Effective results for Vibrio fischeri ES114 (eggnog40)

Summary

Number of putative secreted proteins: 35
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 19 eukaryotic-like domains, contained in 35 proteins (1 high, 34 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
312309.VF_1322				(PF01773) (PF07662)	ER
312309.VF_A0209				(PF06742) (PF06863)	(ER)
312309.VF_A1059				(PF06742) (PF06863)	ER
312309.VF_A0967				(PF01773) (PF07662)	ER
312309.VF_2065				(PF01773) (PF07662)	ER
312309.VF_1096				(PF01773) (PF07662)	ER
312309.VF_1071				(PF06742) (PF06863)	ER
312309.VF_1070				(PF06742) (PF06863)	ER
312309.VF_A0491				(PF06742) (PF06863)	ER
312309.VF_0502				(PF01773) (PF07662)	ER
312309.VF_A0490				(PF06742) (PF06863)	ER
312309.VF_A0123				(PF00854)	ER; (ER)
312309.VF_0802				(PF00854)	ER
312309.VF_A0899				(PF14707)	(ER)
312309.VF_0575				(PF01679)	ER
312309.VF_1427				(PF14707)	ER
312309.VF_A0090				(PF00030)	ER
312309.VF_1256				(PF02112)	ER
312309.VF_1280				(PF08180)	ER
312309.VF_A0621				(PF00030)	ER
312309.VF_0984				(PF00031)	ER
312309.VF_1430				(PF14707)	(ER)
312309.VF_A1060				(PF06742) (PF06863)
312309.VF_2629				(PF01679)	ER; not used
312309.VF_0976				(PF03199) (PF03917)
312309.VF_1472				(PF10013)	plastid
312309.VF_2359				(PF05706)
312309.VF_A0124				(PF00854)
312309.VF_A0532				PF04927	not used
312309.VF_0578				(PF01786)
312309.VF_1428				(PF14707)
312309.VF_2066				(PF10063)
312309.VF_1850				(PF09811)
312309.VF_A0021				(PF00854)
312309.VF_1124				(PF00854)

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 = 1.625 (13/8 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=
==========================================================