Effective results for Novosphingobium nitrogenifigens DSM 19370 (eggnog40)

Summary

Number of putative secreted proteins: 78
- Predicted by T4SEpre: 59
- Predicted by EffectiveELD: 12 eukaryotic-like domains, contained in 32 proteins (5 high, 27 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
983920.Y88_0814			+		(mitochondrial)
983920.Y88_2095			+		ER
983920.Y88_3102			+		mitochondrial
983920.Y88_0468			+		ER
983920.Y88_0288				PF06351	ER
983920.Y88_1882			+		(ER)
983920.Y88_0894			+		mitochondrial
983920.Y88_0969				PF03901	(mitochondrial)
983920.Y88_0629			+		(mitochondrial)
983920.Y88_1372			+		ER
983920.Y88_1623				(PF13871)	ER; (ER)
983920.Y88_2823			+		ER
983920.Y88_0456			+		(mitochondrial)
983920.Y88_1910			+		ER
983920.Y88_1132				PF16058	ER; (ER)
983920.Y88_2116			+		ER
983920.Y88_1644				(PF13604)	mitochondrial
983920.Y88_0732			+		ER
983920.Y88_2097			+		(ER)
983920.Y88_3782				(PF13428) (PF13469)
983920.Y88_3757				(PF03171) (PF14226)
983920.Y88_2432				(PF03171) (PF14226)
983920.Y88_0462			+		(ER)
983920.Y88_0844				(PF03171) (PF14226)
983920.Y88_2287			+	(PF13604)
983920.Y88_3366				(PF13428) (PF13469)
983920.Y88_1289				(PF13428) (PF13469)
983920.Y88_1579			+		plastid
983920.Y88_1581			+		plastid
983920.Y88_2730			+		(mitochondrial)
983920.Y88_3863			+	(PF13604)
983920.Y88_1836				(PF03171) (PF14226)
983920.Y88_3872				(PF13871)	(ER)
983920.Y88_0358				(PF13469)	(plastid)
983920.Y88_2863				(PF03171) (PF14226)
983920.Y88_3313				(PF03171) (PF14226)
983920.Y88_1811			+		(mitochondrial)
983920.Y88_1780			+
983920.Y88_1382			+
983920.Y88_0696				(PF13469)
983920.Y88_1263			+
983920.Y88_3426			+
983920.Y88_2337			+
983920.Y88_0470				PF10520
983920.Y88_3352			+
983920.Y88_2564			+
983920.Y88_3582			+
983920.Y88_2760				(PF13604)
983920.Y88_3362			+
983920.Y88_3145			+
983920.Y88_3034			+
983920.Y88_1950				(PF13661)
983920.Y88_0559			+
983920.Y88_1171			+
983920.Y88_2553			+
983920.Y88_1381				(PF13604)
983920.Y88_2014				(PF13469)
983920.Y88_3613			+
983920.Y88_2220			+
983920.Y88_2909			+
983920.Y88_0503			+
983920.Y88_1569			+
983920.Y88_3526			+
983920.Y88_3675			+
983920.Y88_3294				(PF13469)
983920.Y88_0999			+
983920.Y88_1002			+
983920.Y88_1130			+
983920.Y88_2203				(PF11927)
983920.Y88_0698				(PF13469)
983920.Y88_1834			+
983920.Y88_2908				(PF13604)
983920.Y88_3252			+
983920.Y88_0222				PF03901
983920.Y88_0300			+
983920.Y88_1668				(PF13469)
983920.Y88_1466				(PF11927)
983920.Y88_3314				(PF13469)

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 = 0.3 (3/10 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=
==========================================================