Effective results for Pseudomonas sp. LAMO17WK12:I4 (refseq)

Summary

Number of putative secreted proteins: 611
- Predicted by EffectiveT3: 194 (high confidence), 271 (low confidence)
- Predicted by EffectiveCCBD: 15 within, 11 before, 33 behind expected region 25..70aa
- Predicted by T4SEpre: 91
- Predicted by EffectiveELD: 9 eukaryotic-like domains, contained in 20 proteins (0 high, 20 medium Z-score)
Predicted protein secretion systems (parentheses indicate weak positive predictions lacking more than 50% of core proteins of a secretion system): Type III, (Type IV), Type VI

Protein based results

Putative secreted proteins (weak evidence indicated by parentheses)

Protein	EffectiveT3	EffectiveCCBD	T4SEpre	EffectiveELD	Predotar
WP_019096853.1			+		ER
WP_019096642.1	+				(ER)
WP_019099211.1		(<)			ER
WP_025753015.1			+		ER
WP_025752712.1			+		ER
WP_019098457.1			+		(mitochondrial)
WP_027614739.1	+				(ER); (plastid)
WP_025752686.1			+		ER; (ER)
WP_025754189.1				(PF06039)	ER
WP_019098764.1			+		ER
WP_025754570.1			+		ER
WP_019098440.1	+				(ER)
WP_016711770.1		(>)			ER
WP_019096676.1		+			mitochondrial
WP_025754027.1		+			ER
WP_016711968.1				(PF13488)	ER
WP_025754641.1				(PF07678)	ER
WP_019099069.1			+		ER
WP_019098576.1			+		ER
WP_025753723.1	+				(mitochondrial); (plastid)
WP_025754060.1		+			(ER); (mitochondrial)
WP_019098571.1			+		ER
WP_019099709.1		(>)			ER
WP_016712435.1			+		ER
WP_025753930.1		+			ER
WP_019096309.1				(PF01852)	ER
WP_025754268.1			+		ER
WP_016714320.1			+		ER
WP_019099532.1		(>)			ER
WP_019098460.1			+		ER
WP_016712981.1			+		ER
WP_025753699.1				(PF13488)	ER
WP_019096891.1				(PF13488)	ER
WP_016713393.1			+		ER
WP_016714764.1	+				(mitochondrial)
WP_019097068.1			+		ER; (ER)
WP_025754319.1			+		ER
WP_019096961.1		+			ER
WP_016715101.1		(>)			ER
WP_016714007.1		+			ER
WP_019099837.1		(>)			ER
WP_050547883.1	+				(mitochondrial); (plastid)
WP_016501466.1				(PF13488)	ER
WP_019099272.1			+		ER
WP_016714458.1		(>)			ER
WP_019098485.1				(PF06039)	ER
WP_025753125.1			+		ER
WP_025752850.1			+		ER
WP_016712836.1			+		ER
WP_012271091.1		(<)			ER
WP_016712983.1			+		(ER)
WP_016713141.1		(>)			(mitochondrial)
WP_003254755.1			+		ER
WP_025754410.1			+		ER
WP_019098500.1			+		ER
WP_025753288.1				(PF01852)	ER
WP_025754941.1		(>)			ER
WP_025753975.1			+		ER
WP_025753853.1	+				(mitochondrial); plastid
WP_033695389.1	(+)			(PF13582)	ER
WP_016712750.1			+		ER
WP_019099759.1		(>)			ER; (ER)
WP_019098496.1			+		ER
WP_025754050.1				(PF06293)	(ER)
WP_025754630.1			+		ER
WP_025754052.1		+			ER
WP_019097481.1			+		ER
WP_010954645.1		(>)			mitochondrial; (ER)
WP_016711925.1	+				ER; (ER)
WP_025753952.1		(<)			ER
WP_025755037.1		(>)			mitochondrial; (mitochondrial)
WP_025754698.1	+				(mitochondrial); (ER)
WP_025754943.1			+		ER
WP_019096535.1			+		ER
WP_016715472.1		(>)			(ER)
WP_016711914.1		+			ER
WP_016714784.1	+				(mitochondrial); (plastid)
WP_016713291.1				(PF06039)	(ER)
WP_019097559.1		(>)			(mitochondrial)
WP_025753837.1	+				plastid
WP_025753234.1	+		+
WP_025754944.1	(+)				(ER)
WP_025754048.1	(+)				ER
WP_025754407.1	+				(plastid)
WP_016713817.1	+				(plastid)
WP_019099471.1			+		(mitochondrial)
WP_016714563.1	+		+
WP_019099758.1	(+)				ER
WP_025754466.1	(+)				(ER)
WP_025754458.1	(+)				(mitochondrial)
WP_025752678.1	+				plastid
WP_019097042.1	(+)				mitochondrial
WP_019097235.1	(+)				mitochondrial; (plastid)
WP_025754503.1	+				plastid
WP_025755064.1		(<)			(plastid)
WP_019099718.1	+				plastid
WP_025753769.1	(+)				(ER)
WP_016715506.1	+				(plastid)
WP_004575843.1	+				(plastid)
WP_016714299.1	(+)				ER
WP_016713789.1	(+)				ER; (ER)
WP_025754279.1			+		(mitochondrial)
WP_019098256.1	+				(plastid)
WP_019096813.1		+			(ER)
WP_019098105.1	+				(ER)
WP_019097653.1	(+)				(mitochondrial); (plastid)
WP_016714822.1	(+)				ER
WP_016713139.1		(>)			(mitochondrial)
WP_025753956.1	(+)				mitochondrial; (mitochondrial)
WP_025753918.1	(+)				(mitochondrial); (plastid)
WP_025752372.1	(+)				(ER)
WP_019097414.1	(+)				mitochondrial
WP_019096846.1	(+)				(mitochondrial); mitochondrial
WP_020371258.1	+	(<)
WP_025752781.1	(+)				(ER); (mitochondrial)
WP_025752561.1	+		+
WP_025753380.1			+		(mitochondrial)
WP_025753856.1	+				plastid
WP_019096368.1	+				(mitochondrial)
WP_016487339.1			+		(ER)
WP_025753417.1	+				plastid
WP_016711993.1	(+)				(ER)
WP_019097667.1	(+)				mitochondrial
WP_016713152.1		(<)	+
WP_003256968.1	+				(plastid)
WP_025753070.1	(+)				(mitochondrial); plastid
WP_019098301.1	(+)				(ER)
WP_025754091.1	(+)				mitochondrial
WP_025753961.1	(+)				(mitochondrial); (plastid)
WP_025752342.1	+				(plastid)
WP_025753340.1	+				(plastid)
WP_016713768.1	+				(mitochondrial)
WP_016488335.1	+				(ER)
WP_025755030.1				(PF16473)
WP_025754925.1	(+)				(mitochondrial)
WP_019099166.1		+
WP_025752538.1	+
WP_019097158.1	+
WP_025755060.1	+
WP_016715226.1	+
WP_019096460.1	+
WP_019098777.1	(+)				(ER)
WP_025754222.1			+
WP_016713890.1	+
WP_025754571.1		+
WP_019098265.1	+
WP_003254214.1	(+)				(mitochondrial)
WP_025754491.1	(+)				(mitochondrial)
WP_019098106.1	+
WP_016714890.1		(>)
WP_019098761.1		(>)
WP_012273542.1	+
WP_003254393.1	+
WP_019096627.1	+
WP_019096355.1				(PF07720)
WP_019096689.1	+
WP_019097103.1	+
WP_019096343.1		+
WP_019096516.1	+
WP_016498176.1			+
WP_016712222.1	+
WP_025754958.1	+
WP_019096402.1	+
WP_016711148.1	(+)				(mitochondrial)
WP_019098470.1			+
WP_019098833.1	+
WP_016715779.1	(+)	(>)
WP_010952367.1	(+)	(>)
WP_019096186.1	+
WP_025754386.1	(+)		+
WP_019096756.1	+
WP_019097478.1	+
WP_013974710.1	(+)		+
WP_025753211.1			+
WP_016713489.1	+
WP_025753241.1	+
WP_025754360.1	(+)		+
WP_016714157.1	+
WP_025753745.1	+
WP_025754885.1	(+)				(plastid)
WP_025754476.1	+
WP_025754231.1	(+)		+
WP_019096883.1	+
WP_019099720.1	+
WP_019096344.1	+
WP_019096936.1	+
WP_016489386.1		(>)
WP_012273515.1	+
WP_025753051.1	+
WP_016712237.1			+
WP_016713342.1			+
WP_025752615.1			+
WP_016714470.1	+
WP_027609415.1	+
WP_025754776.1		(>)
WP_019097913.1	+
WP_019097915.1	+
WP_025752182.1	+
WP_025754796.1	+
WP_019098437.1			+
WP_050587803.1	+
WP_025754697.1	+
WP_025752437.1			+
WP_019099786.1	+
WP_025752165.1	+
WP_019097820.1	+
WP_019097854.1	+
WP_003253504.1	+
WP_025754510.1	+
WP_019098253.1	+
WP_025754676.1	+
WP_016713335.1	+
WP_019099603.1	+
WP_019097691.1	+
WP_003253387.1	+
WP_016714029.1	(+)				(plastid)
WP_019096272.1	(+)				(mitochondrial)
WP_025754950.1	+
WP_019096860.1	+
WP_025753429.1	+
WP_019097491.1	+
WP_025754165.1	+
WP_010955104.1		(>)
WP_025754514.1	+
WP_025754668.1	+
WP_025754349.1	+
WP_016715632.1	+
WP_025754814.1			+
WP_010952562.1		(>)
WP_025754853.1			+
WP_019099727.1	+
WP_025752939.1	+
WP_019099794.1		+
WP_016713590.1				(PF06293)
WP_025753189.1	+
WP_019097861.1	+
WP_016392438.1			+
WP_025752145.1			+
WP_025754953.1		(>)
WP_025754702.1	+
WP_025754414.1	+
WP_016713804.1	+
WP_025754472.1	+
WP_019099292.1	(+)				(plastid)
WP_025754969.1	+
WP_025754273.1	(+)		+
WP_016713866.1	+
WP_019099444.1	+
WP_019096167.1	(+)				(plastid)
WP_025754238.1	+
WP_016711177.1	+
WP_025752803.1	+
WP_016712689.1			+
WP_019097462.1	(+)				(plastid)
WP_019098912.1		(>)
WP_025754428.1	(+)				(plastid)
WP_019096759.1	+
WP_019096567.1	+
WP_033695407.1			+
WP_025752401.1	+
WP_003255454.1			+
WP_025754009.1	(+)		+
WP_009682777.1	+
WP_016713270.1		(<)
WP_025752750.1	+
WP_025752344.1			+
WP_016711773.1			+
WP_025754443.1	+
WP_025754038.1	+
WP_025754964.1			+
WP_019097850.1	+
WP_025754540.1	(+)				(plastid)
WP_019098656.1	+
WP_016712556.1			+
WP_016711199.1	+
WP_019099131.1	+
WP_019098505.1	+
WP_019098439.1	+
WP_019096647.1	(+)				(plastid)
WP_019096212.1			+
WP_016714545.1				(PF06293)
WP_016711981.1	+
WP_003255391.1	+
WP_050547878.1	+
WP_019097123.1		(<)
WP_016712122.1	+
WP_016712973.1			+
WP_019096764.1				(PF07653)
WP_025753147.1	+
WP_016715525.1		(>)
WP_019096469.1	+
WP_025753962.1	+
WP_016714324.1	+
WP_016715205.1	+
WP_016715227.1	+
WP_025753672.1	+
WP_025754471.1	(+)				(plastid)
WP_025754334.1	+
WP_019096232.1	(+)				(ER)
WP_016711468.1	+
WP_019096501.1	+
WP_025753110.1	+
WP_016715412.1			+
WP_019098699.1	+
WP_025752210.1	+
WP_019098633.1	+
WP_019097888.1	+
WP_016712620.1	+
WP_019098086.1	+
WP_019098885.1		(<)
WP_050547871.1	+
WP_016712182.1	+
WP_025752237.1			+
WP_019099472.1	+
WP_019098928.1	+
WP_019098754.1	+
WP_025754584.1	+
WP_016712962.1		(>)
WP_016712341.1	(+)				(plastid)
WP_025754198.1	+
WP_025753786.1			+
WP_019098413.1	+
WP_016714939.1	+
WP_016714311.1		(>)
WP_019098088.1	+
WP_019099589.1	+
WP_019097649.1			+
WP_019099531.1	+
WP_023128610.1	+
WP_019097138.1	+
WP_016712457.1	(+)				(mitochondrial)
WP_025753863.1	+
WP_025753841.1	+
WP_025754811.1	+
WP_025752915.1	+
WP_019098396.1	+
WP_025753986.1	+
WP_019098668.1	+
WP_016714544.1				(PF06293)
WP_016711767.1	(+)				(ER)
WP_025754528.1	+
WP_013972924.1	+
WP_016715096.1	+
WP_033695273.1	(+)				(plastid)
WP_025754806.1	(+)				plastid
WP_025754074.1	+
WP_025754120.1	+
WP_025755042.1	+
WP_025753337.1	+
WP_025754419.1	+
WP_019096162.1		(>)
WP_016711876.1		(>)
WP_025754746.1	+
WP_019099088.1		(>)
WP_019096267.1	+
WP_019097920.1	+
WP_016715296.1	+
WP_019097922.1		+
WP_016711142.1			+
WP_019096887.1		(>)
WP_025752816.1			+
WP_019098547.1		(>)
WP_025754427.1	+
WP_025754208.1	+
WP_016711585.1	+
WP_025754815.1	(+)	(<)
WP_025754789.1			+
WP_025752453.1			+
WP_016715680.1			+
WP_019098681.1	+
WP_025754382.1	(+)				(mitochondrial)
WP_025754051.1				(PF06293)
WP_016715684.1	+
WP_025753886.1	+
WP_025752418.1	+
WP_025753746.1		+
WP_025753123.1	+
WP_004575216.1			+
WP_025754013.1	+
WP_025754543.1	+
WP_025754826.1	(+)				(ER)
WP_016713275.1	+
WP_019099200.1	(+)				(mitochondrial)
WP_025754683.1	+
WP_025754488.1			+
WP_019097175.1	+
WP_025753896.1	+
WP_016712705.1	+
WP_025752361.1	+
WP_019096486.1	+
WP_019099359.1			+
WP_025754069.1	+
WP_016712422.1	+
WP_016715787.1		(<)
WP_025752859.1				(PF16473)
WP_050547859.1		(>)
WP_019099492.1			+
WP_025754724.1	+
WP_016712659.1	(+)
WP_019097027.1	(+)
WP_016713426.1	(+)
WP_019096839.1	(+)
WP_025753143.1	(+)
WP_019099533.1	(+)
WP_016713836.1	(+)
WP_016712467.1	(+)
WP_016711135.1	(+)
WP_025754627.1	(+)
WP_016712029.1	(+)
WP_025752601.1	(+)
WP_025753232.1	(+)
WP_019099761.1	(+)
WP_003249375.1	(+)
WP_016715487.1	(+)
WP_016713158.1	(+)
WP_019097372.1	(+)
WP_019097997.1	(+)
WP_025752240.1	(+)
WP_019099693.1	(+)
WP_025753733.1	(+)
WP_003252287.1	(+)
WP_019099314.1	(+)
WP_025754417.1	(+)
WP_019098523.1	(+)
WP_025754817.1	(+)
WP_025753694.1	(+)
WP_003252148.1	(+)
WP_033695325.1	(+)
WP_016713912.1	(+)
WP_019096401.1	(+)
WP_025752528.1	(+)
WP_025752428.1	(+)
WP_025754829.1	(+)
WP_016711342.1	(+)
WP_025753450.1	(+)
WP_025752737.1	(+)
WP_016713891.1	(+)
WP_025754389.1	(+)
WP_019098193.1	(+)
WP_016486361.1	(+)
WP_025754245.1	(+)
WP_019098442.1	(+)
WP_019099209.1	(+)
WP_016715071.1	(+)
WP_010953293.1	(+)
WP_019098153.1	(+)
WP_025753160.1	(+)
WP_012273535.1	(+)
WP_019098850.1	(+)
WP_016711143.1	(+)
WP_025753166.1	(+)
WP_050587800.1	(+)
WP_025754774.1	(+)
WP_025754049.1	(+)
WP_025752839.1	(+)
WP_012274251.1	(+)
WP_016711545.1	(+)
WP_016713391.1	(+)
WP_019099146.1	(+)
WP_016713864.1	(+)
WP_025752720.1	(+)
WP_025754557.1	(+)
WP_025754290.1	(+)
WP_027614779.1	(+)
WP_003250422.1	(+)
WP_019096711.1	(+)
WP_025754546.1	(+)
WP_019096315.1	(+)
WP_025754084.1	(+)
WP_019098358.1	(+)
WP_016713325.1	(+)
WP_025753877.1	(+)
WP_019098729.1	(+)
WP_016715379.1	(+)
WP_019096631.1	(+)
WP_019096526.1	(+)
WP_019096834.1	(+)
WP_025753427.1	(+)
WP_019096403.1	(+)
WP_019098511.1	(+)
WP_025752848.1	(+)
WP_019098114.1	(+)
WP_025754599.1	(+)
WP_019098501.1	(+)
WP_016712527.1	(+)
WP_016713837.1	(+)
WP_019098831.1	(+)
WP_019098658.1	(+)
WP_025753926.1	(+)
WP_025752326.1	(+)
WP_019099867.1	(+)
WP_025754498.1	(+)
WP_009684718.1	(+)
WP_019099803.1	(+)
WP_016711107.1	(+)
WP_004375483.1	(+)
WP_025754898.1	(+)
WP_016715339.1	(+)
WP_019098700.1	(+)
WP_016713177.1	(+)
WP_025752590.1	(+)
WP_019097046.1	(+)
WP_016715077.1	(+)
WP_019099282.1	(+)
WP_025754141.1	(+)
WP_016711413.1	(+)
WP_019096893.1	(+)
WP_025754154.1	(+)
WP_003255452.1	(+)
WP_025754892.1	(+)
WP_025754834.1	(+)
WP_016715611.1	(+)
WP_019099097.1	(+)
WP_016712172.1	(+)
WP_016714744.1	(+)
WP_025752348.1	(+)
WP_019098310.1	(+)
WP_016714319.1	(+)
WP_025753992.1	(+)
WP_016715704.1	(+)
WP_019097169.1	(+)
WP_016711728.1	(+)
WP_016714596.1	(+)
WP_025753214.1	(+)
WP_019096198.1	(+)
WP_025754504.1	(+)
WP_019098624.1	(+)
WP_016711905.1	+
WP_019096909.1	(+)
WP_025752791.1	(+)
WP_019099431.1	(+)
WP_019099730.1	(+)
WP_025754938.1	(+)
WP_025754581.1	(+)
WP_025754336.1	(+)
WP_016714249.1	(+)
WP_025754822.1	(+)
WP_025754605.1	(+)
WP_025752446.1	(+)
WP_025752647.1	(+)
WP_025754742.1	(+)
WP_019098055.1	(+)
WP_025754558.1	(+)
WP_019097859.1	(+)
WP_016484539.1	(+)
WP_025754330.1	(+)
WP_019098120.1	(+)
WP_025752163.1	(+)
WP_016713714.1	(+)
WP_019096964.1	(+)
WP_025753368.1	(+)
WP_025752491.1	(+)
WP_019096867.1	(+)
WP_025754684.1	(+)
WP_019096755.1	(+)
WP_019096869.1	(+)
WP_016715517.1	(+)
WP_025752930.1	(+)
WP_025755055.1	(+)
WP_016712524.1	(+)
WP_003255135.1	(+)
WP_012051225.1	(+)
WP_025753788.1	(+)
WP_016711140.1	(+)
WP_019097864.1	(+)
WP_025754158.1	(+)
WP_019097551.1	(+)
WP_016712768.1	(+)
WP_025754830.1	(+)
WP_025753204.1	(+)
WP_003254203.1	(+)
WP_019099205.1	(+)
WP_025752734.1	(+)
WP_025752652.1	(+)
WP_025754637.1	(+)
WP_019096504.1	(+)
WP_016711158.1	(+)
WP_019096349.1	(+)
WP_016713349.1	(+)
WP_019099109.1	(+)
WP_019096470.1	(+)
WP_012271110.1	(+)
WP_025754377.1	(+)
WP_025754628.1	(+)
WP_016715155.1	(+)
WP_003250537.1	(+)
WP_025753933.1	(+)
WP_019096564.1	(+)
WP_019098132.1	(+)
WP_050591172.1	(+)
WP_025754536.1	(+)
WP_019097582.1	(+)
WP_019098473.1	(+)
WP_019097584.1	(+)
WP_009684590.1	(+)
WP_025755076.1	(+)
WP_025754232.1	(+)
WP_025752571.1	(+)
WP_025753083.1	(+)
WP_025754067.1	(+)
WP_019096283.1	(+)
WP_016715068.1	(+)
WP_025754650.1	(+)
WP_025754316.1	(+)
WP_016712231.1	(+)
WP_019099426.1	(+)
WP_019098157.1	(+)
WP_025754890.1	(+)
WP_025754653.1	(+)
WP_019096831.1	(+)
WP_016713411.1	(+)

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

• EffectiveT3 predictions using new standard model 2.0.1 (PROTEINS.NEW.EFFECTIVET3)
• EffectiveT3 predictions using old standard model 1.0.1 (PROTEINS.OLD.EFFECTIVET3)
• EffectiveCCBD predictions (PROTEINS.CHAPERONES.TXT)
• 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: YES (FDR = 12.5 %)
  Estimated copy number = 1.3 (13/10 KEGG proteins)
• 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 = 1.375 (11/8 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
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=GENOTYPE
EMAIL=
==========================================================