TABLE 2.

SOS boxes identified in the M. tuberculosis genome and potentially LexA-regulated genes^a

No. of mismatches	Position of SOS box in genome sequenceb	Sequence of SOS boxg	Strand	Potential gene or ORF regulated	Location relative to ORFc	Induction ratiof
0	1552510-1552525	tcgaacacatgttcga	−	Rv1378c	+129	15.1 ± 7.0
		tcgaacatgtgttcga	+	Rv1379 (pyrR)	−144	1.7 ± 0.2
	3436770-3436785	tcgaacatgtgttcga	−	Rv3073c	−101	1.1 ± 0.1
		tcgaacacatgttcga	+	Rv3074	−8	21.3 ± 6.6
	3784789-3784804	tcgaacaattgttcga	−	Rv3370c (dnaE2)	−65	13.4 ± 7.6
		tcgaacaattgttcga	+	Rv3371	−142	1.3 ± 0.2
	4221081-4221096	tcgaacgtatgttcga	+	Rv3776	−8	13.1 ± 4.7
1, predicted to bind LexA	79480-79495	tcgaaTatgagttcga	+	Rv0071	−6	2.1 ± 0.8
	400160-400175	tcgaacatacTttcga	−	Rv0335c	−125	1.6 ± 0.4
		tcgaaAgtatgttcga	+	Rv0336	−32	16.1 ± 3.1
	606519-606534	tcgaaAgtatgttcga	+	Rv0515	−32	13.6 ± 3.0
	1117141-1117156	tcgaacgaatgtGcga	−	Rv1000c	−8	6.7 ± 1.4
		tcgCacattcgttcga	+	Rv1001 (arcA)	−44	0.9 ± 0.1
	1928566-1928581	tcgaacatgtAttcga	−	Rv1702c	−6	3.1 ± 0.6
	2358495-2358510	tcgCacacatgttcga	+	Rv2100	+106	6.8 ± 1.3
	2903540-2903555	tAgaacggttgttcga	−	Rv2578c	−24	2.9 ± 0.7
		tcgaacaaccgttcTa	+	Rv2579 (linB)	−99	7.9 ± 2.5
	2925405-2925420	tcgaacgattgttcgG	−	Rv2594c (ruvC)	−37	6.4 ± 1.4
		Ccgaacaatcgttcga	+	Rv2595	−87	1.3 ± 0.2
	3031739-3031754	tcAaacatgtgttcga	−	Rv2719c	−218d	18.1 ± 8.7
		tcgaacacatgttTga	+	Rv2720 (lexA)	−105	7.2 ± 1.6
	3051531-3051546	tcgaacaggtgttcgG	−	Rv2737c (recA)	−123	17.3 ± 3.1
	3453546-3453561	tcgaacgggagttcgC	+
	3811650-3811665	tcgaacatatTttcga	−	Rv3395c	+240	16.8 ± 3.8
1, thought unlikely to bind LexA	6327-6342	Gcgaaccgcagttcga	+
	2265299-2265314	tGgaactgcggttcga	+	Rv2018	+19	1.8 ± 0.5
	2358405-2358420	Gcgaacgacggttcga	−	Rv2099c	−214	1.7 ± 0.2
		tcgaaccgtcgttcgC	+	Rv2100	+16e	6.8 ± 1.3
	2950938-2950953	tcgaacccaagAtcga	+
	3534096-3534111	tcgCacgacggttcga	−	Rv3164c (moxR3)	−207	0.9 ± 0.1
	3640311-3640326	tcgaTcacttgttcga	−	Rv3260c (whiB2)	−186	0.5 ± 0.1
		tcgaacaagtgAtcga	+	Rv3261	−231	0.8 ± 0.1
	3866007-3866022	tcgaacggccgAtcga	+
	3973763-3973778	Acgaaccgcagttcga	−	Rv3534c	−187	1.2 ± 0.2

^aThose potentially LexA-regulated genes which were DNA damage inducible and their induction ratios are highlighted in bold.

^bThe coordinates in the M. tuberculosis genome sequence of the motif matching the SOS box.

^cThe location of the first base of the SOS box relative to the predicted translational start site of the ORF is given; a negative number indicates that the SOS box is upstream and a positive number indicates that it is within the coding region.

^dAlthough Rv2719c is DNA damage inducible, it is not regulated by this site (unpublished data).

^eAlthought Rv2100 is DNA damage inducible, it may not be regulated by this site, as the site at 2358495 is also within the coding region of Rv2100.

^fMean ± standard deviation.

^gThe consensus sequence used to search the genome is in bold, with mismatches from it in uppercase.