Effective results for Treponema phagedenis F0421 (eggnog40)

Summary

Number of putative secreted proteins: 41
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 21 eukaryotic-like domains, contained in 41 proteins (2 high, 39 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
754027.HMPREF9554_02890				(PF09112) (PF09113)	ER
754027.HMPREF9554_02499				(PF13306)	ER
754027.HMPREF9554_02691				(PF13306)	ER
754027.HMPREF9554_01006				(PF12799)	mitochondrial
754027.HMPREF9554_00362				(PF05704)	(mitochondrial)
754027.HMPREF9554_02541				(PF02544)	ER
754027.HMPREF9554_02955				(PF01715)	ER
754027.HMPREF9554_01936				(PF12799)	ER
754027.HMPREF9554_02778				(PF00958)	(mitochondrial)
754027.HMPREF9554_00448				(PF13306)	(ER)
754027.HMPREF9554_01887				(PF13306)	mitochondrial
754027.HMPREF9554_02018				(PF07837) (PF02971)
754027.HMPREF9554_01085				PF03727 PF00349
754027.HMPREF9554_03111				(PF12862)
754027.HMPREF9554_01689				(PF13306)
754027.HMPREF9554_01116				(PF13306)
754027.HMPREF9554_00640				(PF13306)
754027.HMPREF9554_00638				(PF13306)	not used
754027.HMPREF9554_02840				(PF12799)
754027.HMPREF9554_01399				(PF12799)
754027.HMPREF9554_02943				(PF01715)
754027.HMPREF9554_01706				(PF07892)
754027.HMPREF9554_01571				(PF01813)
754027.HMPREF9554_00978				(PF01496)
754027.HMPREF9554_00973				(PF16886)
754027.HMPREF9554_02096				(PF12799)
754027.HMPREF9554_01663				(PF12799)
754027.HMPREF9554_01261				(PF13306)	not used
754027.HMPREF9554_01079				(PF01496)
754027.HMPREF9554_02776				(PF00958)
754027.HMPREF9554_00734				(PF13306)
754027.HMPREF9554_01469				(PF04970)
754027.HMPREF9554_00443				(PF07892)
754027.HMPREF9554_01084				(PF01991)
754027.HMPREF9554_01082				(PF16886)
754027.HMPREF9554_01080				(PF01813)
754027.HMPREF9554_02345				(PF13306)
754027.HMPREF9554_02344				(PF04970)	not used
754027.HMPREF9554_01871				(PF12799)
754027.HMPREF9554_03066				PF04733
754027.HMPREF9554_01404				(PF16314)

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