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BasR,PhoP,SoxR,SoxS regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
SoxS Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator SoxS, regulation of superoxide response regulon
Gene name(s): soxS
Functional conformation(s): SoxS
Coregulator(s): AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, H-NS, HU, IHF, Lrp, MarA, MarR, Mlc, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, Zur
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
PhoP Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): DNA-binding transcriptional dual regulator PhoP, PhoP response regulator
Gene name(s): phoP
Functional conformation(s): PhoP , PhoP-Phosphorylated
Coregulator(s): AcrR, ArcA, ArgR, BasR, CRP, CysB, EnvR, EvgA, FNR, FadR, FliZ, GadE, GadW, GadX, H-NS, HypT, Lrp, MalT, MarA, MetJ, MprA, NagC, NarL, NarP, NtrC, OmpR, PdhR, PhoP, PurR, RbsR, RcsB, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, UvrY, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
SoxR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator SoxR, MarC
Gene name(s): soxR
Functional conformation(s): SoxR , SoxR-[2Fe-2S]2+ reduced
Coregulator(s): AcrR, ArcA, BasR, CRP, FNR, Fur, IHF, MarA, PhoP, Rob, SoxR, SoxS, TyrR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
BasR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External-Two-component systems
Synonym(s): BasR response regulator, DNA-binding transcriptional dual regulator BasR, PmrA
Gene name(s): basR
Functional conformation(s): BasR-Phosphorylated
Coregulator(s): BasR, CRP, CpxR, Cra, CsgD, DksA, DksA-ppGpp, Fis, FliZ, H-NS, IHF, MarA, MlrA, MqsA, NagC, NanR, OmpR, PdhR, PhoP, PutA, QseB, RcdA, RcsB, RstA, SoxR, SoxS, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY BasR,PhoP,SoxR,SoxS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
BasR repressor PhoP activator SoxR activator SoxS activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
PhoP-Phosphorylated activator yrbLp yrbL 3348385 3348401 -28.0 taagaggcatTGTTTAGGTTTTGTTTAagttaatcga [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[1]
[2]
BasR-Phosphorylated repressor yrbLp yrbL 3348359 3348378 -52.5 ctttcagaagAACCTTAAGAAAACCTTAAGaggcattgtt [BPP]
[GEA]
[HIBSCS]
[3]
SoxR activator yrbLp yrbL 3348447 3348464 36.0 tttccaggagATGGCATGATTCGCTTATctgaacaaag [CEUMA]
[IHBCE]
[RE]
[4]
SoxS activator yrbLp yrbL 3348385 3348404 -26.0 taagaggcatTGTTTAGGTTTTGTTTAAGTtaatcgacca [CEUMA]
[IHBCE]
[RE]
[4]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[HIBSCS] Human inference based on similarity to consensus sequences
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Minagawa S., et al., 2003
[2] Monsieurs P., et al., 2005
[3] Ogasawara H., et al., 2012
[4] Seo SW., et al., 2015



Reference(s)    

 [1] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

 [2] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [3] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92

 [4] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99


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