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)
Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides
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)
K01870
-
6.1.1.5
4.148e-260
834.0
BYDH3_k127_10177621_1
Phosphoglycerate mutase family
K02226
-
3.1.3.73
0.00000000000000000129
93.0
BYDH3_k127_10177621_2
Involved in DNA repair and RecF pathway recombination
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
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
K03550
-
3.6.4.12
0.00000000000000000000000000000002787
130.0
BYDH3_k127_10437839_0
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
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
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
-
-
0.000000000001962
70.0
BYDH3_k127_10513986_0
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)
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
COG0494 NTP pyrophosphohydrolases including oxidative damage repair enzymes
-
-
-
0.00000000000000000000000000003572
123.0
BYDH3_k127_10513986_6
Thiol-disulfide oxidoreductase which is required in disulfide reduction during c-type cytochrome synthesis. May accept reducing equivalents from CcdA, leading to breakage of disulfide bonds in apocytochrome c
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
K03701
-
-
6.275e-290
918.0
BYDH3_k127_1054463_1
PFAM Bacterial type II secretion system protein F domain
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
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
K01803
-
5.3.1.1
0.00000000000000000000000000006869
127.0
BYDH3_k127_10973166_0
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
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)
K09765
-
1.17.99.6
0.0000000000000000000000000000000000000000000897
165.0
BYDH3_k127_10994176_3
-
-
-
-
0.000000000000000000000000013
123.0
BYDH3_k127_10994176_4
methylated-DNA- protein -cysteine S-methyltransferase
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
K03282
-
-
0.000000009583
61.0
BYDH3_k127_11550092_0
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
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
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
K01358
-
3.4.21.92
0.000000000000000000000000000000000000000007686
155.0
BYDH3_k127_11550092_4
Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions
K03530
-
-
0.0000000000000000000000003558
108.0
BYDH3_k127_11579267_0
Belongs to the NAD(P)-dependent epimerase dehydratase family
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)
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)
K02563
-
2.4.1.227
0.00000000000000000000000000000000000002928
149.0
BYDH3_k127_12102599_0
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
K02469
-
5.99.1.3
3.526e-281
886.0
BYDH3_k127_12102599_1
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction
K00962
-
2.7.7.8
2.523e-234
745.0
BYDH3_k127_12102599_10
Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
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
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
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
Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
K02652
-
-
0.0000000000000009384
81.0
BYDH3_k127_12370679_0
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
Catalyzes the reversible phosphorylation of UMP to UDP
K09903
-
2.7.4.22
0.000007923
49.0
BYDH3_k127_1248444_0
Glycosyl transferases group 1
K13668
-
2.4.1.346
0.0000000000000000000000000000000000009226
143.0
BYDH3_k127_12595297_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
K04066
-
-
0.0000003658
60.0
BYDH3_k127_12595297_1
Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester
K01975
-
3.1.4.58
0.0000003738
56.0
BYDH3_k127_12595297_2
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
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
May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO
K06187
-
-
0.000000000000000000002595
95.0
BYDH3_k127_13113550_0
Catalyzes the addition of an amino 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
0.000000000000000000000000000003844
123.0
BYDH3_k127_13113550_1
ATP-dependent DNA helicase
K03657
-
3.6.4.12
0.0000000000000000000000000000574
117.0
BYDH3_k127_13113550_2
PFAM Divergent PAP2 family
K09775
-
-
0.0000000000000008044
83.0
BYDH3_k127_13402_0
4-amino-4-deoxy-L-arabinose transferase activity
K16648
-
-
0.0004154
53.0
BYDH3_k127_1343642_0
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 NADPH and FADH(2) as the reductant
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
RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme
K03536
-
3.1.26.5
0.000005493
53.0
BYDH3_k127_1382669_2
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
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
-
-
0.0000000000000000000000009487
110.0
BYDH3_k127_1473787_6
Endonuclease containing a URI domain
K07461
-
-
0.0000000005694
61.0
BYDH3_k127_1473787_7
3D domain
-
-
-
0.00000003677
55.0
BYDH3_k127_1662653_0
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
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
Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
K02988
-
-
0.000000000000000000000000000000000000000007658
160.0
BYDH3_k127_1662653_11
One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome
K02926
-
-
0.000000000000000000000000000000000000001375
155.0
BYDH3_k127_1662653_12
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
K00939
-
2.7.4.3
0.00000000000000000000000000000000000004985
153.0
BYDH3_k127_1662653_13
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
K02906
-
-
0.0000000000000000000000000000000000002916
150.0
BYDH3_k127_1662653_14
Involved in the binding of tRNA to the ribosomes
K02946
-
-
0.000000000000000000000000000000000002575
141.0
BYDH3_k127_1662653_15
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
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
K02965
-
-
0.0000000000000000000000000000006098
124.0
BYDH3_k127_1662653_17
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
-
-
0.0000000000000000000000000000236
120.0
BYDH3_k127_1662653_18
One of the proteins that surrounds the polypeptide exit tunnel on the outside of the 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
One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity
One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome
K02892
-
-
0.00007723
49.0
BYDH3_k127_1662653_26
Belongs to the universal ribosomal protein uL29 family
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
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
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
K03086
-
-
0.0000000000000000000000000085
121.0
BYDH3_k127_1691066_4
Glycosyl hydrolase family 3 C-terminal domain
-
-
-
0.000000006056
70.0
BYDH3_k127_1691066_5
-
-
-
-
0.000125
50.0
BYDH3_k127_1719913_0
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
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 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
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
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
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
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
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
K04066
-
-
0.00000000000000000000000002438
112.0
BYDH3_k127_3300037_2
O-Antigen ligase
-
-
-
0.000000000001493
80.0
BYDH3_k127_3300037_3
Glycosyl transferases group 1
-
-
-
0.00000000001585
76.0
BYDH3_k127_3300037_4
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
Membrane protein involved in the export of O-antigen and teichoic acid
-
-
-
0.0002695
50.0
BYDH3_k127_3394640_0
DNA polymerase III, alpha subunit
K02337,K14162
-
2.7.7.7
1.869e-282
906.0
BYDH3_k127_3394640_1
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)
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation
K02935
-
-
0.000000000000000000000000000000000000004844
149.0
BYDH3_k127_3394640_12
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
Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
K02864
-
-
0.00000000000000000000000000001291
125.0
BYDH3_k127_3394640_14
Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
K02005,K13888
-
-
0.00000000000000000000000000002227
130.0
BYDH3_k127_3394640_15
Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
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)
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
Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions
K03530
-
-
0.00000008438
53.0
BYDH3_k127_3446203_3
-
-
-
-
0.0002535
46.0
BYDH3_k127_3504174_0
Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA
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
Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with geranylgeranyl diphosphate (GGPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30E,34E,38E)-undecaprenyl diphosphate (tritrans,heptacis-UPP). It is probably the precursor of glycosyl carrier lipids
the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide , a short internal open reading frame. During trans-translation Ala- aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA
K03664
-
-
0.000000000000000000000000000000000000000398
154.0
BYDH3_k127_3569730_3
IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins
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
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
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)
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
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
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
K07738
-
-
0.0000000000000000000000000000000000000005109
157.0
BYDH3_k127_4037048_2
Domain of unknown function (DUF4131)
K02238
-
-
0.00000000009181
73.0
BYDH3_k127_4076047_0
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)
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
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 as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
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
K03168
-
5.99.1.2
0.000000000000000000000000000000000002705
141.0
BYDH3_k127_449024_0
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
Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
K01611
-
4.1.1.50
0.00000000000000000000001685
104.0
BYDH3_k127_4495538_4
Cbs domain
-
-
-
0.0000000000000002713
88.0
BYDH3_k127_4495538_5
HD domain
-
-
-
0.0000000000000007641
87.0
BYDH3_k127_4495538_6
membrane
K08978
-
-
0.0000000007284
70.0
BYDH3_k127_4495538_7
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)
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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
K03702
-
-
3.98e-231
733.0
BYDH3_k127_4850211_1
Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
Involved in formation and maintenance of cell shape
K03570
-
-
0.000000000000000000000001623
111.0
BYDH3_k127_5018776_0
GTP-binding protein LepA C-terminus
K03596
-
-
4.978e-210
669.0
BYDH3_k127_5018776_1
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
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
Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP)
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
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
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
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
K02343
-
2.7.7.7
0.000000002433
68.0
BYDH3_k127_5967691_4
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
K03086
-
-
0.000001533
60.0
BYDH3_k127_6099013_0
DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA
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
0.0000000000000000000000000000000002257
135.0
BYDH3_k127_6099013_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)
Function proposed based on presence of conserved amino acid motif, structural feature or limited homology
-
-
-
0.0000000000533
70.0
BYDH3_k127_6249021_1
Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair
Peptidoglycan hydrolase involved in the splitting of the septum during cell division
K22409
-
3.5.1.28
0.0000000000000004758
91.0
BYDH3_k127_6350063_0
Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine
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
K17247
-
-
0.00000000001127
75.0
BYDH3_k127_6550354_5
ATP-dependent DNA helicase RecQ
K03654
-
3.6.4.12
0.0000000002612
64.0
BYDH3_k127_6583914_0
Peptidoglycan polymerase that is essential for cell wall elongation
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
K15633
-
5.4.2.12
0.00000000000000000000004111
101.0
BYDH3_k127_6604672_8
PFAM response regulator receiver
K03413
-
-
0.000000000000000002097
89.0
BYDH3_k127_6673723_0
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
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
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)
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 as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
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)
K02563
-
2.4.1.227
0.00000000001364
68.0
BYDH3_k127_6943381_4
Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
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
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
K02952
-
-
0.0000000000000000000000000000000000000002168
153.0
BYDH3_k127_7294723_3
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
K02871
-
-
0.000000000000000000000000000000000000005326
149.0
BYDH3_k127_7294723_4
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
K02948
-
-
0.00000000000000000000000000000000000005406
147.0
BYDH3_k127_7294723_5
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
K02518
-
-
0.0000000000000000000000002734
110.0
BYDH3_k127_7294723_6
Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
Belongs to the bacterial ribosomal protein bL36 family
K02919
-
-
0.00000000005596
66.0
BYDH3_k127_7294723_9
Belongs to the universal ribosomal protein uS9 family
K02996
-
-
0.000000002124
62.0
BYDH3_k127_7344895_0
Hep Hag repeat protein
-
-
-
0.000000000000003341
83.0
BYDH3_k127_7344895_1
Bacterial protein of unknown function (DUF916)
-
-
-
0.0000001444
63.0
BYDH3_k127_7502836_0
PFAM Type II secretion system protein E
K02454
-
-
0.0000000000000000000000000000000000000002305
155.0
BYDH3_k127_7627726_1
Probable zinc-ribbon domain
-
-
-
0.000008955
55.0
BYDH3_k127_772408_0
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
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
Belongs to the small heat shock protein (HSP20) family
K13993
-
-
0.0000000000000000004196
94.0
BYDH3_k127_772408_6
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
COGs COG1670 Acetyltransferase including N-acetylase of ribosomal protein
-
-
-
0.000000000000000000000000000000000000000004134
161.0
BYDH3_k127_8006814_7
Immunoglobulin-like domain of bacterial spore germination
-
-
-
0.000000000000000000000000198
111.0
BYDH3_k127_8006814_8
Domain of unknown function (DUF4395)
-
-
-
0.00000000000000000000005937
108.0
BYDH3_k127_8056319_0
Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
-
-
-
0.000000000000000000000009032
115.0
BYDH3_k127_8056319_1
Domain of unknown function (DUF4105)
-
-
-
0.00000000000000001051
87.0
BYDH3_k127_8139162_2
Protein involved in outer membrane biogenesis
K17230
-
-
0.0000000000000000009276
95.0
BYDH3_k127_8229826_0
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
K07056
-
2.1.1.198
0.000000000000000000000001825
107.0
BYDH3_k127_8347548_7
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
Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
K02109
-
-
0.000000000007061
72.0
BYDH3_k127_8347548_9
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
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
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
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
Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA
K07042
-
-
0.00000000000000123
88.0
BYDH3_k127_9191768_6
Prokaryotic diacylglycerol kinase
K00887,K00901
-
2.7.1.107,2.7.1.66
0.0000000000001466
79.0
BYDH3_k127_9191768_7
protocatechuate 3,4-dioxygenase
-
-
-
0.0006114
53.0
BYDH3_k127_9326822_0
COG0189 Glutathione synthase Ribosomal protein S6 modification enzyme (glutaminyl transferase)
-
-
-
0.0000000000000000000000000000000000000000008429
173.0
BYDH3_k127_9326822_1
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
K01159
-
3.1.22.4
0.00000000000000000000135
95.0
BYDH3_k127_9326822_2
7 transmembrane helices usually fused to an inactive transglutaminase
-
-
-
0.000000000000005877
83.0
BYDH3_k127_9351143_0
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
Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves
K05896
-
-
0.000000000000000000000000001761
121.0
BYDH3_k127_9351143_2
Belongs to the bacterial ribosomal protein bL27 family
May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO
K06187
-
-
0.0000000000000000000000001026
119.0
BYDH3_k127_9402671_0
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
Belongs to the bacterial solute-binding protein 9 family
K09815,K09818
-
-
0.000000000000001806
85.0
BYDH3_k127_9402671_3
Uncharacterized ACR, COG1430
K09005
-
-
0.0000000000000528
80.0
BYDH3_k127_9402671_4
Glycosyl transferase family 4
-
-
-
0.00001225
51.0
BYDH3_k127_9427104_0
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
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
-
-
-
0.000000000000000000000006884
108.0
BYDH3_k127_9427104_3
PFAM RNP-1 like RNA-binding protein
-
-
-
0.00000000000000000000001237
104.0
BYDH3_k127_9427104_4
Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
K02005
-
-
0.00000000000000000000001266
112.0
BYDH3_k127_9427104_5
helix_turn_helix multiple antibiotic resistance protein
-
-
-
0.0000000000000000000004411
102.0
BYDH3_k127_9429365_0
Type II secretory pathway component PulF
K02505,K12278
-
-
0.000000000000000003327
90.0
BYDH3_k127_9429365_1
Endonuclease Exonuclease Phosphatase
-
-
-
0.00002434
56.0
BYDH3_k127_9429365_2
Protein of unknown function (DUF1559)
-
-
-
0.000135
51.0
BYDH3_k127_9429365_3
Prokaryotic N-terminal methylation motif
-
-
-
0.000558
50.0
BYDH3_k127_9524482_0
DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA
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)
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
0.0000000000000000000000000000003729
141.0
BYDH3_k127_9745519_3
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
K00943
-
2.7.4.9
0.00000000000000000000002188
111.0
BYDH3_k127_9745519_4
COG1278 Cold shock
-
-
-
0.00000000000001863
74.0
BYDH3_k127_9745519_5
Belongs to the peptidase S8 family
-
-
-
0.00000001494
68.0
BYDH3_k127_9745519_6
Peptidase family M23
-
-
-
0.0001217
53.0
BYDH3_k127_9745519_7
C-terminal domain of CHU protein family
-
-
-
0.0004289
53.0
BYDH3_k127_9781163_0
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)
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
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
