Effective results for Cupriavidus metallidurans CH34 (eggnog40)

Summary

Number of putative secreted proteins: 104
- Predicted by T4SEpre: 68
- Predicted by EffectiveELD: 6 eukaryotic-like domains, contained in 45 proteins (0 high, 45 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
266264.Rmet_2016			+		mitochondrial; (mitochondrial)
266264.Rmet_0501				(PF00162)	mitochondrial; (mitochondrial)
266264.Rmet_1704				(PF13441)	ER
266264.Rmet_2000				(PF00665)	(ER)
266264.Rmet_2008				(PF00665)	(ER)
266264.Rmet_0980			+		(mitochondrial); (plastid)
266264.Rmet_3227			+		(mitochondrial)
266264.Rmet_2552				(PF00665)	(ER)
266264.Rmet_3172				(PF02239)	ER
266264.Rmet_3171			+		ER
266264.Rmet_2954			+		ER
266264.Rmet_1046			+		(mitochondrial)
266264.Rmet_3169				(PF02239)	ER; (ER)
266264.Rmet_2080				(PF02239)	ER
266264.Rmet_0993			+		mitochondrial; (mitochondrial)
266264.Rmet_2405				(PF00665)	(ER)
266264.Rmet_0483				(PF00665)	mitochondrial; (mitochondrial)
266264.Rmet_1264				(PF00665)	(mitochondrial)
266264.Rmet_2826			+		(ER)
266264.Rmet_3365				(PF00665)	mitochondrial; (mitochondrial)
266264.Rmet_2205			+		ER
266264.Rmet_2991				(PF00665)	mitochondrial
266264.Rmet_1511				(PF00316)	(mitochondrial)
266264.Rmet_0305			+		ER; (ER)
266264.Rmet_2524				(PF13401)	(mitochondrial)
266264.Rmet_0908			+		mitochondrial
266264.Rmet_3010				(PF00665)	mitochondrial
266264.Rmet_1507				(PF00316)	(mitochondrial)
266264.Rmet_2837				(PF00665)	(ER)
266264.Rmet_3150			+		ER
266264.Rmet_3331				(PF02239)	ER
266264.Rmet_1792			+		(mitochondrial)
266264.Rmet_0312			+		ER
266264.Rmet_2251			+		ER
266264.Rmet_0532			+		(mitochondrial)
266264.Rmet_3472				(PF13441)	ER
266264.Rmet_0321				(PF00665)	(ER)
266264.Rmet_1233			+		(mitochondrial); (plastid)
266264.Rmet_3142				(PF00665)	(ER)
266264.Rmet_0665			+		ER
266264.Rmet_2009				(PF13401)	(ER)
266264.Rmet_2284			+		(mitochondrial)
266264.Rmet_1714			+		(ER)
266264.Rmet_3141				(PF13401)	(ER)
266264.Rmet_2551				(PF13401)	(ER)
266264.Rmet_3543			+		(mitochondrial)
266264.Rmet_1725			+		(mitochondrial)
266264.Rmet_2406				(PF13401)	(ER)
266264.Rmet_1999				(PF13401)	(ER)
266264.Rmet_1280				(PF00665)	(mitochondrial)
266264.Rmet_2768				(PF13441)	plastid
266264.Rmet_2836				(PF13401)	(ER)
266264.Rmet_1251				(PF00665)	(mitochondrial)
266264.Rmet_1404			+		(mitochondrial)
266264.Rmet_1301				(PF00665)	(mitochondrial)
266264.Rmet_0320				(PF13401)	(ER)
266264.Rmet_2874			+
266264.Rmet_2160			+
266264.Rmet_0349			+
266264.Rmet_0359			+
266264.Rmet_2670			+
266264.Rmet_2922			+
266264.Rmet_1015			+
266264.Rmet_2663			+
266264.Rmet_2842				(PF00665)
266264.Rmet_1627			+
266264.Rmet_1923			+
266264.Rmet_0619			+
266264.Rmet_1564				(PF00665)
266264.Rmet_2556				(PF00665)
266264.Rmet_2135			+
266264.Rmet_1557			+
266264.Rmet_2382				(PF00665)
266264.Rmet_2092			+
266264.Rmet_0525			+
266264.Rmet_1612				(PF00665)
266264.Rmet_1055			+
266264.Rmet_1449			+
266264.Rmet_1993				(PF00665)
266264.Rmet_1285			+
266264.Rmet_0132			+
266264.Rmet_0981			+
266264.Rmet_0031				(PF00665)
266264.Rmet_0854			+
266264.Rmet_1529				(PF00665)
266264.Rmet_0853			+
266264.Rmet_1073			+
266264.Rmet_1516				(PF00162)
266264.Rmet_0111			+
266264.Rmet_1884			+
266264.Rmet_3348				(PF00665)
266264.Rmet_2523			+
266264.Rmet_1592				(PF00665)
266264.Rmet_0057			+
266264.Rmet_0875				(PF00316)
266264.Rmet_2899			+
266264.Rmet_2681			+
266264.Rmet_3241			+
266264.Rmet_2031			+
266264.Rmet_3329			+
266264.Rmet_3495			+
266264.Rmet_1421			+
266264.Rmet_0079			+
266264.Rmet_3267			+

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 = 1.25 (10/8 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=
==========================================================