Effective results for Roseovarius sp. TM1035 (eggnog40)

Summary

Number of putative secreted proteins: 81
- Predicted by T4SEpre: 0
- Predicted by EffectiveELD: 27 eukaryotic-like domains, contained in 81 proteins (3 high, 78 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
391613.RTM1035_08464				(PF16350) (PF01571) (PF08669)	ER
391613.RTM1035_08454				(PF16350) (PF01571) (PF08669)	ER
391613.RTM1035_00900				(PF16350) (PF01571) (PF08669)	(ER)
391613.RTM1035_05848				(PF01571) (PF08669)	(mitochondrial)
391613.RTM1035_16187				(PF16350) (PF01571) (PF08669)	(ER)
391613.RTM1035_12998				(PF01571) (PF08669)	(mitochondrial)
391613.RTM1035_03430				(PF01571) (PF08669)	(mitochondrial)
391613.RTM1035_17447				(PF13704)	mitochondrial
391613.RTM1035_08024				(PF06258)	(ER)
391613.RTM1035_11695				(PF02230)	(mitochondrial)
391613.RTM1035_02998				(PF16350) (PF01571) (PF08669)
391613.RTM1035_16607				(PF02230)	ER
391613.RTM1035_06963				(PF05990)	ER
391613.RTM1035_05460				(PF02230)	ER
391613.RTM1035_17367				(PF11977)	ER
391613.RTM1035_12078				(PF03209)	(ER)
391613.RTM1035_06453				(PF03567)	(mitochondrial); mitochondrial
391613.RTM1035_13623				(PF00685)	mitochondrial
391613.RTM1035_17935				(PF13704)	(mitochondrial); plastid
391613.RTM1035_02975				(PF16350) (PF01571) (PF08669)
391613.RTM1035_01585				(PF09585)	(mitochondrial)
391613.RTM1035_12028				(PF03209)	ER
391613.RTM1035_18140				(PF05990)	ER
391613.RTM1035_17462				(PF02230)	ER
391613.RTM1035_06023				(PF01571) (PF08669)
391613.RTM1035_07649				(PF01571) (PF08669)
391613.RTM1035_16272				(PF00549) (PF08442)
391613.RTM1035_17452				(PF02485)	plastid
391613.RTM1035_12373				(PF01571) (PF08669)
391613.RTM1035_16632				(PF01571) (PF08669)
391613.RTM1035_12728				(PF00549) (PF08442)
391613.RTM1035_12743				(PF00549) (PF08442)
391613.RTM1035_13618				(PF00685)	(mitochondrial)
391613.RTM1035_05480				(PF01571) (PF08669)
391613.RTM1035_05360				(PF06119) PF00094
391613.RTM1035_07609				(PF01571) (PF08669)
391613.RTM1035_04885				(PF00549)	(mitochondrial)
391613.RTM1035_04890				(PF00549) (PF08442)
391613.RTM1035_09099				(PF01571) (PF08669)
391613.RTM1035_11320				PF12873
391613.RTM1035_11215				(PF13683)
391613.RTM1035_07468				(PF13683)
391613.RTM1035_09623				(PF05990)
391613.RTM1035_09713				(PF13683)
391613.RTM1035_00140				(PF13683)
391613.RTM1035_09573				(PF03567)
391613.RTM1035_19856				(PF03092)
391613.RTM1035_13563				(PF10013)
391613.RTM1035_13748				(PF09458)
391613.RTM1035_02285				(PF13683)
391613.RTM1035_17457				(PF03567)
391613.RTM1035_16267				(PF00549)
391613.RTM1035_04445				(PF04325)
391613.RTM1035_08019				(PF00685)
391613.RTM1035_19391				(PF03567)
391613.RTM1035_19396				(PF02485)
391613.RTM1035_07549				(PF00070)
391613.RTM1035_12733				(PF00549)
391613.RTM1035_08044				(PF06258)
391613.RTM1035_08049				(PF00685)
391613.RTM1035_14807				(PF01786)
391613.RTM1035_15997				(PF13875)
391613.RTM1035_17287				(PF03567)
391613.RTM1035_07098				PF00094
391613.RTM1035_19506				(PF04325)	not used
391613.RTM1035_03740				(PF13683)
391613.RTM1035_20226				(PF13704)
391613.RTM1035_20221				(PF13704)
391613.RTM1035_20131				(PF04325)
391613.RTM1035_14592				(PF04325)
391613.RTM1035_07984				(PF06258)
391613.RTM1035_20231				(PF13704)
391613.RTM1035_13333				(PF05990)
391613.RTM1035_03295				(PF00685)
391613.RTM1035_01590				(PF09585)
391613.RTM1035_10540				(PF11927)
391613.RTM1035_05745				(PF05990)
391613.RTM1035_09543				(PF13704)
391613.RTM1035_04655				(PF13683)
391613.RTM1035_07664				(PF11927)
391613.RTM1035_05928				(PF13683)

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