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:

ArcA	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

External-Two-component systems

Synonym(s):

ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein

Gene name(s):

arcA

Functional conformation(s):

ArcA-phosphorylated , ArcA

Coregulator(s):

AdiY, AppY, ArcA, BetI, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

NarL	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator NarL, FrdR, NarR, nitrate/nitrite response regulator NarL

Gene name(s):

narL

Functional conformation(s):

NarL , NarL-phosphorylated

Coregulator(s):

AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, Fur, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, SoxS, TorR, UvrY, YdeO

Summary:

TF Summary ...[more]

REGULATION EXERTED BY ArcA,FNR,NarL

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
ArcA activator FNR activator NarL activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
NarL-phosphorylated	activator	cydDp	cydC , cydD	931108	931114	-80.0	tgcggaacgcTACCTCGatggtttagc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
NarL-phosphorylated	activator	cydDp	cydC , cydD	931154	931160	-126.0	gccaggccatTACTTCGgccggtacag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
FNR	activator	cydDp	cydC , cydD	931115	931128	-90.5	atggcagcacTTGATGCGGAACGCtacctcgatg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
ArcA-phosphorylated	activator	cydDp	cydC , cydD	931068	931083	-44.0	gcaaaataatTTTACAAATCAGTAACaaaagtaaag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IEP-MICROARRAY]	[2] [3]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IEP-MICROARRAY] high throughput expression microarray evidence
Reference(s):	[1] Cook GM., et al., 1997 [2] Federowicz S., et al., 2014 [3] Shalel-Levanon S., et al., 2005

Reference(s)
[1] Cook GM., Membrillo-Hernandez J., Poole RK., 1997, Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors., J Bacteriol 179(20):6525-30
[2] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264
[3] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli., Metab Eng 7(5-6):364-74