Effective results for Ralstonia solanacearum GMI1000 (eggnog40)

Summary

Number of putative secreted proteins: 492
- Predicted by EffectiveT3: 141 (high confidence), 224 (low confidence)
- Predicted by EffectiveCCBD: 15 within, 8 before, 30 behind expected region 25..70aa
- Predicted by T4SEpre: 68
- Predicted by EffectiveELD: 11 eukaryotic-like domains, contained in 35 proteins (3 high, 32 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): (Type III), Type IV, (Type VI)

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
267608.RSc0337				PF12143 PF12142	mitochondrial
267608.RSc2440		+			(ER)
267608.RSc1259			+		ER
267608.RSc1492				(PF13276)	(mitochondrial)
267608.RSc0805	+				(mitochondrial); plastid
267608.RSc2405				(PF13276)	(mitochondrial)
267608.RSc2408				(PF13276)	mitochondrial
267608.RSc2530		+			mitochondrial
267608.RSc1910		+			(mitochondrial)
267608.RSc0495	+				(mitochondrial)
267608.RSc2511		+			ER
267608.RSc3350			+		ER
267608.RSc0586			+		ER
267608.RSc1436				(PF13276)	mitochondrial
267608.RSc0664			+		ER
267608.RSc1085		(>)			(mitochondrial)
267608.RSc3376		(>)			(mitochondrial)
267608.RSc3390		+			ER
267608.RSc0610	+				ER
267608.RSc0949		(>)			ER; (ER)
267608.RSc1702		(<)			ER
267608.RSc2143	+				(mitochondrial); plastid
267608.RSc3382		(>)			ER
267608.RSc3034		(>)			(mitochondrial)
267608.RSc0423				(PF13276)	mitochondrial
267608.RSc1555	+				(mitochondrial)
267608.RSc1778			+		mitochondrial; (mitochondrial)
267608.RSc2391		(>)			(mitochondrial); mitochondrial
267608.RSc0638			+		mitochondrial
267608.RSc2958			+		ER
267608.RSc2135			+		mitochondrial
267608.RSc1624			+		mitochondrial
267608.RSc3264			+		ER
267608.RSc2328			+		ER; (ER)
267608.RSc0106			+		ER
267608.RSc2926			+		(mitochondrial)
267608.RSc0147			+		ER
267608.RSc2819		(>)			mitochondrial
267608.RSc0516		(>)			(mitochondrial); (plastid)
267608.RSc2936		+			ER
267608.RSc1647			+		ER
267608.RSc2029			+		(mitochondrial)
267608.RSc3083			+		ER
267608.RSc3089				(PF13276)	mitochondrial
267608.RSc3249			+		ER
267608.RSc1830			+	(PF13276)	(mitochondrial)
267608.RSc1655	+				mitochondrial; (mitochondrial)
267608.RSc2305		(>)			(ER)
267608.RSc1031		(>)			ER; (ER)
267608.RSc0736			+		ER
267608.RSc0828				(PF13276)	(mitochondrial)
267608.RSc2265				(PF13276)	mitochondrial; (mitochondrial)
267608.RSc2484	(+)		+		mitochondrial; plastid
267608.RSc1475	+	(>)
267608.RSc1260	+				plastid
267608.RSc2882		(<)
267608.RSc2331			+	(PF13276)
267608.RSc0232		+
267608.RSc2358	+				(mitochondrial)
267608.RSc2995			+		(mitochondrial)
267608.RSc3355	+				(plastid)
267608.RSc2741		(>)			(mitochondrial)
267608.RSc1439				(PF13276)	(ER)
267608.RSc1721	+		+
267608.RSc2182	(+)				mitochondrial
267608.RSc2161	+				plastid
267608.RSc3013	(+)				mitochondrial; (mitochondrial)
267608.RSc0666	+				(plastid)
267608.RSc0060			+		(ER)
267608.RSc0119	(+)				(mitochondrial); plastid
267608.RSc0547	+				(plastid)
267608.RSc0942	+				(plastid)
267608.RSc1175	+				(plastid)
267608.RSc0958	(+)				ER
267608.RSc0723			+		(ER)
267608.RSc1779		(>)			(ER)
267608.RSc2390	+				(plastid)
267608.RSc2555	(+)		+		(plastid)
267608.RSc0898	(+)				mitochondrial
267608.RSc1385				PF01607	(ER)
267608.RSc2014	(+)				(mitochondrial); (plastid)
267608.RSc2011	+				(plastid)
267608.RSc2706				(PF13276)	(ER)
267608.RSc0889	+	(>)
267608.RSc1599		+			(mitochondrial)
267608.RSc2826	(+)				(mitochondrial)
267608.RSc1293	+		+
267608.RSc1297	(+)				mitochondrial
267608.RSc1749		(>)			(plastid)
267608.RSc2107	+			PF07938
267608.RSc2102	+				(mitochondrial)
267608.RSc2583	(+)				(mitochondrial)
267608.RSc3077	+	+
267608.RSc2445	(+)				(mitochondrial); (plastid)
267608.RSc1641	+				(plastid)
267608.RSc2200	+				(plastid)
267608.RSc0409	+				(plastid)
267608.RSc0732		(>)			(ER)
267608.RSc0230	(+)				(mitochondrial)
267608.RSc2055	(+)				ER
267608.RSc1936	(+)				(mitochondrial)
267608.RSc0688	+	(>)
267608.RSc0227	+		+
267608.RSc0826	(+)				mitochondrial
267608.RSc3318		(<)	+
267608.RSc0321	+				mitochondrial
267608.RSc1251	+
267608.RSc1250	+
267608.RSc1621	+
267608.RSc0257			+
267608.RSc1495	(+)				(mitochondrial)
267608.RSc1473	+
267608.RSc2073		(>)
267608.RSc1786	(+)				(plastid)
267608.RSc1798		(>)
267608.RSc3232				(PF13392)
267608.RSc3236				(PF13392)
267608.RSc3129	+
267608.RSc1860	+
267608.RSc1861	(+)				(ER)
267608.RSc0249	+
267608.RSc2661			+
267608.RSc2407	(+)				(mitochondrial)
267608.RSc1442	+
267608.RSc2888				(PF10908)
267608.RSc1040			+
267608.RSc2085	(+)				(mitochondrial)
267608.RSc2080			+
267608.RSc1477	+
267608.RSc1870			+
267608.RSc2657	+
267608.RSc0876	+
267608.RSc1691	(+)				(plastid)
267608.RSc1690			+
267608.RSc1698	+
267608.RSc2856	+
267608.RSc3219			+
267608.RSc3210	+
267608.RSc3216	+
267608.RSc3324	+
267608.RSc0480	+
267608.RSc1844			+
267608.RSc1842				(PF13565)
267608.RSc0005	+
267608.RSc0260	+
267608.RSc0266	+
267608.RSc0464			+
267608.RSc1512	+
267608.RSc0860	(+)	(<)
267608.RSc1192			+
267608.RSc2357	+
267608.RSc0071			+
267608.RSc0103				(PF13565)
267608.RSc0456	+
267608.RSc0850	+
267608.RSc1187			+
267608.RSc2744	+
267608.RSc1435			+
267608.RSc2639	+
267608.RSc2567	+
267608.RSc1998			+
267608.RSc0466	+
267608.RSc2187	+
267608.RSc1451	+
267608.RSc0066			+
267608.RSc2241			+
267608.RSc0110				(PF13565)
267608.RSc2246	+
267608.RSc2756	+
267608.RSc2570	+
267608.RSc1719	(+)				plastid
267608.RSc2194			+
267608.RSc2199	+
267608.RSc2198	+
267608.RSc2176				(PF13565)
267608.RSc2282	+
267608.RSc3159	+
267608.RSc3151	+
267608.RSc3395	(+)				(ER)
267608.RSc3393				(PF13565)
267608.RSc2059		(>)
267608.RSc1894		(>)
267608.RSc2767	+
267608.RSc2852			+
267608.RSc2962	+
267608.RSc2613		(<)
267608.RSc2388				(PF10908)
267608.RSc0240	(+)				(ER)
267608.RSc3362	(+)				(mitochondrial)
267608.RSc2549			+
267608.RSc2356	+
267608.RSc3039	+
267608.RSc0602	+
267608.RSc0042			+
267608.RSc1959	(+)	+
267608.RSc0428	+
267608.RSc1394	+
267608.RSc1395	+
267608.RSc1392	(+)				(ER)
267608.RSc1687		+
267608.RSc1770	+
267608.RSc2775	+
267608.RSc2772	+
267608.RSc2155	+
267608.RSc2158			+
267608.RSc2805	+
267608.RSc2804	+
267608.RSc0637				(PF13565)
267608.RSc0631	+
267608.RSc0639	+
267608.RSc1943			+
267608.RSc1942				(PF05990)
267608.RSc2535	+
267608.RSc0389	+
267608.RSc0387	(+)				(ER)
267608.RSc0896	+
267608.RSc1382	+
267608.RSc1384		(<)
267608.RSc0960				(PF05990)
267608.RSc1549				(PF13276)
267608.RSc1542	+
267608.RSc2831	+
267608.RSc2232			+
267608.RSc0548	+
267608.RSc0625	+
267608.RSc1790	(+)				(plastid)
267608.RSc1797	+
267608.RSc1060		(>)
267608.RSc1379	+
267608.RSc0575	+
267608.RSc0571		(>)
267608.RSc0578				(PF13276)
267608.RSc1281	+
267608.RSc1598	+
267608.RSc2481	+
267608.RSc2480		(<)			not used
267608.RSc2485	+
267608.RSc2965	+
267608.RSc3440	+
267608.RSc1629	+
267608.RSc2139	+
267608.RSc1627			+
267608.RSc3193				(PF13392)
267608.RSc2225	+
267608.RSc1997	+
267608.RSc2223	+
267608.RSc1551	+
267608.RSc3284	+
267608.RSc3069	+
267608.RSc0760	+
267608.RSc0367	+
267608.RSc0365		(>)
267608.RSc1298	+
267608.RSc2928		+
267608.RSc2104		+
267608.RSc2101	+
267608.RSc1631	+
267608.RSc1639	+
267608.RSc2938	(+)				(mitochondrial)
267608.RSc2540	+
267608.RSc1916	(+)				plastid
267608.RSc0374	+
267608.RSc0372	+
267608.RSc1353	+
267608.RSc1356	+
267608.RSc1357				(PF00646)
267608.RSc0193		(>)
267608.RSc1822	+
267608.RSc0200			+
267608.RSc1008	(+)				(mitochondrial)
267608.RSc1003	+
267608.RSc2735	+
267608.RSc2448	+
267608.RSc1640	(+)				(plastid)
267608.RSc0155	+
267608.RSc0742			+
267608.RSc1907	(+)	(>)
267608.RSc2909	+
267608.RSc1019	(+)	(>)
267608.RSc1129			+
267608.RSc1304	+
267608.RSc3095	+
267608.RSc0758	+
267608.RSc1935	+
267608.RSc0356	+
267608.RSc0687		+
267608.RSc1242	+
267608.RSc2914	+
267608.RSc0226				(PF05189)
267608.RSc0220	(+)		+
267608.RSc0827				(PF05990)
267608.RSc0821		+
267608.RSc1487	+
267608.RSc1027	+
267608.RSc1662			+
267608.RSc2267				(PF13276)
267608.RSc2319			+
267608.RSc2317	+
267608.RSc2313				(PF13276)	not used
267608.RSc1919	+
267608.RSc3139		(>)
267608.RSc3135	+
267608.RSc0225	+
267608.RSc1920	+
267608.RSc0322	+
267608.RSc0031	+
267608.RSc2545	(+)
267608.RSc1322	(+)
267608.RSc1079	(+)
267608.RSc2412	(+)
267608.RSc2413	(+)
267608.RSc1676	(+)
267608.RSc2897	(+)
267608.RSc2077	(+)
267608.RSc3234	(+)
267608.RSc2323	(+)
267608.RSc2324	(+)
267608.RSc3126	(+)
267608.RSc2224	(+)
267608.RSc0333	(+)
267608.RSc1866	(+)
267608.RSc0029	(+)
267608.RSc0028	(+)
267608.RSc1311	(+)
267608.RSc0248	(+)
267608.RSc2662	(+)
267608.RSc2402	(+)
267608.RSc2081	(+)
267608.RSc2334	(+)
267608.RSc2332	(+)
267608.RSc3111	(+)
267608.RSc3114	(+)
267608.RSc0235	(+)
267608.RSc0474	(+)
267608.RSc2650	(+)
267608.RSc2656	(+)
267608.RSc2658	(+)
267608.RSc1276	(+)
267608.RSc1692	(+)
267608.RSc1457	(+)
267608.RSc1456	(+)
267608.RSc1533	(+)
267608.RSc1453	(+)
267608.RSc2502	(+)
267608.RSc3213	(+)
267608.RSc3326	(+)
267608.RSc0482	(+)
267608.RSc0484	(+)
267608.RSc0317	(+)
267608.RSc0434	(+)
267608.RSc1991	(+)
267608.RSc0868	(+)
267608.RSc1199	(+)
267608.RSc1202	(+)
267608.RSc1207	(+)
267608.RSc2421	(+)
267608.RSc2352	(+)
267608.RSc3174	(+)
267608.RSc0588	(+)
267608.RSc0079	(+)
267608.RSc0457	(+)
267608.RSc1505	(+)
267608.RSc1433	(+)
267608.RSc2638	(+)
267608.RSc2630	(+)
267608.RSc1728	(+)
267608.RSc2188	(+)
267608.RSc1106	(+)
267608.RSc3349	(+)
267608.RSc3163	(+)
267608.RSc0665	(+)
267608.RSc0597	(+)
267608.RSc0064	(+)
267608.RSc1536	(+)
267608.RSc1538	(+)
267608.RSc0841	(+)
267608.RSc1748	(+)
267608.RSc1226	(+)
267608.RSc1221	(+)
267608.RSc1883	(+)
267608.RSc1228	(+)
267608.RSc2759	(+)
267608.RSc2623	(+)
267608.RSc2577	(+)
267608.RSc1718	(+)
267608.RSc3371	(+)
267608.RSc2286	(+)
267608.RSc3399	(+)
267608.RSc0619	(+)
267608.RSc0791	(+)
267608.RSc0053	(+)
267608.RSc0439	(+)
267608.RSc0540	(+)
267608.RSc1419	(+)
267608.RSc2763	(+)
267608.RSc1099	(+)
267608.RSc1705	(+)
267608.RSc1388	(+)
267608.RSc2386	(+)
267608.RSc0242	(+)
267608.RSc2544	(+)
267608.RSc3148	+
267608.RSc3367	(+)
267608.RSc0043	(+)
267608.RSc0041	(+)
267608.RSc0048	(+)
267608.RSc0135	(+)
267608.RSc0134	(+)
267608.RSc0425	(+)
267608.RSc1393	(+)
267608.RSc0555	(+)
267608.RSc0950	(+)
267608.RSc0952	(+)
267608.RSc2600	(+)
267608.RSc2609	(+)
267608.RSc1772	(+)
267608.RSc2153	(+)
267608.RSc2556	(+)
267608.RSc1441	(+)
267608.RSc0635	(+)
267608.RSc2069	(+)
267608.RSc0703	(+)
267608.RSc1945	(+)				not used
267608.RSc1941	(+)
267608.RSc0143	(+)
267608.RSc0412	(+)
267608.RSc0890	(+)
267608.RSc0895	(+)
267608.RSc0566	(+)
267608.RSc0964	(+)
267608.RSc1543	(+)
267608.RSc1544	(+)
267608.RSc2702	(+)				not used
267608.RSc2700	(+)
267608.RSc2705	(+)
267608.RSc2122	(+)				not used
267608.RSc2120	(+)
267608.RSc3059	(+)
267608.RSc1238	(+)
267608.RSc0082	(+)
267608.RSc0089	(+)
267608.RSc1975	(+)
267608.RSc1372	(+)
267608.RSc0824	(+)
267608.RSc0572	(+)
267608.RSc1028	(+)
267608.RSc1595	(+)
267608.RSc1858	(+)
267608.RSc2615	(+)
267608.RSc3442	(+)
267608.RSc2226	(+)
267608.RSc2220	(+)
267608.RSc0224	(+)
267608.RSc0364	(+)				not used
267608.RSc0363	(+)
267608.RSc0985	(+)
267608.RSc2037	(+)
267608.RSc2584	(+)
267608.RSc2211	(+)
267608.RSc3278	(+)
267608.RSc0779	(+)
267608.RSc0770	(+)
267608.RSc0172	(+)
267608.RSc1359	(+)
267608.RSc0190	(+)
267608.RSc0998	(+)
267608.RSc1004	(+)
267608.RSc1007	(+)
267608.RSc2117	(+)
267608.RSc1836	(+)
267608.RSc2905	(+)
267608.RSc1349	(+)
267608.RSc2876	(+)
267608.RSc1037	(+)
267608.RSc0753	(+)
267608.RSc0751	(+)
267608.RSc1145	(+)
267608.RSc0686	(+)
267608.RSc1801	(+)
267608.RSc1759	(+)
267608.RSc2009	(+)
267608.RSc2868	(+)
267608.RSc3407	(+)
267608.RSc3405	(+)
267608.RSc3136	(+)
267608.RSc1922	(+)
267608.RSc1924	(+)
267608.RSc0326	(+)
267608.RSc1819	(+)
267608.RSc1815	(+)
267608.RSc1812	(+)
267608.RSc0784	(+)

Detailed merged results for each protein sequence

• Detailed merged results as table (merge_results.html)
• Detailed merged results as tab delimited file (merge_results.csv)

Individual results for each protein sequence

• EffectiveT3 predictions using new standard model 2.0.1 (PROTEINS.NEW.EFFECTIVET3)
• EffectiveT3 predictions using old standard model 1.0.1 (PROTEINS.OLD.EFFECTIVET3)
• EffectiveCCBD predictions (PROTEINS.CHAPERONES.TXT)
• T4SEpre bpbAac predictions (T4SEpre_bpbAac_FinalResult.csv)
• T4SEpre psAac predictions (T4SEpre_psAac_FinalResult.csv)
• EffectiveELD predictions (PROTEINS.ELD.TXT)
• Predotar predictions using animal/human model (Predotar_output_modelANIMAL.TXT)
• Predotar predictions using plant model (Predotar_output_modelPLANT.TXT)

Genome based results

Summary

• Gram negative: YES (FDR = 0.5 %)
• Functional Type III secretion system: YES (FDR = 12.5 %)
  Estimated copy number = 0.1 (1/10 KEGG proteins)
• Functional Type IV secretion system: YES (FDR = 7.2 %)
  Estimated copy number = 0.6 (6/10 KEGG proteins)
• Functional Type VI secretion system: YES (FDR = 7.7 %)
  Estimated copy number = 0.5 (4/8 KEGG proteins)

Individual results for each secretion system

• List of 100 most important COGs/NOGs for prediction of functional Type III secretion system (T3_top100_COGS.xls)
• List of 100 most important COGs/NOGs for prediction of functional Type IV secretion system (T4_top100_COGS.xls)
• List of 100 most important COGs/NOGs for prediction of functional Type VI secretion system (T6_top100_COGS.xls)
• List of COGs assigned to Type III secretion system in KEGG (T3SS_KEGG_cmp.xls)
• List of COGs assigned to Type IV secretion system in KEGG (T4SS_KEGG_cmp.xls)
• List of COGs assigned to Type VI secretion system in KEGG (T6SS_KEGG_cmp.xls)

Parameters:

==========================================================
EFFECTIVE_T3_OLD=selective
EFFECTIVE_T3_NEW=selective
PREDOTAR_ANIMAL_OR_PLANT=a
PROTEINS=INPUT PROTEINS
MODUS=genome
RUN_PREDOTAR=T
RUN_EFFECTIVE_T3=T
RUN_T4SEpre=0.5
RUN_EFFECTIVE_CCBD=T
RUN_EFFECTIVE_ELD=4
CheckM_COMPLETENESS=
RUN_EffectiveS346=T
GENOTYPE=COG Profile
EMAIL=
==========================================================