SII-SWORD/CoKE huggingface dataset:
Sulfate transporter CysZ (Sulfate_CysZ)
Type: Family

CysZ is a high affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake .
Uncharacterised protein family UPF0237, ACT-type (UPF0237_ACT)
Type: Family

The proteins in this entry are functionally uncharacterised. They contain an ACT domain; ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold .
Uncharacterised protein family UPF0227 (UPF0227)
Type: Family

The proteins in this entry, which include the Escherichia coli (strain K12) protein YcfP, are functionally uncharacterised.
Nickel-responsive transcriptional regulator NikR (Ni_resp_reg_NikR)
Type: Family

NikR is the transcriptional repressor of the nickel-specific transport system nikABCDE. NikR is a protein of the ribbon-helix-helix family of transcription factors and is active in the presence of excessive concentrations of intracellular nickel .
Ribosome rescue factor SmrB (SmrB-like)
Type: Family

This entry represents the Ribosome rescue factor SmrB from Escherichia coli and related proteins mainly from gammaproteobacteria. SmrB acts as a ribosome collision sensor . It detects stalled/collided disomes (pairs of ribosomes where the leading ribosome is stalled and a second ribosome has collided with it) and cleaves mRNA at the 5' end of the stalled ribosome. The cleaved mRNA becomes available for tmRNA ligation, leading to ribosomal subunit dissociation and rescue of stalled ribosomes .
Large ribosomal subunit protein eL30, conserved site (Ribosomal_eL30_CS)
Type: Conserved_site

A number of eukaryotic, bacterial and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. This entry represents two conserved sites found in large ribosomal subunit protein eL30 family of proteins, which consists of:

Mammalian eL30 .

Leishmania major L30.

Yeast eL30 (also known as L32) .

Thermococcus celer eL30 .

eL30 from Methanococcus vannielii .

eL30 from Sulfolobus acidocaldarius .

These proteins have 82 to 114 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 .
Uncharacterised protein family UPF0213, GIY-YIG endonuclease (UPF0213_GIY-YIG_endonuc)
Type: Family

The proteins in this entry are functionally uncharacterised but belong to the GIY-YIG endonuclease superfamily.
Uncharacterised protein family UPF0310 (UPF0310)
Type: Family

The proteins in this entry are functionally uncharacterised.
NADH-quinone oxidoreductase chain 4 (NADH_Q_OxRdtase_chain4)
Type: Family

This entry represents the chain 4 of NAD(P)H-quinone oxidoreductase from plants and cyanobacteria.
Thiamine phosphate synthase/TenI (ThiamineP_synth_TenI)
Type: Domain

Thiamine phosphate synthase (TPS) catalyses the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway .

TenI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group . While TenI shows high sequence similarity with thiamin phosphate synthase , the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase .

This entry refers to a domain found in thiamine phosphate synthase, thiazole tautomerase and similar proteins.
Transaldolase type 3B, putative (Transaldolase_3B)
Type: Family

Transaldolase (

) catalyses the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34kDa whose sequence has been well conserved throughout evolution. A lysine has been implicated in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate.

This entry represents the transaldolase type 3B family.
Shikimate kinase, conserved site (Shikimate_kinase_CS)
Type: Conserved_site

This entry represents shikimate kinase (

) catalyzes the fifth step in the biosynthesis from chorismate of the aromatic amino acids (the shikimate pathway) in bacteria (gene aroK or aroL), plants and in fungi (where it is part of a multifunctional enzyme which catalyzes five consecutive steps in this pathway). Shikimate kinase is a small protein of about 200 residues. Proteins belonging to this family also contain a copy of the ATP/GTP- binding motif 'A' (P-loop).

The signature pattern used in this entry covers a conserved region that contains a run of three glycines.
Fructose-6-phosphate aldolase (F6P_aldolase)
Type: Family

Fructose-6-phosphate aldolases were originally thought to be transaldolases or transaldolase-related proteins. Instead, they perform a novel reaction, the cleavage or formation of fructose 6-phosphate . They belong to the class I aldolase family.
Glycerol-1-phosphate dehydrogenase, archaea (G1P_dehydrogenase_arc)
Type: Family

This entry represents archaeal glycerol-1-phosphate dehydrogenase

. Glycerol-1-phosphate dehydrogenase is responsible for the formation of the archaeal-specific glycerophosphate backbone of phospholipids, G-1-P, from glycerone phosphate , using either NADH or NADPH as a coenzyme , and is primarily Zn
2+
-dependent in archaea . This is the key step in the in biosynthesis of archaeal enantiomeric phospholipids . One characteristic feature of archaea is that their cellular membrane has an ether linkage between the glycerol backbone and the hydrocarbon residues. The polar lipids of the members of Archaea consist of di- and tetraethers of glycerol with isoprenoid alcohols bound at the sn-2 and sn-3 positions of the glycerol moiety. The archaeal polar lipids have the enantiomeric configuration of a glycerophosphate backbone [sn- glycerol-1-phosphate (G-1-P)]. that is the mirror image structure of the bacterial or eukaryal counterpart [sn-glycerol- 3-phosphate (G-3-P)]. The absolute stereochemistry of the glycerol moiety in all archaeal polar lipids is opposite to that of glycerol ester lipids in bacteria and eukarya. This protein family is only found in Archaea .
Glycerol-1-phosphate dehydrogenase, bacteria (G1P_dehydrogenase_bac)
Type: Family

Glycerol-1-phosphate dehydrogenase is found primarily as a Zn
2+
-dependent form in archaea (see

); however a Ni
2+
-dependent form has been found in Gram-positive bacteria .
Nucleoside diphosphate kinase, active site (Nucleoside_diP_kinase_AS)
Type: Active_site

The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism . This entry covers the active site histidine.

Nucleoside diphosphate kinases (

) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation. In eukaryotes, there seems to be a small family of NDK isozymes each of which acts in a different subcellular compartment and/or has a distinct biological function. Eukaryotic NDK isozymes are hexamers of two highly related chains (A and B) . By random association (A6, A5B...AB5, B6), these two kinds of chain form isoenzymes differing in their isoelectric point. NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP. NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23.
YchJ-like (YchJ-like)
Type: Family

This entry represents UPF0225 protein YchJ and structurally related uncharacterised proteins from bacteria. These proteins contain a middle domain represented by

.
Uncharacterised protein family UPF0232, actinobacteria (UPF0232_actinobac)
Type: Family

The proteins in this entry are functionally uncharacterised.
Uncharacterized MFS-type transporter YhhS-like (MFS_YhhS-like)
Type: Family

This is a family of uncharacterised bacterial transporters that includes YhhS .
Tyrosine recombinase XerC/XerD (Tyrosine_recombinase_XerC/XerD)
Type: Family

This entry represents a site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. XerD binds cooperatively to specific DNA consensus sequences that are separated from XerC binding sites by a short central region, forming the heterotetrameric XerC-XerD complex that recombines DNA substrates. The complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids . XerD forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD, in which XerC interacts with XerD via its C-terminal region, XerD interacts with XerC via its C-terminal region and so on .
Probable glycine dehydrogenase (decarboxylating) subunit 1 (GcvPA)
Type: Family

The subunit composition of glycine cleavage system P-proteins have been classified into two types. Those from eukaryotes and some of the P-proteins from prokaryotes (e.g. Escherichia coli) are in the homodimeric form. The rest of those from prokaryotes are heterotetrameric, with two different subunits which, based on sequence similarities, correspond respectively to the N and C-terminal halves of the eukariotic-subunit .

This entry represents the probable glycine dehydrogenase (decarboxylating) subunit 1 from prokaryotes.
ATP synthase, F0 complex, subunit A, active site (ATP_synth_F0_asu_AS)
Type: Active_site

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents the active site of subunit A (or subunit 6) found in the F0 complex of F-ATPases. This subunit is a key component of the proton channel, and may play a direct role in the translocation of protons across the membrane. Catalysis in the F1 complex depends upon the rotation of the central stalk and F0 c-ring, which in turn is driven by the flux of protons through the membrane via the interface between the F0 c-ring and subunit A. The peripheral stalk links subunit A to the external surface of the F1 domain, and is thought to act as a stator to counter the tendency of subunit A and the F1 α(3)β(3) catalytic portion to rotate with the central rotary element
.

Sequence comparison of a subunits from all available sources reveals very few conserved regions. The best conserved region is located in what is predicted to be the fifth transmembrane domain. This region contains three perfectly conserved residues: an arginine, a leucine and an asparagine. Mutagenesis experiments carried out in Escherichia coli have shown that the arginine is necessary for proton translocation and that its replacement by another amino acid results in loss of ATPase activity. The signature pattern of this entry contains the arginine residue.
Probable glycine dehydrogenase (decarboxylating) subunit 2 (GcvPB)
Type: Family

The P protein, also known as Glycine dehydrogenase (decarboxylating), is part of the glycine decarboxylase multienzyme complex (GDC), also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T . The P protein (

) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. The reaction catalysed by this protein is:

Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2

The subunit composition of glycine cleavage system P proteins have been classified into two types. Those from eukaryotes and some of the P proteins from prokaryotes (e.g. Escherichia coli) are in the homodimeric form. The rest of those from prokaryotes are heterotetrameric, with two different subunits which, based on sequence similarities, correspond respectively to the N and C-terminal halves of the eukaryotic subunit .

This entry represents the probable glycine dehydrogenase (decarboxylating) subunit 2 from prokaryotes.
N-acetyl-gamma-glutamyl-phosphate reductase, active site (AGPR_AS)
Type: Active_site

N -Acetylglutamate (NAG) fulfils distinct biological roles in lower and higher organisms. In prokaryotes, lower eukaryotes and plants it is the first intermediate in the biosynthesis of arginine, whereas in ureotelic (excreting nitrogen mostly in the form of urea) vertebrates, it is an essential allosteric cofactor for carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle. The pathway that leads from glutamate to arginine in lower organisms employs eight steps, starting with the acetylation of glutamate to form NAG. In these species, NAG can be produced by two enzymatic reactions: one catalysed by NAG synthase (NAGS) and the other by ornithine acetyltransferase (OAT). In ureotelic species, NAG is produced exclusively by NAGS. In lower organisms, NAGS is feedback-inhibited by L-arginine, whereas mammalian NAGS activity is significantly enhanced by this amino acid. The NAGS genes of bacteria, fungi and mammals are more diverse than other arginine-biosynthesis and urea-cycle genes. The evolutionary relationship between the distinctly different roles of NAG and its metabolism in lower and higher organisms remains to be determined .

The pathway from glutamate to arginine is:

NAGS; N-acetylglutamate synthase (

) (glutamate to N-acetylglutamate)

NAGK; N-acetylglutamate kinase (

) (N-acetylglutamate to N-acetylglutamate-5P)

N-acetyl-gamma-glutamyl-phosphate reductase (

) (N-acetylglutamate-5P to N-acetylglumate semialdehyde)

Acetylornithine aminotransferase (

) (N-acetylglumate semialdehyde to N-acetylornithine)

Acetylornithine deacetylase (

) (N-acetylornithine to ornithine)

Arginase (

) (ornithine to arginine)

N-acetyl-gamma-glutamyl-phosphate reductase (

) (AGPR) is the enzyme that catalyzes the third step in the biosynthesis of arginine from glutamate, the NADP-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde.
In bacteria it is a monofunctional protein of 35 to 38kDa (gene argC) while in fungi it is part of a bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) which contains a N-terminal acetylglutamate kinase ((

) domain and a C-terminal AGPR domain.
In the Mycobacterium tuberculosis enzyme, a cysteine has been shown to be implicated in the catalytic activity; the region around this residue is well conserved and is used as a signature pattern for the proteins in this entry .
Fructose-bisphosphate aldolase class I, Gram-positive bacteria-type (FBA_I_Gram+-type)
Type: Family

Fructose-bisphosphate aldolase (

) is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms: class I enzymes do not require a metal ion, and are characterised by the formation of a Schiff base intermediate between a highly conserved active site lysine and a substrate carbonyl group, while the class II enzymes require an active-site divalent metal ion.

This entry represents class I enzymes from Gram-positive and some Gram-negative bacteria.
HisA/PriA (HisA/PriA)
Type: Family

This protein family consists of HisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, also known as 1-(5-phosphoribosyl)-5-(5-phosphoribosylamino methylideneamino) imidazole-4-carboxamide isomerase (

), the enzyme catalyzing the fourth step in histidine biosynthesis. It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity .
Transport protein YbjL, putative (Transp_YbjL_put)
Type: Family

The proteins in this entry are putative transport proteins.
Transport protein YidE, putative (Transpt_YidE_put)
Type: Family

This entry represents a family of putative transport proteins from Gammaproteobacteria.
Histidine biosynthesis bifunctional protein HisIE (His_synth_HisIE)
Type: Family

The HisI and HisE functions, phosphoribosyl-AMP cyclohydrolase

and phosphoribosyl-ATP pyrophosphatase

, are coded by a a single gene in E. coli and other bacteria . This entry represents bifunctional HisIE proteins. This entry also includes its plant homologues, such as HISN2 (At1g31860) from Arabidopsis .
dNTP triphosphohydrolase, type 2 (dNTPase_2)
Type: Family

This entry represents a subgroup of dNTP triphosphohydrolases, classified as type 2 dNTPases . Proteins in this entry includes TTHA0412 (

) from Thermus thermophilus HB8. It hydrolyzes multiple kinds of dNTP upon activation by binding of an activator. Its dNTP triphosphohydrolase activity is stimulated by dATP and dTTP .
dNTP triphosphohydrolase, type 3 (dNTPase_3)
Type: Family

This entry represents a subgroup of dNTP triphosphohydrolases, classified as type 3 dNTPases .

This entry includes PA3043 (

) from Pseudomonas aeruginosa. It is a dNTP triphosphohydrolase that hydrolyzes multiple kinds of dNTP without an activator .
Serine/threonine transporter SstT (Ser_Thr_transp_SstT)
Type: Family

This entry represents the SstT family of serine/threonine transporters. It is involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system) .
Tryptophan synthase beta chain/beta chain-like (Trp_synth_beta/beta-like)
Type: Family

Tryptophan synthase catalyses the last step in the biosynthesis of tryptophan :

L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H
2
O

It has two functional domains, each found in bacteria and plants on a separate subunit: alpha chain (

) is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and beta chain is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together on a single multifunctional protein .

The beta chain of the enzyme, represented here, requires pyridoxal-phosphate as a cofactor. The pyridoxal-phosphate group is attached to a lysine residue. The region around this lysine residue also contains two histidine residues which are part of the pyridoxal-phosphate binding site.
Mannitol dehydrogenase, conserved site (Mannitol_DH_CS)
Type: Conserved_site

Mannitol dehydrogenases catalyse the NAD-dependent reduction of mannitol-1-phosphates as part of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTS facilitates the vectorial translocation of metabolisable carbohydrates to form the corresponding sugar phosphates, which are then converted to glycolytic intermediates . Mannitol 2-dehydrogenase catalyses the NAD-dependent reduction of mannitol to fructose .
Several dehydrogenases have been shown to be evolutionary related, including mannitol-1-phosphate 5-dehydrogenase (

) (gene mtlD), mannitol 2-dehydrogenase (

) (gene mtlK); mannonate oxidoreductase (

) (fructuronate reductase) (gene uxuB); Escherichia coli hypothetical proteins ydfI and yeiQ; and yeast hypothetical protein YEL070w.

This entry represents a conserved site found in mannitol dehydrogenases.
Mannitol-1-phosphate 5-dehydrogenase (Mannitol_1_phos_5_DH)
Type: Family

Mannitol dehydrogenases catalyse the NAD-dependent reduction of mannitol-1-phosphates as part of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTS facilitates the vectorial translocation of metabolisable carbohydrates to form the corresponding sugar phosphates, which are then converted to glycolytic intermediates . Mannitol 2-dehydrogenase catalyses the NAD-dependent reduction of mannitol to fructose .
Several dehydrogenases have been shown to be evolutionary related, including mannitol-1-phosphate 5-dehydrogenase (

) (gene mtlD), mannitol 2-dehydrogenase (

) (gene mtlK); mannonate oxidoreductase (

) (fructuronate reductase) (gene uxuB); Escherichia coli hypothetical proteins ydfI and yeiQ; and yeast hypothetical protein YEL070w.

This entry represents the mannitol-1-phosphate 5-dehydrogenase family, which catalyses the reaction

D-mannitol-1-phosphate + NAD
+
=>beta-D-fructose-6-phosphate + H
+
+ NADH