Effective results for Beijerinckia indica subsp. indica ATCC 9039 (eggnog40)

Summary

Number of putative secreted proteins: 81
- Predicted by T4SEpre: 79
- Predicted by EffectiveELD: 11 eukaryotic-like domains, contained in 18 proteins (2 high, 16 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
395963.Bind_0024			+		mitochondrial
395963.Bind_0252			+		ER
395963.Bind_2756				(PF07250)	(mitochondrial)
395963.Bind_2752				(PF02230)	ER
395963.Bind_1951			+		ER
395963.Bind_1556			+		ER
395963.Bind_1190			+		ER
395963.Bind_3201			+		mitochondrial
395963.Bind_1985			+		ER
395963.Bind_2853			+		(mitochondrial); (plastid)
395963.Bind_0110			+		(mitochondrial)
395963.Bind_1640			+		ER
395963.Bind_1645			+		ER
395963.Bind_0124			+		ER
395963.Bind_1725			+		(mitochondrial); mitochondrial
395963.Bind_2387				(PF06455)	ER
395963.Bind_0137			+		ER
395963.Bind_2248			+		ER
395963.Bind_3620			+		ER
395963.Bind_1451			+		ER
395963.Bind_0858			+		(mitochondrial)
395963.Bind_2000				(PF13207)	ER; mitochondrial
395963.Bind_3630			+		ER
395963.Bind_0447				(PF13506)	(mitochondrial)
395963.Bind_3067			+		(mitochondrial)
395963.Bind_1755			+		(ER)
395963.Bind_1840			+		(mitochondrial)
395963.Bind_0284				PF08557	(mitochondrial)
395963.Bind_3654			+		(ER)
395963.Bind_2724			+		(mitochondrial)
395963.Bind_0684			+
395963.Bind_0446				(PF02230)
395963.Bind_2117			+
395963.Bind_3084			+
395963.Bind_3089				(PF06080)
395963.Bind_1497			+
395963.Bind_0304			+
395963.Bind_1301				(PF06080)
395963.Bind_1013				(PF02844)
395963.Bind_1018			+
395963.Bind_3416			+
395963.Bind_2348				(PF01442)
395963.Bind_2578				(PF14330)
395963.Bind_3046			+
395963.Bind_0782			+
395963.Bind_1662			+
395963.Bind_0025			+
395963.Bind_0487			+
395963.Bind_0486			+
395963.Bind_0571			+
395963.Bind_0801				PF16575
395963.Bind_2331			+
395963.Bind_2183			+
395963.Bind_2637			+
395963.Bind_3580			+
395963.Bind_0007			+
395963.Bind_1249			+
395963.Bind_3268			+
395963.Bind_0432				(PF02230)
395963.Bind_3673				(PF13506)
395963.Bind_3675			+
395963.Bind_3499			+
395963.Bind_1066				(PF02230)
395963.Bind_0382			+
395963.Bind_0251			+
395963.Bind_1383				(PF02844)
395963.Bind_2707			+
395963.Bind_1587			+
395963.Bind_0400			+
395963.Bind_1667			+
395963.Bind_3286			+
395963.Bind_1670			+
395963.Bind_1050			+
395963.Bind_2904			+
395963.Bind_3390			+
395963.Bind_0468			+
395963.Bind_2730			+
395963.Bind_3172			+
395963.Bind_0451				(PF13506)
395963.Bind_2109			+
395963.Bind_1356			+

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