Effective results for Variovorax paradoxus EPS (eggnog40)

Summary

Number of putative secreted proteins: 110
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 26 eukaryotic-like domains, contained in 110 proteins (1 high, 109 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): None

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
595537.Varpa_1656				(PF13458)	ER
595537.Varpa_0816				(PF13458)	ER; (ER)
595537.Varpa_4456				(PF13091)	mitochondrial; (mitochondrial)
595537.Varpa_0156				(PF13458)	(mitochondrial)
595537.Varpa_0155				(PF13091)	ER
595537.Varpa_1425				(PF07519)	mitochondrial
595537.Varpa_2993				(PF13091)	ER
595537.Varpa_5714				(PF13458)	ER
595537.Varpa_3476				(PF13458)	(mitochondrial)
595537.Varpa_3804				(PF13458)	ER
595537.Varpa_1660				(PF13458)	ER; (ER)
595537.Varpa_5950				(PF13458)	ER
595537.Varpa_3281				(PF02643)	ER
595537.Varpa_5978				(PF06414)	(mitochondrial); (plastid)
595537.Varpa_2832				(PF13458)	ER
595537.Varpa_1751				(PF13458)	ER
595537.Varpa_0090				(PF13458)	(ER)
595537.Varpa_2587				(PF13458)	ER
595537.Varpa_2305				(PF13458)	ER
595537.Varpa_2894				(PF13599)	mitochondrial
595537.Varpa_5458				(PF13458)	ER
595537.Varpa_1207				(PF13091)	ER
595537.Varpa_4000				(PF13458)	ER
595537.Varpa_2526				(PF13091)	ER
595537.Varpa_1745				(PF13458)	ER
595537.Varpa_0216				(PF13458)	(mitochondrial); (plastid)
595537.Varpa_0211				(PF13458)	(ER)
595537.Varpa_0988				(PF01148)	ER
595537.Varpa_0485				(PF13091)	ER
595537.Varpa_0845				(PF13458)	(ER)
595537.Varpa_2439				(PF13458)	ER
595537.Varpa_4309				(PF07519)	ER
595537.Varpa_3445				(PF13458)	ER
595537.Varpa_3322				(PF01148)	ER
595537.Varpa_0162				(PF13458)	ER
595537.Varpa_0349				(PF13458)	mitochondrial
595537.Varpa_3877				(PF13091)	ER; (ER)
595537.Varpa_1657				(PF13458)	ER
595537.Varpa_0385				(PF13458)	ER
595537.Varpa_5290				(PF01148)	(ER)
595537.Varpa_3192				(PF13458)	ER
595537.Varpa_3191				(PF13458)	ER
595537.Varpa_3999				(PF13458)	ER
595537.Varpa_0505				(PF02643)	(mitochondrial)
595537.Varpa_1920				(PF13458)	ER
595537.Varpa_1925				(PF07519)	ER
595537.Varpa_4033				(PF13458)	mitochondrial
595537.Varpa_5429				(PF13091)	ER
595537.Varpa_4927				(PF02643)	(mitochondrial)
595537.Varpa_0100				(PF13458)	ER
595537.Varpa_5402				(PF07519)	ER
595537.Varpa_5409				(PF13458)	ER
595537.Varpa_5615				(PF13458)	ER
595537.Varpa_5634				PF15240	ER
595537.Varpa_2911				(PF13599)	mitochondrial
595537.Varpa_1323				(PF13458)	ER
595537.Varpa_3083				(PF06884)	ER
595537.Varpa_5331				(PF13458)	ER
595537.Varpa_5332				(PF13458)	ER
595537.Varpa_3552				(PF13458)	(ER)
595537.Varpa_3111				(PF07519)	plastid
595537.Varpa_3898				(PF13458)	(mitochondrial)
595537.Varpa_3952				(PF02201)	(mitochondrial)
595537.Varpa_4969				(PF14336)	(plastid)
595537.Varpa_3629				(PF07519)	(ER)
595537.Varpa_0328				(PF10994)	(mitochondrial)
595537.Varpa_2990				(PF12899)
595537.Varpa_2466				(PF13458)
595537.Varpa_0115				(PF09298)
595537.Varpa_5281				(PF14521)
595537.Varpa_1914				(PF13091)
595537.Varpa_4202				(PF10994)
595537.Varpa_5930				(PF02201)
595537.Varpa_0537				(PF13091)
595537.Varpa_5269				(PF00847)
595537.Varpa_0944				(PF06189)
595537.Varpa_0947				(PF14521)
595537.Varpa_2893				(PF13599)
595537.Varpa_2151				(PF13599)
595537.Varpa_1565				(PF00180)
595537.Varpa_0570				(PF13599)
595537.Varpa_3262				(PF13091)
595537.Varpa_0012				(PF13091)
595537.Varpa_0149				(PF16158)
595537.Varpa_3246				(PF07958)
595537.Varpa_3245				(PF12471)
595537.Varpa_0297				(PF09298)
595537.Varpa_3386				(PF13816)
595537.Varpa_1267				(PF11969)
595537.Varpa_4752				(PF00180)
595537.Varpa_0458				(PF13458)
595537.Varpa_0305				(PF13599)
595537.Varpa_5684				(PF03162)
595537.Varpa_1152				(PF06189)
595537.Varpa_3812				(PF09298)
595537.Varpa_5965				(PF00180)
595537.Varpa_2105				(PF13458)
595537.Varpa_2374				(PF13091)
595537.Varpa_4883				(PF00180)
595537.Varpa_4888				(PF16155)
595537.Varpa_1552				(PF05637)
595537.Varpa_4907				(PF13458)
595537.Varpa_0104				(PF16155)
595537.Varpa_0569				(PF13599)
595537.Varpa_1963				(PF00180)
595537.Varpa_4346				(PF00180)
595537.Varpa_3278				(PF00180)
595537.Varpa_5239				(PF06414)
595537.Varpa_0614				(PF00180)
595537.Varpa_2912				(PF13599)

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

• 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: NO (FDR = 7.2 %)
• 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=
==========================================================