Effective results for Granulibacter bethesdensis CGDNIH1 (eggnog40)

Summary

Number of putative secreted proteins: 46
- Predicted by T4SEpre: 44
- Predicted by EffectiveELD: 5 eukaryotic-like domains, contained in 9 proteins (0 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
391165.GbCGDNIH1_2146			+		ER
391165.GbCGDNIH1_2028				(PF13436)	ER
391165.GbCGDNIH1_1820			+		mitochondrial
391165.GbCGDNIH1_2057			+		mitochondrial
391165.GbCGDNIH1_1330			+		ER
391165.GbCGDNIH1_1327			+		mitochondrial
391165.GbCGDNIH1_1720			+		ER
391165.GbCGDNIH1_1276			+		mitochondrial
391165.GbCGDNIH1_0803			+		(mitochondrial)
391165.GbCGDNIH1_0060				(PF13704)	(mitochondrial)
391165.GbCGDNIH1_0596			+		(ER); (plastid)
391165.GbCGDNIH1_0703			+		mitochondrial
391165.GbCGDNIH1_0517			+		(mitochondrial)
391165.GbCGDNIH1_2160			+		(ER)
391165.GbCGDNIH1_2390			+
391165.GbCGDNIH1_0771			+
391165.GbCGDNIH1_0373			+
391165.GbCGDNIH1_0419			+
391165.GbCGDNIH1_0963			+
391165.GbCGDNIH1_0988			+
391165.GbCGDNIH1_1163				(PF14832)
391165.GbCGDNIH1_1839			+
391165.GbCGDNIH1_0577			+
391165.GbCGDNIH1_1141				(PF13704)
391165.GbCGDNIH1_1936			+
391165.GbCGDNIH1_1249			+
391165.GbCGDNIH1_0324				(PF13704)
391165.GbCGDNIH1_0780			+
391165.GbCGDNIH1_2167			+
391165.GbCGDNIH1_2092			+
391165.GbCGDNIH1_0534			+
391165.GbCGDNIH1_2181			+
391165.GbCGDNIH1_1066			+
391165.GbCGDNIH1_1501				(PF13704)
391165.GbCGDNIH1_1935			+
391165.GbCGDNIH1_0809			+
391165.GbCGDNIH1_0062				(PF13704)
391165.GbCGDNIH1_0470			+
391165.GbCGDNIH1_1059			+
391165.GbCGDNIH1_2435			+
391165.GbCGDNIH1_0866			+
391165.GbCGDNIH1_2422				(PF09731)
391165.GbCGDNIH1_2289			+
391165.GbCGDNIH1_1435			+
391165.GbCGDNIH1_1546				(PF00648)
391165.GbCGDNIH1_1997			+

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 = 0.4 (4/10 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=
==========================================================