Effective results for Methylocella silvestris BL2 (eggnog40)

Summary

Number of putative secreted proteins: 91
- Predicted by T4SEpre: 73
- Predicted by EffectiveELD: 15 eukaryotic-like domains, contained in 35 proteins (2 high, 33 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
395965.Msil_1075			+	(PF05990)	ER
395965.Msil_0460				(PF14295) (PF03659)	mitochondrial
395965.Msil_0468			+		ER
395965.Msil_3149				(PF01011)	ER
395965.Msil_0171			+		ER
395965.Msil_2884			+		ER
395965.Msil_3913			+		ER; (ER)
395965.Msil_2611				(PF05050)	(mitochondrial)
395965.Msil_3471			+		ER; mitochondrial
395965.Msil_0808			+		ER
395965.Msil_0110				(PF00190)	mitochondrial
395965.Msil_0605			+		ER
395965.Msil_1502				(PF13506)	ER
395965.Msil_0914			+		mitochondrial
395965.Msil_0919			+		ER
395965.Msil_0130				(PF13506)	ER
395965.Msil_2062				(PF03209)	ER
395965.Msil_1094				PF03080	ER
395965.Msil_3387				(PF01011)	(ER)
395965.Msil_2260				(PF01011)	(mitochondrial)
395965.Msil_3028			+		ER
395965.Msil_3733				(PF01011)	ER
395965.Msil_3035				(PF13506)	ER
395965.Msil_0411				(PF14269)	ER
395965.Msil_1588			+		(ER)
395965.Msil_2037				(PF03209)	ER; (mitochondrial)
395965.Msil_3560			+		ER; (ER)
395965.Msil_1041				(PF05990)	ER
395965.Msil_3185			+		ER
395965.Msil_0471				(PF01011)	(ER)
395965.Msil_0473			+		ER
395965.Msil_1587				(PF01011)	ER
395965.Msil_2903			+		mitochondrial; (mitochondrial)
395965.Msil_1758				(PF10162)	(mitochondrial)
395965.Msil_1750				(PF14494)	ER
395965.Msil_1927				(PF14269)	mitochondrial
395965.Msil_3163			+		ER
395965.Msil_0203				(PF14494)	ER
395965.Msil_1320			+		(ER)
395965.Msil_1742			+		(ER)
395965.Msil_1889			+		(mitochondrial)
395965.Msil_2841			+		(mitochondrial)
395965.Msil_0043			+		plastid
395965.Msil_2115				(PF05050)	(plastid)
395965.Msil_0265			+
395965.Msil_1540			+
395965.Msil_0165			+
395965.Msil_1160				(PF05050)
395965.Msil_3461			+
395965.Msil_2433			+
395965.Msil_0763			+
395965.Msil_1569				(PF05990)
395965.Msil_0619			+
395965.Msil_2183				(PF00190)
395965.Msil_3116			+
395965.Msil_2609			+
395965.Msil_1351				PF08557
395965.Msil_3803			+
395965.Msil_2459			+
395965.Msil_2678				(PF00190)
395965.Msil_3220			+
395965.Msil_3009			+
395965.Msil_0288			+
395965.Msil_2548			+
395965.Msil_0722				(PF00190)
395965.Msil_0729			+
395965.Msil_1389			+
395965.Msil_1718			+
395965.Msil_2733				(PF05050)
395965.Msil_2732				(PF05050)
395965.Msil_2734				(PF05050)
395965.Msil_0376			+
395965.Msil_3616			+
395965.Msil_2810			+
395965.Msil_1103				(PF00102)
395965.Msil_0711				(PF13506)
395965.Msil_2233			+
395965.Msil_2345			+
395965.Msil_2691			+
395965.Msil_0317			+
395965.Msil_1482			+
395965.Msil_2912			+
395965.Msil_2914			+
395965.Msil_3160			+
395965.Msil_3548				(PF01442)
395965.Msil_1148			+
395965.Msil_2377			+
395965.Msil_3522			+
395965.Msil_0444			+
395965.Msil_2559			+
395965.Msil_2799			+

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 = 0.3 (3/10 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=
==========================================================