Effective results for Delftia acidovorans SPH-1 (eggnog40)

Summary

Number of putative secreted proteins: 120
- Predicted by T4SEpre: 97
- Predicted by EffectiveELD: 15 eukaryotic-like domains, contained in 40 proteins (1 high, 39 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, Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
398578.Daci_3415			+		(mitochondrial)
398578.Daci_1306			+		mitochondrial
398578.Daci_5291				(PF11937)	mitochondrial; (mitochondrial)
398578.Daci_3985			+		(mitochondrial)
398578.Daci_0871			+		(ER); plastid
398578.Daci_3564			+		(ER); (plastid)
398578.Daci_2769			+		ER
398578.Daci_0318				(PF05704)	ER
398578.Daci_0315			+		ER
398578.Daci_3378			+		ER
398578.Daci_5001			+		ER
398578.Daci_2841			+		ER
398578.Daci_0763			+		(mitochondrial); plastid
398578.Daci_4899			+		mitochondrial
398578.Daci_1666			+		ER
398578.Daci_1145			+		(mitochondrial)
398578.Daci_1495			+		mitochondrial
398578.Daci_2325			+		ER
398578.Daci_2920			+		ER
398578.Daci_0978			+		ER
398578.Daci_0425			+		ER
398578.Daci_0863			+		(mitochondrial)
398578.Daci_4619				(PF02201)	(mitochondrial); (plastid)
398578.Daci_3930			+		(mitochondrial)
398578.Daci_4630			+		(mitochondrial)
398578.Daci_1046			+		(mitochondrial)
398578.Daci_0322				(PF05704)	(mitochondrial)
398578.Daci_3363			+		(mitochondrial)
398578.Daci_0367			+		ER
398578.Daci_0567			+		ER
398578.Daci_3806				(PF11937)	mitochondrial
398578.Daci_1805			+		ER
398578.Daci_3857			+		ER
398578.Daci_4241			+		ER
398578.Daci_5892			+		ER
398578.Daci_4757			+		ER; (ER)
398578.Daci_5500			+		(mitochondrial)
398578.Daci_0683			+		(ER)
398578.Daci_0660			+		(ER)
398578.Daci_4340			+		(mitochondrial)
398578.Daci_4853			+		plastid
398578.Daci_2243			+		(ER)
398578.Daci_5798				(PF01070)	plastid
398578.Daci_1575			+		(mitochondrial)
398578.Daci_5413			+		(mitochondrial)
398578.Daci_0884			+	(PF02201)
398578.Daci_4573			+		(ER)
398578.Daci_2195			+		(ER)
398578.Daci_0905			+		(plastid)
398578.Daci_5508			+		(mitochondrial)
398578.Daci_4923			+
398578.Daci_3220				(PF03796)
398578.Daci_2958			+
398578.Daci_4271			+
398578.Daci_3201				(PF00847)
398578.Daci_3200				(PF13392)
398578.Daci_2456			+
398578.Daci_2455				PF07716
398578.Daci_2452				(PF13565)
398578.Daci_1933				(PF03796)
398578.Daci_5108			+
398578.Daci_5294				(PF01070)
398578.Daci_2472				(PF09791)
398578.Daci_1773			+
398578.Daci_0431			+
398578.Daci_0419			+
398578.Daci_4149			+
398578.Daci_5651			+
398578.Daci_4628			+
398578.Daci_1409				(PF13565)
398578.Daci_6008			+
398578.Daci_0680				(PF05189)
398578.Daci_0749			+
398578.Daci_4092				(PF13392)
398578.Daci_4110				(PF03796)
398578.Daci_4620				(PF01070)
398578.Daci_4554			+
398578.Daci_1624				(PF08707)
398578.Daci_4396			+
398578.Daci_4702				(PF13392)
398578.Daci_5778				(PF14832)
398578.Daci_3251			+
398578.Daci_3804			+
398578.Daci_1567				(PF13565)
398578.Daci_2308				(PF13565)
398578.Daci_1962				(PF13392)
398578.Daci_0954				(PF13565)
398578.Daci_5796			+
398578.Daci_0179				(PF03069)
398578.Daci_0789				(PF01070)
398578.Daci_5499			+
398578.Daci_5805				(PF09791)
398578.Daci_0225				(PF03069)
398578.Daci_3426				(PF08707)
398578.Daci_5455			+
398578.Daci_3380			+
398578.Daci_2522			+
398578.Daci_5900			+
398578.Daci_4360			+
398578.Daci_3463			+
398578.Daci_3346				(PF01070)
398578.Daci_1271			+
398578.Daci_3168				(PF13565)
398578.Daci_0635			+
398578.Daci_3571			+
398578.Daci_4867			+
398578.Daci_3143			+
398578.Daci_5225				(PF03796)
398578.Daci_0566			+
398578.Daci_4086			+
398578.Daci_0888			+
398578.Daci_0886				(PF13565)
398578.Daci_3724			+
398578.Daci_1384				(PF01070)
398578.Daci_4963				(PF03069)
398578.Daci_4962				(PF03069)
398578.Daci_1719			+
398578.Daci_1711			+
398578.Daci_3242				(PF12949)
398578.Daci_4742			+

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 = 1.2 (12/10 KEGG proteins)
• Functional Type VI secretion system: YES (FDR = 7.7 %)
  Estimated copy number = 2.0 (16/8 KEGG proteins)

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=
==========================================================