Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system
K03116
-
-
0.00000000000861
66.0
DYD1_k127_1683503_12
O-methyltransferase activity
-
-
-
0.0000000006331
68.0
DYD1_k127_1683503_13
Hep Hag repeat protein
-
-
-
0.000000001301
73.0
DYD1_k127_1683503_14
Transposase IS200 like
-
-
-
0.000000005798
68.0
DYD1_k127_1683503_15
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
calcium- and calmodulin-responsive adenylate cyclase activity
-
-
-
0.00000000000000000000384
111.0
DYD1_k127_1683503_8
-
-
-
-
0.00000000000000000005912
107.0
DYD1_k127_1683503_9
PFAM Glycosyl transferase family 2
-
-
-
0.00000000000000007879
86.0
DYD1_k127_1885619_0
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate
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
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
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
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)
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
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)
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
-
-
0.00000000000000000000000000000000000000000003952
166.0
DYD1_k127_1885619_133
COG3476 Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog)
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
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)
Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue
K02654
-
3.4.23.43
0.000000000000000000000000000000000000001515
157.0
DYD1_k127_1885619_143
D-isomer specific 2-hydroxyacid dehydrogenase catalytic
K00058
-
1.1.1.399,1.1.1.95
0.000000000000000000000000000000000000002072
160.0
DYD1_k127_1885619_144
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
-
-
0.000000000000000000000000000000000000002782
152.0
DYD1_k127_1885619_145
Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
K03431
-
5.4.2.10
0.000000000000000000000000000000000000004657
162.0
DYD1_k127_1885619_146
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
K02520
-
-
0.00000000000000000000000000000000000002339
150.0
DYD1_k127_1885619_147
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
-
-
0.00000000000000000000000000000000000002697
149.0
DYD1_k127_1885619_148
PFAM peptidase M50
-
-
-
0.00000000000000000000000000000000000003271
153.0
DYD1_k127_1885619_149
domain protein
K02238
-
-
0.00000000000000000000000000000000000004892
154.0
DYD1_k127_1885619_15
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
Bacterial extracellular solute-binding proteins, family 5 Middle
K02035
-
-
0.0000000000000000000000000000000000002864
157.0
DYD1_k127_1885619_152
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
K02357
-
-
0.0000000000000000000000000000000000007295
145.0
DYD1_k127_1885619_153
Cell wall formation
-
-
-
0.000000000000000000000000000000000001053
152.0
DYD1_k127_1885619_154
glycosyl transferase family 2
K12984
-
-
0.000000000000000000000000000000000001618
149.0
DYD1_k127_1885619_155
maltose O-acetyltransferase activity
K03818
-
-
0.000000000000000000000000000000000001625
145.0
DYD1_k127_1885619_156
Methionine biosynthesis protein MetW
-
-
-
0.00000000000000000000000000000000000199
146.0
DYD1_k127_1885619_157
pilus assembly protein
K02662
-
-
0.000000000000000000000000000000000004382
150.0
DYD1_k127_1885619_158
HAD-hyrolase-like
-
-
-
0.000000000000000000000000000000000007626
144.0
DYD1_k127_1885619_159
Glycosyltransferase like family 2
-
-
-
0.00000000000000000000000000000000001873
147.0
DYD1_k127_1885619_16
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
Belongs to the aspartate glutamate racemases family
K01779
-
5.1.1.13
0.0000000000000000000000000000000000255
143.0
DYD1_k127_1885619_161
Glycosyl transferase family 2
-
-
-
0.00000000000000000000000000000000005643
142.0
DYD1_k127_1885619_162
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
0.0000000000000000000000000000000002732
137.0
DYD1_k127_1885619_163
Catalyzes the conversion of GlcNAc-PP-undecaprenol into ManNAc-GlcNAc-PP-undecaprenol, the first committed lipid intermediate in the de novo synthesis of teichoic acid
K05946
-
2.4.1.187
0.0000000000000000000000000000000006291
142.0
DYD1_k127_1885619_164
PFAM glycosyl transferase family 39
-
-
-
0.0000000000000000000000000000000007867
149.0
DYD1_k127_1885619_165
ADP-glyceromanno-heptose 6-epimerase activity
-
-
-
0.000000000000000000000000000000003514
148.0
DYD1_k127_1885619_166
-
-
-
-
0.00000000000000000000000000000001199
145.0
DYD1_k127_1885619_167
Methyltransferase domain
-
-
-
0.00000000000000000000000000000002963
136.0
DYD1_k127_1885619_168
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
0.00000000000000000000000000000008615
130.0
DYD1_k127_1885619_17
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
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
-
-
0.000000000000000000000000000001255
123.0
DYD1_k127_1885619_174
Tetratricopeptide repeat
-
-
-
0.000000000000000000000000000002352
129.0
DYD1_k127_1885619_175
Immunoglobulin-like domain of bacterial spore germination
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
PMT family glycosyltransferase, 4-amino-4-deoxy-L-arabinose transferase
-
-
-
0.0000000000000000000001689
112.0
DYD1_k127_1885619_194
PFAM deoxynucleoside kinase
-
-
-
0.000000000000000000000496
104.0
DYD1_k127_1885619_195
Binds the 23S rRNA
K02909
-
-
0.0000000000000000000007009
98.0
DYD1_k127_1885619_196
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
0.0000000000000000000007033
103.0
DYD1_k127_1885619_197
PFAM Major Facilitator Superfamily
-
-
-
0.000000000000000000001436
108.0
DYD1_k127_1885619_198
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
K00943
-
2.7.4.9
0.000000000000000000003739
103.0
DYD1_k127_1885619_199
Involved in DNA repair and RecF pathway recombination
K03584
-
-
0.0000000000000000000116
98.0
DYD1_k127_1885619_2
Bacterial DNA polymerase III alpha subunit
K02337
-
2.7.7.7
1.369e-276
889.0
DYD1_k127_1885619_20
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
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
-
-
0.0000000000000000007642
90.0
DYD1_k127_1885619_208
This protein binds to 23S rRNA in the presence of protein L20
Evidence 5 No homology to any previously reported sequences
K09005
-
-
0.00000000000000003058
89.0
DYD1_k127_1885619_214
phosphoribosyl-ATP pyrophosphohydrolase
-
-
-
0.0000000000000000357
86.0
DYD1_k127_1885619_215
Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
K02864
-
-
0.00000000000000005296
87.0
DYD1_k127_1885619_217
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
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)
7 transmembrane helices usually fused to an inactive transglutaminase
-
-
-
0.0000000000000007296
88.0
DYD1_k127_1885619_221
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)
Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl- L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway
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
-
-
0.00000001108
62.0
DYD1_k127_1885619_244
Plays a major role in protein secretion by helping the post-translocational extracellular folding of several secreted proteins
K07533
-
5.2.1.8
0.00000001185
64.0
DYD1_k127_1885619_245
TIGRFAM Sporulation protein YteA
-
-
-
0.00000001503
62.0
DYD1_k127_1885619_246
PFAM peptidase U32
K08303
-
-
0.00000001956
58.0
DYD1_k127_1885619_247
-
-
-
-
0.00000002132
58.0
DYD1_k127_1885619_248
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
K03545
-
-
0.0000000264
64.0
DYD1_k127_1885619_249
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation
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
Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection
K09747
-
-
0.0000478
49.0
DYD1_k127_1885619_283
PEGA domain
-
-
-
0.00005435
55.0
DYD1_k127_1885619_284
bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding
K06042
-
5.4.99.60,5.4.99.61
0.00007212
56.0
DYD1_k127_1885619_285
TIGRFAM cell envelope-related function transcriptional attenuator, LytR CpsA family
-
-
-
0.00008181
53.0
DYD1_k127_1885619_286
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
K03073
-
-
0.00008354
49.0
DYD1_k127_1885619_287
Acyltransferase
K00655
-
2.3.1.51
0.0001042
53.0
DYD1_k127_1885619_288
Pfam:DUF2233
-
-
-
0.000133
53.0
DYD1_k127_1885619_289
Uncharacterized conserved protein (DUF2304)
K09153
-
-
0.0001353
49.0
DYD1_k127_1885619_29
TIGRFAM cell shape determining protein, MreB Mrl family
Produces ATP from ADP in the presence of a proton gradient across the membrane
K02114
-
-
0.0002586
47.0
DYD1_k127_1885619_292
Belongs to the UPF0109 family
K06960
-
-
0.0002688
47.0
DYD1_k127_1885619_293
Uncharacterised nucleotidyltransferase
-
-
-
0.000318
53.0
DYD1_k127_1885619_294
-
-
-
-
0.0003379
51.0
DYD1_k127_1885619_295
Transcriptional regulator
-
-
-
0.0003393
47.0
DYD1_k127_1885619_297
-
-
-
-
0.000447
42.0
DYD1_k127_1885619_298
-
-
-
-
0.0006183
48.0
DYD1_k127_1885619_299
Carboxypeptidase
-
-
-
0.0007342
50.0
DYD1_k127_1885619_3
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
5.661e-263
836.0
DYD1_k127_1885619_30
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP
Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine
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)
Catalyzes the addition of an amino acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes
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)
damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage
K03702
-
-
3.791e-238
753.0
DYD1_k127_1885619_70
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate- limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth
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
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
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
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
Belongs to the bacterial ribosomal protein bL34 family
K02914
-
-
0.0000000002542
62.0
DYD1_k127_2134998_103
protein serine/threonine phosphatase activity
-
-
-
0.00000000406
70.0
DYD1_k127_2134998_104
Belongs to the NUDIX hydrolase family
K03574
-
3.6.1.55
0.00000002231
62.0
DYD1_k127_2134998_105
Bacterial PH domain
-
-
-
0.0000000231
64.0
DYD1_k127_2134998_106
ParB-like nuclease domain
-
-
-
0.00000008603
63.0
DYD1_k127_2134998_107
Serine hydrolase
-
-
-
0.000000803
51.0
DYD1_k127_2134998_108
Thioredoxin
-
-
-
0.00000269
55.0
DYD1_k127_2134998_109
Psort location Extracellular, score
-
-
-
0.000003731
56.0
DYD1_k127_2134998_11
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
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
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
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
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
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
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
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
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
7.609e-223
719.0
DYD1_k127_2134998_40
Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
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
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
K07738
-
-
0.00000000000000000000000000000000000000000000647
166.0
DYD1_k127_2134998_5
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
1.651e-211
677.0
DYD1_k127_2134998_50
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
COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase
K01247
-
3.2.2.21
0.0000000000000000000000000000000000000000000596
166.0
DYD1_k127_2134998_52
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
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
-
-
0.0000000000000000000008328
100.0
DYD1_k127_2134998_74
Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
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
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
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
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
6-O-methylguanine DNA methyltransferase, DNA binding domain
K07443
-
-
0.0000000000000000000000006695
107.0
DYD1_k127_4746303_32
Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
Catalyzes the 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
0.000000000000003526
84.0
DYD1_k127_4746303_41
Protein of unknown function (DUF3105)
-
-
-
0.0000000000002762
79.0
DYD1_k127_4746303_42
-
-
-
-
0.000000000001055
69.0
DYD1_k127_4746303_43
Peptidase family M23
-
-
-
0.00000000001147
74.0
DYD1_k127_4746303_44
COG NOG15344 non supervised orthologous group
-
-
-
0.0000000002005
63.0
DYD1_k127_4746303_45
Belongs to the cytidylate kinase family. Type 2 subfamily
K00945
-
2.7.4.25
0.0000000002274
70.0
DYD1_k127_4746303_47
Heavy metal translocating P-type atpase
-
-
-
0.000000001036
63.0
DYD1_k127_4746303_48
-
-
-
-
0.00000000115
60.0
DYD1_k127_4746303_49
COG NOG15344 non supervised orthologous group
-
-
-
0.000000001292
61.0
DYD1_k127_4746303_5
DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
K17758,K17759
-
4.2.1.136,5.1.99.6
0.0001187
48.0
DYD1_k127_4746303_63
Cell wall-associated hydrolase
-
-
-
0.0001777
46.0
DYD1_k127_4746303_64
-
-
-
-
0.0002263
45.0
DYD1_k127_4746303_65
Protein of unknown function (DUF1573)
-
-
-
0.0003759
49.0
DYD1_k127_4746303_66
phosphohydrolase
K06950
-
-
0.0007889
49.0
DYD1_k127_4746303_67
-
-
-
-
0.0009726
42.0
DYD1_k127_4746303_7
Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family
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
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
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)
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
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
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
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)
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
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
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
rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality
Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
K02988
-
-
0.00000000000000000000000000000000000000001271
158.0
DYD1_k127_5126590_33
Transport permease protein
K01992,K09690
-
-
0.0000000000000000000000000000000000000003178
159.0
DYD1_k127_5126590_34
Protein of unknown function (DUF3048) C-terminal domain
-
-
-
0.000000000000000000000000000000000000005615
160.0
DYD1_k127_5126590_35
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
-
-
0.000000000000000000000000000000000000006939
149.0
DYD1_k127_5126590_36
Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome
K02948
-
-
0.000000000000000000000000000000000002812
141.0
DYD1_k127_5126590_37
Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
K02874
-
-
0.0000000000000000000000000000000003387
134.0
DYD1_k127_5126590_38
transferase activity, transferring glycosyl groups
K20444
-
-
0.0000000000000000000000000000000009019
144.0
DYD1_k127_5126590_39
AI-2E family transporter
-
-
-
0.0000000000000000000000000000005435
134.0
DYD1_k127_5126590_4
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)
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
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
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
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
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
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
-
-
0.0000001051
57.0
DYD1_k127_5126590_72
general secretion pathway protein
K02456
-
-
0.0000007522
57.0
DYD1_k127_5126590_73
Pfam:N_methyl_2
-
-
-
0.000001544
57.0
DYD1_k127_5126590_74
Major Facilitator
-
-
-
0.0002637
53.0
DYD1_k127_5126590_75
domain protein
-
-
-
0.0008054
51.0
DYD1_k127_5126590_8
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. 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
-
-
2.257e-276
878.0
DYD1_k127_880556_1
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
K01338
-
3.4.21.53
2.851e-228
732.0
DYD1_k127_880556_10
Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4- hexulose to yield dTDP-L-rhamnose
K00067
-
1.1.1.133
0.000000000000000000000000000000001068
141.0
DYD1_k127_880556_42
Involved in the biosynthesis of branched-chain polyamines, which support the growth of thermophiles under high- temperature conditions. Catalyzes the sequential condensation of spermidine with the aminopropyl groups of decarboxylated S- adenosylmethionines to produce N(4)-bis(aminopropyl)spermidine via N(4)-aminopropylspermidine
K07057
-
2.5.1.128
0.000000000000000000000000000000003389
141.0
DYD1_k127_880556_43
PFAM glycosyl transferase family 39
-
-
-
0.00000000000000000000000000000002437
135.0
DYD1_k127_880556_44
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
Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA RNA and avoiding chromosomal lesions
K02428
-
3.6.1.66
0.0000000000000000000000000003247
121.0
DYD1_k127_880556_47
Catalyzes the formation of CDP-2,3-bis-(O- geranylgeranyl)-sn-glycerol (CDP-archaeol) from 2,3-bis-(O- geranylgeranyl)-sn-glycerol 1-phosphate (DGGGP) and CTP. This reaction is the third ether-bond-formation step in the biosynthesis of archaeal membrane lipids
K19664
-
2.7.7.67
0.000000000000000000000000000695
119.0
DYD1_k127_880556_48
glycosyl transferase family 2
K07011
-
-
0.0000000000000000000000000009647
130.0
DYD1_k127_880556_49
COG2931 RTX toxins and related Ca2 -binding proteins
-
-
-
0.000000000000000000000000002847
124.0
DYD1_k127_880556_5
Belongs to the NAD(P)-dependent epimerase dehydratase family
Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
K01611
-
4.1.1.50
0.000000001032
64.0
DYD1_k127_880556_77
COG1214 Inactive homolog of metal-dependent proteases
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
K07738
-
-
0.000958
45.0
DYD1_k127_880556_9
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)
