Table 1.

Peptide sharing between bacterial proteomes and the human proteome at the 5-, 6-, 7- and 8-mer level

Taxa Id	Bacterium name	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
299768	Streptococcus thermophilus	450402	3863966	35961	92.8	448812	345526	33679	31.8	447222	29009	13533	3.5	445632	5821	2258	0.5
367928	Bifidobacterium adolescentis	593219	4720571	35984	91.6	591592	464558	34565	31.8	589965	41915	16817	3.6	588338	7312	3025	0.4
206672	Bifidobacterium longum	631639	4930744	35983	91.7	629916	507033	34673	32.5	628193	46282	17784	3.7	626470	7796	3266	0.4
257314	Lactobacillus johnsonii	580247	4373499	35966	91.6	578438	394509	34122	29.9	576629	32622	14862	3.2	574820	5814	2354	0.4
272621	Lactobacillus acidophilus	576525	4285917	35956	91.4	574666	378992	33885	29.0	572807	31372	14409	3.0	570948	5704	2190	0.4
203120	Leuconostoc mesenteroides	598355	4551589	35963	92.0	596353	419771	34303	30.4	594351	34970	15491	3.3	592349	6662	2432	0.5
416870	Lactococcus lactis	672683	4980061	35981	92.1	670299	495503	34595	31.5	667915	41383	17246	3.5	665531	6919	2831	0.4
393595	Alcanivorax borkumensis	896972	6304479	35999	91.5	894220	736390	35320	33.5	891468	62704	21456	4.1	888716	9487	4176	0.5
220668	Lactobacillus plantarum	904305	5835444	35989	90.8	901306	623037	35071	30.0	898307	52498	19685	3.3	895308	8195	3575	0.4
226185	Enterococcus faecalis	940332	6145880	35988	91.6	937095	668944	35158	31.1	933858	57666	20168	3.3	930621	9470	3796	0.4
420662	Methylibium petroleiphilum	1363510	7268505	36004	91.3	1359155	1153424	35558	35.9	1354800	123368	26348	5.1	1350445	19643	7555	0.7
251221	Gloeobacter violaceus	1359892	7559021	36004	91.7	1355488	1155772	35593	35.8	1351084	114279	26125	4.7	1346680	18514	7090	0.5
369723	Salinispora tropica	1499556	7020220	35995	91.6	1495034	1268110	35537	37.5	1490512	142761	27415	5.5	1485990	20474	8513	0.6
78245	Xanthobacter autotrophicus	1598054	7692783	36005	91.6	1593085	1285165	35609	35.8	1588116	136687	27146	4.9	1583147	21199	7980	0.6
138119	Desulfuobacterium hafniense	1580893	8351354	36000	90.5	1575878	1125244	35636	31.4	1570863	97706	25570	3.5	1565848	14124	6018	0.4
318586	Paracoccus denitrificans	1541153	7483126	35998	90.8	1536137	1192734	35649	34.5	1531121	122240	26532	4.7	1526105	17463	7217	0.6
351746	Pseudomonas putida	1734619	8415989	36006	90.5	1729375	1327148	35661	33.9	1724131	126059	27425	4.3	1718887	16807	7352	0.5
222523	Bacillus cereus	1505863	7776742	36005	90.0	1499864	981068	35501	29.7	1493866	82158	23724	3.2	1487873	10991	4881	0.4
366394	Sinorhizobium medicae	1896855	8634389	36006	90.6	1890710	1395567	35700	33.6	1884565	133621	27663	4.2	1878420	20378	7549	0.5
224911	Bradyrhizobium japonicum	2582736	9728471	36007	89.8	2574488	1816906	35804	32.9	2566240	183683	29933	4.1	2557992	27201	9643	0.5
471472	Chlamydia trachomatis	306365	3176212	35959	93.3	305482	276387	33051	34.4	304599	22712	11834	4.1	303716	3440	1592	0.5
455434	Treponema pallidum	345928	3356569	35952	93.0	344863	299569	33510	33.8	343798	26743	12789	3.9	342733	5561	2064	0.5
392021	Rickettsia rickeitsii	313106	2762374	35941	92.6	311761	226202	31809	30.7	310416	21699	10218	3.6	309071	5559	1605	0.7
458234	Frunciselia tularensis	450826	3551140	35966	91.8	449318	298668	33231	29.6	447810	24243	12135	3.2	446302	4463	1687	0.5
85962	Helicobacter pylori	485536	3780814	35963	92.2	483971	359383	33668	31.3	482406	29876	13919	3.5	480841	4281	1925	0.4
224326	Borrelia burgdorferi	412046	2867951	35918	93.1	410464	257661	32030	30.8	408882	20885	11291	3.3	407300	3026	1426	0.4
195099	Campylobacter jejuni	531256	3866438	35955	92.2	529420	374675	33686	30.7	527584	30421	14358	3.4	525748	5188	2141	0.4
374833	Neisseria meningitidis	559567	4473458	35977	92.2	557569	433384	34379	32.4	555571	38343	16154	3.8	553573	6201	2582	0.6
516950	Streptococcus pneumoniae	624663	4783135	35976	92.2	622474	467024	34432	31.7	620285	38722	16550	3.5	618096	6560	2702	0.4
257309	Corynebacterium diphtheriae	716248	5461966	35986	92.2	713983	601188	34952	34.0	711718	51983	19542	4.0	709453	7482	3527	0.5
212717	Clostridium tetani	799625	4942017	35972	91.3	797211	519578	34461	29.5	794797	42607	17049	3.1	792383	6520	2876	0.4
273036	Staphylococcus aureus	725020	4995196	35982	91.2	722512	465501	34460	28.8	720004	36783	16275	3.0	717496	5780	2508	0.4
262698	Brucella abortus	874969	6056419	35991	92.0	871895	714382	35165	33.8	868821	65769	21087	4.2	865747	12203	4314	0.7
400673	Legionella pneumophila	1021398	6572966	35999	90.7	1018194	703289	35287	30.2	1014990	57003	20586	3.3	1011786	9586	3736	0.4
520	Bordetella pertussis	1051997	6271766	35998	91.6	1048737	884648	35324	35.3	1045477	91024	23660	4.9	1042217	14756	5916	0.7
243277	Vibrio cholerae	1138797	7077244	36000	90.7	1134997	833801	35408	31.2	1131197	70647	22617	3.5	1127398	12337	4680	0.4
349746	Yersinia pestis	1123279	7065400	36001	90.8	1119462	846102	35433	31.9	1115645	73246	22780	3.7	1111828	11446	4709	0.5
83331	Mycobacterium tuberculosis	1307195	6877511	35993	91.5	1302949	1082521	35477	35.8	1298704	115970	25679	4.9	1294460	19203	7141	0.6
99287	Salmonella typhimurium	1401436	7838576	36001	90.0	1396908	1015124	35570	31.4	1392380	89038	24671	3.6	1387852	12184	5316	0.4
261594	Bacillus anthracis	1439159	7615447	36005	90.1	1433570	944793	35483	29.7	1427981	76954	23306	3.2	1422392	11356	4851	0.4
	Total bacterial overlap*:		15260383	36014			9133718	36014			1643139	35906			200708	31170

The level of peptide overlap between 40 bacterial proteomes and the human proteome is shown. The filtered bacterial proteomes consisted of 128,248 unique proteins, while the human proteome contained 36,014 proteins at the time of the analysis. Bacteria that are pathogenic to humans are shown in bold. Information for each bacterium can be found at ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi. Column details are as follows: (1) Number of 5-mer occurrences in the bacterial proteome (including duplicate instances of same unique 5-mer); (2) Observed bacterial 5-mer occurrences in the human proteome (including multiple occurrences); (3) Number of human proteins involved in the pentapeptide overlap; (4) Percent of unique bacterial 5-mers which occur in the human proteome; (5) Number of 6-mer occurrences in the bacterial proteome (including duplicate instances of same unique 6-mer); (6) Observed bacterial 6-mer occurrences in the human proteome (including multiple occurrences); (7) Number of human proteins involved in the hexapeptide overlap; (8) Percent of unique bacterial 6-mers which occur in the human proteome; (9) Number of 7-mer occurrences in the bacterial proteome (including duplicate instances of same unique7-mer); (10) Observed bacterial 7-mer occurrences in the human proteome (including multiple occurrences); (11) Number of human proteins involved in the heptapeptide overlap; (12) Percent of unique bacterial 7-mers which occur in the human proteome; (13) Number of 8-mer occurrences in the bacterial proteome (including duplicate instances of same unique 8-mer); (14) Observed bacterial 8-mer occurrences in the human proteome (including multiple occurrences); (15) Number of human proteins involved in the octapeptide overlap; (16) Percent of unique bacterial 8-mers which occur in the human proteome.

^*Obtained by combining all bacterial proteomes into one protein set, and computing the overlap of this set with the human proteome. The human proteome was downloaded from UniProtKB²³ and analyzed by custom programs written in C24 (see under Methods).