------------------------------------------------------------ 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 SUA5 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 SUA5.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: SUA5_YEAST 426 YCIO_ECOLI 218 YCIO_HAEIN 207 YRDC_ECOLI 176 YRDC_HAEIN 183 YRFE_MYCLE 220 YWLC_BACSU 346 Pratt run started at Thu Feb 6 21:16:00 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.1802 7( 7) P-x(4)-A-x(2,3)-L-x(0,2)-L 2: 12.5102 7( 7) P-x(5)-G-x-G 3: 12.0102 7( 7) L-x(5)-S-x(0,1)-L 4: 12.0102 7( 7) P-x(5)-I-x(0,1)-L 5: 12.0102 9( 7) L-x(5)-P-x(4,5)-L 6: 12.0102 8( 7) A-x(2,3)-L-L 7: 12.0102 8( 7) P-T-x(1,2)-V 8: 12.0102 10( 7) V-x(2,3)-P-T 9: 11.5102 10( 7) A-L-x(2,4)-L 10: 11.5102 7( 7) E-x(0,1)-G-x(4,5)-P 11: 11.5102 9( 7) V-x(0,1)-V-x(2,3)-T 12: 11.5102 9( 7) V-x(3,4)-E-x(1,2)-G 13: 11.5102 8( 7) V-x(4)-T-x(3,5)-L 14: 11.5102 7( 7) L-x(3)-P-x(1,3)-T 15: 11.5102 10( 7) A-x(0,1)-L-x(1,2)-L 16: 11.5102 10( 7) T-x(2,3)-L-x(3,4)-P 17: 11.5102 10( 7) V-x(1,2)-L-x(3,4)-G 18: 11.5102 8( 7) T-x(0,2)-T-x(3)-L 19: 11.5102 8( 7) P-x(0,1)-T-x(0,1)-T 20: 11.5102 11( 7) V-x(2,3)-P-x(0,1)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 66.5390 9( 7) V-x(2,3)-P-T-[DE]-[AST]-[GV]-[FY]-[AG]-[ILV]-G-[ACG]-x(3)-[DNS]-x(2)-[AS]-[MV]-x(2)-[IL]-x(2)-[AIL]-[KR]-x(2)-[GP]-x-[DEG]-x-[GNP]-[FLV] B 2: 27.7177 7( 7) P-T-x(1,2)-V-x-[DG]-[ILV]-[GT]-x-[DENS]-[APST]-x-[DNSV] C 3: 19.6623 7( 7) P-x(4)-A-x(2,3)-L-x(0,2)-L-x-[ADEQ]-x(2)-[ILPV] D 4: 19.5451 7( 7) T-x(0,2)-T-[PV]-x(2)-L-x-[ADEG]-x(3)-[NSV] E 5: 19.4926 7( 7) P-[TV]-x(4)-G-x-G-[ACDGS]-[DNSTV] F 6: 19.0806 7( 7) P-[GLV]-x(2)-[AGTV]-x-I-x(0,1)-L-x-[ACDG] G 7: 18.6713 7( 7) P-x(0,1)-T-x(0,1)-T-x(3)-[ILP]-[AGT]-x-[DENRS] H 8: 17.0456 7( 7) L-x(5)-P-x(4,5)-L-[IMV]-x-[AIPV] I 9: 16.4527 7( 7) V-[GIV]-x(3)-T-x(3,5)-L-[CGNV] J 10: 13.7126 8( 7) A-L-x(2,4)-L-x(3)-[AGLP] K 11: 13.1613 9( 7) V-x(3,4)-E-x(1,2)-G-x(3)-[ADGNPT] L 12: 12.0102 7( 7) L-x(5)-S-x(0,1)-L M 13: 12.0102 8( 7) A-x(2,3)-L-L N 14: 11.5102 7( 7) E-x(0,1)-G-x(4,5)-P O 15: 11.5102 9( 7) V-x(0,1)-V-x(2,3)-T P 16: 11.5102 7( 7) L-x(3)-P-x(1,3)-T Q 17: 11.5102 10( 7) A-x(0,1)-L-x(1,2)-L R 18: 11.5102 10( 7) T-x(2,3)-L-x(3,4)-P S 19: 11.5102 10( 7) V-x(1,2)-L-x(3,4)-G T 20: 11.5102 8( 7) P-x(0,1)-T-x(0,1)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 66.5390 9( 7) V-x(2,3)-P-T-[DE]-[AST]-[GV]-[FY]-[AG]-[ILV]-G-[ACG]-x(3)-[DNS]-x(2)-[AS]-[MV]-x(2)-[IL]-x(2)-[AIL]-[KR]-x(2)-[GP]-x-[DEG]-x-[GNP]-[FLV] Occurences: 9(7) SUA5_YEAST : 66- 101: dtdet Vaf-PTETVYGLGGsalNdnSVlsIyrAKnrPsDnPL ithvs YCIO_ECOLI : 41- 77: vrkgg VivyPTDSGYALGCkieDknAMerIcrIRqlPdGhNF tlmcr YCIO_HAEIN : 29- 65: lqkgg VivyPTDSGYALGCmmgDkhAMdrIvaIRklPeGhNF tlvcs YRDC_ECOLI : 8- 44: smker ViayPTEAVFGVGCdpdSetAVmrLleLKqrPvDkGL iliaa YRDC_HAEIN : 15- 51: lrqnq VvayPTEAVFGLGCnpqSesAVkkLldLKqrPvEkGL ilvap YRDC_HAEIN : 16- 51: rqnqv Vay-PTEAVFGLGCnpqSesAVkkLldLKqrPvEkGL ilvap YRFE_MYCLE : 33- 68: kggrl Vvm-PTDTVYGIGAdafDraAVaaLlsAKgrGrDmPV gvlvg YWLC_BACSU : 33- 69: lrene VvafPTETVYGLGAnakNtdAVkkIyeAKgrPsDnPL ivhia YWLC_BACSU : 34- 69: renev Vaf-PTETVYGLGAnakNtdAVkkIyeAKgrPsDnPL ivhia B 2: 27.7177 7( 7) P-T-x(1,2)-V-x-[DG]-[ILV]-[GT]-x-[DENS]-[APST]-x-[DNSV] Occurences: 7(7) SUA5_YEAST : 69- 82: etvaf PTetVyGLGgSAlN dnsvl YCIO_ECOLI : 193- 205: ylgqk PTt-ViDLTdDTpV vvreg YCIO_HAEIN : 182- 194: ylgqe PTt-VvDLTeESpV ilreg YRDC_ECOLI : 12- 25: rviay PTeaVfGVGcDPdS etavm YRDC_HAEIN : 19- 32: qvvay PTeaVfGLGcNPqS esavk YRFE_MYCLE : 36- 49: rlvvm PTdtVyGIGaDAfD raava YWLC_BACSU : 37- 50: evvaf PTetVyGLGaNAkN tdavk C 3: 19.6623 7( 7) P-x(4)-A-x(2,3)-L-x(0,2)-L-x-[ADEQ]-x(2)-[ILPV] Occurences: 7(7) SUA5_YEAST : 176- 192: favri PanpvAra-LiaLsDtpI aapsa YCIO_ECOLI : 136- 153: igmrv PsnpiAqalLeaLgEpmL stslm YCIO_HAEIN : 124- 141: iglrv PdnkiAldlLsaLgEpiL scslm YRDC_ECOLI : 23- 40: gvgcd PdsetAvmrLleLkQrpV dkgli YRDC_HAEIN : 30- 47: glgcn PqsesAvkkLldLkQrpV ekgli YRFE_MYCLE : 127- 141: vmlrm PlhsvAie-L--LcEvgP mavss YWLC_BACSU : 19- 33: lstnd PqiaqAaa-L--LrEneV vafpt D 4: 19.5451 7( 7) T-x(0,2)-T-[PV]-x(2)-L-x-[ADEG]-x(3)-[NSV] Occurences: 7(7) SUA5_YEAST : 70- 82: tvafp Te-TVygLgGsalN dnsvl YCIO_ECOLI : 194- 205: lgqkp T--TVidLtDdtpV vvreg YCIO_HAEIN : 183- 194: lgqep T--TVvdLtEespV ilreg YRDC_ECOLI : 88- 99: fpapa T--TPrwLtGrfdS lavrv YRDC_HAEIN : 95- 106: vpaks T--TPhfLtGkfdS iairl YRFE_MYCLE : 190- 203: tivdl TeaTPriLrAgpvS varia YWLC_BACSU : 38- 50: vvafp Te-TVygLgAnakN tdavk E 5: 19.4926 7( 7) P-[TV]-x(4)-G-x-G-[ACDGS]-[DNSTV] Occurences: 7(7) SUA5_YEAST : 69- 79: etvaf PTetvyGlGGS alndn YCIO_ECOLI : 204- 214: ltddt PVvvreGvGDV kpfl YCIO_HAEIN : 193- 203: ltees PVilreGsGST apfi YRDC_ECOLI : 12- 22: rviay PTeavfGvGCD pdset YRDC_HAEIN : 19- 29: qvvay PTeavfGlGCN pqses YRFE_MYCLE : 36- 46: rlvvm PTdtvyGiGAD afdra YWLC_BACSU : 37- 47: evvaf PTetvyGlGAN akntd F 6: 19.0806 7( 7) P-[GLV]-x(2)-[AGTV]-x-I-x(0,1)-L-x-[ACDG] Occurences: 7(7) SUA5_YEAST : 179- 189: ripan PVarAlIaLsD tpiaa YCIO_ECOLI : 106- 115: mknnt PGnyTfI-LkG tkevp YCIO_HAEIN : 94- 103: iknnt PGryTfI-LtA tkelp YRDC_ECOLI : 39- 48: elkqr PVdkGlI-LiA anyeq YRDC_HAEIN : 46- 55: dlkqr PVekGlI-LvA psldf YRFE_MYCLE : 127- 137: vmlrm PLhsVaIeLlC evgpm YWLC_BACSU : 99- 108: mkrfw PGalTlI-LpC kpdal G 7: 18.6713 7( 7) P-x(0,1)-T-x(0,1)-T-x(3)-[ILP]-[AGT]-x-[DENRS] Occurences: 7(7) SUA5_YEAST : 69- 79: etvaf P-TeTvygLGgS alndn YCIO_ECOLI : 193- 202: ylgqk P-T-TvidLTdD tpvvv YCIO_HAEIN : 182- 191: ylgqe P-T-TvvdLTeE spvil YRDC_ECOLI : 86- 96: fvfpa PaT-TprwLTgR fdsla YRDC_HAEIN : 85- 94: gkyer P-T-TwivPAkS ttphf YRFE_MYCLE : 36- 46: rlvvm P-TdTvygIGaD afdra YWLC_BACSU : 37- 47: evvaf P-TeTvygLGaN akntd H 8: 17.0456 7( 7) L-x(5)-P-x(4,5)-L-[IMV]-x-[AIPV] Occurences: 7(7) SUA5_YEAST : 40- 55: hidgs LptitdPeteaaLVeA ariir YCIO_ECOLI : 145- 160: iaqal LealgePmlstsLMlP gseft YCIO_HAEIN : 133- 148: ialdl LsalgePilscsLMlP neeht YRDC_ECOLI : 33- 47: avmrl LelkqrPvdkg-LIlI aanye YRDC_HAEIN : 40- 54: avkkl LdlkqrPvekg-LIlV apsld YRFE_MYCLE : 92- 106: dgare LirafwPgals-LVvV hapsl YWLC_BACSU : 93- 107: ekakt LmkrfwPgalt-LIlP ckpda I 9: 16.4527 7( 7) V-[GIV]-x(3)-T-x(3,5)-L-[CGNV] Occurences: 7(7) SUA5_YEAST : 230- 241: ggack VGvesTvvdg-LC npptl YCIO_ECOLI : 41- 53: vrkgg VIvypTdsgyaLG ckied YCIO_HAEIN : 29- 41: lqkgg VIvypTdsgyaLG cmmgd YRDC_ECOLI : 150- 160: gaafp VVpgeTggr--LN pseir YRDC_HAEIN : 15- 27: lrqnq VVaypTeavfgLG cnpqs YRFE_MYCLE : 72- 82: pvgvl VGswhTieg--LV ytmpd YWLC_BACSU : 33- 45: lrene VVafpTetvygLG anakn J 10: 13.7126 8( 7) A-L-x(2,4)-L-x(3)-[AGLP] Occurences: 8(7) SUA5_YEAST : 183- 191: npvar ALia--LsdtP iaaps YCIO_ECOLI : 147- 157: qalle ALgepmLstsL mlpgs YCIO_HAEIN : 129- 137: pdnki ALdl--LsalG epils YCIO_HAEIN : 135- 145: ldlls ALgepiLscsL mlpne YRDC_ECOLI : 167- 176: seird ALtge-LfrqG YRDC_HAEIN : 119- 127: hpsvk ALce--LtgfA ltsts YRFE_MYCLE : 26- 36: asava ALkggrLvvmP tdtvy YWLC_BACSU : 101- 110: rfwpg ALtli-LpckP dalsp K 11: 13.1613 9( 7) V-x(3,4)-E-x(1,2)-G-x(3)-[ADGNPT] Occurences: 9(7) SUA5_YEAST : 302- 313: kvvll Vphc-EgdGilkG vdrme SUA5_YEAST : 399- 410: vdlif VeginEe-GeglA vmnrl YCIO_ECOLI : 205- 216: tddtp Vvvr-EgvGdvkP fl YCIO_HAEIN : 194- 205: teesp Vilr-EgsGstaP fi YRDC_ECOLI : 150- 160: gaafp Vvpg-Et-GgrlN pseir YRDC_ECOLI : 150- 161: gaafp Vvpg-EtgGrlnP seird YRDC_HAEIN : 117- 129: cdhps VkalcEltGfalT stsan YRFE_MYCLE : 204- 216: agpvs VariaEvlGvvpA slia YWLC_BACSU : 54- 66: kntda VkkiyEakGrpsD npliv YWLC_BACSU : 272- 284: grrvg VltteEkaGvysA dyvks L 12: 12.0102 7( 7) L-x(5)-S-x(0,1)-L Occurences: 7(7) SUA5_YEAST : 260- 267: eeivk LggeawS-L ckven YCIO_ECOLI : 79- 87: ghnft LmcrdlSeL stysf YCIO_HAEIN : 67- 75: ghnft LvcsdlSeL styar YRDC_ECOLI : 93- 100: ttprw LtgrfdS-L avrvt YRDC_HAEIN : 51- 58: pvekg LilvapS-L dffrp YRFE_MYCLE : 211- 218: riaev LgvvpaS-L ia YWLC_BACSU : 135- 143: dhpla LalireSgL piaap M 13: 12.0102 8( 7) A-x(2,3)-L-L Occurences: 8(7) SUA5_YEAST : 296- 301: hysps AkvvLL vphce YCIO_ECOLI : 141- 145: psnpi Aqa-LL ealge YCIO_HAEIN : 129- 133: pdnki Ald-LL salge YRDC_ECOLI : 28- 33: pdset AvmrLL elkqr YRDC_HAEIN : 35- 40: pqses AvkkLL dlkqr YRFE_MYCLE : 52- 57: afdra AvaaLL sakgr YRFE_MYCLE : 132- 136: plhsv Aie-LL cevgp YWLC_BACSU : 24- 28: pqiaq Aaa-LL renev N 14: 11.5102 7( 7) E-x(0,1)-G-x(4,5)-P Occurences: 7(7) SUA5_YEAST : 277- 285: nkktv EkGekvrtP gmkyr YCIO_ECOLI : 209- 216: pvvvr E-GvgdvkP fl YCIO_HAEIN : 198- 205: pvilr E-GsgstaP fi YRDC_ECOLI : 154- 161: pvvpg EtGgrln-P seird YRDC_HAEIN : 48- 56: kqrpv EkGlilvaP sldff YRFE_MYCLE : 79- 86: swhti E-GlvytmP dgare YWLC_BACSU : 140- 148: lalir EsGlpiaaP sanls O 15: 11.5102 9( 7) V-x(0,1)-V-x(2,3)-T Occurences: 9(7) SUA5_YEAST : 230- 235: ggack VgVes-T vvdgl YCIO_ECOLI : 41- 46: vrkgg ViVyp-T dsgya YCIO_HAEIN : 29- 34: lqkgg ViVyp-T dsgya YCIO_HAEIN : 185- 189: qeptt V-Vdl-T eespv YRDC_ECOLI : 150- 155: gaafp V-VpgeT ggrln YRDC_HAEIN : 15- 20: lrqnq V-VaypT eavfg YRFE_MYCLE : 33- 37: kggrl V-Vmp-T dtvyg YWLC_BACSU : 33- 38: lrene V-VafpT etvyg YWLC_BACSU : 270- 275: qggrr VgVlt-T eekag P 16: 11.5102 7( 7) L-x(3)-P-x(1,3)-T Occurences: 7(7) SUA5_YEAST : 141- 147: pliss LwpgPl--T illpv YCIO_ECOLI : 189- 195: ihggy LgqkPt--T vidlt YCIO_HAEIN : 178- 184: ihggy LgqePt--T vvdlt YRDC_ECOLI : 128- 136: stsan LsglPpcrT vdevr YRDC_HAEIN : 135- 143: stsan LtgePpcrT adevr YRFE_MYCLE : 32- 39: lkggr LvvmPtd-T vygig YWLC_BACSU : 152- 159: apsan LsgkPsp-T kaehv Q 17: 11.5102 10( 7) A-x(0,1)-L-x(1,2)-L Occurences: 10(7) SUA5_YEAST : 159- 163: ssehs A-LskL ttadq SUA5_YEAST : 183- 187: npvar A-LiaL sdtpi SUA5_YEAST : 338- 343: nikki AiLtsL klrds YCIO_ECOLI : 143- 148: npiaq AlLeaL gepml YCIO_HAEIN : 129- 132: pdnki A-Ld-L lsalg YCIO_HAEIN : 129- 133: pdnki A-LdlL salge YRDC_ECOLI : 126- 131: lvsts AnLsgL ppcrt YRDC_HAEIN : 119- 123: hpsvk A-LceL tgfal YRFE_MYCLE : 100- 103: afwpg A-Ls-L vvvha YWLC_BACSU : 101- 104: rfwpg A-Lt-L ilpck YWLC_BACSU : 134- 137: pdhpl A-La-L iresg R 18: 11.5102 10( 7) T-x(2,3)-L-x(3,4)-P Occurences: 10(7) SUA5_YEAST : 18- 25: kalfd Tki-Lkvn-P lsiif YCIO_ECOLI : 195- 204: gqkpt TvidLtddtP vvvre YCIO_HAEIN : 184- 193: gqept TvvdLteesP vilre YRDC_ECOLI : 124- 132: kplvs TsanLsgl-P pcrtv YRDC_ECOLI : 124- 133: kplvs TsanLsglpP crtvd YRDC_HAEIN : 131- 139: falts TsanLtge-P pcrta YRDC_HAEIN : 131- 140: falts TsanLtgepP crtad YRFE_MYCLE : 77- 86: vgswh TiegLvytmP dgare YRFE_MYCLE : 185- 194: qqaas TivdLteatP rilra YRFE_MYCLE : 193- 201: dltea TpriLrag-P vsvar YWLC_BACSU : 11- 19: wfvdv Tde-LstndP qiaqa YWLC_BACSU : 103- 110: wpgal Tli-Lpck-P dalsp S 19: 11.5102 10( 7) V-x(1,2)-L-x(3,4)-G Occurences: 10(7) SUA5_YEAST : 394- 401: dendk Vd-LifveG ineeg YCIO_ECOLI : 180- 186: rlekq Vd-Liih-G gylgq YCIO_ECOLI : 180- 187: rlekq Vd-LiihgG ylgqk YCIO_HAEIN : 21- 28: linqa VeiLqkg-G vivyp YCIO_HAEIN : 169- 175: rlehq Vd-Liih-G gylgq YCIO_HAEIN : 169- 176: rlehq Vd-LiihgG ylgqe YCIO_HAEIN : 194- 201: teesp Vi-LregsG stapf YRDC_ECOLI : 110- 118: tdhpl VvaLcqayG kplvs YRDC_ECOLI : 111- 118: dhplv Va-LcqayG kplvs YRDC_HAEIN : 117- 125: cdhps VkaLceltG falts YRFE_MYCLE : 53- 61: fdraa VaaLlsakG rgrdm YWLC_BACSU : 198- 204: addip Vl-Lrpg-G itkeq T 20: 11.5102 8( 7) P-x(0,1)-T-x(0,1)-T Occurences: 8(7) SUA5_YEAST : 41- 44: idgsl P-TiT dpete SUA5_YEAST : 69- 72: etvaf P-TeT vyglg YCIO_ECOLI : 193- 195: ylgqk P-T-T vidlt YCIO_HAEIN : 182- 184: ylgqe P-T-T vvdlt YRDC_ECOLI : 86- 89: fvfpa PaT-T prwlt YRDC_HAEIN : 85- 87: gkyer P-T-T wivpa YRFE_MYCLE : 36- 39: rlvvm P-TdT vygig YWLC_BACSU : 37- 40: evvaf P-TeT vyglg Number of patterns evaluated by Pratt:1729 Total running time: 1 seconds