------------------------------------------------------------ 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 MAM 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 MAM.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: A5_XENLA 928 MEPA_MOUSE 760 MEPB_RAT 668 PTPK_MOUSE 1457 PTPM_HUMAN 1452 PTPM_MOUSE 1452 Pratt run started at Thu Feb 6 20:13:21 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.8503 7( 6) G-x(2,3)-S-x(0,1)-G-G-x(3)-D 2: 19.8503 7( 6) G-x(1,2)-G-x(2,3)-G-x(5)-D-I 3: 19.8503 6( 6) R-x(4)-G-x(1,3)-G-x-P-G 4: 19.3503 7( 6) G-x(1,3)-S-x(0,1)-G-G-x(3)-D 5: 19.3503 6( 6) R-x(4)-G-x(1,3)-G-x(0,1)-P-G 6: 19.3503 6( 6) R-x(3,4)-G-x(1,3)-G-x-P-G 7: 16.1802 6( 6) G-Q-x(2)-P-x(1,2)-R 8: 16.1802 8( 6) S-x(0,1)-G-G-x(3)-D 9: 16.1802 6( 6) S-x-G-x(0,1)-G-x(5)-I 10: 16.1802 6( 6) C-x(3)-L-x(4)-G-x(2,3)-S 11: 16.1802 6( 6) F-x(3)-Q-S-x(2,3)-D 12: 16.1802 6( 6) I-x(5)-S-x(3)-S-x(1,2)-G 13: 15.6802 6( 6) I-x(2)-A-x(2,3)-S-x(4,5)-A 14: 15.6802 6( 6) G-D-x(2,3)-I-x(4,5)-E 15: 15.6802 7( 6) S-x(0,1)-G-x-G-x(1,2)-G 16: 15.6802 7( 6) S-x(1,2)-L-x(2,3)-R-x(4)-G 17: 15.6802 6( 6) T-x(1,2)-D-x(0,1)-N-x(2)-Y 18: 15.6802 8( 6) D-x(3,4)-D-x(1,2)-N-x(2)-Y 19: 15.6802 6( 6) L-x(1,3)-T-x(2)-P-x(5)-I 20: 15.6802 6( 6) G-x(2,3)-G-x(1,2)-S-x-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 34.4984 7( 6) G-x(1,2)-G-x(2,3)-G-[CG]-x(2)-[ILV]-x-D-I-x-[IL]-[ADST]-x(4)-[EP] B 2: 33.7478 7( 6) G-x(2,3)-S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] C 3: 33.2478 7( 6) G-x(1,3)-S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] D 4: 32.9324 6( 6) S-[AS]-G-x(0,1)-G-x(2)-[GILV]-[CD]-x-I-x-[IL]-[ADST]-x(3)-[CDS] E 5: 30.0777 8( 6) S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] F 6: 29.1680 6( 6) G-x(2,3)-G-x(1,2)-S-[AGP]-G-[GILP]-x(3)-[DT]-x(4)-[AE]-[CDNT] G 7: 24.1856 6( 6) R-x-[DGV]-x(2)-G-x(1,3)-G-x(0,1)-P-G-x-[AGPS] H 8: 22.4139 6( 6) S-x(1,2)-L-x(2,3)-R-x(4)-G-[CDNTV]-[EGS]-x(4)-[ANTV] I 9: 22.0531 6( 6) R-x(4)-G-x(1,3)-G-x-P-G-x-[AGPS] J 10: 21.5531 6( 6) R-x(3,4)-G-x(1,3)-G-x-P-G-x-[AGPS] K 11: 21.0235 6( 6) I-x-[AIP]-A-x(2,3)-S-x(4,5)-A-x(2)-[AIV] L 12: 20.5265 6( 6) S-x(0,1)-G-x-G-x(1,2)-G-[ACTV]-x(4)-[DNT] M 13: 19.4164 6( 6) F-x(3)-Q-S-x(2,3)-D-x-[AD] N 14: 18.8487 6( 6) C-x(3)-L-x(2)-[GIV]-x-G-x(2,3)-S O 15: 17.8127 6( 6) R-x-[DGV]-x(2)-G-x(1,3)-G-x(0,1)-P P 16: 16.1802 6( 6) G-Q-x(2)-P-x(1,2)-R Q 17: 16.1802 6( 6) I-x(5)-S-x(3)-S-x(1,2)-G R 18: 15.6802 6( 6) G-D-x(2,3)-I-x(4,5)-E S 19: 15.6802 7( 6) S-x(1,2)-L-x(2,3)-R-x(4)-G T 20: 15.6802 6( 6) T-x(1,2)-D-x(0,1)-N-x(2)-Y Best patterns with alignements: fitness hits(seqs) Pattern A 1: 34.4984 7( 6) G-x(1,2)-G-x(2,3)-G-[CG]-x(2)-[ILV]-x-D-I-x-[IL]-[ADST]-x(4)-[EP] Occurences: 7(6) A5_XENLA : 787- 807: vegtv Gk-Gsa-GGiaVdDIiIAnhisP sqcra MEPA_MOUSE : 422- 444: flgtk GdpGnssGGiyLdDItLTetpcP agvwt MEPB_RAT : 407- 429: vfegv GgpGassGGlsIdDInLSetrcP hhiwh MEPB_RAT : 408- 429: fegvg Gp-GassGGlsIdDInLSetrcP hhiwh PTPK_MOUSE : 1103- 1123: vhcsa Ga-Grt-GCyiViDImLDmaerE gvvdi PTPM_HUMAN : 1098- 1118: vhcsa Ga-Grt-GCfiViDImLDmaerE gvvdi PTPM_MOUSE : 1098- 1118: vhcsa Ga-Grt-GCfiViDImLDmaerE gvvdi B 2: 33.7478 7( 6) G-x(2,3)-S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] Occurences: 7(6) A5_XENLA : 787- 807: vegtv Gkg-SaGGiaVDDIiiAnhisP sqcra MEPA_MOUSE : 425- 444: tkgdp Gns-S-GGiyLDDItlTetpcP agvwt MEPB_RAT : 408- 429: fegvg GpgaSsGGlsIDDInlSetrcP hhiwh MEPB_RAT : 410- 429: gvggp Gas-S-GGlsIDDInlSetrcP hhiwh PTPK_MOUSE : 28- 48: lgsal Gqf-SaGGctFDDGpgAcdyhQ dlydd PTPM_HUMAN : 20- 40: lltaa GetfS-GGclFDEPysTcgysQ segdd PTPM_MOUSE : 20- 40: lltaa GetfS-GGclFDEPysTcgysQ adedd C 3: 33.2478 7( 6) G-x(1,3)-S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] Occurences: 7(6) A5_XENLA : 787- 807: vegtv Gkg-SaGGiaVDDIiiAnhisP sqcra MEPA_MOUSE : 425- 444: tkgdp Gns-S-GGiyLDDItlTetpcP agvwt MEPA_MOUSE : 425- 444: tkgdp Gn--SsGGiyLDDItlTetpcP agvwt MEPB_RAT : 408- 429: fegvg GpgaSsGGlsIDDInlSetrcP hhiwh MEPB_RAT : 410- 429: gvggp Gas-S-GGlsIDDInlSetrcP hhiwh MEPB_RAT : 410- 429: gvggp Ga--SsGGlsIDDInlSetrcP hhiwh PTPK_MOUSE : 28- 48: lgsal Gqf-SaGGctFDDGpgAcdyhQ dlydd PTPM_HUMAN : 20- 40: lltaa GetfS-GGclFDEPysTcgysQ segdd PTPM_MOUSE : 20- 40: lltaa GetfS-GGclFDEPysTcgysQ adedd D 4: 32.9324 6( 6) S-[AS]-G-x(0,1)-G-x(2)-[GILV]-[CD]-x-I-x-[IL]-[ADST]-x(3)-[CDS] Occurences: 6(6) A5_XENLA : 790- 806: tvgkg SAG-GiaVDdIiIAnhiS psqcr MEPA_MOUSE : 427- 443: gdpgn SSG-GiyLDdItLTetpC pagvw MEPB_RAT : 412- 428: ggpga SSG-GlsIDdInLSetrC phhiw PTPK_MOUSE : 1101- 1118: ivvhc SAGaGrtGCyIvIDimlD maere PTPM_HUMAN : 1096- 1113: lvvhc SAGaGrtGCfIvIDimlD maere PTPM_MOUSE : 1096- 1113: lvvhc SAGaGrtGCfIvIDimlD maere E 5: 30.0777 8( 6) S-x(0,1)-G-G-x(2)-[FILV]-D-[DE]-[GIP]-x(2)-[AST]-x(4)-[PQ] Occurences: 8(6) A5_XENLA : 790- 807: tvgkg SaGGiaVDDIiiAnhisP sqcra MEPA_MOUSE : 427- 444: gdpgn SsGGiyLDDItlTetpcP agvwt MEPA_MOUSE : 428- 444: dpgns S-GGiyLDDItlTetpcP agvwt MEPB_RAT : 412- 429: ggpga SsGGlsIDDInlSetrcP hhiwh MEPB_RAT : 413- 429: gpgas S-GGlsIDDInlSetrcP hhiwh PTPK_MOUSE : 31- 48: algqf SaGGctFDDGpgAcdyhQ dlydd PTPM_HUMAN : 24- 40: agetf S-GGclFDEPysTcgysQ segdd PTPM_MOUSE : 24- 40: agetf S-GGclFDEPysTcgysQ adedd F 6: 29.1680 6( 6) G-x(2,3)-G-x(1,2)-S-[AGP]-G-[GILP]-x(3)-[DT]-x(4)-[AE]-[CDNT] Occurences: 6(6) A5_XENLA : 784- 803: qvive Gtv-GkgSAGGiavDdiiiAN hisps MEPA_MOUSE : 422- 441: flgtk Gdp-GnsSGGIyldDitltET pcpag MEPB_RAT : 407- 426: vfegv Ggp-GasSGGLsidDinlsET rcphh PTPK_MOUSE : 24- 44: pwpll GsalGqfSAGGctfDdgpgAC dyhqd PTPM_HUMAN : 359- 378: lltrp Geg-GtgSPGPalrTrtkcAD pmrgp PTPM_MOUSE : 359- 378: lltrp Geg-GtgSPGPalrTrtkcAD pmrgp G 7: 24.1856 6( 6) R-x-[DGV]-x(2)-G-x(1,3)-G-x(0,1)-P-G-x-[AGPS] Occurences: 6(6) A5_XENLA : 207- 221: ggqtc RyDwlGiwdGfPGvG phigr MEPA_MOUSE : 414- 427: eekkf RyVflGtk-GdPGnS sggiy MEPB_RAT : 400- 412: vtekf RvVfeGvg-G-PGaS sggls MEPB_RAT : 400- 412: vtekf RvVfeGv--GgPGaS sggls PTPK_MOUSE : 366- 378: rvllt RpGegGt--GlPGpP litrt PTPM_HUMAN : 357- 369: svllt RpGegGt--GsPGpA lrtrt PTPM_MOUSE : 357- 369: svllt RpGegGt--GsPGpA lrtrt H 8: 22.4139 6( 6) S-x(1,2)-L-x(2,3)-R-x(4)-G-[CDNTV]-[EGS]-x(4)-[ANTV] Occurences: 6(6) A5_XENLA : 573- 590: erasa Sg-Lal-RlellGCEvetpT siptt MEPA_MOUSE : 586- 605: wgqai ShqLlkrRnflkGDSliifV dfkdl MEPB_RAT : 530- 547: tddng Sy-Lwd-RpskvGVEaffpN gtqfs PTPK_MOUSE : 853- 872: ataes SrlLdvpRylceGTEspyqT gqlhp PTPM_HUMAN : 352- 369: teyei Sv-Llt-RpgegGTGspgpA lrtrt PTPM_MOUSE : 352- 369: teyei Sv-Llt-RpgegGTGspgpA lrtrt I 9: 22.0531 6( 6) R-x(4)-G-x(1,3)-G-x-P-G-x-[AGPS] Occurences: 6(6) A5_XENLA : 207- 221: ggqtc RydwlGiwdGfPGvG phigr MEPA_MOUSE : 414- 427: eekkf RyvflGtk-GdPGnS sggiy MEPB_RAT : 400- 412: vtekf RvvfeGv--GgPGaS sggls PTPK_MOUSE : 366- 378: rvllt RpgegGt--GlPGpP litrt PTPM_HUMAN : 357- 369: svllt RpgegGt--GsPGpA lrtrt PTPM_MOUSE : 357- 369: svllt RpgegGt--GsPGpA lrtrt J 10: 21.5531 6( 6) R-x(3,4)-G-x(1,3)-G-x-P-G-x-[AGPS] Occurences: 6(6) A5_XENLA : 207- 221: ggqtc RydwlGiwdGfPGvG phigr MEPA_MOUSE : 414- 427: eekkf RyvflGtk-GdPGnS sggiy MEPB_RAT : 400- 412: vtekf RvvfeGv--GgPGaS sggls PTPK_MOUSE : 366- 378: rvllt RpgegGt--GlPGpP litrt PTPK_MOUSE : 366- 378: rvllt Rpge-Ggt-GlPGpP litrt PTPM_HUMAN : 357- 369: svllt RpgegGt--GsPGpA lrtrt PTPM_HUMAN : 357- 369: svllt Rpge-Ggt-GsPGpA lrtrt PTPM_MOUSE : 357- 369: svllt RpgegGt--GsPGpA lrtrt PTPM_MOUSE : 357- 369: svllt Rpge-Ggt-GsPGpA lrtrt K 11: 21.0235 6( 6) I-x-[AIP]-A-x(2,3)-S-x(4,5)-A-x(2)-[AIV] Occurences: 6(6) A5_XENLA : 799- 815: iavdd IiIAnhiSpsqcrApeI ddsan MEPA_MOUSE : 17- 32: aimlw IqPAcllSlifs-AhiA avsik MEPB_RAT : 608- 622: pprls ImPAlr-Snvrt-AasA lskka PTPK_MOUSE : 1248- 1263: essny InAAlmdSyrqp-AafI vtqyp PTPK_MOUSE : 1248- 1264: essny InAAlmdSyrqpaAfiV tqypl PTPM_HUMAN : 1243- 1259: essny InAAlmdSykqpsAfiV tqhpl PTPM_MOUSE : 1243- 1259: essny InAAlmdSykqpsAfiV tqhpl L 12: 20.5265 6( 6) S-x(0,1)-G-x-G-x(1,2)-G-[ACTV]-x(4)-[DNT] Occurences: 6(6) A5_XENLA : 337- 349: nlrfv S-GiGtqGAiskeT kkkyf MEPA_MOUSE : 474- 486: prfyn SeGyGv-GVtlypN grits MEPB_RAT : 552- 564: ngtqf SrGrGy-GTsvfiT qerlk PTPK_MOUSE : 1101- 1114: ivvhc SaGaGrtGCyiviD imldm PTPM_HUMAN : 1096- 1109: lvvhc SaGaGrtGCfiviD imldm PTPM_MOUSE : 1096- 1109: lvvhc SaGaGrtGCfiviD imldm M 13: 19.4164 6( 6) F-x(3)-Q-S-x(2,3)-D-x-[AD] Occurences: 6(6) A5_XENLA : 262- 272: gffan FsvvQSnt-DeD fqcke MEPA_MOUSE : 175- 185: lhalg FfheQSrt-DrD dyvni MEPB_RAT : 161- 171: lhalg FwheQSra-DrD dyiti PTPK_MOUSE : 906- 917: eeyes FfegQSaswDvA kkdqn PTPM_HUMAN : 907- 918: eeyes FfegQSapwDsA kkden PTPM_MOUSE : 907- 918: eeyes FfegQSapwDsA kkden N 14: 18.8487 6( 6) C-x(3)-L-x(2)-[GIV]-x-G-x(2,3)-S Occurences: 6(6) A5_XENLA : 431- 443: itdyp CsrmLgmVsGli-S dsqit MEPA_MOUSE : 573- 586: dkdcd CfrsLdwGwGqaiS hqllk MEPB_RAT : 266- 279: sfmds CdfeLenIcGmiqS sqdsa PTPK_MOUSE : 1233- 1245: lppdr ClpfLitIdGes-S nyina PTPM_HUMAN : 1228- 1240: lppdr ClpfLitIdGes-S nyina PTPM_MOUSE : 1228- 1240: lppdr ClpfLitIdGes-S nyina O 15: 17.8127 6( 6) R-x-[DGV]-x(2)-G-x(1,3)-G-x(0,1)-P Occurences: 6(6) A5_XENLA : 207- 218: ggqtc RyDwlGiwdGfP gvgph MEPA_MOUSE : 414- 424: eekkf RyVflGtk-GdP gnssg MEPB_RAT : 400- 409: vtekf RvVfeGvg-G-P gassg MEPB_RAT : 400- 409: vtekf RvVfeGv--GgP gassg PTPK_MOUSE : 366- 375: rvllt RpGegGt--GlP gppli PTPM_HUMAN : 357- 366: svllt RpGegGt--GsP gpalr PTPM_MOUSE : 357- 366: svllt RpGegGt--GsP gpalr P 16: 16.1802 6( 6) G-Q-x(2)-P-x(1,2)-R Occurences: 6(6) A5_XENLA : 229- 235: igryc GQntPg-R vrsft MEPA_MOUSE : 658- 664: lpssl GQrhPs-R qkrsv MEPB_RAT : 599- 605: taavp GQspPp-R lsimp PTPK_MOUSE : 873- 880: spyqt GQlhPaiR vadll PTPM_HUMAN : 874- 881: vpyqt GQlhPaiR vadll PTPM_MOUSE : 874- 881: vpyqt GQlhPaiR vadll Q 17: 16.1802 6( 6) I-x(5)-S-x(3)-S-x(1,2)-G Occurences: 6(6) A5_XENLA : 31- 43: kcgdt IkitspSyltSa-G yphsy MEPA_MOUSE : 132- 145: gessy IifqklSgcwSmiG dqqvg MEPB_RAT : 117- 130: geeny IsvfkgSgcwSsvG nihag PTPK_MOUSE : 1082- 1094: gllsf IrrvklSnppSa-G pivvh PTPM_HUMAN : 530- 543: sfdpe IdlsnqSgrvSklG nethf PTPM_MOUSE : 530- 543: sfdpe IdlsnqSgrvSklG nethf R 18: 15.6802 6( 6) G-D-x(2,3)-I-x(4,5)-E Occurences: 6(6) A5_XENLA : 689- 700: vqdht GDgnfIyseadE rhegr MEPA_MOUSE : 505- 516: fhlys GDndaIlewpvE nrqai MEPB_RAT : 576- 586: reflk GDdvyIlltv-E dishl PTPK_MOUSE : 318- 328: ansii GDgpiIlkev-E yrmts PTPK_MOUSE : 318- 328: ansii GDgp-IilkevE yrmts PTPM_HUMAN : 309- 319: ansin GDgp-IvarevE yctas PTPM_MOUSE : 309- 319: ansin GDgp-IvarevE yctas S 19: 15.6802 7( 6) S-x(1,2)-L-x(2,3)-R-x(4)-G Occurences: 7(6) A5_XENLA : 573- 583: erasa Sg-Lal-RlellG cevet MEPA_MOUSE : 586- 598: wgqai ShqLlkrRnflkG dslii MEPB_RAT : 530- 540: tddng Sy-Lwd-RpskvG veaff PTPK_MOUSE : 777- 788: vivkk Sk-LakkRkdamG ntrqe PTPK_MOUSE : 853- 865: ataes SrlLdvpRylceG tespy PTPM_HUMAN : 352- 362: teyei Sv-Llt-RpgegG tgspg PTPM_MOUSE : 352- 362: teyei Sv-Llt-RpgegG tgspg T 20: 15.6802 6( 6) T-x(1,2)-D-x(0,1)-N-x(2)-Y Occurences: 6(6) A5_XENLA : 688- 695: pvqdh Tg-DgNfiY seade MEPA_MOUSE : 210- 218: tyddn TitDlNtpY dyesl MEPB_RAT : 525- 531: tdpkm Td-D-NgsY lwdrp PTPK_MOUSE : 685- 692: epapf TvgD-NrtY kgfwn PTPM_HUMAN : 677- 684: aaqpf TigD-NktY ngywn PTPM_MOUSE : 677- 684: aaqpf TigD-NktY ngywn Number of patterns evaluated by Pratt:60443 Total running time: 74 seconds