Effective results for Photobacterium leiognathi subsp. mandapamensis svers.1.1. (eggnog40)

Summary

Number of putative secreted proteins: 46
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 20 eukaryotic-like domains, contained in 46 proteins (2 high, 44 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
1001530.PMSV_1237				(PF01773) (PF07662)	ER
1001530.PMSV_711				(PF02839) (PF10462)	ER
1001530.PMSV_3675				(PF01773) (PF07662)	ER
1001530.PMSV_2268				(PF01773) (PF07662)	ER
1001530.PMSV_2064				(PF02839) (PF02010)	ER; (ER)
1001530.PMSV_824				(PF01773) (PF07662)	ER
1001530.PMSV_1202				(PF01773) (PF07662)	ER
1001530.PMSV_1764				(PF02275)	ER
1001530.PMSV_1232				(PF03222)	ER
1001530.PMSV_1235				(PF02839)	(ER)
1001530.PMSV_1247				(PF03724)	ER
1001530.PMSV_2054				(PF03724)	ER
1001530.PMSV_1738				(PF02839)	ER
1001530.PMSV_469				(PF01179)	ER
1001530.PMSV_468				(PF01179)	ER
1001530.PMSV_1892				(PF10462)	ER
1001530.PMSV_2120				(PF02839)	(ER)
1001530.PMSV_2000				(PF02839)	ER
1001530.PMSV_543				(PF03724)	ER
1001530.PMSV_541				(PF03222)	ER
1001530.PMSV_1138				(PF00031)	ER
1001530.PMSV_371				(PF02275)	ER
1001530.PMSV_159				(PF03724)	ER
1001530.PMSV_1128				PF00362	(mitochondrial)
1001530.PMSV_1303				(PF03724)	ER
1001530.PMSV_2301				(PF02839)	ER; (ER)
1001530.PMSV_66				(PF03222)	(ER)
1001530.PMSV_941				(PF08180)	ER
1001530.PMSV_1157				(PF02839)	(ER)
1001530.PMSV_2427				PF00531
1001530.PMSV_1432				(PF12344)
1001530.PMSV_1984				(PF12344)
1001530.PMSV_2632				(PF10063)
1001530.PMSV_1243				(PF01786)
1001530.PMSV_2624				(PF02275)
1001530.PMSV_2610				(PF04399)
1001530.PMSV_726				(PF00677)
1001530.PMSV_1472				(PF03222)
1001530.PMSV_803				(PF12588)
1001530.PMSV_1846				(PF00677)
1001530.PMSV_1599				(PF04399)
1001530.PMSV_597				(PF03222)
1001530.PMSV_178				(PF00677)
1001530.PMSV_144				(PF01490)
1001530.PMSV_1823				(PF02839)
1001530.PMSV_1838				(PF00677)

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