Effective results for Novosphingobium sp. PP1Y (eggnog40)

Summary

Number of putative secreted proteins: 101
- Predicted by T4SEpre: 70
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 43 proteins (0 high, 43 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type IV

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
702113.PP1Y_AT27326				(PF06455)	ER
702113.PP1Y_AT31415			+		(mitochondrial)
702113.PP1Y_AT12522			+		mitochondrial
702113.PP1Y_AT16773				(PF13207)	(mitochondrial)
702113.PP1Y_AT6403			+		ER
702113.PP1Y_AT24345			+		mitochondrial
702113.PP1Y_AT29061			+		ER
702113.PP1Y_AT19175			+		ER
702113.PP1Y_AT35138			+		mitochondrial
702113.PP1Y_AT31957			+		(mitochondrial)
702113.PP1Y_AT24777			+		ER
702113.PP1Y_AT26940			+		(mitochondrial); mitochondrial
702113.PP1Y_AT21281			+		(mitochondrial)
702113.PP1Y_AT32302				(PF13872) (PF13871)	(plastid)
702113.PP1Y_AT192			+		ER; plastid
702113.PP1Y_AT5105			+		ER
702113.PP1Y_AT5449			+		ER
702113.PP1Y_AT6032			+		ER
702113.PP1Y_AT14195			+		ER
702113.PP1Y_AT7107			+		ER
702113.PP1Y_AT10866				(PF00355) (PF00848)
702113.PP1Y_AT33003			+		(ER)
702113.PP1Y_AT14814			+		(mitochondrial)
702113.PP1Y_AT31241				(PF00355) (PF00848)
702113.PP1Y_AT31065				(PF00355) (PF00848)
702113.PP1Y_AT30726			+		(mitochondrial)
702113.PP1Y_AT31705				(PF00355) (PF00848)
702113.PP1Y_AT31674				(PF00355) (PF00848)
702113.PP1Y_AT15610				(PF00355) (PF00848)
702113.PP1Y_AT34423			+		(plastid)
702113.PP1Y_AT8063			+		(mitochondrial)
702113.PP1Y_AT15992				(PF00355) (PF00848)
702113.PP1Y_AT15854				(PF00355) (PF00848)
702113.PP1Y_AT31297				(PF00355) (PF00848)
702113.PP1Y_AT13595				(PF00355) (PF00848)
702113.PP1Y_AT22200				(PF13872) (PF13871)
702113.PP1Y_AT4063			+		plastid
702113.PP1Y_AT37066			+		(ER)
702113.PP1Y_AT15795				(PF00355) (PF00848)
702113.PP1Y_AT15780				(PF00355) (PF00848)
702113.PP1Y_AT18786			+		(mitochondrial)
702113.PP1Y_AT13576				(PF00355) (PF00848)
702113.PP1Y_AT31315				(PF00355) (PF00848)
702113.PP1Y_AT14538				(PF13872) (PF13871)
702113.PP1Y_AT11936				(PF00355)	(ER)
702113.PP1Y_AT13423				(PF00355) (PF00848)
702113.PP1Y_AT13500				(PF00355) (PF00848)
702113.PP1Y_AT13437				(PF00355) (PF00848)
702113.PP1Y_AT4418				(PF00355) (PF00848)
702113.PP1Y_AT13537				(PF00355) (PF00848)
702113.PP1Y_AT36501				(PF00355) (PF00848)
702113.PP1Y_AT31645				(PF00355) (PF00848)
702113.PP1Y_AT15578				(PF00355) (PF00848)
702113.PP1Y_AT13649				(PF00355) (PF00848)
702113.PP1Y_AT15637				(PF00355) (PF00848)
702113.PP1Y_AT4161				(PF02933)
702113.PP1Y_AT13724			+
702113.PP1Y_AT3663			+
702113.PP1Y_AT22937				(PF00162)
702113.PP1Y_AT13327				(PF00355)
702113.PP1Y_AT4579			+
702113.PP1Y_AT30722			+
702113.PP1Y_AT4105			+
702113.PP1Y_AT7586			+
702113.PP1Y_AT26651			+
702113.PP1Y_AT20235			+
702113.PP1Y_AT28131			+
702113.PP1Y_AT35170				(PF03901)
702113.PP1Y_AT25461			+
702113.PP1Y_AT16177			+
702113.PP1Y_AT3119				(PF13872)
702113.PP1Y_AT28107			+
702113.PP1Y_AT1927			+
702113.PP1Y_AT18960			+
702113.PP1Y_AT23747			+
702113.PP1Y_AT17927				(PF09298)
702113.PP1Y_AT34430			+
702113.PP1Y_AT32377			+
702113.PP1Y_AT6695			+
702113.PP1Y_AT29047			+
702113.PP1Y_AT29868			+
702113.PP1Y_AT12562				(PF09298)
702113.PP1Y_AT208			+
702113.PP1Y_AT12150			+
702113.PP1Y_AT3187				(PF13871)
702113.PP1Y_AT23239			+
702113.PP1Y_AT34482			+
702113.PP1Y_AT15594				(PF00355)
702113.PP1Y_AT20282			+
702113.PP1Y_AT34666			+
702113.PP1Y_AT31695				(PF00355)
702113.PP1Y_AT28745				(PF00162)
702113.PP1Y_AT2399			+
702113.PP1Y_AT13619			+
702113.PP1Y_AT9744			+
702113.PP1Y_AT36990			+
702113.PP1Y_AT33074				(PF09298)
702113.PP1Y_AT26756			+
702113.PP1Y_AT17145			+
702113.PP1Y_AT4735			+
702113.PP1Y_AT1286				(PF00355)

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

• 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: NO (FDR = 12.5 %)
• Functional Type IV secretion system: YES (FDR = 7.2 %)
  Estimated copy number = 1.7 (17/10 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=
==========================================================