Effective results for Shewanella denitrificans OS217 (eggnog40)

Summary

Number of putative secreted proteins: 55
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 16 eukaryotic-like domains, contained in 55 proteins (2 high, 53 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
318161.Sden_3684				(PF01391)	ER
318161.Sden_3685				(PF01391)	ER
318161.Sden_3686				(PF01391)	ER
318161.Sden_1914				(PF11999)	ER
318161.Sden_1915				(PF11999)	ER
318161.Sden_2258				(PF01117)	ER
318161.Sden_2876				(PF00849)	(mitochondrial)
318161.Sden_2616				(PF14521)	(ER)
318161.Sden_1380				(PF14521)	ER
318161.Sden_0482				(PF00849)	(mitochondrial); plastid
318161.Sden_0236				(PF14240)	(ER)
318161.Sden_2402				(PF13127)	ER
318161.Sden_0595				(PF02371)	mitochondrial
318161.Sden_0685				(PF00849)	mitochondrial; (mitochondrial)
318161.Sden_1926				(PF01391)	ER
318161.Sden_1925				(PF01391)	ER
318161.Sden_1924				(PF01391)	ER
318161.Sden_3681				(PF02371)	(mitochondrial)
318161.Sden_1691				(PF03538) (PF00045)
318161.Sden_0793				(PF00849)
318161.Sden_0881				(PF02371)
318161.Sden_1680				(PF00305)
318161.Sden_1134				(PF02371)
318161.Sden_2806				(PF02371)
318161.Sden_3048				(PF00849)
318161.Sden_0401				(PF13936)
318161.Sden_3445				(PF02371)
318161.Sden_1574				(PF13936)
318161.Sden_2279				PF01536
318161.Sden_0291				(PF02732)
318161.Sden_2863				(PF00849)
318161.Sden_2262				(PF13936)
318161.Sden_1546				(PF00849)
318161.Sden_1014				(PF00849)
318161.Sden_1830				(PF00849)
318161.Sden_1748				(PF00849)
318161.Sden_0371				(PF14240)
318161.Sden_2436				(PF00849)
318161.Sden_2438				PF00277
318161.Sden_3360				(PF02371)
318161.Sden_0037				(PF13936)
318161.Sden_0038				(PF13936)
318161.Sden_0804				(PF00026)
318161.Sden_3589				(PF13936)
318161.Sden_0238				(PF13936)
318161.Sden_1879				(PF13936)
318161.Sden_0592				(PF02371)
318161.Sden_1090				(PF00849)
318161.Sden_0199				(PF02371)
318161.Sden_0688				(PF00849)
318161.Sden_3311				(PF02371)
318161.Sden_0111				(PF00849)
318161.Sden_1332				(PF02371)
318161.Sden_2524				(PF00849)
318161.Sden_2301				(PF00849)

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 = 0.875 (7/8 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=
==========================================================