------------------------------------------------------------ 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 YCR59C_YIGZ 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 YCR59C_YIGZ.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: YCU9_YEAST 258 YIGZ_ECOLI 205 YIGZ_HAEIN 206 YPOL_THEFL 179 YVYE_BACSU 171 Pratt run started at Thu Feb 6 21:36:07 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.5203 7( 5) V-V-x(0,1)-R-x(2)-G-G-x(3)-G 2: 24.5203 6( 5) V-x(0,1)-V-x-R-x(2)-G-G-x(3)-G 3: 20.8503 5( 5) V-x-R-x(2)-G-G-x(3)-G 4: 19.8503 5( 5) D-D-G-E-x(2,4)-G 5: 19.3503 5( 5) G-x(3)-L-x(3,4)-L-x(4)-G-x(1,3)-V 6: 16.6802 5( 5) R-x(2)-G-G-x(3)-G 7: 15.6802 9( 5) G-x(2,3)-L-x(3,4)-L-x(4)-G 8: 15.6802 5( 5) E-x(4,5)-A-x(2,3)-P-x-L 9: 15.6802 5( 5) D-G-E-x(2,4)-G 10: 15.1802 5( 5) G-x(1,3)-A-x(0,1)-G-x(3)-L 11: 15.1802 5( 5) G-x(2,4)-G-x(3)-L-x(1,2)-L 12: 12.5102 5( 5) G-G-x(3)-G 13: 12.5102 6( 5) E-x(4)-A-x(4)-L 14: 12.5102 5( 5) A-x-H-x(3)-A 15: 12.5102 5( 5) I-x(3)-R-F 16: 12.0102 9( 5) V-V-x(0,1)-R 17: 12.0102 7( 5) V-x(0,1)-V-x-R 18: 12.0102 6( 5) G-V-x(3,4)-L 19: 12.0102 7( 5) G-x(0,1)-V-x(3)-L 20: 12.0102 6( 5) G-x(3)-A-x(0,1)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 94.5197 5( 5) G-x(1,3)-A-x(0,1)-G-x(2)-[IM]-L-x(2)-[IL]-x(4)-[LV]-x-[DENR]-x(2)-[AV]-[LV]-V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ] B 2: 72.7110 6( 5) V-x(0,1)-V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] C 3: 70.1044 7( 5) V-V-x(0,1)-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] D 4: 69.0409 5( 5) V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] E 5: 62.2643 5( 5) R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] F 6: 51.5658 5( 5) G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] G 7: 36.1258 5( 5) G-[GS]-[IV]-x-L-x(3,4)-L-x-[EKR]-[AL]-x-G-x(1,3)-V-[AENQS]-x-[AEG] H 8: 27.3060 9( 5) G-x(2,3)-L-x(3,4)-L-x-[EKR]-[AL]-x-G-x(4)-[EQ]-[AGP] I 9: 23.1777 5( 5) I-x(2)-[DS]-R-F-x(4)-[AQS]-x-[ATV]-x-[EGST] J 10: 22.8984 5( 5) G-x(3)-A-x(0,1)-G-x(2)-[IMV]-x(2)-[AGL]-[IL]-x(3)-[DEGT] K 11: 19.8503 5( 5) D-D-G-E-x(2,4)-G L 12: 18.4155 1( 1) G-[GS]-[IV]-x-L-x(3,4)-L M 13: 15.8020 5( 5) A-x-H-x(3)-A-x(2)-[AI] N 14: 15.6802 5( 5) E-x(4,5)-A-x(2,3)-P-x-L O 15: 15.6802 5( 5) D-G-E-x(2,4)-G P 16: 15.1802 5( 5) G-x(2,4)-G-x(3)-L-x(1,2)-L Q 17: 14.7256 6( 5) E-x(4)-A-x(2)-[ADPS]-x-L R 18: 12.5102 5( 5) I-x(3)-R-F S 19: 12.0102 7( 5) V-V-x(0,1)-R T 20: 12.0102 7( 5) V-x(0,1)-V-x-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 94.5197 5( 5) G-x(1,3)-A-x(0,1)-G-x(2)-[IM]-L-x(2)-[IL]-x(4)-[LV]-x-[DENR]-x(2)-[AV]-[LV]-V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ] Occurences: 5(5) YCU9_YEAST : 202- 250: dsddd GetaA-GsrMLhlItimdVwNviVVVARWFGGAhIGPDrFkHInStArEA vvrag YCU9_YEAST : 202- 250: dsddd Get-AaGsrMLhlItimdVwNviVVVARWFGGAhIGPDrFkHInStArEA vvrag YIGZ_ECOLI : 78- 124: dgepa Gt--A-GkpMLaqLmgsgVgEitAVVVRYYGGIlLGTGgLvKAyGgGvNQ alrql YIGZ_HAEIN : 77- 123: dgepa Gt--A-GkpMLsaLqgsqLgEisAVVVRYYGGIlLGTGgLvRAyGnGvQQ alkli YPOL_THEFL : 51- 100: rfsdd GeprApGrpILhaIeaagLdRvvVLVVRYFGGVkLGAGgLvRAyGgVaAE alrra YVYE_BACSU : 76- 122: dgeps Gt--A-GvpMLevLkkrrLkDtcAVVTRYFGGIkLGAGgLiRAyGkSvSE glnhi B 2: 72.7110 6( 5) V-x(0,1)-V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] Occurences: 6(5) YCU9_YEAST : 224- 255: vwnvi VvVARWFGGAhIGPDrFkHInStArEAVVraG fds YCU9_YEAST : 225- 255: wnviv V-VARWFGGAhIGPDrFkHInStArEAVVraG fds YIGZ_ECOLI : 99- 129: geita V-VVRYYGGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_HAEIN : 98- 128: geisa V-VVRYYGGIlLGTGgLvRAyGnGvQQALklI eseik YPOL_THEFL : 74- 105: ldrvv VlVVRYFGGVkLGAGgLvRAyGgVaAEALrrA pkapl YVYE_BACSU : 97- 127: kdtca V-VTRYFGGIkLGAGgLiRAyGkSvSEGLnhI gvver C 3: 70.1044 7( 5) V-V-x(0,1)-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] Occurences: 7(5) YCU9_YEAST : 225- 255: wnviv VVaRWFGGAhIGPDrFkHInStArEAVVraG fds YIGZ_ECOLI : 99- 129: geita VVvRYYGGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_ECOLI : 100- 129: eitav VV-RYYGGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_HAEIN : 98- 128: geisa VVvRYYGGIlLGTGgLvRAyGnGvQQALklI eseik YIGZ_HAEIN : 99- 128: eisav VV-RYYGGIlLGTGgLvRAyGnGvQQALklI eseik YPOL_THEFL : 76- 105: rvvvl VV-RYFGGVkLGAGgLvRAyGgVaAEALrrA pkapl YVYE_BACSU : 97- 127: kdtca VVtRYFGGIkLGAGgLiRAyGkSvSEGLnhI gvver D 4: 69.0409 5( 5) V-[ATV]-R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] Occurences: 5(5) YCU9_YEAST : 226- 255: nvivv VARWFGGAhIGPDrFkHInStArEAVVraG fds YIGZ_ECOLI : 100- 129: eitav VVRYYGGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_HAEIN : 99- 128: eisav VVRYYGGIlLGTGgLvRAyGnGvQQALklI eseik YPOL_THEFL : 76- 105: rvvvl VVRYFGGVkLGAGgLvRAyGgVaAEALrrA pkapl YVYE_BACSU : 98- 127: dtcav VTRYFGGIkLGAGgLiRAyGkSvSEGLnhI gvver E 5: 62.2643 5( 5) R-[WY]-[FY]-G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] Occurences: 5(5) YCU9_YEAST : 228- 255: ivvva RWFGGAhIGPDrFkHInStArEAVVraG fds YIGZ_ECOLI : 102- 129: tavvv RYYGGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_HAEIN : 101- 128: savvv RYYGGIlLGTGgLvRAyGnGvQQALklI eseik YPOL_THEFL : 78- 105: vvlvv RYFGGVkLGAGgLvRAyGgVaAEALrrA pkapl YVYE_BACSU : 100- 127: cavvt RYFGGIkLGAGgLiRAyGkSvSEGLnhI gvver F 6: 51.5658 5( 5) G-G-[AIV]-x-[IL]-G-[APT]-[DG]-x-[FL]-x-[HKR]-[AI]-x-[GS]-x-[AGSV]-x-[AENQS]-[AEQ]-[AGV]-[LV]-x(2)-[AGIL] Occurences: 5(5) YCU9_YEAST : 231- 255: varwf GGAhIGPDrFkHInStArEAVVraG fds YIGZ_ECOLI : 105- 129: vvryy GGIlLGTGgLvKAyGgGvNQALrqL ttqrk YIGZ_HAEIN : 104- 128: vvryy GGIlLGTGgLvRAyGnGvQQALklI eseik YPOL_THEFL : 81- 105: vvryf GGVkLGAGgLvRAyGgVaAEALrrA pkapl YVYE_BACSU : 103- 127: vtryf GGIkLGAGgLiRAyGkSvSEGLnhI gvver G 7: 36.1258 5( 5) G-[GS]-[IV]-x-L-x(3,4)-L-x-[EKR]-[AL]-x-G-x(1,3)-V-[AENQS]-x-[AEG] Occurences: 5(5) YCU9_YEAST : 96- 116: svfhr GSVcLfdf-LtELdGvlyVEpE eetep YIGZ_ECOLI : 105- 125: vvryy GGIlLgtggLvKAyGgg-VNqA lrqlt YIGZ_HAEIN : 104- 124: vvryy GGIlLgtggLvRAyGng-VQqA lklie YPOL_THEFL : 81- 100: vvryf GGVkLgaggLvRAyGg--VAaE alrra YVYE_BACSU : 103- 123: vtryf GGIkLgaggLiRAyGks-VSeG lnhig H 8: 27.3060 9( 5) G-x(2,3)-L-x(3,4)-L-x-[EKR]-[AL]-x-G-x(4)-[EQ]-[AGP] Occurences: 9(5) YCU9_YEAST : 96- 115: svfhr GsvcLfdf-LtELdGvlyvEP eeete YIGZ_ECOLI : 105- 125: vvryy GgilLgtggLvKAyGggvnQA lrqlt YIGZ_ECOLI : 106- 125: vryyg Gil-LgtggLvKAyGggvnQA lrqlt YIGZ_HAEIN : 104- 124: vvryy GgilLgtggLvRAyGngvqQA lklie YIGZ_HAEIN : 105- 124: vryyg Gil-LgtggLvRAyGngvqQA lklie YPOL_THEFL : 81- 101: vvryf GgvkLgaggLvRAyGgvaaEA lrrap YPOL_THEFL : 82- 101: vryfg Gvk-LgaggLvRAyGgvaaEA lrrap YVYE_BACSU : 103- 123: vtryf GgikLgaggLiRAyGksvsEG lnhig YVYE_BACSU : 104- 123: tryfg Gik-LgaggLiRAyGksvsEG lnhig I 9: 23.1777 5( 5) I-x(2)-[DS]-R-F-x(4)-[AQS]-x-[ATV]-x-[EGST] Occurences: 5(5) YCU9_YEAST : 235- 249: fggah IgpDRFkhinStArE avvra YIGZ_ECOLI : 18- 32: tvvee IkkSRFitmlAhTdG veaak YIGZ_HAEIN : 17- 31: vfeee IkkSRFitylQhTeG ledar YPOL_THEFL : 2- 16: i IqrSRFlakaApAaS eeeal YVYE_BACSU : 18- 32: eheiv IekSRFichlSrVsT eqeaq J 10: 22.8984 5( 5) G-x(3)-A-x(0,1)-G-x(2)-[IMV]-x(2)-[AGL]-[IL]-x(3)-[DEGT] Occurences: 5(5) YCU9_YEAST : 202- 218: dsddd GetaA-GsrMlhLItimD vwnvi YIGZ_ECOLI : 113- 130: llgtg GlvkAyGggVnqALrqlT tqrkt YIGZ_HAEIN : 112- 129: llgtg GlvrAyGngVqqALkliE seikv YPOL_THEFL : 51- 68: rfsdd GeprApGrpIlhAIeaaG ldrvv YVYE_BACSU : 111- 128: klgag GlirAyGksVseGLnhiG vverk K 11: 19.8503 5( 5) D-D-G-E-x(2,4)-G Occurences: 5(5) YCU9_YEAST : 200- 207: yqdsd DDGEtaa-G srmlh YIGZ_ECOLI : 72- 78: qlgfs DDGEpa--G tagkp YIGZ_HAEIN : 71- 77: qlgfs DDGEpa--G tagkp YPOL_THEFL : 49- 57: lyrfs DDGEprapG rpilh YVYE_BACSU : 70- 76: iqkan DDGEps--G tagvp L 12: 18.4155 1( 1) G-[GS]-[IV]-x-L-x(3,4)-L Occurences: 1(1) YPOL_THEFL : 81- 90: vvryf GGVkLgaggL vrayg M 13: 15.8020 5( 5) A-x-H-x(3)-A-x(2)-[AI] Occurences: 5(5) YCU9_YEAST : 177- 186: skmrk AnHvmsAwrI kqdgs YIGZ_ECOLI : 50- 59: aehpd ArHhcvAwvA gapdd YIGZ_HAEIN : 49- 58: qehpn ArHhcwAavA gkptd YPOL_THEFL : 32- 41: hrepq AtHnayAyrI gplyr YVYE_BACSU : 50- 59: kqhwn AtHncsAyvI gendh N 14: 15.6802 5( 5) E-x(4,5)-A-x(2,3)-P-x-L Occurences: 5(5) YCU9_YEAST : 11- 22: eqlve EleaveAiy-PdL lskkq YIGZ_ECOLI : 75- 85: fsddg Epagt-Agk-PmL aqlmg YIGZ_HAEIN : 74- 84: fsddg Epagt-Agk-PmL salqg YPOL_THEFL : 100- 111: ggvaa Ealrr-ApkaPlL dwvev YVYE_BACSU : 73- 83: anddg Epsgt-Agv-PmL evlkk O 15: 15.6802 5( 5) D-G-E-x(2,4)-G Occurences: 5(5) YCU9_YEAST : 201- 207: qdsdd DGEtaa-G srmlh YIGZ_ECOLI : 73- 78: lgfsd DGEpa--G tagkp YIGZ_HAEIN : 72- 77: lgfsd DGEpa--G tagkp YPOL_THEFL : 50- 57: yrfsd DGEprapG rpilh YVYE_BACSU : 71- 76: qkand DGEps--G tagvp P 16: 15.1802 5( 5) G-x(2,4)-G-x(3)-L-x(1,2)-L Occurences: 5(5) YCU9_YEAST : 202- 213: dsddd GetaaGsrmLh-L itimd YIGZ_ECOLI : 78- 88: dgepa Gta--GkpmLaqL mgsgv YIGZ_HAEIN : 77- 87: dgepa Gta--GkpmLsaL qgsql YPOL_THEFL : 157- 167: lrlpp Gge--GgpcLkaL sdltr YVYE_BACSU : 76- 86: dgeps Gta--GvpmLevL kkrrl Q 17: 14.7256 6( 5) E-x(4)-A-x(2)-[ADPS]-x-L Occurences: 6(5) YCU9_YEAST : 158- 168: ahvts EeqafAmlDlL ktdsk YIGZ_ECOLI : 75- 85: fsddg EpagtAgkPmL aqlmg YIGZ_HAEIN : 74- 84: fsddg EpagtAgkPmL salqg YIGZ_HAEIN : 179- 189: ilgis EktieAfsSeL tekss YPOL_THEFL : 100- 110: ggvaa EalrrApkApL ldwve YVYE_BACSU : 73- 83: anddg EpsgtAgvPmL evlkk R 18: 12.5102 5( 5) I-x(3)-R-F Occurences: 5(5) YCU9_YEAST : 235- 240: fggah IgpdRF khins YIGZ_ECOLI : 18- 23: tvvee IkksRF itmla YIGZ_HAEIN : 17- 22: vfeee IkksRF itylq YPOL_THEFL : 2- 7: i IqrsRF lakaa YVYE_BACSU : 18- 23: eheiv IeksRF ichls S 19: 12.0102 7( 5) V-V-x(0,1)-R Occurences: 7(5) YCU9_YEAST : 225- 228: wnviv VVaR wfgga YIGZ_ECOLI : 99- 102: geita VVvR yyggi YIGZ_ECOLI : 100- 102: eitav VV-R yyggi YIGZ_HAEIN : 98- 101: geisa VVvR yyggi YIGZ_HAEIN : 99- 101: eisav VV-R yyggi YPOL_THEFL : 76- 78: rvvvl VV-R yfggv YVYE_BACSU : 97- 100: kdtca VVtR yfggi T 20: 12.0102 7( 5) V-x(0,1)-V-x-R Occurences: 7(5) YCU9_YEAST : 224- 228: vwnvi VvVaR wfgga YCU9_YEAST : 225- 228: wnviv V-VaR wfgga YIGZ_ECOLI : 99- 102: geita V-VvR yyggi YIGZ_HAEIN : 98- 101: geisa V-VvR yyggi YPOL_THEFL : 74- 78: ldrvv VlVvR yfggv YVYE_BACSU : 97- 100: kdtca V-VtR yfggi YVYE_BACSU : 129- 132: lnhig V-VeR klmri Number of patterns evaluated by Pratt:1533 Total running time: 0 seconds