Table 3.

Validated new operon pairs containing ubiquitous single-copy (non-HGT) genes

Upstream gene	Downstream gene	Known operon?	Microarray similarity	Age of pair
yfhB	*yfhC^		0.51	Salmonella
*yrdC*	aroE		0.80	HPVS
yrdD	*yrdC*		0.76	HPVS
yhbE	*yhbZ^		0.73	HPVS
*pyrF^	yciH		0.71	HPVS
*murB*	birA^*		0.67	HPVS
ygiM	*cca^		0.65	HPVS
kdtA^*	*kdtB^	Yes	0.61	HPVS
*yggJ*	gshB^*		0.58	HPVS
*yhhF^	yhhL^*		0.54	HPVS
*pyrE*	rph	Yes	−0.13	HPVS
*lgt^	thyA^*	Yes	0.81	γ-Proteo.
*lspA^	slpA	Yes	0.76	γ-Proteo.
holC^*	*valS^		0.74	γ-Proteo.
rnhB^*	*dnaE^		0.73	γ-Proteo.
*ygbB^	ygbO		0.69	γ-Proteo.
*ksgA*	apaG	Yes	0.59	γ-Proteo.
*dapF^	yigA		0.54	γ-Proteo.
ycfC	*purB*	Yes	0.34	γ-Proteo.
priB^*	*rpsR^	Yes	0.93	βγ-Proteo.
rpsF	priB^*	Yes	0.92	βγ-Proteo.
nlpB	*dapA^	Yes	0.87	βγ-Proteo.
atpI	*atpB^	Yes	0.85	βγ-Proteo.
*ftsJ*	hflB	Yes	0.72	βγ-Proteo.
*yacE^	yacF		0.69	βγ-Proteo.
*folC*	dedD		0.64	βγ-Proteo.
yffB^*	*dapE^		0.54	βγ-Proteo.
slpA	*lytB^	Yes	—	βγ-Proteo.
*sucB^	sucC	Yes	0.98	Proteo.
*rnc^	era^*	Yes	0.85	Proteo.
yaeL	*yaeT^		0.83	Proteo.
ydgQ	*nth*		0.76	Proteo.
ndk	*yfgB*		0.74	Proteo.
pdxA	*ksgA*	Yes	0.73	Proteo.
*pepA^	holC^*		0.73	Proteo.
*pheT*	himA	Yes	0.64	Proteo.
*ribF^	*ileS^	Yes	0.63	Proteo.
b2512	*b2511^		0.52	Proteo.

Ubiquitous single-copy genes are in bold face type. Asterisks (^*) mark the genes reported to be essential (Gerdes et al. 2003). Known operons are taken from Karp et al. (2002). The microarray similarity is the Pearson (linear) correlation of normalized log-ratios across 74 E. coli microarray experiments that compared mRNA levels (Gollub et al. 2003). We used a microarray similarity of 0.5 or greater as confirmation that the predicted pair is a true operon pair. We validated this threshold against a database of known transcripts (Karp et al. 2002): 72% of known operon pairs and only 27% of known not-operon adjacent pairs had correlation coefficients greater than 0.5.

Operon formation is driven by co-regulation and not by horizontal gene transfer