TABLE 2.

Number of peptides from each individual M. tuberculosis protein binding to three MHC class II alleles^a

Protein	No. of peptides	No. of epitopes				No. of epitopes/peptideb
		DR1	DR2	DR4	Total
Immunogenic protein MPT63 CAB06500	49	4	7	17	28	0.57
PPE family protein CAE55334	137	23	16	25	64	0.47
Probable lipoprotein LPRJ CAB10947	39	3	4	9	16	0.41
Periplasmic phosphate-binding lipoprotein PSTS1 YP_177770	121	17	12	20	49	0.40
Secreted antigen 85-B FBPB (85B) CAB10044	105	16	8	18	42	0.40
10-kDa chaperonin GROES CAB01005	30	6	2	4	12	0.40
PE family protein CAE55335	29	1	2	8	11	0.38
Possible glycosyltransferase CAB05418	139	12	10	28	50	0.36
Secreted ESAT-6-like protein ESXR CAA16104	28	5	0	5	10	0.36
Low-molecular-weight protein antigen 7 ESXH CAA17363	28	3	1	5	9	0.32
Conserved hypothetical protein TB18.5CAD93033	50	6	4	6	16	0.32
Probable isocitrate dehydrogenase CAA16247	245	30	9	28	67	0.27
Possible hemolysin-like protein CAA17201	77	9	3	9	21	0.27
Heat shock protein HSPX CAA17245	44	3	3	6	12	0.27
Immunogenic protein MPT64 CAA98382	72	8	2	8	18	0.25
Possible glycosyltransferase CAB05415	146	10	7	19	36	0.25
Putative cyclopropane-fatty-acyl-phospholipid synthase UFAA1 NP_854118	139	11	6	16	33	0.24
Major secreted immunogenic protein CAA98373	61	2	0	11	13	0.21
Conserved hypothetical protein CFP17 CAB01474	50	2	2	6	10	0.20
Probable isocitrate dehydrogenase CAA17111	133	12	5	9	26	0.20
MCE family protein MCE1AYP_177701	148	15	4	9	28	0.19
Heat shock protein HSP CAA17343	49	2	2	5	9	0.18
Conserved hypothetical protein TB16.3CAD97060	44	5	2	1	8	0.18
Possible hemolysin CAA16235	36	3	1	2	6	0.17
M. bovis mycocerosic acid synthase gene; M95808	700	35	16	61	112	0.16
Probable cutinase precursor CFP21 NP_216500	69	1	3	7	11	0.16
Two-component transcriptional regulatory protein DEVR NP_217649	69	2	5	4	11	0.16
Possible glycosyltransferase CAB05419	88	6	4	4	14	0.16
Probable molybdopterin-guanine dinucleotide biosynthesis protein CAA16030	63	1	3	6	10	0.16
Hypothetical protein RV2623 NP_217139	95	4	0	11	15	0.16
Transmembrane serine/threonine-protein kinase D PKND NP_215446	218	13	7	12	32	0.15
M. bovis acyl-coenzyme A synthase gene; U75685	190	7	6	14	27	0.14
ESAT-6-Like protein ESXQ CAA16102	36	0	1	4	5	0.14
Conserved hypothetical protein TB9.8 CAD93159	29	2	1	1	4	0.14
RNA polymerase beta subunit AAA21416	389	19	11	23	53	0.14
PPE family protein CAE55371	127	4	1	12	17	0.13
Conserved hypothetical protein CAB08634	121	2	2	11	15	0.12
Secreted l-alanine dehydrogenase ALD CAA15575	120	3	1	9	13	0.11
10-kDa culture filtrate antigen ESXB CAA17966	30	0	0	3	3	0.10
3-oxoacyl-[acyl-carrier protein] synthase 2 KASB CAA94642	142	4	3	7	14	0.10
PPE family protein YP_177963	1,037	33	24	44	101	0.10
MTB81	243	7	10	6	23	0.09
Low-molecular-weight T-cell antigen TB8.4 NP_215690	33	0	1	2	3	0.09
Iron-regulated conserved hypothetical protein CAB08889	45	0	0	4	4	0.09
MTB48 AAK31576	150	4	3	6	13	0.09
Probable serine protease PEPD CAA17582	151	4	3	6	13	0.09
Cell surface lipoprotein MPT83 CAA98350	70	2	0	4	6	0.09
Probable serine protease PEPA CAB09453	115	0	1	8	9	0.08
60-kDa chaperonin 2 P0A521	176	3	5	5	13	0.07
Conserved hypothetical protein CAA15739	39	0	0	2	2	0.05
Conserved hypothetical protein CAB06237	130	0	3	2	5	0.04
Probable 50S ribosomal protein L7/L12 RPLL CAB07109	40	0	0	1	1	0.03
Alternate RNA polymerase sigma factor SIGF CAB07069	83	0	0	2	2	0.02
Lipoprotein LPQH precursor P0A5J0	49	0	0	1	1	0.02

^aDRB1*0101, DRB1*1501, and DRB1*0401.

^bThe “epitope density” of each protein.