The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing
K03551
-
3.6.4.12
0.00000000000000002212
81.0
BYDH3_k127_1005639_0
The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently
K03076
-
-
1.633e-260
805.0
BYDH3_k127_1005639_1
Acts as a magnesium transporter
K06213
-
-
5.946e-255
793.0
BYDH3_k127_1005639_10
This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome
Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits
Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome
Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
K00822,K12256
-
2.6.1.113,2.6.1.18
2.903e-267
826.0
BYDH3_k127_10291335_2
Belongs to the aldehyde dehydrogenase family
K00135,K00137
-
1.2.1.16,1.2.1.19,1.2.1.20,1.2.1.79
1.248e-266
826.0
BYDH3_k127_10291335_3
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl- acyl-carrier-protein (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA
Belongs to the bacterial ribosomal protein bL32 family
K02911
-
-
0.000000000000000000000000000000007076
127.0
BYDH3_k127_10359792_2
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched- chain and or straight-chain of fatty acids
Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length
K04760
-
-
0.00000000000000000000000000000000000000007413
151.0
BYDH3_k127_10597223_0
Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
K01703
-
4.2.1.33,4.2.1.35
1.616e-271
839.0
BYDH3_k127_10597223_1
Belongs to the argininosuccinate synthase family. Type 1 subfamily
K01940
-
6.3.4.5
9.208e-259
799.0
BYDH3_k127_10597223_2
LeuA allosteric (dimerisation) domain
-
-
-
9.599e-254
790.0
BYDH3_k127_10597223_3
PFAM Aminotransferase class-III
K00821
-
2.6.1.11,2.6.1.17
1.51e-205
644.0
BYDH3_k127_10597223_4
Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate
Belongs to the acetyltransferase family. ArgA subfamily
K14682
-
2.3.1.1
4.058e-267
830.0
BYDH3_k127_10791788_1
Catalyzes the addition and repair of the essential 3'- terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'- nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases
K00974
-
2.7.7.72
4.581e-206
649.0
BYDH3_k127_10791788_2
Belongs to the acetylglutamate kinase family. ArgB subfamily
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
K00343
-
1.6.5.3
5.444e-241
751.0
BYDH3_k127_10856118_1
TIGRFAM proton-translocating NADH-quinone oxidoreductase, chain M
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
K03070
-
-
0.0
1168.0
BYDH3_k127_10856290_1
Proton pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for proton movement across the membrane. Generates a proton motive force
IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatB, TatC is part of a receptor directly interacting with Tat signal peptides
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatC, TatB is part of a receptor directly interacting with Tat signal peptides. TatB may form an oligomeric binding site that transiently accommodates folded Tat precursor proteins before their translocation
K03117
-
-
0.000000000000000000000000003112
113.0
BYDH3_k127_1087364_8
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
double-stranded DNA 3'-5' exodeoxyribonuclease activity
-
-
-
0.00000000000000306
75.0
BYDH3_k127_10882230_12
-
-
-
-
0.0000000000000375
79.0
BYDH3_k127_10882230_13
PFAM Endonuclease Exonuclease phosphatase
-
-
-
0.00000000000005562
72.0
BYDH3_k127_10882230_14
This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site
K02884
-
-
0.000000000000472
69.0
BYDH3_k127_10882230_15
PFAM Endonuclease Exonuclease phosphatase
-
-
-
0.000003815
50.0
BYDH3_k127_10882230_2
Catalyzes the transfer of an acyl group from acyl- phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH
Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation
K11085
-
-
8.009e-283
878.0
BYDH3_k127_10966408_1
Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
DNA internalization-related competence protein ComEC Rec2
K02238
-
-
0.00000000000000000000000000000000007201
135.0
BYDH3_k127_10966408_19
DNA internalization-related competence protein ComEC Rec2
K02238
-
-
0.0000000000000000000000000000000002247
133.0
BYDH3_k127_10966408_2
Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit
DNA internalization-related competence protein ComEC Rec2
K02238
-
-
0.0000000000000000000006487
98.0
BYDH3_k127_10966408_22
DNA internalization-related competence protein ComEC Rec2
K02238
-
-
0.00000000000000000006684
90.0
BYDH3_k127_10966408_23
Immunity protein 49
-
-
-
0.00006767
49.0
BYDH3_k127_10966408_3
Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit
Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1- P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA)
Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol- acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3- dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3- hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate
K00053
-
1.1.1.86
1.613e-208
649.0
BYDH3_k127_10988403_1
Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer)
Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
K18303
-
-
5.054e-299
922.0
BYDH3_k127_11018163_0
Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
An FAD assembly protein, which accelerates covalent attachment of the cofactor into other proteins. Plays an essential role in the assembly of succinate dehydrogenase (SDH, respiratory complex II), an enzyme complex that is a component of both the tricarboxylic acid cycle and the electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit SdhA of SDH
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth
K03086
-
-
0.0
1137.0
BYDH3_k127_11036651_1
Cytochrome c-type biogenesis protein CcmF
K02198
-
-
1.499e-271
850.0
BYDH3_k127_11036651_10
subunit of a heme lyase
K02200
-
-
0.000000000000000000000000000000000000006641
149.0
BYDH3_k127_11036651_11
Cupredoxin-like domain
-
-
-
0.00000000000000000000000000000000000002911
145.0
BYDH3_k127_11036651_12
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP
K09458
-
2.3.1.179
0.000000000000000000001664
94.0
BYDH3_k127_11036651_13
Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
K02196
-
-
0.00000000001628
65.0
BYDH3_k127_11036651_14
glycosyl transferase
-
-
-
0.00001726
51.0
BYDH3_k127_11036651_2
Outer membrane protein transport protein (OMPP1/FadL/TodX)
Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH
PFAM extracellular solute-binding protein family 5
K02035
-
-
6.234e-221
694.0
BYDH3_k127_11074412_20
Sigma 54 modulation protein / S30EA ribosomal protein
-
-
-
0.00000000000000000000000000000000000000001449
156.0
BYDH3_k127_11074412_21
-
-
-
-
0.000000000000000000000000000000000001161
143.0
BYDH3_k127_11074412_22
-
-
-
-
0.0000000000000002396
85.0
BYDH3_k127_11074412_23
-
-
-
-
0.000000000009057
67.0
BYDH3_k127_11074412_3
Protein conserved in bacteria
-
-
-
1.327e-202
649.0
BYDH3_k127_11074412_4
Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides
DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N- glycosidic bond, leaving an AP (apurinic apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Part of a membrane complex involved in electron transport
K03615
-
-
1.42e-268
841.0
BYDH3_k127_11092207_20
Catalyzes the formation of 6,7-dimethyl-8- ribityllumazine by condensation of 5-amino-6-(D- ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin
Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length
K04760
-
-
0.000000000000000000000000000000000000006225
146.0
BYDH3_k127_11092398_4
PFAM Heavy metal transport detoxification protein
-
-
-
0.0000000000000000000000000000009574
124.0
BYDH3_k127_11092398_5
Uncharacterized protein conserved in bacteria (DUF2331)
-
-
-
0.00000000000000000000002826
99.0
BYDH3_k127_11163455_0
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate
K00615
-
2.2.1.1
0.0
1234.0
BYDH3_k127_11163455_1
Belongs to the pyruvate kinase family
K00873
-
2.7.1.40
4.448e-239
746.0
BYDH3_k127_11163455_2
Belongs to the phosphoglycerate kinase family
K00927
-
2.7.2.3
2.589e-226
704.0
BYDH3_k127_11163455_3
Belongs to the glyceraldehyde-3-phosphate dehydrogenase family
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
K15726
-
-
0.0
1695.0
BYDH3_k127_11194035_1
damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage
Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit
K02963
-
-
0.000000000000000000000000000000000000000007335
154.0
BYDH3_k127_11194035_26
Binds single-stranded DNA at the primosome assembly site (PAS)
K02686
-
-
0.00000000000000000000000000000000000006421
143.0
BYDH3_k127_11194035_28
-
-
-
-
0.000000000000000000001903
99.0
BYDH3_k127_11194035_29
Outer membrane efflux protein
-
-
-
0.000000000000000000022
94.0
BYDH3_k127_11194035_3
PFAM Aminotransferase class I and II
K00812
-
2.6.1.1
4.689e-232
721.0
BYDH3_k127_11194035_30
it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins
Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation
K03771
-
5.2.1.8
4.916e-211
662.0
BYDH3_k127_11261352_1
Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane
Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP)
Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates
Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA RNA and avoiding chromosomal lesions
first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA
Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm. This transfer involves a cascade of disulfide bond formation and reduction steps
K04084
-
1.8.1.8
7.842e-226
715.0
BYDH3_k127_11369047_5
Involved in the biosynthesis of porphyrin-containing compound
Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner
Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr)
Catalyzes the specific phosphorylation of 1,6-anhydro-N- acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
K02470
-
5.99.1.3
1.931e-231
718.0
BYDH3_k127_11622359_0
3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs
Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism
K00600
-
2.1.2.1
4.931e-252
781.0
BYDH3_k127_11703928_1
Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP
K09458
-
2.3.1.179
1.108e-258
799.0
BYDH3_k127_11794045_1
Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide
Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. MsrQ provides electrons for reduction to the reductase catalytic subunit MsrP, using the quinone pool of the respiratory chain
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched- chain and or straight-chain of fatty acids
Catalyzes the ATP- as well as the pyrophosphate- dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P- Ser-HPr)
Catalyzes the ATP- as well as the pyrophosphate- dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P- Ser-HPr)
This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex
Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr)
Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A)
Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
K03072
-
-
0.0
1050.0
BYDH3_k127_12201126_10
non-haem dioxygenase in morphine synthesis N-terminal
Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
K01649
-
2.3.3.13
1.528e-303
934.0
BYDH3_k127_12201126_4
Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components
K03106
-
3.6.5.4
1.507e-264
818.0
BYDH3_k127_12201126_5
Transporter associated domain
-
-
-
2.44e-239
743.0
BYDH3_k127_12201126_6
Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2- cyclopenten-1-yl)amino)methyl)-7-deazaguanosine)
K00773
-
2.4.2.29
6.716e-226
701.0
BYDH3_k127_12201126_7
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
K01895
-
6.2.1.1
0.0
1225.0
BYDH3_k127_12308216_1
Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP
Involved in the regulation of glutamine synthetase GlnA, a key enzyme in the process to assimilate ammonia. When cellular nitrogen levels are high, the C-terminal adenylyl transferase (AT) inactivates GlnA by covalent transfer of an adenylyl group from ATP to specific tyrosine residue of GlnA, thus reducing its activity. Conversely, when nitrogen levels are low, the N-terminal adenylyl removase (AR) activates GlnA by removing the adenylyl group by phosphorolysis, increasing its activity. The regulatory region of GlnE binds the signal transduction protein PII (GlnB) which indicates the nitrogen status of the cell
K00982
-
2.7.7.42,2.7.7.89
0.00000000001187
66.0
BYDH3_k127_12317863_0
PFAM GGDEF domain containing protein
K13590
-
2.7.7.65
6.101e-247
775.0
BYDH3_k127_12317863_1
Required for morphogenesis and for the elongation of the flagellar filament by facilitating polymerization of the flagellin monomers at the tip of growing filament. Forms a capping structure, which prevents flagellin subunits (transported through the central channel of the flagellum) from leaking out without polymerization at the distal end
K02407
-
-
1.066e-224
709.0
BYDH3_k127_12317863_2
histidine kinase dimerisation and phosphoacceptor region
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position
K00700
-
2.4.1.18
0.0
1201.0
BYDH3_k127_12462401_1
PFAM Phosphoglucose isomerase
K01810
-
5.3.1.9
0.0
1017.0
BYDH3_k127_12462401_2
Belongs to the glycosyl hydrolase 57 family
-
-
-
1.061e-268
835.0
BYDH3_k127_12462401_3
Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
K03628
-
-
3.983e-263
813.0
BYDH3_k127_12530942_1
-
-
-
-
4.268e-237
742.0
BYDH3_k127_12530942_10
BON domain
-
-
-
0.00000000000000000000000000000000000000000000114
171.0
BYDH3_k127_12530942_11
Cell division protein FtsL
-
-
-
0.00000000000000000000000000000000000403
139.0
BYDH3_k127_12530942_12
Catalyzes cross-linking of the peptidoglycan cell wall at the division septum
K03587
-
3.4.16.4
0.00000000000000000000000000000002594
126.0
BYDH3_k127_12530942_13
Belongs to the UPF0102 family
K07460
-
-
0.0000000000000000000000000008797
113.0
BYDH3_k127_12530942_14
-
-
-
-
0.000000000000001011
79.0
BYDH3_k127_12530942_15
Belongs to the UPF0102 family
K07460
-
-
0.00000000000001576
74.0
BYDH3_k127_12530942_17
-
-
-
-
0.00002197
50.0
BYDH3_k127_12530942_2
Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision
K03703
-
-
0.0
1033.0
BYDH3_k127_1258657_2
TIGRFAM type I secretion membrane fusion protein, HlyD family
K12542
-
-
5.861e-231
723.0
BYDH3_k127_1258657_3
TIGRFAM cation diffusion facilitator family transporter
Catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7- carboxy-7-deazaguanine (CDG), a step common to the biosynthetic pathways of all 7-deazapurine-containing compounds
An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes
This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site
The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine
K01696
-
4.2.1.20
2.096e-252
779.0
BYDH3_k127_12820130_10
Catalyzes the phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and the respective free bases. Can use uridine, adenosine, guanosine, cytidine, thymidine, inosine and xanthosine as substrates. Also catalyzes the reverse reactions
Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
K00133
-
1.2.1.11
1.077e-208
653.0
BYDH3_k127_12820130_3
Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
K03296
-
-
0.0
1377.0
BYDH3_k127_12920014_0
Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs
One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
K02519
-
-
0.0
1344.0
BYDH3_k127_12943068_1
Participates in both transcription termination and antitermination
K02600
-
-
2.62e-279
862.0
BYDH3_k127_12943068_2
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction
K00962
-
2.7.7.8
8.408e-247
765.0
BYDH3_k127_12943068_3
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA
Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
K00764
-
2.4.2.14
0.000000002856
58.0
BYDH3_k127_13046177_0
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
K01338
-
3.4.21.53
0.0
1418.0
BYDH3_k127_13046177_1
Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions
ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP
K03544
-
-
0.000000000000002902
75.0
BYDH3_k127_13111782_0
PFAM FAD dependent oxidoreductase
K00303
-
1.5.3.1
5.618e-266
820.0
BYDH3_k127_13111782_1
glycine cleavage T protein (aminomethyl transferase)
RuBisCO catalyzes two reactions the carboxylation of D- ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site
Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
K01255
-
3.4.11.1
8.952e-265
821.0
BYDH3_k127_1445993_1
PFAM sigma-54 factor interaction domain-containing protein
Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome
K02355
-
-
0.0
1364.0
BYDH3_k127_1457257_1
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
K03046
-
2.7.7.6
0.0
1124.0
BYDH3_k127_1457257_2
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
K02358
-
-
3.844e-249
770.0
BYDH3_k127_1457257_3
One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA
Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit
Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
K07277
-
-
0.0
1083.0
BYDH3_k127_1640153_0
Glycyl-tRNA synthetase beta subunit
K01879
-
6.1.1.14
0.0
1032.0
BYDH3_k127_1640153_1
Transfers the fatty acyl group on membrane lipoproteins
K03820
-
-
7.498e-225
706.0
BYDH3_k127_1640153_10
Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell
Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA
Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
K00820
-
2.6.1.16
0.0
1007.0
BYDH3_k127_1652081_1
Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
K02111
-
3.6.3.14
1.945e-316
971.0
BYDH3_k127_1652081_2
Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits
K02112
-
3.6.3.14
1.086e-293
903.0
BYDH3_k127_1652081_3
Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP- GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5- monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain
K04042
-
2.3.1.157,2.7.7.23
5.29e-243
756.0
BYDH3_k127_1652081_4
Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
The M ring may be actively involved in energy transduction
K02409
-
-
0.00000000000000000000000000000000000001494
145.0
BYDH3_k127_1652587_3
FlhB HrpN YscU SpaS Family
K04061
-
-
0.00000000000000000000000000000000000006307
144.0
BYDH3_k127_1745489_0
Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP)
K01662
-
2.2.1.7
0.0
1044.0
BYDH3_k127_1745489_1
Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system
Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen
Purine nucleoside phosphorylase which is highly specific for 6-oxopurine nucleosides. Cleaves guanosine or inosine to respective bases and sugar-1-phosphate molecules. Involved in purine salvage
Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions
DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back- translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner
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). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS
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). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS
Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine- binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
Phosphoribosylformylglycinamidine synthase involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate
Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo- MPT) cofactor (Moco or molybdenum cofactor) to form Mo- molybdopterin guanine dinucleotide (Mo-MGD) cofactor
Involved in the regulation of glutamine synthetase GlnA, a key enzyme in the process to assimilate ammonia. When cellular nitrogen levels are high, the C-terminal adenylyl transferase (AT) inactivates GlnA by covalent transfer of an adenylyl group from ATP to specific tyrosine residue of GlnA, thus reducing its activity. Conversely, when nitrogen levels are low, the N-terminal adenylyl removase (AR) activates GlnA by removing the adenylyl group by phosphorolysis, increasing its activity. The regulatory region of GlnE binds the signal transduction protein PII (GlnB) which indicates the nitrogen status of the cell
) H( ) antiporter that extrudes sodium in exchange for external protons
K03313
-
-
0.000000000000000000000000000000000000000203
151.0
BYDH3_k127_2238049_0
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate- limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth
Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane)
Required for the insertion and or proper folding and or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins
K03217
-
-
2.785e-279
866.0
BYDH3_k127_2461554_1
Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine
K07304
-
1.8.4.11
0.00000000000000000000000006539
106.0
BYDH3_k127_2538931_2
The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
K00627
-
2.3.1.12
3.068e-243
756.0
BYDH3_k127_2538931_3
Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain
K01872
-
6.1.1.7
0.0
1071.0
BYDH3_k127_2624334_1
Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
K03553
-
-
3.803e-207
646.0
BYDH3_k127_2624334_2
Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG)
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease
Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme
K02302
-
1.3.1.76,2.1.1.107,4.99.1.4
3.896e-259
803.0
BYDH3_k127_2767128_1
Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine
K06168
-
2.8.4.3
1.763e-256
795.0
BYDH3_k127_2767128_2
fructose-bisphosphate aldolase, class II, Calvin cycle subtype
Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln)
K02433
-
6.3.5.6,6.3.5.7
6.966e-283
872.0
BYDH3_k127_278067_1
TIGRFAM cell shape determining protein, MreB Mrl family
K03569
-
-
7.37e-212
659.0
BYDH3_k127_278067_2
Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
K02435
-
6.3.5.6,6.3.5.7
0.00000000000000000000000000000000000000000005208
162.0
BYDH3_k127_2849171_0
In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
Proton pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for proton movement across the membrane. Generates a proton motive force
Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
Catalyzes the rearrangement of 1-deoxy-D-xylulose 5- phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S
Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties
K00688
-
2.4.1.1
0.0
1437.0
BYDH3_k127_3252003_1
Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre- crRNA and tracrRNA of type II CRISPR loci if present in the organism
Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone
Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine cysteine desulfurase (IscS) system
Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr)
This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control
Belongs to the bacterial ribosomal protein bL35 family
K02916
-
-
0.0000000000000000000000000000008623
121.0
BYDH3_k127_3327343_14
One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex
Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit
TIGRFAM PQQ-dependent dehydrogenase, methanol ethanol family
-
-
-
0.000000000000000000000000000000000001806
139.0
BYDH3_k127_3386207_2
Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis
Catalyzes the transfer of a formyl group from 5-formyl tetrahydromethanopterin (5-formyl-H(4)MPT) to methanofuran (MFR) so as to produce formylmethanofuran (formyl-MFR) and tetrahydromethanopterin (H(4)MPT)
Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control
Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate
Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2- polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2)
Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and or for immediate growth after restoration of oxygen
K00525
-
1.17.4.1
0.0
1343.0
BYDH3_k127_4156960_1
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
K18303
-
-
5.217e-232
723.0
BYDH3_k127_4156960_2
TIGRFAM type I secretion outer membrane protein, TolC family
K12340
-
-
1.177e-200
633.0
BYDH3_k127_4156960_3
PFAM Three-deoxy-D-manno-octulosonic-acid transferase domain protein
Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
K03526
-
1.17.7.1,1.17.7.3
0.0000000000000001177
80.0
BYDH3_k127_4243150_0
Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA
Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis
Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
K01874
-
6.1.1.10
0.0
1088.0
BYDH3_k127_4634005_20
Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis
This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control
Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
K00036
-
1.1.1.363,1.1.1.49
3e-305
938.0
BYDH3_k127_4634005_4
S1 RNA binding domain
K02945
-
-
1.318e-291
899.0
BYDH3_k127_4634005_5
Modulates cellular lipopolysaccharide (LPS) levels by regulating LpxC, which is involved in lipid A biosynthesis. May act by modulating the proteolytic activity of FtsH towards LpxC. May also coordinate assembly of proteins involved in LPS synthesis at the plasma membrane
K19804
-
-
9.828e-218
680.0
BYDH3_k127_4634005_6
Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3- phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate
K00800
-
2.5.1.19
1.382e-210
661.0
BYDH3_k127_4634005_7
Binds and transfers iron-sulfur (Fe-S) clusters to target apoproteins. Can hydrolyze ATP
Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits
One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
K02961
-
-
0.0000000000000000000000000000000000000007295
149.0
BYDH3_k127_4678744_11
Belongs to the universal ribosomal protein uL29 family
K02904
-
-
0.0000000000000000000000000005665
113.0
BYDH3_k127_4678744_12
This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
K02881
-
-
0.0000000000006459
68.0
BYDH3_k127_4678744_2
This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center
One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome
NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
Catalyzes cross-linking of the peptidoglycan cell wall at the division septum
K03587
-
3.4.16.4
4.498e-273
845.0
BYDH3_k127_482784_1
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
K01928
-
6.3.2.13
2.227e-198
624.0
BYDH3_k127_4881184_0
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate
Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters
Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34
Belongs to the bacterial ribosomal protein bL28 family
K02902
-
-
0.000000000000000000000000000000000000000001436
157.0
BYDH3_k127_4944337_12
Protein of unknown function (DUF2805)
-
-
-
0.000000000000000000000000000000000002294
139.0
BYDH3_k127_4944337_13
TIGRFAM DNA repair protein RadC
K03630
-
-
0.0000000000000000000000000000000921
124.0
BYDH3_k127_4944337_14
Selenoprotein, putative
-
-
-
0.000000000000000000000001568
104.0
BYDH3_k127_4944337_15
Belongs to the bacterial ribosomal protein bL33 family
K02913
-
-
0.0000000000000000000006636
96.0
BYDH3_k127_4944337_16
TIGRFAM DNA repair protein RadC
K03630
-
-
0.0000000000004961
68.0
BYDH3_k127_4944337_18
Belongs to the UPF0149 family
K07039
-
-
0.000009034
58.0
BYDH3_k127_4944337_2
TonB-dependent Receptor Plug
K02014
-
-
0.0
1020.0
BYDH3_k127_4944337_3
Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine
This enzyme is involved in nucleotide metabolism it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate
Flavin transferase that catalyzes the transfer of the FMN moiety of FAD and its covalent binding to the hydroxyl group of a threonine residue in a target flavoprotein
Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P)
This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
K02897
-
-
0.00000000000000000000001926
100.0
BYDH3_k127_5197749_0
Putative diguanylate phosphodiesterase
K21023
-
2.7.7.65
1.795e-212
681.0
BYDH3_k127_5197749_1
Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves
Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance
K01139
-
2.7.6.5,3.1.7.2
0.0
1254.0
BYDH3_k127_5333748_1
Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA)
K03655
-
3.6.4.12
0.0
1146.0
BYDH3_k127_5333748_10
A predicted alpha-helical domain with a conserved ER motif.
Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of ubiquinone-8 (UQ-8) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB, generating the first membrane-bound Q intermediate 3- octaprenyl-4-hydroxybenzoate
Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
K03060
-
2.7.7.6
0.0000000000000000000000000000000001716
132.0
BYDH3_k127_5451660_0
PFAM Flavocytochrome c sulphide dehydrogenase, flavin-binding
Catalyzes the interconversion between ADP-D-glycero- beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose
Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP
Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis
Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis
Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria
K02338
-
2.7.7.7
4.396e-200
627.0
BYDH3_k127_5679203_1
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP
Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate
An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
Cell division protein that is involved in the assembly of the Z ring. May serve as a membrane anchor for the Z ring
K03590
-
-
1.585e-248
769.0
BYDH3_k127_6217067_2
Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity
K03531
-
-
1.022e-223
696.0
BYDH3_k127_6217067_3
Catalyzes the hydrolysis of UDP-3-O-myristoyl-N- acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis
Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. May control correct divisome assembly
Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives
Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate
Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines
Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site
K03723
-
-
0.0
1697.0
BYDH3_k127_6580351_0
Belongs to the MurCDEF family
K01924
-
6.3.2.8
4.742e-260
806.0
BYDH3_k127_6580351_1
Peptidoglycan polymerase that is essential for cell division
K03588
-
-
5.292e-227
706.0
BYDH3_k127_6580351_2
First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
K01000
-
2.7.8.13
2.928e-217
676.0
BYDH3_k127_6580351_3
Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA)
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. May control correct divisome assembly
K03589
-
-
0.0000000000000000000000000001983
119.0
BYDH3_k127_6580351_9
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit
it can initiate unwinding at a nick in the DNA. It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction
Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
K00817
-
2.6.1.9
1.651e-201
631.0
BYDH3_k127_6837772_2
amino acid-binding ACT domain protein
K14170
-
4.2.1.51,5.4.99.5
6.792e-199
623.0
BYDH3_k127_6837772_3
Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism
it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins
K02314
-
3.6.4.12
5.221e-255
788.0
BYDH3_k127_7178579_1
DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division
K09888
-
-
0.0000000000000000000000000000000000000000004581
158.0
BYDH3_k127_7184143_4
S4 domain
K14761
-
-
0.0000000000000000000000002072
106.0
BYDH3_k127_7184143_5
-
-
-
-
0.0000000000000000000003781
98.0
BYDH3_k127_7184143_6
-
-
-
-
0.00000000000004329
74.0
BYDH3_k127_7212090_0
Involved in the TonB-independent uptake of proteins
Catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7- carboxy-7-deazaguanine (CDG), a step common to the biosynthetic pathways of all 7-deazapurine-containing compounds
K10026
-
4.3.99.3
0.000000000000000000000000002213
111.0
BYDH3_k127_7305299_0
histidine kinase HAMP region domain protein
-
-
-
3.071e-228
712.0
BYDH3_k127_7305299_1
Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus
Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
-
-
-
3.774e-315
977.0
BYDH3_k127_7329000_1
Protein of unknown function (DUF2892)
-
-
-
0.000000000000000000000000001916
112.0
BYDH3_k127_7329000_2
Outer membrane efflux protein
K12340
-
-
0.000001215
54.0
BYDH3_k127_7385784_0
amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile)
Cell division factor that enhances FtsZ-ring assembly. Directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity
Hydrolyzes the pyrophosphate bond of UDP-2,3- diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane
K03980
-
-
3.32e-284
878.0
BYDH3_k127_7385784_20
PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
Belongs to the bacterial ribosomal protein bL27 family
K02899
-
-
0.0000000000000000000000000000000000000000008831
157.0
BYDH3_k127_7385784_31
Protein of unknown function (DUF2946)
-
-
-
0.000000000000000000000000000000001024
134.0
BYDH3_k127_7385784_32
Ferredoxin
-
-
-
0.00000000000000000000000000002693
119.0
BYDH3_k127_7385784_33
Inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. Acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase
K09862
-
-
0.00000000000000004447
82.0
BYDH3_k127_7385784_34
Cro/C1-type HTH DNA-binding domain
-
-
-
0.00000000000000005729
84.0
BYDH3_k127_7385784_4
cysteine-tRNA ligase activity
-
-
-
2.085e-249
775.0
BYDH3_k127_7385784_5
TonB-dependent receptor
K02014
-
-
2.654e-234
741.0
BYDH3_k127_7385784_6
Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate
K00620
-
2.3.1.1,2.3.1.35
3.782e-217
678.0
BYDH3_k127_7385784_7
An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control
K03979
-
-
1.802e-208
650.0
BYDH3_k127_7385784_8
Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
K00145
-
1.2.1.38
5.209e-194
608.0
BYDH3_k127_7414143_1
This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly
PFAM ATPase associated with various cellular activities, AAA_3
-
-
-
6.631e-203
634.0
BYDH3_k127_7454163_2
Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl- ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)- decenoyl-ACP. Can catalyze the dehydratase reaction for beta- hydroxyacyl-ACPs with saturated chain lengths up to 16 0, being most active on intermediate chain length
Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine
K12960
-
3.5.4.28,3.5.4.31
1.268e-221
695.0
BYDH3_k127_7596229_1
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
ATPase, P-type (transporting), HAD superfamily, subfamily IC
K01533
-
3.6.3.4
0.0000000000000000000000000000000001477
136.0
BYDH3_k127_7697571_0
PFAM type II secretion system
K12276
-
-
2.644e-214
668.0
BYDH3_k127_7697571_1
Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits
Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP)
ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins
Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components
Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components
Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5- carboxylate
K00147
-
1.2.1.41
7.66e-220
687.0
BYDH3_k127_7799312_2
Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4- diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP)
Carbamoyl-phosphate synthetase large chain domain protein
K01941
-
6.3.4.6
2.774e-313
970.0
BYDH3_k127_793033_1
Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln)
amino acids such as threonine, to avoid such errors, it has a posttransfer editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner
Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn)
The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB
Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA
K01754
-
4.3.1.19
1.392e-283
875.0
BYDH3_k127_8047519_10
EVE domain
-
-
-
0.00000000000001342
73.0
BYDH3_k127_8047519_2
TIGRFAM 40-residue YVTN family beta-propeller repeat
Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and or repair of Fe-S clusters in biosynthetic enzymes
Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs
K08300
-
3.1.26.12
8.861e-305
936.0
BYDH3_k127_8069840_1
Responsible for synthesis of pseudouridine from uracil
Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
K03688
-
-
5.116e-254
791.0
BYDH3_k127_8157406_2
Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves 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
Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2- polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2)
K03183
-
2.1.1.163,2.1.1.201
0.00000000000000007088
79.0
BYDH3_k127_8203718_0
Polyketide cyclase / dehydrase and lipid transport
Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene
Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene
K03664
-
-
0.000000000000000000000007175
101.0
BYDH3_k127_8203718_4
-
-
-
-
0.00002848
47.0
BYDH3_k127_8209923_0
TIGRFAM proton-translocating NADH-quinone oxidoreductase, chain L
K00341
-
1.6.5.3
0.0
1130.0
BYDH3_k127_8209923_1
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)- butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP MEP pathway for isoprenoid precursor biosynthesis
Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates
K01937
-
6.3.4.2
0.0
1036.0
BYDH3_k127_8363301_1
Sodium:solute symporter family
K14393
-
-
8.221e-246
769.0
BYDH3_k127_8363301_2
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
K00333
-
1.6.5.3
1.117e-269
831.0
BYDH3_k127_8383487_10
PFAM Preprotein translocase SecG subunit
K03075
-
-
0.0000000000000000000000000000000001144
135.0
BYDH3_k127_8383487_2
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain
K00335
-
1.6.5.3
5.674e-265
820.0
BYDH3_k127_8383487_3
Putative RNA methylase family UPF0020
-
-
-
4.207e-205
642.0
BYDH3_k127_8383487_4
Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides
K01207
-
3.2.1.52
1.838e-200
627.0
BYDH3_k127_8383487_5
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone
Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)
K01875
-
6.1.1.11
5.343e-222
691.0
BYDH3_k127_8398372_1
Murein-degrading enzyme that degrades murein glycan strands and insoluble, high-molecular weight murein sacculi, with the concomitant formation of a 1,6-anhydromuramoyl product. Lytic transglycosylases (LTs) play an integral role in the metabolism of the peptidoglycan (PG) sacculus. Their lytic action creates space within the PG sacculus to allow for its expansion as well as for the insertion of various structures such as secretion systems and flagella
The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes
Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX
Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the phosphoenolpyruvate synthase (PEPS) by catalyzing its phosphorylation dephosphorylation
Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34
Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain
Phosphoribosylformylglycinamidine synthase involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate
K01952
-
6.3.5.3
0.0
1174.0
BYDH3_k127_8659133_0
Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
K02400
-
-
0.0
1151.0
BYDH3_k127_869379_1
Required for formation of the rod structure in the basal body of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins
K03798
-
-
0.0
1154.0
BYDH3_k127_8726636_1
Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives
Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity
IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of IGP and AICAR
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
K15633
-
5.4.2.12
8.634e-275
852.0
BYDH3_k127_8821998_1
Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide
Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring
K01935
-
6.3.3.3
0.000000000000000000000000000000000000000006982
155.0
BYDH3_k127_8821998_13
Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
K03676
-
-
0.000000000000000000000000000000000000001843
147.0
BYDH3_k127_8821998_14
-
-
-
-
0.0000000000000000000007369
100.0
BYDH3_k127_8821998_2
Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters
Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl- L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway
Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide
One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA
Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation
Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome
Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another
Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB
K04044
-
-
2.666e-283
881.0
BYDH3_k127_8856478_1
Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur atoms from cysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins
A scaffold on which IscS assembles Fe-S clusters. It is likely that Fe-S cluster coordination is flexible as the role of this complex is to build and then hand off Fe-S clusters
Condensation of UDP-2,3-diacylglucosamine and 2,3- diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu)
K01885
-
6.1.1.17
3.678e-257
797.0
BYDH3_k127_894895_2
-
-
-
-
2.905e-211
670.0
BYDH3_k127_894895_3
TIGRFAM RND efflux system, outer membrane lipoprotein, NodT family
K18139
-
-
9.135e-204
643.0
BYDH3_k127_894895_4
GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs
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). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS
Required for chromosome condensation and partitioning
K03529
-
-
0.0
1556.0
BYDH3_k127_9096875_1
Essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and that serves as a cytoplasmic membrane anchor for the Z ring. Also required for the recruitment to the septal ring of downstream cell division proteins
Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5- dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon
CAAX prenyl protease N-terminal, five membrane helices
K06013
-
3.4.24.84
0.0001561
44.0
BYDH3_k127_9193220_0
PFAM peptidase M3A and M3B thimet oligopeptidase F
K01414
-
3.4.24.70
0.0
1064.0
BYDH3_k127_9193220_1
General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr)
Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE
K03695
-
-
0.0
1509.0
BYDH3_k127_9210165_1
PFAM EAL domain protein
-
-
-
2.954e-258
807.0
BYDH3_k127_9210165_2
SMART Sel1 domain protein repeat-containing protein
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
-
-
-
0.0
1752.0
BYDH3_k127_9231748_1
ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP
Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins
Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase
Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate
K08289
-
2.1.2.2
1.105e-215
674.0
BYDH3_k127_9287939_2
PFAM sigma-54 factor interaction domain-containing protein
-
-
-
4.88e-212
667.0
BYDH3_k127_9287939_3
Domain present in phytochromes and cGMP-specific phosphodiesterases.
Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA
Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine
Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase
Oxygenase that introduces the hydroxyl group at carbon five of 2-nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinol resulting in the formation of 2-nonaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4- benzoquinol
Functions in complex with FlhD as a master transcriptional regulator that regulates transcription of several flagellar and non-flagellar operons by binding to their promoter region. Activates expression of class 2 flagellar genes, including fliA, which is a flagellum-specific sigma factor that turns on the class 3 genes. Also regulates genes whose products function in a variety of physiological pathways
Functions in complex with FlhC as a master transcriptional regulator that regulates transcription of several flagellar and non-flagellar operons by binding to their promoter region. Activates expression of class 2 flagellar genes, including fliA, which is a flagellum-specific sigma factor that turns on the class 3 genes. Also regulates genes whose products function in a variety of physiological pathways
May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine
K01251
-
3.3.1.1
2.296e-294
906.0
BYDH3_k127_9508728_1
Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme
K00789
-
2.5.1.6
7.437e-229
711.0
BYDH3_k127_9508728_2
PFAM metal-dependent phosphohydrolase HD sub domain
Catalyzes the stereoinversion of LL-2,6- diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso- DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan
Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and or degradation of damaged proteins
Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides
Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group
Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs
Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate
Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation
