------------------------------------------------------------ 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 23 sequences from file ALKALINE_PHOSPHATASE PATTERN CONSERVATION: CM: min Nr of Seqs to Match 23 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 ALKALINE_PHOSPHATASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PPB1_HUMAN 535 PPB2_HUMAN 530 PPB3_BACSU 462 PPB3_HUMAN 535 PPB4_BACSU 461 PPBE_MOUSE 529 PPBH_PSEAE 19 PPBI_BOVIN 44 PPBI_HUMAN 528 PPBI_MOUSE 559 PPBI_RAT 540 PPBL_PSEAE 14 PPBN_HUMAN 532 PPBT_BOVIN 524 PPBT_HUMAN 524 PPBT_MOUSE 524 PPBT_RAT 524 PPB_BOMMO 547 PPB_ECOLI 471 PPB_ESCFE 472 PPB_SERMA 475 PPB_YEAST 566 STRK_STRGR 449 Pratt run started at Thu Feb 6 18:35:20 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 247( 23) A-x(1,2)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 9.4893 147( 23) A-x(1,2)-L-x-[AGILPV] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 9.4893 147( 23) A-x(1,2)-L-x-[AGILPV] Occurences: 147(23) PPB1_HUMAN : 39- 44: wnrea AeaLgA akklq PPB1_HUMAN : 45- 50: ealga AkkLqP aqtaa PPB1_HUMAN : 55- 60: paqta AknLiI flgdg PPB1_HUMAN : 74- 79: stvta AriLkG qkkdk PPB1_HUMAN : 120- 124: gatat Ay-LcG vkgnf PPB1_HUMAN : 278- 282: telmq As-LdP svthl PPB1_HUMAN : 316- 320: memte Aa-LrL lsrnp PPB1_HUMAN : 487- 492: hvmaf AacLeP ytacd PPB1_HUMAN : 488- 492: vmafa Ac-LeP ytacd PPB1_HUMAN : 495- 500: lepyt AcdLaP pagtt PPB1_HUMAN : 517- 521: rsvvp Al-LpL lagtl PPB1_HUMAN : 523- 528: llpll AgtLlL letat PPB2_HUMAN : 34- 39: wnrea AeaLgA akklq PPB2_HUMAN : 40- 45: ealga AkkLqP aqtaa PPB2_HUMAN : 50- 55: paqta AknLiI flgdg PPB2_HUMAN : 69- 74: stvta AriLkG qkkdk PPB2_HUMAN : 115- 119: gatat Ay-LcG vkgnf PPB2_HUMAN : 273- 277: telmq As-LdP svthl PPB2_HUMAN : 311- 315: memte Aa-LrL lsrhp PPB2_HUMAN : 482- 487: hvmaf AacLeP ytacd PPB2_HUMAN : 483- 487: vmafa Ac-LeP ytacd PPB2_HUMAN : 490- 495: lepyt AcdLaP pagtt PPB2_HUMAN : 512- 516: rsvvp Al-LpL lagtl PPB2_HUMAN : 518- 523: llpll AgtLlL letat PPB3_BACSU : 141- 146: kekgk AtgLvA tseit PPB3_HUMAN : 39- 44: wnrea AeaLgA akklq PPB3_HUMAN : 45- 50: ealga AkkLqP aqtaa PPB3_HUMAN : 55- 60: paqta AknLiI flgdg PPB3_HUMAN : 74- 79: stvta AriLkG qkkdk PPB3_HUMAN : 120- 124: gatat Ay-LcG vkgnf PPB3_HUMAN : 278- 282: telmr As-LdP svahl PPB3_HUMAN : 285- 289: ldpsv Ah-LmG lfepg PPB3_HUMAN : 316- 320: memte Aa-LrL lsrnp PPB3_HUMAN : 487- 492: hvmaf AacLeP ytacd PPB3_HUMAN : 488- 492: vmafa Ac-LeP ytacd PPB3_HUMAN : 495- 500: lepyt AcdLaP pagtt PPB3_HUMAN : 517- 521: rsvvp Al-LpL lagtl PPB3_HUMAN : 523- 528: llpll AgtLlL letat PPB4_BACSU : 378- 382: vlary An-LkV tseei PPBE_MOUSE : 4- 8: mwg Ac-LlL lglsl PPBE_MOUSE : 4- 9: mwg AclLlL glslq PPBE_MOUSE : 35- 40: wnrka AeaLdA akklk PPBE_MOUSE : 41- 46: ealda AkkLkP iqtsa PPBE_MOUSE : 51- 56: piqts AknLvI lmgdg PPBE_MOUSE : 116- 120: agtgt Af-LcG vktnm PPBE_MOUSE : 483- 488: hvmaf AacLeP ytdcg PPBE_MOUSE : 484- 488: vmafa Ac-LeP ytdcg PPBH_PSEAE : 13- 18: fnrqa AgeLsV r PPBI_BOVIN : 17- 22: wnrqa AqaLdV akklq PPBI_BOVIN : 23- 28: qaldv AkkLqP iqtaa PPBI_HUMAN : 36- 41: wnrqa AeaLdA akklq PPBI_HUMAN : 42- 47: ealda AkkLqP iqkva PPBI_HUMAN : 52- 57: piqkv AknLiL flgdg PPBI_HUMAN : 117- 121: aatat Ay-LcG vkanf PPBI_HUMAN : 313- 317: memte Aa-LrL lsrnp PPBI_HUMAN : 484- 489: hvmaf AacLeP ytacd PPBI_HUMAN : 485- 489: vmafa Ac-LeP ytacd PPBI_HUMAN : 492- 497: lepyt AcdLaP pactt PPBI_HUMAN : 509- 514: aahpv AasLpL lagtl PPBI_HUMAN : 510- 514: ahpva As-LpL lagtl PPBI_HUMAN : 516- 521: slpll AgtLlL lgasa PPBI_MOUSE : 36- 41: wnkka AeaLdA akklq PPBI_MOUSE : 42- 47: ealda AkkLqP iqtsa PPBI_MOUSE : 52- 57: piqts AknLiI flgdg PPBI_MOUSE : 117- 121: astat Ay-LcG vktny PPBI_MOUSE : 343- 347: hhlgt Ay-LaL teavm PPBI_MOUSE : 397- 401: sifgl Ap-LnA ldgkp PPBI_MOUSE : 483- 488: hvmas AgcLeP ytdcg PPBI_MOUSE : 530- 535: pvhns ArsLgP atapl PPBI_MOUSE : 538- 542: lgpat Ap-LaL allag PPBI_MOUSE : 541- 546: atapl AlaLlA gmlml PPBI_MOUSE : 543- 547: aplal Al-LaG mlmll PPBI_MOUSE : 546- 551: alall AgmLmL llgap PPBI_RAT : 43- 48: ealdv AkkLqP iqtsa PPBI_RAT : 53- 58: piqts AknLiL flgdg PPBI_RAT : 118- 122: agtat Ay-LcG vkany PPBI_RAT : 344- 348: hhagt Ay-LaL teavm PPBI_RAT : 398- 402: sifgl Ap-LnA qdgks PPBI_RAT : 485- 490: hvmaf AgcLeP ytdcg PPBL_PSEAE : 6- 10: vtggg As-LpA elyr PPBN_HUMAN : 36- 41: wnrqa AeaLgA akklq PPBN_HUMAN : 42- 47: ealga AkkLqP aqtaa PPBN_HUMAN : 52- 57: paqta AknLiI flgdg PPBN_HUMAN : 71- 76: stvta AriLkG qkkdk PPBN_HUMAN : 117- 121: gatat Ay-LcG vkgnf PPBN_HUMAN : 275- 279: tellq As-LdP svthl PPBN_HUMAN : 313- 317: memte Aa-LlL lsrnp PPBN_HUMAN : 313- 318: memte AalLlL srnpr PPBN_HUMAN : 314- 318: emtea Al-LlL srnpr PPBN_HUMAN : 443- 448: yrqqs AvpLdG ethag PPBN_HUMAN : 484- 489: hvmaf AacLeP ytacd PPBN_HUMAN : 485- 489: vmafa Ac-LeP ytacd PPBN_HUMAN : 492- 497: lepyt AcdLaP pagtt PPBN_HUMAN : 514- 518: psvvp Al-LpL lagtl PPBN_HUMAN : 520- 525: llpll AgtLlL lgtat PPBT_BOVIN : 15- 20: igtcf AssLvP ekekd PPBT_BOVIN : 70- 75: stvta AriLkG qlhhs PPBT_BOVIN : 116- 120: agtat Ay-LcG vkane PPBT_BOVIN : 412- 416: kkpft Ai-LyG ngpgy PPBT_BOVIN : 468- 473: akgpm AhlLhG vqeqn PPBT_BOVIN : 516- 520: lllll Al-LpL gslf PPBT_HUMAN : 70- 75: stvta AriLkG qlhhn PPBT_HUMAN : 116- 120: agtat Ay-LcG vkane PPBT_HUMAN : 412- 416: kkpft Ai-LyG ngpgy PPBT_HUMAN : 468- 473: skgpm AhlLhG vheqn PPBT_HUMAN : 503- 508: apass AgsLaA gplll PPBT_HUMAN : 508- 513: agsla AgpLlL alaly PPBT_HUMAN : 514- 519: gplll AlaLyP lsvlf PPBT_MOUSE : 70- 75: stvta AriLkG qlhhn PPBT_MOUSE : 116- 120: agtat Ay-LcG vkane PPBT_MOUSE : 412- 416: kkpft Ai-LyG ngpgy PPBT_MOUSE : 468- 473: akgpm AhlLhG vheqn PPBT_MOUSE : 510- 514: apspg Al-LlP lavls PPBT_MOUSE : 510- 515: apspg AllLpL avlsl PPBT_MOUSE : 516- 520: lllpl Av-LsL ptlf PPBT_RAT : 70- 75: stvta AriLkG qlhhn PPBT_RAT : 116- 120: agtat Ay-LcG vkane PPBT_RAT : 412- 416: kkpft Ai-LyG ngpgy PPBT_RAT : 468- 473: akgpm AhlLhG vheqn PPBT_RAT : 510- 514: spspg Al-LlP lalfp PPBT_RAT : 510- 515: spspg AllLpL alfpl PPB_BOMMO : 90- 95: ptlaa ArtLlG qrrgq PPB_BOMMO : 136- 140: sctat Ay-LcG vkanq PPB_BOMMO : 366- 370: hhdny Ah-LaL detie PPB_BOMMO : 528- 533: atvpt AalLsL llaaf PPB_BOMMO : 529- 533: tvpta Al-LsL llaaf PPB_ECOLI : 7- 12: kqsti AlaLlP llftp PPB_ECOLI : 9- 13: stial Al-LpL lftpv PPB_ECOLI : 44- 49: tapgg ArrLtG dqtaa PPB_ECOLI : 99- 104: fkgid AlpLtG qythy PPB_ECOLI : 179- 183: qdatp Aa-LvA hvtsr PPB_ECOLI : 466- 470: fytmk Aa-LgL k PPB_ESCFE : 5- 10: mkqs AiaLaL lscli PPB_ESCFE : 45- 50: tmpgg ArrLsG dqtea PPB_ESCFE : 100- 105: fkgid AlpLtG qythy PPB_ESCFE : 263- 268: qivsd AasLaA vtqag PPB_ESCFE : 264- 268: ivsda As-LaA vtqag PPB_ESCFE : 467- 471: fytmk Aa-LgL q PPB_SERMA : 4- 9: mqp AvsLiA gavls PPB_SERMA : 11- 15: sliag Av-LsA llcss PPB_SERMA : 48- 53: vepgg ArrLaG dqtta PPB_SERMA : 103- 108: fkgid AlpLtG qythy PPB_SERMA : 266- 271: qwvsn AdeLqA vtlan PPB_YEAST : 156- 161: gtvle AakLaG yltgl PPB_YEAST : 157- 161: tvlea Ak-LaG yltgl PPB_YEAST : 160- 165: eaakl AgyLtG lvvtt STRK_STRGR : 19- 23: avlgs Al-LvL vtapa STRK_STRGR : 155- 159: adatp Aa-LtA hvtdr STRK_STRGR : 297- 301: aestr Aa-LdL ltara STRK_STRGR : 383- 387: hdarp Ag-LsA tlvtd STRK_STRGR : 444- 448: fgtvt Aa-LgL r Number of patterns evaluated by Pratt:2 Total running time: 1 seconds