Table 2.

Number of Motifs Scoring Above Different Cutoffs

Cutoffs		Number of motifs found in all organisms
Cutoffs		WIT		KEGG		Regulons		total
MAP	S _site	additional	indiv.	pooled	indiv.	indiv.	pooled	total
0	1	(no cutoffs)	22,134	32,760	21,677	9967	17,744	104,282
5	1		4924	4228	13,416	4696	2988	30,252
10	1		2706	1829	8484	2830	1480	17,329
5	1e-10		606	252	2035	794	219	3906
10	1e-10		316	125	1231	485	147	2304
10	1e-15		63	20	321	139	50	593
10	1e-20		7	4	90	58	24	183
10	1e-25		0	2	23	18	16	59
10	1e-10	pal	18	27	128	74	53	300
10	1e-10	pal, AT < 80	7	23	44	50	42	166

↵See Table 1.
↵May contain multiple instances of the same motif (motifs are not clustered by similarity).
↵Groups derived from conserved gene adjacencies from the WIT database (Overbeek et al., 1999).
↵Groups derived from KEGG metabolic pathways (Ogata et al., 1999).
↵Groups derived from E. coli footprinted regulons.
↵AlignACE runs in individual organisms.
↵AlignACE runs on groups of closely related organisms pooled together.

Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes