Effective results for Shewanella loihica PV-4 (eggnog40)

Summary

Number of putative secreted proteins: 37
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 11 eukaryotic-like domains, contained in 37 proteins (1 high, 36 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
323850.Shew_2246				(PF00849)	(mitochondrial)
323850.Shew_0807				(PF02225)	ER
323850.Shew_0935				(PF02225)	ER
323850.Shew_1510				(PF02225)	ER
323850.Shew_2529				(PF00849)	ER; (ER)
323850.Shew_2208				(PF02225)	ER
323850.Shew_2051				(PF09317)	ER
323850.Shew_0781				(PF02225)	ER; (ER)
323850.Shew_3152				(PF02225)	ER; (ER)
323850.Shew_2367				(PF04970)	ER
323850.Shew_2960				(PF02225)	ER
323850.Shew_3180				(PF00849)	mitochondrial
323850.Shew_2108				(PF09317)	ER
323850.Shew_2720				(PF02225)	ER
323850.Shew_3418				(PF06468)	ER
323850.Shew_3417				(PF06468)	mitochondrial
323850.Shew_1678				(PF07766)	mitochondrial
323850.Shew_0916				(PF00849)	(mitochondrial)
323850.Shew_1562				(PF00849)	plastid
323850.Shew_1028				(PF14216)
323850.Shew_1253				(PF04970)
323850.Shew_0814				(PF00849)
323850.Shew_1620				PF01536
323850.Shew_2643				(PF00849)
323850.Shew_2975				(PF00849)
323850.Shew_2443				(PF02225)
323850.Shew_3003				(PF09317)
323850.Shew_2996				(PF00026)
323850.Shew_2547				(PF00849)
323850.Shew_0783				(PF00849)
323850.Shew_2950				(PF00849)
323850.Shew_0099				(PF00849)
323850.Shew_1594				(PF00849)
323850.Shew_3348				(PF00849)
323850.Shew_1460				(PF00849)
323850.Shew_0508				(PF16983)
323850.Shew_1642				(PF05548)

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: YES (FDR = 7.7 %)
  Estimated copy number = 0.625 (5/8 KEGG proteins)

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