Table 5.

CodY-binding motifs of the nupN gene

Motifa	Sequenceb	No. of mismatches	Scorec	Location with respect to transcription start point
Consensus	AATTTTCWGAAAATT	0	13.8–14.1
1a	AtTTTTaAGcAAATa	4	4.0	−94–−80
1b	AtaaTTCTaAAAATa	5	4.6	−82–−68
1b p21	AtaaTTCTGAAAATa	4	6.6
1b p22	AtaaTTgTaAAAATa	6	1.9
1b p23	AtaaTTCTacAAATa	6	0.85
1b p24	AtaaaTCTaAAAATa	6	3.7
1cd	tAaTTTtTaAAAAaT	5	4.6	−65–−51
1 p+	AATTTTtAaAAAATT	2	10.1	−64–−50
1 p1	AATTTTCAGAAAATT	0	14.1
1 p2	AATTTTtAacAAATT	3	6.4
1 p3	AAaTTTtAaAAAATT	3	8.3
2 p+	tATTaTCAGAAAATT	2	12.0	+169–+183
2 p11	AATTTTCAGAAAATT	0	14.1
2 p12	tATTaTCAcAAAATT	3	8.0

^aShown are strong CodY-binding motifs 1 and 2 and weaker motifs found upstream of motif 1 and analyzed in this work. Additional weak motifs can be found downstream of motifs 1 and 2 (see Discussion).

^bMismatches to the proposed CodY-binding consensus are indicated by lowercase letters. Mutations are in boldface. Overlapping parts of motifs 1a and 1b and the part of motif 1c that overlaps motif 1 are underlined.

^cThe scores for individual CodY-binding motifs have been generated using the position-specific weight matrix, as described in reference 6.

^dMotif 1c almost completely overlaps strong motif 1 and therefore is unlikely to have a separate functional role. This is supported by the fact that the p1 mutation that increased CodY-mediated repression is a strong down mutation in motif 1c.