RegulonDB RegulonDB 10.8: Regulon Form
   
   


AraC,GadX,NagC regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
Name:
GadX Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Synonym(s): DNA-binding transcriptional dual regulator GadX, YhiX
Gene name(s): gadX
Functional conformation(s): GadX
Coregulator(s): AdiY, AraC, ArcA, CRP, CadC, CspA, EvgA, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, Lrp, MarA, MqsA, NagC, NtrC, OmpR, PhoB, PhoP, RcsB, RutR, SdiA, TorR, YdeO, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
NagC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class External sensing using transported metabolites
Synonym(s): DNA-binding transcriptional dual regulator NagC, NagR, transcriptional repressor of nag (N-acetylglucosamine) operon
Gene name(s): nagC
Functional conformation(s): NagC , NagC-N-acetyl-D-glucosamine 6-phosphate
Coregulator(s): AraC, BasR, CRP, ChbR, Cra, DksA, DksA-ppGpp, EvgA, FNR, Fur, GadX, GalR, GalS, H-NS, IHF, LexA, Mlc, NagC, NanR, NarL, NarP, PhoP, RcsB, UvrY, ppGpp
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
AraC Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator AraC
Gene name(s): araC
Functional conformation(s): AraC-D-fucose , AraC , AraC-arabinose , AraC
Coregulator(s): AraC, CRP, GadX, NagC, XylR
Summary: TF Summary ...[more]

REGULATION EXERTED BY AraC,GadX,NagC Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
AraC repressor GadX repressor NagC repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
NagC repressor ydeNp ydeM , ydeN 1582559 1582581 -16.0 cttacatccaCTTATTTCTCTTCGTAAAATTACtttggaatta [AIBSCS] [1]
NagC repressor ydeNp ydeM , ydeN 1582683 1582705 -140.0 caataaattaGTTGTTTATCGGCGAGAAATTACttaatagaac [AIBSCS] [1]
AraC-arabinose repressor ydeNp ydeM , ydeN         [GEA] [2]
GadX repressor ydeNp ydeM , ydeN 1582613 1582632 -69.0 tttttcccttTTTTTAGCTAAATCTGCTATctctttatgt [CEUMA]
[IHBCE]
[RE]
[3]
GadX repressor ydeNp ydeM , ydeN 1582778 1582797 -233.5 cacatatttaTGCACTTGCATAACCTGTTGcatgattatt [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] Oberto J. 2010
[2] Stringer AM., et al., 2014
[3] Seo SW., et al., 2015



Reference(s)    

 [1] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [2] Stringer AM., Currenti S., Bonocora RP., Baranowski C., Petrone BL., Palumbo MJ., Reilly AA., Zhang Z., Erill I., Wade JT., 2014, Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon., J Bacteriol 196(3):660-71

 [3] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970


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