Effective results for Sphingomonas sp. SKA58 (eggnog40)

Summary

Number of putative secreted proteins: 82
- Predicted by T4SEpre: 43
- Predicted by EffectiveELD: 17 eukaryotic-like domains, contained in 45 proteins (5 high, 40 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
314266.SKA58_03650				(PF10435) (PF13363)	ER
314266.SKA58_09461			+		mitochondrial
314266.SKA58_17208			+		ER
314266.SKA58_17203			+		ER
314266.SKA58_17023				(PF03050)	(mitochondrial)
314266.SKA58_03024			+		ER
314266.SKA58_08869			+		ER
314266.SKA58_13827			+		ER
314266.SKA58_13007			+		ER; (ER)
314266.SKA58_06125			+		ER
314266.SKA58_06535			+		(mitochondrial)
314266.SKA58_03280			+		(mitochondrial)
314266.SKA58_13373			+		ER; (ER)
314266.SKA58_12517				PF10712	(mitochondrial); mitochondrial
314266.SKA58_18207			+		(mitochondrial)
314266.SKA58_09761				(PF06455)	ER
314266.SKA58_14707			+		mitochondrial
314266.SKA58_07113			+		ER
314266.SKA58_14127			+		ER
314266.SKA58_01225				(PF03050)	(mitochondrial)
314266.SKA58_10435				(PF15892)	(mitochondrial)
314266.SKA58_10440				(PF15892)	(ER)
314266.SKA58_01900			+		(mitochondrial)
314266.SKA58_09201			+		(mitochondrial)
314266.SKA58_14017				(PF13621)	(plastid)
314266.SKA58_16933				PF06087
314266.SKA58_06605			+
314266.SKA58_19585			+
314266.SKA58_13052			+
314266.SKA58_17213			+
314266.SKA58_02440			+
314266.SKA58_12030				(PF03050)
314266.SKA58_17038				(PF03050)
314266.SKA58_09896			+
314266.SKA58_18970				PF03332
314266.SKA58_14272			+
314266.SKA58_18895				PF03332
314266.SKA58_02010				(PF02958)
314266.SKA58_19175				(PF01786)
314266.SKA58_08504			+
314266.SKA58_01280				(PF03050)
314266.SKA58_16012				(PF01695)
314266.SKA58_02000				(PF02958)
314266.SKA58_05600				PF03332
314266.SKA58_19150				(PF03050)
314266.SKA58_18685				(PF01695)
314266.SKA58_03995				(PF01695)
314266.SKA58_03375				(PF00614)
314266.SKA58_06400			+
314266.SKA58_02345				(PF03050)
314266.SKA58_16993				(PF01695)	not used
314266.SKA58_16998				(PF03050)
314266.SKA58_10123				(PF01695)
314266.SKA58_18072				(PF02933)
314266.SKA58_16988				(PF03050)
314266.SKA58_19370			+
314266.SKA58_19475			+
314266.SKA58_01550			+
314266.SKA58_00945				(PF13621)
314266.SKA58_13628			+
314266.SKA58_19490			+
314266.SKA58_09176				(PF10013)	not used
314266.SKA58_09191			+
314266.SKA58_08649				(PF01695)
314266.SKA58_11720			+
314266.SKA58_08809			+
314266.SKA58_02310				(PF01695)
314266.SKA58_01375				(PF01695)
314266.SKA58_19710				(PF01695)	not used
314266.SKA58_02080				(PF03492)
314266.SKA58_05995			+
314266.SKA58_12060				(PF01695)	not used
314266.SKA58_01985				(PF02958)
314266.SKA58_16913				(PF11074)
314266.SKA58_00615				(PF13621)
314266.SKA58_13703				(PF13621)
314266.SKA58_06620				(PF01695)
314266.SKA58_03900			+
314266.SKA58_01090				(PF01695)
314266.SKA58_12547			+
314266.SKA58_10295				(PF01695)
314266.SKA58_04045				(PF00614)

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 = 2.1 (21/10 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=
==========================================================