RegulonDB RegulonDB 10.7: Regulon Form
   
   


CRP,GntR,IdnR regulon in Escherichia coli K-12 genome


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:
GntR Weight Matrix      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional repressor GntR
Gene name(s): gntR
Functional conformation(s): GntR-D-gluconate , GntR
Coregulator(s): CRP, Cra, GntR, IdnR, KdgR
Summary: TF Summary ...[more]
TRANSCRIPTION FACTOR: Info
Name:
IdnR      Tractordb tool
Connectivity class Local Regulator
Sensing Class Sensing external and internal signals
Synonym(s): DNA-binding transcriptional dual regulator IdnR, GntH, YjgS
Gene name(s): idnR
Functional conformation(s): IdnR-Idonate , IdnR , IdnR-5-ketogluconate
Coregulator(s): CRP, GntR, IdnR
Summary: TF Summary ...[more]

REGULATION EXERTED BY CRP,GntR,IdnR Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
CRP activator GntR repressor IdnR activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator idnKp idnK 4494466 4494488 -120.5 aactgtcattATTTGTGATGAAGATCACGTCAGaaaattgtta [AIBSCS]
[APIORCISFBSCS]
[GEA]
[1]
[2]
[3]
[4]
CRP-cAMP activator idnKp idnK 4494516 4494537 -70.5 atgttacgcaTAACGTGATGTGCCTTGTAATTcttatcagta [APIORCISFBSCS]
[GEA]
[1]
[2]
[4]
GntR repressor idnKp idnK 4494504 4494523 -83.5 tgttacattaCTATGTTACGCATAACGTGAtgtgccttgt [AIBSCS]
[APIORCISFBSCS]
[GEA]
[2]
[5]
[4]
GntR repressor idnKp idnK 4494484 4494503 -103.5 tgaagatcacGTCAGAAAATTGTTACATTActatgttacg [APIORCISFBSCS]
[GEA]
[4]
GntR repressor idnKp idnK 4494534 4494553 -53.5 tgtgccttgtAATTCTTATCAGTAGAAATAaaaaaacgtg [AIBSCS]
[APIORCISFBSCS]
[GEA]
[5]
[4]
CRP-cAMP activator idnDp idnR , idnT , idnO , idnD 4494516 4494537 -91.5 tactgataagAATTACAAGGCACATCACGTTAtgcgtaacat [APIORCISFBSCS]
[GEA]
[1]
[2]
[4]
IdnR-5-ketogluconate activator idnDp idnR , idnT , idnO , idnD 4494506 4494521 -78.5 aaggcacatcACGTTATGCGTAACATagtaatgtaa [AIBSCS]
[GEA]
[6]
[1]
[4]
CRP-cAMP activator idnDp idnR , idnT , idnO , idnD 4494466 4494488 -41.5 taacaattttCTGACGTGATCTTCATCACAAATaatgacagtt [AIBSCS]
[APIORCISFBSCS]
[GEA]
[1]
[2]
[3]
[4]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494534 4494553 -108.5 cacgttttttTATTTCTACTGATAAGAATTacaaggcaca [AIBSCS]
[APIORCISFBSCS]
[GEA]
[5]
[4]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494484 4494503 -58.5 cgtaacatagTAATGTAACAATTTTCTGACgtgatcttca [APIORCISFBSCS]
[GEA]
[4]
GntR repressor idnDp idnR , idnT , idnO , idnD 4494504 4494523 -78.5 acaaggcacaTCACGTTATGCGTAACATAGtaatgtaaca [AIBSCS]
[APIORCISFBSCS]
[GEA]
[2]
[5]
[4]
IdnR activator idnKp idnK 4494506 4494521 -83.5 ttacattactATGTTACGCATAACGTgatgtgcctt [AIBSCS]
[GEA]
[6]
[1]
[4]
CRP activator GntR repressor IdnR repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
CRP-cAMP activator gntKp gntU , gntK 3577703 3577724 -68.5 ttaagcccacAAATTTGAAGTAGCTCACACTTatacacttaa [APIORCISFBSCS]
[BCE]
[GEA]
[7]
[2]
[8]
IdnR-5-ketogluconate repressor gntKp gntU , gntK 3577623 3577638 15.5 ttaccgataaCAGTTACCCGTAACATttttaattct [GEA] [9]
IdnR-5-ketogluconate repressor gntKp gntU , gntK 3577636 3577651 2.5 cggctggacaATGTTACCGATAACAGttacccgtaa [GEA] [9]
GntR repressor gntKp gntU , gntK 3577621 3577640 15.5 tgttaccgatAACAGTTACCCGTAACATTTttaattcttg [AIBSCS]
[APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[2]
[5]
[9]
GntR repressor gntKp gntU , gntK 3577634 3577653 2.5 tccggctggaCAATGTTACCGATAACAGTTacccgtaaca [AIBSCS]
[APIORCISFBSCS]
[BPP]
[GEA]
[SM]
[7]
[2]
[5]
[8]
[9]

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.
[GEA] Gene expression analysis
[BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[SM] Site mutation
Reference(s): [1] Bausch C., et al., 2004
[2] Rodionov DA., et al., 2000
[3] Tsai MJ., et al., 2018
[4] Tsunedomi R., et al., 2003
[5] Suvorova IA., et al., 2015
[6] Bausch C., et al., 1998
[7] Izu H., et al., 1997
[8] Tong S., et al., 1996
[9] Tsunedomi R., et al., 2003



Reference(s)    

 [1] Bausch C., Ramsey M., Conway T., 2004, Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli., J Bacteriol 186(5):1388-97

 [2] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol 38(4):673-83

 [3] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [4] Tsunedomi R., Izu H., Kawai T., Yamada M., 2003, Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli., J Mol Microbiol Biotechnol 6(1):41-56

 [5] Suvorova IA., Korostelev YD., Gelfand MS., 2015, GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution., PLoS One 10(7):e0132618

 [6] Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T., 1998, Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli., J Bacteriol 180(14):3704-10

 [7] Izu H., Adachi O., Yamada M., 1997, Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli., J Mol Biol 267(4):778-93

 [8] Tong S., Porco A., Isturiz T., Conway T., 1996, Cloning and molecular genetic characterization of the Escherichia coli gntR, gntK, and gntU genes of GntI, the main system for gluconate metabolism., J Bacteriol 178(11):3260-9

 [9] Tsunedomi R., Izu H., Kawai T., Matsushita K., Ferenci T., Yamada M., 2003, The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli., J Bacteriol 185(6):1783-95


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