Effective results for Nitrococcus mobilis Nb-231 (eggnog40)

Summary

Number of putative secreted proteins: 109
- Predicted by T4SEpre: 62
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 60 proteins (50 high, 10 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), Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
314278.NB231_03125				PF01609 (PF05598)	(mitochondrial)
314278.NB231_10458				PF01609 (PF05598)	(mitochondrial)
314278.NB231_03565				PF01609 (PF05598)	(mitochondrial)
314278.NB231_08217				PF01609 (PF05598)	(mitochondrial)
314278.NB231_10048				PF01609 (PF05598)	(mitochondrial)
314278.NB231_02323				PF01609 (PF05598)	(mitochondrial)
314278.NB231_08257				PF01609 (PF05598)	(mitochondrial)
314278.NB231_11349				PF01609 (PF05598)	(mitochondrial)
314278.NB231_11399				PF01609 (PF05598)	(mitochondrial)
314278.NB231_12429				PF01609 (PF05598)	(mitochondrial)
314278.NB231_02838			+		ER
314278.NB231_08585			+		ER
314278.NB231_07227			+		ER
314278.NB231_02153			+		ER
314278.NB231_17048			+		(mitochondrial); (plastid)
314278.NB231_05180				PF01609 (PF05598)	plastid
314278.NB231_14006			+		ER
314278.NB231_16093			+		(ER)
314278.NB231_04135				(PF06258)	(mitochondrial)
314278.NB231_00935			+		ER
314278.NB231_03575				PF01609	(mitochondrial)
314278.NB231_16078			+		(mitochondrial)
314278.NB231_04205			+		ER
314278.NB231_01499			+		ER; (ER)
314278.NB231_03530			+		ER
314278.NB231_16033			+		mitochondrial; (mitochondrial)
314278.NB231_03185			+		ER
314278.NB231_16973			+		ER
314278.NB231_09828				PF01609	mitochondrial
314278.NB231_08908			+		ER
314278.NB231_01883				PF01609	(mitochondrial)
314278.NB231_08943				PF09139	(mitochondrial)
314278.NB231_00585			+		(mitochondrial)
314278.NB231_01019			+		(ER)
314278.NB231_14148			+		(plastid)
314278.NB231_05726			+		(plastid)
314278.NB231_12936			+	(PF09414)
314278.NB231_00410				PF01609
314278.NB231_12139			+
314278.NB231_10803				PF01609
314278.NB231_09888			+
314278.NB231_08335				PF01609
314278.NB231_00280			+
314278.NB231_00600				PF01609
314278.NB231_04835				PF01609
314278.NB231_13761				PF01609
314278.NB231_05886				(PF06080)
314278.NB231_16638				PF01609
314278.NB231_16633			+
314278.NB231_14233				PF01609
314278.NB231_07917			+
314278.NB231_11064			+
314278.NB231_06885			+
314278.NB231_07070				PF01609
314278.NB231_13636				PF00955
314278.NB231_05971			+
314278.NB231_09233				PF01609
314278.NB231_09308				PF01609
314278.NB231_14738				PF01609
314278.NB231_04130				(PF06258)
314278.NB231_17058			+
314278.NB231_17293			+
314278.NB231_07202			+
314278.NB231_05501			+
314278.NB231_01868			+
314278.NB231_10478				PF01609
314278.NB231_03590				PF01609
314278.NB231_13651			+
314278.NB231_09143				PF01609
314278.NB231_02228				(PF13875)
314278.NB231_00820				PF01609
314278.NB231_13801			+
314278.NB231_04840			+
314278.NB231_09023			+
314278.NB231_09578				PF01609
314278.NB231_15898			+
314278.NB231_15478			+
314278.NB231_13676				PF01609
314278.NB231_10413				PF01609
314278.NB231_17540				(PF00889)	not used
314278.NB231_06346				(PF01457)
314278.NB231_05826			+
314278.NB231_09583				PF01609
314278.NB231_01234				PF01609
314278.NB231_04195				PF01609
314278.NB231_00015			+
314278.NB231_13041				(PF09414)
314278.NB231_07982			+
314278.NB231_10688			+
314278.NB231_13996				PF01609
314278.NB231_12916				PF01609
314278.NB231_17218				PF01609
314278.NB231_06176				PF01609
314278.NB231_15928				PF01609
314278.NB231_15108				PF01609
314278.NB231_16378				PF01609
314278.NB231_17353				(PF06080)
314278.NB231_03045			+
314278.NB231_06940				PF01609
314278.NB231_09703			+
314278.NB231_09708				PF01609
314278.NB231_14443			+
314278.NB231_02063			+
314278.NB231_01289				(PF00889)
314278.NB231_16918			+
314278.NB231_00405				PF01609
314278.NB231_02623			+
314278.NB231_14283				PF01609
314278.NB231_08297				PF01609

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: YES (FDR = 7.7 %)
  Estimated copy number = 1.5 (12/8 KEGG proteins)

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