------------------------------------------------------------ Pratt version 2.1, Sept. 1996 Written by Inge Jonassen, University of Bergen Norway email: inge@ii.uib.no For more information, see http://www.ii.uib.no/~inge/Pratt.html ------------------------------------------------------------ Please quote: I.Jonassen, J.F.Collins, D.G.Higgins. Protein Science 1995;4(8):1587-1595. ------------------------------------------------------------ Pratt version 2.1 Analysing 5 sequences from file TERPENE_SYNTHASES PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 C%: min Percentage Seqs to Match 100.0 PATTERN RESTRICTIONS : PP: pos in seq [off,complete,start] off PL: max Pattern Length 50 PN: max Nr of Pattern Symbols 50 PX: max Nr of consecutive x's 5 FN: max Nr of flexible spacers 2 FL: max Flexibility 2 FP: max Flex.Product 10 BI: Input Pattern Symbol File off BN: Nr of Pattern Symbols Initial Search 20 PATTERN SCORING: S: Scoring [info,mdl,tree,dist,ppv] info SEARCH PARAMETERS: G: Pattern Graph from [seq,al,query] seq E: Search Greediness 3 R: Pattern Refinement on RG: Generalise ambiguous symbols off OUTPUT: OF: Output Filename TERPENE_SYNTHASES.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CAS1_ARATH 759 ERG7_CANAL 728 ERG7_YEAST 730 SQHC_ALIAC 626 SQHC_ZYMMO 658 Pratt run started at Thu Feb 6 21:25:08 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 31.8604 5( 5) Q-x(2,3)-D-G-S-W-x-G-x-W-x(3,5)-Y 2: 29.1904 5( 5) Y-x(2)-Y-x(3)-F-P-x(2)-A-L-x(2)-Y 3: 29.1904 5( 5) D-G-S-W-x-G-x-W-x(5)-Y 4: 28.1904 5( 5) D-G-S-W-x-G-x-W-x(3,5)-Y 5: 25.0203 5( 5) Y-x(3)-F-P-x(2)-A-L-x(2)-Y 6: 25.0203 5( 5) L-x(3)-Q-x(2)-D-G-G-W 7: 25.0203 5( 5) G-S-W-x-G-x-W-x(5)-Y 8: 24.5203 5( 5) Y-x(2,3)-F-P-x(2)-A-L-x(2)-Y 9: 24.0203 5( 5) S-x(5)-A-W-A-x(0,1)-L-x(1,2)-L 10: 24.0203 5( 5) G-S-W-x-G-x-W-x(3,5)-Y 11: 24.0203 5( 5) V-x(0,1)-K-x(4)-L-x(3)-Q-x(4)-G-x(0,1)-W 12: 24.0203 6( 5) Q-x(2,3)-D-G-S-W-x(0,1)-G 13: 20.8503 6( 5) Q-x(2)-D-G-G-W 14: 20.8503 6( 5) Q-x(3)-G-G-W-x-E 15: 20.8503 6( 5) D-G-G-W-G 16: 20.8503 6( 5) D-x(5)-Q-x(2)-D-G-x-W 17: 20.8503 9( 5) L-x(3)-Q-x(2)-D-G-x-W 18: 20.3503 6( 5) D-G-S-W-x(0,1)-G 19: 19.8503 5( 5) Y-x(2)-Y-x(3)-F-P-x(1,3)-L 20: 19.8503 5( 5) A-W-A-x(0,1)-L-x(1,2)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 77.8072 5( 5) D-G-S-W-[FY]-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] B 2: 77.7927 5( 5) Q-x(2,3)-D-G-S-W-x(0,1)-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] C 3: 74.1227 5( 5) D-G-S-W-x(0,1)-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] D 4: 73.6371 5( 5) G-S-W-[FY]-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] E 5: 67.7213 5( 5) Q-x(2,3)-D-G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] F 6: 64.0512 5( 5) D-G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] G 7: 59.8812 5( 5) G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] H 8: 53.2977 5( 5) S-x-[APV]-[SV]-[NQ]-[ST]-A-W-A-x(0,1)-L-x(1,2)-L-[ILM]-x-[AGV]-[EGN]-x-[AP]-[DEN]-x-[DE] I 9: 49.6324 5( 5) V-x(0,1)-K-[AG]-[CGV]-[ADE]-[FW]-L-x-[DST]-x-Q-x(2)-[DSV]-[GP]-G-x(0,1)-W-[AGS]-x(4)-[GNS] J 10: 39.5425 5( 5) Q-x(2)-[DS]-G-G-W-[DGS]-E-[DNPS]-x(2)-[GS]-x-[AEQ]-x(4)-[AGSV]-x(4)-[DNS] K 11: 36.9901 5( 5) A-W-A-x(0,1)-L-x(1,2)-L-[ILM]-x-[AGV]-[EGN]-x-[AP]-[DEN]-x-[DE] L 12: 36.8636 5( 5) L-x-[ENST]-x-Q-x(2)-D-G-G-W-[DGS]-x(4)-[GST]-x-[AEST]-x(4)-[DGSV] M 13: 36.2952 5( 5) Q-x(2)-D-G-G-W-[DGS]-x(3)-[DEKR]-[GS]-x-[AES]-x(4)-[AGSV]-x(4)-[DSV] N 14: 33.2432 5( 5) D-G-G-W-G-x(4)-[DGS]-x-[AES]-x(4)-[AGSTV]-x(2)-[GNP]-x-[DSV] O 15: 32.3605 5( 5) Y-x(2)-Y-x(3)-F-P-x(2)-A-L-[AG]-x-Y P 16: 32.0550 5( 5) D-[FWY]-x(4)-Q-x(2)-D-G-x-W-x-[EG]-[DRS]-x(2)-[GSV] Q 17: 30.5439 5( 5) L-x-[ENST]-[HKR]-Q-x(2)-D-G-x-W-[GSV]-x(4)-[AGPS] R 18: 30.4096 5( 5) Y-x(2)-Y-[RS]-x(2)-F-P-x(1,3)-L-[AG]-x-Y S 19: 28.1904 5( 5) Y-x(3)-F-P-x(2)-A-L-[AG]-x-Y T 20: 27.6904 5( 5) Y-x(2,3)-F-P-x(2)-A-L-[AG]-x-Y Best patterns with alignements: fitness hits(seqs) Pattern A 1: 77.8072 5( 5) D-G-S-W-[FY]-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 603- 633: siqaa DGSWYGsWAVCFtYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 576- 606: sqdni DGSWYGcWGICYtYASmfALeALhTVGlDyE sssav ERG7_YEAST : 579- 609: ksqlp DGSWYGsWGICFtYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 477- 507: reqkp DGSWFGrWGVNYlYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 500- 530: keqee DGSWFGrWGVNYiYGTwsALcALnVAAlPhD hlavq B 2: 77.7927 5( 5) Q-x(2,3)-D-G-S-W-x(0,1)-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 600- 633: fiesi Qaa-DGSWyGsWAVCFtYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 572- 606: yilds QdniDGSWyGcWGICYtYASmfALeALhTVGlDyE sssav ERG7_YEAST : 576- 609: fikks Qlp-DGSWyGsWGICFtYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 474- 507: ylkre Qkp-DGSWfGrWGVNYlYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 497- 530: yllke Qee-DGSWfGrWGVNYiYGTwsALcALnVAAlPhD hlavq C 3: 74.1227 5( 5) D-G-S-W-x(0,1)-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 603- 633: siqaa DGSWyGsWAVCFtYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 576- 606: sqdni DGSWyGcWGICYtYASmfALeALhTVGlDyE sssav ERG7_YEAST : 579- 609: ksqlp DGSWyGsWGICFtYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 477- 507: reqkp DGSWfGrWGVNYlYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 500- 530: keqee DGSWfGrWGVNYiYGTwsALcALnVAAlPhD hlavq D 4: 73.6371 5( 5) G-S-W-[FY]-G-x-W-[AG]-[IV]-[CN]-[FY]-x-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 604- 633: iqaad GSWYGsWAVCFtYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 577- 606: qdnid GSWYGcWGICYtYASmfALeALhTVGlDyE sssav ERG7_YEAST : 580- 609: sqlpd GSWYGsWGICFtYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 478- 507: eqkpd GSWFGrWGVNYlYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 501- 530: eqeed GSWFGrWGVNYiYGTwsALcALnVAAlPhD hlavq E 5: 67.7213 5( 5) Q-x(2,3)-D-G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 600- 633: fiesi Qaa-DGSWYGsWavcftYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 572- 606: yilds QdniDGSWYGcWgicytYASmfALeALhTVGlDyE sssav ERG7_YEAST : 576- 609: fikks Qlp-DGSWYGsWgicftYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 474- 507: ylkre Qkp-DGSWFGrWgvnylYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 497- 530: yllke Qee-DGSWFGrWgvnyiYGTwsALcALnVAAlPhD hlavq F 6: 64.0512 5( 5) D-G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 603- 633: siqaa DGSWYGsWavcftYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 576- 606: sqdni DGSWYGcWgicytYASmfALeALhTVGlDyE sssav ERG7_YEAST : 579- 609: ksqlp DGSWYGsWgicftYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 477- 507: reqkp DGSWFGrWgvnylYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 500- 530: keqee DGSWFGrWgvnyiYGTwsALcALnVAAlPhD hlavq G 7: 59.8812 5( 5) G-S-W-[FY]-G-x-W-x(3,5)-Y-[AG]-[GST]-x(2)-[AGV]-[LV]-x-[AG]-L-x-[ATV]-[AV]-[AG]-x-[DPT]-x-[DEKR] Occurences: 5(5) CAS1_ARATH : 604- 633: iqaad GSWYGsWavcftYGTwfGVkGLvAVGkTlK nsphv ERG7_CANAL : 577- 606: qdnid GSWYGcWgicytYASmfALeALhTVGlDyE sssav ERG7_YEAST : 580- 609: sqlpd GSWYGsWgicftYAGmfALeALhTVGeTyE nsstv SQHC_ALIAC : 478- 507: eqkpd GSWFGrWgvnylYGTgaVVsALkAVGiDtR epyiq SQHC_ZYMMO : 501- 530: eqeed GSWFGrWgvnyiYGTwsALcALnVAAlPhD hlavq H 8: 53.2977 5( 5) S-x-[APV]-[SV]-[NQ]-[ST]-A-W-A-x(0,1)-L-x(1,2)-L-[ILM]-x-[AGV]-[EGN]-x-[AP]-[DEN]-x-[DE] Occurences: 5(5) CAS1_ARATH : 675- 696: ldgnr ShVVNTAWAmLa-LIgAGqAEvD rkplh ERG7_CANAL : 646- 667: vngen SlVVQSAWA-LigLIlGNyPDeE pikrg ERG7_YEAST : 649- 670: vdsek SlVVQTAWA-LiaLLfAEyPNkE vidrg SQHC_ALIAC : 546- 567: agkga StPSQTAWA-LmaLIaGGrAEsE aarrg SQHC_ZYMMO : 570- 591: yepmd StASQTAWAlLg-LMaVGeANsE avtkg SQHC_ZYMMO : 570- 591: yepmd StASQTAWA-LlgLMaVGeANsE avtkg I 9: 49.6324 5( 5) V-x(0,1)-K-[AG]-[CGV]-[ADE]-[FW]-L-x-[DST]-x-Q-x(2)-[DSV]-[GP]-G-x(0,1)-W-[AGS]-x(4)-[GNS] Occurences: 5(5) CAS1_ARATH : 638- 661: knsph VaKACEFLlSkQqpSGG-WGesylS cqdkv ERG7_CANAL : 611- 634: esssa VkKGCDFLiSkQlpDGG-WSesmkG ceths ERG7_YEAST : 614- 637: ensst VrKGCDFLvSkQmkDGG-WGesmkS selhs SQHC_ALIAC : 330- 353: dhdrl V-KAGEWLlDrQitVPGdWAvkrpN lkpgg SQHC_ZYMMO : 534- 557: hdhla VqKAVAWLkTiQneDGG-WGencdS yaldy J 10: 39.5425 5( 5) Q-x(2)-[DS]-G-G-W-[DGS]-E-[DNPS]-x(2)-[GS]-x-[AEQ]-x(4)-[AGSV]-x(4)-[DNS] Occurences: 5(5) CAS1_ARATH : 649- 673: fllsk QqpSGGWGESylScQdkvySnldgN rshvv ERG7_CANAL : 622- 646: flisk QlpDGGWSESmkGcEthsyVngenS lvvqs ERG7_YEAST : 625- 649: flvsk QmkDGGWGESmkSsElhsyVdsekS lvvqt SQHC_ALIAC : 522- 546: wveqh QnpDGGWGEDcrSyEdpayAgkgaS tpsqt SQHC_ZYMMO : 545- 569: wlkti QneDGGWGENcdSyAldysGyepmD stasq K 11: 36.9901 5( 5) A-W-A-x(0,1)-L-x(1,2)-L-[ILM]-x-[AGV]-[EGN]-x-[AP]-[DEN]-x-[DE] Occurences: 5(5) CAS1_ARATH : 681- 696: hvvnt AWAmLa-LIgAGqAEvD rkplh ERG7_CANAL : 652- 667: lvvqs AWA-LigLIlGNyPDeE pikrg ERG7_YEAST : 655- 670: lvvqt AWA-LiaLLfAEyPNkE vidrg SQHC_ALIAC : 552- 567: tpsqt AWA-LmaLIaGGrAEsE aarrg SQHC_ZYMMO : 576- 591: tasqt AWAlLg-LMaVGeANsE avtkg SQHC_ZYMMO : 576- 591: tasqt AWA-LlgLMaVGeANsE avtkg L 12: 36.8636 5( 5) L-x-[ENST]-x-Q-x(2)-D-G-G-W-[DGS]-x(4)-[GST]-x-[AEST]-x(4)-[DGSV] Occurences: 5(5) CAS1_ARATH : 154- 177: emrry LyNhQneDGGWGlhieGpStmfgS vlnyv ERG7_CANAL : 618- 641: kgcdf LiSkQlpDGGWSesmkGcEthsyV ngens ERG7_YEAST : 621- 644: kgcdf LvSkQmkDGGWGesmkSsElhsyV dseks SQHC_ALIAC : 576- 599: rgvqy LvEtQrpDGGWDepyyTgTaspgD fylgy SQHC_ZYMMO : 541- 564: kavaw LkTiQneDGGWGencdSyAldysG yepmd M 13: 36.2952 5( 5) Q-x(2)-D-G-G-W-[DGS]-x(3)-[DEKR]-[GS]-x-[AES]-x(4)-[AGSV]-x(4)-[DSV] Occurences: 5(5) CAS1_ARATH : 158- 182: ylynh QneDGGWGlhiEGpStmfgSvlnyV tlrll ERG7_CANAL : 622- 646: flisk QlpDGGWSesmKGcEthsyVngenS lvvqs ERG7_YEAST : 625- 649: flvsk QmkDGGWGesmKSsElhsyVdsekS lvvqt SQHC_ALIAC : 522- 546: wveqh QnpDGGWGedcRSyEdpayAgkgaS tpsqt SQHC_ZYMMO : 545- 569: wlkti QneDGGWGencDSyAldysGyepmD stasq N 14: 33.2432 5( 5) D-G-G-W-G-x(4)-[DGS]-x-[AES]-x(4)-[AGSTV]-x(2)-[GNP]-x-[DSV] Occurences: 5(5) CAS1_ARATH : 161- 182: nhqne DGGWGlhieGpStmfgSvlNyV tlrll ERG7_CANAL : 132- 153: tahpv DGGWGlhsvDkStcfgTtmNyV clrll ERG7_YEAST : 139- 160: tahpv DGGWGlhsvDkStvfgTvlNyV ilrll SQHC_ALIAC : 525- 546: qhqnp DGGWGedcrSyEdpayAgkGaS tpsqt SQHC_ZYMMO : 548- 569: tiqne DGGWGencdSyAldysGyePmD stasq O 15: 32.3605 5( 5) Y-x(2)-Y-x(3)-F-P-x(2)-A-L-[AG]-x-Y Occurences: 5(5) CAS1_ARATH : 734- 749: ncmit YaaYrniFPiwALGeY rcqvl ERG7_CANAL : 703- 718: scaie YpsYrflFPikALGlY knkyg ERG7_YEAST : 706- 721: scaie YpsYrflFPikALGmY sraye SQHC_ALIAC : 604- 619: dfylg YtmYrhvFPtlALGrY kqaie SQHC_ZYMMO : 628- 643: vfylr YhgYskyFPlwALArY rnlkk P 16: 32.0550 5( 5) D-[FWY]-x(4)-Q-x(2)-D-G-x-W-x-[EG]-[DRS]-x(2)-[GSV] Occurences: 5(5) CAS1_ARATH : 102- 120: lkrgl DFystiQahDGhWpGDygG pmfll ERG7_CANAL : 616- 634: vkkgc DFliskQlpDGgWsESmkG ceths ERG7_YEAST : 619- 637: vrkgc DFlvskQmkDGgWgESmkS selhs SQHC_ALIAC : 516- 534: iqkal DWveqhQnpDGgWgEDcrS yedpa SQHC_ZYMMO : 491- 509: mkaav DYllkeQeeDGsWfGRwgV nyiyg Q 17: 30.5439 5( 5) L-x-[ENST]-[HKR]-Q-x(2)-D-G-x-W-[GSV]-x(4)-[AGPS] Occurences: 5(5) CAS1_ARATH : 154- 170: emrry LyNHQneDGgWGlhieG pstmf ERG7_CANAL : 618- 634: kgcdf LiSKQlpDGgWSesmkG ceths ERG7_YEAST : 621- 637: kgcdf LvSKQmkDGgWGesmkS selhs SQHC_ALIAC : 245- 261: raldw LlERQagDGsWGgiqpP wfyal SQHC_ZYMMO : 29- 45: katra LlEKQqqDGhWVfeleA datip R 18: 30.4096 5( 5) Y-x(2)-Y-[RS]-x(2)-F-P-x(1,3)-L-[AG]-x-Y Occurences: 5(5) CAS1_ARATH : 734- 749: ncmit YaaYRniFPiwaLGeY rcqvl ERG7_CANAL : 703- 718: scaie YpsYRflFPikaLGlY knkyg ERG7_YEAST : 706- 721: scaie YpsYRflFPikaLGmY sraye SQHC_ALIAC : 604- 619: dfylg YtmYRhvFPtlaLGrY kqaie SQHC_ZYMMO : 628- 643: vfylr YhgYSkyFPlwaLArY rnlkk S 19: 28.1904 5( 5) Y-x(3)-F-P-x(2)-A-L-[AG]-x-Y Occurences: 5(5) CAS1_ARATH : 737- 749: ityaa YrniFPiwALGeY rcqvl ERG7_CANAL : 706- 718: ieyps YrflFPikALGlY knkyg ERG7_YEAST : 709- 721: ieyps YrflFPikALGmY sraye SQHC_ALIAC : 607- 619: lgytm YrhvFPtlALGrY kqaie SQHC_ZYMMO : 631- 643: lryhg YskyFPlwALArY rnlkk T 20: 27.6904 5( 5) Y-x(2,3)-F-P-x(2)-A-L-[AG]-x-Y Occurences: 5(5) CAS1_ARATH : 737- 749: ityaa YrniFPiwALGeY rcqvl ERG7_CANAL : 706- 718: ieyps YrflFPikALGlY knkyg ERG7_YEAST : 709- 721: ieyps YrflFPikALGmY sraye SQHC_ALIAC : 607- 619: lgytm YrhvFPtlALGrY kqaie SQHC_ZYMMO : 631- 643: lryhg YskyFPlwALArY rnlkk Number of patterns evaluated by Pratt:34487 Total running time: 23 seconds