Effective results for Grimontia hollisae CIP 101886 (eggnog40)

Summary

Number of putative secreted proteins: 25
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 15 eukaryotic-like domains, contained in 25 proteins (3 high, 22 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
675812.VHA_001502				(PF02010)	(ER); ER
675812.VHA_000904				(PF00165)	ER
675812.VHA_002617				(PF13582)	ER
675812.VHA_002766				(PF08180)	ER
675812.VHA_001299				PF02205	(mitochondrial); (plastid)
675812.VHA_002466				(PF03199) (PF03917)
675812.VHA_001300				(PF00102)
675812.VHA_003121				PF01536
675812.VHA_001222				(PF02371)
675812.VHA_002538				(PF02371)
675812.VHA_001224				(PF02371)
675812.VHA_002988				(PF14216)
675812.VHA_001221				(PF02371)
675812.VHA_002539				(PF02371)
675812.VHA_002010				(PF10462)
675812.VHA_001155				(PF13402)
675812.VHA_001397				(PF02371)
675812.VHA_001396				(PF02371)
675812.VHA_000892				(PF02371)
675812.VHA_001146				(PF13402)
675812.VHA_001569				(PF08732)
675812.VHA_002541				(PF02371)
675812.VHA_002546				(PF02371)
675812.VHA_002545				(PF02371)
675812.VHA_003521				PF10393

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 = 0.375 (3/8 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=
==========================================================