RegulonDB

TRANSCRIPTION FACTOR:

Name:

RutR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator RutR, YcdC

Gene name(s):

rutR

Functional conformation(s):

RutR , RutR-thymine , RutR-uracil

Coregulator(s):

ArcA, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, IHF, NemR, NtrC, PepA, PhoB, PhoP, PurR, RutR

Summary:

TF Summary ...[more]

REGULATION EXERTED BY RutR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
RutR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
RutR	repressor	rutRp2	rutR	1074120	1074138	16.5	tggtaaaaagTGGACTAAACGGTCAAAACagttgcacat	[AIBSCS] [BPP] [CV(GEA)] [CV(GEA)] [CV(GEA/SM)] [CV(SM)] [GEA] [SM]	[1] [2] [3]

Evidence:	[AIBSCS] Automated inference based on similarity to consensus sequences [BPP] Binding of purified proteins [CV(GEA)] cross validation(GEA) [CV(GEA/SM)] cross validation(GEA/SM) [CV(SM)] cross validation(SM) [GEA] Gene expression analysis [SM] Site mutation
Reference(s):	[1] Nguyen Le Minh P., et al., 2015 [2] Shimada T., et al., 2007 [3] Shimada T., et al., 2008

Reference(s)
[1] Nguyen Le Minh P., de Cima S., Bervoets I., Maes D., Rubio V., Charlier D., 2015, Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli., FEBS Open Bio 5:76-84
[2] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57
[3] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5