TABLE 2.

Mass spectrometric identification of proteins from D. vulgaris separated by 2DE

Spot no.a	IDb	Sequence coverage (%)c	Significanced	pIe	Mrf	Locationg	Possible function (gene)h
1a	ORF02977	32	5.8 e-22	6.8	41.8	C	Alcohol dehydrogenase
1b	ORF02977	44	5.7 e-27	6.8	41.8	C	Alcohol dehydrogenase
2	ORF03570	26	3.0 e-06	6.0	28.5	P	Conserved hypothetical protein (periplasmic)
3	ORF04254	13	1.5 e-04	6.7	28.4*	C	Ubiquinone/menaquinone biosynthesis methyltransferase (ubiE)
4	ORF02836	68	6.5 e-50	5.1	94.1*	M	Cation-transporting ATPase, E1-E2 family
5	ORF02836	58	2.0 e-37	5.1	94.1*	M	Cation-transporting ATPase, E1-E2 family
6	ORF00572	40	1.9 e-31	4.7	87.1*	C	PTS system, fructose-specific EIIA/HPr/EI components (ptsI)
7	ORF00572	41	7.7 e-39	4.7	87.1*	C	PTS system, fructose-specific EIIA/HPr/EI components (ptsI)
8	ORF00988	63	1.4 e-29	5.8	26.8	P	Arginine ABC transporter, periplasmic arginine-binding protein, putative
9	ORF02865	52	1.3 e-19	7.0	29.7	P	Amino acid ABC transporter, amino acid-binding protein, putative
10	ORF00176	32	2.1 e-14	7.1	30.4	P	Amino acid ABC transporter, amino acid-binding protein, putative
11	ORF04661	42	1.1 e-19	4.9	20.2	C	Nigerythrin
12	ORF04056	9	2.2 e-04	5.7	63.5*	C	Sensory box/GGDEF family protein
13	ORF00383	56	4.6 e-29	5.0	30.5	C	Translation elongation factor Ts (tsf)
14	ORF00347	54	5.6 e-18	4.9	20.2*	C	Hypothetical protein
15	ORF00590	57	1.4 e-23	5.4	21.2	C	ThiJ/PfpI family superfamily
16	ORF01081	45	2.8 e-37	6.0	47.5	C	Sulfate adenylyltransferase (sat)
17	ORF01081	52	1.7 e-41	6.0	47.5	C	Sulfate adenylyltransferase (sat)
18	ORF03883	69	3.4 e-17	5.4	17.0	C	Nitrogen assimilation regulatory protein (Klebsiella, putative)
19	ORF02097	42	2.4 e-13	4.6	17.7	C	Purine-binding chemotaxis protein CheW (cheW-1)
20	ORF03811	43	5.9 e-25	4.8	43.4	C	Translation elongation factor Tu (tuf)
21	ORF03178	60	1.6 e-36	5.1	41.4	C	Phosphoglycerate kinases
22	ORF03040	54	4.3 e-37	5.3	42.4	C	S-Adenosylmethionine synthetase (metK)
23	ORF01685	46	6.5 e-45	5.2	42.7	C	Aminotransferase, class I (aspC4)
24	ORF04028	42	3.6 e-30	5.2	38.3	C	Aspartate-semialdehyde dehydrogenase (asd)
25	ORF03996	54	1.3 e-37	5.8	36.7	C	Acetate kinase (ackA)
26	ORF05210	26	5.1 e-20	4.9	28.9	C	3-Deoxy-d-manno-octulosonate cytidylyltransferase (kdsB)
27	ORF04793	58	2.3 e-35	5.5	38.9	P	Periplasmic spermidine/putrescine-binding protein (potD-1)
28	ORF00568	52	3.8 e-42	5.2	38.1	C	Dihydroxyacetone kinase family protein (b1200)

^aSpot numbers in 2DE gels shown in Fig. 1 and 2.

^bIdentification by mass spectrometry in a database of coding genes (http://www.tigr.org). Spots 1a and 1b were also identified by N-terminal sequence analysis.

^cExtent to which the combined peptide masses cover the indicated sequence. Low coverage of proteins 3 and 12 was due to problems with mass spectrometry calibration and N-terminal truncation, respectively.

^dSignificance of the match between experimental and theoretical peptide masses as expressed by the probability that the match is due to random chance.

^epI is the average theoretical value calculated with programs found at http://www.embl-heidelberg.de/cgi/pi-wrapper.pl and http://www.biologie.uni-freiburg.de/data/PcIP.html.

^fM_r is the theoretical molecular mass derived from the genome sequence. *, disagreement with M_r observed in Fig. 3.

^gMost likely location—periplasmic (P), cytoplasmic (C), or in the membrane (M)—based on evaluation of the amino acid sequence.

^hAnnotated function.