RegulonDB

Regulon
Regulated gene(s)	amtB, asnB, btuB, cadA, cadB, dctR, dtpA, gadA, gadB, gadC, gadE, gadF, gadW, gadX, gadY, glnK, glsA, hdeA, hdeB, hdeD, hns, lon, mdtE, mdtF, murI, rpoS, slp, speG, uspE, ybaT, ydeM, ydeN, yhiD, ynfB
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) pH (9) cadA, dctR, gadA, gadB, gadE, glsA, hdeA, hdeB, hdeD membrane (5) amtB, cadB, dtpA, gadC, mdtF Porters (Uni-, Sym- and Antiporters) (4) amtB, cadB, dtpA, gadC Transcription related (4) gadE, gadW, gadX, hns activator (3) gadE, gadX, hns prophage genes and phage related functions (2) btuB, lon unknown (2) dctR, glnK repressor (2) gadW, hns drug resistance/sensitivity (2) mdtE, mdtF amino acids (1) asnB asparagine (1) asnB Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (1) btuB antisense RNA (1) gadY nitrogen metabolism (1) glnK metabolism (1) glsA defense/survival (1) hdeA nucleoproteins, basic proteins (1) hns proteins/peptides/glycopeptides (1) lon turnover, degradation (1) lon proteases, cleavage of compounds (1) lon cell division (1) lon plasmid related (1) lon Accessory Factors Involved in Transport (1) mdtE Electrochemical potential driven transporters (1) mdtF murein (peptidoglycan) (1) murI murein (1) murI sigma factors, anti-sigmafactors (1) rpoS starvation (1) slp polyamine biosynthesis (1) speG adaptations (1) uspE radiation (1) uspE Putative uncharacterized transport protein (1) ybaT chaperoning, repair (refolding) (1) ydeM sulfur metabolism (1) ydeN Read more >
Regulated operon(s)	asnB, btuB-murI, cadBA, clpPX-lon, dtpA, gadAXW, gadBC, gadEF-mdtEF, gadY, glnK-amtB, glsA-ybaT, hdeAB-yhiD, hdeD, hns, nlpD-rpoS, slp-dctR, uspE, ydeNM, ynfB-speG
First gene in the operon(s)	asnB, btuB, cadB, gadA, gadB, gadE, gadW, gadX, gadY, glnK, glsA, hdeA, hdeD, hns, lon, rpoS, slp, dtpA, uspE, ydeN, ynfB
Simple and complex regulons	AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR,ppGpp AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB AraC,GadX,NagC ArcA,CRP,Fur,GadX,MqsA,ppGpp ArcA,CadC,GadE-RcsB,GadX,H-NS,Lrp,OmpR ArcA,GadX,YdeO CRP,EvgA,FliZ,GadE,GadW,GadX,H-NS,YdeO CspA,Fis,GadX,H-NS,ppGpp FNR,Fur,GadX,NtrC FNR,GadE,GadW,GadX,H-NS,PhoB,RutR FliZ,GadE,GadW,GadX,H-NS,Lrp,MarA,PhoP,RcsB,TorR GadE,GadX,H-NS,PhoP,RcsB GadE-RcsB,GadW,GadX,H-NS,MarA,YdeO GadW,GadX,H-NS,PhoP,SdiA GadW,GadX,RcsB,SdiA GadX GadX,OmpR GadX,ppGpp Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase) [GadX,-](7) btuBp, gadWp2, hdeAp, hdeAp2, tppBp, ydeNp, ynfBp [GadX,+](22) asnBp, cadBp, gadAp, gadAp2, gadBp, gadBp2, gadEp2, gadEp3, gadXp, gadYp, glnKp, glsAp, hdeAp, hdeAp2, hdeDp, hdeDp2, hnsp, lonp, lonp2, rpoSp, slpp, uspEp

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
GadX	activator	asnBp	nd	nd	nd	asnB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	repressor	btuBp	Sigma70	74.5	-166.5	btuB, murI	cggtaaggaaAGGTGCGATGATTGCGTTATgcggacactg cggtaaggaaAGGTGCGATGATTGCGTTATgcggacactg	4163463	4163482	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[2]
GadX	repressor	btuBp	Sigma70	105.5	-135.5	btuB, murI	cggacactgcCATTCGGTGGGAAGTCATCAtctcttagta atgattctctACTACTGAAGGGTGGCTTACcgtcacaggc	4163494	4163513	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[2]
GadX	repressor	btuBp	Sigma70	134.5	-106.5	btuB, murI	atctcttagtATCTTAGATACCCCTCCAAGcccgaagacc atctcttagtATCTTAGATACCCCTCCAAGcccgaagacc	4163523	4163542	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[2]
GadX	activator	cadBp	Sigma70	nd	nd	cadB, cadA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	gadAp	Sigma70	-121.5	-148.5	gadA, gadX	tacgataataAAGTCTGTTTTTAATATTATcatgttaaat tacgataataAAGTCTGTTTTTAATATTATcatgttaaat	3667719	3667738	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp	Sigma70	-100.5	-127.5	gadA, gadX	taatattatcATGTTAAATGTTTATATTATaaaaagtcgt nd	3667698	3667717	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp	Sigma70	-78.0	-105.0	gadA, gadX	tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta nd	3667676	3667695	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp	Sigma70	-57.5	-84.5	gadA, gadX	tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc nd	3667655	3667674	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp	Sigma70	-31.5	-58.5	gadA, gadX	taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta	3667629	3667648	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp	Sigma70	-10.5	-37.5	gadA, gadX	ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata	3667608	3667627	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-121.5	-148.5	gadA, gadX	tacgataataAAGTCTGTTTTTAATATTATcatgttaaat nd	3667719	3667738	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-100.5	-127.5	gadA, gadX	taatattatcATGTTAAATGTTTATATTATaaaaagtcgt nd	3667698	3667717	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-78.0	-105.0	gadA, gadX	tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta nd	3667676	3667695	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-57.5	-84.5	gadA, gadX	tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc nd	3667655	3667674	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-31.5	-58.5	gadA, gadX	taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta nd	3667629	3667648	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadAp2	Sigma38	-10.5	-37.5	gadA, gadX	ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata nd	3667608	3667627	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp	Sigma70	-268.0	-295.0	gadB, gadC	ctatttttatGTAATAATTTTATAAATGCGttcaaaataa nd	1572330	1572349	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	gadBp	Sigma70	-231.5	-258.5	gadB, gadC	ataataatcaAGTACTAATAGTGATATTTTaaggtctgat ataataatcaAGTACTAATAGTGATATTTTaaggtctgat	1572294	1572313	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [5], [8]
GadX	activator	gadBp	Sigma70	-210.5	-237.5	gadB, gadC	tgatattttaAGGTCTGATTTTTACGTGATaattcaggag tgatattttaAGGTCTGATTTTTACGTGATaattcaggag	1572273	1572292	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[4], [5]
GadX	activator	gadBp	Sigma70	-184.0	-211.0	gadB, gadC	gataattcagGAGACACAGAATGCGCATAAaaataacagc nd	1572246	1572265	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	gadBp	Sigma70	-119.5	-146.5	gadB, gadC	gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat	1572182	1572201	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp	Sigma70	-98.5	-125.5	gadB, gadC	ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa nd	1572161	1572180	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp	Sigma70	-39.5	-66.5	gadB, gadC	atttaaacacGAGTCCTTTGCACTTGCTTActttatcgat atcgataaagTAAGCAAGTGCAAAGGACTCgtgtttaaat	1572102	1572121	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp	Sigma70	-17.5	-44.5	gadB, gadC	cttgcttactTTATCGATAAATCCTACTTTtttaatgcga tcgcattaaaAAAGTAGGATTTATCGATAAagtaagcaag	1572080	1572099	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp2	Sigma38	-268.0	-295.0	gadB, gadC	ctatttttatGTAATAATTTTATAAATGCGttcaaaataa nd	1572330	1572349	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	gadBp2	Sigma38	-231.5	-258.5	gadB, gadC	ataataatcaAGTACTAATAGTGATATTTTaaggtctgat nd	1572294	1572313	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [5], [8]
GadX	activator	gadBp2	Sigma38	-210.5	-237.5	gadB, gadC	tgatattttaAGGTCTGATTTTTACGTGATaattcaggag nd	1572273	1572292	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[4], [5]
GadX	activator	gadBp2	Sigma38	-184.0	-211.0	gadB, gadC	gataattcagGAGACACAGAATGCGCATAAaaataacagc nd	1572246	1572265	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	gadBp2	Sigma38	-119.5	-146.5	gadB, gadC	gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat nd	1572182	1572201	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp2	Sigma38	-98.5	-125.5	gadB, gadC	ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa nd	1572161	1572180	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp2	Sigma38	-39.5	-66.5	gadB, gadC	atttaaacacGAGTCCTTTGCACTTGCTTActttatcgat nd	1572102	1572121	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadBp2	Sigma38	-17.5	-44.5	gadB, gadC	cttgcttactTTATCGATAAATCCTACTTTtttaatgcga nd	1572080	1572099	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[3], [4], [5], [6], [7]
GadX	activator	gadEp2	Sigma38	-595.5	-616.5	gadE, gadF, mdtE, mdtF	ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat	3657740	3657759	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[7], [9], [10], [11], [12]
GadX	activator	gadEp2	Sigma38	-574.5	-595.5	gadE, gadF, mdtE, mdtF	aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa	3657761	3657780	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[7], [9], [10], [11], [12]
GadX	activator	gadEp3	Sigma70	-50.5	-616.5	gadE, gadF	ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat	3657740	3657759	[COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	S	[7], [9], [10], [11], [12]
GadX	activator	gadEp3	Sigma70	-29.5	-595.5	gadE, gadF	aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa	3657761	3657780	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	S	[7], [9], [10], [11], [12]
GadX	repressor	gadWp2	nd	-96.5	-259.5	gadW	tccctgttggCACGGGAAACTTTGTGCTCTcagtaagtta nd	3664868	3664887	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	repressor	gadWp2	nd	-68.5	-231.5	gadW	ctcagtaagtTAAATATAACTTTTACTGGAaataagatca nd	3664840	3664859	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	repressor	gadWp2	nd	-53.5	-216.5	gadW	ataacttttaCTGGAAATAAGATCAGCCATttttttataa ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat	3664825	3664844	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[12]
GadX	repressor	gadWp2	nd	-32.5	-195.5	gadW	atcagccattTTTTTATAAACATAAGCTATacgctgtgcg cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat	3664804	3664823	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[12]
GadX	activator	gadXp	Sigma38	nd	nd	gadX, gadW	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1], [4], [12]
GadX	activator	gadYp	Sigma38	-50.5	-50.5	gadY	cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat	3664804	3664823	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[12]
GadX	activator	gadYp	Sigma38	-29.5	-29.5	gadY	ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat	3664825	3664844	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[12]
GadX	activator	glnKp	Sigma54	nd	nd	glnK, amtB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	glsAp	Sigma38	11.5	-57.5	glsA, ybaT	gttaaatcagGATGCCTGAAAATCGGCACCggggtgagga nd	511574	511593	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[1], [7], [8]
GadX	activator	hdeAp	Sigma70	-126.5	-177.5	hdeA, hdeB, yhiD	gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat	3656908	3656927	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[7], [13]
GadX	repressor	hdeAp	Sigma70	-126.5	-177.5	hdeA, hdeB, yhiD	gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd	3656908	3656927	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[7], [13]
GadX	activator	hdeAp	Sigma70	-74.5	-125.5	hdeA, hdeB, yhiD	tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd	3656856	3656875	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	repressor	hdeAp	Sigma70	-74.5	-125.5	hdeA, hdeB, yhiD	tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat	3656856	3656875	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	activator	hdeAp	Sigma70	-53.5	-104.5	hdeA, hdeB, yhiD	tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd	3656835	3656854	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	repressor	hdeAp	Sigma70	-53.5	-104.5	hdeA, hdeB, yhiD	tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd	3656835	3656854	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	activator	hdeAp2	Sigma38	-126.5	-177.5	hdeA, hdeB, yhiD	gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd	3656908	3656927	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[7], [13]
GadX	repressor	hdeAp2	Sigma38	-126.5	-177.5	hdeA, hdeB, yhiD	gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd	3656908	3656927	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[7], [13]
GadX	activator	hdeAp2	Sigma38	-74.5	-125.5	hdeA, hdeB, yhiD	tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd	3656856	3656875	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	repressor	hdeAp2	Sigma38	-74.5	-125.5	hdeA, hdeB, yhiD	tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd	3656856	3656875	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	activator	hdeAp2	Sigma38	-53.5	-104.5	hdeA, hdeB, yhiD	tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd	3656835	3656854	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	repressor	hdeAp2	Sigma38	-53.5	-104.5	hdeA, hdeB, yhiD	tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd	3656835	3656854	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[1], [7], [12], [13]
GadX	activator	hdeDp	Sigma70	-115.5	-150.5	hdeD	atgttgatggAAAATATCAAAATCAGATATttttatttca nd	3656835	3656854	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[1], [7], [12], [13]
GadX	activator	hdeDp	Sigma70	-94.5	-129.5	hdeD	atcagatattTTTATTTCAATACAATGAGTtacagatgca tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat	3656856	3656875	[COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[1], [7], [12], [13]
GadX	activator	hdeDp2	Sigma38	-115.5	-150.5	hdeD	atgttgatggAAAATATCAAAATCAGATATttttatttca nd	3656835	3656854	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[1], [7], [12], [13]
GadX	activator	hdeDp2	Sigma38	-94.5	-129.5	hdeD	atcagatattTTTATTTCAATACAATGAGTtacagatgca nd	3656856	3656875	[COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[1], [7], [12], [13]
GadX	activator	hnsp	Sigma70	nd	nd	hns	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	lonp	Sigma70	nd	nd	lon	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	lonp2	Sigma32	nd	nd	lon	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	rpoSp	Sigma70	nd	nd	rpoS	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]
GadX	activator	slpp	Sigma70	-81.5	-106.5	slp, dctR	ctaaacagaaAGGATATAAACATCAGACAGgtttacgtta taacgtaaacCTGTCTGATGTTTATATCCTttctgtttag	3653845	3653864	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[7], [8], [12]
GadX	activator	slpp	Sigma70	-70.5	-95.5	slp, dctR	ggatataaacATCAGACAGGTTTACGTTACtatcaggcat nd	3653856	3653875	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	slpp	Sigma70	-60.5	-85.5	slp, dctR	atcagacaggTTTACGTTACTATCAGGCATatcacctcag nd	3653866	3653885	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[7], [12]
GadX	activator	slpp	Sigma70	-3.0	-28.0	slp, dctR	aaagaaatatCTATTATGGTTTTAATATTTgttgataagg nd	3653923	3653942	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	slpp	Sigma70	17.0	-9.0	slp, dctR	ttttaatattTGTTGATAAGGATAGTAACAtgaacatgac nd	3653942	3653961	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	repressor	tppBp	Sigma70	-151.0	-249.0	dtpA	cgttaagccaTCACCCCCCTCTCAGTGCAGtgaaaaaatc nd	1712510	1712529	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	activator	uspEp	nd	nd	nd	uspE	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[14]
GadX	repressor	ydeNp	Sigma70	-233.5	-263.5	ydeN, ydeM	cacatatttaTGCACTTGCATAACCTGTTGcatgattatt nd	1582778	1582797	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	repressor	ydeNp	Sigma70	-69.0	-99.0	ydeN, ydeM	tttttcccttTTTTTAGCTAAATCTGCTATctctttatgt nd	1582613	1582632	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]
GadX	repressor	ynfBp	Sigma38	-94.5	-193.5	ynfB, speG	ttaaccacaaCCAGGGCAGAAAGCATCCAAtaatttcaca nd	1655605	1655624	[EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL]	S	[8]

	Sequence
	ctatggcaaaTTAGCCATTTCAAACATTATcatggctgat	[-595.5, gadEp2, forward] [-50.5, gadEp3, forward]
	aaacattatcATGGCTGATATTTTCCGTAGtcaggtttaa	[-574.5, gadEp2, forward] [-29.5, gadEp3, forward]
	ctatttttatGTAATAATTTTATAAATGCGttcaaaataa	[-268.0, gadBp, reverse] [-268.0, gadBp2, reverse]
	cacatatttaTGCACTTGCATAACCTGTTGcatgattatt	[-233.5, ydeNp, reverse]
	ataataatcaAGTACTAATAGTGATATTTTaaggtctgat	[-231.5, gadBp, reverse] [-231.5, gadBp2, reverse]
	tgatattttaAGGTCTGATTTTTACGTGATaattcaggag	[-210.5, gadBp, reverse] [-210.5, gadBp2, reverse]
	gataattcagGAGACACAGAATGCGCATAAaaataacagc	[-184.0, gadBp, reverse] [-184.0, gadBp2, reverse]
	cgttaagccaTCACCCCCCTCTCAGTGCAGtgaaaaaatc	[-151.0, tppBp, forward]
	gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat	[-126.5, hdeAp, reverse] [-126.5, hdeAp2, reverse]
	tacgataataAAGTCTGTTTTTAATATTATcatgttaaat	[-121.5, gadAp, reverse] [-121.5, gadAp2, reverse]
	gaatttcataTTGTATTGTTTTTCAATGAAaaaatattat	[-119.5, gadBp, reverse] [-119.5, gadBp2, reverse]
	atgttgatggAAAATATCAAAATCAGATATttttatttca	[-53.5, hdeAp, reverse] [-53.5, hdeAp2, reverse] [-115.5, hdeDp, forward] [-115.5, hdeDp2, forward]
	taatattatcATGTTAAATGTTTATATTATaaaaagtcgt	[-100.5, gadAp, reverse] [-100.5, gadAp2, reverse]
	ttcaatgaaaAAATATTATTCGCGTAATATctcacgataa	[-98.5, gadBp, reverse] [-98.5, gadBp2, reverse]
	tccctgttggCACGGGAAACTTTGTGCTCTcagtaagtta	[-96.5, gadWp2, reverse]
	atcagatattTTTATTTCAATACAATGAGTtacagatgca	[-74.5, hdeAp, reverse] [-74.5, hdeAp2, reverse] [-94.5, hdeDp, forward] [-94.5, hdeDp2, forward]
	ttaaccacaaCCAGGGCAGAAAGCATCCAAtaatttcaca	[-94.5, ynfBp, forward]
	ctaaacagaaAGGATATAAACATCAGACAGgtttacgtta	[-81.5, slpp, forward]
	tatattataaAAAGTCGTTTTTCTGCTTAGgattttgtta	[-78.0, gadAp, reverse] [-78.0, gadAp2, reverse]
	ggatataaacATCAGACAGGTTTACGTTACtatcaggcat	[-70.5, slpp, forward]
	tttttcccttTTTTTAGCTAAATCTGCTATctctttatgt	[-69.0, ydeNp, reverse]
	ctcagtaagtTAAATATAACTTTTACTGGAaataagatca	[-68.5, gadWp2, reverse]
	atcagacaggTTTACGTTACTATCAGGCATatcacctcag	[-60.5, slpp, forward]
	tctgcttaggATTTTGTTATTTAAATTAAGcctgtaatgc	[-57.5, gadAp, reverse] [-57.5, gadAp2, reverse]
	ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat	[-53.5, gadWp2, reverse] [-29.5, gadYp, forward]
	cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat	[-32.5, gadWp2, reverse] [-50.5, gadYp, forward]
	atttaaacacGAGTCCTTTGCACTTGCTTActttatcgat	[-39.5, gadBp, reverse] [-39.5, gadBp2, reverse]
	taagcctgtaATGCCTTGCTTCCATTGCGGataaatccta	[-31.5, gadAp, reverse] [-31.5, gadAp2, reverse]
	cttgcttactTTATCGATAAATCCTACTTTtttaatgcga	[-17.5, gadBp, reverse] [-17.5, gadBp2, reverse]
	ccattgcggaTAAATCCTACTTTTTTATTGccttcaaata	[-10.5, gadAp, reverse] [-10.5, gadAp2, reverse]
	aaagaaatatCTATTATGGTTTTAATATTTgttgataagg	[-3.0, slpp, forward]
	gttaaatcagGATGCCTGAAAATCGGCACCggggtgagga	[11.5, glsAp, forward]
	ttttaatattTGTTGATAAGGATAGTAACAtgaacatgac	[17.0, slpp, forward]
	cggtaaggaaAGGTGCGATGATTGCGTTATgcggacactg	[74.5, btuBp, forward]
	cggacactgcCATTCGGTGGGAAGTCATCAtctcttagta	[105.5, btuBp, forward]
	atctcttagtATCTTAGATACCCCTCCAAGcccgaagacc	[134.5, btuBp, forward]

Alignment and PSSM for GadX TFBSs

Aligned TFBS of GadX

	Sequence
	AAATATCAAAATCAGATATTTT
	TCACGTAAAAATCAGACCTTAA
	TAATATTAAAAACAGACTTTAT
	TACGGAAAATATCAGCCATGAT
	GGATATAAACATCAGACAGGTT
	TAACGCAATCATCGCACCTTTC
	AAATATTAAAACCATAATAGAT
	TAATATAAACATTTAACATGAT
	TCATTGAAAAACAATACAATAT
	TTACGTTACTATCAGGCATATC
	TTATCGATAAATCCTACTTTTT
	TTTTATAAACATAAGCTATACG
	TGGAAATAAGATCAGCCATTTT
	AATTAGCCATTTCAAACATTAT
	TACTATCCTTATCAACAAATAT
	CTAAGCAGAAAAACGACTTTTT
	ATTTATAAAATTATTACATAAA
	CAATAAAAAAGTAGGATTTATC
	TATTACGCGAATAATATTTTTT
	TGCAGTCGATTTAATAAAAATT
	CGCAATGGAAGCAAGGCATTAC
	TTTTAGCTAAATCTGCTATCTC
	TTATTTCAATACAATGAGTTAC
	CAGGGCAGAAAGCATCCAATAA
	TAATTTAAATAACAAAATCCTA
	TTATGCACTTGCATAACCTGTT
	TCAAGTACTAATAGTGATATTT
	AGATGATGACTTCCCACCGAAT
	AGACACAGAATGCGCATAAAAA
	TATCTTAGATACCCCTCCAAGC
	TACTGAGAGCACAAAGTTTCCC
	TAAAGTAAGCAAGTGCAAAGGA
	ATGCCTGAAAATCGGCACCGGG
	AGCCATCACCCCCCTCTCAGTG

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

A	8	15	19	6	16	5	18	20	25	16	25	4	12	19	6	19	8	17	10	8	14	6
C	4	3	6	7	2	6	7	5	2	8	1	8	20	5	4	9	18	7	2	3	2	8
G	1	7	3	2	12	4	4	7	3	1	3	2	1	5	14	5	0	1	2	8	3	3
T	21	9	6	19	4	19	5	2	4	9	5	20	1	5	10	1	8	9	20	15	15	17

Consensus

;	consensus.strict             	taatgtaaaaatCagacatttt
;	consensus.strict.rc          	AAAATGTCTGATTTTTACATTA
;	consensus.IUPAC              	tratrtaramayMagmcawkwy
;	consensus.IUPAC.rc           	RWMWTGKCTKRTKTYTAYATYA
;	consensus.regexp             	t[ag]at[ag]ta[ag]a[ac]a[ct][AC]ag[ac]ca[at][gt][at][ct]
;	consensus.regexp.rc          	[AG][AT][AC][AT]TG[GT]CT[GT][AG]T[GT]T[CT]TA[CT]AT[CT]A

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-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IEP-RNA-SEQ] RNA-seq evidence
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

Reference(s)
[1] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72
[2] Lei GS., Syu WJ., Liang PH., Chak KF., Hu WS., Hu ST., 2011, Repression of btuB gene transcription in Escherichia coli by the GadX protein., BMC Microbiol 11(1):33
[3] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M., 2005, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli., J Biol Chem 280(22):21498-505
[4] Ma Z., Richard H., Tucker DL., Conway T., Foster JW., 2002, Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)., J Bacteriol 184(24):7001-12
[5] Tramonti A., De Canio M., Delany I., Scarlato V., De Biase D., 2006, Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli., J Bacteriol 188(23):8118-27
[6] Tramonti A., Visca P., De Canio M., Falconi M., De Biase D., 2002, Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system., J Bacteriol 184(10):2603-13
[7] Tucker DL., Tucker N., Ma Z., Foster JW., Miranda RL., Cohen PS., Conway T., 2003, Genes of the GadX-GadW regulon in Escherichia coli., J Bacteriol 185(10):3190-201
[8] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970
[9] Nishino K., Senda Y., Yamaguchi A., 2008, The AraC-family regulator GadX enhances multidrug resistance in Escherichia coli by activating expression of mdtEF multidrug efflux genes., J Infect Chemother 14(1):23-9
[10] Sayed AK., Foster JW., 2009, A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator., Mol Microbiol 71(6):1435-50
[11] Sayed AK., Odom C., Foster JW., 2007, The Escherichia coli AraC-family regulators GadX and GadW activate gadE, the central activator of glutamate-dependent acid resistance., Microbiology 153(Pt 8):2584-92
[12] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82
[13] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol 190(4):1290-7
[14] Hodges AP., Dai D., Xiang Z., Woolf P., Xi C., He Y., 2010, Bayesian Network Expansion Identifies New ROS and Biofilm Regulators., PLoS One 5(3):e9513
[15] Tramonti A, De Canio M, Bossa F, De Biase D, 2003, Stability and oligomerization of recombinant GadX, a transcriptional activator of the Escherichia coli glutamate decarboxylase system., Biochim Biophys Acta, 1647(1-2):376 10.1016/s1570-9639(03)00098-0
[16] Shin S, Castanie-Cornet MP, Foster JW, Crawford JA, Brinkley C, Kaper JB, 2001, An activator of glutamate decarboxylase genes regulates the expression of enteropathogenic Escherichia coli virulence genes through control of the plasmid-encoded regulator, Per., Mol Microbiol, 41(5):1133 10.1046/j.1365-2958.2001.02570.x
[17] Richard H, Foster JW, 2007, Sodium regulates Escherichia coli acid resistance, and influences GadX- and GadW-dependent activation of gadE., Microbiology (Reading), 153(Pt 9):3154 10.1099/mic.0.2007/007575-0
[18] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410
[19] Martin RG, Rosner JL, 2001, The AraC transcriptional activators., Curr Opin Microbiol, 4(2):132 10.1016/s1369-5274(00)00178-8
[20] Opdyke JA., Kang JG., Storz G., 2004, GadY, a small-RNA regulator of acid response genes in Escherichia coli., J Bacteriol 186(20):6698-705
[21] Gallegos MT, Michán C, Ramos JL, 1993, The XylS/AraC family of regulators., Nucleic Acids Res, 21(4):807 10.1093/nar/21.4.807
[22] Yamanaka Y, Aizawa SI, Yamamoto K, 2022, The hdeD Gene Represses the Expression of Flagellum Biosynthesis via LrhA in Escherichia coli K-12., J Bacteriol, 204(1):e0042021 10.1128/JB.00420-21
[23] Hong SH, Wang X, O'Connor HF, Benedik MJ, Wood TK, 2012, Bacterial persistence increases as environmental fitness decreases., Microb Biotechnol, 5(4):509 10.1111/j.1751-7915.2011.00327.x

RegulonDB

DNA binding site length:	20
DNA binding site symmetry:	asymmetric