Effective results for Xenorhabdus nematophila ATCC 19061 (eggnog40)

Summary

Number of putative secreted proteins: 393
- Predicted by T4SEpre: 128
- Predicted by EffectiveELD: 27 eukaryotic-like domains, contained in 286 proteins (168 high, 118 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
406817.XNC1_0714				PF13358 PF13551	(mitochondrial)
406817.XNC1_4407				PF13358 PF13592 PF13384	plastid
406817.XNC1_1608				PF13358 PF13551	(mitochondrial)
406817.XNC1_0841				PF13358 PF13592	mitochondrial
406817.XNC1_1739				PF13358 PF13592 PF13384	plastid
406817.XNC1_0716			+		(ER)
406817.XNC1_3824				PF13551	(mitochondrial)
406817.XNC1_1914				(PF00665)	mitochondrial
406817.XNC1_2348				(PF01527)	(ER)
406817.XNC1_4085			+		(mitochondrial)
406817.XNC1_2395				PF13358 PF13592 PF13551
406817.XNC1_0871				PF13551	(mitochondrial)
406817.XNC1_0876				PF01375	ER
406817.XNC1_3513				(PF00665)	(mitochondrial)
406817.XNC1_3831			+		ER
406817.XNC1_1021				PF13358 PF13592 PF13384
406817.XNC1_1595			+		ER
406817.XNC1_4171			+		ER
406817.XNC1_3998			+		ER
406817.XNC1_2136			+		ER
406817.XNC1_4417			+		ER
406817.XNC1_0527				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_2223			+		ER
406817.XNC1_4348			+		(mitochondrial); mitochondrial
406817.XNC1_1620			+		ER
406817.XNC1_0997			+		(ER)
406817.XNC1_4234				PF13358 PF13592 PF13384
406817.XNC1_2971			+		mitochondrial; (mitochondrial)
406817.XNC1_4535				PF13358 PF13592 PF13384
406817.XNC1_0834				PF02371	(mitochondrial)
406817.XNC1_2568				(PF12256) (PF03534) PF12255
406817.XNC1_3365			+		(mitochondrial)
406817.XNC1_2308			+		ER
406817.XNC1_1200			+	PF13358 PF13551
406817.XNC1_2956			+		ER
406817.XNC1_3898			+		ER
406817.XNC1_1783				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_3229			+		ER
406817.XNC1_3224				PF13358	(mitochondrial)
406817.XNC1_3135				(PF01527)	(ER)
406817.XNC1_1816				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_2545				PF13551	mitochondrial
406817.XNC1_0962				PF13358 PF13592 PF13551
406817.XNC1_2090				PF13551	(mitochondrial)
406817.XNC1_2432			+		ER
406817.XNC1_0807				PF13358	(mitochondrial)
406817.XNC1_0809				PF13384	(mitochondrial)
406817.XNC1_4272				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_4270				(PF01527)	(ER)
406817.XNC1_2889				(PF02899)	(mitochondrial); mitochondrial
406817.XNC1_1999				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_3687				(PF00665)	mitochondrial; (mitochondrial)
406817.XNC1_0580				(PF01527)	(ER)
406817.XNC1_2335				(PF12256) (PF03534) PF12255
406817.XNC1_4640				PF13358 PF13592 PF13384
406817.XNC1_4483			+		ER
406817.XNC1_1239			+	PF13358 PF13551
406817.XNC1_2423				(PF00665) PF13551	(mitochondrial)
406817.XNC1_1988				(PF01609)	ER
406817.XNC1_3328				PF13358 PF13592 PF13384
406817.XNC1_0599				PF13358 PF13384	(plastid)
406817.XNC1_2186				(PF12256) (PF03534) PF12255
406817.XNC1_2994				(PF00665)	mitochondrial
406817.XNC1_2789			+		ER
406817.XNC1_2840			+		ER
406817.XNC1_3488			+		(mitochondrial); (ER)
406817.XNC1_1903				PF13551	(mitochondrial)
406817.XNC1_1905				PF13358 PF13592 PF13384
406817.XNC1_2419				(PF01396) (PF01131)	(plastid)
406817.XNC1_2191			+		(mitochondrial)
406817.XNC1_3715				(PF01527)	mitochondrial
406817.XNC1_2875				PF13358	mitochondrial
406817.XNC1_0600				PF13358 PF13592 PF13384
406817.XNC1_2050				(PF03400)	(mitochondrial)
406817.XNC1_1649			+		ER
406817.XNC1_2865				PF13358 PF13592	(mitochondrial)
406817.XNC1_2046				PF13358 PF13592 PF13551
406817.XNC1_0411				(PF02899)	ER; (ER)
406817.XNC1_0257				PF02371	(mitochondrial)
406817.XNC1_0131				PF02371	(mitochondrial)
406817.XNC1_4387				(PF00665)	mitochondrial
406817.XNC1_1667				PF13358	(ER); not used
406817.XNC1_2387				(PF01396) (PF01131)
406817.XNC1_2381				(PF00665) PF13551
406817.XNC1_4635				(PF00665) PF13551
406817.XNC1_4568				PF02371	(plastid)
406817.XNC1_3538				(PF01396) (PF01131)
406817.XNC1_3826				PF13358	(ER); not used
406817.XNC1_3827				(PF00665) PF13551
406817.XNC1_3825				PF13358	(mitochondrial)
406817.XNC1_2646				(PF00665) PF13551
406817.XNC1_3754				PF13358	(ER)
406817.XNC1_0863				PF13358 PF13592
406817.XNC1_1901				PF13358	(ER); not used
406817.XNC1_1900				PF02371	(plastid)
406817.XNC1_2012				(PF01527)	(ER)
406817.XNC1_3450				(PF01396) (PF01131)
406817.XNC1_2644				(PF00665) PF13551
406817.XNC1_2641				(PF00665) PF13551
406817.XNC1_1610				PF13358 PF13592
406817.XNC1_2005				PF13358	(mitochondrial)
406817.XNC1_2004				PF13358	(ER); not used
406817.XNC1_0181			+		(mitochondrial)
406817.XNC1_2918			+		(mitochondrial)
406817.XNC1_1858				PF02371	(plastid)
406817.XNC1_4513			+		(mitochondrial)
406817.XNC1_4204				(PF00665) PF13551
406817.XNC1_0680				PF13592 PF13384
406817.XNC1_0686				(PF01931)	(plastid)
406817.XNC1_2217				PF13358	(ER); not used
406817.XNC1_4233				PF13358 PF13592
406817.XNC1_0201				(PF00665) PF13551
406817.XNC1_1010				(PF01527)	(mitochondrial)
406817.XNC1_4320				(PF00665)	(mitochondrial)
406817.XNC1_4321				PF13592 PF13384
406817.XNC1_3225				PF13592 PF13384
406817.XNC1_1961				PF13592 PF13384
406817.XNC1_0778				(PF00665)	(mitochondrial)
406817.XNC1_2091				PF13358	(mitochondrial)
406817.XNC1_2092				PF13358	(ER); not used
406817.XNC1_1193			+		(mitochondrial)
406817.XNC1_0803				(PF00665)	(mitochondrial)
406817.XNC1_4312			+		(mitochondrial)
406817.XNC1_0016				(PF00665) PF13551
406817.XNC1_3200				PF13358	(mitochondrial)
406817.XNC1_3201				PF13358	(ER); not used
406817.XNC1_4264				PF02371	(plastid)
406817.XNC1_0341			+		(mitochondrial)
406817.XNC1_0869				PF13358	(ER); not used
406817.XNC1_3588				(PF00665) PF13551
406817.XNC1_3325				PF16485	(ER)
406817.XNC1_3323				PF16485	(ER)
406817.XNC1_4298				(PF01609)	plastid
406817.XNC1_1902				PF13358	(mitochondrial)
406817.XNC1_2610				PF13592 PF13384
406817.XNC1_2874				PF13592 PF13384
406817.XNC1_0117			+		(mitochondrial)
406817.XNC1_2058				(PF03400)	(mitochondrial)
406817.XNC1_0738			+	PF13384
406817.XNC1_0735				PF13592 PF13384
406817.XNC1_3018				PF13358	(mitochondrial)
406817.XNC1_3010				PF13358 PF13592
406817.XNC1_3649				(PF01396) (PF01131)
406817.XNC1_2042				(PF08964) PF14564
406817.XNC1_2928				(PF01527)	(ER)
406817.XNC1_4382				PF13358	(ER); not used
406817.XNC1_4383				PF13358	(mitochondrial)
406817.XNC1_2618			+
406817.XNC1_0715			+
406817.XNC1_1668				PF13358
406817.XNC1_0718				PF02371
406817.XNC1_2389			+
406817.XNC1_2496				(PF01131)
406817.XNC1_2664			+
406817.XNC1_2661			+
406817.XNC1_3626				(PF01527)
406817.XNC1_3629				(PF00665)
406817.XNC1_2713				(PF13745)
406817.XNC1_3829				(PF01609)
406817.XNC1_0248				(PF01094)
406817.XNC1_1912				(PF01527)
406817.XNC1_2933				PF02371
406817.XNC1_2930				PF02371
406817.XNC1_2939				PF13358
406817.XNC1_4394				PF02371
406817.XNC1_1704				(PF13745)
406817.XNC1_1674				(PF02899)
406817.XNC1_2397				PF02371
406817.XNC1_2394				PF13358
406817.XNC1_2390			+
406817.XNC1_2398			+
406817.XNC1_2485			+
406817.XNC1_3541			+
406817.XNC1_4405				PF13358
406817.XNC1_0898			+
406817.XNC1_3637				PF13358
406817.XNC1_3632				PF02371
406817.XNC1_0879			+
406817.XNC1_3832				(PF01609)
406817.XNC1_2901				(PF02899)
406817.XNC1_0086			+
406817.XNC1_2017				PF13358
406817.XNC1_2018				PF13384
406817.XNC1_0463			+
406817.XNC1_1022				(PF01609)
406817.XNC1_2234				(PF02899)
406817.XNC1_2230				(PF13745)
406817.XNC1_2233				(PF13745)
406817.XNC1_3457				(PF03400)
406817.XNC1_3453			+
406817.XNC1_4172			+
406817.XNC1_2916			+
406817.XNC1_1085			+
406817.XNC1_2006				PF13551
406817.XNC1_2002				PF13358
406817.XNC1_0188				(PF05929)
406817.XNC1_3138				(PF01609)
406817.XNC1_4416			+
406817.XNC1_0526				(PF01527)
406817.XNC1_2229				(PF13745)
406817.XNC1_2228				(PF13745)
406817.XNC1_2747				PF02371
406817.XNC1_0853				(PF10014)
406817.XNC1_3506				(PF02899)
406817.XNC1_0065			+
406817.XNC1_1624			+
406817.XNC1_2038				(PF13745)
406817.XNC1_2039				(PF13745)
406817.XNC1_1137			+
406817.XNC1_1134				(PF02899)
406817.XNC1_2219				(PF01609)
406817.XNC1_1005				(PF10014)
406817.XNC1_0843				PF13384
406817.XNC1_0842				PF13358
406817.XNC1_2598				PF02371
406817.XNC1_1957			+
406817.XNC1_3697				PF13358
406817.XNC1_2022				(PF13745)
406817.XNC1_1120			+
406817.XNC1_1129			+
406817.XNC1_1018				(PF01609)
406817.XNC1_3081				(PF05929)
406817.XNC1_3698				PF13358
406817.XNC1_1270			+
406817.XNC1_3154				PF13384
406817.XNC1_4531				PF13358
406817.XNC1_4532			+
406817.XNC1_0835				(PF01609)
406817.XNC1_0832				PF02371
406817.XNC1_0831				PF02371
406817.XNC1_1837			+
406817.XNC1_0459			+
406817.XNC1_2569				PF03538
406817.XNC1_2560				PF03538
406817.XNC1_2566				PF03538
406817.XNC1_0237				PF13358
406817.XNC1_4225			+
406817.XNC1_4322				PF13358
406817.XNC1_1943				PF13358
406817.XNC1_2781				(PF13745)
406817.XNC1_2782				(PF13745)
406817.XNC1_2783				(PF13745)
406817.XNC1_2943				(PF01609)
406817.XNC1_1038				PF14564
406817.XNC1_2161				(PF13745)
406817.XNC1_1790				(PF01609)
406817.XNC1_0558				PF13358
406817.XNC1_2300				(PF13745)
406817.XNC1_3781				PF13384
406817.XNC1_0826			+
406817.XNC1_1802				PF13358
406817.XNC1_1803			+
406817.XNC1_1801			+
406817.XNC1_1804				PF13358
406817.XNC1_0488			+
406817.XNC1_1972				(PF01609)
406817.XNC1_1978				PF13358
406817.XNC1_1979			+
406817.XNC1_3957			+
406817.XNC1_2950			+
406817.XNC1_3426			+
406817.XNC1_3425			+
406817.XNC1_3421				PF13358
406817.XNC1_0786			+
406817.XNC1_1143			+
406817.XNC1_1784				(PF01609)
406817.XNC1_1789				(PF01527)
406817.XNC1_0493			+
406817.XNC1_1219				(PF01609)
406817.XNC1_2400				PF13358
406817.XNC1_2407				PF13358
406817.XNC1_3131				PF02371
406817.XNC1_1817				(PF01527)
406817.XNC1_1811				PF02371
406817.XNC1_2544				PF02371
406817.XNC1_2540				PF13358
406817.XNC1_4242				(PF01931)
406817.XNC1_1962				PF13358
406817.XNC1_0026			+
406817.XNC1_1771				PF02371
406817.XNC1_1776			+
406817.XNC1_1777				PF13358
406817.XNC1_3307				(PF07678)
406817.XNC1_0776				PF13358
406817.XNC1_0775			+
406817.XNC1_0575				PF13358
406817.XNC1_0576				PF13384
406817.XNC1_2093				PF13358
406817.XNC1_3239				PF13358
406817.XNC1_3232				(PF01527)	not used
406817.XNC1_3235				(PF00665)
406817.XNC1_3129				(PF02899)
406817.XNC1_2557				(PF01609)
406817.XNC1_0806				(PF01527)
406817.XNC1_0808				PF13592
406817.XNC1_4317				(PF01527)	not used
406817.XNC1_1990				(PF01609)
406817.XNC1_1992				PF13358
406817.XNC1_1995				PF13358
406817.XNC1_3682				(PF01609)
406817.XNC1_0219			+
406817.XNC1_0015			+
406817.XNC1_3590				PF13358
406817.XNC1_3598				(PF02899)
406817.XNC1_1517			+
406817.XNC1_1420			+
406817.XNC1_1767			+
406817.XNC1_2333				PF03538
406817.XNC1_4481				(PF01609)
406817.XNC1_1233				(PF07653)	not used
406817.XNC1_3408			+
406817.XNC1_4267				PF13358
406817.XNC1_2631				(PF01609)
406817.XNC1_2637				PF13358	not used
406817.XNC1_3695				PF02371
406817.XNC1_2988				PF13592
406817.XNC1_2989				PF13384
406817.XNC1_0870				PF13358
406817.XNC1_4078			+
406817.XNC1_2882			+
406817.XNC1_2853			+
406817.XNC1_3631				PF02371
406817.XNC1_4101			+
406817.XNC1_0945			+
406817.XNC1_3327				PF02371
406817.XNC1_0596				PF13384
406817.XNC1_0594				PF13358
406817.XNC1_2187				PF03538
406817.XNC1_2184			+
406817.XNC1_2180				(PF01609)
406817.XNC1_2457			+
406817.XNC1_2539				PF13358
406817.XNC1_4581				(PF00665)
406817.XNC1_4294				(PF00665)
406817.XNC1_4297				(PF01527)
406817.XNC1_3638			+
406817.XNC1_2991				(PF01609)
406817.XNC1_2992				(PF01527)
406817.XNC1_2995				(PF01609)
406817.XNC1_0352				(PF01396)
406817.XNC1_4112				PF13358
406817.XNC1_1749			+
406817.XNC1_3526				(PF00665)
406817.XNC1_0728				PF02371
406817.XNC1_0727				(PF01609)
406817.XNC1_0721				(PF01609)
406817.XNC1_1908				(PF01609)
406817.XNC1_3265			+
406817.XNC1_2445			+
406817.XNC1_3007				PF13358
406817.XNC1_3000				(PF01609)
406817.XNC1_3002				PF13358
406817.XNC1_0298			+
406817.XNC1_2616			+
406817.XNC1_2611				PF13358
406817.XNC1_2872				(PF01527)
406817.XNC1_0952			+
406817.XNC1_2299				(PF13745)
406817.XNC1_0734				PF13358
406817.XNC1_1641				PF02371
406817.XNC1_1642				PF13551
406817.XNC1_3657			+
406817.XNC1_1264			+
406817.XNC1_2517			+
406817.XNC1_3019				PF13358
406817.XNC1_3016				PF02371
406817.XNC1_3015				PF02371
406817.XNC1_3012				(PF01609)
406817.XNC1_4548			+
406817.XNC1_2869				(PF00665)
406817.XNC1_0125				PF02371
406817.XNC1_2040				(PF13745)
406817.XNC1_2286				PF13358
406817.XNC1_0702			+
406817.XNC1_1389			+
406817.XNC1_0412			+
406817.XNC1_3339				(PF01609)
406817.XNC1_2465				(PF13745)
406817.XNC1_2464				(PF13745)
406817.XNC1_2467				(PF13745)
406817.XNC1_2466				(PF13745)
406817.XNC1_2269				(PF13745)
406817.XNC1_0848				PF13358
406817.XNC1_3656				PF13358
406817.XNC1_3659			+
406817.XNC1_1899				PF02371
406817.XNC1_2705			+
406817.XNC1_0256				(PF01609)
406817.XNC1_3818			+
406817.XNC1_4143			+
406817.XNC1_0130				(PF03400)
406817.XNC1_4385				(PF01527)
406817.XNC1_1477				PF13358

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 = 0.0 (0/10 KEGG proteins)
• Functional Type VI secretion system: YES (FDR = 7.7 %)
  Estimated copy number = 1.875 (15/8 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=
==========================================================