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| | rapA | Hypothetical protein; Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair; Belongs to the SNF2/RAD54 helicase family. RapA subfamily. (968 aa) |
| | polB | DNA polymerase II; Residues 1 to 783 of 783 are 98.85 pct identical to residues 1 to 783 of 783 from Escherichia coli K-12 Strain MG1655: B0060. (783 aa) |
| | mutT | 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP, causes AT-GC transversions; Residues 1 to 129 of 132 are 97.67 pct identical to residues 1 to 129 of 129 from Escherichia coli K-12 Strain MG1655: B0099; Belongs to the Nudix hydrolase family. (132 aa) |
| | dnaE | DNA polymerase III, alpha subunit; 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. The alpha chain is the DNA polymerase; Belongs to the DNA polymerase type-C family. DnaE subfamily. (1160 aa) |
| | dnaQ | DNA polymerase III, epsilon subunit; 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. (243 aa) |
| | dinP | Damage-inducible protein P; 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. (351 aa) |
| | yaiD | Orf, hypothetical protein; May be involved in recombination; Belongs to the RdgC family. (303 aa) |
| | sbcC | ATP-dependent dsDNA exonuclease; SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'->5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity; Belongs to the SMC family. SbcC subfamily. (1047 aa) |
| | sbcD | ATP-dependent dsDNA exonuclease; SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'->5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity (By similarity); Belongs to the SbcD family. (400 aa) |
| | priC | Primosomal replication protein N'; Residues 1 to 175 of 175 are 97.71 pct identical to residues 1 to 175 of 175 from Escherichia coli K-12 Strain MG1655: B0467. (175 aa) |
| | dnaX | DNA polymerase III, tau and gamma subunits; 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. (643 aa) |
| | recR | Recombination and repair; 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. (201 aa) |
| | holA | DNA polymerase III, delta subunit; Residues 1 to 343 of 343 are 99.41 pct identical to residues 1 to 343 of 343 from Escherichia coli K-12 Strain MG1655: B0640. (343 aa) |
| | uvrB | DNA repair; The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative 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 [...] (673 aa) |
| | dinG | Putative ATP-dependent helicase; DNA-dependent ATPase and 5'-3' DNA helicase. (716 aa) |
| | Z1129 | Putative helicase; Residues 428 to 792 of 794 are 32.46 pct identical to residues 87 to 440 of 459 from GenPept 118 : gi|1131497|gb|AAC96521.1| (U42580) similar to phage T5 helicase, corresponds to Swiss-Prot Accession Number P11107 [Paramecium bursaria Chlorella virus 1]. (794 aa) |
| | sulA | Suppressor of lon; Component of the SOS system and an inhibitor of cell division. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, binds a polymerization-competent form of FtsZ in a 1:1 ratio, thus inhibiting FtsZ polymerization and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division. (169 aa) |
| | dinI | Putative damage induced protein I; Involved in SOS regulation. Inhibits RecA by preventing RecA to bind ssDNA. Can displace ssDNA from RecA (By similarity). (81 aa) |
| | holB | DNA polymerase III, delta prime subunit; Residues 1 to 334 of 334 are 99.70 pct identical to residues 1 to 334 of 334 from Escherichia coli K-12 Strain MG1655: B1099. (334 aa) |
| | umuD | SOS mutagenesis; Involved in UV protection and mutation. Essential for induced (or SOS) mutagenesis. May modify the DNA replication machinery to allow bypass synthesis across a damaged template (By similarity). (139 aa) |
| | umuC | SOS mutagenesis and repair; Residues 1 to 422 of 422 are 99.28 pct identical to residues 1 to 422 of 422 from Escherichia coli K-12 Strain MG1655: B1184; Belongs to the DNA polymerase type-Y family. (422 aa) |
| | dcm-2 | Putative DNA modification methyltransferase encoded within prophage CP-933R; Residues 4 to 368 of 383 are 40.90 pct identical to residues 7 to 367 of 424 from GenPept 118 : gi|458402|gb|AAA50432.1| (U06424) M-XorII [Xanthomonas oryzae]. (383 aa) |
| | topA | DNA topoisomerase type I, omega protein; 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, th [...] (865 aa) |
| | nth | Endonuclease III; 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. (211 aa) |
| | cho | Putative excinuclease subunit; Incises the DNA at the 3' side of a lesion during nucleotide excision repair. Incises the DNA farther away from the lesion than UvrC. Not able to incise the 5' site of a lesion. When a lesion remains because UvrC is not able to induce the 3' incision, Cho incises the DNA. Then UvrC makes the 5' incision. The combined action of Cho and UvrC broadens the substrate range of nucleotide excision repair (By similarity). (295 aa) |
| | xthA | Exonuclease III; Residues 1 to 268 of 268 are 98.13 pct identical to residues 1 to 268 of 268 from Escherichia coli K-12 Strain MG1655: B1749. (268 aa) |
| | yoaA | Putative enzyme; Residues 1 to 636 of 636 are 99.84 pct identical to residues 1 to 636 of 636 from Escherichia coli K-12 Strain MG1655: B1808. (636 aa) |
| | holE | DNA polymerase III theta subunit; 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 (By similarity). (76 aa) |
| | exoX | Orf, hypothetical protein; Residues 1 to 220 of 220 are 99.54 pct identical to residues 1 to 220 of 220 from Escherichia coli K-12 Strain MG1655: B1844. (220 aa) |
| | ruvB | Holliday junction helicase subunit A; 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. (336 aa) |
| | ruvA | Holliday junction helicase subunit B; 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. (203 aa) |
| | ruvC | Holliday junction nuclease; 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 (By similarity). (173 aa) |
| | yebC | Orf, hypothetical protein; Residues 1 to 246 of 246 are 99.59 pct identical to residues 1 to 246 of 246 from Escherichia coli K-12 Strain MG1655: B1864. (246 aa) |
| | uvrC | Excinuclease ABC, subunit C; 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 (By similarity). (588 aa) |
| | vsr | DNA mismatch endonuclease, patch repair protein; May nick specific sequences that contain T:G mispairs resulting from m5C-deamination. (156 aa) |
| | dcm | DNA cytosine methylase; This methylase recognizes the double-stranded sequence CCWGG, causes specific methylation on C-2 on both strands; Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family. (472 aa) |
| | yedJ | Orf, hypothetical protein; Residues 1 to 231 of 231 are 96.96 pct identical to residues 1 to 231 of 231 from Escherichia coli K-12 Strain MG1655: B1962. (231 aa) |
| | Z3056 | Hypothetical protein; Residues 1 to 88 of 102 are 97.72 pct identical to residues 7 to 94 of 127 from Escherichia coli K-12 Strain MG1655: B1963. (102 aa) |
| | sbcB | Exonuclease I, 3' --> 5' specific; Residues 1 to 475 of 475 are 98.94 pct identical to residues 1 to 475 of 475 from Escherichia coli K-12 Strain MG1655: B2011. (475 aa) |
| | alkA | 3-methyl-adenine DNA glycosylase II, inducible; Residues 1 to 282 of 282 are 97.16 pct identical to residues 1 to 282 of 282 from Escherichia coli K-12 Strain MG1655: B2068. (282 aa) |
| | nfo | Endonuclease IV; Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. (285 aa) |
| | yejH | Putative ATP-dependent helicase; Residues 1 to 586 of 586 are 99.65 pct identical to residues 1 to 586 of 586 from Escherichia coli K-12 Strain MG1655: B2184. (586 aa) |
| | alkB | DNA repair system specific for alkylated DNA; Residues 1 to 216 of 216 are 99.53 pct identical to residues 1 to 216 of 216 from Escherichia coli K-12 Strain MG1655: B2212. (216 aa) |
| | ada | O6-methylguanine-DNA methyltransferase; Residues 1 to 354 of 354 are 98.58 pct identical to residues 1 to 354 of 354 from Escherichia coli K-12 Strain MG1655: B2213. (354 aa) |
| | hda | Putative DNA replication factor; Mediates the interaction of DNA replication initiator protein DnaA with DNA polymerase subunit beta sliding clamp (dnaN). Stimulates hydrolysis of ATP-DnaA to ADP-DnaA, rendering DnaA inactive for reinitiation, a process called regulatory inhibition of DnaA or RIDA (By similarity); Belongs to the DnaA family. HdA subfamily. (248 aa) |
| | recO | Protein interacts with RecR and possibly RecF proteins; Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. (242 aa) |
| | ung | uracil-DNA-glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (229 aa) |
| | recN | Protein used in recombination and DNA repair; May be involved in recombinational repair of damaged DNA. (553 aa) |
| | oraA | Regulator, OraA protein; Modulates RecA activity through direct physical interaction. Can inhibit both RecA recombinase and coprotease activities. May have a regulatory role during the SOS response. Inhibits DNA strand exchange in vitro (By similarity); Belongs to the RecX family. (166 aa) |
| | recA | DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease; 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; Belongs to the RecA family. (353 aa) |
| | mutS | Methyl-directed mismatch repair; This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. (853 aa) |
| | exo | 5'-3' exonuclease; Has flap endonuclease activity. During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. (281 aa) |
| | recD | DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the [...] (608 aa) |
| | recB | DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the [...] (1180 aa) |
| | ptr | Protease III; Endopeptidase that degrades small peptides of less than 7 kDa, such as glucagon and insulin. (962 aa) |
| | recC | DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the [...] (1122 aa) |
| | ppdC | Prepilin peptidase dependent protein C; Residues 1 to 107 of 107 are 98.13 pct identical to residues 1 to 107 of 107 from Escherichia coli K-12 Strain MG1655: B2823. (107 aa) |
| | ygdB | Hypothetical protein; Residues 1 to 121 of 121 are 92.56 pct identical to residues 1 to 121 of 121 from Escherichia coli K-12 Strain MG1655: B2824. (121 aa) |
| | mutH | Methyl-directed mismatch repair; Sequence-specific endonuclease that cleaves unmethylated GATC sequences. It is involved in DNA mismatch repair; Belongs to the MutH family. (229 aa) |
| | recJ | ssDNA exonuclease, 5' --> 3' specific; Residues 1 to 577 of 577 are 99.65 pct identical to residues 1 to 577 of 577 from Escherichia coli K-12 Strain MG1655: B2892. (577 aa) |
| | mutY | Adenine glycosylase; Adenine glycosylase active on G-A mispairs. (350 aa) |
| | dnaG | DNA biosynthesis; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (581 aa) |
| | mutM | Formamidopyrimidine DNA glycosylase; 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. (269 aa) |
| | recF | ssDNA and dsDNA binding, ATP binding; The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP (By similarity). (357 aa) |
| | dnaN | DNA polymerase III, beta-subunit; 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; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...] (366 aa) |
| | dnaA | DNA biosynthesis; Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; 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. (467 aa) |
| | rep | Rep helicase, a single-stranded DNA dependent ATPase; Rep helicase is a single-stranded DNA-dependent ATPase involved in DNA replication; it can initiate unwinding at a nick in the DNA. It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction. (673 aa) |
| | uvrD | DNA-dependent ATPase I and helicase II; Residues 1 to 720 of 720 are 99.86 pct identical to residues 1 to 720 of 720 from Escherichia coli K-12 Strain MG1655: B3813. (720 aa) |
| | recQ | ATP-dependent DNA helicase; Residues 1 to 611 of 611 are 99.67 pct identical to residues 1 to 610 of 610 from Escherichia coli K-12 Strain MG1655: B3822. (611 aa) |
| | polA | DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (928 aa) |
| | priA | Primosomal protein N'(= factor Y)(putative helicase); 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; Belongs to the helicase family. PriA subfamily. (732 aa) |
| | lexA | Regulator for SOS(lexA) regulon; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. Binds to the 16 bp palindromic sequence 5'-CTGTATATATATACAG-3'. 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. (202 aa) |
| | dnaB | Replicative DNA helicase; Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins. (471 aa) |
| | uvrA | Excision nuclease subunit A; 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. (940 aa) |
| | ssb | ssDNA-binding protein; 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. (178 aa) |
| | mutL | Enzyme in methyl-directed mismatch repair; This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. (615 aa) |
| | priB | Primosomal replication protein N; Binds single-stranded DNA at the primosome assembly site (PAS). During primosome assembly it facilitates the complex formation between PriA and DnaT; Belongs to the PriB family. (104 aa) |
| | holC | DNA polymerase III, chi subunit; Residues 1 to 147 of 147 are 99.31 pct identical to residues 1 to 147 of 147 from Escherichia coli K-12 Strain MG1655: B4259. (147 aa) |
| | dnaC | Chromosome replication; This protein is required for chromosomal replication. It forms, in concert with DnaB protein and other prepriming proteins DnaT, N, N', N'' a prepriming protein complex on the specific site of the template DNA recognized by protein N' (By similarity). (245 aa) |
| | dnaT | DNA biosynthesis; This protein is required for primosome-dependent normal DNA replication; it is also involved in inducing stable DNA replication during SOS response. It forms, in concert with DnaB protein and other prepriming proteins DnaC, N, N', N'' a prepriming protein complex on the specific site of the template DNA recognized by protein N' (By similarity). (179 aa) |
| | holD | DNA polymerase III, psi subunit; 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. The exact function of the psi subunit is unknown. (137 aa) |
| | sms | Probable ATP-dependent protease; 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. (460 aa) |
