RegulonDB

Regulon
Regulated gene(s)	aceE, aceF, bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fhlA, fliA, fliZ, grxD, hcp, hcr, hmp, hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI, hypA, hypB, hypC, hypD, hypE, ihfA, infC, lrp, mepH, mhpT, moeA, moeB, ndh, norR, nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG, pgpC, pheM, pheS, pheT, poxB, rfe, rffC, rffG, rffH, rffM, rplT, rpmI, rybB, sodB, sufA, sufB, sufC, sufD, sufE, tadA, tcyJ, tehA, tehB, thrS, tsgA, waaH, wecB, wecC, wecE, wecF, wzxE, wzyE, wzzE, ydbD, yeaE, yeaR, ygbA, yoaG, ytfE Read more >
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) membrane (16) bamE, hycC, hycD, hycF, mhpT, nrfC, nrfD, nrfE, pgpC, poxB, tehA, tsgA, waaH, wzxE, wzyE, wzzE anaerobic respiration (11) hypA, hypC, hypD, hypE, nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG enterobacterial common antigen (surface glycolipid) (11) rfe, rffG, rffH, rffM, wecB, wecC, wecE, wecF, wzxE, wzyE, wzzE surface antigens (ECA, O antigen of LPS) (11) rfe, rffC, rffG, rffH, rffM, wecB, wecC, wecE, wecF, wzyE, wzzE fermentation (10) fhlA, hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hypB Transcription related (7) dsdC, feaR, fhlA, fliA, ihfA, lrp, norR chaperoning, repair (refolding) (7) hycI, hypB, hypC, nrfE, nrfF, nrfG, ytfE activator (6) dsdC, feaR, fhlA, ihfA, lrp, norR sulfur metabolism (6) sufA, sufB, sufC, sufD, sufE, sufS detoxification (5) dkgB, norR, sodB, ydbD, yeaE operon (5) dsdC, feaR, fhlA, hycA, lrp cytochromes (5) nrfA, nrfB, nrfE, nrfF, nrfG incorporation of metal ions (5) sufA, sufB, sufC, sufD, sufE carbon compounds (4) aceE, aceF, dkgB, poxB amino acid -activation (4) pheM, pheS, pheT, thrS repressor (3) dsdC, ihfA, lrp posttranslational modification (3) hycI, hypD, hypE translation (3) infC, rplT, rpmI Porters (Uni-, Sym- and Antiporters) (3) mhpT, tehA, tsgA electron acceptors (3) nrfA, nrfB, nrfC pyruvate dehydrogenase (2) aceE, aceF glyoxylate degradation (2) aceE, aceF methylglyoxal metabolism (2) dkgB, yeaE amino acids (2) dsdC, feaR amines (2) feaB, feaR nicotinamide adenine dinucleotide (2) feaB, rffG unknown (2) fliZ, wzzE molybdenum (2) moeA, moeB electron donors (2) ndh, poxB O antigen (2) rffG, rffH ribosomal proteins (2) rplT, rpmI ribosomes (2) rplT, rpmI drug resistance/sensitivity (2) tehA, tehB nucleotide and nucleoside conversions (1) cdd sigma factors, anti-sigmafactors (1) fliA stimulon (1) fliA motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (1) fliA flagella (1) fliA thioredoxin, glutaredoxin (1) grxD nitrogen metabolism (1) hcp metabolism (1) hcr unassigned reversible reactions (1) hmp DNA recombination (1) ihfA isoleucine/valine (1) lrp leucine (1) lrp nucleoproteins, basic proteins (1) lrp murein (peptidoglycan) (1) mepH fatty acids (1) mhpT aerobic respiration (1) ndh phospholipid (1) pgpC pyruvate oxidation (1) poxB posttranscriptional (1) rplT RNA related (1) rybB inhibition / activation of enzymes (1) sufE RNA modification (1) tadA ABC superfamily, periplasmic binding component (1) tcyJ translation attenuation and efficiency (1) thrS other (mechanical, nutritional, oxidative stress) (1) waaH transport (1) wzxE Read more >
Regulated operon(s)	bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fliAZ-tcyJ, grxD, hcp-hcr-poxB-ltaE-ybjT, hmp, hycABCDEFGHI, hypABCDE-fhlA, lrp, mepH, mhpT, moeAB, ndh, norR, nrfABCDEFG, pdhR-aceEF-lpd, pgpC-tadA, rfe-wzzE-wecBC-rffGHC-wecE-wzxE-wecF-wzyE-rffM, rybB, sodB, sufABCDSE, tehAB, thrS-infC-rpmI-rplT-pheMST-ihfA, tsgA, waaH, ydbD, yeaE, yeaR-yoaG, ygbA, ytfE
First gene in the operon(s)	aceE, bamE, bdcA, cdd, dkgB, dsdC, feaB, feaR, fliA, grxD, hcp, hmp, hycA, hypA, lrp, mepH, mhpT, moeA, ndh, norR, nrfA, pgpC, rfe, rybB, sodB, sufA, tehA, thrS, tsgA, ydbD, yeaE, yeaR, ygbA, waaH, ytfE
Simple and complex regulons	ArcA,FNR,Fis,Fur,IHF,NsrR,PdhR ArcA,FNR,NarL,NsrR ArcA,FNR,NsrR CRP,CytR,NsrR CRP,FeaR,NsrR CRP,IHF,NsrR CRP,Nac,NsrR,PhoB,QseB CpxR,NsrR CsgD,FlhDC,H-NS,IHF,MatA,NsrR,SutR DksA,DksA-ppGpp,NsrR DksA-ppGpp,NsrR DsdC,NsrR FNR,Fis,FlhDC,IHF,NarL,NarP,NsrR FNR,Fur,MetR,NsrR,ppGpp FNR,NarL,NarP,NsrR FNR,NarL,NarP,NsrR,OxyR FNR,NsrR FhlA,IHF,ModE,NsrR FhlA,IHF,NsrR Fis,NarL,NarP,NsrR Fur,IHF,IscR,NsrR,OxyR GadE,H-NS,Lrp,NsrR,ppGpp NorR,NsrR NsrR NsrR,PhoB Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase) [NsrR,-](36) aceEp1, aceEp2, bamEp, bdcAp, cddp, dkgBp, dsdCp, feaBp1, feaRp2, fliAp1, fliAp2, grxD, hcpp1, hmpp, hycAp, hypAp, lrpp, mepHp, mhpTp, ndhp, norRp, nrfAp, pgpCp, rfep, rybBp, sodBp, sufAp, tehAp, thrSp, tsgAp, ydbDp, yeaEp, yeaRp, ygbAp, yibDp1, ytfEp [NsrR,+](1) moeAp

Transcription factor binding sites (TFBSs) arrangements

Functional conformation	Function	Promoter	Sigma factor	Central Rel-Pos	Distance to first Gene	Genes	Sequence	LeftPos	RightPos	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	References
NsrR	repressor	aceEp1	Sigma70	-81.0	-129.0	aceE, aceF	aattatccagAAGATGTTGTAAatcaagcgca nd	122883	122894	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	aceEp2	Sigma38	-81.0	-129.0	aceE, aceF	aattatccagAAGATGTTGTAAatcaagcgca nd	122883	122894	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	bamEp	Sigma24	67.0	-53.0	bamE	gtctattatcATCGGCATATTAcagatgagcc nd	2753547	2753558	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	bdcAp	Sigma70	-18.0	-29.0	bdcA	aaacagttttGTAATGCATGTTacataataaa nd	4474077	4474088	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	cddp	Sigma70	9.0	-17.0	cdd	gttatcccatTACATGATTATGaggcaacgcc nd	2231822	2231833	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	dkgBp	Sigma38	-11.0	-80.0	dkgB	cgcaaaaatcCTCTGCATTTTAcgctcttttt nd	229082	229093	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	dkgBp	Sigma38	64.0	-6.0	dkgB	tagcattaaaAGAGGCATATTAtggctatccc nd	229156	229167	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	dsdCp	Sigma70	14.0	-104.0	dsdC	atcaatggagTGATTTACATCTaaaaatgaag nd	2477728	2477739	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	feaBp1	Sigma70	-184.0	-211.0	feaB	tcgctctgtgAAATGTATTTTTattgttgcat nd	1447303	1447314	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [2]
NsrR	repressor	feaRp2	Sigma70	2.0	-25.0	feaR	atgcaacaatAAAAATACATTTcacagagcga nd	1447303	1447314	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	fliAp1	Sigma70	-207.0	-237.0	fliA, fliZ, tcyJ	cctacaagttGAATTGCAATTTattgaatttg nd	2002021	2002032	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	fliAp1	Sigma70	7.0	-24.0	fliA, fliZ, tcyJ	taatcatgccGATAACTCATATaacgcagggc nd	2001808	2001819	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION]	S	[1], [1]
NsrR	repressor	fliAp2	Sigma28	-218.0	-237.0	fliA, fliZ, tcyJ	cctacaagttGAATTGCAATTTattgaatttg nd	2002021	2002032	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	fliAp2	Sigma28	-5.0	-24.0	fliA, fliZ, tcyJ	taatcatgccGATAACTCATATaacgcagggc nd	2001808	2001819	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	grxD	Sigma70	-13.0	-74.0	grxD	aaagcgtgatGAAAATGTTATTttccgatgcc nd	1734170	1734181	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	hcpp1	nd	6.0	-26.0	hcp, hcr, poxB	taaccttaaaCATGTATATTAAATATAACtttaaaaggt nd	913831	913849	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [3], [3], [4], [5]
NsrR	repressor	hmpp	Sigma38	-38.0	-76.0	hmp	aaaacaccaaAGAACCATTTACattgcagggc nd	2685754	2685765	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[1], [1], [5]
NsrR	repressor	hmpp	Sigma38	2.0	-37.0	hmp	tttttataagATGCATTTGAGATACATCAattaagatgc nd	2685789	2685807	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[5], [6], [6]
NsrR	repressor	hmpp	Sigma38	20.0	-19.0	hmp	tacatcaattAAGATGCAAAAAaaggaagacc nd	2685811	2685822	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[1], [1], [5]
NsrR	repressor	hycAp	Sigma54	-70.0	-96.0	hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI	acacggcgacGAAATTCATCTTtagcttaaaa nd	2850526	2850537	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	hypAp	Sigma54	-96.0	-116.0	hypA, hypB, hypC, hypD, hypE, fhlA	ttttaagctaAAGATGAATTTCgtcgccgtgt nd	2850526	2850537	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	lrpp	Sigma70	52.0	-216.0	lrp	catgcatgtaAATACCATGTTTaccgtgctag nd	932374	932385	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	mepHp	Sigma70	-61.0	-139.0	mepH	tagctttcacTGCTGCATTTTTttgcgctcgc nd	1734291	1734302	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	mhpTp	Sigma32	-484.0	-557.0	mhpT	actgccgagaACGTGCATTTTGtatgcccatc nd	374897	374908	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	activator	moeAp	Sigma70	nd	nd	moeA, moeB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[7], [7]
NsrR	repressor	ndhp	Sigma70	6.0	-88.0	ndh	ctcaatagcgAAGAACATTTTCattgctgtaa nd	1165992	1166003	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	norRp	nd	21.0	3.0	norR	acagtgaggcAAAGATGAGTTTttccgttgat nd	2832282	2832293	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	nrfAp	Sigma70	-121.0	-214.0	nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG	ttctttgaggAACATGCAGTTAtgcatgctgt nd	4287545	4287556	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [4]
NsrR	repressor	nrfAp	Sigma70	-63.0	-156.0	nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG	taactctaaaGTGGTATTTTACATGCACTtacaattgat nd	4287599	4287617	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [8], [8]
NsrR	repressor	pgpCp	Sigma32	131.0	43.0	pgpC, tadA	gttttttgacTTAGATGGAACAttgcatcagc nd	2698503	2698514	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	rfep	Sigma70	-1.0	-117.0	rfe, wzzE, wecB, wecC, rffG, rffH, rffC, wecE, wzxE, wecF, wzyE, rffM	catgttatgcAATTTGCATATCaaatggttaa nd	3967794	3967805	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	rybBp	Sigma24	nd	nd	rybB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[9]
NsrR	repressor	sodBp	Sigma70	-37.0	-92.0	sodB	gcaacagggtAAGTTCATCTTTtgtctcacct nd	1735281	1735292	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	sufAp	Sigma70	-68.0	-100.0	sufA, sufB, sufC, sufD, sufS, sufE	aaaagcaggcAAAAAGCATGTTttacggtaaa nd	1764481	1764492	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [10]
NsrR	repressor	sufAp	Sigma70	-6.0	-38.0	sufA, sufB, sufC, sufD, sufS, sufE	tcattatcacTAACATGCTGTTatacgctgaa nd	1764419	1764430	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [10]
NsrR	repressor	tehAp	nd	-1.0	-38.0	tehA, tehB	aattccataaAATGCATTTCAAATATACTttataaatta nd	1500526	1500544	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [6], [6]
NsrR	repressor	tehAp	nd	28.0	-10.0	tehA, tehB	taaattaaacAAAATGAGTAAGaagatgcaga nd	1500558	1500569	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	thrSp	nd	80.0	-84.0	thrS, infC, rpmI, rplT, pheM, pheS, pheT, ihfA	catttgttggCTAGATGGTTTCgcaatgaact nd	1802649	1802660	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	tsgAp	nd	-64.0	-113.0	tsgA	atcacctcttAAAATGCAATTTagcaaccgat nd	3492450	3492461	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	ydbDp	Sigma38	39.0	-40.0	ydbD	acaaaagggaAAGATGCATTTCcctttttttc nd	1475099	1475110	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	yeaEp	Sigma70	5.0	-84.0	yeaE	acaaattctgATAATGCATCTTtccagggcat nd	1865715	1865726	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	yeaRp	Sigma70	-32.0	-78.0	yeaR, yoaG	taaccaataaATGGTATTTAAAATGCAAAttatcaggcg nd	1880017	1880035	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
NsrR	repressor	ygbAp	nd	-118.0	-140.0	ygbA	tggttccgggAAAGATGCTGTTttgcagcttt nd	2856941	2856952	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	ygbAp	nd	-7.0	-29.0	ygbA	ttaagattaaGATGTAATATAAATACATCttaatgaggt nd	2856826	2856844	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1], [6], [6]
NsrR	repressor	ygbAp	nd	-1.0	-23.0	ygbA	agatgtaataTAAATACATCTTaatgaggtgg nd	2856824	2856835	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	yibDp1	Sigma70	-115.0	-183.0	waaH	ataatctgttAAATATGTAAAAtcctgtcagt nd	3790259	3790270	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[1], [1]
NsrR	repressor	ytfEp	nd	-12.0	-38.0	ytfE	ttgccttaaaGATGCATTTAAAATACATCttatcttatt nd	4432012	4432030	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [4], [5], [6], [6]

	Sequence
	actgccgagaACGTGCATTTTGtatgcccatc	[-484.0, mhpTp, forward]
	cctacaagttGAATTGCAATTTattgaatttg	[-207.0, fliAp1, reverse] [-218.0, fliAp2, reverse]
	tcgctctgtgAAATGTATTTTTattgttgcat	[-184.0, feaBp1, forward]
	ttctttgaggAACATGCAGTTAtgcatgctgt	[-121.0, nrfAp, forward]
	tggttccgggAAAGATGCTGTTttgcagcttt	[-118.0, ygbAp, reverse]
	ataatctgttAAATATGTAAAAtcctgtcagt	[-115.0, yibDp1, reverse]
	ttttaagctaAAGATGAATTTCgtcgccgtgt	[-70.0, hycAp, reverse] [-96.0, hypAp, forward]
	aattatccagAAGATGTTGTAAatcaagcgca	[-81.0, aceEp1, forward] [-81.0, aceEp2, forward]
	aaaagcaggcAAAAAGCATGTTttacggtaaa	[-68.0, sufAp, reverse]
	atcacctcttAAAATGCAATTTagcaaccgat	[-64.0, tsgAp, forward]
	taactctaaaGTGGTATTTTACATGCACTtacaattgat	[-63.0, nrfAp, forward]
	tagctttcacTGCTGCATTTTTttgcgctcgc	[-61.0, mepHp, forward]
	aaaacaccaaAGAACCATTTACattgcagggc	[-38.0, hmpp, forward]
	gcaacagggtAAGTTCATCTTTtgtctcacct	[-37.0, sodBp, forward]
	taaccaataaATGGTATTTAAAATGCAAAttatcaggcg	[-32.0, yeaRp, reverse]
	aaacagttttGTAATGCATGTTacataataaa	[-18.0, bdcAp, reverse]
	aaagcgtgatGAAAATGTTATTttccgatgcc	[-13.0, grxD, reverse]
	ttgccttaaaGATGCATTTAAAATACATCttatcttatt	[-12.0, ytfEp, reverse]
	cgcaaaaatcCTCTGCATTTTAcgctcttttt	[-11.0, dkgBp, forward]
	ttaagattaaGATGTAATATAAATACATCttaatgaggt	[-7.0, ygbAp, reverse]
	tcattatcacTAACATGCTGTTatacgctgaa	[-6.0, sufAp, reverse]
	taatcatgccGATAACTCATATaacgcagggc	[-5.0, fliAp2, reverse]
	aattccataaAATGCATTTCAAATATACTttataaatta	[-1.0, tehAp, forward]
	agatgtaataTAAATACATCTTaatgaggtgg	[-1.0, ygbAp, reverse]
	catgttatgcAATTTGCATATCaaatggttaa	[-1.0, rfep, forward]
	atgcaacaatAAAAATACATTTcacagagcga	[2.0, feaRp2, reverse]
	tttttataagATGCATTTGAGATACATCAattaagatgc	[2.0, hmpp, forward]
	acaaattctgATAATGCATCTTtccagggcat	[5.0, yeaEp, reverse]
	ctcaatagcgAAGAACATTTTCattgctgtaa	[6.0, ndhp, forward]
	taaccttaaaCATGTATATTAAATATAACtttaaaaggt	[6.0, hcpp1, reverse]
	taatcatgccGATAACTCATATaacgcagggc	[7.0, fliAp1, reverse]
	gttatcccatTACATGATTATGaggcaacgcc	[9.0, cddp, forward]
	atcaatggagTGATTTACATCTaaaaatgaag	[14.0, dsdCp, reverse]
	tacatcaattAAGATGCAAAAAaaggaagacc	[20.0, hmpp, forward]
	acagtgaggcAAAGATGAGTTTttccgttgat	[21.0, norRp, reverse]
	taaattaaacAAAATGAGTAAGaagatgcaga	[28.0, tehAp, forward]
	acaaaagggaAAGATGCATTTCcctttttttc	[39.0, ydbDp, forward]
	catgcatgtaAATACCATGTTTaccgtgctag	[52.0, lrpp, forward]
	tagcattaaaAGAGGCATATTAtggctatccc	[64.0, dkgBp, forward]
	gtctattatcATCGGCATATTAcagatgagcc	[67.0, bamEp, forward]
	catttgttggCTAGATGGTTTCgcaatgaact	[80.0, thrSp, reverse]
	gttttttgacTTAGATGGAACAttgcatcagc	[131.0, pgpCp, reverse]

Alignment and PSSM for NsrR TFBSs

Aligned TFBS of NsrR

	Sequence
	TAAGATGCATTTGAG
	AAAGATGCATTTAAA
	AAAGATGCATTTCCC
	TAAAATGCATTTCAA
	TAAAATGCAATTTAG
	AAAGATGCATTATCA
	TAACATGCATTACAA
	AAAGATGCTGTTTTG
	AAACATGCTTTTTGC
	TAAGATGTATTTATA
	TAAAATGCAAATTAT
	AAACATGTATATTAA
	GAACATGCAGTTATG
	TAAGATGCAAAAAAA
	TAACATGCTGTTATA
	AAAGATGAATTTCGT
	AAACATGGTATTTAC
	AAAGATGAGTTTTTC
	AAAGATGAACTTACC
	TTAGATGTAAATCAC
	TAAATTGCAATTCAA
	AAAGAGGCATATTAT
	TTACATGCACTTACA
	AAAAATACATTTCAC
	GAAAATGTTATTTTC
	AAAAATGCAGCAGTG
	TTACATGATTATGAG
	GAAGATGTTGTAAAT
	TAAAATGCAGAGGAT
	GAACGTGCATTTTGT
	AAATATGTAAAATCC
	GAAAATGTTCTTCGC
	CAATTTGCATATCAA
	TAATATGCCGATGAT
	TTAGATGGAACATTG
	CAAAATGAGTAAGAA
	GTAAATGGTTCTTTG
	TTATATGAGTTATCG
	CTAGATGGTTTCGCA

Position weight matrix (PWM). NsrR matrix-quality result

A	14	32	39	11	36	0	1	6	25	9	11	9	8	19	13
C	3	0	0	9	0	0	0	22	1	3	3	1	9	7	10
G	6	0	0	15	1	1	38	4	3	7	0	1	7	4	9
T	16	7	0	4	2	38	0	7	10	20	25	28	15	9	7

Consensus

;	consensus.strict             	tAAgATGcattttac
;	consensus.strict.rc          	GTAAAATGCATCTTA
;	consensus.IUPAC              	wAAsATGcatttyav
;	consensus.IUPAC.rc           	BTRAAATGCATSTTW
;	consensus.regexp             	[at]AA[cg]ATGcattt[ct]a[acg]
;	consensus.regexp.rc          	[CGT]T[AG]AAATGCAT[CG]TT[AT]

PWM logo

Evolutionary conservation of regulatory elements

Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.

TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation

Evidence
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IMP-SITE-MUTATION] Site mutation
[EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

Reference(s)
[1] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94
[2] Rankin LD., Bodenmiller DM., Partridge JD., Nishino SF., Spain JC., Spiro S., 2008, Escherichia coli NsrR regulates a pathway for the oxidation of 3-nitrotyramine to 4-hydroxy-3-nitrophenylacetate., J Bacteriol 190(18):6170-7
[3] Chismon DL., Browning DF., Farrant GK., Busby SJ., 2010, Unusual organization, complexity and redundancy at the Escherichia coli hcp-hcr operon promoter., Biochem J 430(1):61-8
[4] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7
[5] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2
[6] Bodenmiller DM., Spiro S., 2006, The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator., J Bacteriol 188(3):874-81
[7] Fujita D., Tobe R., Tajima H., Anma Y., Nishida R., Mihara H., 2021, Genetic analysis of tellurate reduction reveals the selenate/tellurate reductase genes ynfEF and the transcriptional regulation of moeA by NsrR in Escherichia coli., J Biochem 169(4):477-484
[8] Browning DF., Lee DJ., Spiro S., Busby SJ., 2010, Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site., J Bacteriol 192(14):3824-8
[9] Thompson KM., Rhodius VA., Gottesman S., 2007, {sigma}E Regulates and Is Regulated by a Small RNA in Escherichia coli., J Bacteriol 189(11):4243-56
[10] Chhabra S., Spiro S., 2015, Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli., Microbiology 161(10):2029-38
[11] Lin HY., Bledsoe PJ., Stewart V., 2007, Activation of yeaR-yoaG operon transcription by the nitrate-responsive regulator NarL is independent of oxygen- responsive regulator Fnr in Escherichia coli K-12., J Bacteriol 189(21):7539-48
[12] Beaumont HJ, Lens SI, Reijnders WN, Westerhoff HV, van Spanning RJ, 2004, Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor., Mol Microbiol, 54(1):148 10.1111/j.1365-2958.2004.04248.x
[13] Schwartz CJ., Giel JL., Patschkowski T., Luther C., Ruzicka FJ., Beinert H., Kiley PJ., 2001, IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins., Proc Natl Acad Sci U S A 98(26):14895-900
[14] Todd JD, Wexler M, Sawers G, Yeoman KH, Poole PS, Johnston AWB, 2002, RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum., Microbiology (Reading), 148(Pt 12):4059 10.1099/00221287-148-12-4059
[15] Rodionov DA., Dubchak IL., Arkin AP., Alm EJ., Gelfand MS., 2005, Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks., PLoS Comput Biol 1(5):e55
[16] Tucker NP, Hicks MG, Clarke TA, Crack JC, Chandra G, Le Brun NE, Dixon R, Hutchings MI, 2008, The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster., PLoS One, 3(11):e3623 10.1371/journal.pone.0003623
[17] Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, Barras F, 2013, In vivo [Fe-S] cluster acquisition by IscR and NsrR, two stress regulators in Escherichia coli., Mol Microbiol, 87(3):493 10.1111/mmi.12135
[18] Cairrao F., Cruz A., Mori H., Arraiano CM., 2003, Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA., Mol Microbiol 50(4):1349-60
[19] Lövgren JM, Wikström PM, 2001, The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli., J Bacteriol, 183(23):6957 10.1128/JB.183.23.6957-6960.2001

RegulonDB

DNA binding site length:	23
DNA binding site symmetry:	inverted-repeat