------------------------------------------------------------ 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 7 sequences from file PREPHENATE_DEHYDR_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 PREPHENATE_DEHYDR_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: PHEA_BACSU 285 PHEA_CORGL 315 PHEA_ECOLI 386 PHEA_ERWHE 387 PHEA_HAEIN 385 PHEA_LACLA 279 PHEA_PSEST 365 Pratt run started at Thu Feb 6 20:50:35 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.1802 10( 7) V-x(2,3)-E-N-x(3)-G 2: 15.6802 7( 7) E-x(4)-G-x(2,4)-N-x(3)-D 3: 15.1802 8( 7) A-x(2,3)-V-x(3,5)-P-x(3)-A 4: 15.1802 11( 7) A-x(3,4)-V-x(3,5)-P-x(3)-A 5: 15.1802 7( 7) S-x(2)-A-x(0,1)-A-x(1,3)-V 6: 15.1802 7( 7) A-x(0,1)-L-x(1,3)-G-S 7: 12.5102 9( 7) A-x(2)-E-L 8: 12.5102 8( 7) E-x-R-P 9: 12.5102 7( 7) T-R-F 10: 12.5102 7( 7) E-N-x(3)-G 11: 12.0102 9( 7) V-x(1,2)-L-G 12: 12.0102 7( 7) V-x(1,2)-L-x(4)-S 13: 12.0102 14( 7) A-x(0,1)-L-G 14: 12.0102 9( 7) L-E-x(1,2)-L 15: 12.0102 11( 7) L-x(0,1)-E-x-L 16: 12.0102 13( 7) A-L-x(0,1)-E 17: 12.0102 8( 7) S-x(5)-A-x(3,4)-A 18: 12.0102 7( 7) P-x(4,5)-L-G 19: 12.0102 8( 7) L-x(2)-A-x(0,1)-L 20: 12.0102 12( 7) L-x(1,2)-A-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 44.7959 10( 7) V-x(2,3)-E-N-x(2)-[DES]-G-[APST]-[IV]-[NT]-x-[STV]-x-D-x-[FIL]-x(3)-[DQS]-x(4)-[GIV]-[AEG] B 2: 41.1258 7( 7) E-N-x(2)-[DES]-G-[APST]-[IV]-[NT]-x-[STV]-x-D-x-[FIL]-x(3)-[DQS]-x(4)-[GIV]-[AEG] C 3: 20.9822 7( 7) S-[NQST]-[AGNQS]-A-x(0,1)-A-x(1,3)-V-x-[ADENQS] D 4: 20.0527 7( 7) E-x-[ASTV]-x(2)-G-x(2,4)-N-x-[ASTV]-x-D E 5: 19.6465 7( 7) T-R-F-x-[AILV]-[ILV]-[AGQS] F 6: 19.0629 7( 7) V-x(1,2)-L-G-x(2)-[AGS]-x(2)-[EQST]-x(2)-[AEGQ] G 7: 17.8457 7( 7) A-x(0,1)-L-x(1,3)-G-S-x(4)-[AIV] H 8: 15.7078 7( 7) E-[DS]-R-P I 9: 15.1802 8( 7) A-x(2,3)-V-x(3,5)-P-x(3)-A J 10: 15.1802 11( 7) A-x(3,4)-V-x(3,5)-P-x(3)-A K 11: 14.6091 12( 7) A-x(0,1)-L-G-x(2)-[AGV] L 12: 13.6700 9( 7) L-E-x(1,2)-L-x-[CDGNTV] M 13: 12.5102 9( 7) A-x(2)-E-L N 14: 12.0102 7( 7) V-x(1,2)-L-x(4)-S O 15: 12.0102 11( 7) L-x(0,1)-E-x-L P 16: 12.0102 13( 7) A-L-x(0,1)-E Q 17: 12.0102 8( 7) S-x(5)-A-x(3,4)-A R 18: 12.0102 7( 7) P-x(4,5)-L-G S 19: 12.0102 8( 7) L-x(2)-A-x(0,1)-L T 20: 12.0102 12( 7) L-x(1,2)-A-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 44.7959 10( 7) V-x(2,3)-E-N-x(2)-[DES]-G-[APST]-[IV]-[NT]-x-[STV]-x-D-x-[FIL]-x(3)-[DQS]-x(4)-[GIV]-[AEG] Occurences: 10(7) PHEA_BACSU : 50- 77: vdfaf Vpl-ENalEGSVNlTiDyLiheQplpiVG emtlp PHEA_CORGL : 60- 88: taqfa VvaiENfvDGPVTpTfDaLdqgSnvqiIA eeeld PHEA_CORGL : 61- 88: aqfav Vai-ENfvDGPVTpTfDaLdqgSnvqiIA eeeld PHEA_ECOLI : 155- 183: qadya VvpiENtsSGAINdVyDlLqhtSlsivGE mtlti PHEA_ECOLI : 156- 183: adyav Vpi-ENtsSGAINdVyDlLqhtSlsivGE mtlti PHEA_ERWHE : 155- 183: vadya VmpiENtsSGSINdVyDlLqqtSlsivGE ltlpi PHEA_HAEIN : 155- 183: eadfg VlplENttSGAINeVyDlLqhtDlslvGE laypi PHEA_LACLA : 49- 76: cdfal Vpi-ENstEGTVNmSiDkIfhdSnakvVA efvlp PHEA_PSEST : 143- 171: avnfg VvpvENstEGAVNhTlDsFlehDivicGE velri PHEA_PSEST : 144- 171: vnfgv Vpv-ENstEGAVNhTlDsFlehDivicGE velri B 2: 41.1258 7( 7) E-N-x(2)-[DES]-G-[APST]-[IV]-[NT]-x-[STV]-x-D-x-[FIL]-x(3)-[DQS]-x(4)-[GIV]-[AEG] Occurences: 7(7) PHEA_BACSU : 53- 77: afvpl ENalEGSVNlTiDyLiheQplpiVG emtlp PHEA_CORGL : 64- 88: avvai ENfvDGPVTpTfDaLdqgSnvqiIA eeeld PHEA_ECOLI : 159- 183: avvpi ENtsSGAINdVyDlLqhtSlsivGE mtlti PHEA_ERWHE : 159- 183: avmpi ENtsSGSINdVyDlLqqtSlsivGE ltlpi PHEA_HAEIN : 159- 183: gvlpl ENttSGAINeVyDlLqhtDlslvGE laypi PHEA_LACLA : 52- 76: alvpi ENstEGTVNmSiDkIfhdSnakvVA efvlp PHEA_PSEST : 147- 171: gvvpv ENstEGAVNhTlDsFlehDivicGE velri C 3: 20.9822 7( 7) S-[NQST]-[AGNQS]-A-x(0,1)-A-x(1,3)-V-x-[ADENQS] Occurences: 7(7) PHEA_BACSU : 131- 141: yeyan STGAaAkf-VsD hpeln PHEA_BACSU : 131- 141: yeyan STGA-AakfVsD hpeln PHEA_CORGL : 140- 150: ylsas SNGAgAqm-VaE gtada PHEA_ECOLI : 233- 243: ieyte STSA-AmekVaQ aksph PHEA_ERWHE : 233- 243: ieyte STAA-AmekVaA lnspk PHEA_HAEIN : 305- 314: llmtt SQQAgAl--VdA llvfk PHEA_LACLA : 126- 136: veite STSAaAef-VkN npdlp PHEA_LACLA : 126- 136: veite STSA-AaefVkN npdlp PHEA_PSEST : 221- 232: ervav SSNAdAakrVkS ewnsa D 4: 20.0527 7( 7) E-x-[ASTV]-x(2)-G-x(2,4)-N-x-[ASTV]-x-D Occurences: 7(7) PHEA_BACSU : 53- 65: afvpl EnAleGsv--NlTiD ylihe PHEA_CORGL : 273- 287: hlqae ElVfvGswpsNrAeD stpqt PHEA_ECOLI : 159- 171: avvpi EnTssGai--NdVyD llqht PHEA_ERWHE : 159- 171: avmpi EnTssGsi--NdVyD llqqt PHEA_HAEIN : 159- 171: gvlpl EnTtsGai--NeVyD llqht PHEA_LACLA : 52- 64: alvpi EnSteGtv--NmSiD kifhd PHEA_PSEST : 147- 159: gvvpv EnSteGav--NhTlD sfleh E 5: 19.6465 7( 7) T-R-F-x-[AILV]-[ILV]-[AGQS] Occurences: 7(7) PHEA_BACSU : 176- 182: yrdnh TRFvILS pdeni PHEA_CORGL : 183- 189: vrgar TRFvAVQ aqaav PHEA_ECOLI : 278- 284: qrqnf TRFvVLA rkain PHEA_ERWHE : 278- 284: qqqnh TRFiVLA rkaie PHEA_HAEIN : 278- 284: qenni TRFiVVA kepre PHEA_LACLA : 171- 177: lagns TRFwLLG kekqs PHEA_PSEST : 265- 271: rpdns TRFlIIG sqevp F 6: 19.0629 7( 7) V-x(1,2)-L-G-x(2)-[AGS]-x(2)-[EQST]-x(2)-[AEGQ] Occurences: 7(7) PHEA_BACSU : 3- 16: mk VgyLGpaAtfThlA vsscf PHEA_CORGL : 8- 21: daptv VayLGpaGtfTeeA lykfa PHEA_ECOLI : 249- 262: aksph VaaLGseAggTlyG lqvle PHEA_ERWHE : 249- 262: lnspk VaaLGseAggElyQ lqvle PHEA_HAEIN : 132- 144: yqkqf Ve-LGcqSfeQvfE kvqtg PHEA_LACLA : 265- 278: glgvn VrlLGnySvySlgE v PHEA_PSEST : 97- 110: eqplr VayLGpeGtfSqaA alkhf G 7: 17.8457 7( 7) A-x(0,1)-L-x(1,3)-G-S-x(4)-[AIV] Occurences: 7(7) PHEA_BACSU : 55- 64: vplen A-Le--GSvnltI dylih PHEA_CORGL : 77- 87: tptfd A-Ldq-GSnvqiI aeeel PHEA_ECOLI : 107- 119: hsari AfLgpkGSyshlA arqya PHEA_ERWHE : 107- 119: haari AfLgpkGSyshlA arnya PHEA_HAEIN : 107- 119: qnlhi AfLgkrGSysnlA arnya PHEA_LACLA : 4- 16: mki AyLgprGSfcsvV aeaaf PHEA_PSEST : 353- 364: dheav A-LkvlGSypkaV l H 8: 15.7078 7( 7) E-[DS]-R-P Occurences: 7(7) PHEA_BACSU : 234- 237: nlski ESRP tktgl PHEA_CORGL : 234- 237: dltri ESRP trkvf PHEA_ECOLI : 329- 332: imtrl ESRP ihgnp PHEA_ERWHE : 329- 332: imskl ESRP ingnp PHEA_HAEIN : 329- 332: nmtkl ESRP iygkp PHEA_LACLA : 224- 227: dmtki ESRP lrtrl PHEA_PSEST : 258- 261: laeki EDRP dnstr I 9: 15.1802 8( 7) A-x(2,3)-V-x(3,5)-P-x(3)-A Occurences: 8(7) PHEA_BACSU : 42- 55: idaav Age-VdfafvPlenA legsv PHEA_CORGL : 271- 285: alhlq AeelVfvgswPsnrA edstp PHEA_ECOLI : 237- 251: estsa AmekVaqaksPhvaA lgsea PHEA_ERWHE : 237- 251: estaa AmekVaalnsPkvaA lgsea PHEA_HAEIN : 237- 251: esssh AmqlVaslnkPniaA lgned PHEA_LACLA : 130- 142: estsa AaefVknn--PdlpA aavan PHEA_LACLA : 131- 142: stsaa Aef-Vknn--PdlpA aavan PHEA_PSEST : 46- 58: aswpk AeeaVfyr--PereA wvlkh J 10: 15.1802 11( 7) A-x(3,4)-V-x(3,5)-P-x(3)-A Occurences: 11(7) PHEA_BACSU : 40- 55: ecida AvageVdfafvPlenA legsv PHEA_CORGL : 62- 77: qfavv AienfVdgpvtPtfdA ldqgs PHEA_CORGL : 271- 285: alhlq Aeel-VfvgswPsnrA edstp PHEA_ECOLI : 236- 251: tests AamekVaqaksPhvaA lgsea PHEA_ECOLI : 237- 251: estsa Amek-VaqaksPhvaA lgsea PHEA_ERWHE : 236- 251: testa AamekVaalnsPkvaA lgsea PHEA_ERWHE : 237- 251: estaa Amek-VaalnsPkvaA lgsea PHEA_HAEIN : 237- 251: esssh Amql-VaslnkPniaA lgned PHEA_LACLA : 129- 142: tests AaaefVknn--PdlpA aavan PHEA_LACLA : 130- 142: estsa Aaef-Vknn--PdlpA aavan PHEA_PSEST : 46- 58: aswpk Aeea-Vfyr--PereA wvlkh K 11: 14.6091 12( 7) A-x(0,1)-L-G-x(2)-[AGV] Occurences: 12(7) PHEA_BACSU : 269- 274: mqele A-LGckV rllga PHEA_CORGL : 9- 15: aptvv AyLGpaG tftee PHEA_ECOLI : 107- 113: hsari AfLGpkG syshl PHEA_ECOLI : 250- 256: ksphv AaLGseA ggtly PHEA_ECOLI : 251- 256: sphva A-LGseA ggtly PHEA_ERWHE : 107- 113: haari AfLGpkG syshl PHEA_ERWHE : 250- 256: nspkv AaLGseA ggely PHEA_ERWHE : 251- 256: spkva A-LGseA ggely PHEA_HAEIN : 107- 113: qnlhi AfLGkrG sysnl PHEA_LACLA : 4- 10: mki AyLGprG sfcsv PHEA_LACLA : 259- 265: aleel AgLGvnV rllgn PHEA_PSEST : 98- 104: qplrv AyLGpeG tfsqa L 12: 13.6700 9( 7) L-E-x(1,2)-L-x-[CDGNTV] Occurences: 9(7) PHEA_BACSU : 52- 58: fafvp LEnaLeG svnlt PHEA_BACSU : 267- 272: gamqe LEa-LgC kvrll PHEA_CORGL : 168- 173: aelfg LEr-LvD dvadv PHEA_ECOLI : 56- 61: rerdl LEr-LiT lgkah PHEA_ERWHE : 56- 61: reral LEn-LiV lgkah PHEA_ERWHE : 266- 272: yqlqv LErnLaN qqqnh PHEA_HAEIN : 359- 364: dtkqa LEe-LkN ysnyl PHEA_LACLA : 255- 260: kipya LEe-LaG lgvnv PHEA_PSEST : 91- 97: sscla LEqpLrV aylgp M 13: 12.5102 9( 7) A-x(2)-E-L Occurences: 9(7) PHEA_BACSU : 96- 100: psren AwkEL dkiys PHEA_BACSU : 263- 267: vlipg AmqEL ealgc PHEA_CORGL : 88- 92: nvqii AeeEL diafs PHEA_ECOLI : 358- 362: aemqk AlkEL geitr PHEA_ERWHE : 256- 260: algse AggEL yqlqv PHEA_ERWHE : 358- 362: ermqq AlqEL qtmtr PHEA_HAEIN : 358- 362: pdtkq AleEL knysn PHEA_LACLA : 254- 258: lkipy AleEL aglgv PHEA_PSEST : 295- 299: rnkpg AlhEL lmpfh N 14: 12.0102 7( 7) V-x(1,2)-L-x(4)-S Occurences: 7(7) PHEA_BACSU : 274- 282: algck VrlLgayqS yql PHEA_CORGL : 228- 235: fgirg Vd-LtrieS rptrk PHEA_ECOLI : 169- 177: gaind VydLlqhtS lsivg PHEA_ERWHE : 169- 177: gsind VydLlqqtS lsivg PHEA_HAEIN : 155- 163: eadfg VlpLenttS gaine PHEA_LACLA : 265- 272: glgvn Vr-LlgnyS vyslg PHEA_PSEST : 352- 359: idhea Va-LkvlgS ypkav O 15: 12.0102 11( 7) L-x(0,1)-E-x-L Occurences: 11(7) PHEA_BACSU : 267- 270: gamqe L-EaL gckvr PHEA_CORGL : 168- 171: aelfg L-ErL vddva PHEA_ECOLI : 17- 21: ekisa LdEkL lalla PHEA_ECOLI : 55- 59: drerd LlErL itlgk PHEA_ECOLI : 56- 59: rerdl L-ErL itlgk PHEA_ECOLI : 311- 315: qqaga LvEaL lvlrn PHEA_ERWHE : 55- 59: erera LlEnL ivlgk PHEA_ERWHE : 56- 59: reral L-EnL ivlgk PHEA_HAEIN : 359- 362: dtkqa L-EeL knysn PHEA_LACLA : 255- 258: kipya L-EeL aglgv PHEA_PSEST : 296- 300: nkpga LhElL mpfhs P 16: 12.0102 13( 7) A-L-x(0,1)-E Occurences: 13(7) PHEA_BACSU : 55- 57: vplen AL-E gsvnl PHEA_CORGL : 219- 222: gslvr ALnE fgirg PHEA_ECOLI : 9- 12: enpll ALrE kisal PHEA_ECOLI : 16- 19: rekis ALdE kllal PHEA_ECOLI : 310- 313: gqqag ALvE allvl PHEA_ECOLI : 358- 361: aemqk ALkE lgeit PHEA_ERWHE : 54- 57: verer ALlE nlivl PHEA_ERWHE : 358- 361: ermqq ALqE lqtmt PHEA_HAEIN : 2- 4: m AL-E lsdir PHEA_HAEIN : 358- 360: pdtkq AL-E elkny PHEA_HAEIN : 358- 361: pdtkq ALeE lknys PHEA_LACLA : 254- 256: lkipy AL-E elagl PHEA_LACLA : 254- 257: lkipy ALeE laglg PHEA_PSEST : 90- 92: msscl AL-E qplrv PHEA_PSEST : 295- 298: rnkpg ALhE llmpf Q 17: 12.0102 8( 7) S-x(5)-A-x(3,4)-A Occurences: 8(7) PHEA_BACSU : 19- 29: hlavs ScfqngAehv-A yrtip PHEA_BACSU : 123- 134: hrhfp SvpyeyAnstgA aakfv PHEA_CORGL : 139- 149: mylsa SsngagAqmv-A egtad PHEA_ECOLI : 114- 124: lgpkg SyshlaArqy-A arhfe PHEA_ECOLI : 114- 125: lgpkg SyshlaArqyaA rhfeq PHEA_ERWHE : 114- 124: lgpkg SyshlaArny-A srhfd PHEA_HAEIN : 114- 124: lgkrg SysnlaArny-A aryqk PHEA_HAEIN : 114- 125: lgkrg SysnlaArnyaA ryqkq PHEA_LACLA : 248- 259: nnatn SlkipyAleelA glgvn PHEA_PSEST : 26- 36: ildli SerarcAqev-A rvkta R 18: 12.0102 7( 7) P-x(4,5)-L-G Occurences: 7(7) PHEA_BACSU : 237- 243: kiesr Ptktg-LG hyffi PHEA_CORGL : 5- 12: msda PtvvayLG pagtf PHEA_ECOLI : 247- 253: aqaks Phvaa-LG seagg PHEA_ERWHE : 247- 253: aalns Pkvaa-LG seagg PHEA_HAEIN : 247- 253: aslnk Pniaa-LG nedgg PHEA_LACLA : 227- 233: kiesr Plrtr-LG qyffi PHEA_PSEST : 94- 101: laleq PlrvayLG pegtf S 19: 12.0102 8( 7) L-x(2)-A-x(0,1)-L Occurences: 8(7) PHEA_BACSU : 52- 56: fafvp LenA-L egsvn PHEA_CORGL : 216- 220: nvpgs LvrA-L nefgi PHEA_ECOLI : 311- 315: qqaga LveA-L lvlrn PHEA_ECOLI : 311- 316: qqaga LveAlL vlrnh PHEA_ERWHE : 311- 315: qqaga LvdA-L lvlrq PHEA_ERWHE : 311- 316: qqaga LvdAlL vlrqh PHEA_HAEIN : 104- 109: qrnqn LhiAfL gkrgs PHEA_HAEIN : 311- 315: qqaga LvdA-L lvfkk PHEA_HAEIN : 311- 316: qqaga LvdAlL vfkkh PHEA_LACLA : 202- 206: tlpdn LpgA-L hkais PHEA_PSEST : 95- 100: aleqp LrvAyL gpegt T 20: 12.0102 12( 7) L-x(1,2)-A-L Occurences: 12(7) PHEA_BACSU : 52- 56: fafvp LenAL egsvn PHEA_BACSU : 267- 270: gamqe Le-AL gckvr PHEA_CORGL : 216- 220: nvpgs LvrAL nefgi PHEA_CORGL : 264- 267: pvaea Lr-AL hlqae PHEA_ECOLI : 7- 10: tsenp Ll-AL rekis PHEA_ECOLI : 21- 24: aldek Ll-AL laerr PHEA_ECOLI : 311- 315: qqaga LveAL lvlrn PHEA_ERWHE : 7- 10: npdnp Ll-AL rdkis PHEA_ERWHE : 311- 315: qqaga LvdAL lvlrq PHEA_HAEIN : 311- 315: qqaga LvdAL lvfkk PHEA_LACLA : 202- 206: tlpdn LpgAL hkais PHEA_PSEST : 7- 10: seadq Lk-AL rvrid Number of patterns evaluated by Pratt:4695 Total running time: 3 seconds