Effective results for Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (eggnog40)

Summary

Number of putative secreted proteins: 388
- Predicted by T4SEpre: 520
- Predicted by EffectiveELD: 23 eukaryotic-like domains, contained in 41 proteins (6 high, 35 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
272624.lpg0276			+	(PF00617)	(mitochondrial)
272624.lpg0257			+		ER
272624.lpg0041			+		ER
272624.lpg2686			+		ER
272624.lpg2206			+		ER
272624.lpg1017				(PF13246)	ER
272624.lpg0301				PF11901	ER
272624.lpg1905				PF01150	ER
272624.lpg0696			+		mitochondrial; (mitochondrial)
272624.lpg1273			+		(mitochondrial)
272624.lpg1868			+		mitochondrial
272624.lpg2351			+		ER; (ER)
272624.lpg0403			+		ER
272624.lpg1264				(PF00854)	(ER)
272624.lpg1071				(PF01610)	ER; (ER)
272624.lpg1108			+		mitochondrial
272624.lpg0181			+		(mitochondrial)
272624.lpg0721			+		ER
272624.lpg2344			+		mitochondrial; (mitochondrial)
272624.lpg2588			+		ER
272624.lpg1299			+		ER
272624.lpg0081			+		mitochondrial
272624.lpg0407			+		ER
272624.lpg0401			+		(mitochondrial); (plastid)
272624.lpg0402			+		ER
272624.lpg1667			+		ER
272624.lpg1666			+		mitochondrial
272624.lpg1660			+		(mitochondrial)
272624.lpg2804			+		(mitochondrial)
272624.lpg2577			+		mitochondrial
272624.lpg1289			+		ER
272624.lpg2628			+		ER
272624.lpg2623			+		ER
272624.lpg0234			+		mitochondrial
272624.lpg1945				(PF02112)	ER
272624.lpg0708			+		ER
272624.lpg2819				(PF14566)	ER
272624.lpg1726			+		ER
272624.lpg2176			+		ER
272624.lpg2148			+		mitochondrial; (mitochondrial)
272624.lpg0896			+		ER
272624.lpg0558				(PF01610)	ER
272624.lpg2954				(PF08123)	ER
272624.lpg1962			+		ER
272624.lpg0170			+		(mitochondrial)
272624.lpg0172			+		(mitochondrial)
272624.lpg0955			+		ER
272624.lpg1147			+		(mitochondrial)
272624.lpg1144			+		ER
272624.lpg1965			+		(mitochondrial)
272624.lpg2831			+		(mitochondrial)
272624.lpg1158			+		ER
272624.lpg1151			+		ER
272624.lpg1154			+		mitochondrial
272624.lpg1082			+		mitochondrial; (mitochondrial)
272624.lpg0286			+		ER
272624.lpg0285			+		(mitochondrial)
272624.lpg1972			+		mitochondrial
272624.lpg2999			+		ER
272624.lpg2444			+		ER
272624.lpg2443			+		ER
272624.lpg0971				PF01150	ER
272624.lpg2199			+		(mitochondrial); (plastid)
272624.lpg2815			+		ER
272624.lpg1366			+		(mitochondrial)
272624.lpg0365			+		(ER)
272624.lpg0796			+		(mitochondrial)
272624.lpg2851			+		mitochondrial
272624.lpg2529			+		(mitochondrial); mitochondrial
272624.lpg0746				(PF00854)	(mitochondrial)
272624.lpg2884			+		ER
272624.lpg0120			+		ER
272624.lpg1741			+		ER
272624.lpg0902			+		ER; (ER)
272624.lpg0249				(PF01610)	ER
272624.lpg2222			+		ER
272624.lpg1533				(PF00854)	mitochondrial; (mitochondrial)
272624.lpg0926			+		(ER)
272624.lpg1803			+		(ER)
272624.lpg2203			+		(ER)
272624.lpg1491			+		(mitochondrial)
272624.lpg0196			+		(ER)
272624.lpg1481			+		(mitochondrial)
272624.lpg1484			+		(plastid)
272624.lpg1642			+	(PF05677)
272624.lpg2805				(PF00854)	(ER)
272624.lpg1109			+		(mitochondrial)
272624.lpg2160			+		(ER)
272624.lpg2372			+		(mitochondrial)
272624.lpg1129			+		(plastid)
272624.lpg1950			+	PF01369
272624.lpg0770			+		(ER)
272624.lpg0171			+	(PF00646)
272624.lpg2826			+		(ER)
272624.lpg2830			+	(PF04564)
272624.lpg1978			+	(PF04488)
272624.lpg2538			+		(mitochondrial)
272624.lpg1718			+		plastid
272624.lpg2198				(PF00854)	(mitochondrial)
272624.lpg0294			+		(mitochondrial)
272624.lpg2525			+		(ER)
272624.lpg2526			+		(mitochondrial)
272624.lpg1760			+		plastid
272624.lpg0439			+		(ER)
272624.lpg2637			+		(plastid)
272624.lpg2885			+		(plastid)
272624.lpg1340			+		plastid
272624.lpg2874			+		(mitochondrial)
272624.lpg1358			+		(mitochondrial)
272624.lpg1684			+	PF07065
272624.lpg1328			+	(PF00314)
272624.lpg2411			+
272624.lpg2410			+
272624.lpg2416			+
272624.lpg0675			+
272624.lpg0921			+
272624.lpg2239			+
272624.lpg2301			+
272624.lpg2300			+
272624.lpg1259			+
272624.lpg0260			+
272624.lpg2215			+
272624.lpg0046			+
272624.lpg2424			+
272624.lpg2425			+
272624.lpg2420			+
272624.lpg2421			+
272624.lpg2338			+
272624.lpg2118				(PF01610)
272624.lpg2117				(PF01610)
272624.lpg1797			+
272624.lpg1798			+
272624.lpg2200			+
272624.lpg1242			+
272624.lpg0275			+
272624.lpg1907			+
272624.lpg0059			+
272624.lpg2434			+
272624.lpg0695			+
272624.lpg0693			+
272624.lpg1496			+
272624.lpg1654			+
272624.lpg2694			+
272624.lpg2692			+
272624.lpg2328			+
272624.lpg2322			+
272624.lpg0870			+
272624.lpg2745			+
272624.lpg2744			+
272624.lpg2216			+
272624.lpg1476			+
272624.lpg1312			+
272624.lpg1316			+
272624.lpg1005			+
272624.lpg1752			+
272624.lpg0191			+
272624.lpg0195			+
272624.lpg0208			+
272624.lpg0422			+
272624.lpg0515			+
272624.lpg0518			+
272624.lpg0519			+
272624.lpg0733			+
272624.lpg2910			+
272624.lpg2912			+
272624.lpg2504			+
272624.lpg1483			+
272624.lpg1489			+
272624.lpg1488			+
272624.lpg2359			+
272624.lpg2591			+
272624.lpg2771			+
272624.lpg1268			+
272624.lpg1266			+
272624.lpg1072				(PF01610)
272624.lpg2806			+
272624.lpg1106			+
272624.lpg1101			+
272624.lpg0182			+
272624.lpg0210			+
272624.lpg0437			+
272624.lpg0436			+
272624.lpg1924			+
272624.lpg1851			+
272624.lpg2907			+
272624.lpg1670			+
272624.lpg2391			+
272624.lpg2584			+
272624.lpg2762			+
272624.lpg2761			+
272624.lpg1290			+
272624.lpg1453			+
272624.lpg1111			+
272624.lpg1110			+
272624.lpg0227			+
272624.lpg1529			+
272624.lpg1933			+
272624.lpg0080			+
272624.lpg0086			+
272624.lpg0716			+
272624.lpg2975			+
272624.lpg0405			+
272624.lpg2482			+
272624.lpg1661			+
272624.lpg2370			+
272624.lpg2571			+
272624.lpg1598			+
272624.lpg2154			+
272624.lpg2717			+
272624.lpg2718			+
272624.lpg1288			+
272624.lpg1449			+
272624.lpg2155			+
272624.lpg2156			+
272624.lpg2153			+
272624.lpg1056				(PF07700)
272624.lpg1053			+
272624.lpg1120			+
272624.lpg1121			+
272624.lpg1124			+
272624.lpg1947			+
272624.lpg1948			+
272624.lpg1949			+
272624.lpg1602			+
272624.lpg0096			+
272624.lpg0095				(PF05761)
272624.lpg0094			+
272624.lpg0090			+
272624.lpg0144				(PF01610)
272624.lpg0143				(PF01610)
272624.lpg2490			+
272624.lpg2498			+
272624.lpg2363				(PF01610)
272624.lpg2566			+
272624.lpg2173				(PF01610)
272624.lpg2382			+
272624.lpg0963			+
272624.lpg2149			+
272624.lpg2147			+
272624.lpg0894				(PF09265)
272624.lpg1545			+
272624.lpg1137			+
272624.lpg0794			+
272624.lpg1953			+
272624.lpg1959			+
272624.lpg1958			+
272624.lpg0390			+
272624.lpg2828			+
272624.lpg2829			+
272624.lpg2552			+
272624.lpg2555			+
272624.lpg2556			+
272624.lpg1639			+
272624.lpg0953			+
272624.lpg1425			+
272624.lpg1426			+
272624.lpg2603			+
272624.lpg2936			+
272624.lpg2422			+
272624.lpg1551			+
272624.lpg1148			+
272624.lpg1145			+
272624.lpg1387			+
272624.lpg1669				(PF14701)
272624.lpg1093				(PF13246)
272624.lpg0543			+
272624.lpg1890			+
272624.lpg0160			+
272624.lpg1964			+
272624.lpg1966			+
272624.lpg1960			+
272624.lpg1961				(PF04488)
272624.lpg1633				PF14360
272624.lpg2832			+
272624.lpg2546			+
272624.lpg2541			+
272624.lpg1701			+
272624.lpg1702			+
272624.lpg2720			+
272624.lpg2050			+
272624.lpg0945			+
272624.lpg0944			+
272624.lpg0940			+
272624.lpg0948			+
272624.lpg0030			+
272624.lpg1152			+
272624.lpg1083			+
272624.lpg1089			+
272624.lpg0284			+
272624.lpg1884			+
272624.lpg1881			+
272624.lpg0376			+
272624.lpg0375			+
272624.lpg0116			+
272624.lpg1976			+
272624.lpg1975			+
272624.lpg1621			+
272624.lpg1625			+
272624.lpg0621			+
272624.lpg2844			+
272624.lpg2539			+
272624.lpg3000			+
272624.lpg0021			+
272624.lpg1717			+
272624.lpg1716			+
272624.lpg1711			+
272624.lpg2283			+
272624.lpg1578			+
272624.lpg1164			+
272624.lpg1166			+
272624.lpg2813			+
272624.lpg0364			+
272624.lpg1183			+
272624.lpg1986			+
272624.lpg0103			+
272624.lpg0634			+
272624.lpg2528			+
272624.lpg2523			+
272624.lpg2527			+
272624.lpg0038			+
272624.lpg2298			+
272624.lpg2456			+
272624.lpg2451			+
272624.lpg2452			+
272624.lpg2459				(PF07700)
272624.lpg0969			+
272624.lpg0968			+
272624.lpg2271			+
272624.lpg1171			+
272624.lpg1378				(PF00854)
272624.lpg0135			+
272624.lpg0130			+
272624.lpg0642			+
272624.lpg2862			+
272624.lpg2510			+
272624.lpg2511			+
272624.lpg2519			+
272624.lpg0008			+
272624.lpg1773			+
272624.lpg1774			+
272624.lpg1776			+
272624.lpg2461			+
272624.lpg2464			+
272624.lpg2144			+
272624.lpg2248			+
272624.lpg2241				(PF12471)
272624.lpg2242				(PF07958)
272624.lpg2244			+
272624.lpg2888			+
272624.lpg2889			+
272624.lpg0967			+
272624.lpg0898			+
272624.lpg1836			+
272624.lpg0126			+
272624.lpg2465			+
272624.lpg2879			+
272624.lpg2505			+
272624.lpg2509			+
272624.lpg1888			+
272624.lpg0012			+
272624.lpg1588			+
272624.lpg2166			+
272624.lpg1692			+
272624.lpg2651			+
272624.lpg1969			+
272624.lpg1355			+
272624.lpg2691			+
272624.lpg1827			+
272624.lpg0483			+
272624.lpg0246			+
272624.lpg0240			+
272624.lpg1963			+
272624.lpg1751			+
272624.lpg2793			+
272624.lpg2409			+
272624.lpg2406			+
272624.lpg2407			+
272624.lpg2223			+
272624.lpg2224			+
272624.lpg1683			+
272624.lpg1685			+
272624.lpg1687			+
272624.lpg1689			+
272624.lpg2311			+
272624.lpg2433			+
272624.lpg2137			+
272624.lpg2131			+
272624.lpg1227			+

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 = 0.8 (8/10 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=
==========================================================