Effective results for Ruegeria sp. R11 (eggnog40)

Summary

Number of putative secreted proteins: 36
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 36 proteins (1 high, 35 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
439497.RR11_142				(PF16350) (PF08669)	ER; (ER)
439497.RR11_1052				(PF16350) (PF08669)	(ER)
439497.RR11_2615				(PF16350) (PF08669)	ER
439497.RR11_3440				(PF08669)	(mitochondrial)
439497.RR11_2179				(PF13704)	(mitochondrial)
439497.RR11_1101				(PF16350) (PF08669)
439497.RR11_2998				(PF16350) (PF08669)
439497.RR11_3173				(PF02485)	(plastid)
439497.RR11_2177				(PF16350) (PF08669)
439497.RR11_1645				(PF07366)
439497.RR11_80				(PF08669)
439497.RR11_3082				(PF07366)
439497.RR11_1644				(PF08669)
439497.RR11_3389				(PF08669)
439497.RR11_3060				(PF07366)
439497.RR11_770				(PF07366)
439497.RR11_2394				(PF08669)
439497.RR11_3271				(PF08669)
439497.RR11_1729				(PF10013)	not used
439497.RR11_3613				(PF13704)
439497.RR11_2668				(PF08669)
439497.RR11_2984				(PF13704)
439497.RR11_1564				(PF07366)
439497.RR11_2698				(PF02485)
439497.RR11_1969				(PF09585)
439497.RR11_2047				(PF01755)
439497.RR11_413				(PF09585)
439497.RR11_1206				(PF13704)
439497.RR11_2494				(PF01755)
439497.RR11_2491				(PF02475)
439497.RR11_3165				(PF13704)
439497.RR11_3169				(PF13704)
439497.RR11_1928				(PF07366)
439497.RR11_2315				PF11781
439497.RR11_215				(PF01755)
439497.RR11_1124				(PF13704)

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