Effective results for Novosphingobium aromaticivorans DSM 12444 (eggnog40)

Summary

Number of putative secreted proteins: 70
- Predicted by T4SEpre: 58
- Predicted by EffectiveELD: 13 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
279238.Saro_2161			+		ER
279238.Saro_1621				(PF03537)	(mitochondrial)
279238.Saro_0025			+		ER
279238.Saro_0838			+		ER
279238.Saro_1184				(PF03537)	ER; (ER)
279238.Saro_1721				PF11578	ER
279238.Saro_0052			+		ER
279238.Saro_2690			+		ER
279238.Saro_1078			+		ER; (ER)
279238.Saro_0458			+		ER
279238.Saro_2523			+		(mitochondrial)
279238.Saro_1429			+		(mitochondrial)
279238.Saro_2829			+		ER
279238.Saro_1359			+		ER
279238.Saro_1126			+		ER
279238.Saro_2991			+		mitochondrial
279238.Saro_2057				(PF13436)	ER
279238.Saro_1377			+		ER
279238.Saro_0349				(PF11074)	(mitochondrial)
279238.Saro_3189			+		(mitochondrial)
279238.Saro_3181				PF11578	ER
279238.Saro_2282				(PF03901)	ER
279238.Saro_2289				(PF06455)	ER
279238.Saro_0612			+		ER; (ER)
279238.Saro_1748			+		ER; (ER)
279238.Saro_2131			+		mitochondrial
279238.Saro_0424			+		(mitochondrial); mitochondrial
279238.Saro_1955			+		ER
279238.Saro_0377				(PF13872) (PF13871)	(mitochondrial)
279238.Saro_0370			+		mitochondrial
279238.Saro_3298			+		plastid
279238.Saro_2208				(PF13872) (PF13871)
279238.Saro_2543			+
279238.Saro_0573				(PF02933)
279238.Saro_1145			+
279238.Saro_0925			+
279238.Saro_2378			+
279238.Saro_0724				(PF04765)
279238.Saro_2888			+
279238.Saro_0801				PF11578
279238.Saro_2772			+
279238.Saro_0128			+
279238.Saro_0912			+
279238.Saro_2507			+
279238.Saro_2500				(PF03537)
279238.Saro_1085			+
279238.Saro_1292			+
279238.Saro_0451			+
279238.Saro_2528			+
279238.Saro_2237				PF11578
279238.Saro_0530				(PF03537)
279238.Saro_0663			+
279238.Saro_1794			+
279238.Saro_0891				(PF10013)	not used
279238.Saro_2656			+
279238.Saro_2318			+
279238.Saro_0868			+
279238.Saro_1135			+
279238.Saro_0259				(PF05706)
279238.Saro_2182			+
279238.Saro_2877				PF11578
279238.Saro_1576				(PF01786)
279238.Saro_0180			+
279238.Saro_0299			+
279238.Saro_3055			+
279238.Saro_0436			+
279238.Saro_2596			+
279238.Saro_2595			+
279238.Saro_3241			+
279238.Saro_1769			+

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 = 0.8 (8/10 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=
==========================================================