. 2009 Apr 29;4(4):e5368. doi: 10.1371/journal.pone.0005368

Table 2. List of differentially expressed proteins identified by MALDI-TOF-MS.

Spot no	NCBI GI	Locus	Gene	Protein description	Theoretical/Exptl		sequence coverage	COG^a	Location^b	Change fold^c
					MW(kDa)	pI
Energy production and conversion
Q39	gi\|17986535	BMEI0251	atpD	ATP synthase subunit B	55/34	5.48/4.95	0.51	C	U	Y
Q1	gi\|17989212	BMEII0867	adh	alcohol dehydrogenase class III	40/41	6.03/6.63	0.29	C	C	−6.7
Q47	gi\|17988739	BMEII0394	-	glycerol trinitrate reductase	40/43	5.80/5.91	0.35	C	C	−4.8
Q77	gi\|17986535	BMEI0251	atpD	ATP synthase subunit B	55/31	5.48/4.88	0.31	C	U	−2.6
Q3	gi\|17989214	BMEII0869	putA	succinate-semialdehyde dehydrogenase (NADP+)	52/46	6.42/6.42	0.41	C	C	−2.0
Q74	gi\|17986422	BMEI0138	sucC	succinyl-CoA synthetase subunit beta	43/44	4.90/5.03	0.54	C	C	−2.0
Q4	gi\|17988102	BMEI1819	adh	alcohol dehydrogenase class III	40/44	5.72/6.18	0.44	C	C	2.0
Amino acid transport and metabolism
Q27	gi\|17989216	BMEII0871	aroE	shikimate 5-dehydrogenase	30/31	5.99/6.64	0.27	E	U	−4.0
Q10	gi\|17987926	BMEI1643	argE	N-carbamoyl-L-amino acid amidohydrolase	45/51	5.17/5.30	0.36	E	C	−2.9
Q51	gi\|17989218	BMEII0873	livF	high-affinity branched-chain amino acid transport ATP-binding protein LivF	28/30	6.99/6.45	0.70	E	C	−2.7
Q49	gi\|17987935	BMEI1652	ureC	urease subunit alpha	61/33	5.43/5.97	0.31	E	C	−2.6
Q7	gi\|17988264	BMEI1981	-	aminopeptidase T	46/45	5.65/5.90	0.32	E	C	−2.5
Q50	gi\|17987454	BMEI1171	argC	N-acetyl-gamma-glutamyl-phosphate reductase	34/37	5.89/6.27	0.54	E	C	−2.2
Q35	gi\|17987387	BMEI1104	-	arginine/ornithine-binding periplasmic protein precursor	27/31	4.77/4.72	0.61	ET	P	T
Q53	gi\|17988946	BMEII0601	-	cystine-binding periplasmic protein precursor	28/30	7.74/6.77	0.54	ET	P	9.3
Q65	gi\|17988895	BMEII0550	proX	glycine betaine/l-proline-binding protein ProX	32/32	5.57/5.34	0.58	E	P	2.2
Q71	gi\|17988978	BMEII0633	livK	leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein precursor	39/40	5.52/5.62	0.56	E	P	2.2
Q54	gi\|17988946	BMEII0601	-	cystine-binding periplasmic protein precursor	28/30	7.74/6.90	0.54	ET	P	2.1
Nucleotide transport and metabolism
Q30	gi\|17987061	BMEI0778	adk	adenylate kinase	21/31	6.63/6.59	0.57	F	C	−2.1
Carbohydrate transport and metabolism
Q34	gi\|17988062	BMEI1779	pfkB	Fructokinase	36/42	4.85/4.94	0.60	G	C	T
Q43	gi\|17986593	BMEI0310	gapA	glyceraldehyde-3-phosphate dehydrogenase	36/38	6.13/6.91	0.71	G	C	2.7
Lipid transport and metabolism
Q63	gi\|17988859	BMEII0514	fabG	3-ketoacyl-(acyl-carrier-protein) reductase	27/31	5.44/5.52	0.59	IQR	C	−3.2
Q73	gi\|17988206	BMEI1923	caiA	isovaleryl-CoA dehydrogenase	42/42	5.36/5.33	0.53	I	U	−2.2
Q44	gi\|17986323	BMEI0039	accA	acetyl-CoA carboxylase carboxyltransferase subunit alpha	35/34	6.14/6.62	0.70	I	C	−2.1
Q9	gi\|17988206	BMEI1923	caiA	isovaleryl CoA dehydrogenase	41/42	5.36/5.45	0.44	I	U	−2.0
Q72	gi\|17987756	BMEI1473	-	3-oxoacyl-(acyl carrier protein) synthase II	44/48	5.36/5.50	0.49	IQ	C	2.3
Translation
Q8	gi\|17987120	BMEI0837	gltX	glutamyl-tRNA synthetase	55/49	5.85/5.66	0.42	J	C	−6.4
Q24	gi\|17988198	BMEI1915	rpsA	30S ribosomal protein S1	64/33	5.19/5.67	0.20	J	C	−3.9
Q46	gi\|17983840	BMEI1806	trpRS	tryptophanyl-tRNA synthetase	42/41	6.28/6.02	0.27	J	C	−2.6
Q31	gi\|17987025	BMEI0742	tuf	elongation factor Tu	43/43	5.29/5.57	0.54	J	C	T
Q64	gi\|17988070	BMEI1787	raiA	putative sigma54 modulation protein/SSU ribosomal protein S30P	22/31	5.24/5.50	0.67	J	U	2.9
Transcription
Q26	gi\|17989223	BMEII0878	gntR	transcriptional regulator, GntR family	26/32	6.15/6.61	0.47	K	C	−12.2
Q29	gi\|17989461	BMEII1116	vjbR	transcriptional activator, LuxR family	26/32	6.21/6.41	0.80	K	U	−2.0
Cell wall/membrane biogenesis
Q13	gi\|17989189	BMEII0844	omp31	31 kDa outer-membrane immunogenic protein precursor	23/45	5.21/5.08	0.38	M	OM	Y
Q15	gi\|17988112	BMEI1829	omp25c	25 KDa outer-membrane immunogenic protein precursor	25/45	4.79/4.57	0.42	M	OM	Y
Q36	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/30	8.58/5.26	0.31	M	OM	Y
Q37	gi\|17988725	BMEII0380	acrA	acriflavin resistance protein A precursor	42/41	5.68/5.51	0.30	M	CM	Y
Q38	gi\|17987010	BMEI0727	ddl	D-alanine–D-alanine ligase A	39/43	4.96/5.17	0.41	M	C	Y
Q19	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/28	8.58/5.07	0.47	M	OM	−34.8
Q17	gi\|17988112	BMEI1829	omp25c	25 KDa outer-membrane immunogenic protein precursor	25/31	4.79/4.37	0.42	M	OM	−19.9
Q23	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/26	8.58/5.67	0.31	M	OM	−19.2
Q22	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/27	8.58/5.26	0.44	M	OM	−9.6
Q12	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/41	8.58/5.26	0.50	M	OM	−9.1
Q18	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/28	8.58/4.88	0.21	M	OM	−8.6
Q16	gi\|17987290	BMEI1007	omp25a	25 KDa outer-membrane immunogenic protein precursor	25/34	4.72/4.37	0.42	M	OM	−5.7
Q58	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/25	8.58/5.68	0.62	M	OM	−3.9
Q11	gi\|17989189	BMEII0844	omp31	31 kDa outer-membrane immunogenic protein precursor	23/48	5.21/5.20	0.38	M	OM	−3.1
Q20	gi\|17987532	BMEI1249	omp25	25 KDa outer-membrane immunogenic protein precursor	23/28	8.58/4.69	0.41	M	OM	−2.8
Q76	gi\|17989189	BMEII0844	omp31	31 kDa outer-membrane immunogenic protein precursor	23/32	5.21/4.88	0.49	M	OM	−2.1
Posttranslational modification, protein turnover, chaperones
Q14	gi\|17988285	BMEI2002	dnaK	molecular chaperone DnaK	69/40	4.86/4.82	0.16	O	C	Y
Q75	gi\|17988746	BMEII0401	-	thioredoxin	35/37	4.94/5.03	0.37	O	C	−2.9
Q6	gi\|17987613	BMEI1330	htrA	protease DO	53/40	5.81/5.99	0.17	O	U	−2.4
Q68	gi\|17989393	BMEII1048	groEL	chaperonin GroEL	57/34	5.04/5.13	0.27	O	C	−2.3
Q40	gi\|17987352	BMEI1069	tf	trigger factor	54/58	4.94/5.07	0.55	O	C	−2.0
Inorganic ion transport and metabolism
Q60	gi\|17988349	BMEII0005	modA	molybdate-binding periplasmic protein	25/29	5.31/5.44	0.45	P	P	−2.2
Q32	gi\|17988929	BMEII0584	afuA	iron(iii)-binding periplasmic protein precursor	36/38	5.20/5.17	0.49	P	P	−2.0
Q28	gi\|17988124	BMEI1841	sbp	sulfate-binding protein precursor	36/41	5.47/6.07	0.34	P	P	4.0
Q69	gi\|17986956	BMEI0673	cysP	thiosulfate-binding protein precursor	37/37	5.31/5.23	0.29	P	P	2.3
Q70	gi\|17986956	BMEI0673	cysP	thiosulfate-binding protein precursor	37/37	5.31/5.34	0.41	P	P	2.3
Q62	gi\|17988952	BMEII0607	fatB	ferric anguibactin-binding protein	31/33	5.36/5.64	0.34	P	P	2.2
General function prediction only
Q5	gi\|17987208	BMEI0925	adh	alcohol dehydrogenase	35/37	5.56/5.99	0.28	R	C	Y
Q21	gi\|17986557	BMEI0273	glcG	GlcG protein	14/21	5.10/5.39	0.61	R	U	−5.0
Q48	gi\|17989217	BMEII0872	fabG	3-ketoacyl-(acyl-carrier-protein) reductase	28/36	5.57/6.07	0.45	QR	C	−3.0
Q33	gi\|17988824	BMEII0479	-	ABC transporter substrate-binding protein	40/40	5.11/5.33	0.39	R	U	3.5
Q52	gi\|17987518	BMEI1235	fabG	short-chain dehydrogenase	25/29	6.15/6.79	0.61	QR	C	3.4
Intracellular trafficking and secretion
Q25	gi\|17986405	BMEI0121	secA	protein translocase, chain secA	103/31	5.15/5.66	0.20	U	C	−5.3
Function unknown
Q59	gi\|17986596	BMEI0313	zapA	Hypothetical Cytosolic Protein	13/15	4.78/4.81	0.84	S	C	−2.5
Q42	gi\|17987476	BMEI1193	-	cell wall degradation protein	45/43	7.03/6.90	0.45	S	U	2.2
not in COGs
Q41	gi\|17986462	BMEI0178	-	hypothetical protein BMEI0178	18/52	4.79/5.03	0.66	-	U	−5.9
Q56	gi\|17986457	BMEI0173	-	YciI-like protein	40/14	5.52/5.74	0.92	-	U	−5.0
Q45	gi\|17988858	BMEII0513	gpd	glucose-6-phosphate 1-dehydrogenase	55/31	5.74/6.54	0.28	-	U	−3.6
Q61	gi\|17988500	BMEII0156	motD	chemotaxis motd protein	40/31	5.12/5.82	0.17	-	C	−2.5
Q2	gi\|17987549	BMEI1266	pdxA	4-hydroxythreonine-4-phosphate dehydrogenase	43/39	9.13/6.63	0.40	-	C	−2.3
Q78	gi\|17986825	BMEI0542	-	hypothetical protein BMEI0542	30/30	4.83/4.79	0.64	-	U	−2.2
Q57	gi\|17986528	BMEI0244	-	putative translaldolase	23/30	5.69/5.72	0.60	-	U	2.8
Q55	gi\|17987937	BMEI1654	-	urease gamma subunit	9/14	5.54/6.49	0.89	-	C	2.1

Abbreviation of cellular role categories of theoretical (http://www.ncbi.nlm.gov/COG/).

Abbreviation of cellular location. Protein cellular location was annotated by PSORTb V. 2.0 (http://www.psort.org/). C: Cytoplasmic, P: Periplasmic, U: Unknown, OM: OuterMembrane, CM: CytoplasmicMembrane.

Proteins upshifted in the BMΔvirB mutant are marked with “+”, and those downshifted with “−”; unique protein spots in BM are marked with “Y”, and in BMΔvirB with “T”.