Effective results for Sphingomonas sp. S17 (eggnog40)

Summary

Number of putative secreted proteins: 108
- Predicted by T4SEpre: 52
- Predicted by EffectiveELD: 16 eukaryotic-like domains, contained in 64 proteins (3 high, 61 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
1007104.SUS17_1114			+		ER
1007104.SUS17_2490			+		ER
1007104.SUS17_2496				(PF07971)	ER; (ER)
1007104.SUS17_2498				(PF16670)	mitochondrial
1007104.SUS17_499			+		ER
1007104.SUS17_202			+		ER
1007104.SUS17_356				(PF05433)	mitochondrial; ER
1007104.SUS17_2024			+		(mitochondrial); mitochondrial
1007104.SUS17_754				(PF05433)	(ER)
1007104.SUS17_3084				(PF01790)	(ER)
1007104.SUS17_1550			+		ER
1007104.SUS17_2908				(PF05433)	(ER)
1007104.SUS17_2902				(PF05433)	ER
1007104.SUS17_2274			+		ER
1007104.SUS17_784				(PF05433)	ER
1007104.SUS17_1164			+		mitochondrial; (mitochondrial)
1007104.SUS17_1499			+		ER
1007104.SUS17_1380				(PF05433)	ER
1007104.SUS17_2040			+		mitochondrial; (mitochondrial)
1007104.SUS17_1530				(PF16670)	ER
1007104.SUS17_315				(PF07971)	ER
1007104.SUS17_3146			+		ER
1007104.SUS17_522			+		ER
1007104.SUS17_3289				(PF06824)	mitochondrial; (mitochondrial)
1007104.SUS17_3592			+		ER
1007104.SUS17_921				(PF07971)	mitochondrial
1007104.SUS17_851				(PF06455)	ER
1007104.SUS17_3297				(PF07971)	ER
1007104.SUS17_1189				(PF03203)	mitochondrial; (mitochondrial)
1007104.SUS17_3672			+		ER
1007104.SUS17_2737			+		ER
1007104.SUS17_139			+		mitochondrial; (mitochondrial)
1007104.SUS17_3922				(PF04820)	(ER)
1007104.SUS17_73			+		(mitochondrial); (plastid)
1007104.SUS17_388			+		ER
1007104.SUS17_2987				(PF05433)	ER
1007104.SUS17_2695			+		ER; (ER)
1007104.SUS17_3121				(PF04041)	(mitochondrial)
1007104.SUS17_2235				(PF05433)	ER
1007104.SUS17_2839				(PF01790)	ER
1007104.SUS17_2649			+		ER
1007104.SUS17_3554			+		(mitochondrial)
1007104.SUS17_1744				(PF16387)	(ER)
1007104.SUS17_1957				(PF01790)	(ER)
1007104.SUS17_2907				(PF05433)	plastid
1007104.SUS17_3288				(PF07971)	(ER)
1007104.SUS17_920				(PF06824)	(plastid)
1007104.SUS17_3295				(PF07971)	(mitochondrial)
1007104.SUS17_3231			+		(ER)
1007104.SUS17_3003				(PF11911)	(ER)
1007104.SUS17_3211				(PF03203)	(plastid)
1007104.SUS17_513				(PF04041)
1007104.SUS17_3196				(PF02796)
1007104.SUS17_1593			+
1007104.SUS17_741			+
1007104.SUS17_3734				(PF02796)
1007104.SUS17_3427			+
1007104.SUS17_251			+
1007104.SUS17_3098				(PF02796)
1007104.SUS17_1542				(PF00028)
1007104.SUS17_244			+
1007104.SUS17_3404			+
1007104.SUS17_4073				(PF02796)
1007104.SUS17_875			+
1007104.SUS17_28			+
1007104.SUS17_861			+
1007104.SUS17_3145				(PF04041)
1007104.SUS17_485				(PF11911)
1007104.SUS17_3776				(PF03203)
1007104.SUS17_2369				(PF13668)
1007104.SUS17_587				(PF04820)
1007104.SUS17_3290				(PF07971)
1007104.SUS17_3906				(PF02933)
1007104.SUS17_3586			+
1007104.SUS17_1616				(PF13668)
1007104.SUS17_938				(PF04820)
1007104.SUS17_1984			+
1007104.SUS17_2370				(PF13668)
1007104.SUS17_440				(PF04041)
1007104.SUS17_3112				(PF02796)
1007104.SUS17_3629				(PF04820)
1007104.SUS17_3244				(PF04041)
1007104.SUS17_1263			+
1007104.SUS17_541			+
1007104.SUS17_544			+
1007104.SUS17_3631				(PF04820)
1007104.SUS17_3630				(PF04820)
1007104.SUS17_1678			+
1007104.SUS17_953			+
1007104.SUS17_2996				(PF01790)
1007104.SUS17_1646				(PF04820)
1007104.SUS17_894				(PF04820)
1007104.SUS17_2504				(PF00028)
1007104.SUS17_3128				PF03332
1007104.SUS17_3716				PF03332
1007104.SUS17_3150			+
1007104.SUS17_1782				(PF04820)
1007104.SUS17_2204				PF03332
1007104.SUS17_578				(PF13668)
1007104.SUS17_579				(PF13668)
1007104.SUS17_3461			+
1007104.SUS17_1225				(PF04820)
1007104.SUS17_985			+
1007104.SUS17_2013			+
1007104.SUS17_3074				(PF02796)
1007104.SUS17_176				(PF04820)
1007104.SUS17_3039			+
1007104.SUS17_2311			+

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 = 0.8 (8/10 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=
==========================================================