Table 4

Analysis of cre boxes with apparent low affinity to CcpA
Gene Cre sequencea Scoreb
1 2 3 4 5 6 7 8 9 10 11 12 13 14
abnA T G T A A G C G C T T T C T 5
acoA T G T A A G C G T T T G C T 4
citZ T G T A A G C A T T T T C T 3
csbX T G A A A A C G G T G C C A 4
cydA T G A A A T G A A T C G T T 2
drm T G A A A A C G G T T T A T 4
gntR-1 T G A A A G T G T T T G C A 4
gntR-2 T G A A A G C G G T A C C A 4
hutP T G A A A C C G C T T C C A 5
lcfA T G A A A A C G T T A T C A 6
levD T G A A A A C G C T T A A C 3
malA T G T A A A C G T T A T C A 5
mleN T G A A A G C G T T T T A G 4
msmR T G T A A C C G C T T A C T 5
mtlR T G A A A G C G T T T T A T 4
odhA T G G A A G C G T T T T T A 4
pbuG T G A A A A C G T T T T T T 5
pta T G A A A G C G C T A T A A 5
resA T A A A A A C G C T T T C T 4
sigL G G A A A A C G C T T T C A 5
wprA T G T A A G C G G T A T C T 3
yckB T G A A A A C G C G A T C A 4
ycsA A G A A A G C G C T T A C G 5
ydzA T G A A A A C G T G T C C A 5
yesL T G A A A G C G T T T T C C 4
yfiG A G A A A G C G G T T A C A 4
yncC T G T A A A C G G T T A C A 6
yojA T G A A A G C G C T T T C T 6
yqgW T G A A A A C G C T A T C G 4
yqgY T G A A A A T G T T T A C A 5
ysbA T G T A A G C G C T T T A T 4
ysfC T G A A A G C G T T T T T T 4
yugN T G A A T G C G C T T T C T 5
yuxG T G A A A A C G G A T A C A 4
yvdG T G T A A C C G C T T T C T 5
yxlH T T G A A A C G C T T T C A 4
yydK T G T A A G C G G T T T A T 3
yyzE T G A A A G C G T A A C C A 3
palindrome %c 40 66 42 74 87 32 90 90 32 87 74 42 66 40 Average score = 4.3

a In bold – palindromic residues.

b Score - a number of palindromic pairs.

c Occurrence of palindromic residue at each position.

Cre boxes of repressed genes are aligned.

Marciniak et al.

Marciniak et al. BMC Genomics 2012 13:401   doi:10.1186/1471-2164-13-401

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