Effective results for Pseudoxanthomonas suwonensis 11-1 (eggnog40)

Summary

Number of putative secreted proteins: 43
- Predicted by T4SEpre: 41
- Predicted by EffectiveELD: 8 eukaryotic-like domains, contained in 10 proteins (1 high, 9 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
743721.Psesu_2935			+		ER; (ER)
743721.Psesu_2658			+		(mitochondrial)
743721.Psesu_0260			+		(mitochondrial)
743721.Psesu_1930			+		ER
743721.Psesu_1591			+		ER
743721.Psesu_0519			+		(mitochondrial)
743721.Psesu_2709			+		ER
743721.Psesu_1925			+		ER
743721.Psesu_0661			+		ER
743721.Psesu_2568			+		ER
743721.Psesu_1159			+		ER
743721.Psesu_1976			+		ER
743721.Psesu_0030			+		ER
743721.Psesu_1369			+		ER
743721.Psesu_2097				(PF06884)	ER
743721.Psesu_1545			+		ER
743721.Psesu_2157				(PF03901)	(ER); ER
743721.Psesu_1182			+		ER
743721.Psesu_3008			+		ER
743721.Psesu_1777			+		ER
743721.Psesu_0493				(PF11539)	(mitochondrial)
743721.Psesu_0228				(PF04505) (PF14237)
743721.Psesu_2313			+		(mitochondrial)
743721.Psesu_1219			+		(mitochondrial)
743721.Psesu_0259			+
743721.Psesu_1278			+
743721.Psesu_2817			+
743721.Psesu_0395				(PF04505)
743721.Psesu_2248				PF17067	not used
743721.Psesu_1292			+
743721.Psesu_2227			+
743721.Psesu_2732			+
743721.Psesu_0075				(PF13661)
743721.Psesu_2682			+
743721.Psesu_2168			+
743721.Psesu_2303			+
743721.Psesu_0226				(PF14237)
743721.Psesu_0227				(PF14237)
743721.Psesu_1229				(PF04768)
743721.Psesu_1165			+
743721.Psesu_0528			+
743721.Psesu_1422			+
743721.Psesu_0639			+

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: 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=
==========================================================