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Table 2 High- and low-affinity cre boxes of the first genes of operons

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

     Gene expression fold changea  
  Gene Strand cresequence Low CcpA induction Medium CcpA induction High CcpA induction crebox to TSS distanceb
High affinity cre boxes
1 acoR upper TGAAAGCGCTTTAT −4.8 −18.7 −21.7 −27
2 acsA lower TGAAAGCGTTACCA −2.3 −2.5 −2.7 +44
3 acuA upper TGAAAACGCTTTAT −2.2 −4.6 −7.7 −26
4 amyE upper TGTAAGCGTTAACA −2.6 −10.7 −12.9 +4
5 bglP lower TGAAAGCGTTGACA −2.5 −4.7 −4.6 −36
6 cccA lower TGTAAGCGTATACA −2.2 −1.8 −2.8 −29
7 citM upper TGTAAGCGGATTCA −2.6 −2.7 −2.9 +46
8 cstA lower TGAATGCGGTTACA −2.2 −1.9 −2.4 +32
9 dctP upper TGAAAACGCTATCA −7.4 −12.3 −16.6 −14
10 glpF upper TGACACCGCTTTCA −4.3 −21.9 −35.6 −27
11 gmuB upper TGTAAGCGTTTTAA −3.0 −15.6 −35.8 +6
12 iolA-1 lower TGAAAGCGTTTAAT −1.8 −1.9 −2.1 +93
13 iolA-2 (within iolB) lower TGAAAACGTTGTCA −2.2 −2.5 −2.4 +2404
14 manR upper TGTAAACGGTTTCT −2.0 −3.7 −8.0 0
15 msmX lower AGAAAGCGTTTACA −2.0 −2.6 −3.1 −15
16 rbsR upper TGTAAACGGTTACA −6.7 −15.2 −23.1 +6
17 rocG lower TTAAAGCGCTTACA −2.6 −3.5 −3.1 +43
18 sacP lower CGAAAACGCTATCA −2.1 −7.9 −8.1 −19
19 sucC upper TGAAAGCGCAGTCT −2.0 −5.8 −3.4 0
20 treP upper TGAAAACGCTTGCA −3.2 −13.0 −17.5 +372
21 uxaC upper TGAAAGCGTTATCA −2.5 −3.7 −8.9 +1237
22 xsa lower TAAAAGCGCTTACA −1.9 −1.8 −2.6 +7
23 xylA upper TGGAAGCGCAAACA −2.4 −11.9 −11.1 +144
24 xynP upper TGAAAGCGCTTTTA −4.0 −11.0 −17.9 +230
25 yisS upper AGAAAACGCTTTCT −1.9 −3.5 −3.7 +74
26 yjmD upper TGAAAGCGGTTCAA −2.2 −2.4 −8.8 ND
27 ykoM upper TGCAAGGGCTTTCA −2.0 −3.4 −3.5 +150
28 yrpD upper TGATAGCGTTTTCT −1.9 −8.0 −6.8 +127
29 ytkA lower TGTAAGCGTTTGCT −1.9 −6.4 −6.8 ND
30 yulD lower TGAAAGCGCTATCT −2.3 −4.9 −5.3 ND
31 yvfK lower TTAAAGCGCTTTCA −4.0 −6.1 −10.6 +5
Low affinity cre boxes
1 abnA lower TGTAAGCGCTTTCT −1.8 −1.7 −2.5 +85
2 acoA lower TGTAAGCGTTTGCT −1.1 −1.0 −1.8 +462
3 citZ lower TGTAAGCATTTTCT −1.5 −1.8 −2.1 +88
4 csbX lower TGAAAACGGTGCCA −1.4 −2.8 −2.1 −401
5 cydA lower TGAAATGAATCGTT 1.6 1.0 −2.7 −21
6 drm lower TGAAAACGGTTTAT −1.3 −3.6 −3.2 −16
7 gntR-1 upper TGAAAGTGTTTGCA −1.3 −2.8 −3.2 −41
8 gntR-2 upper TGAAAGCGGTACCA −1.3 −2.8 −3.2 +148
9 hutP upper TGAAACCGCTTCCA −1.3 −1.9 −2.6 +209
10 lcfA lower TGAAAACGTTATCA −1.4 −2.6 −2.6 +450
11 levD lower TGAAAACGCTTAAC −1.5 −1.2 −2.2 −45
12 malA upper TGTAAACGTTATCA −1.7 −2.0 −2.6 +6
13 mleN lower TGAAAGCGTTTTAG −1.5 −3.5 −2.4 +21
14 msmR upper TGTAACCGCTTACT −1.7 −4.2 −12.2 −28
15 mtlR upper TGAAAGCGTTTTAT −1.5 −2.7 −2.5 −16
16 odhA lower TGGAAGCGTTTTTA −1.6 −6.6 −3.4 +21
17 pbuG upper TGAAAACGTTTTTT −1.1 −1.5 −1.9 +245
18 pta lower TGAAAGCGCTATAA 1.3 −3.2 −2.7 −55
19 resA lower TAAAAACGCTTTCT −1.1 −1.9 −1.9 −72
20 sigL lower GGAAAACGCTTTCA −1.1 −3.1 −3.3 ND
21 wprA upper TGTAAGCGGTATCT −1.6 −5.5 −4.2 +43
22 yckB lower TGAAAACGCGATCA −1.4 −3.5 −2.1 −48
23 ycsA upper AGAAAGCGCTTACG −1.7 −6.0 −10.3 +67
24 ydzA lower TGAAAACGTGTCCA −1.3 −6.4 −6.4 +9
25 yesL upper TGAAAGCGTTTTCC −1.3 −1.6 −2.0 +125
26 yfiG upper AGAAAGCGGTTACA −1.6 −2.7 −4.6 +38
27 yncC upper TGTAAACGGTTACA −1.3 −2.4 −3.8 +84
28 yojA lower TGAAAGCGCTTTCT 1.1 −1.5 −1.8 +57
29 yqgW upper TGAAAACGCTATCG −1.1 −4.5 −4.2 −39
30 yqgY upper TGAAAATGTTTACA −1.4 −5.4 −4.1 −38
31 ysbA lower TGTAAGCGCTTTAT 1.0 −3.8 −7.6 ND
32 ysfC upper TGAAAGCGTTTTTT −1.5 −1.5 −2.0 +196
33 yugN lower TGAATGCGCTTTCT −1.7 −2.4 −2.3 ND
34 yuxG lower TGAAAACGGATACA −1.2 −4.2 −6.1 0
35 yvdG lower TGTAACCGCTTTCT −1.4 −1.5 −2.1 −28
36 yxlH upper TTGAAACGCTTTCA −1.4 −2.0 −2.3 +260
37 yydK upper TGTAAGCGGTTTAT −1.5 −3.2 −2.4 −21
38 yyzE lower TGAAAGCGTAACCA −1.2 −3.0 −2.1 0
Activating cre boxes
1 ilvB lower TGAAAGCGTATACA 3.0 6.2 2.7 +88
2 opuE lower TGAAAGCGTTTTAT 2.3 2.5 2.3 −103
3 ycbP lower TGAAAGCGCTCGCT 2.5 3.3 2.6 +30
  1. a In bold – genes significantly regulated (1.8 < fold < −1.8).
  2. bcre box distance to transcriptional start site calculated from the conserved G residue in the middle CpG of the cre box.
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