Effective results for Stenotrophomonas maltophilia R551-3 (eggnog40)

Summary

Number of putative secreted proteins: 89
- Predicted by T4SEpre: 44
- Predicted by EffectiveELD: 18 eukaryotic-like domains, contained in 47 proteins (1 high, 46 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type IV

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
391008.Smal_2875				(PF01431) (PF05649)	ER
391008.Smal_1199				(PF01431) (PF05649)	ER
391008.Smal_0428				(PF01431) (PF05649)	ER
391008.Smal_2116			+		ER
391008.Smal_0065				(PF11720)	ER
391008.Smal_0398				(PF03203)	ER
391008.Smal_3458			+		(ER); ER
391008.Smal_3293			+		ER
391008.Smal_3294			+		ER
391008.Smal_0126				(PF03544)	ER
391008.Smal_2734			+		(mitochondrial)
391008.Smal_1195			+		ER
391008.Smal_2675				(PF03544)	ER
391008.Smal_3582				(PF03901)	ER
391008.Smal_4024			+		ER
391008.Smal_2985			+		ER
391008.Smal_0697			+		ER
391008.Smal_2326			+		ER
391008.Smal_2327			+		ER
391008.Smal_0368				(PF03544)	(mitochondrial); plastid
391008.Smal_2661			+		(ER)
391008.Smal_3483				(PF08212)	ER
391008.Smal_3832			+		ER
391008.Smal_3308				(PF03544)	ER
391008.Smal_0417			+		ER
391008.Smal_1950				(PF08212)	ER
391008.Smal_3813			+		(ER)
391008.Smal_2775				(PF08212)	ER
391008.Smal_3224				(PF03544)	ER
391008.Smal_3351				(PF04450)	ER
391008.Smal_1840				(PF03544)	(mitochondrial); (ER)
391008.Smal_1841				(PF03544)	ER
391008.Smal_3696				(PF04505)	ER
391008.Smal_2357				(PF11720)	ER
391008.Smal_3007			+		ER
391008.Smal_0623				(PF03544)	ER
391008.Smal_3748				(PF07653)	mitochondrial
391008.Smal_2112			+		(ER)
391008.Smal_0078				(PF11720)	ER
391008.Smal_2391				(PF03544)	ER
391008.Smal_3868				(PF03544)	ER; (ER)
391008.Smal_2874				(PF01431) (PF05649)
391008.Smal_2989				(PF05684)	(ER)
391008.Smal_2536				(PF03544)	(ER)
391008.Smal_1092				(PF05684)	(ER)
391008.Smal_0790			+		(mitochondrial)
391008.Smal_3697				(PF04505)	(ER)
391008.Smal_1215				(PF03203)	(mitochondrial)
391008.Smal_2903				(PF03544)	(mitochondrial)
391008.Smal_3741			+		(mitochondrial)
391008.Smal_3412			+		(ER)
391008.Smal_3091				(PF03544)	(plastid)
391008.Smal_3071			+		(mitochondrial)
391008.Smal_3864				(PF08695)	plastid
391008.Smal_0719			+
391008.Smal_1659			+
391008.Smal_3590				(PF14237)
391008.Smal_0008				(PF03544)
391008.Smal_2678			+
391008.Smal_3589				(PF14237)
391008.Smal_0361			+
391008.Smal_2662			+
391008.Smal_2537				(PF03544)
391008.Smal_3131			+
391008.Smal_2847			+
391008.Smal_1886			+
391008.Smal_1887			+
391008.Smal_1647			+
391008.Smal_2543			+
391008.Smal_3173			+
391008.Smal_0309			+
391008.Smal_0794				(PF05076)
391008.Smal_3964				(PF05076)
391008.Smal_3960			+
391008.Smal_3995				(PF14237)
391008.Smal_3993			+
391008.Smal_2160				(PF03203)
391008.Smal_3760				(PF08212)
391008.Smal_3765			+
391008.Smal_1216				PF17067	not used
391008.Smal_2900			+
391008.Smal_2176			+
391008.Smal_2352				(PF11397)
391008.Smal_0622				(PF11539)
391008.Smal_2726				(PF04768)
391008.Smal_4030				(PF05076)
391008.Smal_0281			+
391008.Smal_1736			+
391008.Smal_3389			+

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

• T4SEpre bpbAac predictions (T4SEpre_bpbAac_FinalResult.csv)
• T4SEpre psAac predictions (T4SEpre_psAac_FinalResult.csv)
• 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: YES (FDR = 7.2 %)
  Estimated copy number = 0.7 (7/10 KEGG proteins)
• 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=
==========================================================