SII-SWORD/CoKE huggingface dataset:
GMP synthase (glutamine-hydrolyzing) subunit A (GMP_synthase_A)
Type: Family

This enzyme catalyzes the synthesis of GMP from XMP in the reaction

ATP + xanthosine 5'-phosphate + L-glutamine +H(2)O = AMP + diphosphate + GMP + L-glutamate.

The enzyme is a heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit and contains 1 glutamine amidotransferase type-1 domain.
Oxaloacetate decarboxylase, bacterial (Oxaloacetate_deCOase_bac)
Type: Family

This entry describes a class of bacterial oxaloacetate decarboxylases from the PEP mutase/isocitrate lyase superfamily. The enzyme plays a role in the maintenance of cellular concentrations of bicarbonate and pyruvate .
Cell division protein ZapA, firmicutes (Cell_div_ZapA_firmicutes)
Type: Family

This entry represents the cell division protein ZapA. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring. ZapA is recruited early at mid-cell but it is not essential for cell division . In sporulating cells, ZapA localizes near the cell poles. The proteins in this entry belongs to the ZapA Type 2 subfamily.
2,3-diketo-L-gulonate reductase (Diketo_gul_Rdtase)
Type: Family

This entry represents a family of bacterial 2,3-diketo-L-gulonate reductases, which catalyse the reduction of 2,3-diketo-L-gulonate in the presence of NADH . The gene operon yiaK-S (of which yiaK encodes for the 2,3-diketo-L-gulonate reductase) is believed to encode proteins which are involved in the utilisation of rare sugars for growth. This enzyme relies on NAD-tartrate binding to produce a more open active site; the conformation of the free enzyme is incompatible with substrate binding .
Cytoskeleton protein RodZ (RodZ)
Type: Family

RodZ are cytoskeletal proteins that are involved in bacterial cell-shape control through regulation of the length of the long axis . They are transmembrane proteins, with a cytoplasmic N-terminal domain that includes a helix-turn-helix motif, and a large periplasmic C-terminal domain.
ABC transporter, vitamin B12 import, permease protein BtuC (ABC_transptr_BtuC)
Type: Family

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.

Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets . The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin .

This entry represents bacterial BtuC, which is a component of the vitamin B12 ABC transporter complex . The BtuC proteins are the membrane-spanning subunits which engage with the ATP binding cassette BtuD. Its crystal structure has been resolved .
Multidrug resistance protein MdtG (Mutidrug-R_MdtG)
Type: Family

MdtG is found in enterobacteria and confers resistance to fosfomycin and deoxycholate . It belongs to the major facilitator superfamily.
Agmatinase (Agmatinase)
Type: Family

This enzyme belongs to the arginase family and more specifically the agmatinase (agmatine ureohydrolase

) subfamily. Agmatinase catalyses the hydrolysis of agmatine to putrescine and urea. Manganese is required as a cofactor in this reaction .

Agmatinase may play important regulatory roles by modulating the cellular levels of agmatine, which is a metabolic intermediate in the biosynthesis of putrescine and higher polyamines .
Thiosulfate sulfurtransferase, bacterial (Thiosulf_sulfurTrfase)
Type: Family

This entry represents the GlpE cytoplasmic bacterial family of rhodanese thiosulphate sulphurtransferases . They are responsible for the transfer of sulphur from thiosulphate to thiophilic acceptors. The related periplasmic thiosulphate sulphurtransferases, PspE, are responsible for a much greater proportion of rhodanese activity .
Ureohydrolase domain superfamily (Ureohydrolase_dom_sf)
Type: Homologous_superfamily

This entry represents hydrolases that cleave carbon-nitrogen bonds other than peptide bonds ([ec:3.5.-.-]). It includes mainly members of the ureohydrolase superfamily. It also represents the histone deacetylase family (

) and other related hydrolases.

The ureohydrolase superfamily includes arginase (

), agmatinase (

), formimidoylglutamase (also known as formiminoglutamase;

) and proclavaminate amidinohydrolase (

) . These enzymes share a 3-layer α-β-α structure , and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.

Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion . There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.

Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals.
Multidrug resistance protein MdtL (Multidrug-R_MdtL)
Type: Family

MdtL confers resistance to chloramphenicol .
3-isopropylmalate dehydrogenase, actinobacteria (LeuB_actb)
Type: Family

This entry represents 3-isopropylmalate dehydrogenases found in actinobacteria. This enzyme is responsible for the catalysis of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate .
Transcription activator HTH, RhaR (Tscrpt_act_RhaR)
Type: Family

RhaR activates expression of the rhaSR operon in response to L-rhamnose . It is one of numerous bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif.
Divalent cation tolerance protein CutA, Enterobacteria (CutA_Enterobact)
Type: Family

This entry represents CutA, which is involved in resistance toward heavy metals . It binds 1 copper ion per subunit. Similar sequences to CutA are found in several genomes. The metal binding sites are not conserved in many of the family members and their is currently unknown.
4-hydroxy-2-oxo-heptane-1,7-dioate aldolase, Enterobacteriales (HKHD_aldolase_ent)
Type: Family

This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde . The gene for this enzyme is generally found adjacent to other genes for this pathway .

The reaction catalysed is:

4-hydroxy-2-ketoheptane-1,7-dioate = pyruvate+ succinate semialdehyde.

This enzyme belongs to the hpcH/hpaI aldolase family and the proteins found in this entry are specific to the enterobacteriales.
D-cysteine desulphhydrase, bacterial (D_Cys_desulphydr_bac)
Type: Family

This entry represents a family of bacterial D-cysteine desulphydrases, which are responsible for the decomposition of D-cysteine, which is a powerful inhibitor of E. coli growth. D-cysteine is decomposed into pyruvate, H
2
S and NH
3
, and restricts growth through inhibition of key amino acid biosynthethis.
Membrane-bound lytic murein transglycosylase F (MltF)
Type: Family

This entry represents membrane-bound lytic murein transglycosylase F (MltF). In Escherichia coli, MltF function as an lytic transglycosylases; it degrades peptidoglycan producing 1,6-anhydromuramoyl residues in the process .
Glucan biosynthesis protein G (MdoG_OpgG)
Type: Family

Membrane-derived oligosaccharides (MDO) are members of a family of glucans found in the periplasmic space of Gram-negative bacteria. MdoG has been shown to be necessary for the synthesis of MDO , but its exact function is not known yet. This entry contains proteins that are involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs). They belong to the opgD/opgG family.
Nucleoid occlusion protein (Nucleoid_occlusion_protein)
Type: Family

This entry represents nucleoid occlusion proteins belonging to the parB family. Nucleoid occlusion protein effects nucleoid occlusion by binding relatively nonspecifically to DNA and preventing the assembly of the division machinery in the vicinity of the nucleoid, especially under conditions that disturb the cell cycle. It helps to coordinate cell division and chromosome segregation by preventing the formation of the Z ring through the nucleoid, which would cause chromosome breakage .
Para-hydroxybenzoic acid efflux pump, subunit AaeB (PHBA_efflux_pump_AaeB)
Type: Family

The para-hydroxybenzoic acid efflux pump's substrates are p-hydroxybenzoic acid (pHBA), 6-hydroxy-2-naphthoic and 2-hydroxycinnamate. It could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell . Both AaeB and AaeA subunits are required for the function of the efflux system. This entry represents subunit AaeB.
Outer membrane protein assembly factor BamA (OM_assembly_BamA)
Type: Family

This entry represents the BamA (also known as YaeT) family of proteins. BamA forms part of the outer membrane protein assembly complex, which is involved in assembly and insertion of β-barrel proteins into the outer membrane in Gram-negative bacteria .
Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase (Guo-5TP_3DP_PyrP)
Type: Family

Guanosine pentaphosphate (pppGpp) is a cytoplasmic signalling molecule which together with ppGpp controls the "stringent response", an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities. Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase (GppA), also known as guanosine pentaphosphate phosphohydrolase, catalyses the conversion of pppGpp to ppGpp.
Probable phosphatase YcdX (Phosphatase_YcdX_put)
Type: Family

This phosphatase is a homotrimer. Each subunit binds 3 zinc ions .
Transcription regulator HTH, UlaR (Tscrpt_reg_HTH_UlaR)
Type: Family

The HTH-type transcription regulator UlaR represses ulaG and the ulaABCDEF operon. Two UlaR binding sites have been identified in each promoter. Full activity requires simultaneous interaction of UlaR with both divergent promoters and seems to be dependent on repressor-mediated DNA loop formation, which is helped by the action of integration host factor .
3-phenylpropionate/cinnamic acid dioxygenase, beta subunit (HcaF)
Type: Family

Phenylpropanoid compounds are widely available in natural environments, and they can originate from putrefaction of proteins in soil or as breakdown products of several constituents of plants, such as lignin, various oils, and resins. Microbial catabolism of phenylpropanoid compounds plays an important role not only in the natural degradative cycle of these aromatic molecules but also in their industrial applications such as wine making, aging, and storage. In particular, degradation of cinnamic acid (CI), 3-phenylpropionic acid (PP), and their hydroxylated derivatives has been reported in several bacteria, including Pseudomonas species , Arthrobacter species , Escherichia coli (strain K12) , and Rhodococcus globerulus .

This entry represents HcaF, the beta subunit of PP/CI dioxygenase.
Endonuclease VIII (Endonuclease-VIII)
Type: Family

This entry represents the endonuclease 8 (also known as Nei) enzyme involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Endonuclease 8 acts as DNA glycosylase that recognises and removes damaged bases . The enzyme has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouraciland 5,6-dihydrothymine. It also has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand.The enzyme binds 1 zinc ion per subunit and acts by cleaving the DNA backbone by beta-delta elimination to generate a single-strand-break at the site of the removed base with both 3'- and 5'-phosphates. The C-O-P bond 3' to the apurinic orapyrimidinic site in DNA which is broken by the beta-elimination reaction leaves a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. This enzyme belongs to the FPG family and contains 1 FPG-type zinc finger .
Zinc transport protein ZntB (Zn_transp_ZntB)
Type: Family

ZntB is integral membrane protein consisting largely of two independent domains. The first 266 amino acids form a large, highly charged domain within the cytoplasm, while the remaining 61 residues form a small membrane domain containing two membrane-spanning segments . ZntB mediates efflux of zinc ions .
Trehalase, cytoplasmic (Cyt_trehalase)
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.

Glycoside hydrolase family 37

comprises enzymes with only one known activity; trehalase (

).

Trehalase is the enzyme responsible for the degradation of the disaccharide alpha,alpha-trehalose yielding two glucose subunits . It is an enzyme found in a wide variety of organisms and whose sequence has been highly conserved throughout evolution.

This entry represents a family of bacterial cytoplasic trehalases, a product of the TreF gene. It does not include the related TreA family of periplasmic trehalases. Under conditions of osmotic stress, E. coli may synthesize trehalose and utilise trehalose as a carbon source .
Proline-tRNA ligase, class IIa, type 2 (Prolyl-tRNA_ligase_IIa_type2)
Type: Family

Proline-tRNA ligase (also known as Prolyl-tRNA synthetase) belongs to class IIa. Proline-tRNA ligase(

) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota.

Proline-tRNA ligase catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). It can inadvertently accommodate and process cysteine .

The proline-tRNA ligaseform presents in most eubacteria can be divided in 2 types. This entry represents proline-tRNA ligase type 2 from eubacteria.

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 .
Prolyl-tRNA synthetase, class IIa, type 1 (Pro-tRNA-Synthase_IIa_type1)
Type: Family

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 .

Proline-tRNA ligase (also known as Prolyl-tRNA synthetase) belongs to class IIa. Proline-tRNA ligase(

) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota.

The prolyl-tRNA synthetase form presents in most eubacteria can be divided in 2 types. This entry represents type 1. This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases .
Aliphatic amidase (Aliphatic_amidase)
Type: Family

These enzymes catalyzes the hydrolysis of short-chain aliphatic amides to their corresponding organic acids with release of ammonia . They also exhibit in vitro acyl transferase activity,transferring the acyl moiety of short-chain amides to hydroxylamine to form hydroxamates. Aliphatic amidases contain 1 CN hydrolase domain. This group of enzyme belongs to the nitrilase superfamily.
Trehalase, periplasmic (Trehalase_periplasmic)
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.

Glycoside hydrolase family 37

comprises enzymes with only one known activity; trehalase (

).

Trehalase is the enzyme responsible for the degradation of the disaccharide alpha,alpha-trehalose yielding two glucose subunits . It is an enzyme found in a wide variety of organisms and whose sequence has been highly conserved throughout evolution.

This entry represents a family of bacterial cytoplasic trehalases, a product of the treA gene. It does not include the related TreF family of periplasmic trehalases. Under conditions of osmotic stress, E. coli may synthesize trehalose and utilise trehalose as a carbon source .
Multidrug resistance protein MdtD (Multi-R_MdtD)
Type: Family

This putative multidrug resistance protein is transcriptionally regulated by the response regulator BaeR .
Enterobactin exporter, EntS (Enterobactin_exp_EntS)
Type: Family

This group of proteins exports the siderophore enterobactin out of the cell and belongs to the major facilitator superfamily .
Glucan biosynthesis protein C (Glucans_biosynth_C)
Type: Family

This entry represents bacterial glucans biosynthesis proteins, which are responsible for the succinyl substitution of periplasmic glucans .
Glucan biosynthesis, MdoD (Glucan_biosyn_MdoD)
Type: Family

Membrane-derived oligosaccharides (MDO) are members of a family of glucans found in the periplasmic space of Gram-negative bacteria. MdoG has been shown to be necessary for the synthesis of MDO , but its exact function is not known yet. MdoD, an MdoG paralog, is a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures ; see also .

This entry represents bacterial MdoD proteins . They are thought to be involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans (OPGs).
Glucan biosynthesis glucosyltransferase H (Glucans_biosynth_gluTrFase_H)
Type: Family

Proteins in this entry are thought to be glucan biosynthesis glucosyltransferases, which play a role in the synthesis of osmoregulated periplasmic glycoproteins.
Threonine/serine transporter TdcC (Thr/Ser_transpt_TdcC)
Type: Family

This entry represents the threonine/serine transporter TdcC . It is involved in the import of threonine and serine into the cell, with the concomitant import of a proton (symport system). TdcC is a multi-pass membrane protein .
Lysophospholipid transporter LplT (LysoPLipid__transptr_LplT)
Type: Family

Lysophospholipid transporter LplT catalyzes the facilitated diffusion of 2-acyl-glycero-3-phosphoethanolamine (2-acyl-GPE) into the cell .
Small heat shock protein IbpA (HSP20_IbpA)
Type: Family

Small heat shock proteins IbpA associate with aggregated proteins, together with IbpB, 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, .

These proteins form homomultimers of about 100-150 subunits at optimal growth temperatures. The conformation changes to monomers at high temperatures or high ionic concentrations. Proteins in this entry belong to the small heat shock protein (HSP20) family.
K(+)/H(+) antiporter NhaP2 (NhaP2)
Type: Family

This entry represents the NhaP2 family of bacterial K(+)/H(+) antiporters. They are thought to be involved in control of cell volumes under low osmotic conditions . Vc-NhaP2 from Vibrio cholerae functions as a specific K+/H+ antiporter while retaining the ability to exchange H+ for Na+ and bind (but not exchange with H+) Li+ in a competitive manner .