TABLE 3.

NreA operator motifs identified in the mesorhizobium C089B genome

Matched sequence	Start	Stop	Strand	Scorea	P valueb	Q valuec	Region	Upstream	Predicted function
Search with nreA operator sequence TATCCTCTCGGGGGGGATA
TATCCTCTCGGGGGGGATAd	3,145,188	3,145,206	+	36.6402	2.48E−12	1.31E−5	Intergenic	nreA	Ni-sensing transcriptional regulator
CATCCTCCCCGGGGGGATA	1,073,223	1,073,241	+	15.4756	1.50E−7	0.265	Intergenic	nreA2	Metal-sensing transcriptional regulator
TCTCCCCCACGAGGGGAGA	4,657,185	4,657,203	+	15.4756	1.50E−7	0.265	Intergenic	glcB	Malate synthase G
TATCCCCTCCTAGAGGTTT	3,437,282	3,437,300	+	15.2561	2.43E−7	0.322	Intergenic	KPGJNAOJ_03459	ATP-dependent nuclease
Search with degenerate consensus sequence (Fig. 4A) TATCCYCTCCRGGRGGATA
CATCCTCCCCGGGGGGATA	1,073,223	1,073,241	+	23.2744	6.29E−9	0.0329	Intergenic	nreA2	Metal-sensing transcriptional regulator
TATCCCCCCCGAGAGGATA	3,145,188	3,145,206	+	23.0244	1.12E−8	0.0329	Intergenic	nreA	Ni-sensing transcriptional regulator
TAACCCCTCGGGGAGGAAA	4,855,066	4,855,084	+	17.7195	1.75E7	0.344	Intergenic	malK-5	Maltose/maltodextrin import ATP binding
TATCCCCTCCTAGAGGTTT	3,437,282	3,437,300	+	13.3963	6.33E−7	0.908	Intergenic	KPGJNAOJ_03459	ATP-dependent nuclease

^a The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.

^b The P value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.

^c The Q value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.

^d The underlined characters match the associated search sequence.