TABLE 3.

LSP groups and their attributes

Group	LSP	Locusa	Coordinatesb	Gene	Other genes in deleted region in CDC1551 or H37Rv reference strainsc	Strain(s) containing adjacent IS6110	No. of independent LSP deletions
A	1	MT0676	744149-744392	Alpha-mannosidase			1
	9	MT2081, MT2082	2268479-2268702	Hypd/helicase	MT2080 (Hyp) and MT2080.1 (Hyp)		1
	13	Rv0793, Rv0794c	886934-887397	Hyp/dihydrolipoamide dehydrogenase			1
	16	Rv3519	3955704-3956104	Hyp			1
B	12	MT2423	2633331-2633746	PPE		H37Rv	2
	14	Rv2124c	2381785-2383193	Methionine synthase			2
C	2	MT1360	1481322-1481551	Adenylate cyclase			7
	3	MT1802	198225-1982482	Transporter		H37Rv and CDC1551	5
	4	MT1799	1978754-1978931	Phospholipase	MT1800 (glycosyl transferase), MT1801 (molybdopterin oxidoreductase), MT1802 (mmpL family)	H37Rv and CDC1551	6
	5	MT1812	1994163-1994437	Hyp		H37Rv and CDC1551	4
	6	MT2420	2630855-2631147	Hyp	MT2421 (Hyp)		7
	7	MT2619	2862884-2863033	Membrane lipoprotein			5
	8	MT3248	3526018-3526304	PPE			4
	10	MT3426	3705322-3705665	moaB	MT3427 (moaA), MT3428 (transcript. regulator), MT3429 (Hyp), MT3430 (IS1547, transposase)	H37Rv	6
	11	MT3427	3707462-3707706	moaA	MT3426 (pterin dehydratase), MT3428-MT3430 (see above)	H37Rv	4
	15	Rv3135	3501335-3501499	PPE			3
	17	Rv3343c	3733083-3733353	PPE			6

^aThe MT prefix indicates LSPs present in CDC1551 and absent in H37Rv; the Rv prefix indicates LSPs present in H37Rv but absent in CDC1551.

^bCoordinates of the LSP probes. Note that probes for LSPs 1 to 12 are CDC1551 coordinates (GenBank accession number NC_002755) and probes for LSPs 13 to 17 are H37Rv coordinates (GenBank accession number NC_000962).

^cCoordinates for all LSPs in the reference strains have been described previously (16).

^dHyp, hypothetical.