Effective results for Sinorhizobium fredii NGR234 (eggnog40)

Summary

Number of putative secreted proteins: 396
- Predicted by EffectiveT3: 112 (high confidence), 165 (low confidence)
- Predicted by EffectiveCCBD: 15 within, 13 before, 19 behind expected region 25..70aa
- Predicted by T4SEpre: 70
- Predicted by EffectiveELD: 5 eukaryotic-like domains, contained in 20 proteins (1 high, 19 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
394.NGR_c34730	+		+		(mitochondrial); plastid
394.NGR_c02360	+		+		(mitochondrial); plastid
394.NGR_c18480			+		(ER)
394.NGR_c34280		+			mitochondrial
394.NGR_c27760			+		ER
394.NGR_c27570			+		(mitochondrial)
394.NGR_c04710		+			ER
394.NGR_c17830			+		ER
394.NGR_c27970		+			(ER)
394.NGR_c20430			+		(mitochondrial); mitochondrial
394.NGR_c19320			+		ER
394.NGR_c29180		+			(mitochondrial); plastid
394.NGR_c10300			+		ER
394.NGR_c27010	+				mitochondrial; plastid
394.NGR_c01830			+		ER
394.NGR_c01010				(PF05544)	mitochondrial
394.NGR_c24890			+		ER
394.NGR_c36060	+				(mitochondrial)
394.NGR_c03060			+		ER
394.NGR_c08340				(PF02371)	(mitochondrial)
394.NGR_c29710		(>)			ER
394.NGR_c27840			+		mitochondrial
394.NGR_c19100			+		ER
394.NGR_c08020		(>)			(ER)
394.NGR_c18220			+		ER
394.NGR_c33560			+		ER
394.NGR_c25820			+		ER
394.NGR_c01560	+				(mitochondrial)
394.NGR_c26840	+				(ER); plastid
394.NGR_c17610				(PF05023)	ER
394.NGR_c21690			+		ER
394.NGR_c02840	+				mitochondrial; plastid
394.NGR_c02320	+				(mitochondrial); plastid
394.NGR_c22180		(>)			ER
394.NGR_c13720			+		ER
394.NGR_c32080			+		ER
394.NGR_c26790			+		(mitochondrial)
394.NGR_c02950	+				(mitochondrial); plastid
394.NGR_c24870		(>)			ER; (ER)
394.NGR_c04500			+		ER
394.NGR_c02960	+				(mitochondrial)
394.NGR_c24310				PF12763	ER
394.NGR_c04970				(PF02371)	(mitochondrial)
394.NGR_c31640	(+)		+		(plastid)
394.NGR_c05840			+		(plastid)
394.NGR_c36650	(+)				(mitochondrial)
394.NGR_c06150			+		(ER)
394.NGR_c23020	+				(plastid)
394.NGR_c06540	+				(plastid)
394.NGR_c32540	+				plastid
394.NGR_c20130	(+)				ER
394.NGR_c17390		+			(plastid)
394.NGR_c23990	+				(plastid)
394.NGR_c00800			+		(ER)
394.NGR_c08940	+				(mitochondrial); not used
394.NGR_c36730	(+)				mitochondrial
394.NGR_c02990	+				plastid
394.NGR_c32750		(<)			(mitochondrial)
394.NGR_c14120			+		(mitochondrial)
394.NGR_c01760	+				(plastid)
394.NGR_c17700	+				plastid
394.NGR_c02850	(+)				(mitochondrial); plastid
394.NGR_c16650	(+)				mitochondrial
394.NGR_c32730			+		(mitochondrial)
394.NGR_c28990	+				(plastid)
394.NGR_c34700		(>)			(mitochondrial)
394.NGR_c18630	(+)				ER
394.NGR_c08530		(<)			plastid
394.NGR_c31830	(+)				mitochondrial
394.NGR_c21350	(+)				(mitochondrial)
394.NGR_c09640		(>)
394.NGR_c36360	+
394.NGR_c31120			+
394.NGR_c00420	+
394.NGR_c12270			+
394.NGR_c16990	+
394.NGR_c33880	+
394.NGR_c18660	(+)		+
394.NGR_c17110			+
394.NGR_c28820		+
394.NGR_c18800		(<)
394.NGR_c35920		(>)
394.NGR_c29890		+
394.NGR_c07390	+
394.NGR_c14650		(>)
394.NGR_c05530				(PF02371)
394.NGR_c18320				(PF02371)
394.NGR_c06450	+
394.NGR_c30770	+
394.NGR_c16180		(>)
394.NGR_c19780	+
394.NGR_c18920	+
394.NGR_c33450		(>)
394.NGR_c29210	+
394.NGR_c00920	(+)				(plastid)
394.NGR_c08480	+
394.NGR_c22870		(>)
394.NGR_c26140	+
394.NGR_c24610	+
394.NGR_c27140	+
394.NGR_c27380	(+)				(plastid)
394.NGR_c09460		+
394.NGR_c35050				(PF02371)
394.NGR_c20280	+
394.NGR_c30180				(PF05544)
394.NGR_c21390	+
394.NGR_c25140	+
394.NGR_c34250	+				not used
394.NGR_c33440			+
394.NGR_c18860	+
394.NGR_c07350	(+)				(mitochondrial)
394.NGR_c01700	+
394.NGR_c35660		(>)
394.NGR_c36790	+
394.NGR_c10200	+
394.NGR_c30150				(PF05544)
394.NGR_c18450	+
394.NGR_c30080		(>)
394.NGR_c14920			+
394.NGR_c26550	+
394.NGR_c30380	+
394.NGR_c19470				(PF02371)
394.NGR_c27600		+
394.NGR_c00260	+
394.NGR_c15440			+
394.NGR_c00640	+
394.NGR_c06950	+
394.NGR_c13320		(<)
394.NGR_c10850			+
394.NGR_c10690	+
394.NGR_c30090	+
394.NGR_c14950	+
394.NGR_c22240	+
394.NGR_c33550	+
394.NGR_c22390	+
394.NGR_c04130		(<)
394.NGR_c20890	+
394.NGR_c15940			+
394.NGR_c15160	+
394.NGR_c10990	(+)				(plastid)
394.NGR_c35080	+
394.NGR_c17410		+
394.NGR_c33960		+
394.NGR_c36030		+
394.NGR_c16320	+
394.NGR_c35880		(<)
394.NGR_c15550			+
394.NGR_c01970	+
394.NGR_c29460				(PF02371)
394.NGR_c34100	+
394.NGR_c33800	+
394.NGR_c16680				(PF01442)
394.NGR_c31880		(<)
394.NGR_c03050			+
394.NGR_c02050	+
394.NGR_c32910	+
394.NGR_c23170	+
394.NGR_c12130			+
394.NGR_c15800	+
394.NGR_c01740	+
394.NGR_c17430		(>)
394.NGR_c05930	+
394.NGR_c17980			+
394.NGR_c13350		(>)
394.NGR_c12550	+
394.NGR_c17500	+
394.NGR_c33160	+
394.NGR_c26050	+
394.NGR_c07270	+
394.NGR_c18090	(+)				(plastid)
394.NGR_c31920	+
394.NGR_c08950	+
394.NGR_c18550		(<)
394.NGR_c21480	+
394.NGR_c13160	+
394.NGR_c31450				(PF02371)
394.NGR_c34340		(<)
394.NGR_c34580				(PF02371)
394.NGR_c20530				(PF05544)
394.NGR_c16060		(<)
394.NGR_c12540	+
394.NGR_c32400	+
394.NGR_c24350			+
394.NGR_c04790	+
394.NGR_c23080			+
394.NGR_c31530				(PF02371)
394.NGR_c26310	(+)				(plastid)
394.NGR_c10400			+
394.NGR_c10150		(>)
394.NGR_c30460			+
394.NGR_c21010			+
394.NGR_c35170			+
394.NGR_c28690	+
394.NGR_c32520	(+)				(plastid)
394.NGR_c30870			+
394.NGR_c23360	(+)				(plastid)
394.NGR_c36520	+
394.NGR_c10140	(+)				(plastid)
394.NGR_c13140	+
394.NGR_c13540			+
394.NGR_c22990	(+)				(mitochondrial)
394.NGR_c12700				(PF02371)
394.NGR_c10560		(>)
394.NGR_c17060	+
394.NGR_c18900	+
394.NGR_c34380			+
394.NGR_c25260	+
394.NGR_c02940	(+)				(mitochondrial)
394.NGR_c17710			+
394.NGR_c22880		+
394.NGR_c06190	+
394.NGR_c29800		(>)
394.NGR_c29150	+
394.NGR_c26230			+
394.NGR_c22400	+
394.NGR_c26420		+
394.NGR_c00300	+
394.NGR_c10350	+
394.NGR_c01320			+
394.NGR_c10910	+
394.NGR_c10820	+
394.NGR_c36450		(<)
394.NGR_c28520	(+)	+
394.NGR_c34040	+
394.NGR_c03200	+
394.NGR_c02620	+
394.NGR_c21680		(>)
394.NGR_c26940	+
394.NGR_c11760	+
394.NGR_c29810	+
394.NGR_c23120	+
394.NGR_c11360	+
394.NGR_c20480	+
394.NGR_c10290			+
394.NGR_c05360				(PF02371)
394.NGR_c13120				(PF02371)
394.NGR_c21560			+
394.NGR_c35230			+
394.NGR_c36440	+
394.NGR_c17840	(+)				(plastid)
394.NGR_c11420	+
394.NGR_c08610			+
394.NGR_c11370	+
394.NGR_c03210	+
394.NGR_c00980	+
394.NGR_c11240	+
394.NGR_c15110	+
394.NGR_c35750	+
394.NGR_c18830	+
394.NGR_c32670	+
394.NGR_c02570		(<)
394.NGR_c32900	+
394.NGR_c35140	+
394.NGR_c36020		(<)
394.NGR_c36560	(+)
394.NGR_c01110	(+)
394.NGR_c17200	(+)
394.NGR_c02740	(+)
394.NGR_c26280	(+)
394.NGR_c09650	(+)
394.NGR_c05020	(+)
394.NGR_c04950	(+)
394.NGR_c20720	(+)
394.NGR_c08030	(+)
394.NGR_c21410	(+)
394.NGR_c27710	(+)
394.NGR_c12420	(+)
394.NGR_c04140	(+)
394.NGR_c08710	(+)
394.NGR_c04040	(+)
394.NGR_c27430	(+)
394.NGR_c30680	(+)
394.NGR_c10010	(+)
394.NGR_c23800	(+)
394.NGR_c13470	(+)
394.NGR_c13300	(+)
394.NGR_c33660	(+)
394.NGR_c12320	(+)
394.NGR_c11200	(+)
394.NGR_c26220	(+)
394.NGR_c11330	(+)
394.NGR_c03250	(+)
394.NGR_c05280	(+)
394.NGR_c24130	(+)
394.NGR_c00120	(+)
394.NGR_c05990	(+)
394.NGR_c31370	(+)
394.NGR_c10510	(+)
394.NGR_c16300	(+)
394.NGR_c02420	(+)
394.NGR_c22920	(+)
394.NGR_c09190	(+)
394.NGR_c14550	(+)
394.NGR_c01350	(+)
394.NGR_c19860	(+)				not used
394.NGR_c27940	(+)
394.NGR_c21910	(+)				not used
394.NGR_c18420	(+)
394.NGR_c13250	(+)
394.NGR_c23690	(+)
394.NGR_c22710	(+)
394.NGR_c00810	(+)
394.NGR_c32980	(+)
394.NGR_c03850	(+)
394.NGR_c21870	(+)
394.NGR_c28720	(+)
394.NGR_c30220	(+)
394.NGR_c25110	(+)
394.NGR_c17820	(+)
394.NGR_c29380	(+)
394.NGR_c11490	(+)
394.NGR_c32780	(+)
394.NGR_c02400	(+)
394.NGR_c11810	(+)
394.NGR_c14390	(+)
394.NGR_c03620	(+)
394.NGR_c34680	(+)
394.NGR_c24360	(+)
394.NGR_c20640	(+)
394.NGR_c01750	(+)
394.NGR_c14970	(+)
394.NGR_c16040	(+)
394.NGR_c36870	(+)
394.NGR_c04110	(+)
394.NGR_c04840	(+)
394.NGR_c01180	(+)
394.NGR_c20180	(+)
394.NGR_c20320	(+)
394.NGR_c19940	(+)
394.NGR_c17050	(+)
394.NGR_c27880	(+)
394.NGR_c16870	(+)
394.NGR_c16670	(+)
394.NGR_c29610	(+)
394.NGR_c03480	(+)
394.NGR_c05780	(+)
394.NGR_c00170	(+)
394.NGR_c35560	(+)
394.NGR_c20190	(+)
394.NGR_c00680	(+)
394.NGR_c06200	(+)
394.NGR_c13010	(+)
394.NGR_c13380	(+)
394.NGR_c16880	(+)
394.NGR_c17600	(+)
394.NGR_c34900	(+)
394.NGR_c01300	(+)
394.NGR_c01090	(+)
394.NGR_c28270	(+)
394.NGR_c05910	(+)
394.NGR_c22560	(+)
394.NGR_c33720	(+)
394.NGR_c26780	(+)
394.NGR_c07670	(+)
394.NGR_c06530	(+)
394.NGR_c28460	(+)
394.NGR_c12140	(+)
394.NGR_c18970	(+)
394.NGR_c11840	(+)
394.NGR_c11930	(+)
394.NGR_c30860	(+)
394.NGR_c04400	(+)
394.NGR_c03940	(+)
394.NGR_c05200	(+)
394.NGR_c30240	(+)
394.NGR_c13150	(+)
394.NGR_c17490	(+)
394.NGR_c22540	(+)
394.NGR_c18960	(+)
394.NGR_c32380	(+)
394.NGR_c11380	(+)
394.NGR_c04980	(+)
394.NGR_c24010	(+)
394.NGR_c30650	(+)
394.NGR_c20150	(+)
394.NGR_c06800	(+)
394.NGR_c05960	(+)
394.NGR_c12720	(+)
394.NGR_c06240	(+)
394.NGR_c12610	(+)
394.NGR_c34050	(+)
394.NGR_c04770	(+)
394.NGR_c20160	(+)
394.NGR_c21570	(+)
394.NGR_c25560	(+)
394.NGR_c17810	(+)
394.NGR_c09700	(+)
394.NGR_c06580	(+)
394.NGR_c28300	(+)
394.NGR_c28940	(+)
394.NGR_c29780	(+)
394.NGR_c36310	(+)
394.NGR_c28160	(+)
394.NGR_c16720	(+)
394.NGR_c26180	(+)
394.NGR_c37010	(+)

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:

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