Effective results for Cronobacter sakazakii ATCC BAA-894 (eggnog40)

Summary

Number of putative secreted proteins: 97
- Predicted by T4SEpre: 100
- Predicted by EffectiveELD: 9 eukaryotic-like domains, contained in 15 proteins (2 high, 13 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): (Type IV), Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
290339.ESA_01764			+	(PF06884)	ER
290339.ESA_03720				(PF13436)	ER
290339.ESA_02526			+		ER
290339.ESA_02856			+		ER
290339.ESA_00135			+		ER
290339.ESA_03592			+		ER
290339.ESA_01275			+		ER
290339.ESA_03566			+		ER
290339.ESA_02870			+		ER
290339.ESA_03325				PF10712	mitochondrial; (mitochondrial)
290339.ESA_02233			+		mitochondrial
290339.ESA_01658			+		ER
290339.ESA_02747				(PF00959)	(mitochondrial)
290339.ESA_01266			+		ER
290339.ESA_00210			+		ER
290339.ESA_03518			+		ER
290339.ESA_03513			+		ER
290339.ESA_03512			+		ER
290339.ESA_00185			+		ER
290339.ESA_02605			+		ER
290339.ESA_02714			+		ER
290339.ESA_00703			+		ER
290339.ESA_01126			+		ER
290339.ESA_02815			+		mitochondrial
290339.ESA_01958			+		ER
290339.ESA_04387			+		(mitochondrial)
290339.ESA_01890			+		mitochondrial
290339.ESA_02775			+		ER
290339.ESA_01625				(PF00959)	(mitochondrial)
290339.ESA_01395			+		(plastid)
290339.ESA_04299			+		(mitochondrial)
290339.ESA_03035			+		(ER)
290339.ESA_00836			+		plastid
290339.ESA_03062				(PF00959)	(mitochondrial)
290339.ESA_02592			+		(plastid)
290339.ESA_p1			+		(mitochondrial)
290339.ESA_04044			+
290339.ESA_00752				(PF16485)
290339.ESA_02284				(PF04399)
290339.ESA_01628			+
290339.ESA_01366				PF10712
290339.ESA_01161			+
290339.ESA_03920			+
290339.ESA_00647			+
290339.ESA_03935				(PF14113)
290339.ESA_01195			+
290339.ESA_00137			+
290339.ESA_04234			+
290339.ESA_02889			+
290339.ESA_03050			+
290339.ESA_00971			+
290339.ESA_03903			+
290339.ESA_00122			+
290339.ESA_04007			+
290339.ESA_00487			+
290339.ESA_03912			+
290339.ESA_00325			+
290339.ESA_01606			+
290339.ESA_03460			+
290339.ESA_00672				(PF14328)
290339.ESA_02309				(PF00959)
290339.ESA_02303			+
290339.ESA_04158			+
290339.ESA_02787			+
290339.ESA_00267				(PF04399)
290339.ESA_03083			+
290339.ESA_01798			+
290339.ESA_01022			+
290339.ESA_02201			+
290339.ESA_00271			+
290339.ESA_01340			+
290339.ESA_00607			+
290339.ESA_02326				(PF14216)
290339.ESA_02257			+
290339.ESA_02743			+
290339.ESA_02740			+
290339.ESA_02744			+
290339.ESA_00192			+
290339.ESA_03634			+
290339.ESA_01676			+
290339.ESA_00539			+
290339.ESA_00530			+
290339.ESA_00719			+
290339.ESA_01287			+
290339.ESA_02398			+
290339.ESA_03576			+
290339.ESA_03146			+
290339.ESA_02035			+
290339.ESA_02036				(PF14113)
290339.ESA_00094			+
290339.ESA_00773			+
290339.ESA_02556			+
290339.ESA_00357			+
290339.ESA_02739			+
290339.ESA_01966			+
290339.ESA_01565			+
290339.ESA_03181			+

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

• T4SEpre bpbAac predictions (T4SEpre_bpbAac_FinalResult.csv)
• T4SEpre psAac predictions (T4SEpre_psAac_FinalResult.csv)
• 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: YES (FDR = 7.2 %)
  Estimated copy number = 0.0 (0/10 KEGG proteins)
• Functional Type VI secretion system: YES (FDR = 7.7 %)
  Estimated copy number = 2.0 (16/8 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=
==========================================================