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Table 2 Identification of a cep box consensus motif.

From: Identification of potential CepR regulated genes using a cep box motif-based search of the Burkholderia cenocepacia genome

Gene

p-valueb

direction

Sequencec

bp to ORFd

First Generation Motif Sequencesa

cepI

2.23E-11

+

CACCCTGTAAGAGTTACCAGTT ACAGGCTC

72

phuR

6.53E-10

+

TACACTGTTAAAGTTGTCAGTT GCCTTTCA

116

aidA

2.24E-09

-

GAAGCTGTAAAAGTAAACAGGT CGGGAAAA

159

zmpA

2.60E-09

+

TCTTGTTTAAAAGTCATCACTT GATGCATT

54

Acyltransferase

1.13E-07

-

AGGGCTTCAAGTGTAACTCCTT GGAAAGGT

3

scpB

1.25E-07

-

CCAGTTTCCATAGCTGTCAGTT CTGACAAC

115

consensus

  

CTGTAA A AGT TAC CAGTT e

 

Second Generation Motif Sequencesf

cepI

4.79E-11

+

CACCCTGTAAGAGTTACCAGTT ACAGGCTC

72

phuR

6.11E-11

+

TACACTGTTAAAGTTGTCAGTT GCCTTTCA

116

MST072

4.01E-09

+

AAAATTGACAAAGTTATCAGTT ATGACTTT

56

aidA

2.16E-08

-

GAAGCTGTAAAAGTAAACAGGT CGGGAAAA

159

MST028

5.32E-07

-

CTTTCGGCAATAGTTGCCTGTT TCGATTGA

140

zmpA

2.60E-09

+

TCTTGTTTAAAAGTCATCACTT GATGCATT

54

MST005

1.24E-06

+

CAACCAGTAAAACTTGCGCATT CCGGTCGA

206

MST068

1.60E-06

-

CGTTCGCTTAGAGTTGTTCGAT ATTTCGAA

138

MST011

1.80E-06

+

TGTCAAGTCAGACTTGACAGCT TGTAAAGG

76

MST059

2.41e-06

+

ATGGTTGAAAGTGTCATCCGGT GCTACACT

118

consensus

  

C TGT A A A AGTT AC C A G T T g

 
  1. a The promoter regions of 6 genes experimentally determined to be positively regulated by CepR used to search for common motifs with the MEME (Multiple EM for Motif Elicitation) program.
  2. b The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p -value by the MAST algorithm.)
  3. c The boxed region represents the region determined to be required for cepI expression as determined in Fig. 1. Bold lettering represents the motif predicted by the MEME program. In the case of cepI the motif matches the CepR binding site [20].
  4. d The number of base pairs to the start codons predicted by alignment with homologous genes.
  5. e Underlined bases are conserved in at least 4 of 6 sequences.
  6. f The promoter regions of 10 genes experimentally determined to be positively regulated by CepR used to search for common motifs with MEME.
  7. g Underlined bases are conserved in at least 7 of 10 sequences.