RegulonDB

Regulon
Regulated gene(s)	amtB, argT, astA, astB, astC, astD, astE, cbl, ddpA, ddpB, ddpC, ddpD, ddpF, ddpX, glnA, glnG, glnH, glnK, glnL, glnP, glnQ, hisJ, hisM, hisP, hisQ, nac, patA, potF, potG, potH, potI, relA, rpoE, rseA, rseB, rseC, rseD, rutA, rutB, rutC, rutD, rutE, rutF, rutG, yeaG, yeaH, yhdW, yhdX, yhdY, yhdZ
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) membrane (12) amtB, ddpB, ddpC, glnP, hisM, hisQ, potH, potI, rseC, rutG, yhdX, yhdY nitrogen metabolism (11) astC, glnA, glnK, nac, patA, rutA, rutB, rutC, rutD, rutE, rutF ABC superfamily, membrane component (9) ddpB, ddpC, glnP, hisM, hisQ, potH, potI, yhdX, yhdY other (mechanical, nutritional, oxidative stress) (8) hisJ, hisM, hisP, hisQ, rpoE, rseA, rseB, rseC Transcription related (7) cbl, glnG, nac, rpoE, rseA, rseB, rseC ABC superfamily ATP binding cytoplasmic component (6) ddpD, ddpF, glnQ, hisP, potG, yhdZ glutamine (6) glnA, glnG, glnH, glnL, glnP, glnQ ABC superfamily, periplasmic binding component (5) argT, ddpA, glnH, hisJ, potF amino acids (4) astA, astB, astD, astE amines (4) potF, potG, potH, potI sigma factors, anti-sigmafactors (4) rpoE, rseA, rseB, rseC activator (3) cbl, glnG, nac starvation (3) ddpX, rseB, rseC Porters (Uni-, Sym- and Antiporters) (2) amtB, rutG repressor (2) glnG, nac two component regulatory systems (external signal) (2) glnG, glnL operon (2) glnG, nac unknown (2) glnK, relA posttranslational modification (2) glnL, yeaG temperature extremes (2) rpoE, rseA arginine (1) argT lysine (1) argT cysteine (1) cbl sulfur metabolism (1) cbl regulon (1) cbl other compounds (1) ddpX proteins/peptides/glycopeptides (1) ddpX murein (peptidoglycan) (1) ddpX turnover, degradation (1) ddpX osmotic pressure (1) ddpX covalent modification, demodification, maturation (1) glnL nucleotide and nucleoside conversions (1) relA ribosomes (1) relA stimulon (1) rpoE Read more >
Regulated operon(s)	argT-hisJQMP, astCADBE, cbl, ddpXABCDF, glnALG, glnHPQ, glnK-amtB, nac, patA, potFGHI, relA-mazEFG, rseD-rpoE-rseABC, rutABCDEFG, yeaGH, yhdWXYZ
First gene in the operon(s)	argT, astC, cbl, ddpX, glnA, glnH, glnK, glnL, nac, patA, potF, relA, rseD, rutA, yeaG, yhdW
Simple and complex regulons	ArcA,NtrC,PhoP,RutR ArgR,NtrC CRP,Fis,NtrC CRP,GlrR,NtrC,RcsB CRP,NtrC CysB,NtrC FNR,Fur,GadX,NtrC FNR,Fur,Nac,NtrC Fis,IHF,NtrC IHF,NtrC NtrC NtrC,ppGpp Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase) [NtrC,+](18) argTp, astCp2, cblp, crlp2, ddpXp1, glnAp2, glnHp2, glnKp, nacp, patAp, patAp2, potFp1, relAp4, rpoEp2b, rseDp, rutAp, yeaGp1, yhdWp [NtrC,-](3) glnAp1, glnHp2, glnLp

Transcription factor binding sites (TFBSs) arrangements

Functional conformation	Function	Promoter	Sigma factor	Central Rel-Pos	Distance to first Gene	Genes	Sequence	LeftPos	RightPos	Evidence (Confirmed, Strong, Weak)	References
NtrC-phosphorylated	activator	argTp	Sigma54	-190.0	-248.0	argT, hisJ, hisQ, hisM, hisP	actccgctgtTGCCCTGTTTCAGGGCAattttgcaac nd	2428031	2428047	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	argTp	Sigma54	-83.0	-141.0	argT, hisJ, hisQ, hisM, hisP	tatcttcaacTTCAGGACAATAATGCAacgtcttatt nd	2427924	2427940	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	astCp2	Sigma54	-275.0	-337.0	astC, astA, astD, astB, astE	gttgttaatgATGTCAACGATGGCGCAaaaaatgccc nd	1832311	1832327	[GEA], [AIBSCS], [BPP]	[2]
NtrC-phosphorylated	activator	astCp2	Sigma54	-253.0	-315.0	astC, astA, astD, astB, astE	gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca nd	1832289	1832305	[GEA], [AIBSCS], [BPP]	[2]
NtrC-phosphorylated	activator	astCp2	Sigma54	-233.0	-295.0	astC, astA, astD, astB, astE	tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca nd	1832269	1832285	[GEA], [AIBSCS], [BPP]	[2]
NtrC-phosphorylated	activator	cblp	Sigma70	nd	nd	cbl	nd nd	nd	nd	[GEA], [BPP]	[1]
NtrC-phosphorylated	activator	ddpXp1	Sigma54	-109.0	-140.0	ddpX, ddpA, ddpB, ddpC, ddpD, ddpF	cttcccctctTGCACCAAAACTGCACTacgctgcaca nd	1563208	1563224	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	ddpXp1	Sigma54	-88.0	-119.0	ddpX, ddpA, ddpB, ddpC, ddpD, ddpF	tgcactacgcTGCACAAATGTTGATCAaaagttaaaa nd	1563187	1563203	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	repressor	glnAp1	Sigma70	-25.0	-213.0	glnA, glnL, glnG	caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd	4058239	4058255	[GEA], [APIORCISFBSCS], [BPP], [SM]	[3], [4]
NtrC-phosphorylated	repressor	glnAp1	Sigma70	8.0	-181.0	glnA, glnL, glnG	tttccattgaAGCACTATATTGGTGCAacattcacat nd	4058207	4058223	[GEA], [APIORCISFBSCS], [BPP], [SM]	[3], [4]
NtrC-phosphorylated	repressor	glnAp1	Sigma70	27.0	-162.0	glnA, glnL, glnG	ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd	4058188	4058204	[GEA], [APIORCISFBSCS], [BPP], [SM]	[3], [5]
NtrC-phosphorylated	repressor	glnAp1	Sigma70	48.0	-141.0	glnA, glnL, glnG	ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd	4058167	4058183	[GEA], [APIORCISFBSCS], [SM]	[3], [5]
NtrC-phosphorylated	repressor	glnAp1	Sigma70	71.0	-118.0	glnA, glnL, glnG	tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd	4058144	4058160	[GEA], [APIORCISFBSCS]	[3], [5]
NtrC-phosphorylated	activator	glnAp2	Sigma54	-140.0	-213.0	glnA, glnL, glnG	caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd	4058239	4058255	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [6], [7]
NtrC-phosphorylated	activator	glnAp2	Sigma54	-108.0	-181.0	glnA, glnL, glnG	tttccattgaAGCACTATATTGGTGCAacattcacat nd	4058207	4058223	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [7], [8]
NtrC-phosphorylated	activator	glnAp2	Sigma54	-89.0	-162.0	glnA, glnL, glnG	ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd	4058188	4058204	[GEA], [APIORCISFBSCS], [BPP], [SM]	[3], [4], [5], [6], [7]
NtrC-phosphorylated	activator	glnAp2	Sigma54	-68.0	-141.0	glnA, glnL, glnG	ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd	4058167	4058183	[GEA], [APIORCISFBSCS], [SM]	[3], [5]
NtrC-phosphorylated	activator	glnAp2	Sigma54	-45.0	-118.0	glnA, glnL, glnG	tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd	4058144	4058160	[GEA], [APIORCISFBSCS]	[3], [5]
NtrC-phosphorylated	repressor	glnHp2	Sigma54	-135.0	-178.0	glnH, glnP, glnQ	ctgtgttgagTGCACAATTTTAGCGCAccagattggt nd	848174	848190	[APIORCISFBSCS], [BPP]	[9]
NtrC-phosphorylated	activator	glnHp2	Sigma54	-122.0	-165.0	glnH, glnP, glnQ	acaattttagCGCACCAGATTGGTGCCccagaatggt nd	848161	848177	[APIORCISFBSCS], [BPP]	[9]
NtrC-phosphorylated	activator	glnHp2	Sigma54	-109.0	-152.0	glnH, glnP, glnQ	accagattggTGCCCCAGAATGGTGCAtcttcagggt nd	848148	848164	[APIORCISFBSCS], [BPP]	[9]
NtrC-phosphorylated	repressor	glnHp2	Sigma54	-79.0	-122.0	glnH, glnP, glnQ	tcagggtattGCCCTATAAATCGTGCAtcacgttttt nd	848118	848134	[APIORCISFBSCS], [BPP]	[9]
NtrC-phosphorylated	activator	glnKp	Sigma54	-87.0	-129.0	glnK, amtB	taacgcactgTGCACTGTCATAGTGCGttttcatttt nd	472461	472477	[APIORCISFBSCS]	[10]
NtrC-phosphorylated	repressor	glnLp	Sigma70	3.0	-30.0	glnL, glnG	aaagctataaTGCACTAAAATGGTGCAacctgttcag nd	4056361	4056377	[APIORCISFBSCS], [BPP], [SM]	[11]
NtrC-phosphorylated	activator	nacp	Sigma54	-152.0	-197.0	nac	tattgggtaaTGAACCATCGTGGTGCAtaccctcctt nd	2062122	2062138	[APIORCISFBSCS]	[12]
NtrC-phosphorylated	activator	patAp	Sigma38	-543.0	-579.0	patA	atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta nd	3218907	3218924	[IEP], [AIBSCS]	[13]
NtrC-phosphorylated	activator	patAp	Sigma38	-193.0	-229.0	patA	ttaattatctTGCCCAAAAATCAGGCAattattgccc nd	3219257	3219273	[GEA], [AIBSCS]	[14], [15]
NtrC-phosphorylated	activator	patAp	Sigma38	-171.0	-207.0	patA	aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc nd	3219279	3219295	[GEA], [AIBSCS]	[14], [15]
NtrC-phosphorylated	activator	patAp2	Sigma54	-543.0	-579.0	patA	atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta nd	3218907	3218924	[IEP], [AIBSCS]	[13]
NtrC-phosphorylated	activator	patAp2	Sigma54	-193.0	-229.0	patA	ttaattatctTGCCCAAAAATCAGGCAattattgccc nd	3219257	3219273	[GEA], [AIBSCS]	[14], [15]
NtrC-phosphorylated	activator	patAp2	Sigma54	-171.0	-207.0	patA	aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc nd	3219279	3219295	[GEA], [AIBSCS]	[14], [15]
NtrC-phosphorylated	activator	potFp1	Sigma54	nd	nd	potF, potG, potH, potI	nd nd	nd	nd	[GEA], [BPP]	[1]
NtrC-phosphorylated	activator	relAp4	Sigma54	nd	nd	relA	nd nd	nd	nd	[GEA], [BPP]	[16]
NtrC-phosphorylated	activator	rpoEp2b	Sigma70	-33.5	-208.5	rseD, rpoE, rseA, rseB, rseC	tttggtcagcATAGCATCATGTTGTGCGGataaacacct nd	2710364	2710382	[APIORCISFBSCS], [BPP]	[17]
NtrC-phosphorylated	activator	rseDp	Sigma54	-33.5	-208.5	rseD, rpoE, rseA, rseB, rseC	tttggtcagcATAGCATCATGTTGTGCGGataaacacct nd	2710364	2710382	[APIORCISFBSCS], [BPP]	[17]
NtrC-phosphorylated	activator	rutAp	Sigma54	-145.0	-160.0	rutA, rutB, rutC, rutD, rutE, rutF, rutG	ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg nd	1074163	1074179	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	rutAp	Sigma54	-124.0	-139.0	rutA, rutB, rutC, rutD, rutE, rutF, rutG	cgcgcacagaTGCATGTTTTATGTGCAactgttttga nd	1074142	1074158	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	yeaGp1	Sigma54	nd	nd	yeaG, yeaH	nd nd	nd	nd	[GEA], [BPP]	[1]
NtrC-phosphorylated	activator	yhdWp	Sigma54	-126.0	-196.0	yhdW, yhdX, yhdY, yhdZ	gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat nd	3418838	3418854	[GEA], [AIBSCS]	[1]
NtrC-phosphorylated	activator	yhdWp	Sigma54	-96.0	-166.0	yhdW, yhdX, yhdY, yhdZ	gtttcattttCGCACCATTGCGGGGCGctgtttttat nd	3418868	3418884	[GEA], [AIBSCS]	[1]

	Sequence
	atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta	[-543.0, patAp, forward] [-543.0, patAp2, forward]
	gttgttaatgATGTCAACGATGGCGCAaaaaatgccc	[-275.0, astCp2, reverse]
	gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca	[-253.0, astCp2, reverse]
	tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca	[-233.0, astCp2, reverse]
	ttaattatctTGCCCAAAAATCAGGCAattattgccc	[-193.0, patAp, forward] [-193.0, patAp2, forward]
	actccgctgtTGCCCTGTTTCAGGGCAattttgcaac	[-190.0, argTp, reverse]
	aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc	[-171.0, patAp, forward] [-171.0, patAp2, forward]
	tattgggtaaTGAACCATCGTGGTGCAtaccctcctt	[-152.0, nacp, reverse]
	ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg	[-145.0, rutAp, reverse]
	caaaggtcatTGCACCAACATGGTGCTtaatgtttcc	[-25.0, glnAp1, reverse] [-140.0, glnAp2, reverse]
	ctgtgttgagTGCACAATTTTAGCGCAccagattggt	[-135.0, glnHp2, reverse]
	gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat	[-126.0, yhdWp, forward]
	cgcgcacagaTGCATGTTTTATGTGCAactgttttga	[-124.0, rutAp, reverse]
	acaattttagCGCACCAGATTGGTGCCccagaatggt	[-122.0, glnHp2, reverse]
	cttcccctctTGCACCAAAACTGCACTacgctgcaca	[-109.0, ddpXp1, reverse]
	accagattggTGCCCCAGAATGGTGCAtcttcagggt	[-109.0, glnHp2, reverse]
	tttccattgaAGCACTATATTGGTGCAacattcacat	[8.0, glnAp1, reverse] [-108.0, glnAp2, reverse]
	gtttcattttCGCACCATTGCGGGGCGctgtttttat	[-96.0, yhdWp, forward]
	ttggtgcaacATTCACATCGTGGTGCAgcccttttgc	[27.0, glnAp1, reverse] [-89.0, glnAp2, reverse]
	tgcactacgcTGCACAAATGTTGATCAaaagttaaaa	[-88.0, ddpXp1, reverse]
	taacgcactgTGCACTGTCATAGTGCGttttcatttt	[-87.0, glnKp, forward]
	tatcttcaacTTCAGGACAATAATGCAacgtcttatt	[-83.0, argTp, reverse]
	tcagggtattGCCCTATAAATCGTGCAtcacgttttt	[-79.0, glnHp2, reverse]
	ggtgcagcccTTTTGCACGATGGTGCGcatgataacg	[48.0, glnAp1, reverse] [-68.0, glnAp2, reverse]
	tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt	[71.0, glnAp1, reverse] [-45.0, glnAp2, reverse]
	tttggtcagcATAGCATCATGTTGTGCGGataaacacct	[-33.5, rpoEp2b, reverse] [-33.5, rseDp, reverse]
	aaagctataaTGCACTAAAATGGTGCAacctgttcag	[3.0, glnLp, reverse]

Alignment and PSSM for NtrC TFBSs

Aligned TFBS of NtrC

	Sequence
	GATGCACCATTCTGGGGCAC
	TAAGCACCATGTTGGTGCAA
	GTTGCACCATTTTAGTGCAT
	TTCGCACCATTGCGGGGCGC
	AGTGCACAATTTTAGCGCAC
	AATGCACGTTTTCAGGGCAA
	ATTGCCTGATTTTTGGGCAA
	GAAGCACTATATTGGTGCAA
	AATGCCCGCTTTTGGTGCGC
	GTTGCCCTGTTTCAGGGCAA
	TGCGCCACATTTTGGCGCAA
	GGGGCACCAATCTGGTGCGC
	GATGCATGTTTTATGTGCAA
	AACGCACTATGACAGTGCAC
	AATGAACCATCGTGGTGCAT
	GACGCACCATGTTGTGCGGC
	ACTGCGCCATTCTGACGCAG
	ATAACGCCTTTTAGGGGCAA
	GTAGTGCAGTTTTGGTGCAA
	TGTGCGCGATGAGAGTGCAG
	GATGCACGATTTATAGGGCA
	TTTGCACGATGGTGCGCATG
	ATAGCATCATGTTGTGCGGA
	GTTGCATTATTGTCCTGAAG
	GCTGCACAAATGTTGATCAA
	TTTGCGCCATCGTTGACATC
	TTCACATCGTGGTGCAGCCC

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

A	9	10	5	2	1	18	1	3	20	2	1	2	3	6	2	3	0	3	18	12
C	0	2	5	0	25	4	21	13	1	0	2	3	4	1	3	3	4	21	2	9
G	11	4	1	25	0	5	0	7	3	0	7	7	1	15	20	10	22	3	5	4
T	7	11	16	0	1	0	5	4	3	25	17	15	19	5	2	11	1	0	2	2

Consensus

;	consensus.strict             	gttGCaCcaTtttgGgGCac
;	consensus.strict.rc          	GTGCCCCAAAATGGTGCAAC
;	consensus.IUPAC              	rwtGCaCsaTkktgGkGCam
;	consensus.IUPAC.rc           	KTGCMCCAMMATSGTGCAWY
;	consensus.regexp             	[ag][at]tGCaC[cg]aT[gt][gt]tgG[gt]GCa[ac]
;	consensus.regexp.rc          	[GT]TGC[AC]CCA[AC][AC]AT[CG]GTGCA[AT][CT]

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
[GEA] Gene expression analysis
[AIBSCS] Automated inference based on similarity to consensus sequences
[BPP] Binding of purified proteins
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[SM] Site mutation
[IEP] Inferred from expression pattern

Reference(s)
[1] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9
[2] Kiupakis AK., Reitzer L., 2002, ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli., J Bacteriol 184(11):2940-50
[3] Reitzer LJ., Magasanik B., 1985, Expression of glnA in Escherichia coli is regulated at tandem promoters., Proc Natl Acad Sci U S A 82(7):1979-83
[4] Reitzer LJ., Movsas B., Magasanik B., 1989, Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase., J Bacteriol 171(10):5512-22
[5] Atkinson MR., Pattaramanon N., Ninfa AJ., 2002, Governor of the glnAp2 promoter of Escherichia coli., Mol Microbiol 46(5):1247-57
[6] Collado-Vides J., Magasanik B., Gralla JD., 1991, Control site location and transcriptional regulation in Escherichia coli., Microbiol Rev 55(3):371-94
[7] Ninfa AJ., Reitzer LJ., Magasanik B., 1987, Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers., Cell 50(7):1039-46
[8] Reitzer LJ., Magasanik B., 1986, Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter., Cell 45(6):785-92
[9] Claverie-Martin F., Magasanik B., 1991, Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli., Proc Natl Acad Sci U S A 88(5):1631-5
[10] van Heeswijk WC., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff HV., 1996, An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli., Mol Microbiol 21(1):133-46
[11] Ueno-Nishio S., Mango S., Reitzer LJ., Magasanik B., 1984, Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli., J Bacteriol 160(1):379-84
[12] Muse WB., Bender RA., 1998, The nac (nitrogen assimilation control) gene from Escherichia coli., J Bacteriol 180(5):1166-73
[13] Robison K., McGuire AM., Church GM., 1998, A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome., J Mol Biol 284(2):241-54
[14] Samsonova NN., Smirnov SV., Altman IB., Ptitsyn LR., 2003, Molecular cloning and characterization of Escherichia coli K12 ygjG gene., BMC Microbiol 3(1):2
[15] Schneider BL., Hernandez VJ., Reitzer L., 2013, Putrescine catabolism is a metabolic response to several stresses in Escherichia coli., Mol Microbiol 88(3):537-50
[16] Brown DR., Barton G., Pan Z., Buck M., Wigneshweraraj S., 2014, Nitrogen stress response and stringent response are coupled in Escherichia coli., Nat Commun 5:4115
[17] Klein G., Stupak A., Biernacka D., Wojtkiewicz P., Lindner B., Raina S., 2016, Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective., J Biol Chem 291(44):22999-23019

RegulonDB