Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

Table 7 Motifs passing our set of stringent filters, ranked by their degree of conservation

k^a	Cluster #	Motif	MAP score^b	Specificity^c	Known^d	Palind-romicity^e	Conser-vation^f	Motif Logo^g
100	71	1	65.6	1.8E-29	KstR	0.93	46
250	179	1	88.6	4.8E-26	KstR	0.71	43
50	35	1	87.4	1.8E-19	KstR	0.79	40
200	182	1	94.2	5.7E-28	KstR	0.80	36
100	73	2	31.3	1.5E-32	IdeR	0.85	30
100	49	15	16.3	2.8E-18	KstR	0.71	29
250	112	1	25.5	2.1E-25	DosR	0.76	21
100	80	1	15.0	2.2E-14		0.92	21
50	29	1	15.0	2.2E-14		0.92	21	X
50	23	31	21.7	6.7E-24		0.71	18
200	47	64	7.2	1.2E-15		0.75	16
250	87	1	22.1	1.5E-13	ZurB	0.94	16
200	6	1	16.3	2.0E-12	IdeR	0.70	16
200	184	19	12.1	4.7E-13		0.75	16
250	123	18	14.5	3.7E-11		0.82	16
250	224	1	26.9	6.2E-24	DosR	0.73	15
200	46	3	19.8	1.6E-12		0.78	15
100	5	25	12.4	3.8E-15		0.71	14
200	120	62	15.3	2.0E-14		0.74	14
200	71	9	16.6	2.3E-16		0.75	14
200	195	1	25.4	7.2E-26	DosR	0.76	14
50	48	1	68.8	6.4E-35	DosR	0.86	13
100	74	1	66.9	3.6E-34	DosR	0.88	13
50	23	12	26.8	5.0E-22		0.73	13
250	89	1	46.636	4.0E-20		0.75	12
100	81	84	6.4	2.3E-16		0.71	12
250	92	6	5.7	3.7E-17	DosR	0.73	12
100	52	91	9.7	1.5E-18		0.76	11
200	91	1	47.1	4.7E-20		0.70	10
50	36	43	34.8	4.6E-30		0.72	10
100	42	4	15.3	2.8E-17		0.70	10
200	80	9	8.5	4.0E-13		0.72	10
50	43	7	15.7	8.7E-12		0.72	10
50	36	21	48.5	5.3E-12		0.71	10
200	26	17	7.5	2.1E-12		0.70	9
50	6	61	6.3	1.2E-11		0.73	9
50	11	43	13.7	1.4E-11		0.72	14

^ak indicates the value of k in the k-means clustering process (50, 100, 200, or 250)
^bMAP score indicates the AlignACE MAP score [76]
^cSpecificity score [77]
^dCompareACE score ≥ 0.7 to the alignment for this known motif
^eCompareACE score to its reverse complement
^fnumber of ScanACE hits in the genome that are conserved in ≥ 8 genomes
^gsequence logo [78]

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