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Fur,RutR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
RutR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator RutR, YcdC
Gene name(s): rutR
Functional conformation(s): RutR , RutR-thymine , RutR-uracil
Coregulator(s): ArcA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, IHF, NemR, NtrC, PepA, PhoB, PhoP, PurR, RutR
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-Mn2+ , Fur-Fe2+ , 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, NarL, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY Fur,RutR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
Fur repressor RutR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Fur-Fe2+ repressor fepBp fepB 624725 624743 -7.0 ttgtggttacAATGAAAATGAGAAGCATTattgatggat [AIBSCS]
[APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[CV(GEA/SM)]
[CV(SM)]
[GEA]
[SM]
[1]
[2]
[3]
[4]
Fur-Fe2+ repressor fepBp fepB 624719 624737 -1.0 ttacaatgaaAATGAGAAGCATTATTGATggattcgcat [AIBSCS]
[APIORCISFBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[GEA]
[1]
[2]
[3]
[4]
Fur-Fe2+ repressor fepBp fepB 624731 624749 -13.0 atctggttgtGGTTACAATGAAAATGAGAagcattattg [APIORCISFBSCS]
[BPP]
[1]
RutR repressor fepBp fepB 624548 624564 172.5 gattgtgcgcTTTGTCGAATTTGTCATtacgccctta [AIBSCS]
[BPP]
[CV(GEA)]
[CV(GEA)]
[GEA]
[5]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BPP] Binding of purified proteins
[CV(GEA)] cross validation(GEA)
[CV(GEA/SM)] cross validation(GEA/SM)
[CV(SM)] cross validation(SM)
[GEA] Gene expression analysis
[SM] Site mutation
Reference(s): [1] Brickman TJ., et al., 1990
[2] Chen Z., et al., 2007
[3] Newman DL., et al., 1999
[4] Vassinova N., et al., 2000
[5] Shimada T., et al., 2008



Reference(s)    

 [1] Brickman TJ., Ozenberger BA., McIntosh MA., 1990, Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli., J Mol Biol 212(4):669-82

 [2] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [3] Newman DL., Shapiro JA., 1999, Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development., Mol Microbiol 33(1):18-32

 [4] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [5] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5


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