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
Part of the ABC transporter FtsEX involved in cellular division
K09811
-
-
0.0000000000000000000000000000909
127.0
BYDH3_k127_10277192_6
COG0494 NTP pyrophosphohydrolases including oxidative damage repair enzymes
-
-
-
0.0008767
48.0
BYDH3_k127_10308142_0
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
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
K02931
-
-
0.0000000000000000000000000000000000000000127
159.0
BYDH3_k127_10308142_2
Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
K02874
-
-
0.000000000000000000000000000000005086
131.0
BYDH3_k127_10308142_3
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
K02994
-
-
0.00000000000000000000000000000009912
128.0
BYDH3_k127_10308142_4
One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site
K02954
-
-
0.000000000000000001084
88.0
BYDH3_k127_10313414_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)
K01870
-
6.1.1.5
4.716e-235
769.0
BYDH3_k127_10313414_1
Catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
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)
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
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
0.000000000000000000000000000001104
126.0
BYDH3_k127_10782375_7
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
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
transferase activity, transferring glycosyl groups
K01179,K12567,K20276,K21000
-
2.7.11.1,3.2.1.4
0.0000000000000000000000000000000000000000001297
180.0
BYDH3_k127_11052727_8
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
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
1.514e-251
800.0
BYDH3_k127_11366415_1
Beta-lactamase superfamily domain
-
-
-
0.0000000000000000000504
100.0
BYDH3_k127_11366415_2
ubiE/COQ5 methyltransferase family
-
-
-
0.0000000000000003543
85.0
BYDH3_k127_11366415_3
Extracellular solute-binding protein
K02027
-
-
0.0005894
52.0
BYDH3_k127_11393757_0
Transposase IS200 like
-
-
-
0.000000000000000000000002283
111.0
BYDH3_k127_11393757_1
IMG reference gene
-
-
-
0.00000000000000000000003602
107.0
BYDH3_k127_11448305_0
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
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
Evidence 4 Homologs of previously reported genes of
-
-
-
0.000000002539
66.0
BYDH3_k127_12730955_0
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)
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
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
K03625
-
-
0.00000000000000000000000001779
120.0
BYDH3_k127_12847604_3
Belongs to the bacterial ribosomal protein bL32 family
K02911
GO:0003674,GO:0003735,GO:0005198
-
0.0000000002221
66.0
BYDH3_k127_12859479_0
Belongs to the CDP-alcohol phosphatidyltransferase class-I family
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
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
Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit
K09761
-
2.1.1.193
0.00000000000000000000000001989
117.0
BYDH3_k127_1360954_4
-
-
-
-
0.0000000000000000000001715
109.0
BYDH3_k127_1360954_5
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
-
-
0.000000000000000000003341
97.0
BYDH3_k127_1360954_6
addiction module toxin, RelE StbE family
K19157
-
-
0.00000000000000000001123
94.0
BYDH3_k127_1360954_7
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
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
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
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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)
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)
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
K03734
-
2.7.1.180
0.000000000000000000000000001843
123.0
BYDH3_k127_1509857_2
-
-
-
-
0.000002056
53.0
BYDH3_k127_1509857_3
FMN-binding domain protein
-
-
-
0.000002368
59.0
BYDH3_k127_1534038_0
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)
Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
-
-
-
0.000000000000000000000000000000000000000009441
162.0
BYDH3_k127_2313705_7
Necessary for normal cell division and for the maintenance of normal septation
K03978
-
-
0.000000000000000000000000000000000001142
145.0
BYDH3_k127_2313705_8
PFAM inositol monophosphatase
K01082
-
3.1.3.7
0.0000000000000000000000000000000009252
141.0
BYDH3_k127_2313705_9
Belongs to the Fur family
K02076,K03711
-
-
0.0000000000000000000003934
100.0
BYDH3_k127_2483080_0
Catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
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
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
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
TIGRFAM haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
-
-
-
0.00000000000000000000000000000000000000007145
159.0
BYDH3_k127_2838990_21
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
COG0543 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases
K00523
-
1.17.1.1
0.00000000000000000002976
99.0
BYDH3_k127_2838990_31
GIY-YIG catalytic domain
K07461
-
-
0.00000000000000000009855
91.0
BYDH3_k127_2838990_33
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 membrane fusion protein (MFP) (TC 8.A.1) family
K15727
-
-
0.000000002909
70.0
BYDH3_k127_2838990_41
PaaX-like protein
K02616
-
-
0.000000003215
65.0
BYDH3_k127_2838990_42
heme binding
K06194
-
-
0.00000003296
64.0
BYDH3_k127_2838990_43
FMN_bind
-
-
-
0.000003854
55.0
BYDH3_k127_2838990_44
NUDIX domain
K03574
-
3.6.1.55
0.00005434
54.0
BYDH3_k127_2838990_45
Phosphinothricin acetyltransferase
K03823
-
2.3.1.183
0.0000764
51.0
BYDH3_k127_2838990_46
Domain of unknown function (DUF4342)
-
-
-
0.0001187
48.0
BYDH3_k127_2838990_47
Nucleotidyltransferase domain
-
-
-
0.0002344
52.0
BYDH3_k127_2838990_5
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
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)
Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII
An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay
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
Phenylacetic acid degradation operon negative regulatory protein PaaX
K02616
-
-
0.0000005604
58.0
BYDH3_k127_3360255_22
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
K03073
-
-
0.00004313
48.0
BYDH3_k127_3360255_23
Copper binding proteins, plastocyanin/azurin family
-
-
-
0.0003293
49.0
BYDH3_k127_3360255_3
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
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
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
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
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)
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
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
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)
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
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
-
-
0.000000000000000000000001992
112.0
BYDH3_k127_4410147_32
Diguanylate cyclase
-
-
-
0.000000000000000000000002242
110.0
BYDH3_k127_4410147_33
Belongs to the peptidase S11 family
K07258
-
3.4.16.4
0.00000000000000000000001677
112.0
BYDH3_k127_4410147_34
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
K06024
-
-
0.00000000000000000000001704
109.0
BYDH3_k127_4410147_35
Belongs to the bacterial ribosomal protein bL27 family
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)
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 DNA repair and RecF pathway recombination
K03584
-
-
0.00000004243
62.0
BYDH3_k127_4652697_0
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
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
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
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
K02356
-
-
0.000000000000000000000000000000000005949
143.0
BYDH3_k127_4805770_7
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
Belongs to the small heat shock protein (HSP20) family
K13993
-
-
0.000000000000000000386
92.0
BYDH3_k127_4938697_12
Belongs to the acylphosphatase family
K01512
-
3.6.1.7
0.0000000000000000007023
90.0
BYDH3_k127_4938697_13
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
0.00000000000000007167
85.0
BYDH3_k127_4938697_14
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Responsible for synthesis of pseudouridine from uracil
K06180
-
5.4.99.23
0.00000000000000000000000000000000000000000000918
171.0
BYDH3_k127_4938697_8
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
PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
-
-
-
0.00000000000000000000000000000000000000000002534
169.0
BYDH3_k127_4954609_2
PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
K01802
-
5.2.1.8
0.00000000000000000000000004085
110.0
BYDH3_k127_4954609_3
DUF167
K09131
-
-
0.0000000426
57.0
BYDH3_k127_4954609_4
seems to be involved in modulation of the sigma(54) (RpoN) activity for quorum sensing
K05808
-
-
0.0000007958
57.0
BYDH3_k127_4954609_5
-
-
-
-
0.00006612
46.0
BYDH3_k127_5274941_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
K02470
-
5.99.1.3
1.283e-207
666.0
BYDH3_k127_5274941_1
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)
Aminoacyl tRNA synthetase class II, N-terminal domain
K01889
-
6.1.1.20
0.00000000000000000000008098
98.0
BYDH3_k127_542842_0
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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
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
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
TIGRFAM DNA internalization-related competence protein ComEC Rec2
K02238
-
-
0.000000000000171
78.0
BYDH3_k127_5899626_4
Ribosomal L28 family
K02902
-
-
0.0002127
46.0
BYDH3_k127_5924905_0
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
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
K03624
-
-
0.00000000000000000000000000000006176
130.0
BYDH3_k127_6130820_12
Cytochrome C biogenesis protein transmembrane region
-
-
-
0.000000000000000000000000000000365
132.0
BYDH3_k127_6130820_13
23S rRNA-intervening sequence protein
-
-
-
0.00000000000000001799
86.0
BYDH3_k127_6130820_14
RQC
K03654
-
3.6.4.12
0.0000000000000001463
80.0
BYDH3_k127_6130820_15
Cytochrome C biogenesis protein transmembrane region
-
-
-
0.00000000000009308
76.0
BYDH3_k127_6130820_16
Domain of unknown function (DUF4145)
-
-
-
0.000000001267
68.0
BYDH3_k127_6130820_18
Involved in formation and maintenance of cell shape
K03570
-
-
0.00001121
56.0
BYDH3_k127_6130820_19
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
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
Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane
K03980
-
-
0.0000000000000000000000000000000000000002062
169.0
BYDH3_k127_6305536_5
PFAM RNP-1 like RNA-binding protein
-
-
-
0.00000000000000000000000000558
112.0
BYDH3_k127_6305536_6
pfkB family carbohydrate kinase
-
-
-
0.0000000000000000000008135
107.0
BYDH3_k127_6305536_7
This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
K02897
-
-
0.00000000000000000001646
100.0
BYDH3_k127_6305536_8
Uncharacterized ACR, COG1430
K09005
-
-
0.000000000000000004109
90.0
BYDH3_k127_6305536_9
HicA toxin of bacterial toxin-antitoxin,
-
-
-
0.0000000000005005
71.0
BYDH3_k127_6413767_0
Belongs to the class-I aminoacyl-tRNA synthetase family
K01869
-
6.1.1.4
4.642e-287
909.0
BYDH3_k127_6413767_1
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
5.64e-197
623.0
BYDH3_k127_6413767_10
Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2- amino-6-oxopimelate using succinyl-CoA
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
it plays a direct role in the translocation of protons across the membrane
K02108
-
-
0.000000000000000000000000000000000000001464
157.0
BYDH3_k127_6413767_19
acid membrane antigen A
-
-
-
0.000000000000000000000000000000000000007097
158.0
BYDH3_k127_6413767_2
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
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
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
K03086
-
-
0.0000003138
62.0
BYDH3_k127_6413767_32
ATP synthase, delta epsilon subunit, beta-sandwich domain protein
K02114
-
-
0.0000005419
54.0
BYDH3_k127_6413767_34
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
K02113
-
-
0.000004253
54.0
BYDH3_k127_6413767_35
NUDIX domain
K01515,K03574
-
3.6.1.13,3.6.1.55
0.00007719
51.0
BYDH3_k127_6413767_36
helicase activity
K06915,K19172
-
-
0.0001101
54.0
BYDH3_k127_6413767_4
ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner
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)
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
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
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
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
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
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
-
-
-
0.00000000000000000000000000002382
124.0
BYDH3_k127_6743566_8
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
K03625
-
-
0.0000000000000000000000002325
117.0
BYDH3_k127_6743566_9
NUDIX domain
-
-
-
0.000000007055
66.0
BYDH3_k127_7113515_0
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
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
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
-
-
0.0000000000003792
75.0
BYDH3_k127_7376078_9
Type I restriction enzyme R protein N terminus (HSDR_N)
K01153
-
3.1.21.3
0.000000001856
61.0
BYDH3_k127_7689896_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
K01873
-
6.1.1.9
4.487e-209
671.0
BYDH3_k127_7689896_1
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
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
K02952
-
-
0.000000000000000000000000000000004434
131.0
BYDH3_k127_7729827_6
Translation initiation factor 1A / IF-1
K02518
-
-
0.0000000000002662
72.0
BYDH3_k127_7729827_7
Belongs to the bacterial ribosomal protein bS16 family
K02959
-
-
0.0000000000003921
75.0
BYDH3_k127_7729827_8
Ribosomal protein L17
K02879
-
-
0.00000000000155
69.0
BYDH3_k127_7729827_9
Belongs to the bacterial ribosomal protein bL36 family
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
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
K02890
-
-
0.000000000000000000001266
100.0
BYDH3_k127_7964305_3
One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
K02961
-
-
0.00000000000000000009013
91.0
BYDH3_k127_7964305_4
Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
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
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
transferase activity, transferring glycosyl groups
-
-
-
0.000000000000000000001817
107.0
BYDH3_k127_9075170_23
Glycosyl transferases group 1
-
-
-
0.0000000000000000001369
101.0
BYDH3_k127_9075170_24
Iron-sulfur cluster-binding domain
-
-
-
0.0000000000001074
82.0
BYDH3_k127_9075170_25
Methionine biosynthesis protein MetW
-
-
-
0.0000000000002157
81.0
BYDH3_k127_9075170_26
methyltransferase
-
-
-
0.000000000757
68.0
BYDH3_k127_9075170_27
GtrA-like protein
-
-
-
0.0000001182
59.0
BYDH3_k127_9075170_28
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
Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
K00033
-
1.1.1.343,1.1.1.44
0.000000000000000000001716
100.0
BYDH3_k127_9301062_12
-
-
-
-
0.00000000000000000000379
96.0
BYDH3_k127_9301062_13
Membrane-associated phospholipid phosphatase
K19302
-
3.6.1.27
0.00000000000000003132
88.0
BYDH3_k127_9301062_14
SpoVT / AbrB like domain
K07172
-
-
0.00000000000003127
76.0
BYDH3_k127_9301062_15
-
-
-
-
0.0000000002233
61.0
BYDH3_k127_9301062_16
COG NOG14600 non supervised orthologous group
-
-
-
0.0000000004214
60.0
BYDH3_k127_9301062_17
-
-
-
-
0.00000000318
58.0
BYDH3_k127_9301062_18
3-beta hydroxysteroid dehydrogenase/isomerase family
K15856,K22252
-
1.1.1.135,1.1.1.281
0.00007583
54.0
BYDH3_k127_9301062_2
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
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
Bacterial toxin of type II toxin-antitoxin system, YafQ
-
-
-
0.00000001519
59.0
BYDH3_k127_9379124_11
transcriptional
-
-
-
0.000006047
57.0
BYDH3_k127_9379124_13
Transcriptional regulator, TrmB
-
-
-
0.0006012
50.0
BYDH3_k127_9379124_14
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
0.0008631
50.0
BYDH3_k127_9379124_2
Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family
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
-
-
3.954e-293
924.0
BYDH3_k127_9383933_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
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
K02965
-
-
0.00000000000000000000000002396
112.0
BYDH3_k127_9554741_1
Domain of unknown function (DUF4347)
-
-
-
0.0000000000000000000000002464
124.0
BYDH3_k127_9554741_2
negative regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment
-
-
-
0.0000000000000000003196
104.0
BYDH3_k127_9554741_3
Pkd domain containing protein
-
-
-
0.00000000003363
78.0
BYDH3_k127_9554741_4
Tetratricopeptide repeat
-
-
-
0.00003416
54.0
BYDH3_k127_9585298_0
CYTH
-
-
-
0.00000004734
59.0
BYDH3_k127_9585298_1
SWIM zinc finger
-
-
-
0.0003498
50.0
BYDH3_k127_9652062_0
Protein conserved in bacteria
-
-
-
0.00000000108
70.0
BYDH3_k127_9768769_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
