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:

HyfR	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional activator HyfR

Gene name(s):

hyfR

Functional conformation(s):

HyfR

Coregulator(s):

CRP, FNR, FhlA, HyfR

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

FhlA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional activator FhlA, Fhl, formate hydrogen-lyase transcriptional activator for fdhF, hyc and hyp operons

Gene name(s):

fhlA

Functional conformation(s):

FhlA , FhlA-formate

Coregulator(s):

CRP, FNR, FhlA, FlhDC, HyfR, IHF, ModE, NarL, NarP, NsrR

Summary:

TF Summary ...[more]

REGULATION EXERTED BY CRP,FNR,FhlA,HyfR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
CRP activator FNR repressor FhlA activator HyfR activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	hyfAp	hyfA , hyfB , hyfC , hyfD , hyfE , hyfF , hyfG , hyfH , hyfI , hyfJ , hyfR , focB	2601000	2601022	-160.5	atacctcactTCTCGTGATCAAGATCACATTCTcgctttcccc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2]
FhlA-formate	activator	hyfAp	hyfA , hyfB , hyfC , hyfD , hyfE , hyfF , hyfG , hyfH , hyfI , hyfJ , hyfR , focB	2601034	2601047	-130.0	gctttcccctGCGACACGGGTGTCgaatccattt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [3]
HyfR	activator	hyfAp	hyfA , hyfB , hyfC , hyfD , hyfE , hyfF , hyfG , hyfH , hyfI , hyfJ , hyfR , focB	2601033	2601050	-129.5	cgctttccccTGCGACACGGGTGTCGAAtccatttttt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [3]
FNR	repressor	hyfAp	hyfA , hyfB , hyfC , hyfD , hyfE , hyfF , hyfG , hyfH , hyfI , hyfJ , hyfR , focB	2601059	2601072	-105.5	aatccattttTTGCTGAACGTTAAtgaccatcat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[1] Self WT., et al., 2004 [2] Tsai MJ., et al., 2018 [3] Skibinski DA., et al., 2002

Reference(s)
[1] Self WT., Hasona A., Shanmugam KT., 2004, Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli., J Bacteriol 186(2):580-7
[2] 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
[3] Skibinski DA., Golby P., Chang YS., Sargent F., Hoffman R., Harper R., Guest JR., Attwood MM., Berks BC., Andrews SC., 2002, Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR., J Bacteriol 184(23):6642-53