Table 2.

Genes repressed in wild-type M. avium subsp. paratuberculosis, relative to the levels for the M. paratuberculosis ΔsigH mutant following diamide exposure^a

Functional classification	Geneb	Fold expression	FDR P value correction	Old locus tagc	M. tuberculosis ortholog	Protein similarity
Lipid metabolism	fadE3_2	−2.64	0.00	MAP3651c	Rv0215c	90.65
	fadE26_2	−2.72	0.00	MAP2585	Rv3504	65.58
	fadD36	−3.15	0.01	MAP2580c	Rv1193	75.89
	echA14	−3.60	0.00	MAP2306	Rv2486	75.39
	MAPK_2175	−3.81	0.00	MAP1593	Rv1136	55.55
	fadA6_4	−5.15	0.00	MAP3337	Rv3556c	61.05
	fadE14	−5.42	0.00	MAP1553c	Rv1346	84.55
	fadD33_2	−5.60	0.00	MAP1554c	Rv1345	75.09
	mbtC	−3.29	0.00	MAP2175c	Rv2382c	78.87
	MAPK_1126	−4.10	0.00	MAP2642	Rv1665	60.23
	papA3_2	−4.22	0.00	MAP3763c	Rv3820c	66.73
	mbtD	−4.43	0.00	MAP2174c	Rv2381c	52.68
	mbtA	−4.51	0.00	MAP2178	Rv2384	76.87
	MAPK_0028	−4.86	0.00	MAP3740	Rv0035	51.42
	pks2	−5.62	0.00	MAP3764c	Rv1180	79.08
	MAPK_1764	−2.63	0.00	MAP2004	Rv2251	83.94
	MAPK_0895	−4.36	0.00	MAP2873c	Rv2247	47.36
	MAPK_2213	−7.33	0.00	MAP1555c	Rv1344	97.01
Amino acid biosynthesis	trpE2	−2.70	0.00	MAP2205c	Rv2386c	79.33
	metA	−2.70	0.00	MAP3458	Rv3341	75.53
	metC	−2.73	0.00	MAP3457	Rv3340	90.13
	leuD	−3.79	0.00	MAP3025c	Rv2987c	97.19
	leuC	−4.10	0.00	MAP3026c	Rv2988c	92.96
	hacA	−11.23	0.00	MAP2255	Rv2988c	50.28
	argC	−2.80	0.00	MAP1361	Rv1652	83.58
Detoxification	ahpC	−12.47	0.00	MAP1589c	Rv2428	93.33
	ahpD	−15.40	0.00	MAP1588c	Rv2429	78.85
Cell envelope associated	MAPK_0029	−5.69	0.00	MAP3739c	Rv2846c	46.68
	MAPK_0769	−5.93	0.00	MAP2999	Rv2963	79.31
	MAPK_0033	−6.79	0.00	MAP3735c	Rv1348	54
	MAPK_3788	−10.35	0.00	MAP3786	Rv0290	55.43
	MAPK_3789	−10.73	0.00	MAP3787	Rv0291	79.95

^aThe functional categorization of M. avium subsp. paratuberculosis genes was based on their known functions as assigned in the Integrated Microbial Genomes system (http://img.jgi.doe.gov).

^bImproved annotations according to the revised genome sequence of M. avium subsp. paratuberculosis (35).

^cAnnotations according to Li et al. (32).