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, glnA, glnA, 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,-](3) glnAp1, glnHp2, glnLp [NtrC,+](15) argTp, astCp2, cblp, ddpXp, glnAp2, glnHp2, glnKp, nacp, patAp, potFp1, relAp4, rpoEp2b, rutAp, yeaGp1, yhdWp

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-P^asp	activator	argTp	Sigma54	-190.0	-248.0	argT, hisJ, hisQ, hisM, hisP	actccgctgtTGCCCTGTTTCAGGGCAattttgcaac nd	2428031	2428047	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	argTp	Sigma54	-83.0	-141.0	argT, hisJ, hisQ, hisM, hisP	tatcttcaacTTCAGGACAATAATGCAacgtcttatt nd	2427924	2427940	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	astCp2	Sigma54	-275.0	-337.0	astC, astA, astD, astB, astE	gttgttaatgATGTCAACGATGGCGCAaaaaatgccc nd	1832311	1832327	[AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[6]
NtrC-P^asp	activator	astCp2	Sigma54	-253.0	-315.0	astC, astA, astD, astB, astE	gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca nd	1832289	1832305	[AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[6]
NtrC-P^asp	activator	astCp2	Sigma54	-233.0	-295.0	astC, astA, astD, astB, astE	tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca nd	1832269	1832285	[AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA]	[6]
NtrC-P^asp	activator	cblp	Sigma70	nd	nd	cbl	nd nd	nd	nd	[GEA]	[5]
NtrC-P^asp	activator	ddpXp	Sigma54	-109.0	-140.0	ddpX, ddpA, ddpB, ddpC, ddpD, ddpF	cttcccctctTGCACCAAAACTGCACTacgctgcaca nd	1563208	1563224	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	ddpXp	Sigma54	-88.0	-119.0	ddpX, ddpA, ddpB, ddpC, ddpD, ddpF	tgcactacgcTGCACAAATGTTGATCAaaagttaaaa nd	1563187	1563203	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	repressor	glnAp1	Sigma70	-25.0	-213.0	glnA, glnL, glnG	caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd	4058239	4058255	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [8], [9]
NtrC-P^asp	repressor	glnAp1	Sigma70	8.0	-181.0	glnA, glnL, glnG	tttccattgaAGCACTATATTGGTGCAacattcacat nd	4058207	4058223	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [8], [9]
NtrC-P^asp	repressor	glnAp1	Sigma70	27.0	-162.0	glnA, glnL, glnG	ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd	4058188	4058204	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [9], [10]
NtrC-P^asp	repressor	glnAp1	Sigma70	48.0	-141.0	glnA, glnL, glnG	ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd	4058167	4058183	[APIORCISFBSCS], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[7], [10]
NtrC-P^asp	repressor	glnAp1	Sigma70	71.0	-118.0	glnA, glnL, glnG	tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd	4058144	4058160	[APIORCISFBSCS], [CV(GEA)], [GEA]	[7], [10]
NtrC-P^asp	activator	glnAp2	Sigma54	-140.0	-213.0	glnA, glnL, glnG	caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd	4058239	4058255	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [8], [9], [11]
NtrC-P^asp	activator	glnAp2	Sigma54	-108.0	-181.0	glnA, glnL, glnG	tttccattgaAGCACTATATTGGTGCAacattcacat nd	4058207	4058223	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [8], [9]
NtrC-P^asp	activator	glnAp2	Sigma54	-89.0	-162.0	glnA, glnL, glnG	ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd	4058188	4058204	[APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[2], [7], [9], [10], [11]
NtrC-P^asp	activator	glnAp2	Sigma54	-68.0	-141.0	glnA, glnL, glnG	ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd	4058167	4058183	[APIORCISFBSCS], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM]	[7], [10]
NtrC-P^asp	activator	glnAp2	Sigma54	-45.0	-118.0	glnA, glnL, glnG	tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd	4058144	4058160	[APIORCISFBSCS], [CV(GEA)], [GEA]	[7], [10]
NtrC-P^asp	repressor	glnHp2	Sigma54	-135.0	-178.0	glnH, glnP, glnQ	ctgtgttgagTGCACAATTTTAGCGCAccagattggt nd	848174	848190	[APIORCISFBSCS], [BPP]	[12]
NtrC-P^asp	activator	glnHp2	Sigma54	-122.0	-165.0	glnH, glnP, glnQ	acaattttagCGCACCAGATTGGTGCCccagaatggt nd	848161	848177	[APIORCISFBSCS], [BPP]	[12]
NtrC-P^asp	activator	glnHp2	Sigma54	-109.0	-152.0	glnH, glnP, glnQ	accagattggTGCCCCAGAATGGTGCAtcttcagggt nd	848148	848164	[APIORCISFBSCS], [BPP]	[12]
NtrC-P^asp	repressor	glnHp2	Sigma54	-79.0	-122.0	glnH, glnP, glnQ	tcagggtattGCCCTATAAATCGTGCAtcacgttttt nd	848118	848134	[APIORCISFBSCS], [BPP]	[12]
NtrC-P^asp	activator	glnKp	Sigma54	-87.0	-129.0	glnK, amtB	taacgcactgTGCACTGTCATAGTGCGttttcatttt nd	472461	472477	[APIORCISFBSCS]	[13]
NtrC-P^asp	repressor	glnLp	Sigma70	3.0	-30.0	glnL, glnG	aaagctataaTGCACTAAAATGGTGCAacctgttcag nd	4056361	4056377	[APIORCISFBSCS], [BPP], [CV(SM)], [SM]	[4], [14]
NtrC-P^asp	activator	nacp	Sigma54	-152.0	-197.0	nac	tattgggtaaTGAACCATCGTGGTGCAtaccctcctt nd	2062122	2062138	[APIORCISFBSCS]	[15]
NtrC-P^asp	activator	patAp	Sigma38, Sigma54	-543.0	-579.0	patA	atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta nd	3218907	3218924	[AIBSCS], [IEP]	[16]
NtrC-P^asp	activator	patAp	Sigma38, Sigma54	-193.0	-229.0	patA	ttaattatctTGCCCAAAAATCAGGCAattattgccc nd	3219257	3219273	[AIBSCS], [CV(GEA)], [GEA]	[17], [18]
NtrC-P^asp	activator	patAp	Sigma38, Sigma54	-171.0	-207.0	patA	aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc nd	3219279	3219295	[AIBSCS], [CV(GEA)], [GEA]	[17], [18]
NtrC-P^asp	activator	potFp1	Sigma54	nd	nd	potF, potG, potH, potI	nd nd	nd	nd	[GEA]	[5]
NtrC-P^asp	activator	relAp4	Sigma54	nd	nd	relA	nd nd	nd	nd	[BPP], [GEA]	[19]
NtrC-P^asp	activator	rpoEp2b	Sigma70, Sigma54	-33.5	-208.5	rseD, rpoE, rseA, rseB, rseC	tttggtcagcATAGCATCATGTTGTGCGGataaacacct nd	2710364	2710382	[APIORCISFBSCS], [BPP]	[20]
NtrC-P^asp	activator	rutAp	Sigma54	-145.0	-160.0	rutA, rutB, rutC, rutD, rutE, rutF, rutG	ctcgaccttcTGCACTCTCATCGCGCAcagatgcatg nd	1074163	1074179	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	rutAp	Sigma54	-124.0	-139.0	rutA, rutB, rutC, rutD, rutE, rutF, rutG	cgcgcacagaTGCATGTTTTATGTGCAactgttttga nd	1074142	1074158	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	yeaGp1	Sigma54	nd	nd	yeaG, yeaH	nd nd	nd	nd	[GEA]	[5]
NtrC-P^asp	activator	yhdWp	Sigma54	-126.0	-196.0	yhdW, yhdX, yhdY, yhdZ	gtaaatatttTGCGCCAAAATGTGGCGcatgtttcat nd	3418838	3418854	[AIBSCS], [CV(GEA)], [GEA]	[5]
NtrC-P^asp	activator	yhdWp	Sigma54	-96.0	-166.0	yhdW, yhdX, yhdY, yhdZ	gtttcattttCGCACCATTGCGGGGCGctgtttttat nd	3418868	3418884	[AIBSCS], [CV(GEA)], [GEA]	[5]

	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

Evidence
[APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[AIBSCS] Automated inference based on similarity to consensus sequences
[CV(GEA)] cross validation(GEA)
[GEA] Gene expression analysis
[BPP] Binding of purified proteins
[APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[CV(GEA/SM)] cross validation(GEA/SM)
[CV(SM)] cross validation(SM)
[SM] Site mutation
[IEP] Inferred from expression pattern

Reference(s)
[1] Miranda-Rios J., Sanchez-Pescador R., Urdea M., Covarrubias AA., 1987, The complete nucleotide sequence of the glnALG operon of Escherichia coli K12., Nucleic Acids Res 15(6):2757-70
[2] 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
[3] Reitzer L., 2003, Nitrogen assimilation and global regulation in Escherichia coli., Annu Rev Microbiol 57:155-76
[4] 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
[5] 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
[6] 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
[7] 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
[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] 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
[10] Atkinson MR., Pattaramanon N., Ninfa AJ., 2002, Governor of the glnAp2 promoter of Escherichia coli., Mol Microbiol 46(5):1247-57
[11] Collado-Vides J., Magasanik B., Gralla JD., 1991, Control site location and transcriptional regulation in Escherichia coli., Microbiol Rev 55(3):371-94
[12] 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
[13] 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
[14] Rocha M., Vazquez M., Garciarrubio A., Covarrubias AA., 1985, Nucleotide sequence of the glnA-glnL intercistronic region of Escherichia coli., Gene 37(1-3):91-9
[15] Muse WB., Bender RA., 1998, The nac (nitrogen assimilation control) gene from Escherichia coli., J Bacteriol 180(5):1166-73
[16] 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
[17] Samsonova NN., Smirnov SV., Altman IB., Ptitsyn LR., 2003, Molecular cloning and characterization of Escherichia coli K12 ygjG gene., BMC Microbiol 3(1):2
[18] 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
[19] 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
[20] 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

	Sequence
	atccgggtgaCGCACCATGTTGTGCGGCtgcccttgta	[-543.0, patAp, forward]
	gttgttaatgATGTCAACGATGGCGCAaaaaatgccc	[-275.0, astCp2, reverse]
	gcgcaaaaaaTGCCCGCTTTTGGTGCGcgctgcgtca	[-253.0, astCp2, reverse]
	tggtgcgcgcTGCGTCAGAATGGCGCAgtaatttcca	[-233.0, astCp2, reverse]
	ttaattatctTGCCCAAAAATCAGGCAattattgccc	[-193.0, patAp, forward]
	actccgctgtTGCCCTGTTTCAGGGCAattttgcaac	[-190.0, argTp, reverse]
	aggcaattatTGCCCTGAAAACGTGCAtttgcgcagc	[-171.0, patAp, 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, ddpXp, 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, ddpXp, 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]
	aaagctataaTGCACTAAAATGGTGCAacctgttcag	[3.0, glnLp, reverse]

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