Effective results for Sinorhizobium medicae WSM419 (eggnog40)

Summary

Number of putative secreted proteins: 381
- Predicted by EffectiveT3: 99 (high confidence), 170 (low confidence)
- Predicted by EffectiveCCBD: 12 within, 7 before, 21 behind expected region 25..70aa
- Predicted by T4SEpre: 71
- Predicted by EffectiveELD: 12 eukaryotic-like domains, contained in 14 proteins (2 high, 12 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)

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
366394.Smed_0078			+		(ER)
366394.Smed_1476			+		(mitochondrial); (plastid)
366394.Smed_1612				(PF07648)	ER
366394.Smed_3030			+		ER
366394.Smed_1859			+		mitochondrial
366394.Smed_1042			+		ER
366394.Smed_2809		(>)			ER
366394.Smed_1826	+				ER; (ER)
366394.Smed_1827			+		ER
366394.Smed_0278	+				(mitochondrial)
366394.Smed_0187	+				(ER); plastid
366394.Smed_1633				(PF05630)	ER
366394.Smed_1832		+			ER; (ER)
366394.Smed_2764		+			(mitochondrial); plastid
366394.Smed_0265	+				mitochondrial; plastid
366394.Smed_1330	+				(mitochondrial); plastid
366394.Smed_2912		(>)			ER
366394.Smed_0216			+		(mitochondrial); mitochondrial
366394.Smed_2966	+				mitochondrial; (mitochondrial)
366394.Smed_2968				(PF09731)	mitochondrial
366394.Smed_2969			+		ER
366394.Smed_2978	+		+		(mitochondrial)
366394.Smed_2371		(>)			ER
366394.Smed_2373			+		ER
366394.Smed_1041			+		ER
366394.Smed_2623			+		ER
366394.Smed_3469	+				(mitochondrial)
366394.Smed_2987				(PF05023)	ER
366394.Smed_3120		(<)			(mitochondrial)
366394.Smed_2187			+		ER
366394.Smed_2058		(>)			(ER)
366394.Smed_3475			+		ER
366394.Smed_1424				PF02475	mitochondrial
366394.Smed_1426			+		mitochondrial; (mitochondrial)
366394.Smed_2604			+		(mitochondrial)
366394.Smed_0450			+		ER
366394.Smed_0636			+		ER
366394.Smed_2296			+		mitochondrial
366394.Smed_0288			+		ER
366394.Smed_1863				(PF05630)	ER
366394.Smed_0721			+		ER
366394.Smed_1677				(PF14216)	(mitochondrial)
366394.Smed_1865			+		(mitochondrial)
366394.Smed_1129			+		mitochondrial
366394.Smed_2643		+			(ER)
366394.Smed_3098	+				ER
366394.Smed_3231	+				(mitochondrial); (plastid)
366394.Smed_2738			+		(mitochondrial)
366394.Smed_1299	(+)				(mitochondrial); mitochondrial
366394.Smed_2696			+		(mitochondrial)
366394.Smed_1639	+				plastid
366394.Smed_1040	+				(plastid)
366394.Smed_0743	(+)				(mitochondrial)
366394.Smed_0277	+				plastid
366394.Smed_3561	(+)				(mitochondrial)
366394.Smed_2572			+		(mitochondrial)
366394.Smed_0152	+				(mitochondrial)
366394.Smed_0156	+				(plastid)
366394.Smed_2948	(+)				ER
366394.Smed_1682	+				(mitochondrial); not used
366394.Smed_2316	(+)				(mitochondrial); plastid
366394.Smed_2313	(+)				ER; (ER)
366394.Smed_1995	(+)				(ER)
366394.Smed_1692	(+)				ER
366394.Smed_1187	+				(plastid)
366394.Smed_1983	(+)				(mitochondrial); (plastid)
366394.Smed_0376	(+)				(ER)
366394.Smed_2608		+			(ER)
366394.Smed_0297	+				(mitochondrial)
366394.Smed_0912	+				(mitochondrial); not used
366394.Smed_1088	(+)				(mitochondrial); (plastid)
366394.Smed_0932	(+)				mitochondrial
366394.Smed_1387	+		+
366394.Smed_1517			+		(ER)
366394.Smed_2018	+		+
366394.Smed_1872	+				plastid
366394.Smed_2784		+			(ER)
366394.Smed_0700		(>)			(ER)
366394.Smed_3118			+		(mitochondrial)
366394.Smed_0896		(>)
366394.Smed_0073			+
366394.Smed_1617	(+)		+
366394.Smed_1610		(>)
366394.Smed_1107	+
366394.Smed_1105	+
366394.Smed_2923			+
366394.Smed_2043			+
366394.Smed_0558	+
366394.Smed_2744	(+)				(plastid)
366394.Smed_2747	+
366394.Smed_2740	+
366394.Smed_3508		(<)
366394.Smed_1911	+
366394.Smed_1914	+
366394.Smed_3373	+
366394.Smed_1669	(+)				(plastid)
366394.Smed_0873	+
366394.Smed_0877			+
366394.Smed_0477	+
366394.Smed_0479	+
366394.Smed_0185		(>)
366394.Smed_1456			+
366394.Smed_2831		(>)
366394.Smed_1123		(<)
366394.Smed_2582	+
366394.Smed_2586			+
366394.Smed_2167	+
366394.Smed_2761	(+)				(ER)
366394.Smed_2767	+
366394.Smed_1009			+
366394.Smed_2564			+
366394.Smed_1557	(+)				(plastid)
366394.Smed_3413	+
366394.Smed_0821		(>)
366394.Smed_0868			+
366394.Smed_0860	+
366394.Smed_0041	+
366394.Smed_0193	+
366394.Smed_2429	+
366394.Smed_1484	+
366394.Smed_1937		(<)			not used
366394.Smed_1150			+
366394.Smed_1806		(<)
366394.Smed_1320	(+)				(plastid)
366394.Smed_1035	+
366394.Smed_1924			+
366394.Smed_1817	+
366394.Smed_1812				(PF05704)
366394.Smed_2144		+
366394.Smed_2145	+
366394.Smed_3239	+
366394.Smed_3548				(PF07653)
366394.Smed_3439		(>)
366394.Smed_0841	(+)				(plastid)
366394.Smed_0025	+
366394.Smed_0338	+
366394.Smed_1312	(+)	(>)
366394.Smed_1778	(+)				ER; not used
366394.Smed_3155	+
366394.Smed_2152			+
366394.Smed_0810	+
366394.Smed_2556	+
366394.Smed_3204		(>)
366394.Smed_0238		(<)
366394.Smed_0232			+
366394.Smed_1582	+
366394.Smed_0301	+
366394.Smed_0490				PF02475
366394.Smed_0166		+
366394.Smed_1789	+
366394.Smed_0066	+				not used
366394.Smed_0064	+
366394.Smed_1590	+
366394.Smed_1047	+
366394.Smed_2172			+
366394.Smed_3214	+
366394.Smed_2500	+
366394.Smed_0937	+
366394.Smed_0957			+
366394.Smed_1570	+
366394.Smed_2883	+
366394.Smed_2310	(+)		+
366394.Smed_2319				(PF04218)
366394.Smed_3130	+
366394.Smed_1132		(>)
366394.Smed_3045	+
366394.Smed_1204			+
366394.Smed_3462		(>)
366394.Smed_1568	+
366394.Smed_0583	(+)				(plastid)
366394.Smed_1219	(+)				(mitochondrial)
366394.Smed_1218				(PF11523)
366394.Smed_1366	+
366394.Smed_1369			+
366394.Smed_2186		(>)
366394.Smed_1985	(+)				(ER)
366394.Smed_0010			+
366394.Smed_0541	+
366394.Smed_3470	(+)				ER
366394.Smed_0805		+
366394.Smed_0972	+
366394.Smed_2896			+
366394.Smed_0110	+
366394.Smed_0574			+
366394.Smed_1510	+
366394.Smed_0592	(+)				(mitochondrial)
366394.Smed_1228	+
366394.Smed_1428	+
366394.Smed_3276	+
366394.Smed_3112	+
366394.Smed_1259			+
366394.Smed_2465	+
366394.Smed_2826		+
366394.Smed_0748	+
366394.Smed_0349	+
366394.Smed_0344	+
366394.Smed_1653			+
366394.Smed_1233			+
366394.Smed_2455	+
366394.Smed_2077	+
366394.Smed_2074			+
366394.Smed_2079	+
366394.Smed_3255		+
366394.Smed_3250	(+)				(ER)
366394.Smed_3498	+
366394.Smed_2133	+
366394.Smed_0281	+
366394.Smed_0919	+
366394.Smed_1538				(PF01442)
366394.Smed_1404		(>)
366394.Smed_0117			+
366394.Smed_2210	+
366394.Smed_2840		(>)
366394.Smed_1668	+
366394.Smed_2067	+
366394.Smed_2369	+
366394.Smed_2713			+
366394.Smed_2362	+
366394.Smed_2448	+
366394.Smed_0383	+
366394.Smed_1524	+
366394.Smed_1678	+
366394.Smed_2473	(+)				(ER)
366394.Smed_2817		(>)
366394.Smed_2723		+
366394.Smed_2721			+
366394.Smed_2536	+
366394.Smed_1463			+
366394.Smed_1891	+
366394.Smed_1608		+
366394.Smed_1117			+
366394.Smed_1845			+
366394.Smed_2398		(>)
366394.Smed_2391				(PF00026)
366394.Smed_3355		(>)
366394.Smed_0820			+
366394.Smed_2739	+
366394.Smed_2731	(+)				(plastid)
366394.Smed_3517	+
366394.Smed_0255	(+)				(plastid)
366394.Smed_0416			+
366394.Smed_0411		(<)
366394.Smed_0891	(+)
366394.Smed_1290	(+)
366394.Smed_1106	(+)
366394.Smed_2104	(+)
366394.Smed_2743	(+)
366394.Smed_1978	(+)
366394.Smed_0083	(+)
366394.Smed_1048	(+)
366394.Smed_1043	(+)
366394.Smed_0400	(+)
366394.Smed_0406	(+)
366394.Smed_2254	(+)
366394.Smed_3377	(+)
366394.Smed_0276	(+)
366394.Smed_0874	(+)
366394.Smed_0474	(+)
366394.Smed_1054	(+)
366394.Smed_1058	(+)
366394.Smed_0988	(+)
366394.Smed_1121	(+)
366394.Smed_2086	(+)
366394.Smed_2342	(+)
366394.Smed_2169	(+)
366394.Smed_3562	(+)
366394.Smed_3560	(+)
366394.Smed_0269	(+)
366394.Smed_0463	(+)
366394.Smed_1331	(+)
366394.Smed_1333	(+)
366394.Smed_2201	(+)
366394.Smed_0687	(+)
366394.Smed_3423	(+)
366394.Smed_0320	(+)
366394.Smed_0326	(+)
366394.Smed_0515	(+)
366394.Smed_0147	(+)
366394.Smed_1493	(+)
366394.Smed_1921	(+)
366394.Smed_2219	(+)
366394.Smed_2989	(+)
366394.Smed_1814	(+)
366394.Smed_3162	(+)
366394.Smed_3160	(+)
366394.Smed_2141	(+)
366394.Smed_3432	(+)
366394.Smed_1342	(+)
366394.Smed_2126	(+)
366394.Smed_1792	(+)
366394.Smed_2379	(+)
366394.Smed_2156	(+)
366394.Smed_1593	(+)
366394.Smed_0836	(+)
366394.Smed_0307	(+)
366394.Smed_0302	(+)
366394.Smed_0167	(+)
366394.Smed_0160	(+)
366394.Smed_0015	(+)
366394.Smed_1010	(+)
366394.Smed_1787	(+)
366394.Smed_1783	(+)
366394.Smed_1046	(+)
366394.Smed_2895	(+)
366394.Smed_0069	(+)
366394.Smed_2415	(+)
366394.Smed_2092	(+)
366394.Smed_3327	(+)
366394.Smed_0799	(+)
366394.Smed_1579	(+)
366394.Smed_1754	(+)
366394.Smed_1750	(+)
366394.Smed_2887	(+)
366394.Smed_1372	(+)
366394.Smed_2959	(+)
366394.Smed_1991	(+)
366394.Smed_1135	(+)
366394.Smed_3264	(+)
366394.Smed_3263	(+)
366394.Smed_0101	(+)
366394.Smed_0103	(+)
366394.Smed_0585	(+)
366394.Smed_1742	(+)
366394.Smed_1364	(+)
366394.Smed_2431	(+)
366394.Smed_3128	(+)
366394.Smed_1980	(+)
366394.Smed_3052	(+)
366394.Smed_2054	(+)
366394.Smed_2619	(+)
366394.Smed_1782	(+)
366394.Smed_0976	(+)
366394.Smed_0979	(+)
366394.Smed_0575	(+)
366394.Smed_2994	(+)
366394.Smed_2261	(+)
366394.Smed_2824	(+)
366394.Smed_0290	(+)
366394.Smed_0523	(+)
366394.Smed_1438	(+)
366394.Smed_1346	(+)
366394.Smed_1656	(+)
366394.Smed_2851	(+)
366394.Smed_3103	(+)
366394.Smed_1495	(+)
366394.Smed_3496	(+)
366394.Smed_0133	(+)
366394.Smed_0351	(+)
366394.Smed_0911	(+)
366394.Smed_0752	(+)
366394.Smed_0758	(+)
366394.Smed_1537	(+)
366394.Smed_1144	(+)
366394.Smed_2846	(+)
366394.Smed_2449	(+)
366394.Smed_1893	(+)
366394.Smed_2660	(+)
366394.Smed_2711	(+)
366394.Smed_2717	(+)
366394.Smed_2716	(+)
366394.Smed_1414	(+)
366394.Smed_0923	(+)
366394.Smed_0387	(+)
366394.Smed_0720	(+)
366394.Smed_0722	(+)
366394.Smed_1095	(+)
366394.Smed_1255	(+)
366394.Smed_3456	(+)
366394.Smed_0736	(+)
366394.Smed_1461	(+)
366394.Smed_1263	(+)
366394.Smed_1116	(+)
366394.Smed_2007	(+)
366394.Smed_2006	(+)
366394.Smed_0827	(+)
366394.Smed_0822	(+)
366394.Smed_0251	(+)
366394.Smed_1973	(+)
366394.Smed_0257	(+)
366394.Smed_0092	(+)
366394.Smed_1540	(+)

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 = 0.2 (2/10 KEGG proteins)
• Functional Type IV secretion system: YES (FDR = 7.2 %)
  Estimated copy number = 0.0 (0/10 KEGG proteins)
• Functional Type VI secretion system: NO (FDR = 7.7 %)

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=
==========================================================