Effective results for Paracoccus denitrificans PD1222 (eggnog40)

Summary

Number of putative secreted proteins: 40
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 16 eukaryotic-like domains, contained in 40 proteins (0 high, 40 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
318586.Pden_1612				(PF04752)	(ER); ER
318586.Pden_1589				(PF11720)	ER
318586.Pden_1587				(PF04800)	mitochondrial; (mitochondrial)
318586.Pden_1307				(PF11720)	ER
318586.Pden_1309				(PF04800)	mitochondrial; (mitochondrial)
318586.Pden_2622				(PF11720)	ER
318586.Pden_2774				(PF00777)	(mitochondrial)
318586.Pden_4276				(PF03601)	(ER)
318586.Pden_1009				(PF03601)	(ER)
318586.Pden_1641				(PF03601)	(ER)
318586.Pden_1546				(PF07929)
318586.Pden_3164				(PF01555)
318586.Pden_3838				(PF01555)
318586.Pden_1406				(PF04752)
318586.Pden_1574				(PF13883)
318586.Pden_3842				(PF13020)
318586.Pden_0969				(PF01555)
318586.Pden_0341				(PF01555)
318586.Pden_1588				(PF12344)
318586.Pden_1323				(PF13883)
318586.Pden_2101				(PF01555)
318586.Pden_4264				(PF14532)
318586.Pden_2068				(PF01555)
318586.Pden_3157				(PF07929)
318586.Pden_1308				(PF12344)
318586.Pden_3025				(PF04405)
318586.Pden_0224				(PF14532)
318586.Pden_2083				(PF13020)
318586.Pden_3357				(PF01555)
318586.Pden_3350				(PF07929)
318586.Pden_0257				(PF14216)
318586.Pden_1857				(PF02485)
318586.Pden_4224				(PF04405)
318586.Pden_2333				(PF13875)
318586.Pden_0277				(PF04752)
318586.Pden_0120				(PF01555)
318586.Pden_2293				(PF02485)
318586.Pden_4370				(PF03601)
318586.Pden_3820				(PF09458)
318586.Pden_4129				(PF14532)

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: YES (FDR = 7.7 %)
  Estimated copy number = 1.375 (11/8 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=
==========================================================