Effective results for Rickettsia typhi str. Wilmington (eggnog40)

Summary

Number of putative secreted proteins: 44
- Predicted by T4SEpre: 38
- Predicted by EffectiveELD: 6 eukaryotic-like domains, contained in 10 proteins (7 high, 3 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
257363.RT0188			+		ER
257363.RT0295				(PF05637)	ER
257363.RT0107				PF02326	(ER)
257363.RT0031			+		ER
257363.RT0032			+		ER
257363.RT0775			+		ER
257363.RT0092			+		ER
257363.RT0216			+		(ER); ER
257363.RT0399			+		ER
257363.RT0825				(PF03959)	ER
257363.RT0112			+		ER
257363.RT0758			+		ER
257363.RT0724				PF03219	(mitochondrial)
257363.RT0214			+		(mitochondrial)
257363.RT0340			+		(mitochondrial)
257363.RT0640			+		(mitochondrial)
257363.RT0294			+
257363.RT0372			+
257363.RT0474			+
257363.RT0808			+
257363.RT0255			+
257363.RT0449			+
257363.RT0362				PF01369
257363.RT0366				PF03219
257363.RT0405			+
257363.RT0313			+
257363.RT0142			+
257363.RT0035			+
257363.RT0670			+
257363.RT0776			+
257363.RT0489			+
257363.RT0485			+
257363.RT0486				PF03219
257363.RT0079				PF03219
257363.RT0552			+
257363.RT0307			+
257363.RT0732			+
257363.RT0820			+
257363.RT0606			+
257363.RT0464				PF03219
257363.RT0865			+
257363.RT0248			+
257363.RT0332			+
257363.RT0723				(PF09752)

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 = 1.6 (16/10 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=
==========================================================