Effective results for Parvularcula bermudensis HTCC2503 (eggnog40)

Summary

Number of putative secreted proteins: 66
- Predicted by T4SEpre: 63
- Predicted by EffectiveELD: 9 eukaryotic-like domains, contained in 12 proteins (4 high, 8 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
314260.PB2503_10724			+		ER
314260.PB2503_05197			+		ER
314260.PB2503_01767			+		ER
314260.PB2503_02987			+		ER
314260.PB2503_02982			+		ER
314260.PB2503_08969			+		ER; (ER)
314260.PB2503_06982			+		(mitochondrial)
314260.PB2503_02887			+		ER
314260.PB2503_08599			+		(ER)
314260.PB2503_08609			+		ER
314260.PB2503_10569			+		ER
314260.PB2503_06702				PF01731	ER
314260.PB2503_04167			+		ER
314260.PB2503_11099			+		ER
314260.PB2503_09624			+		ER
314260.PB2503_06022				(PF11074)	(mitochondrial)
314260.PB2503_09829			+		mitochondrial; (mitochondrial)
314260.PB2503_10339			+		ER
314260.PB2503_10914			+		(mitochondrial)
314260.PB2503_09589			+		ER
314260.PB2503_04837			+		ER
314260.PB2503_12749			+		ER
314260.PB2503_04817			+		mitochondrial; (mitochondrial)
314260.PB2503_05007			+		ER
314260.PB2503_09734			+		(ER)
314260.PB2503_13489			+		(ER)
314260.PB2503_05862			+		(mitochondrial)
314260.PB2503_01357			+
314260.PB2503_01517				(PF05019)
314260.PB2503_01532				(PF05019)
314260.PB2503_10289			+
314260.PB2503_06632			+
314260.PB2503_06362			+
314260.PB2503_06367			+
314260.PB2503_01527				(PF05019)
314260.PB2503_03497				PF01096
314260.PB2503_07819			+
314260.PB2503_01882			+
314260.PB2503_10974			+
314260.PB2503_03022				(PF09731)
314260.PB2503_12304			+
314260.PB2503_01712			+
314260.PB2503_05382			+
314260.PB2503_07544			+
314260.PB2503_01702			+
314260.PB2503_05757				PF02171
314260.PB2503_01052			+
314260.PB2503_02242			+
314260.PB2503_03527				PF02171
314260.PB2503_04987			+
314260.PB2503_05637				(PF16565)
314260.PB2503_03742			+
314260.PB2503_01592			+
314260.PB2503_09449			+
314260.PB2503_04347			+
314260.PB2503_01137			+
314260.PB2503_10699			+
314260.PB2503_03407			+
314260.PB2503_05667			+
314260.PB2503_10789			+
314260.PB2503_10379			+
314260.PB2503_11059				(PF04768)
314260.PB2503_10279			+
314260.PB2503_01217			+
314260.PB2503_00817			+
314260.PB2503_10959				(PF00102)

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 = 2.3 (23/10 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=
==========================================================