Effective results for Polaromonas sp. JS666 (eggnog40)

Summary

Number of putative secreted proteins: 69
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 13 eukaryotic-like domains, contained in 69 proteins (1 high, 68 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): None

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
296591.Bpro_0035				(PF03480)	(mitochondrial)
296591.Bpro_3107				(PF03480)	(mitochondrial)
296591.Bpro_0556				(PF03480)	ER
296591.Bpro_2896				(PF04654)	ER
296591.Bpro_4499				(PF03480)	ER
296591.Bpro_1780				(PF03480)	ER
296591.Bpro_1006				(PF01177)	mitochondrial; (mitochondrial)
296591.Bpro_2208				(PF03480)	mitochondrial
296591.Bpro_2119				(PF01177)	(mitochondrial); plastid
296591.Bpro_1871				(PF03480)	ER
296591.Bpro_1290				(PF03480)	ER
296591.Bpro_3964				(PF03480)	ER
296591.Bpro_2963				(PF03480)	(ER); ER
296591.Bpro_4736				(PF03480)	ER
296591.Bpro_0088				(PF03480)	(ER)
296591.Bpro_0553				(PF03480)	(ER)
296591.Bpro_1455				(PF03480)	ER
296591.Bpro_2838				(PF03480)	ER
296591.Bpro_4882				(PF03480)	ER
296591.Bpro_2841				(PF03480)	mitochondrial; (mitochondrial)
296591.Bpro_4384				(PF01177)	ER; (ER)
296591.Bpro_2121				(PF03480)	mitochondrial
296591.Bpro_4848				(PF04654)	ER
296591.Bpro_1777				(PF03480)	ER
296591.Bpro_1748				(PF03480)	(ER)
296591.Bpro_1749				(PF03480)	(mitochondrial)
296591.Bpro_1750				(PF03480)	(mitochondrial)
296591.Bpro_0015				PF08538	plastid
296591.Bpro_2811				(PF02201)	(mitochondrial)
296591.Bpro_1964				(PF07958)
296591.Bpro_1965				(PF12471)
296591.Bpro_3050				(PF04324)
296591.Bpro_4342				(PF13510)
296591.Bpro_4051				(PF03480)
296591.Bpro_4819				(PF14031)
296591.Bpro_3276				(PF04324)
296591.Bpro_3279				(PF04324)
296591.Bpro_0661				(PF14031)
296591.Bpro_0689				(PF04324)
296591.Bpro_3944				(PF13510)
296591.Bpro_4577				(PF03480)
296591.Bpro_4755				(PF01177)
296591.Bpro_3250				(PF13510)
296591.Bpro_4374				(PF04324)
296591.Bpro_4375				(PF13510)
296591.Bpro_0690				(PF13510)
296591.Bpro_0049				(PF04324)
296591.Bpro_2805				(PF13510)
296591.Bpro_1474				(PF05189)
296591.Bpro_4817				(PF14031)
296591.Bpro_0050				(PF13510)
296591.Bpro_4424				(PF13510)
296591.Bpro_4425				(PF04324)
296591.Bpro_4341				(PF04324)
296591.Bpro_0550				(PF01177)
296591.Bpro_0552				(PF01177)
296591.Bpro_2001				(PF01177)
296591.Bpro_3943				(PF04324)
296591.Bpro_4398				(PF04324)
296591.Bpro_4399				(PF13510)
296591.Bpro_4713				(PF02201)
296591.Bpro_3705				(PF08837)
296591.Bpro_1626				(PF16155)
296591.Bpro_4092				(PF14031)
296591.Bpro_4415				(PF13510)
296591.Bpro_4414				(PF04324)
296591.Bpro_2637				(PF08837)
296591.Bpro_1774				(PF03480)
296591.Bpro_2045				(PF01177)

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: NO (FDR = 7.7 %)

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