RegulonDB RegulonDB 10.7: Regulon Form
   
   


CRP,FNR,IHF,TdcA,TdcR regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
FNR Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): DNA-binding transcriptional dual regulator FNR, NirA, NirR, OssA, OxrA
Gene name(s): fnr
Functional conformation(s): FNR-[4Fe-4S]2+ reduced , FNR-[2Fe-2S]2+ oxidized , FNR
Coregulator(s): AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlpR, H-NS, HdfR, HprR, HyfR, HypT, IHF, LeuO, Lrp, MalT, MarA, MetR, MlrA, ModE, Nac, NagC, NarL, NarP, NfeR, NikR, NorR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PhoP, PurR, PuuR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, TdcA, TdcR, TorR, YeiL, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
CRP Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class Using internal synthesized signals
Synonym(s): Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB
Gene name(s): crp
Functional conformation(s): CRP , CRP-cAMP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, CRP-Sxy, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FucR, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsAB, RcsB, RcsB-BglJ, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, YjjQ, ZraR, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
TdcA      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional activator TdcA, transcriptional activator of tdc operon
Gene name(s): tdcA
Functional conformation(s): TdcA
Coregulator(s): CRP, FNR, IHF, TdcA, TdcR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
TdcR      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional activator TdcR, threonine dehydratase operon activator protein
Gene name(s): tdcR
Functional conformation(s): TdcR
Coregulator(s): CRP, FNR, IHF, TdcA, TdcR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IHF Weight Matrix      Tractordb tool
Connectivity class Global Regulator
Sensing Class TFs for DNA-bending
Synonym(s): DNA-binding transcriptional dual regulator IHF
Gene name(s): ihfB, ihfA
Functional conformation(s): IHF
Coregulator(s): AcrR, AdiY, ArcA, ArgR, AtoC, BasR, CRP, Cbl, CpxR, Cra, CsgD, CysB, DksA, DksA-ppGpp, EnvY, FNR, FadR, FhlA, Fis, FlhDC, FliZ, Fur, GadE, GlcC, GlpR, GlrR, H-NS, HU, HdfR, HipAB, HipB, IHF, IclR, IscR, LrhA, Lrp, MarA, MatA, MlrA, MntR, ModE, MprA, MqsA, Nac, NagC, NanR, NarL, NarP, NorR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PepA, PhoB, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YiaJ, YjjQ, ppGpp
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,FNR,IHF,TdcA,TdcR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator FNR activator IHF activator TdcA activator TdcR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267126 3267147 -43.5 ttgaaagttaATTTGTGAGTGGTCGCACATATcctgttcatt [APIORCISFBSCS]
[BCE]
[BPP]
[GEA]
[SM]
[1]
[2]
[3]
IHF activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267190 3267202 -103.0 ttaacttgttGATATTTAAAGGTatttaattgt [APIORCISFBSCS]
[BCE]
[BPP]
[SM]
[1]
[3]
TdcA activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267263 3267277 -177.0 tgttatcgccATAAAATATGGTTATccccgtcatt [BCE]
[GEA]
[SM]
[1]
TdcR activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267282 3267293 -195.0 accacataacGAATGATGTTATcgccataaaa [BCE]
[SM]
[1]
FNR activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267235 3267248 -148.5 gtcattttttTTGACAAAAATCAGggtttatgct [AIBSCS]
[GEA]
[4]
FNR activator tdcAp tdcG , tdcF , tdcE , tdcD , tdcC , tdcB , tdcA 3267192 3267205 -105.5 actttaacttGTTGATATTTAAAGgtatttaatt [AIBSCS]
[GEA]
[4]

Evidence: [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[GEA] Gene expression analysis
[SM] Site mutation
[AIBSCS] Automated inference based on similarity to consensus sequences
Reference(s): [1] Hagewood BT., et al., 1994
[2] Sawers G. 2001
[3] Wu Y., et al., 1992
[4] Constantinidou C., et al., 2006



Reference(s)    

 [1] Hagewood BT., Ganduri YL., Datta P., 1994, Functional analysis of the tdcABC promoter of Escherichia coli: roles of TdcA and TdcR., J Bacteriol 176(20):6214-20

 [2] Sawers G., 2001, A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon., Mol Microbiol 39(5):1285-98

 [3] Wu Y., Patil RV., Datta P., 1992, Catabolite gene activator protein and integration host factor act in concert to regulate tdc operon expression in Escherichia coli., J Bacteriol 174(21):6918-27

 [4] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15


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