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Table 3 Analysis of cre boxes with apparent high affinity to CcpA

From: High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis

Gene

Cre sequencea

Scoreb

 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

 

acoR

T

G

A

A

A

G

C

G

C

T

T

T

A

T

5

acsA

T

G

A

A

A

G

C

G

T

T

A

C

C

A

4

acuA

T

G

A

A

A

A

C

G

C

T

T

T

A

T

4

amyE

T

G

T

A

A

G

C

G

T

T

A

A

C

A

5

bglP

T

G

A

A

A

G

C

G

T

T

G

A

C

A

4

cccA

T

G

T

A

A

G

C

G

T

A

T

A

C

A

5

citM

T

G

T

A

A

G

C

G

G

A

T

T

C

A

4

cstA

T

G

A

A

T

G

C

G

G

T

T

A

C

A

4

dctP

T

G

A

A

A

A

C

G

C

T

A

T

C

A

5

glpF

T

G

A

C

A

C

C

G

C

T

T

T

C

A

5

gmuB

T

G

T

A

A

G

C

G

T

T

T

T

A

A

4

iolA-1

T

G

A

A

A

G

C

G

T

T

T

A

A

T

3

iolA-2

T

G

A

A

A

A

C

G

T

T

G

T

C

A

6

manR

T

G

T

A

A

A

C

G

G

T

T

T

C

T

4

msmX

A

G

A

A

A

G

C

G

T

T

T

A

C

A

4

rbsR

T

G

T

A

A

A

C

G

G

T

T

A

C

A

6

rocG

T

T

A

A

A

G

C

G

C

T

T

A

C

A

5

sacP

C

G

A

A

A

A

C

G

C

T

A

T

C

A

4

sucC

T

G

A

A

A

G

C

G

C

A

G

T

C

T

4

treP

T

G

A

A

A

A

C

G

C

T

T

G

C

A

5

uxaC

T

G

A

A

A

G

C

G

T

T

A

T

C

A

5

xsa

T

A

A

A

A

G

C

G

C

T

T

A

C

A

5

xylA

T

G

G

A

A

G

C

G

C

A

A

A

C

A

4

xynP

T

G

A

A

A

G

C

G

C

T

T

T

T

A

6

yisS

A

G

A

A

A

A

C

G

C

T

T

T

C

T

6

yjmD

T

G

A

A

A

G

C

G

G

T

T

C

A

A

4

ykoM

T

G

C

A

A

G

G

G

C

T

T

T

C

A

5

yrpD

T

G

A

T

A

G

C

G

T

T

T

T

C

T

4

ytkA

T

G

T

A

A

G

C

G

T

T

T

G

C

T

4

yulD

T

G

A

A

A

G

C

G

C

T

A

T

C

T

5

yvfK

T

T

A

A

A

G

C

G

C

T

T

T

C

A

6

palindrome % c

68

71

52

61

84

32

97

97

32

84

61

52

71

68

Average score = 4.6

  1. a In bold – palindromic residues.
  2. b Score - a number of palindromic pairs.
  3. c Occurrence of palindromic residue at each position.
  4. Cre boxes of repressed genes are aligned.