Effective results for Pseudoxanthomonas spadix BD-a59 (eggnog40)

Summary

Number of putative secreted proteins: 68
- Predicted by T4SEpre: 56
- Predicted by EffectiveELD: 9 eukaryotic-like domains, contained in 20 proteins (5 high, 15 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

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
1045855.DSC_09615			+		ER
1045855.DSC_05325				(PF13202)	(ER); plastid
1045855.DSC_08695				PF10712	mitochondrial
1045855.DSC_05210			+		mitochondrial; (mitochondrial)
1045855.DSC_14510			+		ER
1045855.DSC_01575			+		ER
1045855.DSC_14385				(PF13202)	ER
1045855.DSC_11265			+		ER
1045855.DSC_00370				(PF13606)	ER
1045855.DSC_00745				(PF13202)	ER
1045855.DSC_06160				(PF13202)	ER
1045855.DSC_00595				PF11074	(mitochondrial)
1045855.DSC_00750				(PF13202)	ER
1045855.DSC_15580			+		ER
1045855.DSC_14240				(PF04505)	(ER); ER
1045855.DSC_11930				(PF01764)	ER
1045855.DSC_04050			+		(ER)
1045855.DSC_15055				(PF13202)	ER
1045855.DSC_09730			+		ER
1045855.DSC_15060				(PF13202)	ER
1045855.DSC_08735			+		(mitochondrial)
1045855.DSC_03310			+		(plastid)
1045855.DSC_09310			+		(plastid)
1045855.DSC_03240			+		(plastid)
1045855.DSC_04140			+		(plastid)
1045855.DSC_04210			+
1045855.DSC_10540			+
1045855.DSC_12545			+
1045855.DSC_05915				(PF01764)
1045855.DSC_00185			+
1045855.DSC_01925				(PF01764)
1045855.DSC_09075			+
1045855.DSC_12505				PF17067	not used
1045855.DSC_14580			+
1045855.DSC_03970			+
1045855.DSC_08085				(PF04768)
1045855.DSC_04815			+
1045855.DSC_14715			+
1045855.DSC_01785			+
1045855.DSC_02545			+
1045855.DSC_11255			+
1045855.DSC_12665			+
1045855.DSC_10820			+
1045855.DSC_10825			+
1045855.DSC_04290			+
1045855.DSC_14830			+
1045855.DSC_04640			+
1045855.DSC_03065			+
1045855.DSC_15710				PF00018	not used
1045855.DSC_04265			+
1045855.DSC_01610			+
1045855.DSC_07915			+
1045855.DSC_02985			+
1045855.DSC_05790			+
1045855.DSC_08315			+
1045855.DSC_08480			+
1045855.DSC_11910				PF11074
1045855.DSC_14245				(PF04505)
1045855.DSC_02385			+
1045855.DSC_13670			+
1045855.DSC_11785			+
1045855.DSC_00095				(PF13606)
1045855.DSC_04230			+
1045855.DSC_14420			+
1045855.DSC_10040			+
1045855.DSC_10045			+
1045855.DSC_07140			+
1045855.DSC_12145			+

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 = 0.6 (6/10 KEGG proteins)
• Functional Type VI secretion system: NO (FDR = 7.7 %)

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