------------------------------------------------------------ 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 CAP_GLY 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 CAP_GLY.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: BIK1_YEAST 440 DY15_DROME 1319 DYNA_RAT 1325 REST_HUMAN 1427 YM94_CAEEL 124 Pratt run started at Thu Feb 6 19:04:14 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 37.5305 6( 5) G-x(3)-G-x(2)-L-x(4)-G-K-x(2)-G-x(3)-G-x(2)-Y-F 2: 33.3604 6( 5) G-x(2)-L-x(4)-G-K-x(2)-G-x(3)-G-x(2)-Y-F 3: 32.8604 6( 5) G-x(1,2)-L-x(4)-G-K-x(2)-G-x(3)-G-x(2)-Y-F 4: 29.1904 6( 5) L-x(4)-G-K-x(2)-G-x(3)-G-x(2)-Y-F 5: 28.6904 8( 5) L-x(3,4)-G-K-x(2)-G-x(3)-G-x(2)-Y-F 6: 25.0203 6( 5) G-K-x(2)-G-x(3)-G-x(2)-Y-F 7: 20.8503 6( 5) K-x(2)-G-x(3)-G-x(2)-Y-F 8: 19.3503 5( 5) S-L-x(0,2)-K-x(0,1)-L-x(2)-A 9: 16.6802 6( 5) G-x(3)-G-x(2)-Y-F 10: 16.1802 6( 5) G-x(2,3)-G-x(2)-Y-F 11: 16.1802 7( 5) G-K-x(1,2)-G-x(3)-G 12: 15.6802 6( 5) L-x(0,1)-K-x(0,1)-L-x(2)-A 13: 15.6802 7( 5) L-x(4,5)-A-x(5)-S-x(0,1)-L 14: 15.6802 7( 5) S-x(3,4)-K-x(0,1)-L-x(3)-N 15: 15.6802 5( 5) D-x(2,3)-E-L-x(1,2)-K 16: 15.6802 5( 5) D-x(2,3)-E-x(0,1)-L-x-K 17: 15.6802 6( 5) L-x(1,2)-E-x-L-x(1,2)-K 18: 15.6802 5( 5) L-x-E-x(2,4)-K-x(5)-Q 19: 15.6802 7( 5) I-x(0,1)-E-L-x(0,1)-E 20: 15.6802 10( 5) L-x(3,4)-G-x(3)-G-x(2,3)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 73.4895 5( 5) G-x-[FW]-[ACV]-G-[IV]-x-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] B 2: 59.9814 5( 5) G-x(2)-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] C 3: 59.4814 5( 5) G-x(1,2)-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] D 4: 55.8114 5( 5) L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] E 5: 49.4221 7( 5) L-x(3,4)-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] F 6: 45.7520 5( 5) G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] G 7: 43.1131 7( 5) L-x(3,4)-G-K-x-[DS]-G-x(2,3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] H 8: 42.0544 5( 5) G-K-x(1,2)-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] I 9: 41.5820 5( 5) K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] J 10: 28.4053 5( 5) G-x(3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] K 11: 27.9053 5( 5) G-x(2,3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] L 12: 22.3559 5( 5) D-x(2,3)-E-x(0,1)-L-x-K-[ADPST]-x(4)-[EPT]-x-[DENS] M 13: 21.1680 7( 5) S-x(3,4)-K-x(0,1)-L-x(2)-[AQ]-N-x(4)-[DEQS] N 14: 19.3503 5( 5) S-L-x(0,2)-K-x(0,1)-L-x(2)-A O 15: 18.2750 5( 5) L-x(1,2)-E-x-L-x(1,2)-K-[DPQ] P 16: 18.2655 5( 5) L-x-E-x(2,4)-K-x(5)-Q-[AGL] Q 17: 15.6802 6( 5) L-x(0,1)-K-x(0,1)-L-x(2)-A R 18: 15.6802 7( 5) L-x(4,5)-A-x(5)-S-x(0,1)-L S 19: 15.6802 5( 5) D-x(2,3)-E-L-x(1,2)-K T 20: 15.6802 5( 5) D-x(2,3)-E-x(0,1)-L-x-K Best patterns with alignements: fitness hits(seqs) Pattern A 1: 73.4895 5( 5) G-x-[FW]-[ACV]-G-[IV]-x-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 33- 66: vdtka GmFAGVdLlANiGKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 63- 96: dqlrv GkWVGVvLdEPkGKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 54- 87: tlfat GkWVGViLdEAkGKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 85- 118: tqfap GqWAGIvLdEPiGKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 46- 79: ihgkd GmFCGIeLlEPnGKhDGTFqGvsYFiATpyhGiF apifr B 2: 59.9814 5( 5) G-x(2)-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 37- 66: agmfa GvdLlANiGKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 67- 96: vgkwv GvvLdEPkGKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 58- 87: tgkwv GviLdEAkGKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 89- 118: pgqwa GivLdEPiGKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 50- 79: dgmfc GieLlEPnGKhDGTFqGvsYFiATpyhGiF apifr C 3: 59.4814 5( 5) G-x(1,2)-L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 37- 66: agmfa GvdLlANiGKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 67- 96: vgkwv GvvLdEPkGKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 58- 87: tgkwv GviLdEAkGKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 89- 118: pgqwa GivLdEPiGKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 50- 79: dgmfc GieLlEPnGKhDGTFqGvsYFiATpyhGiF apifr D 4: 55.8114 5( 5) L-x-[AE]-[ANP]-x-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 40- 66: fagvd LlANiGKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 70- 96: wvgvv LdEPkGKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 61- 87: wvgvi LdEAkGKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 92- 118: wagiv LdEPiGKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 53- 79: fcgie LlEPnGKhDGTFqGvsYFiATpyhGiF apifr E 5: 49.4221 7( 5) L-x(3,4)-G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 7(5) BIK1_YEAST : 40- 66: fagvd LlaniGKnDGSFmGkkYFqTEypqSgL fiqlq BIK1_YEAST : 41- 66: agvdl Lani-GKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 70- 96: wvgvv LdepkGKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 61- 87: wvgvi LdeakGKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 92- 118: wagiv LdepiGKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 53- 79: fcgie LlepnGKhDGTFqGvsYFiATpyhGiF apifr YM94_CAEEL : 54- 79: cgiel Lepn-GKhDGTFqGvsYFiATpyhGiF apifr F 6: 45.7520 5( 5) G-K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 45- 66: llani GKnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 75- 96: ldepk GKnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 66- 87: ldeak GKnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 97- 118: ldepi GKnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 58- 79: llepn GKhDGTFqGvsYFiATpyhGiF apifr G 7: 43.1131 7( 5) L-x(3,4)-G-K-x-[DS]-G-x(2,3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 7(5) BIK1_YEAST : 40- 66: fagvd LlaniGKnDGsfmGkkYFqTEypqSgL fiqlq BIK1_YEAST : 41- 66: agvdl Lani-GKnDGsfmGkkYFqTEypqSgL fiqlq DY15_DROME : 70- 96: wvgvv LdepkGKnSGsikGqqYFqCDencGmF vrptq DYNA_RAT : 61- 87: wvgvi LdeakGKnDGtvqGrkYFtCDeghGiF vrqsq REST_HUMAN : 92- 118: wagiv LdepiGKnDGsvaGvrYFqCEplkGiF trpsk YM94_CAEEL : 53- 79: fcgie LlepnGKhDGtfqGvsYFiATpyhGiF apifr YM94_CAEEL : 54- 79: cgiel Lepn-GKhDGtfqGvsYFiATpyhGiF apifr H 8: 42.0544 5( 5) G-K-x(1,2)-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 45- 66: llani GKndGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 75- 96: ldepk GKnsGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 66- 87: ldeak GKndGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 97- 118: ldepi GKndGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 58- 79: llepn GKhdGTFqGvsYFiATpyhGiF apifr I 9: 41.5820 5( 5) K-x-[DS]-G-[ST]-[FIV]-x-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 46- 66: lanig KnDGSFmGkkYFqTEypqSgL fiqlq DY15_DROME : 76- 96: depkg KnSGSIkGqqYFqCDencGmF vrptq DYNA_RAT : 67- 87: deakg KnDGTVqGrkYFtCDeghGiF vrqsq REST_HUMAN : 98- 118: depig KnDGSVaGvrYFqCEplkGiF trpsk YM94_CAEEL : 59- 79: lepng KhDGTFqGvsYFiATpyhGiF apifr J 10: 28.4053 5( 5) G-x(3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 49- 66: igknd GsfmGkkYFqTEypqSgL fiqlq DY15_DROME : 79- 96: kgkns GsikGqqYFqCDencGmF vrptq DYNA_RAT : 70- 87: kgknd GtvqGrkYFtCDeghGiF vrqsq REST_HUMAN : 101- 118: igknd GsvaGvrYFqCEplkGiF trpsk YM94_CAEEL : 62- 79: ngkhd GtfqGvsYFiATpyhGiF apifr K 11: 27.9053 5( 5) G-x(2,3)-G-x(2)-Y-F-x-[ACT]-[DET]-x(3)-[GS]-x-[FL] Occurences: 5(5) BIK1_YEAST : 49- 66: igknd GsfmGkkYFqTEypqSgL fiqlq DY15_DROME : 79- 96: kgkns GsikGqqYFqCDencGmF vrptq DYNA_RAT : 70- 87: kgknd GtvqGrkYFtCDeghGiF vrqsq REST_HUMAN : 101- 118: igknd GsvaGvrYFqCEplkGiF trpsk YM94_CAEEL : 62- 79: ngkhd GtfqGvsYFiATpyhGiF apifr L 12: 22.3559 5( 5) D-x(2,3)-E-x(0,1)-L-x-K-[ADPST]-x(4)-[EPT]-x-[DENS] Occurences: 5(5) BIK1_YEAST : 321- 335: lrnie Dqf-E-LhKTkwakErE qlkmh DY15_DROME : 757- 772: qekiv DgiiE-LlKSnqldEnS ttdni DYNA_RAT : 698- 714: hersl DfliElLhKDqldeTvN veplt REST_HUMAN : 902- 918: kfrek DereEqLiKAkeklEnD iaeim YM94_CAEEL : 88- 102: frvtl Dae-E-LpKPpppnPsN vslkl M 13: 21.1680 7( 5) S-x(3,4)-K-x(0,1)-L-x(2)-[AQ]-N-x(4)-[DEQS] Occurences: 7(5) BIK1_YEAST : 370- 384: seeva Sltk-K-LeeANekikQ leqaq DY15_DROME : 167- 183: tasss SigprKsLapQNskdkE spsts DY15_DROME : 408- 424: dspgl StyefKqLeqQNirlkE tlvrl DYNA_RAT : 354- 370: sdgaa SsyqlKqLeeQNarlkD alvrm DYNA_RAT : 355- 370: dgaas Syql-KqLeeQNarlkD alvrm REST_HUMAN : 593- 607: skene Slks-K-LehANkensD vialw YM94_CAEEL : 101- 116: pppnp SnvslK-LpvANyfnvS pllts N 14: 19.3503 5( 5) S-L-x(0,2)-K-x(0,1)-L-x(2)-A Occurences: 5(5) BIK1_YEAST : 370- 378: seeva SLtkK-LeeA nekik BIK1_YEAST : 370- 378: seeva SLt-KkLeeA nekik DY15_DROME : 312- 320: mgaqa SLq-KeLlrA kqeak DYNA_RAT : 972- 981: anvrl SLleKkLdsA akdad REST_HUMAN : 593- 601: skene SLksK-LehA nkens YM94_CAEEL : 104- 110: npsnv SL--K-LpvA nyfnv O 15: 18.2750 5( 5) L-x(1,2)-E-x-L-x(1,2)-K-[DPQ] Occurences: 5(5) BIK1_YEAST : 203- 212: lreaq LtiEkLqrKQ lhykr DY15_DROME : 313- 322: gaqas LqkElLraKQ eakda DYNA_RAT : 700- 707: rsldf Li-ElLh-KD qldet REST_HUMAN : 353- 361: sgtta Lq-EaLkeKQ qhieq YM94_CAEEL : 87- 95: ifrvt LdaEeLp-KP pppnp P 16: 18.2655 5( 5) L-x-E-x(2,4)-K-x(5)-Q-[AGL] Occurences: 5(5) BIK1_YEAST : 375- 388: sltkk LeEane-KikqleQA qaqta DY15_DROME : 251- 263: ktrfa LlEaq--KtsaelQA qladl DYNA_RAT : 61- 74: wvgvi LdEakg-KndgtvQG rkyft REST_HUMAN : 353- 367: sgtta LqEalkeKqqhieQL laerd YM94_CAEEL : 53- 66: fcgie LlEpng-KhdgtfQG vsyfi Q 17: 15.6802 6( 5) L-x(0,1)-K-x(0,1)-L-x(2)-A Occurences: 6(5) BIK1_YEAST : 371- 378: eevas LtKkLeeA nekik DY15_DROME : 313- 320: gaqas LqKeLlrA kqeak DYNA_RAT : 974- 981: vrlsl LeKkLdsA akdad REST_HUMAN : 721- 727: emedt LnK-LqeA eikvk REST_HUMAN : 952- 957: veelq L-K-LtkA nenas YM94_CAEEL : 105- 110: psnvs L-K-LpvA nyfnv R 18: 15.6802 7( 5) L-x(4,5)-A-x(5)-S-x(0,1)-L Occurences: 7(5) BIK1_YEAST : 385- 397: ekikq Leqaq-AqtaveS-L pifdp DY15_DROME : 1089- 1103: etmdh LqsdidAlesekSdL rdklk DYNA_RAT : 307- 319: iemat Ldkem-AeeraeS-L qqeve DYNA_RAT : 1091- 1105: kdspl LlqqisAmrlhiSqL qhens DYNA_RAT : 1092- 1105: dspll Lqqis-AmrlhiSqL qhens REST_HUMAN : 522- 535: elrrr LesnkpAgdvdmS-L sllqe YM94_CAEEL : 105- 118: psnvs Lklpv-AnyfnvSpL ltsfp S 19: 15.6802 5( 5) D-x(2,3)-E-L-x(1,2)-K Occurences: 5(5) BIK1_YEAST : 321- 327: lrnie Dqf-ELh-K tkwak DY15_DROME : 757- 764: qekiv DgiiELl-K snqld DYNA_RAT : 698- 706: hersl DfliELlhK dqlde REST_HUMAN : 946- 953: rlker Dve-ELqlK ltkan YM94_CAEEL : 88- 94: frvtl Dae-ELp-K ppppn T 20: 15.6802 5( 5) D-x(2,3)-E-x(0,1)-L-x-K Occurences: 5(5) BIK1_YEAST : 321- 327: lrnie Dqf-E-LhK tkwak DY15_DROME : 757- 764: qekiv DgiiE-LlK snqld DYNA_RAT : 698- 706: hersl DfliElLhK dqlde REST_HUMAN : 902- 910: kfrek DereEqLiK akekl YM94_CAEEL : 88- 94: frvtl Dae-E-LpK ppppn Number of patterns evaluated by Pratt:6586 Total running time: 6 seconds