Table 2.

Numbers of conformational B cell and T cell (MHC class I and II) epitopes

Proteina	PDB IDb	No. of B cell epitopes at prediction cutoff score					No. of T cell epitopesc
							MHC class I T cell epitopes			MHC class II T cell epitopes
		0.5	0.6	0.7	0.8	0.9	L	I	H	L	I	H
MAP1297	2VEP	5	7	9	3	0	234	1		225	4
MAP1653	1Y25	4	4	2	2	2	155	1		138	12
MAP3393c	1O4V	5	4	4	3	2	158	6	1	149	10
MAP2872cc	2ZAT	4	9	5	5	4	241	7	3	213	13
MAP1589c	2BMX	8	7	6	3	3	183	3	1	181
MAP4340	1NW2	8	7	2	2	1	106	3		103
MAP2698ca	1ZA0	7	7	7	4	3	249	9	9	256	5
MAP1168cb	1EZW	9	7	6	4	2	288	7	2	267	20	4
MAP3567ac	1ZBQ	10	12	9	5	2	268	7	4	268	5
MAP1017c	3H81	7	7	6	4	3	249	4	2	249
MAP2487c	1YLK	5	6	4	2	2	148	6		140	9
MAP3268	1SHS	4	4	5	4	2	138	1	1	133
MAP1698c	1SHS	8	8	6	4	2	133	4	1	131	1
MAP3651cac	2PGO	10	10	10	10	6	381	10	6	381	10
MAP3523cabc	2Q27	9	7	9	9	5	570	13	3	539	41
MAP0187cb	1GN3	6	7	4	2	1	188	8	3	175	18
MAP2312cac	1JQI	6	8	7	8	5	364	11	5	373	1
MAP3974c							163	2	1	160

^aProteins are marked as follows. a, proteins with the largest numbers of MHC class I T cell epitopes; b, proteins with the largest numbers of MHC class II T cell epitopes; c, proteins with the largest numbers of conformational B cell epitopes.

^bPDB ID of the 3D structural template for each M. avium subsp. paratuberculosis protein. A detailed description of the source of each template is presented in Table S4 in the supplemental material.

^cL, low-affinity binding; I, intermediate-affinity binding; H, high-affinity binding.