Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Table 2 Binding sites for CRP upstream of Escherichia coli operons and their xenologs

Operon	Organism	Position	Score	Site sequence
yiaKLMNOPQRS	E. coli K12	-175	9.1	aAgTGTGccgtagtTCACgaTc
yiaKLMNOPQRS	Haemophilus influenzae RD KW20	-148	10.3	aAaTagGAtctagaTCACAaaa
araBAD	E. coli K12	-131	9.1	ttaTtTGcacggcgTCACAcTt
araBDA?C	Vibrio parahaemolyticus RIMD 2210633	-177	6.3	tggaGTtcgatgagagcCggTt
		-137	6.5	cgacaTGAtgacgacgAtcgcc
gntKU	E. coli K12	-171	13.1	aAaTtTGAagtagcTCACAcTt
gntK-edd	V. cholerae	-131	11.5	gttTGTGttatagcTCACAtTt

These E. coli operons are regulated by CRP as well as by an adjacent regulator and have been co-transferred, together with their neighbor regulators, between the E. coli lineage and other γ-Proteobacteria. We used a weight matrix to identify potential binding sites for CRP upstream of these operons and their xenologs. For each site we report its sequence, its score in bits, and its position relative to the start codon of the first gene in the operon. The sites that were used to build the weight matrix have 8.41 ± 2.66 bits (mean ± standard deviation). Within each site's sequence, positions that match the consensus nAnTGTGAnnnnnnTCACAnTn are capitalized.