------------------------------------------------------------ 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 6 sequences from file PECTINESTERASE_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 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 PECTINESTERASE_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PME1_LYCES 317 PME2_LYCES 389 PME_ASPTU 331 PME_BRANA 584 PME_BURSO 396 PME_ERWCH 366 Pratt run started at Thu Feb 6 20:31:04 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.1904 6( 6) G-x(2)-D-F-I-F-G-x(1,3)-A 2: 24.0203 6( 6) D-F-I-F-G-x(1,3)-A 3: 19.8503 6( 6) F-I-F-G-x(1,3)-A 4: 16.6802 6( 6) L-G-R-x-W 5: 16.6802 6( 6) Q-D-T-L 6: 16.6802 6( 6) I-x(4)-G-x-Y-x-E 7: 16.1802 8( 6) A-x-A-x(1,2)-V-x(2)-D 8: 15.6802 6( 6) G-x-G-x(0,1)-A-x(3,4)-R 9: 15.6802 6( 6) I-F-G-x(1,3)-A 10: 15.6802 6( 6) T-x(1,2)-F-I-x(1,2)-G 11: 15.6802 6( 6) G-T-x(1,3)-I-x-G 12: 15.6802 7( 6) A-x(3,4)-A-x-A-x(2,3)-G 13: 15.6802 8( 6) A-x(2)-A-x(0,1)-A-x(4,5)-T 14: 15.6802 7( 6) I-x(2,3)-K-x-G-x(1,2)-Y 15: 15.6802 6( 6) A-x(3)-A-x(3,4)-S-x(0,1)-T 16: 15.6802 9( 6) A-x(1,2)-A-x(1,2)-A-A 17: 15.1802 6( 6) E-x(2)-N-x(0,1)-G-x(0,2)-A 18: 15.1802 6( 6) G-x(2,4)-I-x(2,3)-A-x(2)-A 19: 15.1802 6( 6) T-x(0,1)-D-x-I-x(1,3)-G 20: 15.1802 8( 6) A-V-x(0,1)-A-x(3,5)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 34.3137 6( 6) I-x-[IV]-[EK]-x-G-[STV]-Y-x-E-x-[LV]-x-[IV]-[APST] B 2: 33.7992 6( 6) A-x-A-x(1,2)-V-x(2)-D-x(3)-[AIL]-x(3)-[NQRS]-x(2)-[AEG]-x-[QST]-[ADQ]-x(3)-[ALV]-x(4)-[NPQT] C 3: 30.8243 6( 6) G-[ADT]-x-D-F-I-F-G-x(1,3)-A D 4: 26.4867 6( 6) Q-D-T-L-x-[ALV]-x-[AGNST]-[GQT]-x-[NQS] E 5: 24.0203 6( 6) D-F-I-F-G-x(1,3)-A F 6: 23.9955 6( 6) L-G-R-[AP]-W-x(3)-[ASTV]-x(2)-[ACSTV] G 7: 23.8070 6( 6) T-x(1,2)-F-I-x(1,2)-G-x(2)-[ADTV]-x(2)-[FIV]-x(4)-[IL] H 8: 22.3200 6( 6) G-T-x(1,3)-I-x-G-x-[AGSV]-[ADPT]-x-[GILV] I 9: 21.5207 7( 6) I-x(2,3)-K-x-G-x(1,2)-Y-x-[ET]-x(3)-[AIV] J 10: 20.5819 6( 6) T-x(0,1)-D-[FV]-I-x(1,3)-G-x-[AGST] K 11: 20.0804 6( 6) G-[APTV]-G-x(0,1)-A-x(3,4)-R-x(3)-[APST] L 12: 19.8503 6( 6) F-I-F-G-x(1,3)-A M 13: 19.7305 6( 6) G-x(2,4)-I-x(2,3)-A-[GTV]-x-A-x(4)-[CDGNS] N 14: 18.3226 6( 6) A-x(2)-A-x(0,1)-A-x(4,5)-T-x(2)-[NQS] O 15: 17.9167 6( 6) A-x(2)-[ADNS]-A-x(3,4)-S-x(0,1)-T P 16: 17.3830 6( 6) E-x(2)-N-x(0,1)-G-x(0,2)-A-x(2)-[AGPS] Q 17: 15.6802 6( 6) I-F-G-x(1,3)-A R 18: 15.6802 7( 6) A-x(3,4)-A-x-A-x(2,3)-G S 19: 15.6802 6( 6) A-x(3)-A-x(3,4)-S-x(0,1)-T T 20: 15.6802 9( 6) A-x(1,2)-A-x(1,2)-A-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 34.3137 6( 6) I-x-[IV]-[EK]-x-G-[STV]-Y-x-E-x-[LV]-x-[IV]-[APST] Occurences: 6(6) PME1_LYCES : 35- 49: ktryv IyVKrGTYkEnVeVA snkmn PME2_LYCES : 92- 106: ktryv IyVKrGTYkEnVeVS srkmn PME_ASPTU : 57- 71: tetqt IfIEeGSYdEqVyIP alsgk PME_BRANA : 303- 317: pgrci IyIKaGVYkEqVtIP kkvnn PME_BURSO : 111- 125: varky IsVKaGTYnElVcVP esapp PME_ERWCH : 61- 75: stpfv IlIKnGVYnErLtIT rnnll B 2: 33.7992 6( 6) A-x-A-x(1,2)-V-x(2)-D-x(3)-[AIL]-x(3)-[NQRS]-x(2)-[AEG]-x-[QST]-[ADQ]-x(3)-[ALV]-x(4)-[NPQT] Occurences: 6(6) PME1_LYCES : 110- 141: pardq AvAlrVgaDmsvInrcRidAyQDtlyAhsqrQ fyrdd PME2_LYCES : 167- 198: pakhq AvAlrVgaDksvInrcRidAyQDtlyAhsqrQ fyqss PME_ASPTU : 101- 131: ithai AlAd-VdnDdetAtlrNyaEgSAiynLnianT cgqac PME_BRANA : 380- 411: plghq AvAfrVngDravIfncRfdGyQDtlyVnngrQ fyrni PME_BURSO : 210- 241: dnnqs AvAlaVrgDkaiLenvSviGnQDtlyLgatnN tmvir PME_ERWCH : 333- 363: yksyg AgAa-VskDrrqLtdaQaaEyTQskvLgdwtP tlp C 3: 30.8243 6( 6) G-[ADT]-x-D-F-I-F-G-x(1,3)-A Occurences: 6(6) PME1_LYCES : 150- 159: ddyvt GTvDFIFGg--A avvfq PME1_LYCES : 150- 160: ddyvt GTvDFIFGga-A vvfqk PME2_LYCES : 207- 216: ssyvt GTiDFIFGn--A avvfq PME2_LYCES : 207- 217: ssyvt GTiDFIFGna-A vvfqk PME_ASPTU : 179- 189: gtyie GAvDFIFGqh-A rawfh PME_BRANA : 420- 430: nivvs GTvDFIFGks-A tviqn PME_BURSO : 256- 267: nsfiq GDtDFIFGagtA vfhgc PME_ERWCH : 196- 207: dcris GTvDFIFGdgtA lfnnc D 4: 26.4867 6( 6) Q-D-T-L-x-[ALV]-x-[AGNST]-[GQT]-x-[NQS] Occurences: 6(6) PME1_LYCES : 131- 141: riday QDTLyAhSQrQ fyrdd PME2_LYCES : 188- 198: riday QDTLyAhSQrQ fyqss PME_ASPTU : 160- 170: qftgy QDTLlAeTGyQ vyagt PME_BRANA : 401- 411: rfdgy QDTLyVnNGrQ fyrni PME_BURSO : 231- 241: svign QDTLyLgATnN tmvir PME_ERWCH : 177- 187: slvgy QDTLyVsGGrS ffsdc E 5: 24.0203 6( 6) D-F-I-F-G-x(1,3)-A Occurences: 6(6) PME1_LYCES : 153- 159: vtgtv DFIFGg--A avvfq PME1_LYCES : 153- 160: vtgtv DFIFGga-A vvfqk PME2_LYCES : 210- 216: vtgti DFIFGn--A avvfq PME2_LYCES : 210- 217: vtgti DFIFGna-A vvfqk PME_ASPTU : 182- 189: iegav DFIFGqh-A rawfh PME_BRANA : 423- 430: vsgtv DFIFGks-A tviqn PME_BURSO : 259- 267: iqgdt DFIFGagtA vfhgc PME_ERWCH : 199- 207: isgtv DFIFGdgtA lfnnc F 6: 23.9955 6( 6) L-G-R-[AP]-W-x(3)-[ASTV]-x(2)-[ACSTV] Occurences: 6(6) PME1_LYCES : 219- 230: efpty LGRPWkeySrtV vmesy PME2_LYCES : 276- 287: efpty LGRPWkkySrtV vmess PME_ASPTU : 245- 256: sgtyy LGRPWsqyArvC fqkts PME_BRANA : 490- 501: tvksy LGRPWkpfAttA vigte PME_BURSO : 322- 333: nnsth LGRAWdqgVsgT sayin PME_ERWCH : 265- 276: aksyg LGRPWhptTtfS dgrya G 7: 23.8070 6( 6) T-x(1,2)-F-I-x(1,2)-G-x(2)-[ADTV]-x(2)-[FIV]-x(4)-[IL] Occurences: 6(6) PME1_LYCES : 151- 168: dyvtg TvdFIf-GgaAvvFqkcqL varkp PME2_LYCES : 208- 225: syvtg TidFIf-GnaAvvFqkcqL varkp PME_ASPTU : 56- 73: stetq Ti-FIeeGsyDeqVyipaL sgkli PME_BRANA : 421- 438: ivvsg TvdFIf-GksAtvIqnslI lcrkg PME_BURSO : 258- 274: fiqgd Td-FIf-GagTavFhgctI qytaa PME_ERWCH : 197- 214: crisg TvdFIf-GdgTalFnncdL vsryr H 8: 22.3200 6( 6) G-T-x(1,3)-I-x-G-x-[AGSV]-[ADPT]-x-[GILV] Occurences: 6(6) PME1_LYCES : 150- 162: ddyvt GTvdfIfGgAAvV fqkcq PME2_LYCES : 207- 219: ssyvt GTidfIfGnAAvV fqkcq PME_ASPTU : 174- 184: yqvya GTy--IeGaVDfI fgqha PME_BRANA : 420- 432: nivvs GTvdfIfGkSAtV iqnsl PME_BURSO : 332- 344: dqgvs GTsayInGsSPnG qvvir PME_ERWCH : 196- 208: dcris GTvdfIfGdGTaL fnncd I 9: 21.5207 7( 6) I-x(2,3)-K-x-G-x(1,2)-Y-x-[ET]-x(3)-[AIV] Occurences: 7(6) PME1_LYCES : 35- 48: ktryv Iyv-KrGt-YkEnveV asnkm PME2_LYCES : 92- 105: ktryv Iyv-KrGt-YkEnveV ssrkm PME_ASPTU : 28- 43: apsga IvvaKsGgdYdTisaA vdals PME_BRANA : 302- 316: npgrc IiyiKaGv-YkEqvtI pkkvn PME_BRANA : 303- 316: pgrci Iyi-KaGv-YkEqvtI pkkvn PME_BURSO : 111- 124: varky Isv-KaGt-YnElvcV pesap PME_ERWCH : 61- 74: stpfv Ili-KnGv-YnErltI trnnl J 10: 20.5819 6( 6) T-x(0,1)-D-[FV]-I-x(1,3)-G-x-[AGST] Occurences: 6(6) PME1_LYCES : 151- 159: dyvtg TvDFIf--GgA avvfq PME1_LYCES : 151- 160: dyvtg TvDFIfg-GaA vvfqk PME2_LYCES : 208- 216: syvtg TiDFIf--GnA avvfq PME_ASPTU : 263- 272: qktsm T-DVInhlGwT ewsts PME_BRANA : 421- 429: ivvsg TvDFIf--GkS atviq PME_BURSO : 258- 265: fiqgd T-DFIf--GaG tavfh PME_BURSO : 258- 267: fiqgd T-DFIfgaGtA vfhgc PME_ERWCH : 197- 205: crisg TvDFIf--GdG talfn PME_ERWCH : 197- 207: crisg TvDFIfgdGtA lfnnc K 11: 20.0804 6( 6) G-[APTV]-G-x(0,1)-A-x(3,4)-R-x(3)-[APST] Occurences: 6(6) PME1_LYCES : 266- 278: efmnn GPG-AgtskRvkwP gyhvi PME2_LYCES : 323- 335: efmnn GPG-AgtskRvkwP gyhvi PME_ASPTU : 293- 304: eygnt GTG-Aegp-RanfS selte PME_BRANA : 537- 549: efnnr GPG-AntaaRvpwA kmaks PME_BURSO : 69- 81: wdptg GVG-AvsgfRanyA vaadg PME_ERWCH : 332- 345: eyksy GAGaAvskdRrqlT daqaa L 12: 19.8503 6( 6) F-I-F-G-x(1,3)-A Occurences: 6(6) PME1_LYCES : 154- 159: tgtvd FIFGg--A avvfq PME1_LYCES : 154- 160: tgtvd FIFGga-A vvfqk PME2_LYCES : 211- 216: tgtid FIFGn--A avvfq PME2_LYCES : 211- 217: tgtid FIFGna-A vvfqk PME_ASPTU : 183- 189: egavd FIFGqh-A rawfh PME_BRANA : 424- 430: sgtvd FIFGks-A tviqn PME_BURSO : 260- 267: qgdtd FIFGagtA vfhgc PME_ERWCH : 200- 207: sgtvd FIFGdgtA lfnnc M 13: 19.7305 6( 6) G-x(2,4)-I-x(2,3)-A-[GTV]-x-A-x(4)-[CDGNS] Occurences: 6(6) PME1_LYCES : 237- 251: mesyl Ggl--Inp-AGwAewdgD falkt PME2_LYCES : 55- 70: lmess Gkd--IganAVvAkdgtG kyrtl PME_ASPTU : 35- 51: vaksg GdydtIsa-AVdAlsttS tetqt PME_BRANA : 281- 297: akdgs GqfktIse-AVkAcpekN pgrci PME_BURSO : 256- 272: nsfiq GdtdfIfg-AGtAvfhgC tiqyt PME_ERWCH : 88- 102: gesrn Gav--Iaa-ATaAgtlkS dgskw N 14: 18.3226 6( 6) A-x(2)-A-x(0,1)-A-x(4,5)-T-x(2)-[NQS] Occurences: 6(6) PME1_LYCES : 83- 95: ttfrs AtlA-Avgqg-TllQ diciq PME2_LYCES : 14- 28: elisr AkvAlAmlasvTtpN devlr PME_ASPTU : 12- 25: asvlf AatAlAasrm-TapS gaivv PME_BRANA : 552- 565: pwakm AksA-AeverfTvaN wltpa PME_BURSO : 21- 35: gcslf AatAlAatstaTrpQ lsnad PME_ERWCH : 89- 102: esrng AviAaAtaag-TlkS dgskw PME_ERWCH : 89- 102: esrng AviA-AataagTlkS dgskw O 15: 17.9167 6( 6) A-x(2)-[ADNS]-A-x(3,4)-S-x(0,1)-T Occurences: 6(6) PME1_LYCES : 21- 31: qtlae AvaAApdk-SkT ryviy PME2_LYCES : 78- 88: rtlae AvaAApdk-SkT ryviy PME_ASPTU : 42- 52: ydtis AavDAlsttS-T etqti PME_BRANA : 81- 90: kafml AtkDAvtk-S-T nftas PME_BURSO : 311- 320: nstfn AtgNAsnn-S-T hlgra PME_ERWCH : 48- 57: ktiad AiaSApag-S-T pfvil P 16: 17.3830 6( 6) E-x(2)-N-x(0,1)-G-x(0,2)-A-x(2)-[AGPS] Occurences: 6(6) PME1_LYCES : 261- 272: tlyyg EfmNnGpgAgtS krvkw PME2_LYCES : 318- 329: tlyyg EfmNnGpgAgtS krvkw PME_ASPTU : 288- 299: nvtfv EygNtGtgAegP ranfs PME_BRANA : 532- 543: tatyv EfnNrGpgAntA arvpw PME_BURSO : 386- 395: anrff EynNtG--AgsG n PME_ERWCH : 84- 92: lllkg EsrN-G--AviA aataa Q 17: 15.6802 6( 6) I-F-G-x(1,3)-A Occurences: 6(6) PME1_LYCES : 155- 159: gtvdf IFGg--A avvfq PME1_LYCES : 155- 160: gtvdf IFGga-A vvfqk PME2_LYCES : 212- 216: gtidf IFGn--A avvfq PME2_LYCES : 212- 217: gtidf IFGna-A vvfqk PME_ASPTU : 184- 189: gavdf IFGqh-A rawfh PME_BRANA : 425- 430: gtvdf IFGks-A tviqn PME_BURSO : 261- 267: gdtdf IFGagtA vfhgc PME_ERWCH : 201- 207: gtvdf IFGdgtA lfnnc R 18: 15.6802 7( 6) A-x(3,4)-A-x-A-x(2,3)-G Occurences: 7(6) PME1_LYCES : 106- 116: ntagp Ardq-AvAlrvG admsv PME2_LYCES : 163- 173: ntagp Akhq-AvAlrvG adksv PME_ASPTU : 139- 150: qachq AlavsAyAseqG yyacq PME_BRANA : 248- 258: klmaq AgrpgApAde-G igegg PME_BURSO : 95- 105: yktvq AaidaAvAdg-G varky PME_BURSO : 96- 105: ktvqa Aida-AvAdg-G varky PME_ERWCH : 46- 55: tfkti Adai-AsApa-G stpfv S 19: 15.6802 6( 6) A-x(3)-A-x(3,4)-S-x(0,1)-T Occurences: 6(6) PME1_LYCES : 21- 31: qtlae AvaaApdk-SkT ryviy PME2_LYCES : 78- 88: rtlae AvaaApdk-SkT ryviy PME_ASPTU : 42- 52: ydtis AavdAlsttS-T etqti PME_BRANA : 81- 90: kafml AtkdAvtk-S-T nftas PME_BURSO : 311- 320: nstfn AtgnAsnn-S-T hlgra PME_ERWCH : 48- 57: ktiad AiasApag-S-T pfvil T 20: 15.6802 9( 6) A-x(1,2)-A-x(1,2)-A-A Occurences: 9(6) PME1_LYCES : 19- 24: dyqtl Ae-Av-AA apdks PME1_LYCES : 19- 25: dyqtl Ae-AvaAA pdksk PME2_LYCES : 76- 81: kyrtl Ae-Av-AA apdks PME2_LYCES : 76- 82: kyrtl Ae-AvaAA pdksk PME_ASPTU : 12- 18: asvlf AatAl-AA srmta PME_ASPTU : 13- 18: svlfa At-Al-AA srmta PME_BRANA : 549- 556: arvpw AkmAksAA everf PME_BURSO : 21- 27: gcslf AatAl-AA tstat PME_BURSO : 22- 27: cslfa At-Al-AA tstat PME_BURSO : 78- 84: vsgfr AnyAv-AA dgsaq PME_ERWCH : 92- 97: ngavi Aa-At-AA gtlks Number of patterns evaluated by Pratt:8714 Total running time: 4 seconds