RegulonDB

TRANSCRIPTION FACTOR:

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 , FNR-[4Fe-4S]²⁺ reduced , FNR-[2Fe-2S]²⁺ oxidized

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, BtsR, 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-cyclic-AMP

Coregulator(s):

AaeR, 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, RspR, 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:

Lrp	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

AlsB, DNA-binding transcriptional dual regulator Lrp, Ihb, LivR, Lrs, Lss, LstR, Mbf, OppI, RblA

Gene name(s):

lrp

Functional conformation(s):

Lrp , Lrp-L-leucine

Coregulator(s):

AcrR, Ada, AdiY, AidB, ArcA, ArgP, ArgR, CRP, CadC, CpxR, Cra, DksA, DksA-ppGpp, EnvY, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlaR, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, Mlc, ModE, Nac, NarL, NhaR, NsrR, OmpR, PhoP, PurR, QseB, RcsB, Rob, SoxS, StpA, TorR, YeiL, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

GcvA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Sensing external and internal signals

Synonym(s):

DNA-binding transcriptional dual regulator GcvA, positive regulator of gcv operon

Gene name(s):

gcvA

Functional conformation(s):

GcvA-Purine , GcvA , GcvA-glycine

Coregulator(s):

CRP, FNR, GcvA, Lrp, PurR

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

PurR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional repressor PurR

Gene name(s):

purR

Functional conformation(s):

PurR-Guanine , PurR , PurR-hypoxanthine

Coregulator(s):

CRP, DnaA, FNR, Fis, Fur, GadE, GcvA, IHF, Lrp, MarA, MetR, Nac, PepA, PhoP, PurR, RbsR, RutR

Summary:

TF Summary ...[more]

REGULATION EXERTED BY CRP,FNR,GcvA,Lrp,PurR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
CRP activator FNR activator GcvA dual Lrp activator PurR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
GcvA	activator	gcvTp	gcvP , gcvH , gcvT	3051023	3051037	-258.0	ttttcctcatTTGAAATAAACTAATttcacctccg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3] [4] [5] [6] [7] [8]
GcvA	activator	gcvTp	gcvP , gcvH , gcvT	3050991	3051005	-226.0	ccgttttcgcATTATATTTTCTAATgccattattt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3] [4] [5] [6] [7] [8]
Lrp	activator	gcvTp	gcvP , gcvH , gcvT	3050926	3050940	-161.0	gctcttaataTTGTCTTATTCAAATtgactttctc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IEP-RNA-SEQ]	[9] [10]
GcvA	repressor	gcvTp	gcvP , gcvH , gcvT	3050809	3050823	-44.0	aatgtgatgaTCAATTTTACCTTATggttaacagt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] [IC]	[1] [3] [6] [8] [11]
PurR-hypoxanthine	repressor	gcvTp	gcvP , gcvH , gcvT	3050758	3050773	7.5	gttcaggcaaAAGAGAACGATTGCGTtggggaccgg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12] [8]
GcvA	repressor	gcvTp	gcvP , gcvH , gcvT	3050831	3050845	-66.0	ttgcatttttTAACCATAAGCTAATgtgatgatca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [3] [6] [8] [11]
CRP-cyclic-AMP	activator	gcvTp	gcvP , gcvH , gcvT	3051075	3051097	-313.5	tcctctgttgTTTATTTGATACCCATCACACTTtcatctcccg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]
CRP-cyclic-AMP	activator	gcvTp	gcvP , gcvH , gcvT	3050907	3050929	-145.5	tgtcttattcAAATTGACTTTCTCATCACATCAtctttgtata	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]
GcvA	repressor	gcvTp	gcvP , gcvH , gcvT	3050991	3051005	-226.0	ccgttttcgcATTATATTTTCTAATgccattattt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3] [4] [5] [6] [7] [8]
GcvA	repressor	gcvTp	gcvP , gcvH , gcvT	3051023	3051037	-258.0	ttttcctcatTTGAAATAAACTAATttcacctccg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3] [4] [5] [6] [7] [8]
FNR	activator	gcvTp	gcvP , gcvH , gcvT

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence [IC] Inferred by curator
Reference(s):	[1] Jourdan AD., et al., 1999 [2] Jourdan AD., et al., 1998 [3] Stauffer LT., et al., 2005 [4] Stauffer LT., et al., 1998 [5] Stauffer LT., et al., 1998 [6] Wilson RL., et al., 1994 [7] Wilson RL., et al., 1993 [8] Wilson RL., et al., 1995 [9] Kroner GM., et al., 2019 [10] Stauffer LT., et al., 1999 [11] Wonderling LD., et al., 2000 [12] Cho BK., et al., 2011 [13] Wonderling LD., et al., 1999

Reference(s)
[1] Jourdan AD., Stauffer GV., 1999, Genetic analysis of the GcvA binding site in the gcvA control region., Microbiology 145 ( Pt 8):2153-62
[2] Jourdan AD., Stauffer GV., 1998, Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding., J Bacteriol 180(18):4865-71
[3] Stauffer LT., Stauffer GV., 2005, GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon., FEMS Microbiol Lett 242(2):333-8
[4] Stauffer LT., Stauffer GV., 1998, Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 5):1417-22
[5] Stauffer LT., Stauffer GV., 1998, Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 10):2865-72
[6] Wilson RL., Stauffer GV., 1994, DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system., J Bacteriol 176(10):2862-8
[7] Wilson RL., Steiert PS., Stauffer GV., 1993, Positive regulation of the Escherichia coli glycine cleavage enzyme system., J Bacteriol 175(3):902-4
[8] Wilson RL., Urbanowski ML., Stauffer GV., 1995, DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli., J Bacteriol 177(17):4940-6
[9] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)
[10] Stauffer LT., Stauffer GV., 1999, Role for the leucine-responsive regulatory protein (Lrp) as a structural protein in regulating the Escherichia coli gcvTHP operon., Microbiology 145 ( Pt 3):569-76
[11] Wonderling LD., Urbanowski ML., Stauffer GV., 2000, GcvA binding site 1 in the gcvTHP promoter of Escherichia coli is required for GcvA-mediated repression but not for GcvA-mediated activation., Microbiology 146 ( Pt 11):2909-18
[12] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64
[13] Wonderling LD., Stauffer GV., 1999, The cyclic AMP receptor protein is dependent on GcvA for regulation of the gcv operon., J Bacteriol 181(6):1912-9
[14] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55