Effective results for Rhodobacterales bacterium Y4I (eggnog40)

Summary

Number of putative secreted proteins: 83
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 21 eukaryotic-like domains, contained in 83 proteins (2 high, 81 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
439496.RBY4I_3884				(PF01571) (PF16350) (PF08669)	(ER)
439496.RBY4I_4195				(PF01571) (PF16350) (PF08669)	ER
439496.RBY4I_1598				(PF01571) (PF16350) (PF08669)	ER
439496.RBY4I_402				(PF01571) (PF08669)	(ER)
439496.RBY4I_3366				(PF01571) (PF08669)	(mitochondrial)
439496.RBY4I_2898				(PF01571) (PF08669)	(mitochondrial)
439496.RBY4I_420				(PF02485)	(mitochondrial); plastid
439496.RBY4I_4091				(PF02690)	ER
439496.RBY4I_2632				(PF01571) (PF16350) (PF08669)
439496.RBY4I_1932				(PF04325)	mitochondrial
439496.RBY4I_3035				(PF01527)	(mitochondrial)
439496.RBY4I_3101				(PF07298)	ER
439496.RBY4I_3113				(PF13276)	(mitochondrial); (plastid)
439496.RBY4I_103				(PF02690)	ER
439496.RBY4I_1033				(PF01571) (PF16350) (PF08669)
439496.RBY4I_2540				(PF07298)	ER
439496.RBY4I_2300				(PF13704)	mitochondrial; (plastid)
439496.RBY4I_1546				(PF01527)	(mitochondrial)
439496.RBY4I_1826				(PF01571) (PF16350) (PF08669)
439496.RBY4I_3094				(PF13704)	mitochondrial
439496.RBY4I_2922				(PF02690)	ER
439496.RBY4I_3400				(PF01571) (PF16350) (PF08669)
439496.RBY4I_1798				(PF02690)	ER
439496.RBY4I_3430				(PF13276)	(mitochondrial); (plastid)
439496.RBY4I_671				(PF13276)	(mitochondrial); (plastid)
439496.RBY4I_2874				(PF07298)	ER
439496.RBY4I_730				(PF13276) (PF13683)
439496.RBY4I_3666				(PF13276)	mitochondrial; not used
439496.RBY4I_1133				(PF13276) (PF13683)
439496.RBY4I_1070				(PF01571) (PF08669)
439496.RBY4I_2415				(PF03092)	(ER)
439496.RBY4I_2962				(PF01571) (PF08669)
439496.RBY4I_1999				(PF13704)	plastid
439496.RBY4I_3160				(PF01571) (PF08669)
439496.RBY4I_1687				(PF13276) (PF13683)
439496.RBY4I_1199				(PF01571) (PF08669)
439496.RBY4I_3822				(PF09585)	(mitochondrial)
439496.RBY4I_1857				(PF13276) (PF13683)
439496.RBY4I_2305				(PF13276) (PF13683)
439496.RBY4I_1206				(PF13704)	(ER)
439496.RBY4I_311				(PF13276) (PF13683)
439496.RBY4I_864				(PF13276) (PF13683)
439496.RBY4I_2933				(PF13276) (PF13683)
439496.RBY4I_789				(PF01571) (PF08669)
439496.RBY4I_1101				(PF13276) (PF13683)
439496.RBY4I_3188				(PF13276) (PF13683)
439496.RBY4I_3195				(PF13276) (PF13683)
439496.RBY4I_556				(PF01527)
439496.RBY4I_555				(PF01527)
439496.RBY4I_3878				(PF01527)
439496.RBY4I_2832				(PF01527)
439496.RBY4I_419				PF11781
439496.RBY4I_3920				(PF13704)
439496.RBY4I_284				(PF01527)
439496.RBY4I_3937				(PF13875)
439496.RBY4I_1413				(PF01527)
439496.RBY4I_1696				PF03175
439496.RBY4I_1090				(PF01527)
439496.RBY4I_3350				(PF01527)
439496.RBY4I_1464				(PF01527)
439496.RBY4I_3825				(PF04325)
439496.RBY4I_1859				(PF01527)
439496.RBY4I_2880				(PF13683)
439496.RBY4I_3173				(PF12255)
439496.RBY4I_3789				(PF00102)
439496.RBY4I_1148				(PF01527)
439496.RBY4I_648				(PF01527)
439496.RBY4I_2845				(PF04325)
439496.RBY4I_3311				(PF04325)	not used
439496.RBY4I_3539				(PF09585)
439496.RBY4I_3881				(PF01527)
439496.RBY4I_2913				(PF11927)
439496.RBY4I_2869				(PF01527)
439496.RBY4I_693				(PF01527)
439496.RBY4I_566				(PF13276)
439496.RBY4I_2472				(PF01527)
439496.RBY4I_447				(PF02485)
439496.RBY4I_377				(PF13582)
439496.RBY4I_3042				(PF11927)
439496.RBY4I_2075				(PF01527)
439496.RBY4I_1744				(PF03538)
439496.RBY4I_2650				(PF01527)
439496.RBY4I_2491				(PF01527)

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