Effective results for Helicobacter pullorum MIT 98-5489 (eggnog40)

Summary

Number of putative secreted proteins: 17
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 10 eukaryotic-like domains, contained in 17 proteins (2 high, 15 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
537972.HPMG_01910				(PF04305)	ER
537972.HPMG_01655				(PF02516)	ER
537972.HPMG_01983				(PF00059)	ER
537972.HPMG_01682				(PF14113)	(plastid)
537972.HPMG_01839				(PF01501)
537972.HPMG_00685				(PF05704)
537972.HPMG_00196				(PF04305)
537972.HPMG_00438				(PF06176)	not used
537972.HPMG_01913				(PF01501)
537972.HPMG_02004				PF11443	not used
537972.HPMG_00741				(PF01501)
537972.HPMG_00391				(PF01501)
537972.HPMG_01634				(PF01501)
537972.HPMG_01704				(PF14113)
537972.HPMG_01194				(PF00162)	not used
537972.HPMG_01193				(PF00162)
537972.HPMG_00556				PF14640

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 = 0.5 (4/8 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=
==========================================================