Table 2.

Detection of exact sigma consensus sequences in the complete M. tuberculosis H37Rv genome by MyPatternFinder

Sigma factor	Consensus sequence (Ref.)	Total number of hits	Genea,b	Distance from start codonc
SigA	TTGACW-N17-TATAMTd (15)	0	–	–
	TTGACW-N16–21-TATAMT (15,17)	0	–	–
	TTGACW-N16–21-TATAMT (15,17)	20e	Rv0068f	−84
			Rv0305c (PPE)	−163
			Rvnr01 (16S rRNA)	−225
			Rv1403c	−84
			Rv2011cf	−50
			Rv2487c (PE_PGRS)	−288
			Rv2578cf	−35
			Rv3082c (virS)f	−44
			Rv3760	−485
SigF	GTTT-N17-GGGTAT (15)	4	Rv1248c (sucA)	−358
			Rv3287c (rsbW/usfX)g	−35
			Rv3349c	−264
SigH	SGGAAC-N17–22-SGTTS (15)	150	Rv0384c (clpB)g	−72
			Rv0474	−150
			Rv0563 (htpX)	−78
			Rv0569	−475
			Rv1072	−79
			Rv1535	−93
			Rv1786	−448
			Rv1792	−112
			Rv1883c	−217
			Rv2018	−182
			Rv2184c	−178
			Rv2308	−34
			Rv2334 (cysK)	−364
			Rv2373c (dnaJ2)	−138
			Rv2466cg	−77
			Rv2525c	−345
			Rv2694c	−96
			Rv2745c	−66
			Rv2804c	−384
			Rv2839c (infB)	−313
			Rv3179	−321
			Rv3482c	−248
			Rv3597c (lsr2)	−203
			Rv3832c	−481
			Rv3913 (trxB2)g	−66

^aGene is reported only if the distance of consensus sequence is ≤500 bp upstream of the start codon and it has a non-coding upstream region of ≥25 bp.

^bAccording to Cole et al. (36).

^cLocation is relative to the translation start site as determined at http://genolist.pasteur.fr/TubercuList, except for Rv3287c (rsbW/usfX), where location is relative to transcription start site according to Beaucher et al. (37).

^dW = A/T; M = A/C; S = G/C.

^eBy allowing one mismatch in the consensus sequence.

^fAlso predicted to be an E. coli σ⁷⁰ promoter with one mismatch.

^gInvolvement of the particular sigma factor has been experimentally verified (37,38).