Effective results for Sinorhizobium fredii HH103 (eggnog40)

Summary

Number of putative secreted proteins: 457
- Predicted by EffectiveT3: 118 (high confidence), 171 (low confidence)
- Predicted by EffectiveCCBD: 13 within, 10 before, 26 behind expected region 25..70aa
- Predicted by T4SEpre: 74
- Predicted by EffectiveELD: 14 eukaryotic-like domains, contained in 67 proteins (5 high, 62 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
1117943.SFHH103_01746		(>)		(PF04191)	ER
1117943.SFHH103_01157	(+)		+	(PF03959)	ER
1117943.SFHH103_00276	+		+		(mitochondrial); plastid
1117943.SFHH103_03231			+		ER
1117943.SFHH103_01696				(PF05023)	ER
1117943.SFHH103_00090				(PF04191)	ER
1117943.SFHH103_02796			+		mitochondrial
1117943.SFHH103_03446	+				(mitochondrial)
1117943.SFHH103_01310	(+)			(PF04800)	mitochondrial
1117943.SFHH103_00136	+				(mitochondrial)
1117943.SFHH103_00133		+			ER; (ER)
1117943.SFHH103_02928		+			(mitochondrial); plastid
1117943.SFHH103_03328		(>)			mitochondrial
1117943.SFHH103_02810		+			(ER)
1117943.SFHH103_02494		(>)			ER
1117943.SFHH103_02788			+		ER
1117943.SFHH103_01895			+		(ER)
1117943.SFHH103_00784		(>)			(mitochondrial)
1117943.SFHH103_01627				(PF07648)	ER
1117943.SFHH103_02441			+		mitochondrial; (mitochondrial)
1117943.SFHH103_00338	+				(mitochondrial)
1117943.SFHH103_00337	+				(mitochondrial); plastid
1117943.SFHH103_01336				(PF13488)	ER
1117943.SFHH103_01331	+				(mitochondrial)
1117943.SFHH103_01841	+				(mitochondrial); plastid
1117943.SFHH103_00326	+				mitochondrial; plastid
1117943.SFHH103_00696			+		ER
1117943.SFHH103_01033	+				mitochondrial; plastid
1117943.SFHH103_00637		(>)			ER
1117943.SFHH103_02512			+		mitochondrial
1117943.SFHH103_03584			+		(ER)
1117943.SFHH103_03245	+				(mitochondrial); plastid
1117943.SFHH103_02980		(>)			ER
1117943.SFHH103_03924		(>)			ER
1117943.SFHH103_02726			+		(mitochondrial)
1117943.SFHH103_00901			+		mitochondrial
1117943.SFHH103_00348			+		ER
1117943.SFHH103_03060			+		(mitochondrial)
1117943.SFHH103_03847				(PF13488)	ER
1117943.SFHH103_01751			+		ER
1117943.SFHH103_02081				(PF04191)	ER
1117943.SFHH103_00941			+		ER
1117943.SFHH103_00399				(PF13488)	ER
1117943.SFHH103_00546			+		(mitochondrial)
1117943.SFHH103_02095	+				mitochondrial; plastid
1117943.SFHH103_00969			+		ER
1117943.SFHH103_01544	+				mitochondrial
1117943.SFHH103_02066			+		ER
1117943.SFHH103_03601			+		ER
1117943.SFHH103_02952			+		ER
1117943.SFHH103_02774			+		ER
1117943.SFHH103_00737		(>)			(ER)
1117943.SFHH103_00499			+		(ER)
1117943.SFHH103_03099				(PF13488)	ER
1117943.SFHH103_03569				(PF05990)	mitochondrial
1117943.SFHH103_01125				(PF04191)	ER
1117943.SFHH103_01836			+		ER
1117943.SFHH103_03390				(PF01695)	ER; (ER)
1117943.SFHH103_02111		(>)			ER
1117943.SFHH103_03505			+		ER
1117943.SFHH103_00272	+				(mitochondrial); (plastid)
1117943.SFHH103_03041	+				mitochondrial
1117943.SFHH103_02353			+		ER
1117943.SFHH103_02351		(>)			ER; (ER)
1117943.SFHH103_03199	+				(mitochondrial)
1117943.SFHH103_00516			+		ER
1117943.SFHH103_00081	(+)		+		(ER)
1117943.SFHH103_02906	+				(plastid)
1117943.SFHH103_03839	(+)				(mitochondrial); (plastid)
1117943.SFHH103_01307			+		(mitochondrial)
1117943.SFHH103_03784				(PF01609)	(mitochondrial)
1117943.SFHH103_02781			+		(mitochondrial)
1117943.SFHH103_00235	(+)				(mitochondrial)
1117943.SFHH103_02862	+	+
1117943.SFHH103_02310				(PF05990)	plastid
1117943.SFHH103_03018		(>)	+
1117943.SFHH103_02693	(+)				(ER)
1117943.SFHH103_00327	(+)				(mitochondrial); plastid
1117943.SFHH103_03310	+				plastid
1117943.SFHH103_03671	(+)				mitochondrial; (mitochondrial)
1117943.SFHH103_01632	+		+
1117943.SFHH103_00341	+				plastid
1117943.SFHH103_03736	(+)				(mitochondrial); plastid
1117943.SFHH103_01608	(+)				(mitochondrial)
1117943.SFHH103_02552	+				(plastid)
1117943.SFHH103_01779		+
1117943.SFHH103_03294		(<)			(mitochondrial)
1117943.SFHH103_02948				(PF01989)	(mitochondrial)
1117943.SFHH103_03898	(+)				(mitochondrial)
1117943.SFHH103_03888	+				(mitochondrial)
1117943.SFHH103_02103	+				plastid
1117943.SFHH103_02037	(+)				mitochondrial; (mitochondrial)
1117943.SFHH103_02742	(+)				(mitochondrial); plastid
1117943.SFHH103_02744	(+)				mitochondrial; (mitochondrial)
1117943.SFHH103_01106	(+)				mitochondrial; (mitochondrial)
1117943.SFHH103_01111	+				plastid
1117943.SFHH103_01439			+
1117943.SFHH103_03143			+
1117943.SFHH103_00666	+
1117943.SFHH103_02653				(PF04191)
1117943.SFHH103_01473	+
1117943.SFHH103_00871				(PF01609)
1117943.SFHH103_00896		(>)
1117943.SFHH103_00097	+
1117943.SFHH103_00095	+
1117943.SFHH103_03753				(PF05990)
1117943.SFHH103_02931	+
1117943.SFHH103_03355				(PF13455)
1117943.SFHH103_03358	+
1117943.SFHH103_02671		+
1117943.SFHH103_02802				(PF01609)
1117943.SFHH103_01139	+
1117943.SFHH103_03827		(>)
1117943.SFHH103_03824		(<)
1117943.SFHH103_02483	(+)				(plastid)
1117943.SFHH103_01863	+
1117943.SFHH103_01864			+
1117943.SFHH103_00312	+
1117943.SFHH103_01319		(<)
1117943.SFHH103_00131	+
1117943.SFHH103_00132	(+)				(plastid)
1117943.SFHH103_03529	+
1117943.SFHH103_01523	+
1117943.SFHH103_01985	+
1117943.SFHH103_00150	+
1117943.SFHH103_03329			+
1117943.SFHH103_00824	+
1117943.SFHH103_02325	+
1117943.SFHH103_02889		+
1117943.SFHH103_02495				(PF01989)
1117943.SFHH103_02496				(PF04412)
1117943.SFHH103_01783	+
1117943.SFHH103_01098			+
1117943.SFHH103_01521	+
1117943.SFHH103_00412	+
1117943.SFHH103_00417			+
1117943.SFHH103_03642		(>)
1117943.SFHH103_01755	(+)				mitochondrial; not used
1117943.SFHH103_01620	(+)	+
1117943.SFHH103_03809				(PF01609)
1117943.SFHH103_03800		(>)
1117943.SFHH103_01665			+
1117943.SFHH103_02445				PF00292
1117943.SFHH103_01792			+
1117943.SFHH103_01794	+
1117943.SFHH103_01401	+
1117943.SFHH103_02045	+
1117943.SFHH103_01061	+
1117943.SFHH103_01886	+
1117943.SFHH103_00336	(+)				(mitochondrial)
1117943.SFHH103_00878		+
1117943.SFHH103_02618	+
1117943.SFHH103_03494		(>)
1117943.SFHH103_03309	+				not used
1117943.SFHH103_02879	+
1117943.SFHH103_01281			+
1117943.SFHH103_02456	+
1117943.SFHH103_02694	(+)				(plastid)
1117943.SFHH103_02052			+
1117943.SFHH103_01506				(PF01695)
1117943.SFHH103_01505				(PF01695)
1117943.SFHH103_00432			+
1117943.SFHH103_00436				(PF01695)
1117943.SFHH103_03436	+
1117943.SFHH103_02032	(+)				(mitochondrial)
1117943.SFHH103_03483				(PF01609)
1117943.SFHH103_03313	+
1117943.SFHH103_02845	+
1117943.SFHH103_03004		(>)
1117943.SFHH103_02998		+
1117943.SFHH103_03462				(PF01609)
1117943.SFHH103_03261	+
1117943.SFHH103_02514	+
1117943.SFHH103_02204	(+)				(plastid)
1117943.SFHH103_02192	+
1117943.SFHH103_03918				(PF01695)
1117943.SFHH103_03400	+
1117943.SFHH103_01510		(>)
1117943.SFHH103_01421				PF00292
1117943.SFHH103_01359		(>)
1117943.SFHH103_00778	+
1117943.SFHH103_00177	+
1117943.SFHH103_03676				(PF01609)
1117943.SFHH103_02856	+
1117943.SFHH103_01216		(<)
1117943.SFHH103_02987		(>)
1117943.SFHH103_03292				(PF01609)
1117943.SFHH103_02184				(PF01609)
1117943.SFHH103_02185	+
1117943.SFHH103_02436	(+)				(plastid)
1117943.SFHH103_02434	+
1117943.SFHH103_01989	+
1117943.SFHH103_02729		+
1117943.SFHH103_00583	+
1117943.SFHH103_00347			+
1117943.SFHH103_03664				(PF01695)
1117943.SFHH103_03666				PF00292
1117943.SFHH103_03726	+
1117943.SFHH103_03053	+
1117943.SFHH103_03066			+
1117943.SFHH103_03069			+
1117943.SFHH103_02685			+
1117943.SFHH103_03114				(PF01609)
1117943.SFHH103_03113				(PF01609)
1117943.SFHH103_03443				(PF01609)
1117943.SFHH103_03285	+
1117943.SFHH103_03844				(PF01609)
1117943.SFHH103_03937	+
1117943.SFHH103_03933			+
1117943.SFHH103_01198	+
1117943.SFHH103_00974	+
1117943.SFHH103_00480		(<)
1117943.SFHH103_01244	+
1117943.SFHH103_00543	+
1117943.SFHH103_03545		+
1117943.SFHH103_02897	(+)				(mitochondrial)
1117943.SFHH103_01962	+
1117943.SFHH103_02703	+
1117943.SFHH103_00968			+
1117943.SFHH103_01140	+
1117943.SFHH103_01148	+
1117943.SFHH103_00706			+
1117943.SFHH103_00363	+
1117943.SFHH103_00364	+
1117943.SFHH103_01549				(PF01442)
1117943.SFHH103_00634	+
1117943.SFHH103_00146	+
1117943.SFHH103_02153			+
1117943.SFHH103_02065		(>)
1117943.SFHH103_03603		(<)
1117943.SFHH103_03048	(+)				(ER)
1117943.SFHH103_03733	+
1117943.SFHH103_03136				(PF01609)
1117943.SFHH103_02951				(PF01609)
1117943.SFHH103_02174				(PF01695)
1117943.SFHH103_02770		(>)
1117943.SFHH103_01773	+
1117943.SFHH103_00953		+
1117943.SFHH103_01397		(>)
1117943.SFHH103_01391	+
1117943.SFHH103_01808		(<)
1117943.SFHH103_00041	+
1117943.SFHH103_00491	+
1117943.SFHH103_00992		(>)
1117943.SFHH103_01387	+
1117943.SFHH103_03387	(+)				(ER)
1117943.SFHH103_03385				(PF01609)
1117943.SFHH103_03383	+
1117943.SFHH103_03382				(PF01695)
1117943.SFHH103_03380				(PF01695)
1117943.SFHH103_03415				(PF01695)
1117943.SFHH103_02949				(PF04412)
1117943.SFHH103_03149				(PF01609)
1117943.SFHH103_03418			+
1117943.SFHH103_01819	+
1117943.SFHH103_02387	+
1117943.SFHH103_03560	+
1117943.SFHH103_00239				(PF01695)
1117943.SFHH103_01948	(+)				(ER); not used
1117943.SFHH103_02548			+
1117943.SFHH103_02766				(PF01695)
1117943.SFHH103_01493		(<)
1117943.SFHH103_01126	+
1117943.SFHH103_00144	+
1117943.SFHH103_02430			+
1117943.SFHH103_00052				(PF01609)
1117943.SFHH103_03653	(+)				plastid
1117943.SFHH103_03622				(PF01609)
1117943.SFHH103_03170	+				not used
1117943.SFHH103_03391				(PF01695)
1117943.SFHH103_02973				(PF01609)
1117943.SFHH103_01027	+
1117943.SFHH103_03577	+
1117943.SFHH103_02284			+
1117943.SFHH103_03885	+
1117943.SFHH103_03880		(<)
1117943.SFHH103_02575				(PF01695)
1117943.SFHH103_01951				(PF01609)
1117943.SFHH103_01953	+
1117943.SFHH103_03404			+
1117943.SFHH103_03408				(PF04800)
1117943.SFHH103_01005	+
1117943.SFHH103_00445			+
1117943.SFHH103_01827	+
1117943.SFHH103_00198	+
1117943.SFHH103_00197				(PF01609)
1117943.SFHH103_01592	(+)		+
1117943.SFHH103_00191	+
1117943.SFHH103_02964	+
1117943.SFHH103_03180	+
1117943.SFHH103_03504	+
1117943.SFHH103_01925	(+)				(mitochondrial)
1117943.SFHH103_02580	+
1117943.SFHH103_02036	+
1117943.SFHH103_02749			+
1117943.SFHH103_01729			+
1117943.SFHH103_02638	+
1117943.SFHH103_02925	+
1117943.SFHH103_01580	+
1117943.SFHH103_01587	+
1117943.SFHH103_01210			+
1117943.SFHH103_01219		(>)
1117943.SFHH103_03889	+
1117943.SFHH103_00678	+
1117943.SFHH103_00299		(<)
1117943.SFHH103_00074				(PF01609)
1117943.SFHH103_03435	+
1117943.SFHH103_02918				PF00292
1117943.SFHH103_03378				(PF01695)
1117943.SFHH103_03194			+
1117943.SFHH103_03217	+
1117943.SFHH103_02823	+
1117943.SFHH103_02000			+
1117943.SFHH103_01446	(+)				plastid
1117943.SFHH103_01848				(PF01695)
1117943.SFHH103_01021			+
1117943.SFHH103_00868				PF00292
1117943.SFHH103_00883	+
1117943.SFHH103_03748	(+)
1117943.SFHH103_00513	(+)
1117943.SFHH103_03522	(+)
1117943.SFHH103_02839	(+)
1117943.SFHH103_01901	(+)
1117943.SFHH103_00507	(+)
1117943.SFHH103_01271	(+)
1117943.SFHH103_01270	(+)				not used
1117943.SFHH103_00472	(+)
1117943.SFHH103_01672	(+)
1117943.SFHH103_00093	(+)
1117943.SFHH103_01600	(+)
1117943.SFHH103_03758	(+)
1117943.SFHH103_03353	(+)
1117943.SFHH103_02800	(+)
1117943.SFHH103_02240	(+)
1117943.SFHH103_02330	(+)
1117943.SFHH103_01681	(+)
1117943.SFHH103_02469	(+)
1117943.SFHH103_00316	(+)
1117943.SFHH103_03445	(+)
1117943.SFHH103_01316	(+)
1117943.SFHH103_00223	(+)
1117943.SFHH103_00135	(+)
1117943.SFHH103_00134	(+)
1117943.SFHH103_02608	(+)
1117943.SFHH103_00823	(+)
1117943.SFHH103_03031	(+)
1117943.SFHH103_02473	(+)
1117943.SFHH103_02783	(+)
1117943.SFHH103_01077	(+)
1117943.SFHH103_03331	(+)
1117943.SFHH103_02268	(+)
1117943.SFHH103_01406	(+)
1117943.SFHH103_01065	(+)
1117943.SFHH103_00935	(+)
1117943.SFHH103_00682	(+)
1117943.SFHH103_00113	(+)
1117943.SFHH103_03878	(+)
1117943.SFHH103_03872	(+)
1117943.SFHH103_02279	(+)
1117943.SFHH103_02053	(+)
1117943.SFHH103_02056	(+)
1117943.SFHH103_02059	(+)
1117943.SFHH103_00922	(+)
1117943.SFHH103_00749	(+)				not used
1117943.SFHH103_00107	(+)
1117943.SFHH103_02741	(+)
1117943.SFHH103_02038	(+)
1117943.SFHH103_01515	(+)
1117943.SFHH103_02389	(+)
1117943.SFHH103_03511	(+)
1117943.SFHH103_03677	(+)
1117943.SFHH103_03297	(+)
1117943.SFHH103_03926	(+)
1117943.SFHH103_01569	(+)
1117943.SFHH103_00584	(+)
1117943.SFHH103_01187	(+)
1117943.SFHH103_00902	(+)
1117943.SFHH103_00762	(+)
1117943.SFHH103_00015	(+)
1117943.SFHH103_03668	(+)
1117943.SFHH103_00462	(+)
1117943.SFHH103_03116	(+)
1117943.SFHH103_03115	(+)
1117943.SFHH103_01068	(+)
1117943.SFHH103_02536	(+)				not used
1117943.SFHH103_02882	(+)
1117943.SFHH103_02887	(+)
1117943.SFHH103_03931	(+)
1117943.SFHH103_02405	(+)
1117943.SFHH103_02087	(+)				not used
1117943.SFHH103_02084	(+)
1117943.SFHH103_02716	(+)
1117943.SFHH103_02714	(+)
1117943.SFHH103_00578	(+)
1117943.SFHH103_00481	(+)
1117943.SFHH103_00370	(+)
1117943.SFHH103_00027	(+)
1117943.SFHH103_00024	(+)
1117943.SFHH103_00029	(+)
1117943.SFHH103_00028	(+)
1117943.SFHH103_00541	(+)
1117943.SFHH103_00423	(+)
1117943.SFHH103_02702	(+)
1117943.SFHH103_00962	(+)
1117943.SFHH103_01147	(+)
1117943.SFHH103_01144	(+)
1117943.SFHH103_01389	(+)
1117943.SFHH103_02417	(+)
1117943.SFHH103_03259	(+)
1117943.SFHH103_03554	(+)
1117943.SFHH103_03553	(+)
1117943.SFHH103_03953	(+)
1117943.SFHH103_00559	(+)
1117943.SFHH103_00958	(+)
1117943.SFHH103_02604	(+)
1117943.SFHH103_01552	(+)
1117943.SFHH103_00738	(+)
1117943.SFHH103_03094	(+)
1117943.SFHH103_03098	(+)
1117943.SFHH103_00624	(+)
1117943.SFHH103_01018	(+)
1117943.SFHH103_01491	(+)
1117943.SFHH103_00226	(+)
1117943.SFHH103_01231	(+)
1117943.SFHH103_02541	(+)
1117943.SFHH103_02372	(+)
1117943.SFHH103_02151	(+)				not used
1117943.SFHH103_01954	(+)
1117943.SFHH103_01950	(+)
1117943.SFHH103_01952	(+)
1117943.SFHH103_02592	(+)
1117943.SFHH103_03407	(+)
1117943.SFHH103_01711	(+)
1117943.SFHH103_01485	(+)
1117943.SFHH103_01826	(+)
1117943.SFHH103_00848	(+)
1117943.SFHH103_01222	(+)
1117943.SFHH103_00064	(+)
1117943.SFHH103_03169	(+)
1117943.SFHH103_00157	(+)
1117943.SFHH103_03870	(+)
1117943.SFHH103_02104	(+)
1117943.SFHH103_02569	(+)
1117943.SFHH103_01922	(+)
1117943.SFHH103_01107	(+)
1117943.SFHH103_00987	(+)
1117943.SFHH103_00453	(+)
1117943.SFHH103_01586	(+)
1117943.SFHH103_00858	(+)
1117943.SFHH103_01214	(+)
1117943.SFHH103_00674	(+)
1117943.SFHH103_00279	(+)
1117943.SFHH103_02828	(+)
1117943.SFHH103_01939	(+)
1117943.SFHH103_01116	(+)
1117943.SFHH103_01209	(+)
1117943.SFHH103_01200	(+)

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 = 0.3 (3/10 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:

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