Effective results for Campylobacter showae RM3277 (eggnog40)

Summary

Number of putative secreted proteins: 28
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 9 eukaryotic-like domains, contained in 28 proteins (0 high, 28 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
553219.CAMSH0001_0152				(PF08238)	ER
553219.CAMSH0001_1045				(PF05935)	ER
553219.CAMSH0001_2191				(PF08238)	ER
553219.CAMSH0001_0070				(PF08238)	ER
553219.CAMSH0001_2336				(PF08238)	ER
553219.CAMSH0001_1424				(PF08238)	ER
553219.CAMSH0001_0273				(PF08238)	ER
553219.CAMSH0001_0468				(PF08238)	ER
553219.CAMSH0001_0885				(PF08238)	ER
553219.CAMSH0001_1970				(PF03162)	ER
553219.CAMSH0001_1809				(PF08238)	ER
553219.CAMSH0001_1810				(PF08238)	ER
553219.CAMSH0001_1811				(PF08238)	ER
553219.CAMSH0001_1552				(PF08238)	ER
553219.CAMSH0001_1036				(PF05935)	ER
553219.CAMSH0001_2371				(PF08238)	ER
553219.CAMSH0001_1288				(PF03054)	(ER)
553219.CAMSH0001_0532				(PF08238)	(ER)
553219.CAMSH0001_2135				(PF08238)	(mitochondrial)
553219.CAMSH0001_2196				(PF03054)
553219.CAMSH0001_1315				(PF08238)
553219.CAMSH0001_1357				(PF02516)
553219.CAMSH0001_0757				(PF13207)
553219.CAMSH0001_2121				(PF03054)
553219.CAMSH0001_0501				(PF04098)
553219.CAMSH0001_0569				(PF02689)
553219.CAMSH0001_0166				(PF13910)	not used
553219.CAMSH0001_1023				(PF08238)

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 = 0.25 (2/8 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=
==========================================================