Table 3. Operons associated with a FNR ChIP-seq peak and lacking a FNR-dependent change in expression in GMM but are potentially co-activated by CRP and FNR (Category 3).

Peak Center (nt)a	First Gene of Operon Downstreamb	B-number of First Genec	Cellular Functiond	Increase Expression in Other Carbon Sourcese	Distinct FNR and CPR Sitesf	Referenceg
1019175	ompA	b0957	Outer Membrane Protein 3A	+	+	[58], [143], (Park and Kiley, Personal Communication)
1157025	ptsG	b1101	Glucose PTS Permease	+	+	[58], [144]
1608750	uxaB	b1521	Altronate Oxidoreductase	+	−	[19], [145], (Park and Kiley, Personal Communication)
2531550	ptsH	b2415	Phosphoenolpyruvate Dependent Phophotransferase System	+	−	[58], [146]
2632200	guaB	b2508	IMP Dehydrogenase	+	−	[58], [147]
3229415	fadH	b3081	2,4-Dienoyl-CoA Reductase	+	+	[19], [148], (Park and Kiley, Personal Communication)
3242850	uxaC/exuT	b3092/b3093	Glucuronate and Galacturonate Isomerase (uxaC)/Hexuronate Transporter (exuT)	+/+	+/+	[19], [145], (Park and Kiley, Personal Communication)
3408300	dusB	b3260	tRNA Dihydrouridine Synthase	+	+	[58], [145]
3490500	ppiA	b3363	Peptidyl-Prolyl Cis-Trans Isomerase A	+	+	[58], [149], (Park and Kiley, Personal Communication)
3544500	gntT	b3415	Gluconate Transporter	+	+	[19], [150], (Park and Kiley, Personal Communication)
4366425	aspA	b4139	Aspartate Ammonia-Lyase	+	+	[19], [136], (Park and Kiley, Personal Communication)

^aGenomic location within each FNR ChIP-seq peak with the highest read count (the summit of the peak).

^bFirst gene of the operon downstream of the FNR ChIP-seq peak, and operon designation was obtained from EcoCyc [70]. For peaks located within divergent promoters with both operons activated by CRP, both genes are identified, separated by “/”.

^cIdentification number (B-number) for the first gene in each operon, obtained from EcoCyc [70]. For peaks located within divergent promoters with both operons activated by CRP, both B-numbers are identified, separated by “/”.

^dFunctional description of the products of the operons, obtained from EcoCyc [70]. For peaks located within divergent promoters with both operons activated by CRP, the functions of both operons are listed, separated by “/”.

^eIncrease of expression (+) or no change in expression (−) of gene as determined using microarray analyses when WT E. coli was grown with carbon sources other than glucose (e.g. glycerol, xylose, mannose, arabinose). For peaks located within divergent promoters the expression changes of both operons are listed, separated by “/”.

^fIndication if the FNR site different than the CRP site (+) or overlapping the CRP site (−). For peaks located within divergent promoters the FNR and CRP site positions of both operons are listed, separated by “/”.

^gReference for CRP activation of each operon or regulation in alternative carbon sources of each operon.