Effective results for Parvibaculum lavamentivorans DS-1 (eggnog40)

Summary

Number of putative secreted proteins: 73
- Predicted by T4SEpre: 68
- Predicted by EffectiveELD: 12 eukaryotic-like domains, contained in 18 proteins (1 high, 17 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
402881.Plav_2455			+		ER
402881.Plav_2061				(PF14248)	ER
402881.Plav_3539			+		ER
402881.Plav_2398			+		ER
402881.Plav_2484				(PF03959)	ER
402881.Plav_1279			+		ER
402881.Plav_0894			+		ER
402881.Plav_2565			+		ER
402881.Plav_0694			+		ER
402881.Plav_0866			+		ER
402881.Plav_2048			+		(mitochondrial)
402881.Plav_2773				(PF04519)	ER
402881.Plav_3228			+		ER
402881.Plav_1313				(PF14248)	(mitochondrial)
402881.Plav_1928				(PF04519)	mitochondrial
402881.Plav_2097				PF01731	ER
402881.Plav_1196			+		ER
402881.Plav_0552			+		ER
402881.Plav_2414			+		ER
402881.Plav_0360			+		ER
402881.Plav_1565			+		ER
402881.Plav_0746			+	(PF04519)
402881.Plav_3257			+		(mitochondrial)
402881.Plav_1287			+		(mitochondrial)
402881.Plav_3517				(PF13872) (PF13871)
402881.Plav_2214			+		(ER)
402881.Plav_3205			+		(mitochondrial)
402881.Plav_1218				(PF13872) (PF13871)
402881.Plav_1691			+		(ER)
402881.Plav_2678				(PF13759)
402881.Plav_2674			+
402881.Plav_1509				(PF13759)
402881.Plav_0759			+
402881.Plav_0917			+
402881.Plav_1391			+
402881.Plav_0130			+
402881.Plav_3537			+
402881.Plav_0724				(PF02475)
402881.Plav_1092				(PF10994)
402881.Plav_0737				(PF00102)
402881.Plav_1289			+
402881.Plav_0234			+
402881.Plav_1073			+
402881.Plav_0257			+
402881.Plav_2176			+
402881.Plav_3173			+
402881.Plav_1127			+
402881.Plav_2759			+
402881.Plav_1933			+
402881.Plav_0266			+
402881.Plav_3315			+
402881.Plav_2826			+
402881.Plav_1152			+
402881.Plav_1815			+
402881.Plav_3222			+
402881.Plav_0539				(PF14330)
402881.Plav_3450			+
402881.Plav_2942			+
402881.Plav_0004			+
402881.Plav_1198			+
402881.Plav_3231			+
402881.Plav_2508			+
402881.Plav_1560				(PF10994)
402881.Plav_1564			+
402881.Plav_3279			+
402881.Plav_3278			+
402881.Plav_3273				(PF04519)
402881.Plav_3477			+
402881.Plav_0106			+
402881.Plav_1351				(PF09731)
402881.Plav_1354			+
402881.Plav_2427			+
402881.Plav_3069			+

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 = 1.8 (18/10 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=
==========================================================