RegulonDB

TRANSCRIPTION FACTOR:

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-cyclic-AMP , CRP

Coregulator(s):

AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, 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, FrlR, 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, PlaR, 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, YjjQ, ZraR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

PdhR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

AceC, DNA-binding transcriptional dual regulator PdhR, GenA, YacB

Gene name(s):

pdhR

Functional conformation(s):

PdhR-pyruvate , PdhR

Coregulator(s):

ArcA, AscG, BasR, BtsR, CRP, CpxR, Cra, CusR, FNR, Fis, Fur, GadE, GlcC, HprR, HypT, IHF, MraZ, NsrR, PdhR, PhoP

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

AscG	Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External sensing using transported metabolites

Synonym(s):

DNA-binding transcriptional repressor AscG, Sac

Gene name(s):

ascG

Functional conformation(s):

AscG

Coregulator(s):

AscG, CRP, Fur, HypT, PdhR, PhoB, PrpR

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

HypT	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator HypT, QseD, YjiE

Gene name(s):

hypT

Functional conformation(s):

HypT-Met-oxidized

Coregulator(s):

ArcA, AscG, CRP, FNR, Fur, H-NS, HypT, MetJ, PdhR, PhoP

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, AscG, 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 AscG,CRP,Fur,HypT,PdhR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
AscG unknown CRP activator Fur repressor HypT repressor PdhR activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
PdhR	activator	fecAp	fecE , fecD , fecC , fecB , fecA	4516740	4516756	-21.0	taaggaaaatAATTCTTATTTCGATTGtcctttttac	[GEA]	[1]
Fur-Fe²⁺	repressor	fecAp	fecE , fecD , fecC , fecB , fecA	4516747	4516765	-29.0	tcaccactgtAAGGAAAATAATTCTTATTtcgattgtcc	[GEA]	[2] [3] [4]
Fur-Fe²⁺	repressor	fecAp	fecE , fecD , fecC , fecB , fecA	4516744	4516762	-26.0	ccactgtaagGAAAATAATTCTTATTTCGattgtccttt	[GEA]	[5] [3] [4] [6]
Fur-Fe²⁺	repressor	fecAp	fecE , fecD , fecC , fecB , fecA	4516741	4516759	-23.0	ctgtaaggaaAATAATTCTTATTTCGATTgtccttttta	[GEA]	[2] [3] [4]
HypT-Met-oxidized	repressor	fecAp	fecE , fecD , fecC , fecB , fecA

Evidence:	[GEA] Gene expression analysis
Reference(s):	[1] Faith JJ., et al., 2007 [2] Chen Z., et al., 2007 [3] Gerken H., et al., 2020 [4] Zhang F., et al., 2020 [5] Angerer A., et al., 1998 [6] Zhang Z., et al., 2005

Reference(s)
[1] Faith JJ., Hayete B., Thaden JT., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins JJ., Gardner TS., 2007, Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles., PLoS Biol 5(1):e8
[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] Gerken H., Vuong P., Soparkar K., Misra R., 2020, Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli., mBio 11(3)
[4] Zhang F., Li B., Dong H., Chen M., Yao S., Li J., Zhang H., Liu X., Wang H., Song N., Zhang K., Du N., Xu S., Gu L., 2020, YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner., Nucleic Acids Res 48(17):9571-9588
[5] Angerer A., Braun V., 1998, Iron regulates transcription of the Escherichia coli ferric citrate transport genes directly and through the transcription initiation proteins., Arch Microbiol 169(6):483-90
[6] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90
[7] Drazic A., Miura H., Peschek J., Le Y., Bach NC., Kriehuber T., Winter J., 2013, Methionine oxidation activates a transcription factor in response to oxidative stress., Proc Natl Acad Sci U S A 110(23):9493-8
[8] Gebendorfer KM., Drazic A., Le Y., Gundlach J., Bepperling A., Kastenmuller A., Ganzinger KA., Braun N., Franzmann TM., Winter J., 2012, Identification of a Hypochlorite-specific Transcription Factor from Escherichia coli., J Biol Chem 287(9):6892-903