TABLE 1.

Proteins showing differential expression on 2-D gels

Spot no.	Protein	Differential expressiona
		Acetate in W3110 (Fig. 2A)	ackA-pta/W3110 (Fig. 2B)	Formate in W3110 (Fig. 3A)	Formate in ackA-pta (Fig. 3B)	Acetate in ackA-pta (Fig. 4A)	Acetate in W3110 (glycerol) (Fig. 4B)
1		−0.68 ± 0.37				−0.41 ± 0.08
2	OppAb	+	+				(−)
3	OppA	0.46 ± 0.12	0.43 ± 0.15				−0.55 ± 0.11
4	OppA	0.38 ± 0.20	0.45 ± 0.19				−0.26 ± 0.07
5		0.25 ± 0.10
6		+	(+)		(−)	−0.38 ± 0.20
7		(+)	+		−1.11 ± 0.16
8	TnaAc	−			−	−0.70 ± 0.30
9				0.79 ± 0.23
10		−0.55 ± 0.11
11				(+)
12		(+)
13	MalE						−0.81 ± 0.20
14		−
15		−
16		−
17	PfkB	0.40 ± 0.06	0.36 ± 0.10	−0.22 ± 0.12
18			0.32 ± 0.10
19		(−)
20							0.29 ± 0.09
21		(+)	(+)		−
22			0.45 ± 0.18	0.35 ± 0.16
23		(−)
24		−0.29 ± 0.16
25	OmpC		0.55 ± 0.33				(+)
26	Pta	−0.38 ± 0.08	−
27		(+)					0.32 ± 0.16
28							+
29		0.43 ± 0.17		−0.32 ± 0.17
30	ProX	0.38 ± 0.10			0.32 ± 0.21		−0.68 ± 0.22
31						−
32							0.46 ± 0.09
33							0.39 ± 0.09
34	MglB	−0.42 ± 0.12				−0.49 ± 0.10
35		−	(−)
36		+					+
37		+					0.55 ± 0.46
38	GatY	0.53 ± 0.15		−0.24 ± 0.10	−0.35 ± 0.20		0.40 ± 0.23
39			0.71 ± 0.09
40	SucB			−0.32 ± 0.13
41		+		−0.61 ± 0.11	−0.45 ± 0.31
42							0.43 ± 0.18
43		+	(+)		−0.62 ± 0.25
44	Lpd					−0.33 ± 0.21
45		(+)
46		(+)	(+)	−0.47 ± 0.11	−0.52 ± 0.39	−0.38 ± 0.12	−0.34 ± 0.20
47				+
48	FliY	0.28 ± 0.06	0.36 ± 0.08
49	ArtI	0.26 ± 0.10		−0.22 ± 0.06
50		+
51		−	−0.33 ± 0.15			0.42 ± 0.43
52				(+)	0.90 ± 0.45
53		+	(+)	(+)
54	WrbA	0.29 ± 0.09	0.34 ± 0.11
55		+
56			0.73 ± 0.52
57		+
58	Ppa					0.23 ± 0.09
59			+				0.46 ± 0.09
60		(−)		0.74 ± 0.10	+
61		0.74 ± 0.17					−0.32 ± 0.08
62	LuxS	0.40 ± 0.10
63	OsmY	0.45 ± 0.11	0.50 ± 0.20	−0.34 ± 0.14	−0.35 ± 0.15
64	DksA	−0.34 ± 0.10
65	AroK	−0.39 ± 0.16	−0.32 ± 0.10
67		+
68				(+)	0.30 ± 0.17
69						0.33 ± 0.11
70			−0.31 ± 0.19	−0.23 ± 0.08
71				−0.26 ± 0.10	−0.31 ± 0.15
72		0.24 ± 0.12	0.28 ± 0.14	−0.37 ± 0.10	−0.50 ± 0.18
73	TpiA		0.32 ± 0.24
74		+					0.51 ± 0.36
75		(+)	+		(−)
76		0.58 ± 0.43
77		(+)
78	YfiD	0.32 ± 0.11					0.39 ± 0.09
79		(−)
80							0.43 ± 0.29
81	HdeB	(+)	(+)		(−)
82	HdeA	0.41 ± 0.13	0.42 ± 0.18	−0.93 ± 0.24	−
83	GuaB			−0.42 ± 0.25		−0.50 ± 0.15
84							0.38 ± 0.07

^aRelative protein expression shown as LDE ± standard deviation (n = 9) determined as described in Materials and Methods. +, spot unmatched on reference gel (i.p., protein induced in the comparative condition compared to the reference condition); −, repressed; (+), (−), spot showing differential expression based on visual inspection, though not quantifiable by the Z3 software. The column headers indicate the comparative gel/the reference gel, with the figure number of the layered view in parentheses. 

^bProtein identified based on position (http://www.expasy.ch/). 

^cProtein identified based on position and on inducibility at high pH (9).