Table 2.
CodY-binding motifs of the ybgE gene
| Motif | Sequencea | Number of mismatches | Scoreb | Location with respect to the transcription start point |
|---|---|---|---|---|
| Consensus | AATTTTCWGAAAATT | 0 | 13.8–14.1 | |
| ybgE 1a | tgTTTTCTttAAtTT | 5 | 3.7 | −56 to −42 |
| ybgE 1 | AATaTTCTGAAAtTT | 2 | 10.3 | +10 to +24 |
| ybgE 2c | AAaagaCTGAAtATT | 5 | 6.5 | +81 to +95 |
| ybgE 3 | AATaTTtAaAcAATT | 4 | 6.8 | +90 to +104 |
| ybgE 4c | AATTaTgTGAAAggT | 4 | 4.1 | +101 to +115 |
| ybgE 1 p1 | AATaTTCTGgAAtTT | 3 | 6.5 | +10 to +24 |
| ybgE 3 p11 | AATTTTCAGAAAATT | 0 | 14.1 | +90 to +104 |
a
Mismatches to the proposed CodY-binding consensus are indicated by lower case letters. Mutations are in bold face.
b
The scores for individual CodY-binding motifs have been generated using the position-specific weight matrix as described in 15.
c
Parts of motifs 2 and 4 that overlap with motif 3 are underlined.