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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
K00525
-
1.17.4.1
2.639e-320
1002.0
DYD1_k127_119748_1
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
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
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
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
D-isomer specific 2-hydroxyacid dehydrogenase catalytic region
K03778
-
1.1.1.28
0.000000000000000000000000000000000000001724
153.0
DYD1_k127_1314279_0
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
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
K02115
-
-
0.0000000000000000000000000000000002722
143.0
DYD1_k127_1594048_7
it plays a direct role in the translocation of protons across the membrane
K02108
-
-
0.0000000000000000000000378
109.0
DYD1_k127_1594048_8
Protein of unknown function (DUF1003)
-
-
-
0.000000000000000000009095
97.0
DYD1_k127_1594048_9
Produces ATP from ADP in the presence of a proton gradient across the membrane
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)
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
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
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
-
-
4.111e-225
717.0
DYD1_k127_1692462_1
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)
Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
-
-
-
0.00000000000000000000000000000009027
134.0
DYD1_k127_1692462_11
Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide
K08641
-
3.4.13.22
0.000000000000000000000000005774
118.0
DYD1_k127_1692462_12
Involved in formation and maintenance of cell shape
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
Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction proline is first activated by ATP to form Pro- AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS
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
3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs
K12573,K12585
-
-
2.35e-200
642.0
DYD1_k127_1937083_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)
Belongs to the bacterial ribosomal protein bL32 family
K02911
-
-
0.0001226
49.0
DYD1_k127_1937083_2
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
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
-
-
0.0000000000000000000000001756
117.0
DYD1_k127_1937083_8
KH domain
K06960
-
-
0.00000000000000009718
83.0
DYD1_k127_1937083_9
Belongs to the bacterial ribosomal protein bS16 family
Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
K02956
-
-
0.000000000000000000004757
95.0
DYD1_k127_196450_5
Prokaryotic dksA/traR C4-type zinc finger
K06204
-
-
0.000000002169
64.0
DYD1_k127_1988845_0
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
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
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
0.00000000000000000000000000000001471
132.0
DYD1_k127_2053676_7
Vitamin k epoxide reductase
-
-
-
0.000000000000000000000000576
109.0
DYD1_k127_2053676_8
Fibronectin type III domain protein
K21571
-
-
0.0000000000000000001027
106.0
DYD1_k127_2053676_9
Hydrolase, P-loop family
K06925
-
-
0.000000000000000000145
94.0
DYD1_k127_2067962_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
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit
K02986
-
-
0.000000000000000000000000000000000000000003296
162.0
DYD1_k127_2067962_2
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
-
-
0.00000000000000000000000000000006453
129.0
DYD1_k127_2067962_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 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
Belongs to the bacterial ribosomal protein bL36 family
K02919
-
-
0.0000000000007607
68.0
DYD1_k127_2086047_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
1.243e-203
651.0
DYD1_k127_2086047_1
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
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
K01491
-
1.5.1.5,3.5.4.9
0.000005418
57.0
DYD1_k127_2172371_0
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
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
-
-
0.00000000000000000007047
94.0
DYD1_k127_2191280_12
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
-
-
0.000002799
53.0
DYD1_k127_2191280_2
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
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
Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin
K03737
-
1.2.7.1
0.00000000000444
68.0
DYD1_k127_2273061_0
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
-
-
1.867e-289
914.0
DYD1_k127_2273061_1
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
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
Cell division protein that is involved in the assembly of the Z ring. May serve as a membrane anchor for the Z ring
K03590
-
-
0.00000000000000000000000000000000000008658
157.0
DYD1_k127_2273061_5
Protein of unknown function (DUF4446)
-
-
-
0.0000000000000009281
83.0
DYD1_k127_2273061_6
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
-
-
0.00000000000000156
81.0
DYD1_k127_2273061_7
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA
K02834
-
-
0.00002552
51.0
DYD1_k127_2411672_0
PFAM Lecithin cholesterol acyltransferase
-
-
-
0.0000000000000000000000000001204
135.0
DYD1_k127_2411672_1
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
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
Responsible for synthesis of pseudouridine from uracil
K06180
-
5.4.99.23
0.00000000000000000000000000000000000000002593
161.0
DYD1_k127_2523352_4
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
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
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
K01462
-
3.5.1.88
0.000000000000000000000003399
108.0
DYD1_k127_2887656_4
DoxX
K16937
-
1.8.5.2
0.00000000000000000001118
96.0
DYD1_k127_2887656_5
Domain of unknown function (DUF1905)
-
-
-
0.0000000001008
68.0
DYD1_k127_2887656_6
KAP family P-loop domain
-
-
-
0.0000006256
61.0
DYD1_k127_2887656_7
Belongs to the UPF0235 family
K09131
-
-
0.00001675
50.0
DYD1_k127_2887656_8
Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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)
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
K01520
-
3.6.1.23
0.000000000000000000000000000000000001191
142.0
DYD1_k127_3114512_7
HIT domain
-
-
-
0.00000000000004728
78.0
DYD1_k127_3114512_8
Alternative locus ID
K07260
-
3.4.17.14
0.0000000000107
74.0
DYD1_k127_3114512_9
Involved in DNA repair and RecF pathway recombination
K03584
-
-
0.00001029
55.0
DYD1_k127_3235231_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
Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane
K03980
-
-
0.000000000000000000000000001455
129.0
DYD1_k127_3235231_3
Tetratricopeptide repeat
-
-
-
0.0005886
53.0
DYD1_k127_3560898_0
Heat shock 70 kDa protein
K04043
-
-
4.372e-229
725.0
DYD1_k127_3560898_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
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
K02838
-
-
0.00000000000000000000000000000000008049
141.0
DYD1_k127_3708912_4
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
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
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
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 reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
D-isomer specific 2-hydroxyacid dehydrogenase catalytic region
K03778
-
1.1.1.28
0.00000000000000000000000000007636
121.0
DYD1_k127_4441366_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)
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
-
-
0.00000000000000000001321
98.0
DYD1_k127_4441366_14
Peptidase family M23
-
-
-
0.00000000000000000002837
104.0
DYD1_k127_4441366_15
This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
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)
First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
K01000
-
2.7.8.13
0.000000000000000000000000000000000000009388
158.0
DYD1_k127_4441366_9
PFAM RNA recognition motif
-
-
-
0.000000000000000000000000000008748
121.0
DYD1_k127_4498814_0
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
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
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
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 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
K02945,K03527
-
1.17.7.4
0.00000000000000000000000000000000000000000123
170.0
DYD1_k127_5147553_2
Belongs to the peptidase S26 family
K03100
-
3.4.21.89
0.000000000000000000000000000000000002687
146.0
DYD1_k127_5147553_3
The natural substrate for this enzyme may be peptidyl- tRNAs which drop off the ribosome during protein synthesis
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
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
-
-
0.0000000000000000000000000000000003381
136.0
DYD1_k127_5174864_11
Glycosyltransferase like family 2
-
-
-
0.00000000000000000000000000000004606
138.0
DYD1_k127_5174864_12
hmm tigr00010
K03424
-
-
0.0000000000000000000000000000009292
126.0
DYD1_k127_5174864_13
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
-
-
0.000000000000000000000000000001136
128.0
DYD1_k127_5174864_14
COG1091 dTDP-4-dehydrorhamnose reductase
K00067
-
1.1.1.133
0.0000000000000000000000000001579
123.0
DYD1_k127_5174864_15
Protein of unknown function (DUF3431)
-
-
-
0.000000000000000000000000009808
126.0
DYD1_k127_5174864_16
Glycosyl transferase family 2
-
-
-
0.0000000000000000000001796
104.0
DYD1_k127_5174864_18
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
Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene
K03664
-
-
0.000000000000000000000000000001273
126.0
DYD1_k127_5316827_4
Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
K03470
-
3.1.26.4
0.00000000000000000006836
92.0
DYD1_k127_5316827_5
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 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
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
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
-
-
0.000000000000000000000001855
107.0
DYD1_k127_5327175_12
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
K02887
-
-
0.00000000000000000000002467
103.0
DYD1_k127_5327175_13
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
-
-
0.00000000000000000000004328
100.0
DYD1_k127_5327175_14
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
0.000000000000000000004788
100.0
DYD1_k127_5327175_15
Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
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
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
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 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
-
-
2.253e-272
854.0
DYD1_k127_589367_1
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
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
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)
ABC-type transport system involved in lipoprotein release permease component
K02004
-
-
0.00000000000000000003111
100.0
DYD1_k127_6015396_5
Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis
K00287
-
1.5.1.3
0.0000000000000267
77.0
DYD1_k127_6015396_6
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
K03073
-
-
0.0001924
46.0
DYD1_k127_6037136_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
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
Uncharacterized protein conserved in bacteria (DUF2188)
-
-
-
0.00000000000002406
76.0
DYD1_k127_619103_9
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
K01356
-
3.4.21.88
0.000000000000358
78.0
DYD1_k127_6276445_0
Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates
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
0.0000000000000000000000000000000000002288
147.0
DYD1_k127_6421515_10
Cell-wall hydrolase involved in septum cleavage during cell division
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
9.228e-250
795.0
DYD1_k127_6487897_2
Methyltransferase type 11
-
-
-
0.00000003359
62.0
DYD1_k127_6487897_3
Bacterial extracellular solute-binding protein
K02027
-
-
0.0000003
63.0
DYD1_k127_6491408_0
ABC-type polysaccharide polyol phosphate transport system ATPase component
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation
K02935
-
-
0.00000000000000000000000000000000007242
139.0
DYD1_k127_6491408_5
Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
K02864
-
-
0.000000000000000000000004443
107.0
DYD1_k127_6491408_6
transmembrane transport
-
-
-
0.00000000000000000005212
98.0
DYD1_k127_6491408_7
PD-(D/E)XK nuclease superfamily
-
-
-
0.0000000000000002661
83.0
DYD1_k127_6731548_0
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
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
-
-
4.126e-296
932.0
DYD1_k127_791462_1
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
Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue
K02654
-
3.4.23.43
0.000000000000000000000000000002466
130.0
DYD1_k127_855119_4
TIGRFAM type IV pilus assembly protein PilM
K02662
-
-
0.000000000000000000000002759
116.0
DYD1_k127_855119_5
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)
K01866
-
6.1.1.1
0.0000000000000000000005613
102.0
DYD1_k127_855119_6
Phosphoribosyl transferase domain
K00764
-
2.4.2.14
0.0000000000000000006827
94.0
DYD1_k127_855119_7
Transcriptional regulator
-
-
-
0.0000000000000008973
82.0
DYD1_k127_855119_8
prepilin-type N-terminal cleavage methylation
K02456
-
-
0.00000002
62.0
DYD1_k127_855119_9
Prokaryotic N-terminal methylation motif
-
-
-
0.00004328
51.0
DYD1_k127_922330_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)
