Effective results for Photobacterium angustum S14 (eggnog40)

Summary

Number of putative secreted proteins: 65
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 25 eukaryotic-like domains, contained in 65 proteins (2 high, 63 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
314292.VAS14_04678				(PF01773) (PF07662)	ER
314292.VAS14_02221				(PF01773) (PF07662)	ER
314292.VAS14_04513				(PF01773) (PF07662)	ER
314292.VAS14_13894				(PF01773) (PF07662)	ER
314292.VAS14_09224				(PF02839) (PF08329)	ER
314292.VAS14_07249				(PF01773) (PF07662)	ER
314292.VAS14_08870				(PF02839) (PF08329)	ER; (ER)
314292.VAS14_16172				PF00031	ER
314292.VAS14_18454				(PF03724)	ER
314292.VAS14_11649				(PF00854)	(ER)
314292.VAS14_04668				(PF02839)	(ER)
314292.VAS14_06238				(PF00854)	(ER)
314292.VAS14_02938				(PF08180)	ER
314292.VAS14_09469				(PF02839)	ER
314292.VAS14_15514				(PF00854)	(ER)
314292.VAS14_05818				(PF06455)	ER
314292.VAS14_04213				PF00031	ER
314292.VAS14_16501				(PF03724)	ER
314292.VAS14_08875				(PF02839)	ER
314292.VAS14_12974				(PF03222)	ER
314292.VAS14_06098				(PF02112)	ER
314292.VAS14_13944				(PF00854)	ER
314292.VAS14_04313				(PF02839)	(ER)
314292.VAS14_08910				(PF02839)	ER
314292.VAS14_10704				(PF13127)	ER
314292.VAS14_18444				(PF03222)	ER
314292.VAS14_08850				(PF17186)	ER
314292.VAS14_07479				(PF00303)	(ER)
314292.VAS14_04973				(PF03724)	ER
314292.VAS14_17671				(PF02275)	ER
314292.VAS14_15814				(PF02275)	ER
314292.VAS14_15804				(PF00854)	(ER)
314292.VAS14_12244				(PF02275)	ER
314292.VAS14_09174				(PF03724)	ER
314292.VAS14_03383				(PF17186)	ER
314292.VAS14_21046				(PF03222)	(ER)
314292.VAS14_15829				(PF02839)	ER
314292.VAS14_04723				(PF03724)	ER
314292.VAS14_04653				(PF03222)	ER
314292.VAS14_14429				(PF10013)	(mitochondrial); not used
314292.VAS14_04708				(PF01786)
314292.VAS14_07564				(PF00303)
314292.VAS14_10599				(PF01117)
314292.VAS14_12234				(PF00854)
314292.VAS14_22032				(PF01276)	not used
314292.VAS14_09784				(PF00854)
314292.VAS14_02061				(PF12588)
314292.VAS14_22022				(PF01276)	not used
314292.VAS14_22027				(PF01276)
314292.VAS14_05553				(PF12344)
314292.VAS14_22017				(PF01276)
314292.VAS14_06083				(PF08732)
314292.VAS14_19221				(PF03947)
314292.VAS14_19226				(PF03947)	not used
314292.VAS14_15759				(PF12344)
314292.VAS14_00916				(PF03222)
314292.VAS14_16626				(PF01276)
314292.VAS14_18464				(PF01276)
314292.VAS14_14419				(PF03945)
314292.VAS14_07539				(PF00303)
314292.VAS14_09779				(PF00854)
314292.VAS14_06478				(PF04399)
314292.VAS14_12134				(PF04399)
314292.VAS14_05843				(PF03222)
314292.VAS14_14159				(PF02839)

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 = 1.125 (9/8 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=
==========================================================