factor forms a ternary complex with the methionine initiator tRNA and GTP, which binds to the 40S ribosomal subunit as part of the 43S preinitiation complex . The beta and gamma subunits are responsible for recruiting the initiator tRNA and GTP, while the alpha subunit is involved in the regulation of the translation initiation process. The beta subunit has also been shown to interact with other transcription factors. All three subunits of the archaeal and eukaryotic factors are well conserved among the diverse species of eukaryotes and archaea, but do not occur in prokaryotes.

This entry represents the archaeal subunit alpha.
ATP-dependent DNA helicase Hel308 (Helicase_Hel308)
Type: Family

This entry represents ATP-dependent DNA helicase Hel308 from Archaea. It is thought to be implicated in remodelling compromised replication forks .
Ribonuclease II/R, conserved site (RNase_II/R_CS)
Type: Conserved_site

This entry represents a conserved site for the ribonuclease II family. Proteins with this signature include characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II .
16S/18S rRNA aminocarboxypropyltransferase Tsr3 (Tsr3-like)
Type: Family

This entry represents18S rRNA aminocarboxypropyltransferases Tsr3 and its homologues. Tsr3 from fungi and animals are responsible for 18S rRNA hypermodification. It introduces the acp group to the hypermodified m1acp3psi nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA. The crystal structure of archaeal Tsr3 homologues revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes .
Chloride channel YfeO (Chloride_channel_YfeO)
Type: Family

Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport . Some members are plasma membrane Cl channels, while others are Cl/H exchangers .

The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata , and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl-channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl-channels is that some of the isoforms may function as Cl-channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains . Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N-and C-termini residing in the cytoplasm .

A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl-channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia . Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl-channel, lead to several forms of inherited kidney stone disease . These mutations have been demonstrated to reduce or abolish CLC function.

This entry represents chloride channel proteins found in bacteria.
Nucleoside triphosphate hydrolase-related (NTP_hydrolase-rel)
Type: Family

The proteins in this entry are functionally uncharacterised, but belong to the P-loop containing nucleoside triphosphate hydrolases superfamily. Sequence analysis suggests that they may be archaeal dephospho-CoA kinase homologues.
5'-deoxynucleotidase YfbR (YfbR)
Type: Family

This entry contains Escherichia coli (strain K12) YfbR. It is a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant . YfbR contains a conserved HD domain . YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates . Nucleotidase activity of YfbR was discovered in a high-throughput screen of purified proteins . Crystal structures of YfbR have been solved; based on an analysis of crystal packing and size-exclusion chromatography, it was suggested that the biological unit is a dimer. Site-directed mutagenesis confirmed the importance of certain conserved active site residues, and mechanisms for substrate selectivity and catalysis were proposed .

This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab 15497 , which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity, and catalyse the hydrolysis of 2'-deoxyadenine 5'-triphosphate (dATP) to 2'-deoxyadenine (dA) and triphosphate, with the highest activity using Co2+ as the divalent metal cofactor. These enzymes are highly specific for dATP and also catalyse the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host .
Uncharacterised protein family UPF0292 (UPF0292)
Type: Family

The proteins in this entry are functionally uncharacterised.
Large ribosomal subunit protein uL10, bacterial (Ribosomal_uL10_bac)
Type: Family

This entry represents the large ribosomal subunit protein uL10 family found mainly in bacteria and in plant chloroplast.

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 .
Pyrimidine-specific ribonucleoside hydrolase RihA (Pyrim_hydro_RihA)
Type: Family

The rihA gene encodes a ribonucleoside hydrolase that preferentially utilises cytidine and uridine . The k
cat
/K
M
for uridine is approximately 10 times higher than for cytidine, largely due to a lower K
M
value for uridine . There are two other nucleoside hydrolases with differing specificities encoded by the rihB and rihC genes .An rihA null mutant can not use cytidine as a source of pyrimidine and the rihA and rihC genes are subject to catabolite repression .

A crystal structure of RihA bound to the reaction product D-ribose has been solved at 1.8A resolution .
Non-specific ribonucleoside hydrolase RihC (Nucleosid_hydro_RihC_nonspecif)
Type: Family

This entry represents the RihC proteins, which are ribonucleoside hydrolases with a broad substrate specificity. RihC has decreasing activity in the order uridine >xanthosine >inosine >adenosine >cytidine >guanosine . There are two other ribonucleoside hydrolases present in Escherichia coli encoded by the rihA and rihB genes, which have different specificities .
Pyrimidine-specific ribonucleoside hydrolase RihB (Pyrim_hydro_RihB)
Type: Family

This entry represents the RihB ribonucleoside hydrolases, which are homologous to the RihA and RihC hydrolases. RihB hydrolyses cytidine and uridine to ribose and cytosine or uracil respectively; however in contrast to RihA, RihB displays a preference for cytidine .
Monofunctional glycosyl transferase (Monofunct_glyco_trans)
Type: Family

Proteins in this family are thought to be involved in cell wall peptidoglycan biosynthesis. In particular they are thought to be responsible for the elongation of the glycan strands using lipid-linked disaccharide-pentapeptide as the substrate .
Photosystem I, reaction centre subunit XI (PSI_suXI)
Type: Family

The trimeric photosystem I of the cyanobacterium Synechococcus elongatus recomprises 11 protein subunits. Subunit XI, PsaL, from plants and bacteria is one of the smaller subunits with only two transmembrane α helices. PsaL interacts closely with PsaI .
Large ribosomal subunit protein uL16, archaea (Ribosomal_uL16_arc)
Type: Family

This family consists of archaeal large ribosomal subunit protein uL16 (L10).

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 .
DNA double-strand break repair Rad50 ATPase, archaeal type (Rad50_ATPase_archaeal)
Type: Family

Rad50 is involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity. Rad50 provides an ATP-dependent control of Mre11 by unwinding and/or repositioning DNA ends into the Mre11 active site . This entry represents Rad50 from archaea and some bacteria.
M18 family aminopeptidase 1, putative (M18_aminopeptidase_1)
Type: Family

This group of metallopeptidases belong to the MEROPS peptidase family M18, (clan MH). The proteins have two catalytic zinc ions at the active site, bound by His/Asp, Asp, Glu, Asp/Glu and His. The catalysed reaction involves the release of an N-terminal aminoacid, usually neutral or hydrophobic, from a polypeptide .

This entry represents aminopeptidase 1 from bacteria.
M18 family aminopeptidase 2, putative (M18_aminopeptidase_2)
Type: Family

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation, which is usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophilic role.

Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .

This group of metallopeptidases belong to the MEROPS peptidase family M18, (clan MH). The proteins have two catalytic zinc ions at the active site, bound by His/Asp, Asp, Glu, Asp/Glu and His. The catalysed reaction involves the release of an N-terminal aminoacid, usually neutral or hydrophobic, from a polypeptide .

This entry represents aminopeptidase 2 from bacteria.