TABLE 3.

M. avium subsp. paratuberculosis predicted coding sequences not present in M. avium subsp. avium, as determined in silico

Contig	Gene	Identification in TB-parsea	Presence of RBSb	No. of amino acidsc	Best BLAST hit (expect value)d
1427	10	Yes	No	322	No similarity
1427	11	Yes	Yes	191	0.99
1467	38	Yes	Yes	173	4.4
1482	48	Yes	Yes	352	3.8
1482	49	Yes	Yes	267	0.95
1482	50	Yes	Yes	293	5.1
1490	56	Yes	Yes	193	No similarity
1490	57	Yes	Yes	103	4.7
1532	93	No	Yes	183	0.009
1553	128	Yes	No	191	7e−07 (hyp. protein)
1556	134	Yes	Yes	143	2.8
1556	135	Yes	Yes	157	0.13
1578	159	Yes	Yes	185	2e−04
1602	217	Yes	Yes	106	5.1
1602	218	Yes	Yes	835	0.83
1602	219	Yes	Yes	87	1.1
1605	228	No	No	369	0.86
1612	240	Yes	Yes	223	2.8
1612	241	Yes	Yes	123	1e−05
1614	250	Yes	Yes	199	0.030
1614	251	Yes	No	179	No similarity
1614	252	Yes	Yes	96	No similarity
1614	253	Yes	Yes	74	4.7
1614	254	Yes	Yes	146	9.7
1614	255	Yes	Yes	241	3.6
1614	256	Yes	Yes	141	2.1
1614	257	Yes	Yes	87	0.61

^aTB-parse is the gene prediction program used to annotate the M. tuberculosis genome (6). “Yes,” TB-parse identified the listed M. paratuberculosis gene; “No,” TB-parse did not recognize it as a coding sequence.

^bPresence or absence of a consensus ribosome binding site (RBS).

^cNumber of amino acids encoded by the predicted coding sequence.

^dExpect value of the best match in GenBank. The three predicted coding sequences that contain the highest similarity to a sequence in Genbank are in bold. hyp. protein, hypothetical protein in GenBank.