Table 2.
Scoring of PurR cognate binding sites using DNAPROT
| D = 1.0 | D = 0.4 | |||
| Binding Site | Score | p-value | Score | p-value |
| ACGAAACCGTTTGCGT | 3.93 | 1.49E-04 | 5.68 | 6.42E-06 |
| ACGAAAACGTTTGCGC | 3.84 | 1.98E-04 | 5.65 | 7.02E-06 |
| GCGGAAACGTTTTCCT | 3.37 | 8.15E-04 | 5.48 | 1.16E-05 |
| AGGAAAACGGTTGCGT | 3.26 | 1.11E-03 | 5.41 | 1.42E-05 |
| CGGAAAACGTTTGCGT | 3.22 | 1.24E-03 | 5.40 | 1.46E-05 |
| AAGAAAACGTTTGCGT | 3.13 | 1.59E-03 | 5.27 | 2.12E-05 |
| TTGAAATCGTTTGCAT | 2.51 | 7.73E-03 | 5.06 | 3.81E-05 |
| ACGCACACGTTTGCGT | 3.75 | 2.62E-04 | 4.80 | 7.69E-05 |
| AGGCAAACGTTTACCT | 3.27 | 1.08E-03 | 4.58 | 1.37E-04 |
| ACGCAAACGATTACCT | 3.00 | 2.26E-03 | 4.41 | 2.10E-04 |
| GCGTAACCGATTGCAT | 2.91 | 2.87E-03 | 4.37 | 2.32E-04 |
| TCGCAAACGTTTGCTT | 2.80 | 3.80E-03 | 4.35 | 2.44E-04 |
| GAGCAAACGTTTCCAC | 2.26 | 1.37E-02 | 4.14 | 4.08E-04 |
| TCGTTCTCTTTTGCCT | 0.80 | 1.92E-01 | 1.77 | 4.22E-02 |
| CGGCCAGTTTTTGCAG | -0.43 | 7.45E-01 | 0.35 | 2.58E-01 |
The known binding sites of PurR reported in RegulonDB [49] were scored using DNAPROT, maintaining W fixed to 1 and setting D to 1.0 and 0.4. These values of D correspond to the parameterization that renders the worst and the best PWMs for this transcription factor respectively. The first column corresponds to the binding sites, the second and fourth columns report the scoring obtained with DNAPROT and the third and fifth columns show the p-values of the scores obtained in a site recovery assay in a background set of 106 random sequences.