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
-
-
-
0.0000000000000000000000001301
113.0
DPH2_k127_10062527_0
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
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
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)
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
DPH2_k127_10411307_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
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
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
K03086
-
-
0.000006607
51.0
DPH2_k127_10796644_0
EamA-like transporter family
K08978
-
-
0.0000000000000000000000000001039
123.0
DPH2_k127_10796644_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
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
This protein specifically catalyzes the removal of signal peptides from prolipoproteins
K03101
-
3.4.23.36
0.0000000006407
67.0
DPH2_k127_10883293_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
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
K01462
-
3.5.1.88
0.0000000000000000000000000002226
120.0
DPH2_k127_10883293_2
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
K00604
-
2.1.2.9
0.000000000000000000000000005588
113.0
DPH2_k127_10883293_3
Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester
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
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
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
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
K03111
-
-
0.000000000000000000000000000000000007069
141.0
DPH2_k127_11530571_3
-
-
-
-
0.000000000000000000001059
103.0
DPH2_k127_11530571_4
This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
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
0.000000000000000000000000000000000000001616
154.0
DPH2_k127_11573601_1
Methicillin resistance protein
-
-
-
0.000000000000000000000000000000008156
140.0
DPH2_k127_11573601_2
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
0.00000000002726
66.0
DPH2_k127_11619309_0
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
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
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)
K01823
-
5.3.3.2
0.000000000000000000000000002345
119.0
DPH2_k127_11698442_2
-
-
-
-
0.0002665
52.0
DPH2_k127_11698442_3
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
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
DPH2_k127_11699226_1
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
-
-
0.00000000000000000000000002844
110.0
DPH2_k127_11699226_2
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
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
-
-
0.0001269
48.0
DPH2_k127_11872006_0
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
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
0.000000000000000000000004108
104.0
DPH2_k127_1212077_0
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
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
K03070
-
-
4.573e-289
927.0
DPH2_k127_12123886_1
cell wall formation
K00075
-
1.3.1.98
0.0000000000000256
74.0
DPH2_k127_12123886_2
Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
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
-
-
1.908e-297
930.0
DPH2_k127_12238468_1
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
K02358
-
-
0.00000000000000105
77.0
DPH2_k127_12238468_2
hydrolase, family 25
-
-
-
0.0006758
48.0
DPH2_k127_1273298_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
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
DPH2_k127_1273298_5
Oxidoreductase NAD-binding domain
-
-
-
0.00000000001306
68.0
DPH2_k127_1311941_0
First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
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
-
-
0.0000000000000000000000000002091
124.0
DPH2_k127_1531883_0
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 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
DPH2_k127_1648734_2
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
-
-
0.00000000000000000000000000000000002347
138.0
DPH2_k127_1648734_3
Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
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
DPH2_k127_1670371_1
Polysaccharide biosynthesis protein
-
-
-
0.0000000000001495
83.0
DPH2_k127_1670371_2
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
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
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)
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
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
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
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
-
-
0.00000000000728
66.0
DPH2_k127_2513350_0
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
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)
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
-
-
2.326e-224
710.0
DPH2_k127_2683072_1
membrane-associated protein
-
-
-
0.00000006712
62.0
DPH2_k127_2694918_0
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
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
-
-
0.00000000000000000000000004621
115.0
DPH2_k127_2718047_1
D-alanyl-D-alanine carboxypeptidase
K01286,K07258
-
3.4.16.4
0.0000000006281
69.0
DPH2_k127_2718047_2
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
-
-
0.0002896
45.0
DPH2_k127_2745772_0
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
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 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)
K01868
-
6.1.1.3
0.0000000000000000000000000000000000000007331
151.0
DPH2_k127_2929343_1
Staphylococcal nuclease homologues
K01174
-
3.1.31.1
0.000000000000000000000000000000000002329
147.0
DPH2_k127_2929343_2
RNHCP domain
-
-
-
0.0000000000000000000000000000000006646
133.0
DPH2_k127_2943332_0
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily
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
0.0000000004807
61.0
DPH2_k127_3069012_1
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
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
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)
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
-
-
0.000000000000000000000000000000004443
131.0
DPH2_k127_3376022_3
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
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 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
-
-
0.00000000000000000000000000000214
125.0
DPH2_k127_3400965_2
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
K02965
-
-
0.00000000002808
64.0
DPH2_k127_3400965_3
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
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
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
Belongs to the bacterial ribosomal protein bL34 family
K02914
-
-
0.000000000009657
66.0
DPH2_k127_3691109_3
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
DPH2_k127_3746058_0
Glycosyltransferase Family 4
-
-
-
0.00000000000002204
75.0
DPH2_k127_3746058_1
Polymerase
-
-
-
0.000249
53.0
DPH2_k127_3834807_0
ABC-type antimicrobial peptide transport system, permease component
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
ABC-type transport system involved in lipoprotein release permease component
K02004
-
-
0.00000000000000000000000000000000000000000000271
179.0
DPH2_k127_4025956_1
Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
K02005
-
-
0.000000000000000000000003786
114.0
DPH2_k127_4025956_2
helix_turn_helix multiple antibiotic resistance protein
-
-
-
0.0000000000000000000004411
102.0
DPH2_k127_4095006_0
Parallel beta-helix repeats
-
-
-
0.0000000000000000001607
101.0
DPH2_k127_4115193_0
Diacylglycerol kinase
K00887,K00901
-
2.7.1.107,2.7.1.66
0.00000000000008405
79.0
DPH2_k127_4115193_1
Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA
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
Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling
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
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
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
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 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
K07056
-
2.1.1.198
0.0000000000000000001933
90.0
DPH2_k127_5037844_0
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
Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides
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,K03696
-
-
0.0000000000000000000004243
101.0
DPH2_k127_5413420_0
PFAM Bacterial type II secretion system protein F domain
Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
ATPase, P-type transporting, HAD superfamily, subfamily IC
K01531
-
3.6.3.2
9.702e-266
840.0
DPH2_k127_5612531_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
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
DPH2_k127_5612531_2
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
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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
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 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
0.0000000000000000369
83.0
DPH2_k127_6200627_2
PFAM Divergent PAP2 family
K09775
-
-
0.000000000000003857
81.0
DPH2_k127_6210383_0
ATPase, P-type (transporting), HAD superfamily, subfamily IC
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)
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
-
-
4.262e-225
714.0
DPH2_k127_6286337_1
Protein of unknown function (DUF1003)
-
-
-
0.000000000000000000000000000001344
128.0
DPH2_k127_6286337_2
Belongs to the peptidase S8 family
-
-
-
0.0000000000000000000000000000285
138.0
DPH2_k127_6286337_3
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
DPH2_k127_6286337_4
Glycosyl hydrolase family 3 C-terminal domain
-
-
-
0.0000000105
70.0
DPH2_k127_6290875_0
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
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
-
-
0.000001304
58.0
DPH2_k127_6536062_0
it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
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
Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
K02005,K13888
-
-
0.00000000000000000000000000002227
130.0
DPH2_k127_6943139_3
PFAM ribonuclease H
K03469,K06864
-
3.1.26.4
0.000000000000000000000000001393
119.0
DPH2_k127_6943139_4
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
K02867
-
-
0.000000000001516
67.0
DPH2_k127_6943139_5
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
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
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
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
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
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
-
-
0.000000000512
64.0
DPH2_k127_7574167_0
SET domain
K07117
-
-
0.0000000000000000000000000000000003592
136.0
DPH2_k127_7574167_1
Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
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 phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway
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
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
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
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
-
-
0.0000000000000000000000001451
113.0
DPH2_k127_8093484_4
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
0.00000000000000007879
86.0
DPH2_k127_8093484_5
Endonuclease containing a URI domain
K07461
-
-
0.0000000000000005865
87.0
DPH2_k127_8111081_0
Negative regulator of class I heat shock genes (grpE- dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
K03705
-
-
0.00000000000000000000000000000265
130.0
DPH2_k127_8111081_1
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
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)
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
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
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
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
0.0000006232
61.0
DPH2_k127_8531988_2
Probable zinc-ribbon domain
-
-
-
0.00003734
55.0
DPH2_k127_8545117_0
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
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
-
-
0.000000000000000008894
88.0
DPH2_k127_8686823_0
Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor
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
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
Penicillin-binding protein, transpeptidase domain protein
K03587,K08384
-
3.4.16.4
0.0000000000000000000000000000000000001486
148.0
DPH2_k127_9215589_3
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
pyruvate flavodoxin ferredoxin oxidoreductase domain protein
K00174
-
1.2.7.11,1.2.7.3
0.00000000000000000000000000000000008363
136.0
DPH2_k127_9360684_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)
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
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
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
K01409
-
2.3.1.234
0.0000000000000000000000000000000000000004659
152.0
DPH2_k127_9597102_1
ECF sigma factor
K03088
-
-
0.000000000000000000000000000006807
126.0
DPH2_k127_9629179_0
Predicted membrane protein (DUF2339)
-
-
-
0.000002372
59.0
DPH2_k127_963288_0
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
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
-
-
0.0000000000000001681
83.0
DPH2_k127_9832310_0
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)
