Table II. Ubiquitous proteins identified by iTRAQ in the GC cell envelope.

Accession	Name	Gene	Average ratio ± S.D.a			Sb	Tc
			F62:FA1090	MS11:FA1090	1291:FA1090
Extracellular
Q5F7V4	Lipoprotein	NGO1063	1.31 ± 0.26	1.45 ± 0.17	1.18 ± 0.1	Y	N
Outer membrane
Q5F5F6	Adhesin mafA 1/4	mafA1/NGO1067 mafA4/NGO1972	0.63 ± 0.03	1.1 ± 0.01	1.47 ± 0.32	N	N
Q5F9W0	Competence lipoprotein	bamD, comL/NGO0277	1.07 ± 0.09	1.25 ± 0.39	1.06 ± 0.02	Y	N
Q5F679	Efflux pump protein, fatty acid resistance	emrA/NGO1683	1.33 ± 0.22	0.98 ± 0.3	1.42 ± 0.11	N	Y
Q5F651	LPS-assembly protein LptD	lptD, imp, ostA/NGO1715	1.14 ± 0.19	1.34 ± 0.29	1.23 ± 0.1	Y	N
Q5F6J5	OmpA/MotB domain-containing protein	NGO1559	1.33 ± 0.2	1.64 ± 0.31	1.1 ± 0.16	Y	N
Q5F5W8	Outer membrane protein assembly factor BamA	bamA/NGO1801	1.27 ± 0.21	1.15 ± 0.39	1.16 ± 0.03	Y	N
Q5F6I1	Outer membrane protein PIII	rmp/NGO1577	1.22 ± 0.27	1.22 ± 0.17	0.73 ± 0.02	Y	N
Q5F7A4	Nitrite reductased	aniA/NGO1276	1.46 ± 0.26	1.15 ± 0.24	1.13 ± 0.31	Y	Y
Q5F8E4	Periplasmic protein	NGO0834	1.49 ± 0.14	1.16 ± 0.09	0.8 ± 0.07	Y	N
Q5F7F3	Peptidyl-prolyl cis-trans isomerase Ng-MIPe	mip/NGO1225	1.15 ± 0	0.94 ± 0.09	1.17 ± 0.07	Y	Y
Q5F6Q7	Phospholipase	pldA/NGO1492	1.42 ± 0.14	1.37 ± 0.01	1.15 ± 0	N	N
Q5FAG7	Pilus-associated protein	pilC/NGO0055	1.13 ± 0.04	1.14 ± 0.1	1.21 ± 0.14	N	Y
Q5FAC9	Putative pilus assembly protein	pilN/NGO0097	1.01 ± 0.05	1.13 ± 0.06	1.31 ± 0.03	N	N
Q5F7H3	Putative TonB-dependent receptor protein	NGO1205	0.88 ± 0.04	1.11 ± 0.03	0.67 ± 0.13	Y	N
Q5F518	Putative uncharacterized protein	NGO2121	0.69 ± 0.05	1.14 ± 0.09	0.83 ± 0.06	Y	N
Q5F526	Putative uncharacterized protein	NGO2111	1.08 ± 0.18	0.82 ± 0.04	0.81 ± 0.01	N	Y
Q5F5E4	Putative uncharacterized protein	NGO1985	0.88 ± 0.06	1.17 ± 0.01	0.83 ± 0.04	N	N
Q5F5H0	Putative uncharacterized protein	NGO1956	1.18 ± 0.08	1.4 ± 0.17	1.41 ± 0.02	N	N
Q5F5H1	Putative uncharacterized protein	NGO1955	1.2 ± 0.1	1.15 ± 0.24	1.15 ± 0.1	N	N
Q5F743	Putative uncharacterized protein	NGO1344	1.01 ± 0.05	1.05 ± 0.14	0.9 ± 0.11	N	N
Q5FAD2	Type IV pilus biogenesis and competence protein pilQ	pilQ, omc/NGO0094	1.12 ± 0.19	1.15 ± 0.09	0.89 ± 0.13	Y	N
Periplasmic
Q5F601	Catalase	katA/NGO1767	0.92 ± 0.05	1.09 ± 0.39	0.97 ± 0.05	N	N
Q5F544	Ferric enterobactin periplasmic binding protein	fetB/NGO2092	1.06 ± 0.06	0.99 ± 0.33	1.27 ± 0.09	N	N
Q5F581	Genome-derived Neisserial antigen 33	NGO2048	1.38 ± 0.21	1.24 ± 0.01	1.28 ± 0.04	Y	N
Q5F809	Lipid modified azurin protein	azu/NGO0994	1.09 ± 0.24	1.07 ± 0.04	1.15 ± 0.01	Y	Y
Q5F765	Lipoprotein	NGO1321	1.14 ± 0.25	1 ± 0.32	1.1 ± 0.08	N	N
Q5F848	Lipoprotein	NGO0948	1.47 ± 0.21	1.34 ± 0	1.05 ± 0.02	N	N
Q5F8T2	Lipoprotein	NGO0678	1.08 ± 0.22	0.99 ± 0.05	0.78 ± 0.09	Y	N
Q5F8W2	Membrane lipoprotein	NGO0648	1.47 ± 0.12	1.02 ± 0	1.43 ± 0.21	N	N
Q5FAC7	Penicillin-binding protein 1A	mrcA/NGO0099	1.46 ± 0.14	0.7 ± 0	0.82 ± 0.01	N	N
Q5F9Z6	Periplasmic protein	NGO0238	1.1 ± 0.04	1.23 ± 0.07	1.31 ± 0.15	Y	N
Q5F9M1	Putative ABC transporter, periplasmic binding protein, amino acid	NGO0372	0.85 ± 0.05	0.97 ± 0.1	1.04 ± 0	Y	Y
Q5F6Q5	Putative ABC transporter, periplasmic binding protein, polyamine	NGO1494	0.79 ± 0.02	0.74 ± 0	1.24 ± 0.03	Y	N
Q5F7C5	Putative ABC transporter, periplasmic binding protein, polyamine	NGO1253	1.14 ± 0.02	0.93 ± 0.2	1.79 ± 0.01	N	N
Q5FA28	Putative ABC transporter, periplasmic binding protein, polyamine	NGO0206	0.64 ± 0	0.83 ± 0.01	1.5 ± 0.12	Y	N
Q5F574	Putative ABC transporter, thiamine-binding periplasmic protein	NGO2056	1.43 ± 0.29	0.84 ± 0.23	1.41 ± 0	Y	N
Q5FAB9	Putative carboxypeptidase, penicillin binding protein	pbp3/NGO0107	1.05 ± 0.28	1.43 ± 0.18	0.83 ± 0.17	Y	N
Q5F718	Putative cytochrome c oxidase subunit	NGO1371	1.15 ± 0.17	1.1 ± 0.46	1.01 ± 0.12	N	N
Q5F598	Putative cytochrome C1	NGO2031	1.16 ± 0.01	1.3 ± 0.01	1.66 ± 0.04	Y	N
Q5F8Y3	Putative murein hydrolase	mltB/NGO0626	1.4 ± 0.06	1.43 ± 0.01	1.05 ± 0.16	Y	N
Q5FA91	Putative serine protease	NGO0138	1.06 ± 0.11	0.98 ± 0.4	1.11 ± 0.06	Y	N
Q5F515	Putative thioredoxin	NGO2124	0.9 ± 0.05	1.02 ± 0.18	1.12 ± 0.04	N	N
Q5F5C7	Putative uncharacterized protein	NGO2002	1.29 ± 0	1.06 ± 0.07	1.34 ± 0.23	N	N
Q5F6P4	Putative uncharacterized protein	NGO1505	1.18 ± 0.11	1.28 ± 0.14	1.71 ± 0.08	N	N
Q5F7W0	Putative uncharacterized protein	NGO1056	1.17 ± 0.15	1.18 ± 0.45	0.95 ± 0.07	N	Y
Q5F7X1	Putative uncharacterized protein	NGO1044	0.94 ± 0.41	1.02 ± 0.11	1.27 ± 0.1	N	N
Q5F7X2	Putative uncharacterized protein	NGO1043	1.07 ± 0.01	1.06 ± 0.2	0.84 ± 0.11	Y	N
Q5F8C4	Putative uncharacterized protein	NGO0861	1.17 ± 0.19	1.4 ± 0.42	1.23 ± 0.16	Y	N
Q5F571	Putativeptide methionine sulfoxide reductase	msrAB, pilB/NGO2059	1.36 ± 0.31	1.19 ± 0.36	1.29 ± 0.33	Y	N
Q5F649	Thiol:disulphide interchange protein	dsbA/NGO1717	0.98 ± 0.02	1.14 ± 0.13	1.28 ± 0.02	Y	Y
Q5F6V7	Thiol:disulphide interchange protein	dsbC/NGO1438	1.37 ± 0.03	1.01 ± 0.1	1.03 ± 0.1	Y	N
Q5F505	Transglycosylase	NGO2135	1.62 ± 0.22	1.29 ± 0.17	0.98 ± 0.12	Y	N
Q5F912	Type IV pilus assembly protein	pilF/NGO0595	1.3 ± 0.1	1.01 ± 0.09	1.07 ± 0.08	N	N
Inner membrane
Q5F4Z4	ATP synthase subunit b	atpF/NGO2146	1.23 ± 0.03	1.04 ± 0	1.17 ± 0.18	N	N
Q5F9L1	ATP-dependent zinc metalloprotease FtsH	ftsH/NGO0382	1.04 ± 0.05	1.14 ± 0.42	1.29 ± 0.03	N	N
Q5F6M1	Cell division protein FtsQ	ftsQ/NGO1530	0.95 ± 0.05	0.7 ± 0.3	1.01 ± 0.09	N	N
Q5F6L1	Division cell wall protein	dcaA/NGO1540	0.97 ± 0.09	0.88 ± 0.16	1 ± 0.06	N	N
Q5F8I5	Genome-derived Neisseria antigen 1220	NGO0788	1.43 ± 0.03	1.27 ± 0	1.52 ± 0	N	N
Q5F573	Integral membrane protein	NGO2057	1.28 ± 0.09	1.32 ± 0.02	1.26 ± 0.02	N	N
Q5F5L3	Integral membrane protein	NGO1910	0.82 ± 0.06	1.1 ± 0.14	0.94 ± 0.03	Y	N
Q5F795	Integral membrane protein	NGO1288	1.15 ± 0.02	1.06 ± 0.02	1.27 ± 0.03	N	N
Q5F4X8	Lipid A export ATP-binding/permease protein MsbA	msbA/NGO2165	1.07 ± 0.02	1.05 ± 0.16	1.13 ± 0.11	N	N
Q5F6V6	Macrolide export ATP-binding/permease protein MacB	macB/NGO1439	1.25 ± 0.14	0.94 ± 0.4	0.85 ± 0.09	N	N
Q5F4W6	Membrane protein insertase YidC	yidC/NGO2178	1.2 ± 0.07	0.99 ± 0.05	1.2 ± 0.03	N	N
Q5F6K9	Penicillin-binding protein 2	penA/NGO1542	1.15 ± 0	0.79 ± 0.21	1 ± 0.1	N	N
Q5F7H2	Phosphatidylserine decarboxylase proenzyme	psd/NGO1206	1.09 ± 0.02	1.31 ± 0.3	1.32 ± 0.04	N	N
Q5F693	Pilus assembly protein	pilG/NGO1669	1.33 ± 0.05	1.17 ± 0	1.44 ± 0.01	N	N
Q5FAD0	Pilus assembly protein	pilO/NGO0096	1.28 ± 0.15	1.03 ± 0.21	1.35 ± 0.11	N	N
Q5F6W9	Probable ubiquinone biosynthesis protein UbiB	ubiB/NGO1424	1.26 ± 0.1	1.18 ± 0.13	1.39 ± 0.18	N	Y
Q5FA43	Protein translocase subunit SecD	secD/NGO0189	1.24 ± 0.07	1.08 ± 0	1.21 ± 0.11	N	N
Q5F567	Putative 1-acyl-SN-glycerol-3-phosphate acyltransferase	nlaB/NGO2069	1.03 ± 0.08	1.06 ± 0.2	1.48 ± 0.06	N	N
Q5F523	Putative ABC transporter, ATP-binding protein	NGO2116	0.98 ± 0.03	1.12 ± 0.24	1.27 ± 0.05	N	N
Q5F634	Putative ABC transporter, ATP-binding protein	NGO1732	1.22 ± 0.06	1.23 ± 0.03	1.5 ± 0.05	N	N
Q5F969	Putative acyl-CoA ligase	NGO0530	1.13 ± 0.11	1 ± 0.39	1.02 ± 0.06	N	N
Q5F7V3	Putative carbon starvation protein	cstA/NGO1064	1.01 ± 0.04	1.44 ± 0.02	1.55 ± 0.02	N	N
Q5F823	Thiol:disulfide interchange protein DsbD	dsbD/NGO0978	1.11 ± 0.04	1.1 ± 0.21	1.06 ± 0.12	N	N
Q5F952	Putative dnaJ-family protein	NGO0551	1.29 ± 0.23	0.93 ± 0.35	1 ± 0.12	N	N
Q5F7Y5	Putative ferredoxin	NGO1026	0.99 ± 0	0.89 ± 0.03	1.02 ± 0.04	N	Y
Q5F7V7	Putative fimbrial assembly protein	fimB/NGO1060	1.14 ± 0.03	1.01 ± 0.04	1.35 ± 0.09	N	Y
Q5F916	Putative ftsK-like cell division/stress response protein	NGO0590	1.07 ± 0.02	0.98 ± 0.19	1.04 ± 0.08	N	N
Q5F8K3	Putative lipoprotein releasing system transmembrane protein	NGO0769	1.19 ± 0.11	1.17 ± 0.12	1.43 ± 0.05	N	N
Q5F9U8	Putative Na+/H+ antiporter	NGO0291	1.29 ± 0.2	1.2 ± 0.29	1.53 ± 0.02	N	N
Q5F6S7	Putative NADP transhydrogenase, alpha subunit	NGO1470	1.38 ± 0.01	1.14 ± 0.03	1.26 ± 0.02	N	N
Q5F7A5	Putative nitric oxide reductase	NGO1275	1.5 ± 0.16	1.03 ± 0.05	1 ± 0.19	N	N
Q5F8S5	Putative P-type cation-transporting ATPase	NGO0685	1.03 ± 0	1.22 ± 0.03	1.39 ± 0.02	N	N
Q5F7D2	Putative serine protease	NGO1246	1.46 ± 0.29	0.85 ± 0.17	0.87 ± 0	N	N
Q5FAG5	Putative thioredoxin	NGO0057	1.26 ± 0.09	1.13 ± 0.24	1.12 ± 0.11	N	N
Q5F614	Putative uncharacterized protein	NGO1752	1.14 ± 0.11	1.15 ± 0.34	0.73 ± 0.1	N	N
Q5FA44	Putative uncharacterized protein	NGO0188	1.04 ± 0.08	1.45 ± 0.35	1.32 ± 0.25	N	N
Q5F5W9	RIP metalloprotease RseP	rseP/NGO1800	1.02 ± 0.03	0.95 ± 0.12	1.03 ± 0.1	N	N
Q5F5K7	Transmembrane transporter	NGO1917	0.91 ± 0.12	1.25 ± 0.21	1.28 ± 0.59	N	N
Q5F711	Transport protein	exbB/NGO1378	1.05 ± 0.03	0.82 ± 0.2	0.99 ± 0	N	N
Q5F5Q0	Two-component system sensor kinase	NGO1867	1.12 ± 0.01	1 ± 0.14	1.23 ± 0.03	N	N
Q5FA56	Two-component system sensor kinase	NGO0176	1.14 ± 0.01	1.13 ± 0.08	1.26 ± 0.02	N	N
Q5FAA1	UPF0761 membrane protein NGO0127	NGO0127	1.26 ± 0.14	1.14 ± 0.1	1.07 ± 0.2	N	N
Q5F9N3	Uroporphyrin-III C-methyltransferase	hemX/NGO0360	0.9 ± 0.02	0.86 ± 0.15	1.22 ± 0.1	N	N
Q5F7H9	YhbX/YhjW/YijP/YjdB family protein	NGO1198	1.06 ± 0.09	1.18 ± 0.29	1.12 ± 0	N	N
Unknown
Q5F8Z8	1-acyl-SN-glycerol-3-phosphate acyltransferase	plsC/NGO0611	1.36 ± 0.11	1.32 ± 0.02	1.5 ± 0.22	N	Y
Q5F5V0	30S ribosomal protein S11	rpsK/NGO1820	1.14 ± 0.03	0.99 ± 0.06	0.92 ± 0.06	N	Y
Q5F913	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase	ispG/NGO0594	0.82 ± 0.08	0.67 ± 0.08	0.63 ± 0.09	N	N
Q5F9Z8	Cell division protein zipA	zipA/NGO0236	0.99 ± 0.01	1.11 ± 0.05	1.25 ± 0.01	N	N
Q5F501	Genome-derived Neisserial antigen 1946	NGO2139	1.21 ± 0.04	1.23 ± 0.05	1.74 ± 0.03	Y	Y
Q5F9N2	HemY protein	hemY/NGO0361	1.12 ± 0.03	1.15 ± 0.06	1.29 ± 0.03	N	N
Q5F9W2	IgA-specific metalloendopeptidase	iga/NGO0275	0.93 ± 0.03	1.39 ± 0.1	1.05 ± 0	Y	N
Q5F5I3	Lipoprotein	NGO1942	0.99 ± 0.05	1.24 ± 0.06	1 ± 0.02	N	N
Q5F8J5	Membrane protein	NGO0778	1.12 ± 0.01	0.89 ± 0.27	1.01 ± 0.06	N	N
Q5F7J8	Minor pilin ComP	comP/NGO1177	1.17 ± 0.2	0.62 ± 0.33	1.54 ± 0.01	N	N
Q5F521	Outer membrane transporter	NGO2118	0.96 ± 0.2	1.07 ± 0.21	1.05 ± 0.15	N	N
Q5F8S7	Periplasmic protein	NGO0683	1.04 ± 0.4	0.84 ± 0.08	0.87 ± 0.28	Y	N
Q5FAD1	Pilin assembly protein	pilP/NGO0095	1.19 ± 0.04	1.08 ± 0.07	1.45 ± 0.16	Y	N
Q5F4Y0	Putative 3-oxoacyl-[acyl-carrier protein] reductase	fabG/NGO2163	0.62 ± 0.11	0.8 ± 0.21	0.76 ± 0.02	N	Y
Q5FA61	Putative ABC transporter, ATP-binding protein	znuC, troB/NGO0170	0.87 ± 0.2	0.77 ± 0.23	0.7 ± 0.13	N	N
Q5F531	Putative adhesion and penetration protein	NGO2105	1.04 ± 0.27	0.96 ± 0.13	0.94 ± 0.12	N	Y
Q5F6P7	Putative amidase	amiC/NGO1502	1.56 ± 0.09	1.47 ± 0	1.32 ± 0.14	N	Y
Q5F932	Putative carboxy-terminal processing protease	NGO0572	0.82 ± 0.06	0.98 ± 0.36	0.84 ± 0.04	Y	N
Q5F759	Putative cytochrome	NGO1328	1.16 ± 0.01	1.2 ± 0.12	1.28 ± 0.23	N	Y
Q5FA09	Putative MafB-like protein	NGO0225	1.18 ± 0.17	1.2 ± 0.46	1.02 ± 0.01	Y	N
Q5F6X8	Putative Na(+)-translocating NADH-ubiquinone reductase subunit C	nqrC/NGO1415	1.1 ± 0.19	1.04 ± 0.16	1.11 ± 0.19	N	N
Q5F674	Putative outer membrane protein OmpU	ompU/NGO1688	1.73 ± 0.17	1.44 ± 0	1.54 ± 0.31	Y	N
Q5F8E6	Putative oxidoreductase	NGO0831	1.17 ± 0.1	1.33 ± 0.16	1.28 ± 0.25	N	N
Q5F766	Putative paraquat-inducible protein B	NGO1320	1.01 ± 0.02	0.98 ± 0.13	1 ± 0.01	N	N
Q5FAC8	Putative pilus assembly protein	pilM/NGO0098	1.11 ± 0.04	1.34 ± 0.17	1.48 ± 0.09	N	N
Q5F520	Putative uncharacterized protein	NGO2119	1.27 ± 0.05	1.03 ± 0.05	0.7 ± 0.18	Y	N
Q5F5E5	Putative uncharacterized protein	NGO1984	0.9 ± 0.04	0.98 ± 0.14	1.04 ± 0.04	N	N
Q5F5P4	Putative uncharacterized protein	NGO1873	1.34 ± 0.28	1.34 ± 0.1	0.94 ± 0.08	N	N
Q5F5W7	Putative uncharacterized protein	NGO1802	1.06 ± 0.18	1.45 ± 0.02	1.06 ± 0.19	Y	Y
Q5F657	Putative uncharacterized protein	NGO1709	1.22 ± 0.03	1.3 ± 0.07	1.44 ± 0.01	N	Y
Q5F676	Putative uncharacterized protein	NGO1686	1.11 ± 0.01	1.22 ± 0.03	1.29 ± 0	N	N
Q5F6K2	Putative uncharacterized protein	NGO1549	1.15 ± 0.09	1.1 ± 0.29	1.31 ± 0.03	N	Y
Q5F6P5	Putative uncharacterized protein	NGO1504	0.95 ± 0.08	1.38 ± 0.22	1.45 ± 0.09	N	N
Q5F7A6	Putative uncharacterized protein	NGO1274	1.41 ± 0.02	1.62 ± 0.1	1.46 ± 0.01	N	Y
Q5F7C7	Putative uncharacterized protein	NGO1251	0.94 ± 0.06	0.88 ± 0.39	0.62 ± 0.05	N	N
Q5FAK6	Putative uncharacterized protein	NGO0028	1.07 ± 0.17	1.44 ± 0.09	1.31 ± 0.36	N	N
Q5F9Q0	Signal peptidase I	lepB/NGO0343	1.01 ± 0.09	1.07 ± 0.12	1.21 ± 0.1	N	N
Q5F9E3	Type IV pilus assembly protein PilX	pilX/NGO0455	0.57 ± 0.06	0.74 ± 0.03	0.67 ± 0.12	N	N
O87406	UPF0070 protein NGO0425	NGO0425	1.11 ± 0.07	1.12 ± 0.22	0.98 ± 0.01	N	N

^a Average ratios and standard deviations were calculated for proteins ubiquitously expressed in biological replica experiments.

^b Predictions of signal peptide cleavage site using SignalP (47).

^c Presence of twin-arginine signal peptide as determined by TatP (48).

^d The surface localization of AniA was verified experimentally (97).

^e The outer membrane localization of Ng-MIP was verified experimentally (78).