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.

Price et al. Genome Biology 2008 9:R4   doi:10.1186/gb-2008-9-1-r4