Effective results for Ochrobactrum intermedium LMG 3301 (eggnog40)

Summary

Number of putative secreted proteins: 91
- Predicted by T4SEpre: 81
- Predicted by EffectiveELD: 15 eukaryotic-like domains, contained in 25 proteins (1 high, 24 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
641118.OINT_2001866				(PF07364) (PF07171)	mitochondrial; (mitochondrial)
641118.OINT_2001375				(PF07364) (PF07171)	mitochondrial
641118.OINT_1001652				(PF00050) (PF07648)	ER
641118.OINT_2001628				(PF02275)	ER
641118.OINT_2001715			+		mitochondrial
641118.OINT_1001422			+		mitochondrial
641118.OINT_1001738			+		(mitochondrial)
641118.OINT_2001089			+		mitochondrial
641118.OINT_2000142			+		mitochondrial; (mitochondrial)
641118.OINT_1000363				(PF05990)	ER
641118.OINT_2000105			+		mitochondrial; (mitochondrial)
641118.OINT_2000319			+		mitochondrial; (mitochondrial)
641118.OINT_2000008			+		(mitochondrial)
641118.OINT_1001175			+		(ER); ER
641118.OINT_1001614			+		ER
641118.OINT_1000982			+		ER
641118.OINT_1001743			+		(mitochondrial)
641118.OINT_2001810			+		(mitochondrial)
641118.OINT_2001573			+		(mitochondrial); (ER)
641118.OINT_2001802				(PF00344)	(mitochondrial); mitochondrial
641118.OINT_2001800			+		ER
641118.OINT_1001002			+		(mitochondrial); mitochondrial
641118.OINT_2001348			+	(PF02275)	(mitochondrial)
641118.OINT_1000645			+		mitochondrial
641118.OINT_1001017			+		ER
641118.OINT_2001389			+		ER
641118.OINT_2001437			+		mitochondrial
641118.OINT_2001438			+		ER
641118.OINT_1001535			+		ER
641118.OINT_1000901				(PF05990)	ER
641118.OINT_2001271			+		(plastid)
641118.OINT_2001502				(PF07364) (PF07171)
641118.OINT_1002171			+		(mitochondrial)
641118.OINT_2001070			+		(plastid)
641118.OINT_2001315			+		plastid
641118.OINT_1000757				(PF04800)	mitochondrial
641118.OINT_2001490				(PF07364) (PF07171)
641118.OINT_2001000				(PF07364) (PF07171)
641118.OINT_2000095			+		(ER)
641118.OINT_2001285			+		(mitochondrial)
641118.OINT_2000646			+		(plastid)
641118.OINT_2000268				(PF01812)	(mitochondrial)
641118.OINT_1000473			+		(mitochondrial)
641118.OINT_1001197			+	(PF01442)
641118.OINT_2001362			+		(mitochondrial)
641118.OINT_1001183			+
641118.OINT_1000862				(PF05990)
641118.OINT_2001475			+
641118.OINT_1001438			+
641118.OINT_1000634			+
641118.OINT_1000708			+
641118.OINT_1000442			+
641118.OINT_1001400			+
641118.OINT_1000715			+
641118.OINT_1001395			+
641118.OINT_1001349			+
641118.OINT_2000858			+
641118.OINT_2001183			+
641118.OINT_2001857				(PF04800)
641118.OINT_1000426				(PF07653)
641118.OINT_1001147			+
641118.OINT_1001387			+
641118.OINT_2000080			+
641118.OINT_1000349			+
641118.OINT_2001629				(PF02275)
641118.OINT_1000407			+
641118.OINT_1001163			+
641118.OINT_1001166			+
641118.OINT_1000355				(PF00777)
641118.OINT_1001340				(PF00344)
641118.OINT_2001552				(PF01498)
641118.OINT_2000794				PF07823
641118.OINT_1001337			+
641118.OINT_1000515			+
641118.OINT_1001039			+
641118.OINT_2001775			+
641118.OINT_1001649			+
641118.OINT_2001808			+
641118.OINT_1001862				(PF07930)
641118.OINT_2001162			+
641118.OINT_1001497			+
641118.OINT_1000838			+
641118.OINT_1002473			+
641118.OINT_1002097				(PF01812)
641118.OINT_1001383			+
641118.OINT_1001846			+
641118.OINT_2001615			+
641118.OINT_1002326			+
641118.OINT_1000526			+
641118.OINT_2000264				(PF01812)
641118.OINT_2001258			+

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 = 0.9 (9/10 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=
==========================================================