Effective results for Loktanella vestfoldensis SKA53 (eggnog40)

Summary

Number of putative secreted proteins: 15
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 7 eukaryotic-like domains, contained in 15 proteins (1 high, 14 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): None

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
314232.SKA53_10609				(PF03209)	ER
314232.SKA53_00614				(PF11977)	ER
314232.SKA53_12443				(PF04413)	mitochondrial
314232.SKA53_12053				(PF03209)	(mitochondrial)
314232.SKA53_11588				(PF13704)	mitochondrial
314232.SKA53_08311				(PF04413)	(mitochondrial)
314232.SKA53_08316				(PF04413)	ER
314232.SKA53_11578				(PF02485)	(plastid)
314232.SKA53_04738				(PF13704)
314232.SKA53_11583				(PF13704)
314232.SKA53_15096				(PF02485)
314232.SKA53_06042				(PF13704)
314232.SKA53_11633				PF10712
314232.SKA53_04753				(PF13704)
314232.SKA53_07137				(PF10013)	not used

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

• 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: NO (FDR = 7.2 %)
• 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=
==========================================================