Effective results for Sinorhizobium meliloti 1021 (eggnog40)

Summary

Number of putative secreted proteins: 314
- Predicted by EffectiveT3: 87 (high confidence), 128 (low confidence)
- Predicted by EffectiveCCBD: 11 within, 10 before, 22 behind expected region 25..70aa
- Predicted by T4SEpre: 63
- Predicted by EffectiveELD: 5 eukaryotic-like domains, contained in 12 proteins (0 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
266834.SMc00456			+		ER
266834.SMc03234			+		ER
266834.SMc02897			+		ER
266834.SMc02543			+		ER
266834.SMc03971		+			(ER)
266834.SMc00540			+	(PF04305)	(plastid)
266834.SMc01556			+		mitochondrial; (mitochondrial)
266834.SMc03049	+				(mitochondrial)
266834.SMc04226				(PF07648)	ER
266834.SMc04020			+		ER
266834.SMc01825		(>)			ER
266834.SMc01827			+		ER
266834.SMc04091			+		ER
266834.SMc00354			+		ER
266834.SMc00868			+		ER
266834.SMc00523				(PF04305)	(mitochondrial)
266834.SMc01722			+		(ER); ER
266834.SMc00655			+		(mitochondrial)
266834.SMc01652			+		ER
266834.SMc02359		(>)			ER
266834.SMc00612			+		ER; (ER)
266834.SMc03037	+				mitochondrial; plastid
266834.SMc03182		(>)			ER
266834.SMc01660			+		ER
266834.SMc00621			+		ER
266834.SMc04459			+		ER
266834.SMc02419	+				plastid
266834.SMc02088		(<)			(mitochondrial)
266834.SMc02792		(>)			(mitochondrial)
266834.SMc03789	+				plastid
266834.SMc02236	+				(plastid)
266834.SMc04219		+	+
266834.SMc00570	(+)				(mitochondrial)
266834.SMc03048	+				plastid
266834.SMc05011	+				(mitochondrial); not used
266834.SMc00290			+		(mitochondrial)
266834.SMc03880			+		(mitochondrial)
266834.SMc03085	+		+
266834.SMc02599		(>)			(ER)
266834.SMc00002			+		(ER)
266834.SMc02472	+				(plastid)
266834.SMc00775	(+)				(ER)
266834.SMc02240	+				(plastid)
266834.SMc00231		(<)
266834.SMc01931	+				(plastid)
266834.SMc02020	(+)				(mitochondrial)
266834.SMc04240	(+)				ER; (ER)
266834.SMc03926	+				(plastid)
266834.SMc02727	+				(plastid)
266834.SMc00350	(+)				ER; (ER)
266834.SMc01711		+			plastid
266834.SMc03882		(<)			(mitochondrial)
266834.SMc00821	(+)				(mitochondrial)
266834.SMc02975		+			(mitochondrial)
266834.SMc02574	+
266834.SMc01874			+
266834.SMc01871	+
266834.SMc00453			+
266834.SMc04137	+
266834.SMc04261			+
266834.SMc02180	+
266834.SMc02564		+
266834.SMc04361	+
266834.SMc01869	+
266834.SMc04301	+
266834.SMc00155	+
266834.SMc02081			+
266834.SMc02798		(>)
266834.SMc02421		(>)
266834.SMc02423		(<)
266834.SMc02326		(>)
266834.SMc04463	(+)		+
266834.SMc00038			+
266834.SMc04202	+
266834.SMc01144			+
266834.SMc00329	(+)				(mitochondrial)
266834.SMc00498	+
266834.SMc00819	+
266834.SMc00149	+
266834.SMc02162	+
266834.SMc01986	+
266834.SMc03144		(>)
266834.SMc02788	+
266834.SMc02434	+
266834.SMc01339				(PF13384)
266834.SMc00909		(<)
266834.SMc02820		(>)
266834.SMc03975			+
266834.SMc02764	+
266834.SMc03201		+
266834.SMc00042	(+)				(ER)
266834.SMc05008			+
266834.SMc04440	+
266834.SMc00783	+
266834.SMc01016			+
266834.SMc00301			+
266834.SMc00166		(>)
266834.SMc00761	+
266834.SMc02148			+
266834.SMc02452	(+)				plastid
266834.SMc04182		(<)
266834.SMc01952		(>)
266834.SMc00575	+
266834.SMc01002	+
266834.SMc01003	+
266834.SMc01823	+
266834.SMc00378	+
266834.SMc00195	+
266834.SMc00190				(PF01442)
266834.SMc04231	(+)		+
266834.SMc03088				(PF13384)
266834.SMc03313				(PF13384)
266834.SMc00073	+
266834.SMc02912		(>)
266834.SMc01441	+
266834.SMc01797		(>)
266834.SMc02120	+
266834.SMc01920		(>)
266834.SMc02272	+
266834.SMc02690	+
266834.SMc01777		(>)
266834.SMc04092	+
266834.SMc00704	+
266834.SMc01114	+
266834.SMc00091	+
266834.SMc01602	+
266834.SMc03199	(+)				(plastid)
266834.SMc03192		(>)
266834.SMc03193	+
266834.SMc01341	(+)				(mitochondrial); not used
266834.SMc00505	+
266834.SMc00349	+
266834.SMc01904	+
266834.SMc00725	+
266834.SMc01636			+
266834.SMc00652		+
266834.SMc03071		+
266834.SMc02103		(<)
266834.SMc02100		(>)
266834.SMc02109			+
266834.SMc02493	+
266834.SMc02250		+
266834.SMc00931	(+)				plastid
266834.SMc01359	+
266834.SMc01759		+
266834.SMc01286			+
266834.SMc02660		(>)
266834.SMc04386	+
266834.SMc04388	(+)				(ER)
266834.SMc01802	+
266834.SMc00393			+
266834.SMc00394	+
266834.SMc01631	+
266834.SMc00339		(>)
266834.SMc00808	+
266834.SMc02398				(PF13384)
266834.SMc00386		(<)
266834.SMc04350	+
266834.SMc03875			+
266834.SMc03874	+
266834.SMc01651		(>)
266834.SMc00891				(PF13384)
266834.SMc00673	+
266834.SMc03010		(<)
266834.SMc02017	+
266834.SMc01237			+
266834.SMc00460			+
266834.SMc04167	+
266834.SMc04164	+
266834.SMc04340	+
266834.SMc03866			+
266834.SMc00261	+
266834.SMc04297	+
266834.SMc01646	+
266834.SMc04146	+
266834.SMc03132	+
266834.SMc02023	+
266834.SMc02352				(PF16952)
266834.SMc02287				(PF13384)
266834.SMc01090			+
266834.SMc01908			+
266834.SMc01708	+
266834.SMc01258	+
266834.SMc01949			+
266834.SMc04382	+
266834.SMc04045		+
266834.SMc00617			+
266834.SMc00108	+
266834.SMc00104		(<)
266834.SMc03101	+
266834.SMc03052	+
266834.SMc02611	+
266834.SMc02291				(PF13384)
266834.SMc02121	+
266834.SMc02039			+
266834.SMc01241	(+)				(plastid)
266834.SMc03800			+
266834.SMc03801	+
266834.SMc00138	+
266834.SMc03249	+
266834.SMc03027	(+)				(plastid)
266834.SMc02376	(+)				(plastid)
266834.SMc01764	+
266834.SMc02978	+
266834.SMc02575	(+)
266834.SMc00762	(+)
266834.SMc00450	(+)
266834.SMc01509	(+)
266834.SMc03231	(+)
266834.SMc01130	(+)
266834.SMc03764	(+)
266834.SMc01915	(+)
266834.SMc04360	(+)
266834.SMc01862	(+)
266834.SMc01192	(+)
266834.SMc01048	(+)
266834.SMc00800	(+)
266834.SMc02172	(+)
266834.SMc03179	(+)
266834.SMc02888	(+)
266834.SMc02087	(+)
266834.SMc02791	(+)
266834.SMc02427	(+)
266834.SMc01854	(+)
266834.SMc00926	(+)
266834.SMc01323	(+)
266834.SMc04460	(+)
266834.SMc00144	(+)
266834.SMc00922	(+)
266834.SMc02544	(+)
266834.SMc00557	(+)
266834.SMc00550	(+)
266834.SMc01534	(+)
266834.SMc04213	(+)
266834.SMc02353	(+)
266834.SMc00779	(+)
266834.SMc02230	(+)
266834.SMc01307	(+)
266834.SMc00788	(+)
266834.SMc01783	(+)
266834.SMc00576	(+)
266834.SMc01165	(+)
266834.SMc02181	(+)
266834.SMc02217	(+)
266834.SMc02219	(+)
266834.SMc01316	(+)
266834.SMc01171	(+)
266834.SMc00191	(+)
266834.SMc00990	(+)
266834.SMc02044	(+)
266834.SMc03922	(+)
266834.SMc02269	(+)
266834.SMc02463	(+)
266834.SMc01368	(+)
266834.SMc01566	(+)
266834.SMc01581	(+)
266834.SMc00188	(+)
266834.SMc00007	(+)
266834.SMc00988	(+)
266834.SMc03989	(+)
266834.SMc03059	(+)
266834.SMc02587	(+)
266834.SMc02036	(+)
266834.SMc00517	(+)
266834.SMc01778	(+)
266834.SMc00640	(+)
266834.SMc03047	(+)
266834.SMc02117	(+)
266834.SMc02119	(+)
266834.SMc02869	(+)
266834.SMc02649	(+)
266834.SMc02244	(+)
266834.SMc00507	(+)
266834.SMc01905	(+)
266834.SMc01010	(+)
266834.SMc02105	(+)
266834.SMc04403	(+)
266834.SMc00935	(+)
266834.SMc01285	(+)
266834.SMc01139	(+)
266834.SMc03846	(+)
266834.SMc00433	(+)
266834.SMc02841	(+)
266834.SMc00416	(+)
266834.SMc01430	(+)
266834.SMc02286	(+)
266834.SMc02386	(+)
266834.SMc01665	(+)
266834.SMc04161	(+)
266834.SMc00262	(+)
266834.SMc04290	(+)
266834.SMc00609	(+)
266834.SMc00115	(+)
266834.SMc03135	(+)
266834.SMc01490	(+)
266834.SMc00767	(+)
266834.SMc00479	(+)
266834.SMc04339	(+)
266834.SMc00270	(+)
266834.SMc04028	(+)
266834.SMc00013	(+)
266834.SMc03925	(+)
266834.SMc01540	(+)
266834.SMc03108	(+)
266834.SMc01718	(+)
266834.SMc04171	(+)
266834.SMc01796	(+)
266834.SMc02374	(+)				not used
266834.SMc03808	(+)
266834.SMc01666	(+)
266834.SMc00916	(+)
266834.SMc00241	(+)
266834.SMc00825	(+)
266834.SMc03023	(+)

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