RegulonDB

Regulon
Regulated gene(s)	aceA, aceB, aceE, aceF, aceK, acnA, acnB, adhE, aroP, betA, betB, betI, betT, crp, crr, csgD, csgE, csgF, csgG, cydA, cydB, cyoA, cyoB, cyoC, cyoD, cyoE, cysG, eda, edd, eno, envC, epd, fbaA, fbaB, fruA, fruB, fruK, gapA, glcC, glk, gpmM, hypF, icd, lpd, manX, manY, manZ, marA, marB, marR, mpl, mtlA, mtlD, mtlR, nirB, nirC, nirD, pck, pdeL, pdhR, pfkA, pgk, poxB, ppc, ppsA, prpC, prpD, prpE, ptsH, ptsI, pykF, setA, sgrS, sgrT, tpiA, yeaD, yibQ, zwf Read more >
Multifun term(s) of regulated gene(s)	MultiFun Term (List of genes associated to the multifun term) carbon compounds (26) aceE, aceF, acnB, crr, eda, fbaA, fruA, fruB, glcC, glk, gpmM, lpd, manX, manY, manZ, mtlA, mtlD, mtlR, pfkA, poxB, prpB, prpC, prpD, ptsH, ptsI, zwf membrane (19) aroP, betA, betT, csgF, cydA, cydB, cyoA, cyoB, cyoC, cyoD, cyoE, fruA, manX, manY, manZ, mtlA, nirC, poxB, setA Transcription related (8) betI, crp, csgD, glcC, marA, marR, mtlR, pdhR repressor (8) betI, crp, csgD, glcC, marA, marR, mtlR, pdhR Phosphotransferase Systems (PEP-dependent PTS) (7) crr, fruA, fruB, manX, manY, manZ, mtlA glycolysis (7) eno, fbaB, gapA, pdhR, pgk, pykF, tpiA electron acceptors (6) cydA, cydB, cyoA, cyoB, cyoC, cyoD central intermediary metabolism (6) eno, epd, gapA, pck, pgk, ppsA operon (5) betI, glcC, marA, marR, pdhR activator (5) crp, csgD, glcC, marA, pdhR aerobic respiration (5) cyoA, cyoB, cyoC, cyoD, cyoE TCA cycle (4) acnA, acnB, icd, ppc fatty acids (4) prpB, prpC, prpD, prpE glyoxylate bypass (3) aceA, aceB, aceK pyruvate dehydrogenase (3) aceE, aceF, lpd glyoxylate degradation (3) aceE, aceF, eda fermentation (3) adhE, ppc, pykF Porters (Uni-, Sym- and Antiporters) (3) aroP, betT, nirC betaine biosynthesis (3) betA, betB, betT osmotic pressure (3) betA, betB, betI Accessory Factors Involved in Transport (3) csgE, ptsH, ptsI Oxidoreduction-driven Active Transporters (3) cyoA, cyoB, cyoC drug resistance/sensitivity (3) marA, marB, marR nitrogen metabolism (3) nirB, nirC, nirD posttranslational modification (2) aceK, hypF other (mechanical, nutritional, oxidative stress) (2) acnA, setA Entner-Doudoroff (2) eda, edd pyridoxal 5'phosphate (2) epd, gapA detoxification (2) marA, marB inhibition / activation of enzymes (2) ptsH, sgrT covalent modification, demodification, maturation (1) aceK posttranscriptional (1) acnA phenylalanine (1) aroP tyrosine (1) aroP global (1) crp fimbri, pili (1) csgF Channel-type Transporters (1) csgG heme, porphyrine (1) cysG cell division (1) envC energy metabolism, carbon (1) fruK anaerobic respiration (1) hypF amino acids (1) lpd formyl-THF biosynthesis (1) lpd Putative uncharacterized transport protein (1) marB murein turnover, recycling (1) mpl murein (1) mpl regulation (1) pdeL electron donors (1) poxB pyruvate oxidation (1) poxB Electrochemical potential driven transporters (1) setA antisense RNA (1) sgrS metabolism (1) yibQ pentose pwy, oxidative branch (1) zwf Read more >
Regulated operon(s)	aceBAK, acnB, adhE, aroP, betIBA, betT, crp, csgDEFG, cydAB, cyoABCDE, edd-eda, epd-pgk-fbaA, fbaB, fruBKA, gapA-yeaD, glcC, glk, gpmM-envC-yibQ, hcp-hcr-poxB-ltaE-ybjT, hydN-hypF, icd, manXYZ, marRAB, mpl, mtlADR, nirBDC-cysG, pck, pdeL, pdhR-aceEF-lpd, pfkA, ppc, ppsA, prpBCDE, ptsHI-crr, pykF, pyrG-eno, sgrST-setA, tpiA, ymiC-acnA, zwf
First gene in the operon(s)	aceB, acnA, acnB, adhE, aroP, betI, betT, crp, csgD, cydA, cyoA, edd, eno, epd, fbaB, fruB, gapA, glcC, glk, gpmM, hypF, icd, manX, marR, mpl, mtlA, nirB, pck, pdeL, pdhR, pfkA, poxB, ppc, ppsA, prpB, ptsH, pykF, sgrS, tpiA, zwf
Simple and complex regulons	AcrR,CRP,CpxR,Cra,Fis,MarA,MarR,Rob,SoxS ArcA,BetI,Cra ArcA,CRP,Cra,CusR,FNR,Fis,Fur,GadE,HprR,PdhR ArcA,CRP,Cra,FNR,MarA,Rob,SoxS ArcA,CRP,Cra,Fis ArcA,CRP,Cra,IHF,IclR BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA BtsR,CRP,Cra,FNR,PdhR CRP,Cra CRP,Cra,DcuR CRP,Cra,FNR,Fis,H-NS,IHF,NarL,NarP CRP,Cra,Fis CRP,Cra,Fis,GlcC CRP,Cra,Mlc,NagC CRP,Cra,PrpR Cra Cra,DksA,SgrR,ppGpp Cra,FNR,Fur,MarA,Rob,SoxS Cra,Fis,Lrp,NarL Cra,GntR,KdgR Cra,MarA,SoxS Cra,SgrR Cra,TyrR Read more >
Simple and complex regulatory phrases	Regulatory phrase (List of promoters regulated by the phrase) [Cra,+](16) aceBp, acnAp2, aroPp1, aroPp2, betIp, betTp, crpp1, csgDp1, csgDp3, cydAp5, icdAp2, pckp, poxBp1, poxBp2, ppsAp, ptsHp2 [Cra,-](43) acnBp1, adhEp, adhEp1, cyoAp, eddp, enop1, enop2, enop3, epdp, epdp2, fbaBp, fruBp, gapAp, gapAp1, gapAp2, gapAp3, gapAp4, glcCp, glkp2, glkp4, gpmMp1, hypFp2, hypFp3, manXp, marRp, mplp, mplp1, mtlAp, nirBp, pdeLp1, pdhRp, pdhRp2, pfkAp, pfkAp2, ppcp, prpBp, ptsHp1, pykFp, sgrSp, sgrSp2, tpiAp, tpiAp2, zwfp

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
Cra	activator	aceBp	Sigma70	-166.5	-242.5	aceB, aceA, aceK	tgatagtcgaTCGTTAAGCGATTCAGCAccttacctca nd	4215227	4215244	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[2], [2], [3], [4], [5], [6]
Cra	activator	acnAp2	Sigma70	nd	nd	acnA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[7], [7]
Cra	repressor	acnBp1	Sigma70	nd	nd	acnB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[7], [7]
Cra	repressor	adhEp	Sigma38	36.5	-256.5	adhE	cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa nd	1298370	1298386	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION]	C	[4], [6], [8], [8], [9], [9], [10], [10]
Cra	repressor	adhEp1	Sigma70	36.5	-256.5	adhE	cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa nd	1298370	1298386	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION]	C	[4], [6], [8], [8], [9], [9], [10], [10]
Cra	activator	aroPp1	Sigma70	-177.5	-297.5	aroP	taaaaatccgAATTGAACCGATTCACTTaccaattttg nd	121840	121857	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [10], [10], [11], [11]
Cra	activator	aroPp2	Sigma70	-198.5	-297.5	aroP	taaaaatccgAATTGAACCGATTCACTTaccaattttg nd	121840	121857	[COMP-AINF], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [10], [10], [11], [11]
Cra	activator	betIp	Sigma70	nd	nd	betI, betB, betA	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[3]
Cra	activator	betTp	Sigma70	nd	nd	betT	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[3]
Cra	activator	crpp1	Sigma70	-45.5	-212.5	crp	cctgggtcatGCTGAAGCGAGACACCAggagacacaa nd	3485900	3485916	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[6], [12], [12]
Cra	activator	csgDp1	Sigma70	-563.5	-711.5	csgD, csgE, csgF, csgG	catttaagaaATTAAATCATTTCAACTTggttgttaac nd	1103899	1103916	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[13], [13]
Cra	activator	csgDp1	Sigma70	-227.5	-375.5	csgD, csgE, csgF, csgG	tgtggagaaaAAACAAGAACGTTTTACAtgacgaaagg nd	1103563	1103580	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	csgDp1	Sigma70	-196.5	-344.5	csgD, csgE, csgF, csgG	cgaaaggactACACCGAAATATTTTTTAtatgcattat nd	1103532	1103549	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	csgDp1	Sigma70	46.5	-102.5	csgD, csgE, csgF, csgG	tacccatttaGGGCTGATTTATTACTACacacagcagt nd	1103290	1103307	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	csgDp3	Sigma38	-563.5	-711.5	csgD, csgE, csgF, csgG	catttaagaaATTAAATCATTTCAACTTggttgttaac nd	1103899	1103916	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[13], [13]
Cra	activator	csgDp3	Sigma38	-227.5	-375.5	csgD, csgE, csgF, csgG	tgtggagaaaAAACAAGAACGTTTTACAtgacgaaagg nd	1103563	1103580	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	csgDp3	Sigma38	-196.5	-344.5	csgD, csgE, csgF, csgG	cgaaaggactACACCGAAATATTTTTTAtatgcattat nd	1103532	1103549	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	csgDp3	Sigma38	46.5	-102.5	csgD, csgE, csgF, csgG	tacccatttaGGGCTGATTTATTACTACacacagcagt nd	1103290	1103307	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[13], [13]
Cra	activator	cydAp5	Sigma70	-134.5	-224.5	cydA, cydB	cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt nd	771225	771242	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[14], [14]
Cra	activator	cydAp5	Sigma70	-105.5	-195.5	cydA, cydB	aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat nd	771254	771271	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[14], [14]
Cra	repressor	cyoAp	Sigma70	-268.5	-311.5	cyoA, cyoB, cyoC, cyoD, cyoE	aattctatttTTCTTACACGATTCAGCTaatgagtctt nd	451913	451930	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	eddp	Sigma70	4.5	-105.5	edd, eda	ttattacactGACTGAAACGTTTTTGCCctatgagctc nd	1934701	1934718	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [4], [6]
Cra	repressor	enop1	nd	-205.5	-938.5	eno	gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd	2908871	2908888	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	enop1	nd	-8.5	-741.5	eno	cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd	2908674	2908691	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	enop2	nd	-177.5	-938.5	eno	gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd	2908871	2908888	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	enop2	nd	20.5	-741.5	eno	cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd	2908674	2908691	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	enop3	nd	-33.5	-938.5	eno	gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd	2908871	2908888	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	enop3	nd	164.5	-741.5	eno	cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd	2908674	2908691	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	epdp	Sigma70	3.5	-129.5	epd, pgk, fbaA	cgcttatcctAGCTGAAGCGTTTCAGTCgattaaatgt nd	3073812	3073829	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [4], [6]
Cra	repressor	epdp2	Sigma38	3.5	-129.5	epd, pgk, fbaA	cgcttatcctAGCTGAAGCGTTTCAGTCgattaaatgt nd	3073812	3073829	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[1], [1], [4], [6]
Cra	repressor	fbaBp	Sigma38	-35.5	-138.5	fbaB	acattttttcTGATGAATCGAGCCAACAgaaaacgctg nd	2178694	2178711	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[4], [11], [11]
Cra	repressor	fruBp	Sigma70	7.5	-95.5	fruB, fruK, fruA	gtattatgctTTCTTGAAACGTTTCAGCgcgatcttgt nd	2263582	2263599	[AS-NAS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [AS-NAS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[2], [2], [11], [11]
Cra	repressor	fruBp	Sigma70	73.5	-29.5	fruB, fruK, fruA	ttttctcataGAGGCTGAATCGTTTCAAttcagcaaga nd	2263516	2263533	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [11], [11]
Cra	repressor	gapAp	Sigma38	-725.5	-761.5	gapA	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd	1862001	1862018	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [15], [15]
Cra	repressor	gapAp	Sigma38	-43.5	-79.5	gapA	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd	1862683	1862700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[6], [15], [15]
Cra	repressor	gapAp1	Sigma70	-725.5	-761.5	gapA	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd	1862001	1862018	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [15], [15]
Cra	repressor	gapAp1	Sigma70	-43.5	-79.5	gapA	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd	1862683	1862700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[6], [15], [15]
Cra	repressor	gapAp2	Sigma32	-608.5	-761.5	gapA, yeaD	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd	1862001	1862018	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [15], [15]
Cra	repressor	gapAp2	Sigma32	74.5	-79.5	gapA, yeaD	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd	1862683	1862700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[6], [15], [15]
Cra	repressor	gapAp3	Sigma70	-587.5	-761.5	gapA	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd	1862001	1862018	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [15], [15]
Cra	repressor	gapAp3	Sigma70	95.5	-79.5	gapA	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd	1862683	1862700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[6], [15], [15]
Cra	repressor	gapAp4	Sigma70	-516.5	-761.5	gapA	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt nd	1862001	1862018	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [15], [15]
Cra	repressor	gapAp4	Sigma70	166.5	-79.5	gapA	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg nd	1862683	1862700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[6], [15], [15]
Cra	repressor	glcCp	Sigma70	-4.5	-70.5	glcC	aattgatgtaACATAATCACTTACGTGAtgtgcgtgtt nd	3128193	3128210	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	glkp2	Sigma38	-91.5	-126.5	glk	ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac nd	2509544	2509561	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [11], [11], [16], [16]
Cra	repressor	glkp4	Sigma70	-91.5	-126.5	glk	ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac nd	2509544	2509561	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [11], [11], [16], [16]
Cra	repressor	gpmMp1	nd	-31.5	-56.5	gpmM, envC, yibQ	cttcagaggcTATTTTATCGATTCAGCTgtagtaaaat nd	3785195	3785212	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [11], [11]
Cra	repressor	hypFp2	Sigma70	-84.5	-673.5	hypF	ctggagaattTGATGAACCGTTTCATCAttgctgacgc nd	2838090	2838107	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	repressor	hypFp3	Sigma70	7.5	-673.5	hypF	ctggagaattTGATGAACCGTTTCATCAttgctgacgc nd	2838090	2838107	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[15], [15]
Cra	activator	icdAp2	Sigma70	-76.5	-238.5	icd	gaacgttgcgAGCTGAATCGCTTAACCTggtgatttct nd	1194876	1194893	[EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[6], [17], [17]
Cra	repressor	manXp	Sigma70	40.5	-75.5	manX, manY, manZ	tgtagcccttATCTGAATCGATTCGATtgtggacgac nd	1901965	1901981	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [10], [10]
Cra	repressor	marRp	Sigma70	-72.5	-99.5	marR, marA, marB	attgaacaaaACTTGAACCGATTTAGCAaaacgtggca nd	1619012	1619029	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[4], [11], [11]
Cra	repressor	mplp	Sigma38	-36.5	-93.5	mpl	tgttgcgctcAGGTGAATCGCGCCAGCAaattacggat nd	4455683	4455700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	mplp1	Sigma70	-36.5	-93.5	mpl	tgttgcgctcAGGTGAATCGCGCCAGCAaattacggat nd	4455683	4455700	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	mtlAp	Sigma70	-22.5	-115.5	mtlA, mtlD, mtlR	gtcgactggaCAGTTAACCGATTCAGTGccagatttcg nd	3772157	3772174	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[1], [1]
Cra	repressor	nirBp	Sigma70	-15.5	-39.5	nirB, nirD, nirC, cysG	taagcggggtTGCTGAATCGTTAAGGTAggcggtaata nd	3493963	3493980	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	S	[4], [6], [18], [19], [19]
Cra	activator	pckp	Sigma70	-139.5	-278.5	pck	aaagttagcgTGGTGAATCGATACTTTAccggttgaat nd	3532531	3532548	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[1], [1]
Cra	repressor	pdeLp1	Sigma70	-159.5	-491.5	pdeL	ggttatcattTGCTGAATGGATTCAGTCttaatgagtg nd	331871	331888	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [11], [15], [15], [20]
Cra	repressor	pdeLp1	Sigma70	-13.5	-345.5	pdeL	cagttgatctGGATTGTTAAATTCATATaatgcgcctt nd	332017	332034	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[15]
Cra	repressor	pdhRp	Sigma70	-185.5	-243.5	pdhR, aceE, aceF, lpd	caaaattggtAAGTGAATCGGTTCAATTcggattttta nd	121840	121857	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [10], [10], [11], [11]
Cra	repressor	pdhRp2	Sigma38	-185.5	-243.5	pdhR, aceE, aceF, lpd	caaaattggtAAGTGAATCGGTTCAATTcggattttta nd	121840	121857	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ]	S	[4], [6], [10], [10], [11], [11]
Cra	repressor	pfkAp	Sigma38	-35.5	-113.5	pfkA	atttggcctgACCTGAATCAATTCAGCAggaagtgatt nd	4107430	4107447	[EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[4], [6], [21], [21]
Cra	repressor	pfkAp2	Sigma70	-35.5	-113.5	pfkA	atttggcctgACCTGAATCAATTCAGCAggaagtgatt nd	4107430	4107447	[EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[4], [6], [21], [21]
Cra	activator	poxBp1	Sigma70	nd	nd	poxB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[3]
Cra	activator	poxBp2	Sigma38	nd	nd	poxB	nd nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[3]
Cra	repressor	ppcp	nd	-46.5	-138.5	ppc	tttattcgttTGCTGAAGCGATTTCGCAgcatttgacg nd	4153228	4153245	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ]	S	[4], [11], [11]
Cra	activator	ppsAp	Sigma70	-45.5	-94.5	ppsA	aaaatatattTGCTTGAACGATTCACCgtttttttca nd	1787199	1787215	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	S	[2], [2], [3], [10], [10], [11], [11]
Cra	repressor	prpBp	Sigma54	-101.5	-137.5	prpB, prpC, prpD, prpE	ctgaaacgttAACTGAAACGCATATTTGcggattagtt nd	348536	348553	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX]	S	[11], [11], [20]
Cra	repressor	ptsHp1	nd	-55.5	-211.5	ptsH, ptsI, crr	gaaaagccaaAGCTGAATCGATTTTATGatttggttca nd	2533544	2533561	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [11], [11], [22]
Cra	activator	ptsHp2	Sigma70	-48.5	-211.5	ptsH, ptsI, crr	gaaaagccaaAGCTGAATCGATTTTATGatttggttca nd	2533544	2533561	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	C	[4], [6], [11], [11], [22]
Cra	repressor	pykFp	Sigma70	18.5	-213.5	pykF	gccaattgacTCTTGAATGGTTTCAGCActttggactg nd	1755476	1755493	[EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION]	S	[4], [6], [23], [23]
Cra	repressor	sgrSp	Sigma70	-332.5	-332.5	sgrS, sgrT, setA	tgcaccagttGATCGATACGATCCTGCTccagcaggtc nd	77026	77043	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	sgrSp2	Sigma38	-332.5	-332.5	sgrS, sgrT, setA	tgcaccagttGATCGATACGATCCTGCTccagcaggtc nd	77026	77043	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]
Cra	repressor	tpiAp	Sigma38	-91.5	-153.5	tpiA	tgaccttcgcTGTTGAACCGATTAAGCTggcgctatct nd	4111652	4111669	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO]	S	[6], [11], [11]
Cra	repressor	tpiAp2	Sigma70	-91.5	-153.5	tpiA	tgaccttcgcTGTTGAACCGATTAAGCTggcgctatct nd	4111652	4111669	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO]	S	[6], [11], [11]
Cra	repressor	zwfp	Sigma70	-35.5	-97.5	zwf	gggtggataaGCGTTTACAGTTTTCGCAagctcgtaaa nd	1936403	1936420	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS]	W	[11], [11]

	Sequence
	tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt	[-725.5, gapAp, forward] [-725.5, gapAp1, forward] [-608.5, gapAp2, forward] [-587.5, gapAp3, forward] [-516.5, gapAp4, forward]
	catttaagaaATTAAATCATTTCAACTTggttgttaac	[-563.5, csgDp1, reverse] [-563.5, csgDp3, reverse]
	tgcaccagttGATCGATACGATCCTGCTccagcaggtc	[-332.5, sgrSp, forward] [-332.5, sgrSp2, forward]
	aattctatttTTCTTACACGATTCAGCTaatgagtctt	[-268.5, cyoAp, reverse]
	tgtggagaaaAAACAAGAACGTTTTACAtgacgaaagg	[-227.5, csgDp1, reverse] [-227.5, csgDp3, reverse]
	gacgattataTTTGTAAACGATTCAGCTtaaactgccc	[-205.5, enop1, reverse] [-177.5, enop2, reverse] [-33.5, enop3, reverse]
	caaaattggtAAGTGAATCGGTTCAATTcggattttta	[-177.5, aroPp1, reverse] [-198.5, aroPp2, reverse] [-185.5, pdhRp, forward] [-185.5, pdhRp2, forward]
	cgaaaggactACACCGAAATATTTTTTAtatgcattat	[-196.5, csgDp1, reverse] [-196.5, csgDp3, reverse]
	tgatagtcgaTCGTTAAGCGATTCAGCAccttacctca	[-166.5, aceBp, forward]
	ggttatcattTGCTGAATGGATTCAGTCttaatgagtg	[-159.5, pdeLp1, forward]
	aaagttagcgTGGTGAATCGATACTTTAccggttgaat	[-139.5, pckp, forward]
	cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt	[-134.5, cydAp5, forward]
	aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat	[-105.5, cydAp5, forward]
	ctgaaacgttAACTGAAACGCATATTTGcggattagtt	[-101.5, prpBp, forward]
	tgaccttcgcTGTTGAACCGATTAAGCTggcgctatct	[-91.5, tpiAp, reverse] [-91.5, tpiAp2, reverse]
	ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac	[-91.5, glkp2, reverse] [-91.5, glkp4, reverse]
	ctggagaattTGATGAACCGTTTCATCAttgctgacgc	[-84.5, hypFp2, reverse] [7.5, hypFp3, reverse]
	gaacgttgcgAGCTGAATCGCTTAACCTggtgatttct	[-76.5, icdAp2, forward]
	attgaacaaaACTTGAACCGATTTAGCAaaacgtggca	[-72.5, marRp, forward]
	gaaaagccaaAGCTGAATCGATTTTATGatttggttca	[-55.5, ptsHp1, forward] [-48.5, ptsHp2, forward]
	tttattcgttTGCTGAAGCGATTTCGCAgcatttgacg	[-46.5, ppcp, reverse]
	cctgggtcatGCTGAAGCGAGACACCAggagacacaa	[-45.5, crpp1, forward]
	aaaatatattTGCTTGAACGATTCACCgtttttttca	[-45.5, ppsAp, reverse]
	ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg	[-43.5, gapAp, forward] [-43.5, gapAp1, forward] [74.5, gapAp2, forward] [95.5, gapAp3, forward] [166.5, gapAp4, forward]
	tgttgcgctcAGGTGAATCGCGCCAGCAaattacggat	[-36.5, mplp, forward] [-36.5, mplp1, forward]
	acattttttcTGATGAATCGAGCCAACAgaaaacgctg	[-35.5, fbaBp, reverse]
	atttggcctgACCTGAATCAATTCAGCAggaagtgatt	[-35.5, pfkAp, forward] [-35.5, pfkAp2, forward]
	gggtggataaGCGTTTACAGTTTTCGCAagctcgtaaa	[-35.5, zwfp, reverse]
	cttcagaggcTATTTTATCGATTCAGCTgtagtaaaat	[-31.5, gpmMp1, forward]
	gtcgactggaCAGTTAACCGATTCAGTGccagatttcg	[-22.5, mtlAp, forward]
	taagcggggtTGCTGAATCGTTAAGGTAggcggtaata	[-15.5, nirBp, forward]
	cagttgatctGGATTGTTAAATTCATATaatgcgcctt	[-13.5, pdeLp1, forward]
	cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa	[-8.5, enop1, reverse] [20.5, enop2, reverse] [164.5, enop3, reverse]
	aattgatgtaACATAATCACTTACGTGAtgtgcgtgtt	[-4.5, glcCp, forward]
	cgcttatcctAGCTGAAGCGTTTCAGTCgattaaatgt	[3.5, epdp, reverse] [3.5, epdp2, reverse]
	ttattacactGACTGAAACGTTTTTGCCctatgagctc	[4.5, eddp, reverse]
	gtattatgctTTCTTGAAACGTTTCAGCgcgatcttgt	[7.5, fruBp, reverse]
	gccaattgacTCTTGAATGGTTTCAGCActttggactg	[18.5, pykFp, forward]
	cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa	[36.5, adhEp, reverse] [36.5, adhEp1, reverse]
	tgtagcccttATCTGAATCGATTCGATtgtggacgac	[40.5, manXp, forward]
	tacccatttaGGGCTGATTTATTACTACacacagcagt	[46.5, csgDp1, reverse] [46.5, csgDp3, reverse]
	ttttctcataGAGGCTGAATCGTTTCAAttcagcaaga	[73.5, fruBp, reverse]

Alignment and PSSM for Cra TFBSs

Aligned TFBS of Cra

	Sequence
	GAGGCTGAATCGTTTCAATTC
	ACAGCTGAATCGATAAAATAG
	CTAGCTGAAGCGTTTCAGTCG
	GGTGCTGAAACGATAAAGTAA
	CGCGCTGAAACGTTTCAAGAA
	CGAGCTGAATCGCTTAACCTG
	GTTGCTGAATCGTTAAGGTAG
	GGTGCTGAATCGCTTAACGAT
	GCTGCGAAATCGCTTCAGCAA
	CCAGCTTAATCGGTTCAACAG
	CCTGCTGAATTGATTCAGGTC
	TTTGCTGAATGGATTCAGTCT
	CAAGCGGAATCGTGTCAATCA
	TTTGCTAAATCGGTTCAAGTT
	GTTGCTGAATCGTTTTTTCAA
	AGTGCTGAAACCATTCAAGAG
	TTAGCTGAATCGTGTAAGAAA
	TCAGGTGAATCGCGCCAGCAA
	AAAGCTGAATCGATTTTATGA
	TTATCTGAATCGATTCGATTG
	GTAAGTGAATCGGTTCAATTC
	AACGGTGAATCGTTCAAGCAA
	CGTGGTGAATCGATACTTTAC
	TCTGATGAATCGAGCCAACAG
	CATGCTGAAGCGAGACACCAG
	GATGCTGAAAGGTGTCAGCTT
	AATGATGAAACGGTTCATCAA
	TAAGCTGAATCGTTTACAAAT
	AGGGCAAAAACGTTTCAGTCA
	GGCACTGAATCGGTTAACTGT
	GCCGCAAAATCCTTACAATAA
	GGAGCAGGATCGTATCGATCA
	CAAGTTGAAATGATTTAATTT
	AATGCAAATTTGCTTCAACAA
	TCTTGTGAATCGATCAGTTTG
	TTAACTGAAACGCATATTTGC
	AGGGCTGATTTATTACTACAC
	TCATGTAAAACGTTCTTGTTT
	ATTGTTAAATTCATATAATGC
	GTAACATAATCACTTACGTGA
	CTTGCGAAAACTGTAAACGCT
	ATATAAAAAATATTTCGGTGT

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

A	10	10	17	4	3	6	9	41	40	11	0	3	13	2	9	13	29	18	2	20	15
C	10	9	4	0	31	0	0	0	0	0	34	3	7	0	5	24	2	5	12	6	7
G	12	10	3	34	6	3	31	1	0	2	2	35	6	6	0	0	5	14	6	6	10
T	10	13	18	4	2	33	2	0	2	29	6	1	16	34	28	5	6	5	22	10	10

Consensus

;	consensus.strict             	ggtGCtGAAtCGtttcagtaa
;	consensus.strict.rc          	TTACTGAAACGATTCAGCACC
;	consensus.IUPAC              	sbwGCtGAAtCGwttmaryar
;	consensus.IUPAC.rc           	YTRYTKAAWCGATTCAGCWVS
;	consensus.regexp             	[cg][cgt][at]GCtGAAtCG[at]tt[ac]a[ag][ct]a[ag]
;	consensus.regexp.rc          	[CT]T[AG][CT]T[GT]AA[AT]CGATTCAGC[AT][ACG][CG]

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-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-CHIP-EXO] high throughput ChIP-exo evidence
[EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing
[EXP-IMP-SITE-MUTATION] Site mutation
[COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[AS-NAS] Non-traceable author statement
[EXP-GSELEX] high throughput Genomic SELEX-chip evidence

Reference(s)
[1] Ramseier TM., Bledig S., Michotey V., Feghali R., Saier MH., 1995, The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli., Mol Microbiol 16(6):1157-69
[2] Ramseier TM., Negre D., Cortay JC., Scarabel M., Cozzone AJ., Saier MH., 1993, In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium., J Mol Biol 234(1):28-44
[3] Son YJ., Phue JN., Trinh LB., Lee SJ., Shiloach J., 2011, The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth., Microb Cell Fact 10:52
[4] 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
[5] Cortay JC., Negre D., Scarabel M., Ramseier TM., Vartak NB., Reizer J., Saier MH., Cozzone AJ., 1994, In vitro asymmetric binding of the pleiotropic regulatory protein, FruR, to the ace operator controlling glyoxylate shunt enzyme synthesis., J Biol Chem 269(21):14885-91
[6] Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO, 2018, Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP., Nucleic Acids Res 6:46
[7] Cunningham L., Gruer MJ., Guest JR., 1997, Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli., Microbiology 143 ( Pt 12):3795-805
[8] Kaga N., Umitsuki G., Clark DP., Nagai K., Wachi M., 2002, Extensive overproduction of the AdhE protein by rng mutations depends on mutations in the cra gene or in the Cra-box of the adhE promoter., Biochem Biophys Res Commun 295(1):92-7
[9] Mikulskis A., Aristarkhov A., Lin EC., 1997, Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra., J Bacteriol 179(22):7129-34
[10] Sarkar D., Siddiquee KA., Arauzo-Bravo MJ., Oba T., Shimizu K., 2008, Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli., Arch Microbiol 190(5):559-71
[11] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59
[12] Zhang Z., Aboulwafa M., Saier MH., 2014, Regulation of crp Gene Expression by the Catabolite Repressor/Activator, Cra, in Escherichia coli., J Mol Microbiol Biotechnol 24(3):135-41
[13] Reshamwala SM., Noronha SB., 2011, Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis., Arch Microbiol 193(10):711-22
[14] Ramseier TM., Chien SY., Saier MH., 1996, Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli., Curr Microbiol 33(4):270-4
[15] Shimada T., Fujita N., Maeda M., Ishihama A., 2005, Systematic search for the Cra-binding promoters using genomic SELEX system., Genes Cells 10(9):907-18
[16] Meyer D., Schneider-Fresenius C., Horlacher R., Peist R., Boos W., 1997, Molecular characterization of glucokinase from Escherichia coli K-12., J Bacteriol 179(4):1298-306
[17] Prost JF., Negre D., Oudot C., Murakami K., Ishihama A., Cozzone AJ., Cortay JC., 1999, Cra-dependent transcriptional activation of the icd gene of Escherichia coli., J Bacteriol 181(3):893-8
[18] Browning DF., Cole JA., Busby SJ., 2004, Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter., Mol Microbiol 53(1):203-15
[19] Tyson K., Busby S., Cole J., 1997, Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein., Arch Microbiol 168(3):240-4
[20] Ishihama A, Shimada T, Yamazaki Y, 2016, Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors., Nucleic Acids Res, 44(5):2058 10.1093/nar/gkw051
[21] Negre D., Bonod-Bidaud C., Geourjon C., Deleage G., Cozzone AJ., Cortay JC., 1996, Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR., Mol Microbiol 21(2):257-66
[22] Ryu S., Ramseier TM., Michotey V., Saier MH., Garges S., 1995, Effect of the FruR regulator on transcription of the pts operon in Escherichia coli., J Biol Chem 270(6):2489-96
[23] Bledig SA., Ramseier TM., Saier MH., 1996, Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli., J Bacteriol 178(1):280-3
[24] Ramseier TM, 1996, Cra and the control of carbon flux via metabolic pathways., Res Microbiol, 147(6-7):489 10.1016/0923-2508(96)84003-4
[25] Chin AM, Feldheim DA, Saier MH, 1989, Altered transcriptional patterns affecting several metabolic pathways in strains of Salmonella typhimurium which overexpress the fructose regulon., J Bacteriol, 171(5):2424 10.1128/jb.171.5.2424-2434.1989
[26] Chin AM, Feucht BU, Saier MH, 1987, Evidence for regulation of gluconeogenesis by the fructose phosphotransferase system in Salmonella typhimurium., J Bacteriol, 169(2):897 10.1128/jb.169.2.897-899.1987
[27] Cozzone AJ, El-Mansi M, 2005, Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli., J Mol Microbiol Biotechnol, 9(3-4):132 10.1159/000089642
[28] Kochanowski K, Volkmer B, Gerosa L, Haverkorn van Rijsewijk BR, Schmidt A, Heinemann M, 2013, Functioning of a metabolic flux sensor in Escherichia coli., Proc Natl Acad Sci U S A, 110(3):1130 10.1073/pnas.1202582110
[29] Wei LN, Zhu LW, Tang YJ, 2016, Succinate production positively correlates with the affinity of the global transcription factor Cra for its effector FBP in Escherichia coli., Biotechnol Biofuels, 9(None):264 10.1186/s13068-016-0679-7
[30] Bley Folly B, Ortega AD, Hubmann G, Bonsing-Vedelaar S, Wijma HJ, van der Meulen P, Milias-Argeitis A, Heinemann M, 2018, Assessment of the interaction between the flux-signaling metabolite fructose-1,6-bisphosphate and the bacterial transcription factors CggR and Cra., Mol Microbiol, 109(3):278 10.1111/mmi.14008
[31] Chavarría M, de Lorenzo V, 2018, The imbroglio of the physiological Cra effector clarified at last., Mol Microbiol, 109(3):273 10.1111/mmi.14080
[32] Vartak NB, Reizer J, Reizer A, Gripp JT, Groisman EA, Wu LF, Tomich JM, Saier MH, 1991, Sequence and evolution of the FruR protein of Salmonella typhimurium: a pleiotropic transcriptional regulatory protein possessing both activator and repressor functions which is homologous to the periplasmic ribose-binding protein., Res Microbiol, 142(9):951 10.1016/0923-2508(91)90005-u
[33] Weickert MJ, Adhya S, 1992, A family of bacterial regulators homologous to Gal and Lac repressors., J Biol Chem, 267(22):15869 None
[34] Leclerc G., Noel G., Drapeau GR., 1990, Molecular cloning, nucleotide sequence, and expression of shl, a new gene in the 2-minute region of the genetic map of Escherichia coli., J Bacteriol 172(8):4696-700
[35] Neetu N, Katiki M, Mahto JK, Sharma M, Narayanan A, Maity S, Tomar S, Ambatipudi K, Sharma AK, Yernool D, Kumar P, 2021, Deciphering the enigma of missing DNA binding domain of LacI family transcription factors., Arch Biochem Biophys, 713(None):109060 10.1016/j.abb.2021.109060
[36] Gayán E, Van den Bergh B, Michiels J, Michiels CW, Aertsen A, 2020, Synthetic reconstruction of extreme high hydrostatic pressure resistance in Escherichia coli., Metab Eng, 62(None):287 10.1016/j.ymben.2020.09.008
[37] Pandi K., Chauhan AS., Khan WH., Rathore AS., 2020, Phosphate starvation controls lactose metabolism to produce recombinant protein in Escherichia coli., Appl Microbiol Biotechnol 104(22):9707-9718

RegulonDB

DNA binding site length:	14
DNA binding site symmetry:	inverted-repeat