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Fur,OxyR,SoxS,Zur 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:
OxyR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator OxyR, MomR, Mor, bifunctional regulatory protein sensor for oxidative stress
Gene name(s): oxyR
Functional conformation(s): OxyR
Coregulator(s): CRP, ExuR, FNR, Fis, Fur, H-NS, IHF, IscR, MarA, MetJ, MetR, MntR, NarL, NarP, NsrR, OxyR, Rob, SoxS, UxuR, Zur
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Zur      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional repressor Zur, YjbK, ZnuR
Gene name(s): zur
Functional conformation(s): Zur , Zur-Zn2+
Coregulator(s): Fur, OxyR, SoxS, Zur
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
Fur Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator Fur
Gene name(s): fur
Functional conformation(s): Fur-Fe2+ , Fur-Mn2+ , Fur
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY Fur,OxyR,SoxS,Zur Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Fur activator OxyR activator SoxS activator Zur repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Zur-Zn2+ repressor zinTp zinT 2041319 2041341 -16.0 tgcattttgcTATATGTTACAATATAACATTACacatcatata [AIBSCS] [1]
Fur-Fe2+ activator zinTp zinT         [GEA] [2]
SoxS activator zinTp zinT         [GEA] [2]
OxyR activator zinTp zinT 2041358 2041374 21.5 tatacattaaCTCTGGAGGAAACTGTTttggcgattc [CEUMA]
[IHBCE]
[RE]
[3]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[CEUMA] ChIP-exo evidence used in manual assertion
[IHBCE] Inferred by a human based on computational evidence
[RE] RNA-seq evidence
Reference(s): [1] Panina EM., et al., 2003
[2] Puskarova A., et al., 2002
[3] Seo SW., et al., 2015



Reference(s)    

 [1] Panina EM., Mironov AA., Gelfand MS., 2003, Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins., Proc Natl Acad Sci U S A 100(17):9912-7

 [2] Puskarova A., Ferianc P., Kormanec J., Homerova D., Farewell A., Nystrom T., 2002, Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli., Microbiology 148(Pt 12):3801-11

 [3] 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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