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Table 4 Analysis of cre boxes with apparent low 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

 

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

  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.