Effective results for Shewanella piezotolerans WP3 (eggnog40)

Summary

Number of putative secreted proteins: 72
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 18 eukaryotic-like domains, contained in 72 proteins (2 high, 70 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
225849.swp_3545				(PF14864) (PF14863)	ER
225849.swp_4168				(PF14864) (PF14863)	ER; (ER)
225849.swp_4376				(PF14864) (PF14863)	ER
225849.swp_1820				(PF03553)	(mitochondrial); plastid
225849.swp_2110				(PF03553)	ER
225849.swp_4996				(PF00849)	ER
225849.swp_2178				(PF03553)	ER
225849.swp_3944				(PF02460)	ER
225849.swp_0332				(PF01103)	ER
225849.swp_0944				(PF03553)	ER
225849.swp_2312				(PF09317)	ER
225849.swp_2783				(PF01103)	ER
225849.swp_4477				(PF00245)	ER
225849.swp_3470				(PF03553)	ER
225849.swp_0596				(PF01103)	ER
225849.swp_2518				(PF00849)	ER
225849.swp_4598				(PF00849)	mitochondrial
225849.swp_0605				(PF01103)	ER
225849.swp_4023				(PF03553)	ER
225849.swp_4730				(PF06468)	ER
225849.swp_4731				(PF06468)	ER; (ER)
225849.swp_2992				(PF08329)	ER
225849.swp_2454				(PF03553)	ER
225849.swp_2172				PF05887	(mitochondrial)
225849.swp_2386				(PF09317)	ER
225849.swp_3513				(PF01103)	ER
225849.swp_0647				(PF08329)	ER
225849.swp_1292				(PF00245)	ER
225849.swp_4417				(PF00849)	mitochondrial
225849.swp_3648				(PF03199) (PF03917)
225849.swp_1913				(PF02371)
225849.swp_1911				(PF02371)
225849.swp_1910				(PF02371)
225849.swp_3370				(PF02371)
225849.swp_3372				(PF02371)
225849.swp_3422				(PF09317)
225849.swp_3563				(PF02371)
225849.swp_4034				(PF01103)
225849.swp_0862				(PF02371)
225849.swp_1929				(PF00849)
225849.swp_3309				(PF12392)
225849.swp_3435				(PF02371)
225849.swp_3940				(PF00849)
225849.swp_4223				(PF02371)
225849.swp_4339				(PF00849)
225849.swp_3844				(PF00245)
225849.swp_4662				(PF03553)
225849.swp_3865				(PF00849)
225849.swp_4872				(PF01103)
225849.swp_3055				(PF00849)
225849.swp_4585				(PF16983)
225849.swp_4276				(PF12392)
225849.swp_4290				(PF00849)
225849.swp_4126				(PF00849)
225849.swp_2192				(PF02371)
225849.swp_3066				(PF14864)
225849.swp_4914				(PF02371)
225849.swp_4916				(PF02371)
225849.swp_1248				(PF01103)
225849.swp_1245				(PF01103)
225849.swp_1866				(PF00849)
225849.swp_2442				(PF02371)
225849.swp_3530				(PF00849)
225849.swp_3829				(PF08357)
225849.swp_3825				(PF02371)
225849.swp_2473				(PF02371)
225849.swp_1672				(PF00849)
225849.swp_3023				PF01536
225849.swp_0893				(PF00849)
225849.swp_1294				(PF00245)
225849.swp_3299				(PF00849)
225849.swp_4410				(PF03553)

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