RegulonDB

TRANSCRIPTION FACTOR:

Name:

NagC	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External sensing using transported metabolites

Synonym(s):

DNA-binding transcriptional dual regulator NagC, NagR, transcriptional repressor of nag (N-acetylglucosamine) operon

Gene name(s):

nagC

Functional conformation(s):

NagC , NagC-N-acetyl-D-glucosamine 6-phosphate

Coregulator(s):

AraC, BasR, CRP, ChbR, Cra, DksA, DksA-ppGpp, EvgA, FNR, Fur, GadX, GalR, GalS, H-NS, IHF, LexA, Mlc, NagC, NanR, NarL, NarP, PhoP, RcsB, UvrY, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

LexA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional repressor LexA, ExrA, Spr, Tsl, UmuA

Gene name(s):

lexA

Functional conformation(s):

LexA

Coregulator(s):

ArcA, CRP, DinJ-YafQ, DnaA, LexA, NagC, RcdA, RcsB-BglJ, ppGpp

Summary:

TF Summary ...[more]

REGULATION EXERTED BY LexA,NagC

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
LexA repressor NagC repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
NagC	repressor	dinIp	dinI	1121512	1121534	-14.0	ttgtcattagGTTATTTTACCTGTATAAATAACcagtatattc	[AIBSCS]	[1]
LexA	repressor	dinIp	dinI	1121507	1121526	-7.5	aggttattttACCTGTATAAATAACCAGTAtattcaacag	[AIBSCS] [APIORCISFBSCS] [BPP] [CV(GEA)] [CV(GEA)] [CV(GEA/SM)] [CV(SM)] [GEA] [IHBCE] [SM]	[2] [3] [4] [5] [6]

Evidence:

[AIBSCS] Automated inference based on similarity to consensus sequences
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[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
[IHBCE] Inferred by a human based on computational evidence
[SM] Site mutation

Reference(s):

[1] Oberto J. 2010
[2] Fernandez De Henestrosa AR., et al., 2000
[3] Kaleta C., et al., 2010
[4] Lewis LK., et al., 1994
[5] Wade JT., et al., 2005
[6] Yasuda T., et al., 1996

Reference(s)
[1] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554
[2] Fernandez De Henestrosa AR., Ogi T., Aoyagi S., Chafin D., Hayes JJ., Ohmori H., Woodgate R., 2000, Identification of additional genes belonging to the LexA regulon in Escherichia coli., Mol Microbiol 35(6):1560-72
[3] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116
[4] Lewis LK., Harlow GR., Gregg-Jolly LA., Mount DW., 1994, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli., J Mol Biol 241(4):507-23
[5] Wade JT., Reppas NB., Church GM., Struhl K., 2005, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites., Genes Dev 19(21):2619-30
[6] Yasuda T., Nagata T., Ohmori H., 1996, Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli., J Bacteriol 178(13):3854-9