PSORTb v.2.0: Supplementary Information

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PSORTb v.2.0 Supplementary Information

This page contains supplementary information associated with the PSORTb v.2.0 manuscript.

Table S1a. Confusion matrix for Gram-negative proteins analyzed using PSORTb v.2.0
Table S1b. Confusion matrix for Gram-positive proteins analyzed using PSORTb v.2.0
Table S2a. Analysis of Gram-negative proteomes using PSORTb v.2.0 (raw numbers)
Table S2b. Analysis of Gram-positive proteomes using PSORTb v.2.0 (raw numbers)
Table S2c. Analysis of Gram-negative proteomes using PSORTb v.2.0 (percentages)
Table S2d. Analysis of Gram-positive proteomes using PSORTb v.2.0 (percentages)
Table S3. Confusion matrices for performance comparison between PSORTb v.2.0, CELLO v.2.0, and Proteome Analyst v.1.0.
Figure S1. Proportion of proteins at each localization site

Table S1a. Confusion matrix for Gram-negative proteins analyzed using PSORTb v.2.0

Actual localization	Predicted localization
	C	CM	P	OM	EC	C/CM	C/P	CM/P	CM/OM	CM/P/OM	P/OM	OM/EC	U
C	193	7	4	1	0	1	1	0	0	0	0	0	71
CM	4	285	0	2	0	0	1	0	1	0	0	0	16
P	6	6	189	1	3	4	0	0	0	1	1	1	64
OM	1	0	1	371	1	1	0	0	0	0	0	0	16
EC	4	1	4	6	147	0	0	0	0	0	0	3	25
C/CM	6	2	0	1	0	3	0	0	0	0	0	0	4
CM/P	2	18	7	0	0	1	0	8	0	0	0	0	15
P/OM	0	0	0	1	0	0	0	0	0	0	0	1	0
OM/EC	0	0	1	39	5	0	0	0	0	0	0	32	1

Table S1b. Confusion matrix for Gram-positive proteins analyzed using PSORTb v.2.0

Actual localization	Predicted localization
	C	CM	CW	EC	CM/EC	CW/EC	U
C	168	2	0	4	1	0	19
CM	1	94	0	1	0	0	7
CW	0	0	52	3	0	2	4
EC	4	1	3	119	4	1	51
C/CM	6	6	0	0	0	0	3
CM/CW	6	2	1	1	3	0	7

Table S2a. Analysis of Gram-negative proteomes using PSORT-B v.2.0 (raw numbers)

Organism	C	CM	EC	OM	P	U	Mult.	Total # of Predictions	Proteome Size	Coverage
Agrobacterium tumefaciens str. C58 (Cereon) circular chromosome	1025	524	4	23	60	1046	39	1675	2721	61.6%
Agrobacterium tumefaciens str. C58 (Cereon) linear chromosome	636	405	6	19	82	624	61	1209	1833	66.0%
Agrobacterium tumefaciens str. C58 (U. Washington) circular chromosome	1055	523	4	23	60	1076	44	1709	2785	61.4%
Agrobacterium tumefaciens str. C58 (U. Washington) linear chromosome	667	393	6	21	84	646	59	1230	1876	65.6%
Aquifex aeolicus VF5	839	245	6	24	21	365	29	1164	1529	76.1%
Bacteroides thetaiotaomicron VPI-5482	1358	701	26	248	48	2302	95	2476	4778	51.8%
Bdellovibrio bacteriovorus HD100	860	522	31	100	56	1909	109	1678	3587	46.8%
Blochmannia floridanus	210	107	1	8	5	244	8	339	583	58.1%
Bordetella bronchiseptica RB50	1670	916	16	101	175	1968	148	3026	4994	60.6%
Bordetella parapertussis 12822	1461	790	14	87	158	1547	128	2638	4185	63.0%
Bordetella pertussis Tohama 1	1089	596	11	68	111	1471	90	1965	3436	57.2%
Borrelia burgdorferi B31	259	171	4	46	10	347	14	504	851	59.2%
Bradyrhizobium japonicum USDA 110	2661	1533	27	105	215	3568	208	4749	8317	57.1%
Brucella melitensis 16M chromosome 1	806	327	2	25	35	820	44	1239	2059	60.2%
Brucella melitensis 16M chromosome 2	382	253	1	6	52	410	35	729	1139	64.0%
Brucella suis 1330 chromosome 1	765	319	2	25	34	925	46	1191	2116	56.3%
Brucella suis 1330 chromosome 2	357	235	0	9	47	464	36	684	1148	59.6%
Buchnera aphidicola str. APS (Acrythosiphon pisum)	197	84	1	11	5	260	6	304	564	53.9%
Buchnera aphidicola str. Bp (Baizongia pistaciae)	151	88	1	8	5	243	8	261	504	51.8%
Buchnera aphidicola str. Sg (Schizaphis graminum)	192	79	1	10	8	249	7	297	546	54.4%
Campylobacter jejuni subsp. jejuni NCTC 11168	519	288	6	56	31	706	28	928	1634	56.8%
Caulobacter crescentus CB15	1242	583	14	105	70	1638	85	2099	3737	56.2%
Chlamydia muridarum	304	147	1	23	6	396	27	508	904	56.2%
Chlamydia trachomatis D/UW-3/CX	317	143	2	22	9	385	17	510	895	57.0%
Chlamydophila caviae GPIC	318	160	2	25	9	451	33	547	998	54.8%
Chlamydophila pneumoniae AR39	340	170	1	27	9	537	28	575	1112	51.7%
Chlamydophila pneumoniae CWL029	338	171	1	27	9	479	29	575	1054	54.6%
Chlamydophila pneumoniae J138	339	171	1	28	9	483	38	586	1069	54.8%
Chlamydophila pneumoniae TW-183	340	171	1	27	9	532	33	581	1113	52.2%
Chlorobium tepidum TLS	856	323	4	27	21	991	30	1261	2252	56.0%
Chromobacterium violaceum ATCC 12472	1561	781	33	80	94	1747	111	2660	4407	60.4%
Coxiella burnetii RSA 493	662	343	3	18	12	955	16	1054	2009	52.5%
Escherichia coli CFT073	1842	899	38	110	144	2269	77	3110	5379	57.8%
Escherichia coli K12	1574	851	20	91	142	1577	56	2734	4311	63.4%
Escherichia coli O157:H7 EDL933	1818	873	30	117	149	2186	80	3067	5253	58.4%
Escherichia coli O157:H7 EDL933	1805	893	30	126	147	2242	81	3082	5324	57.9%
Fusobacterium nucleatum subsp. nucleatum ATCC 25586	813	372	1	79	20	720	62	1347	2067	65.2%
Geobacter sulfurreducens PCA	1489	639	24	48	54	1119	72	2326	3445	67.5%
Gloeobacter violaceus PCC 7421	1534	648	14	101	47	1997	89	2433	4430	54.9%
Haemophilus ducreyi 35000HP	581	251	3	37	33	789	23	928	1717	54.0%
Haemophilus influenzae Rd KW20	673	296	4	32	45	580	27	1077	1657	65.0%
Helicobacter hepaticus ATCC 51499	579	282	12	49	23	895	35	980	1875	52.3%
Helicobacter pylori 26695	529	238	12	69	13	689	26	887	1576	56.3%
Helicobacter pylori J99	504	238	14	63	14	629	29	862	1491	57.8%
Leptospira interrogans serovar Copenhageni str. Fiocruz LI-130 chromosome 1	929	535	26	93	30	1729	52	1665	3394	49.1%
Leptospira interrogans serovar Copenhageni str. Fiocruz LI-130 chromosome 2	83	58	0	10	1	111	3	155	266	58.3%
Leptospira interrogans serovar lai str. 56601 chromosome 1	1028	550	27	102	29	2572	52	1788	4360	41.0%
Leptospira interrogans serovar lai str. 56601 chromosome 2	98	58	0	11	1	197	2	170	367	46.3%
Mesorhizobium loti MAFF 303099	2319	1198	14	51	157	2846	161	3900	6746	57.8%
Mycoplasma gallisepticum R	180	122	8	66	0	319	31	407	726	56.1%
Mycoplasma genitalium G-37	115	79	1	19	0	258	12	226	484	46.69%
Mycoplasma mycoides subsp. mycoides Sc str. PG1	231	154	1	71	0	536	23	480	1016	47.2%
Mycoplasma penetrans HF-2	247	165	1	105	1	455	63	582	1037	56.1%
Mycoplasma pneumoniae M129	158	97	1	43	1	381	8	308	689	44.7%
Mycoplasma pulmonis UAB CTIP	189	134	3	54	1	376	25	406	782	51.9%
Neisseria meningitidis MC58	761	275	5	53	32	920	33	1159	2079	55.7%
Neisseria meningitidis Z2491	749	274	4	44	32	929	33	1136	2065	55.0%
Nitrosomonas europaea ATCC 19718	1010	398	11	60	41	897	44	1564	2461	63.6%
Nostoc sp. PCC 7120	1542	909	26	101	60	2629	99	2737	5366	51.0%
Onion yellows phytoplasma OY-M	180	119	1	8	3	434	9	320	754	42.4%
Pasteurella multocida Pm70	774	411	4	49	61	679	37	1336	2015	66.3%
Photorhabdus luminescens subsp. laumondii TT01	1580	663	24	115	85	2149	67	2534	4683	54.1%
Pirellula sp. 1	1937	825	18	61	45	4238	201	3087	7325	42.1%
Porphyromonas gingivalis W83	733	257	7	55	11	818	28	1091	1909	57.2%
Prochlorococcus marinus MIT9313	723	348	5	28	18	1108	35	1157	2265	51.1%
Prochlorococcus marinus subsp. marinus str. CCMP1375	590	251	3	27	12	971	28	911	1882	48.4%
Prochlorococcus marinus subsp. pastoris CCMP1986	519	238	3	43	14	870	25	842	1712	49.2%
Pseudomonas aeruginosa PA01	2321	1032	27	165	125	1777	120	3790	5567	68.1%
Pseudomonas putida KT2440	2000	954	15	147	102	2014	118	3336	5350	62.4%
Pseudomonas syringae pv. yomato str. DC3000	1907	946	20	118	110	2230	140	3241	5471	59.2%
Ralstonia solanacearum GMI 1000	1160	519	15	60	71	1532	83	1908	3440	55.5%
Rhodopseudomonas palustris CGA009	1568	957	4	75	122	1951	137	2863	4814	59.5%
Rickettsia conorii str. Malish 7	355	201	2	16	13	760	27	614	1374	44.7%
Rickettsia prowazekii str. Madrid E	250	174	1	19	9	366	16	469	835	56.2%
Salmonella enterica subsp. enterica serovar Typhi str. CT18	1537	801	22	70	124	1766	75	2629	4395	59.8%
Salmonella enterica subsp. enterica serovar Typhi str. Ty2	1525	793	23	67	121	1713	76	2605	4318	60.3%
Salmonella typhimurium LT2	1570	853	32	83	138	1671	78	2754	4425	62.2%
Shewanella oneidensis MR-1	1318	694	23	114	102	1981	91	2342	4323	54.2%
Shigella flexneri 2a str. 2457T	1426	696	13	60	117	1694	62	2374	4068	58.4%
Shigella flexneri 2a str. 301	1441	722	13	72	116	1751	65	2429	4180	58.1%
Sinorhizobium meliloti 1021	1372	574	12	31	79	1193	80	2148	3341	64.3%
Synechococcus sp. WH8102	871	325	14	14	24	1222	47	1295	2517	51.5%
Synechocystis sp. PCC 6803	1014	540	8	40	44	1468	53	1699	3167	53.6%
Thermosynechococcus elongatus BP-1	829	435	2	16	21	1131	41	1344	2475	54.3%
Thermotoga maritima MSB8	1040	321	7	14	29	393	54	1465	1858	78.8%
Treponema denticola ATCC 35405	792	527	7	59	23	1303	56	1464	2767	52.9%
Treponema pallidum subsp. pallidum str. Nichols	408	177	3	18	15	395	20	641	1036	61.9%
Ureaplasma parvum serovar 3 ATCC 700970	172	92	1	28	1	310	10	304	614	49.5%
Vibrio cholerae 01 biovar eltor str. N16961 chromosome 1	991	476	15	54	57	1112	37	1630	2742	59.4%
Vibrio cholerae 01 biovar eltor str. N16961 chromosome 2	312	207	13	14	23	505	19	588	1093	53.8%
Vibrio parahaemolyticus RIMD 2210633 chromosome 1	1177	497	19	75	63	1190	59	1890	3080	61.4%
Vibrio parahaemolyticus RIMD 2210633 chromosome 2	523	343	20	56	46	727	37	1025	1752	58.5%
Vibrio vulnificus CMCP6 chromosome 1	1114	500	16	67	53	1144	58	1808	2952	61.2%
Vibrio vulnificus CMCP6 chromosome 2	509	331	18	45	44	582	33	980	1562	62.7%
Vibrio vulnificus YJ016 chromosome 1	1131	527	15	72	50	1407	57	1852	3259	56.8%
Vibrio vulnificus YJ016 chromosome 2	517	320	18	48	38	715	40	981	1696	57.8%
Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis	156	144	3	19	5	272	12	339	611	55.5%
Wolbachia endosymbiont of Drosophila melanogaster	401	159	1	19	4	589	22	606	1195	50.7%
Wolinella succinogenes DSM 1740	905	420	5	45	41	581	47	1463	2044	71.6%
Xanthomonas axonopodis pv. citri str. 306	1271	707	38	142	83	1971	100	2341	4312	54.3%
Xanthomonas campestris pv. campestris str. ATCC 33913	1238	693	31	136	74	1904	105	2277	4181	54.5%
Xylella fastidiosa 9a5c	834	310	13	43	30	1496	40	1270	2766	45.9%
Xylella fastidiosa Temecula1	710	287	12	43	28	910	44	1124	2034	55.3%
Yersinia pestis biovar Mediaevails str. 91001	1231	728	23	98	122	1625	68	2270	3895	58.3%
Yersinia pestis CO92	1259	713	25	103	122	1598	65	2287	3885	58.9%
Yersinia pestis KIM	1245	729	26	109	122	1788	67	2298	4086	56.2%

Table S2b. Analysis of Gram-positive proteomes using PSORT-B v.2.0 (raw numbers)

Organism	C	CM	CW	EC	U	Multiple	Total # of Predictions	Total Proteome Size	Coverage
Bacillus anthracis str. A2012	2623	1203	66	164	1450	38	4094	5544	73.8%
Bacillus anthracis str. Ames	2475	1151	56	250	1341	38	3970	5311	74.8%
Bacillus cereus ATCC 10987	2528	1195	57	366	1406	51	4197	5603	74.9%
Bacillus cereus ATCC14579	2537	1136	47	184	1276	54	3958	5234	75.6%
Bacillus halodurans C-125	2265	840	9	157	684	111	3382	4066	83.2%
Bacillus subtilis subsp. subtilis str. 168	2080	911	21	107	965	28	3147	4112	76.5%
Bifidobacterium longum NCC2705	945	354	22	19	376	11	1351	1727	78.2%
Clostridium acetobutylicum ATCC824	1723	775	30	92	1038	14	2634	3672	71.7%
Clostridium perfringens str. 13	1450	588	21	57	509	35	2151	2660	80.9%
Clostridium tetani E88	1265	564	29	24	462	29	1911	2373	80.5%
Corynebacterium diphtheriae NCTC 13129	1188	432	17	50	559	26	1713	2272	75.4%
Corynebacterium efficiens YS-314	1618	544	12	57	679	40	2271	2950	77.0%
Corynebacterium glutamicum ATCC 13032	1560	600	14	49	729	41	2264	2993	75.6%
Deinococcus radiodurans str. R1 chromosome 1	1286	395	17	50	869	12	1760	2629	66.9%
Deinococcus radiodurans str. R1 chromosome 2	190	60	2	4	110	2	258	368	70.1%
Enterococcus faecalis V583	1517	622	45	115	804	10	2309	3113	74.2%
Lactobacillus johnsonii NCC 533	802	446	25	18	526	4	1295	1821	71.1%
Lactobacillus plantarum WCFS1	1254	641	46	38	1019	11	1990	3009	66.1%
Lactococcus lactis Il1403	1118	451	23	43	678	8	1643	2321	70.8%
Listeria innocua Clip 11262 chromosome	1626	585	47	41	651	18	2317	2968	78.1%
Listeria monocytogenes EGD-e	1568	600	54	43	560	21	2286	2846	80.3%
Mycobacterium avium subsp. paratuberculosis k10	2399	663	11	68	1192	17	3158	4350	72.6%
Mycobacterium bovis subsp. bovis AF2122/97	2065	593	8	136	1097	21	2823	3920	72.0%
Mycobacterium leprae TN	853	250	0	31	460	11	1145	1605	71.3%
Mycobacterium tuberculosis CDC1551	2090	587	9	211	1271	19	2916	4187	69.6%
Mycobacterium tuberculosis H37Rv	2086	598	8	135	1079	21	2848	3927	72.5%
Oceanobacillus iheyensis HTE831	1752	812	10	81	769	76	2731	3500	78.0%
Staphylococcus aureus subsp. aureus Mu50	1303	561	34	124	681	11	2033	2714	74.9%
Staphylococcus aureus subsp. aureus MW2	1245	560	32	137	646	12	1986	2632	75.5%
Staphylococcus aureus subsp. aureus N315	1248	553	31	116	635	10	1958	2593	75.5%
Staphylococcus epidermidis ATCC 12228	1130	492	29	177	579	12	1840	2419	76.1%
Streptococcus agalactiae 2603V/R	1039	433	34	86	521	11	1603	2124	75.5%
Streptococcus agalactiae NEM316	1042	456	43	33	509	11	1585	2094	75.7%
Streptococcus mutans UA159	944	419	14	66	514	3	1446	1960	73.8%
Streptococcus pneumonia R6	1071	418	19	54	469	12	1574	2043	77.0%
Streptococcus pneumonia TIGR4	1071	411	19	126	458	9	1636	2094	78.1%
Streptococcus pyogenes M1 GAS	866	320	19	37	446	9	1251	1697	73.7%
Streptococcus pyogenes MGAS315	938	317	22	37	545	6	1320	1865	70.8%
Streptococcus pyogenes MGAS8232	918	318	18	46	538	7	1307	1845	70.8%
Streptococcus pyogenes SSI-1	927	315	22	49	543	5	1318	1861	70.8%
Streptomyces avermitilis MA-4680	3975	1261	33	222	2035	49	5540	7575	73.1%
Streptomyces coelicolor A3(2)	3978	1285	33	267	2116	90	5653	7769	72.8%
Thermoanaerobacter tengcongensis	1551	520	13	37	442	25	2146	2588	82.9%
Tropheryma whipplei TW08/27	416	177	6	13	162	9	621	783	79.3%
Tropheryma whipplei Twist	423	174	5	11	189	6	619	808	76.6%

Table S2c. Analysis of Gram-negative proteomes using PSORTb v.2.0 (percentages)

Organism	C	CM	EC	OM	P	U	Mult.
Agrobacterium tumefaciens str. C58 (Cereon) circular chromosome	37.7%	19.3%	0.1%	0.8%	2.2%	38.4%	1.4%
Agrobacterium tumefaciens str. C58 (Cereon) linear chromosome	34.7%	22.1%	0.3%	1.0%	4.5%	34.0%	3.3%
Agrobacterium tumefaciens str. C58 (U. Washington) circular chromosome	37.9%	18.8%	0.1%	0.8%	2.2%	38.6%	1.6%
Agrobacterium tumefaciens str. C58 (U. Washington) linear chromosome	35.6%	20.9%	0.3%	1.1%	4.5%	34.4%	3.1%
Aquifex aeolicus VF5	54.9%	16.0%	0.4%	1.6%	1.4%	23.9%	1.9%
Bacteroides thetaiotaomicron VPI-5482	28.4%	14.7%	0.5%	5.2%	1.0%	48.2%	2.0%
Bdellovibrio bacteriovorus HD100	24.0%	14.6%	0.9%	2.8%	1.6%	53.2%	3.0%
Blochmannia floridanus	36.0%	18.4%	0.2%	1.4%	0.9%	41.9%	1.4%
Bordetella bronchiseptica RB50	33.4%	18.3%	0.3%	2.0%	3.5%	39.4%	3.0%
Bordetella parapertussis 12822	34.9%	18.9%	0.3%	2.1%	3.8%	37.0%	3.1%
Bordetella pertussis Tohama 1	31.7%	17.3%	0.3%	2.0%	3.2%	42.8%	2.6%
Borrelia burgdorferi B31	30.4%	20.1%	0.5%	5.4%	1.2%	40.8%	1.6%
Bradyrhizobium japonicum USDA 110	32.0%	18.4%	0.3%	1.3%	2.6%	42.9%	2.5%
Brucella melitensis 16M chromosome 1	39.1%	15.9%	0.1%	1.2%	1.7%	39.8%	2.1%
Brucella melitensis 16M chromosome 2	33.5%	22.2%	0.1%	0.5%	4.6%	36.0%	3.1%
Brucella suis 1330 chromosome 1	36.2%	15.1%	0.1%	1.2%	1.6%	43.7%	2.2%
Brucella suis 1330 chromosome 2	31.1%	20.5%	0.0%	0.8%	4.1%	40.4%	3.1%
Buchnera aphidicola str. APS (Acrythosiphon pisum)	34.9%	14.9%	0.2%	2.0%	0.9%	46.1%	1.1%
Buchnera aphidicola str. Bp (Baizongia pistaciae)	30.0%	17.5%	0.2%	1.6%	1.0%	48.2%	1.6%
Buchnera aphidicola str. Sg (Schizaphis graminum)	35.2%	14.5%	0.2%	1.8%	1.5%	45.6%	1.3%
Campylobacter jejuni subsp. jejuni NCTC 11168	31.8%	17.6%	0.4%	3.4%	1.9%	43.2%	1.7%
Caulobacter crescentus CB15	33.2%	15.6%	0.4%	2.8%	1.9%	43.8%	2.3%
Chlamydia muridarum	33.6%	16.3%	0.1%	2.5%	0.7%	43.8%	3.0%
Chlamydia trachomatis D/UW-3/CX	35.4%	16.0%	0.2%	2.5%	1.0%	43.0%	1.9%
Chlamydophila caviae GPIC	31.9%	16.0%	0.2%	2.5%	0.9%	45.2%	3.3%
Chlamydophila pneumoniae AR39	30.6%	15.3%	0.1%	2.4%	0.8%	48.3%	2.5%
Chlamydophila pneumoniae CWL029	32.1%	16.2%	0.1%	2.6%	0.9%	45.4%	2.8%
Chlamydophila pneumoniae J138	31.7%	16.0%	0.1%	2.6%	0.8%	45.2%	3.6%
Chlamydophila pneumoniae TW-183	30.5%	15.4%	0.1%	2.4%	0.8%	47.8%	3.0%
Chlorobium tepidum TLS	38.0%	14.3%	0.2%	1.2%	0.9%	44.0%	1.3%
Chromobacterium violaceum ATCC 12472	35.4%	17.7%	0.7%	1.8%	2.1%	39.6%	2.5%
Coxiella burnetii RSA 493	33.0%	17.1%	0.1%	0.9%	0.6%	47.5%	0.8%
Escherichia coli CFT073	34.2%	16.7%	0.7%	2.0%	2.7%	42.2%	1.4%
Escherichia coli K12	36.5%	19.7%	0.5%	2.1%	3.3%	36.6%	1.3%
Escherichia coli O157:H7 EDL933	34.6%	16.6%	0.6%	2.2%	2.8%	41.6%	1.5%
Escherichia coli O157:H7 EDL933	33.9%	16.8%	0.6%	2.4%	2.8%	42.1%	1.5%
Fusobacterium nucleatum subsp. nucleatum ATCC 25586	39.3%	18.0%	0.0%	3.8%	1.0%	34.8%	3.0%
Geobacter sulfurreducens PCA	43.2%	18.5%	0.7%	1.4%	1.6%	32.5%	2.1%
Gloeobacter violaceus PCC 7421	34.6%	14.6%	0.3%	2.3%	1.1%	45.1%	2.0%
Haemophilus ducreyi 35000HP	33.8%	14.6%	0.2%	2.2%	1.9%	46.0%	1.3%
Haemophilus influenzae Rd KW20	40.6%	17.9%	0.2%	1.9%	2.7%	35.0%	1.6%
Helicobacter hepaticus ATCC 51499	30.9%	15.0%	0.6%	2.6%	1.2%	47.7%	1.9%
Helicobacter pylori 26695	33.6%	15.1%	0.8%	4.4%	0.8%	43.7%	1.6%
Helicobacter pylori J99	33.8%	16.0%	0.9%	4.2%	0.9%	42.2%	1.9%
Leptospira interrogans serovar Copenhageni str. Fiocruz LI-130 chromosome 1	27.4%	15.8%	0.8%	2.7%	0.9%	50.9%	1.5%
Leptospira interrogans serovar Copenhageni str. Fiocruz LI-130 chromosome 2	31.2%	21.8%	0.0%	3.8%	0.4%	41.7%	1.1%
Leptospira interrogans serovar lai str. 56601 chromosome 1	23.6%	12.6%	0.6%	2.3%	0.7%	59.0%	1.2%
Leptospira interrogans serovar lai str. 56601 chromosome 2	26.7%	15.8%	0.0%	3.0%	0.3%	53.7%	0.5%
Mesorhizobium loti MAFF 303099	34.4%	17.8%	0.2%	0.8%	2.3%	42.2%	2.4%
Mycoplasma gallisepticum R	24.8%	16.8%	1.1%	9.1%	0.0%	43.9%	4.3%
Mycoplasma genitalium G-37	23.8%	16.3%	0.2%	3.9%	0.0%	53.3%	2.5%
Mycoplasma mycoides subsp. mycoides Sc str. PG1	22.7%	15.2%	0.1%	7.0%	0.0%	52.8%	2.3%
Mycoplasma penetrans HF-2	23.8%	15.9%	0.1%	10.1%	0.1%	43.9%	6.1%
Mycoplasma pneumoniae M129	22.9%	14.1%	0.1%	6.2%	0.1%	55.3%	1.2%
Mycoplasma pulmonis UAB CTIP	24.2%	17.1%	0.4%	6.9%	0.1%	48.1%	3.2%
Neisseria meningitidis MC58	36.6%	13.2%	0.2%	2.5%	1.5%	44.3%	1.6%
Neisseria meningitidis Z2491	36.3%	13.3%	0.2%	2.1%	1.5%	45.0%	1.6%
Nitrosomonas europaea ATCC 19718	41.0%	16.2%	0.4%	2.4%	1.7%	36.4%	1.8%
Nostoc sp. PCC 7120	28.7%	16.9%	0.5%	1.9%	1.1%	49.0%	1.8%
Onion yellows phytoplasma OY-M	23.9%	15.8%	0.1%	1.1%	0.4%	57.6%	1.2%
Pasteurella multocida Pm70	38.4%	20.4%	0.2%	2.4%	3.0%	33.7%	1.8%
Photorhabdus luminescens subsp. laumondii TT01	33.7%	14.2%	0.5%	2.5%	1.8%	45.9%	1.4%
Pirellula sp. 1	26.4%	11.3%	0.2%	0.8%	0.6%	57.9%	2.7%
Porphyromonas gingivalis W83	38.4%	13.5%	0.4%	2.9%	0.6%	42.8%	1.5%
Prochlorococcus marinus MIT9313	31.9%	15.4%	0.2%	1.2%	0.8%	48.9%	1.5%
Prochlorococcus marinus subsp. marinus str. CCMP1375	31.3%	13.3%	0.2%	1.4%	0.6%	51.6%	1.5%
Prochlorococcus marinus subsp. pastoris CCMP1986	30.3%	13.9%	0.2%	2.5%	0.8%	50.8%	1.5%
Pseudomonas aeruginosa PA01	41.7%	18.5%	0.5%	3.0%	2.2%	31.9%	2.2%
Pseudomonas putida KT2440	37.4%	17.8%	0.3%	2.7%	1.9%	37.6%	2.2%
Pseudomonas syringae pv. yomato str. DC3000	34.9%	17.3%	0.4%	2.2%	2.0%	40.8%	2.6%
Ralstonia solanacearum GMI 1000	33.7%	15.1%	0.4%	1.7%	2.1%	44.5%	2.4%
Rhodopseudomonas palustris CGA009	32.6%	19.9%	0.1%	1.6%	2.5%	40.5%	2.8%
Rickettsia conorii str. Malish 7	25.8%	14.6%	0.1%	1.2%	0.9%	55.3%	2.0%
Rickettsia prowazekii str. Madrid E	29.9%	20.8%	0.1%	2.3%	1.1%	43.8%	1.9%
Salmonella enterica subsp. enterica serovar Typhi str. CT18	35.0%	18.2%	0.5%	1.6%	2.8%	40.2%	1.7%
Salmonella enterica subsp. enterica serovar Typhi str. Ty2	35.3%	18.4%	0.5%	1.6%	2.8%	39.7%	1.8%
Salmonella typhimurium LT2	35.5%	19.3%	0.7%	1.9%	3.1%	37.8%	1.8%
Shewanella oneidensis MR-1	30.5%	16.1%	0.5%	2.6%	2.4%	45.8%	2.1%
Shigella flexneri 2a str. 2457T	35.1%	17.1%	0.3%	1.5%	2.9%	41.6%	1.5%
Shigella flexneri 2a str. 301	34.5%	17.3%	0.3%	1.7%	2.8%	41.9%	1.6%
Sinorhizobium meliloti 1021	41.1%	17.2%	0.4%	0.9%	2.4%	35.7%	2.4%
Synechococcus sp. WH8102	34.6%	12.9%	0.6%	0.6%	1.0%	48.5%	1.9%
Synechocystis sp. PCC 6803	32.0%	17.1%	0.3%	1.3%	1.4%	46.4%	1.7%
Thermosynechococcus elongatus BP-1	33.5%	17.6%	0.1%	0.6%	0.8%	45.7%	1.7%
Thermotoga maritima MSB8	56.0%	17.3%	0.4%	0.8%	1.6%	21.2%	2.9%
Treponema denticola ATCC 35405	28.6%	19.0%	0.3%	2.1%	0.8%	47.1%	2.0%
Treponema pallidum subsp. pallidum str. Nichols	39.4%	17.1%	0.3%	1.7%	1.4%	38.1%	1.9%
Ureaplasma parvum serovar 3 ATCC 700970	28.0%	15.0%	0.2%	4.6%	0.2%	50.5%	1.6%
Vibrio cholerae 01 biovar eltor str. N16961 chromosome 1	36.1%	17.4%	0.5%	2.0%	2.1%	40.6%	1.3%
Vibrio cholerae 01 biovar eltor str. N16961 chromosome 2	28.5%	18.9%	1.2%	1.3%	2.1%	46.2%	1.7%
Vibrio parahaemolyticus RIMD 2210633 chromosome 1	38.2%	16.1%	0.6%	2.4%	2.0%	38.6%	1.9%
Vibrio parahaemolyticus RIMD 2210633 chromosome 2	29.9%	19.6%	1.1%	3.2%	2.6%	41.5%	2.1%
Vibrio vulnificus CMCP6 chromosome 1	37.7%	16.9%	0.5%	2.3%	1.8%	38.8%	2.0%
Vibrio vulnificus CMCP6 chromosome 2	32.6%	21.2%	1.2%	2.9%	2.8%	37.3%	2.1%
Vibrio vulnificus YJ016 chromosome 1	34.7%	16.2%	0.5%	2.2%	1.5%	43.2%	1.7%
Vibrio vulnificus YJ016 chromosome 2	30.5%	18.9%	1.1%	2.8%	2.2%	42.2%	2.4%
Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis	25.5%	23.6%	0.5%	3.1%	0.8%	44.5%	2.0%
Wolbachia endosymbiont of Drosophila melanogaster	33.6%	13.3%	0.1%	1.6%	0.3%	49.3%	1.8%
Wolinella succinogenes DSM 1740	44.3%	20.5%	0.2%	2.2%	2.0%	28.4%	2.3%
Xanthomonas axonopodis pv. citri str. 306	29.5%	16.4%	0.9%	3.3%	1.9%	45.7%	2.3%
Xanthomonas campestris pv. campestris str. ATCC 33913	29.6%	16.6%	0.7%	3.3%	1.8%	45.5%	2.5%
Xylella fastidiosa 9a5c	30.2%	11.2%	0.5%	1.6%	1.1%	54.1%	1.4%
Xylella fastidiosa Temecula1	34.9%	14.1%	0.6%	2.1%	1.4%	44.7%	2.2%
Yersinia pestis biovar Mediaevails str. 91001	31.6%	18.7%	0.6%	2.5%	3.1%	41.7%	1.7%
Yersinia pestis CO92	32.4%	18.4%	0.6%	2.7%	3.1%	41.1%	1.7%
Yersinia pestis KIM	30.5%	17.8%	0.6%	2.7%	3.0%	43.8%	1.6%

Table S2d. Analysis of Gram-positive proteomes using PSORTb v.2.0 (percentages)

Organism	C	CM	CW	EC	U	Mult.
Bacillus anthracis str. A2012	47.3%	21.7%	1.2%	3.0%	26.2%	0.7%
Bacillus anthracis str. Ames	46.6%	21.7%	1.1%	4.7%	25.2%	0.7%
Bacillus cereus ATCC 10987	45.1%	21.3%	1.0%	6.5%	25.1%	0.9%
Bacillus cereus ATCC14579	48.5%	21.7%	0.9%	3.5%	24.4%	1.0%
Bacillus halodurans C-125	55.7%	20.7%	0.2%	3.9%	16.8%	2.7%
Bacillus subtilis subsp. subtilis str. 168	50.6%	22.2%	0.5%	2.6%	23.5%	0.7%
Bifidobacterium longum NCC2705	54.7%	20.5%	1.3%	1.1%	21.8%	0.6%
Clostridium acetobutylicum ATCC824	46.9%	21.1%	0.8%	2.5%	28.3%	0.4%
Clostridium perfringens str. 13	54.5%	22.1%	0.8%	2.1%	19.1%	1.3%
Clostridium tetani E88	53.3%	23.8%	1.2%	1.0%	19.5%	1.2%
Corynebacterium diphtheriae NCTC 13129	52.3%	19.0%	0.7%	2.2%	24.6%	1.1%
Corynebacterium efficiens YS-314	54.8%	18.4%	0.4%	1.9%	23.0%	1.4%
Corynebacterium glutamicum ATCC 13032	52.1%	20.0%	0.5%	1.6%	24.4%	1.4%
Deinococcus radiodurans str. R1 chromosome 1	48.9%	15.0%	0.6%	1.9%	33.1%	0.5%
Deinococcus radiodurans str. R1 chromosome 2	51.6%	16.3%	0.5%	1.1%	29.9%	0.5%
Enterococcus faecalis V583	48.7%	20.0%	1.4%	3.7%	25.8%	0.3%
Lactobacillus johnsonii NCC 533	44.0%	24.5%	1.4%	1.0%	28.9%	0.2%
Lactobacillus plantarum WCFS1	41.7%	21.3%	1.5%	1.3%	33.9%	0.4%
Lactococcus lactis Il1403	48.2%	19.4%	1.0%	1.9%	29.2%	0.3%
Listeria innocua Clip 11262 chromosome	54.8%	19.7%	1.6%	1.4%	21.9%	0.6%
Listeria monocytogenes EGD-e	55.1%	21.1%	1.9%	1.5%	19.7%	0.7%
Mycobacterium avium subsp. paratuberculosis k10	55.1%	15.2%	0.3%	1.6%	27.4%	0.4%
Mycobacterium bovis subsp. bovis AF2122/97	52.7%	15.1%	0.2%	3.5%	28.0%	0.5%
Mycobacterium leprae TN	53.1%	15.6%	0.0%	1.9%	28.7%	0.7%
Mycobacterium tuberculosis CDC1551	49.9%	14.0%	0.2%	5.0%	30.4%	0.5%
Mycobacterium tuberculosis H37Rv	53.1%	15.2%	0.2%	3.4%	27.5%	0.5%
Oceanobacillus iheyensis HTE831	50.1%	23.2%	0.3%	2.3%	22.0%	2.2%
Staphylococcus aureus subsp. aureus Mu50	48.0%	20.7%	1.3%	4.6%	25.1%	0.4%
Staphylococcus aureus subsp. aureus MW2	47.3%	21.3%	1.2%	5.2%	24.5%	0.5%
Staphylococcus aureus subsp. aureus N315	48.1%	21.3%	1.2%	4.5%	24.5%	0.4%
Staphylococcus epidermidis ATCC 12228	46.7%	20.3%	1.2%	7.3%	23.9%	0.5%
Streptococcus agalactiae 2603V/R	48.9%	20.4%	1.6%	4.0%	24.5%	0.5%
Streptococcus agalactiae NEM316	49.8%	21.8%	2.1%	1.6%	24.3%	0.5%
Streptococcus mutans UA159	48.2%	21.4%	0.7%	3.4%	26.2%	0.2%
Streptococcus pneumonia R6	52.4%	20.5%	0.9%	2.6%	23.0%	0.6%
Streptococcus pneumonia TIGR4	51.1%	19.6%	0.9%	6.0%	21.9%	0.4%
Streptococcus pyogenes M1 GAS	51.0%	18.9%	1.1%	2.2%	26.3%	0.5%
Streptococcus pyogenes MGAS315	50.3%	17.0%	1.2%	2.0%	29.2%	0.3%
Streptococcus pyogenes MGAS8232	49.8%	17.2%	1.0%	2.5%	29.2%	0.4%
Streptococcus pyogenes SSI-1	49.8%	16.9%	1.2%	2.6%	29.2%	0.3%
Streptomyces avermitilis MA-4680	52.5%	16.6%	0.4%	2.9%	26.9%	0.6%
Streptomyces coelicolor A3(2)	51.2%	16.5%	0.4%	3.4%	27.2%	1.2%
Thermoanaerobacter tengcongensis	59.9%	20.1%	0.5%	1.4%	17.1%	1.0%
Tropheryma whipplei TW08/27	53.1%	22.6%	0.8%	1.7%	20.7%	1.1%
Tropheryma whipplei Twist	52.4%	21.5%	0.6%	1.4%	23.4%	0.7%

Table S3. Confusion matrices for performance comparison between PSORT-B v.2.0, CELLO v.2.0, and Proteome Analyst v.1.0.

PSORT-B v.2.0

Actual localization Predicted localization

C

CM

P

OM

EC

U

C
22

1

0

1

0

6

CM
1

39

0

0

0

2

P
0

0

26

0

0

6

OM
0

0

0

34

0

5

EC
0

0

0

0

1

0

CELLO v.2.0

Actual localization	Predicted localization
	C	CM	P	OM	EC	U
C	27	1	1	1	0	0
CM	5	35	2	0	0	0
P	3	3	16	2	8	0
OM	1	0	3	24	11	0
EC	0	0	0	0	1	0

Proteome Analyst v.1.0

Actual localization	Predicted localization
	C	CM	P	OM	EC	U
C	22	6	1	0	1	0
CM	0	40	0	0	2	0
P	1	0	29	0	2	0
OM	0	0	0	34	3	2
EC	0	0	0	0	1	0

Figure S1. Proportion of proteins at each localization site.

Click here to view this figure in a new window.

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