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Table 2.

Number of Motifs Scoring Above Different Cutoffs

Cutoffs[i]		Number of motifs found in all organisms[ii]
Cutoffs[i]		WIT[iii]		KEGG[iv]		Regulons[v]		total
MAP	S _site	additional	indiv.[vi]	pooled[vii]	indiv.[vi]	indiv.[vi]	pooled[vii]	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

[i] See Table 1.

[ii] May contain multiple instances of the same motif (motifs are not clustered by similarity).

[iii] Groups derived from conserved gene adjacencies from the WIT database (Overbeek et al., 1999).

[iv] Groups derived from KEGG metabolic pathways (Ogata et al., 1999).

[v] Groups derived from E. coli footprinted regulons.

[vi] AlignACE runs in individual organisms.

[vii] AlignACE runs on groups of closely related organisms pooled together.