------------------------------------------------------------ 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 HYDROPHOBIN 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 HYDROPHOBIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RODL_ASPFU 159 RODL_EMENI 157 RODL_NEUCR 108 SC1_SCHCO 109 SC3_SCHCO 125 SC4_SCHCO 111 Pratt run started at Thu Feb 6 19:56:46 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.6802 6( 6) A-x(5)-A-A-x(1,3)-P 2: 15.1802 6( 6) S-x(5)-G-x(2,3)-G-x(2,4)-C 3: 15.1802 7( 6) G-x(2,3)-G-x(0,2)-L-x(2)-L 4: 15.1802 7( 6) C-x(0,2)-S-x(5)-G-x(2,3)-G 5: 15.1802 8( 6) A-x(2)-A-x(4,5)-A-x(2,4)-P 6: 15.1802 6( 6) A-x(4,5)-A-A-x(1,3)-P 7: 15.1802 6( 6) F-x(2,3)-A-x(1,3)-A-x(5)-A 8: 12.5102 6( 6) C-x(5)-C-C 9: 12.0102 7( 6) V-G-x(2,3)-G 10: 12.0102 12( 6) L-x(0,1)-G-x(3)-G 11: 12.0102 7( 6) L-x(3)-L-x(4,5)-G 12: 12.0102 8( 6) L-x(3,4)-L-G 13: 12.0102 10( 6) L-x(4,5)-G-x(3)-G 14: 12.0102 9( 6) G-L-x(0,1)-L 15: 12.0102 6( 6) S-x(0,1)-P-x(4)-G 16: 12.0102 7( 6) S-x(5)-G-x(2,3)-G 17: 12.0102 7( 6) A-x(2)-A-x(1,2)-V 18: 12.0102 8( 6) A-x(0,1)-A-x-P 19: 11.5102 6( 6) L-x(1,2)-N-x(2,3)-C 20: 11.5102 8( 6) F-x(4,5)-A-x(4,5)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 40.9608 6( 6) C-x-[AQT]-[NQS]-x(2)-C-C-x(2)-[DSTV]-x(2)-[DNS]-[AGT]-x(2)-[NS]-[FILV]-[GIL]-x(2)-[GNP]-[AIL]-[ANPS] B 2: 37.3714 6( 6) S-[LP]-x-[CDST]-[AV]-x-G-x(2,3)-G-x-[GQS]-x-[GPST]-[ACT]-x-[ATV]-x-[CG]-[CS] C 3: 36.0850 6( 6) A-[FIL]-[AGP]-x(2)-[AV]-A-A-x(1,3)-P-x(4)-[GNPS]-x(3)-[AGNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] D 4: 29.6096 6( 6) S-[LP]-x-[CDST]-[AV]-x-G-x(2,3)-G-x(2,4)-C-x-[AT]-x-[GTV] E 5: 28.4393 6( 6) F-x(2,3)-A-x(1,3)-A-[FLMV]-[AGPTV]-[AV]-x-[AV]-A-[APS] F 6: 27.0729 6( 6) A-x(4,5)-A-A-x(1,3)-P-x(4)-[GNPS]-x(3)-[AGNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] G 7: 26.7607 8( 6) A-x(0,1)-A-[ALV]-P-x(4)-[GNPS]-x(3)-[GNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] H 8: 22.7462 6( 6) F-x(4,5)-A-x(4,5)-A-[AV]-x-[APV]-x-[AGPV]-x-[GP] I 9: 21.2562 6( 6) A-x-[AGLP]-A-x(1,2)-V-x-[AGPV]-x-[AGP]-x-[AGPT] J 10: 20.1103 6( 6) G-x(2,3)-G-x(0,2)-L-x-[DGN]-L-x-[CGPV] K 11: 20.0097 7( 6) C-x(0,2)-S-x(2)-[DGST]-[APV]-x-G-x(2,3)-G L 12: 19.9865 6( 6) S-x(0,1)-P-x-[DGST]-[ASV]-x-G-x-[GL] M 13: 17.2218 7( 6) A-[FILMV]-x-A-x(4,5)-A-x(2,4)-P N 14: 16.7788 6( 6) L-[AGSV]-[AGL]-x-L-x(4,5)-G O 15: 16.4823 7( 6) G-L-x(0,1)-L-[GNPS]-x-[AILV] P 16: 14.6720 8( 6) L-x(3,4)-L-G-x-[ILV] Q 17: 12.0102 7( 6) V-G-x(2,3)-G R 18: 12.0102 12( 6) L-x(0,1)-G-x(3)-G S 19: 12.0102 10( 6) L-x(4,5)-G-x(3)-G T 20: 12.0102 6( 6) S-x(0,1)-P-x(4)-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 40.9608 6( 6) C-x-[AQT]-[NQS]-x(2)-C-C-x(2)-[DSTV]-x(2)-[DNS]-[AGT]-x(2)-[NS]-[FILV]-[GIL]-x(2)-[GNP]-[AIL]-[ANPS] Occurences: 6(6) RODL_ASPFU : 127- 151: lvnqk CkQNiaCCqnSpsDAsgSLIglGLP cialg RODL_EMENI : 125- 149: lvnqk CkQNiaCCqnSpsSAdgNLIgvGLP cvalg RODL_NEUCR : 80- 104: vigsq CgASvkCCkdDvtNTgnSFLiiNAA ncva SC1_SCHCO : 82- 106: vggns CsTQtvCCegTqfNGlvNVGctPIN vgl SC3_SCHCO : 99- 123: vggsg CsAQtvCCenTqfNGliNIGctPIN il SC4_SCHCO : 86- 110: ltgns CtAQtvCCdhVtqNGlvNVGctPIS l B 2: 37.3714 6( 6) S-[LP]-x-[CDST]-[AV]-x-G-x(2,3)-G-x-[GQS]-x-[GPST]-[ACT]-x-[ATV]-x-[CG]-[CS] Occurences: 6(6) RODL_ASPFU : 137- 157: accqn SPsDAsGsliGlGlPCiAlGS il RODL_EMENI : 135- 155: accqn SPsSAdGnliGvGlPCvAlGS il RODL_NEUCR : 68- 87: vdlsa SLgCVvGvi-GsQcGAsVkCC kddvt SC1_SCHCO : 70- 89: agvnc SPvSViGvg-GnScSTqTvCC egtqf SC3_SCHCO : 87- 106: vgisc SPlTViGvg-GsGcSAqTvCC entqf SC4_SCHCO : 73- 93: vglnc SPiSVvGvltGnScTAqTvCC dhvtq C 3: 36.0850 6( 6) A-[FIL]-[AGP]-x(2)-[AV]-A-A-x(1,3)-P-x(4)-[GNPS]-x(3)-[AGNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] Occurences: 6(6) RODL_ASPFU : 11- 39: saavl AFAvsVAAl--PqhdvNaagNgvGNkgNanV rfpvp RODL_EMENI : 11- 39: aaavv AFAasVAAl--PpahdSqfaGngVGnkGnsN vkfpv RODL_NEUCR : 11- 39: vftil AIAmtAAAa--PaevvPratTigPNtcSidD ykpyc SC1_SCHCO : 9- 39: slail ALPvlAAAtavPrggaSkcnSgpVQccNtlV dtkdk SC3_SCHCO : 15- 43: lyafv AFGalVAAl--PgghpGttyPpsTTtiAagG tcttg SC4_SCHCO : 9- 37: slall ALPalAAAa--PvpggGkgaGqaCNsgPvqC cnett D 4: 29.6096 6( 6) S-[LP]-x-[CDST]-[AV]-x-G-x(2,3)-G-x(2,4)-C-x-[AT]-x-[GTV] Occurences: 6(6) RODL_ASPFU : 137- 156: accqn SPsDAsGsliGlglpCiAlG sil RODL_EMENI : 135- 154: accqn SPsSAdGnliGvglpCvAlG sil RODL_NEUCR : 68- 84: vdlsa SLgCVvGvi-Gsq--CgAsV kcckd SC1_SCHCO : 70- 86: agvnc SPvSViGvg-Gns--CsTqT vcceg SC3_SCHCO : 87- 103: vgisc SPlTViGvg-Gsg--CsAqT vccen SC4_SCHCO : 73- 90: vglnc SPiSVvGvltGns--CtAqT vccdh E 5: 28.4393 6( 6) F-x(2,3)-A-x(1,3)-A-[FLMV]-[AGPTV]-[AV]-x-[AV]-A-[APS] Occurences: 6(6) RODL_ASPFU : 3- 18: mk FslsAavlAFAVsVAA lpqhd RODL_EMENI : 3- 15: mk Fsi-Aa--AVVAfAAS vaalp RODL_EMENI : 3- 18: mk FsiaAavvAFAAsVAA lppah RODL_NEUCR : 7- 20: qftsv FtilAi--AMTAaAAP aevvp SC1_SCHCO : 3- 16: mr Fsl-Ail-ALPVlAAA tavpr SC3_SCHCO : 9- 22: rlpvv Fly-Afv-AFGAlVAA lpggh SC4_SCHCO : 3- 16: mr Fsl-All-ALPAlAAA apvpg F 6: 27.0729 6( 6) A-x(4,5)-A-A-x(1,3)-P-x(4)-[GNPS]-x(3)-[AGNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] Occurences: 6(6) RODL_ASPFU : 11- 39: saavl AfavsvAAl--PqhdvNaagNgvGNkgNanV rfpvp RODL_EMENI : 11- 39: aaavv AfaasvAAl--PpahdSqfaGngVGnkGnsN vkfpv RODL_NEUCR : 11- 39: vftil AiamtaAAa--PaevvPratTigPNtcSidD ykpyc RODL_NEUCR : 11- 39: vftil Aiamt-AAaa-PaevvPratTigPNtcSidD ykpyc SC1_SCHCO : 9- 39: slail AlpvlaAAtavPrggaSkcnSgpVQccNtlV dtkdk SC3_SCHCO : 15- 43: lyafv AfgalvAAl--PgghpGttyPpsTTtiAagG tcttg SC4_SCHCO : 9- 37: slall AlpalaAAa--PvpggGkgaGqaCNsgPvqC cnett SC4_SCHCO : 9- 37: slall Alpal-AAaa-PvpggGkgaGqaCNsgPvqC cnett G 7: 26.7607 8( 6) A-x(0,1)-A-[ALV]-P-x(4)-[GNPS]-x(3)-[GNPST]-x(2)-[CGPTV]-[GNQT]-x(2)-[AGNPS]-x(2)-[CDGNV] Occurences: 8(6) RODL_ASPFU : 17- 39: favsv A-ALPqhdvNaagNgvGNkgNanV rfpvp RODL_EMENI : 17- 39: faasv A-ALPpahdSqfaGngVGnkGnsN vkfpv RODL_NEUCR : 16- 39: aiamt AaAAPaevvPratTigPNtcSidD ykpyc RODL_NEUCR : 17- 39: iamta A-AAPaevvPratTigPNtcSidD ykpyc SC1_SCHCO : 16- 39: pvlaa AtAVPrggaSkcnSgpVQccNtlV dtkdk SC3_SCHCO : 21- 43: fgalv A-ALPgghpGttyPpsTTtiAagG tcttg SC4_SCHCO : 14- 37: alpal AaAAPvpggGkgaGqaCNsgPvqC cnett SC4_SCHCO : 15- 37: lpala A-AAPvpggGkgaGqaCNsgPvqC cnett H 8: 22.7462 6( 6) F-x(4,5)-A-x(4,5)-A-[AV]-x-[APV]-x-[AGPV]-x-[GP] Occurences: 6(6) RODL_ASPFU : 3- 20: mk Fslsa-Avlaf-AVsVaAlP qhdvn RODL_EMENI : 3- 20: mk Fsiaa-Avvaf-AAsVaAlP pahds RODL_NEUCR : 7- 25: qftsv FtilaiAmtaa-AApAeVvP ratti SC1_SCHCO : 3- 22: mr FslailAlpvlaAAtAvPrG gaskc SC3_SCHCO : 9- 28: rlpvv FlyafvAfgalvAAlPgGhP gttyp SC4_SCHCO : 3- 21: mr FslallAlpal-AAaApVpG ggkga SC4_SCHCO : 3- 22: mr FslallAlpalaAAaPvPgG gkgag I 9: 21.2562 6( 6) A-x-[AGLP]-A-x(1,2)-V-x-[AGPV]-x-[AGP]-x-[AGPT] Occurences: 6(6) RODL_ASPFU : 8- 20: fslsa AvLAfaVsVaAlP qhdvn RODL_EMENI : 11- 22: aaavv AfAAs-VaAlPpA hdsqf RODL_NEUCR : 18- 29: amtaa AaPAe-VvPrAtT igpnt SC1_SCHCO : 6- 18: mrfsl AiLAlpVlAaAtA vprgg SC3_SCHCO : 15- 26: lyafv AfGAl-VaAlPgG hpgtt SC4_SCHCO : 14- 25: alpal AaAAp-VpGgGkG agqac J 10: 20.1103 6( 6) G-x(2,3)-G-x(0,2)-L-x-[DGN]-L-x-[CGPV] Occurences: 6(6) RODL_ASPFU : 80- 91: tdide GilaGt-LkNLiG ggsgt RODL_EMENI : 81- 92: ttvde GllsGa-LsGLiG agsga RODL_NEUCR : 53- 62: msgpa Gsp-G--LlNLiP vdlsa SC1_SCHCO : 55- 66: vgall GldlGs-LtGLaG vncsp SC3_SCHCO : 69- 80: vtall Gll-GivLsDLnV lvgis SC4_SCHCO : 62- 72: lgvvv GpitG--LvGLnC spisv K 11: 20.0097 7( 6) C-x(0,2)-S-x(2)-[DGST]-[APV]-x-G-x(2,3)-G Occurences: 7(6) RODL_ASPFU : 134- 147: qniac CqnSpsDAsGsliG lglpc RODL_EMENI : 132- 145: qniac CqnSpsSAdGnliG vglpc RODL_NEUCR : 44- 56: dykpy CcqSmsGPaGsp-G llnli RODL_NEUCR : 45- 56: ykpyc Cq-SmsGPaGsp-G llnli SC1_SCHCO : 69- 79: lagvn C--SpvSViGvg-G nscst SC3_SCHCO : 86- 96: lvgis C--SplTViGvg-G sgcsa SC4_SCHCO : 72- 83: lvgln C--SpiSVvGvltG nscta L 12: 19.9865 6( 6) S-x(0,1)-P-x-[DGST]-[ASV]-x-G-x-[GL] Occurences: 6(6) RODL_ASPFU : 137- 145: accqn S-PsDAsGsL iglgl RODL_EMENI : 135- 143: accqn S-PsSAdGnL igvgl RODL_NEUCR : 49- 58: ccqsm SgPaGSpGlL nlipv SC1_SCHCO : 70- 78: agvnc S-PvSViGvG gnscs SC3_SCHCO : 87- 95: vgisc S-PlTViGvG gsgcs SC4_SCHCO : 73- 81: vglnc S-PiSVvGvL tgnsc M 13: 17.2218 7( 6) A-[FILMV]-x-A-x(4,5)-A-x(2,4)-P Occurences: 7(6) RODL_ASPFU : 8- 20: fslsa AVlAfavsvAal--P qhdvn RODL_EMENI : 8- 20: fsiaa AVvAfaasvAal--P pahds RODL_EMENI : 8- 21: fsiaa AVvAfaasvAalp-P ahdsq RODL_NEUCR : 13- 25: tilai AMtAaaap-Aevv-P ratti SC1_SCHCO : 6- 20: mrfsl AIlAlpvlaAatavP rggas SC3_SCHCO : 12- 24: vvfly AFvAfgalvAal--P gghpg SC4_SCHCO : 6- 18: mrfsl ALlAlpalaAaa--P vpggg SC4_SCHCO : 6- 18: mrfsl ALlAlpal-Aaaa-P vpggg SC4_SCHCO : 6- 20: mrfsl ALlAlpalaAaapvP gggkg SC4_SCHCO : 9- 20: slall ALpAlaaa-Apv--P gggkg N 14: 16.7788 6( 6) L-[AGSV]-[AGL]-x-L-x(4,5)-G Occurences: 6(6) RODL_ASPFU : 82- 91: idegi LAGtLknli-G ggsgt RODL_ASPFU : 82- 92: idegi LAGtLknligG gsgte RODL_EMENI : 83- 92: vdegl LSGaLsgli-G agsga RODL_NEUCR : 65- 74: lipvd LSAsLgcvv-G vigsq SC1_SCHCO : 54- 63: ivgal LGLdLgslt-G lagvn SC3_SCHCO : 19- 29: vafga LVAaLpgghpG ttypp SC4_SCHCO : 53- 62: qkqgl LGGlLgvvv-G pitgl O 15: 16.4823 7( 6) G-L-x(0,1)-L-[GNPS]-x-[AILV] Occurences: 7(6) RODL_ASPFU : 147- 153: sgsli GLgLPcI algsi RODL_EMENI : 81- 86: ttvde GL-LSgA lsgli RODL_NEUCR : 56- 61: pagsp GL-LNlI pvdls SC1_SCHCO : 55- 61: vgall GLdLGsL tglag SC3_SCHCO : 69- 74: vtall GL-LGiV lsdln SC4_SCHCO : 51- 56: naqkq GL-LGgL lgvvv SC4_SCHCO : 55- 60: qgllg GL-LGvV vgpit P 16: 14.6720 8( 6) L-x(3,4)-L-G-x-[ILV] Occurences: 8(6) RODL_ASPFU : 150- 158: liglg LpciaLGsI l RODL_EMENI : 148- 156: ligvg LpcvaLGsI l RODL_NEUCR : 65- 72: lipvd Lsas-LGcV vgvig SC1_SCHCO : 53- 61: nivga LlgldLGsL tglag SC1_SCHCO : 54- 61: ivgal Lgld-LGsL tglag SC3_SCHCO : 67- 74: spvta Llgl-LGiV lsdln SC4_SCHCO : 52- 60: aqkqg LlgglLGvV vgpit SC4_SCHCO : 53- 60: qkqgl Lggl-LGvV vgpit Q 17: 12.0102 7( 6) V-G-x(2,3)-G Occurences: 7(6) RODL_ASPFU : 31- 35: aagng VGnk-G nanvr RODL_EMENI : 32- 36: fagng VGnk-G nsnvk RODL_NEUCR : 73- 77: slgcv VGvi-G sqcga SC1_SCHCO : 50- 55: hqtni VGallG ldlgs SC3_SCHCO : 94- 98: ltvig VGgs-G csaqt SC4_SCHCO : 61- 66: llgvv VGpitG lvgln SC4_SCHCO : 78- 83: spisv VGvltG nscta R 18: 12.0102 12( 6) L-x(0,1)-G-x(3)-G Occurences: 12(6) RODL_ASPFU : 89- 95: gtlkn LiGggsG teglg RODL_EMENI : 83- 89: vdegl LsGalsG ligag RODL_EMENI : 90- 96: galsg LiGagsG aeglg RODL_NEUCR : 69- 74: dlsas L-GcvvG vigsq SC1_SCHCO : 53- 59: nivga LlGldlG sltgl SC1_SCHCO : 54- 59: ivgal L-GldlG sltgl SC1_SCHCO : 58- 63: llgld L-GsltG lagvn SC3_SCHCO : 23- 29: alvaa LpGghpG ttypp SC4_SCHCO : 52- 58: aqkqg LlGgllG vvvgp SC4_SCHCO : 53- 58: qkqgl L-GgllG vvvgp SC4_SCHCO : 56- 62: gllgg LlGvvvG pitgl SC4_SCHCO : 57- 62: llggl L-GvvvG pitgl S 19: 12.0102 10( 6) L-x(4,5)-G-x(3)-G Occurences: 10(6) RODL_ASPFU : 86- 95: ilagt Lknli-GggsG teglg RODL_EMENI : 87- 96: llsga Lsgli-GagsG aeglg RODL_NEUCR : 65- 74: lipvd Lsasl-GcvvG vigsq SC1_SCHCO : 53- 63: nivga LlgldlGsltG lagvn SC1_SCHCO : 54- 63: ivgal Lgldl-GsltG lagvn SC3_SCHCO : 19- 29: vafga LvaalpGghpG ttypp SC4_SCHCO : 52- 62: aqkqg LlggllGvvvG pitgl SC4_SCHCO : 53- 62: qkqgl Lggll-GvvvG pitgl SC4_SCHCO : 56- 66: gllgg LlgvvvGpitG lvgln SC4_SCHCO : 57- 66: llggl Lgvvv-GpitG lvgln T 20: 12.0102 6( 6) S-x(0,1)-P-x(4)-G Occurences: 6(6) RODL_ASPFU : 137- 143: accqn S-PsdasG sligl RODL_EMENI : 135- 141: accqn S-PssadG nligv RODL_NEUCR : 49- 56: ccqsm SgPagspG llnli SC1_SCHCO : 70- 76: agvnc S-PvsviG vggns SC3_SCHCO : 87- 93: vgisc S-PltviG vggsg SC4_SCHCO : 73- 79: vglnc S-PisvvG vltgn Number of patterns evaluated by Pratt:832 Total running time: 0 seconds