A Comparative Genomics Approach to Prediction of New Members of Regulons

Table 1.

Positional Weight Matrices for CRP and FNR Binding Motifs

CRP Weight Matrix FNR Weight Matrix
A C G T Cns A C G T Cns
0.97 −2.16 −1.70 0.61 A 0.80 −0.55 −0.16 −0.55 A
1.09 −6.57 −1.51 0.61 A 0.97 −0.55 −1.09 −0.16 A
0.80 −1.19 −0.14 −0.14 A 1.25 −1.09 −1.94 −0.16 A
−1.69 −1.19 −1.90 1.58 T 0.80 −0.55 −4.26 0.61 A
−2.46 −3.39 1.74 −1.33 G −1.94 −1.94 −4.26 1.78 T
−1.51 −2.16 −4.23 1.75 T −4.26 −4.26 −4.26 1.96 T
−1.51 −6.57 1.80 −2.46 G −4.26 −4.26 1.96 −4.26 G
1.75 −2.16 −2.16 −2.46 A 1.78 −4.26 −4.26 −1.09 A
−0.35 0.06 −0.61 0.61 T −4.26 −0.55 −4.26 1.70 T
−0.20 0.52 −0.14 −0.35 C 0.39 −0.55 −0.16 0.14 A
−1.06 0.33 −0.71 0.72 T 0.14 −1.94 −1.09 1.12 T
0.72 −0.71 0.33 −1.06 A 1.12 −1.09 −1.94 0.14 A
−0.35 −0.14 0.52 −0.20 G 0.14 −0.16 −0.55 0.39 T
0.61 −0.61 0.06 −0.35 A 1.70 −4.26 −0.55 −4.26 A
−2.46 −2.16 −2.16 1.75 T −1.09 −4.26 −4.26 1.78 T
−2.46 1.80 −6.57 −1.51 C −4.26 1.96 −4.26 −4.26 C
1.75 −4.23 −2.16 −1.51 A 1.96 −4.26 −4.26 −4.26 A
−1.33 1.74 −3.39 −2.46 C 1.78 −4.26 −1.94 −1.94 A
1.58 −1.90 −1.19 −1.69 A 0.61 −4.26 −0.55 0.80 T
−0.14 −0.14 −1.19 0.80 T −0.16 −1.94 −1.09 1.25 T
0.61 −1.51 −6.57 1.09 T −0.16 −1.09 −0.55 0.97 T
0.61 −1.70 −2.16 0.97 T −0.55 −0.16 −0.55 0.80 T
I = 12.88 bits I = 13.74 bits

  • Each column displays the weight of the given nucleotide at that position. Highly conserved nucleotides are in bold. Cns, consensus. They are derived at each position by highest value. I, sample-size adjusted information content (in units of bits).

This Article

  1. Genome Res. 11: 566-584

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