------------------------------------------------------------ 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 COMPLEX1_51K_1 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 COMPLEX1_51K_1.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HOXF_ALCEU 602 HOXF_NOCOP 37 NQO1_PARDE 431 NUBM_BOVIN 464 NUBM_NEUCR 493 NUOF_ECOLI 445 NUOF_SALTY 431 Pratt run started at Thu Feb 6 19:08:46 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.1802 7( 7) A-x(5)-G-x-E-x(2,3)-L 2: 15.1802 8( 7) L-x-R-x(3,4)-E-x(1,3)-R 3: 14.6802 7( 7) G-x(3)-A-x(0,2)-L-x(3,5)-G 4: 14.6802 8( 7) G-x(4)-I-x(1,3)-E-x(3,5)-S 5: 12.0102 11( 7) G-x(1,2)-P-x(2)-V 6: 12.0102 7( 7) Y-x(4,5)-D-E 7: 12.0102 8( 7) D-x-L-x(2,3)-V 8: 12.0102 8( 7) D-x(4)-V-x(3,4)-G 9: 12.0102 8( 7) D-x(4,5)-V-x(4)-G 10: 12.0102 7( 7) L-x-D-x(4,5)-V 11: 12.0102 9( 7) T-x(0,1)-L-I 12: 12.0102 9( 7) T-x(3,4)-I-x(2)-D 13: 12.0102 8( 7) E-x(2)-R-x(4,5)-L 14: 12.0102 9( 7) E-x(3)-L-x(2,3)-I 15: 12.0102 15( 7) E-x(2,3)-L-I 16: 12.0102 8( 7) G-x-E-x(2,3)-L 17: 12.0102 12( 7) G-x(2,3)-T-x-L 18: 12.0102 8( 7) R-x-G-x(3,4)-T 19: 12.0102 9( 7) E-x(2)-G-x(4,5)-R 20: 12.0102 9( 7) E-x(2,3)-G-x(2)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 36.8767 7( 7) E-x(2,3)-G-x(2)-R-x(2)-[LP]-x(3)-[ALV]-x(2)-[GPV]-x(2)-[AGL]-x-[GPT]-x(2)-[LPV]-[ADNT]-[EN]-[AV] B 2: 34.3779 7( 7) A-[GI]-x(3)-[CN]-G-[DES]-E-x(2,3)-L-[IL]-[DEN]-x(3)-[DG] C 3: 25.4586 9( 7) T-x(3,4)-I-[LV]-x-D-x-[AQS]-x(4)-[DHKR]-[AGI]-[ILP] D 4: 23.7351 7( 7) G-[DES]-E-x(2,3)-L-[IL]-[DEN]-x(3)-[DG] E 5: 21.7021 7( 7) E-[RS]-[CN]-G-x(4,5)-R-x-[GI] F 6: 17.8508 7( 7) G-[DE]-x(2)-A-x(0,2)-L-x(3,5)-G G 7: 17.2750 8( 7) T-x(0,1)-L-I-[DEN]-x-[AIL] H 8: 15.9178 13( 7) E-x(2,3)-L-I-[ADEGNS]-x-[FILV] I 9: 15.2968 9( 7) G-x(2,3)-T-x-L-x(3)-[IL] J 10: 15.1802 8( 7) L-x-R-x(3,4)-E-x(1,3)-R K 11: 14.6802 8( 7) G-x(4)-I-x(1,3)-E-x(3,5)-S L 12: 14.5960 7( 7) E-x(2)-R-x(4,5)-L-x-[DEP] M 13: 14.2236 7( 7) E-x-[AEGT]-x-L-x(2,3)-I N 14: 14.2170 9( 7) G-x(1,2)-P-[ADST]-x-V O 15: 12.0102 7( 7) Y-x(4,5)-D-E P 16: 12.0102 8( 7) D-x-L-x(2,3)-V Q 17: 12.0102 8( 7) D-x(4)-V-x(3,4)-G R 18: 12.0102 8( 7) D-x(4,5)-V-x(4)-G S 19: 12.0102 7( 7) L-x-D-x(4,5)-V T 20: 12.0102 12( 7) G-x(2,3)-T-x-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 36.8767 7( 7) E-x(2,3)-G-x(2)-R-x(2)-[LP]-x(3)-[ALV]-x(2)-[GPV]-x(2)-[AGL]-x-[GPT]-x(2)-[LPV]-[ADNT]-[EN]-[AV] Occurences: 7(7) HOXF_ALCEU : 349- 377: liesc EgkrGtpRvkPpfpVqqGylGkPtsVNNV etfaa HOXF_NOCOP : 9- 36: ikail Ern-GseRtrLidiLwdVqhLyGhiPDEV l NQO1_PARDE : 184- 212: llesl EgkkGmpRmkPpfpAgaGlyGcPttVNNV esiav NUBM_BOVIN : 217- 245: liesi EgkqGkpRlkPpfpAdvGvfGcPttVANV etvav NUBM_NEUCR : 229- 257: liesl EgkpGkpRlkPpfpAavGlfGcPstVANV etavv NUOF_ECOLI : 275- 303: areil EdyaGgmRdgLkfkAwqPggAgTdfLTEA hldlp NUOF_SALTY : 275- 303: areil EdyaGgmRdgLkfkAwqPggAgTdfLTEA hldlp B 2: 34.3779 7( 7) A-[GI]-x(3)-[CN]-G-[DES]-E-x(2,3)-L-[IL]-[DEN]-x(3)-[DG] Occurences: 7(7) HOXF_ALCEU : 333- 350: riqmg AGayiCGDEsa-LIEsceG krgtp HOXF_NOCOP : 6- 24: sgdik AIlerNGSErtrLIDilwD vqhly NQO1_PARDE : 168- 185: ylhhg AGayiCGEEta-LLEsleG kkgmp NUBM_BOVIN : 201- 218: fvvrg AGayiCGEEta-LIEsieG kqgkp NUBM_NEUCR : 213- 230: ylhrg AGayvCGEEts-LIEsleG kpgkp NUOF_ECOLI : 175- 192: fvhtg AGryiCGEEta-LINsleG rranp NUOF_SALTY : 175- 192: fvhtg AGryiCGEEta-LINsleG rranp C 3: 25.4586 9( 7) T-x(3,4)-I-[LV]-x-D-x-[AQS]-x(4)-[DHKR]-[AGI]-[ILP] Occurences: 9(7) HOXF_ALCEU : 17- 34: yrsdr TrlidILwDvQheygHIP davlp HOXF_NOCOP : 16- 33: ngser TrlidILwDvQhlygHIP devl NQO1_PARDE : 318- 334: rssfg Tacm-IVmDqStdvvKAI wrlsk NUBM_BOVIN : 351- 367: qtglg Taav-IVmDrStdivKAI arlie NUBM_NEUCR : 363- 379: qsglg Taal-IVmDkStdvvRAI srlsh NUOF_ECOLI : 268- 285: elpfg TtareILeDyAggmrDGL kfkaw NUOF_ECOLI : 269- 285: lpfgt Tare-ILeDyAggmrDGL kfkaw NUOF_SALTY : 268- 285: elpfg TtareILeDyAggmrDGL kfkaw NUOF_SALTY : 269- 285: lpfgt Tare-ILeDyAggmrDGL kfkaw D 4: 23.7351 7( 7) G-[DES]-E-x(2,3)-L-[IL]-[DEN]-x(3)-[DG] Occurences: 7(7) HOXF_ALCEU : 339- 350: gayic GDEsa-LIEsceG krgtp HOXF_NOCOP : 12- 24: ilern GSErtrLIDilwD vqhly NQO1_PARDE : 174- 185: gayic GEEta-LLEsleG kkgmp NUBM_BOVIN : 207- 218: gayic GEEta-LIEsieG kqgkp NUBM_NEUCR : 219- 230: gayvc GEEts-LIEsleG kpgkp NUOF_ECOLI : 181- 192: gryic GEEta-LINsleG rranp NUOF_SALTY : 181- 192: gryic GEEta-LINsleG rranp E 5: 21.7021 7( 7) E-[RS]-[CN]-G-x(4,5)-R-x-[GI] Occurences: 7(7) HOXF_ALCEU : 497- 508: qffve ESCGicvpcRaG nvdlh HOXF_NOCOP : 9- 19: ikail ERNGsert-RlI dilwd NQO1_PARDE : 344- 355: kffkh ESCGqctpcReG tgwmm NUBM_BOVIN : 377- 388: efykh ESCGqctpcReG vdwmn NUBM_NEUCR : 389- 400: hfyrh ESCGqctpcReG skwte NUOF_ECOLI : 349- 360: effar ESCGwctpcRdG lpwsv NUOF_SALTY : 349- 360: effar ESCGwctpcRdG lpwsv F 6: 17.8508 7( 7) G-[DE]-x(2)-A-x(0,2)-L-x(3,5)-G Occurences: 7(7) HOXF_ALCEU : 339- 350: gayic GDesA--LiesceG krgtp HOXF_NOCOP : 2- 12: s GDikAi-Lern--G sertr NQO1_PARDE : 174- 185: gayic GEetAl-Lesle-G kkgmp NQO1_PARDE : 174- 185: gayic GEetA--LlesleG kkgmp NUBM_BOVIN : 207- 218: gayic GEetA--LiesieG kqgkp NUBM_NEUCR : 87- 98: hdwii GEvkAsgLrgr--G gagfp NUBM_NEUCR : 87- 99: hdwii GEvkAsgLrgrg-G agfps NUOF_ECOLI : 181- 192: gryic GEetA--LinsleG rranp NUOF_SALTY : 181- 192: gryic GEetA--LinsleG rranp G 7: 17.2750 8( 7) T-x(0,1)-L-I-[DEN]-x-[AIL] Occurences: 8(7) HOXF_ALCEU : 17- 23: yrsdr TrLIDiL wdvqh HOXF_NOCOP : 16- 22: ngser TrLIDiL wdvqh NQO1_PARDE : 104- 109: rhdph T-LIEgA liasf NUBM_BOVIN : 210- 216: icgee TaLIEsI egkqg NUBM_NEUCR : 222- 228: vcgee TsLIEsL egkpg NUOF_ECOLI : 184- 190: icgee TaLINsL egrra NUOF_ECOLI : 430- 436: qpfsn ThLINgI qpnll NUOF_SALTY : 184- 190: icgee TaLINsL egrra H 8: 15.9178 13( 7) E-x(2,3)-L-I-[ADEGNS]-x-[FILV] Occurences: 13(7) HOXF_ALCEU : 123- 131: glsdq EpamLIDkV vftrl HOXF_NOCOP : 14- 22: erngs ErtrLIDiL wdvqh NQO1_PARDE : 107- 114: phtli Ega-LIAsF amgah NUBM_BOVIN : 208- 216: ayicg EetaLIEsI egkqg NUBM_BOVIN : 209- 216: yicge Eta-LIEsI egkqg NUBM_NEUCR : 220- 228: ayvcg EetsLIEsL egkpg NUBM_NEUCR : 221- 228: yvcge Ets-LIEsL egkpg NUOF_ECOLI : 114- 121: phllv Egm-LISaF alkay NUOF_ECOLI : 182- 190: ryicg EetaLINsL egrra NUOF_ECOLI : 183- 190: yicge Eta-LINsL egrra NUOF_SALTY : 114- 121: phllv Egm-LISaF alkay NUOF_SALTY : 182- 190: ryicg EetaLINsL egrra NUOF_SALTY : 183- 190: yicge Eta-LINsL egrra I 9: 15.2968 9( 7) G-x(2,3)-T-x-L-x(3)-[IL] Occurences: 9(7) HOXF_ALCEU : 224- 233: grgga Gfs-TgLkwrL crdae HOXF_NOCOP : 12- 22: ilern GserTrLidiL wdvqh NQO1_PARDE : 174- 183: gayic Gee-TaLlesL egkkg NUBM_BOVIN : 207- 216: gayic Gee-TaLiesI egkqg NUBM_NEUCR : 219- 228: gayvc Gee-TsLiesL egkpg NUOF_ECOLI : 66- 75: grgga Gfs-TgLkwsL mpkde NUOF_ECOLI : 181- 190: gryic Gee-TaLinsL egrra NUOF_SALTY : 66- 75: grgga Gfs-TgLkwsL mpkde NUOF_SALTY : 181- 190: gryic Gee-TaLinsL egrra J 10: 15.1802 8( 7) L-x-R-x(3,4)-E-x(1,3)-R Occurences: 8(7) HOXF_ALCEU : 300- 308: ylkdy LeRqlq-El--R edgll HOXF_NOCOP : 8- 17: dikai LeRngs-Ert-R lidil NQO1_PARDE : 405- 416: wpiqg LiRnfreEiedR ikakr NUBM_BOVIN : 438- 449: wpvqg LiRhfrpEleeR mqqfa NUBM_NEUCR : 16- 25: asart LsRaaa-Eqc-R tfatv NUBM_NEUCR : 450- 461: wpiqg LiRhfrpEleaR irkfa NUOF_ECOLI : 338- 348: inmvs LvRnle-EffaR escgw NUOF_SALTY : 338- 348: igmvs LvRnle-EffaR escgw K 11: 14.6802 8( 7) G-x(4)-I-x(1,3)-E-x(3,5)-S Occurences: 8(7) HOXF_ALCEU : 332- 347: iriqm GagayIcgdEsalieS cegkr HOXF_NOCOP : 2- 13: s GdikaIl--Erng--S ertrl NQO1_PARDE : 39- 50: aiiqr GrdkiId--Emka--S glrgr NQO1_PARDE : 167- 182: lylhh GagayIcgeEtalleS legkk NUBM_BOVIN : 200- 215: vfvvr GagayIcgeEtalieS iegkq NUBM_NEUCR : 81- 92: eillk GhdwiIg--Evka--S glrgr NUOF_ECOLI : 174- 189: lfvht GagryIcgeEtalinS legrr NUOF_SALTY : 174- 189: lfvht GagryIcgeEtalinS legrr L 12: 14.5960 7( 7) E-x(2)-R-x(4,5)-L-x-[DEP] Occurences: 7(7) HOXF_ALCEU : 10- 21: ittil EryRsdrtrLiD ilwdv HOXF_NOCOP : 14- 24: erngs ErtRlidi-LwD vqhly NQO1_PARDE : 96- 107: tckdr EimRhdphtLiE galia NUBM_BOVIN : 129- 140: tckdr EiiRhdphkLvE gclvg NUBM_NEUCR : 141- 152: tckdr EimRkdphkLvE gclva NUOF_ECOLI : 36- 47: skngy EgaRkaltgLsP deivn NUOF_SALTY : 36- 47: skngy EgaRkaltgLsP deivs M 13: 14.2236 7( 7) E-x-[AEGT]-x-L-x(2,3)-I Occurences: 7(7) HOXF_ALCEU : 309- 317: lqelr EdGlLgraI ggrag HOXF_NOCOP : 14- 21: erngs ErTrLid-I lwdvq NQO1_PARDE : 132- 140: gefir ErEaLqaaI decyd NUBM_BOVIN : 208- 216: ayicg EeTaLiesI egkqg NUBM_NEUCR : 177- 185: gefiq EaAiLqnaI neaya NUOF_ECOLI : 152- 160: iaeat EaGlLgknI mgtgf NUOF_SALTY : 152- 160: iaeat EaGlLgknI mgtgf N 14: 14.2170 9( 7) G-x(1,2)-P-[ADST]-x-V Occurences: 9(7) HOXF_ALCEU : 31- 37: vqhey GhiPDaV lpqlg HOXF_ALCEU : 369- 374: qqgyl Gk-PTsV nnvet HOXF_NOCOP : 30- 36: vqhly GhiPDeV l NQO1_PARDE : 204- 209: gagly Gc-PTtV nnves NUBM_BOVIN : 10- 16: rrllg GslPArV svrfs NUBM_BOVIN : 237- 242: dvgvf Gc-PTtV anvet NUBM_NEUCR : 249- 254: avglf Gc-PStV anvet NUOF_ECOLI : 211- 216: tsgaw Gk-PTcV nnvet NUOF_SALTY : 211- 216: tsgvw Gk-PTcV nnvet O 15: 12.0102 7( 7) Y-x(4,5)-D-E Occurences: 7(7) HOXF_ALCEU : 243- 250: eseqk YvicnaDE gepgt HOXF_NOCOP : 29- 35: dvqhl Yghip-DE vl NQO1_PARDE : 79- 86: dgrps YlvinaDE sepat NUBM_BOVIN : 112- 119: dgrpk YlvvnaDE gepgt NUBM_NEUCR : 124- 131: ddkpr YlvvnaDE gepgt NUOF_ECOLI : 86- 93: smnir YllcnaDE mepgt NUOF_SALTY : 86- 93: smnir YllcnaDE mepgt P 16: 12.0102 8( 7) D-x-L-x(2,3)-V Occurences: 8(7) HOXF_ALCEU : 21- 26: rtrli DiLwd-V qheyg HOXF_ALCEU : 482- 487: fnckr DlLei-V rdhmq HOXF_NOCOP : 20- 25: rtrli DiLwd-V qhlyg NQO1_PARDE : 377- 382: eveei DmLfd-V tkqve NUBM_BOVIN : 312- 317: vtggw DnLla-V ipggs NUBM_NEUCR : 324- 329: vrggw DnLla-V ipggs NUOF_ECOLI : 359- 365: ctpcr DgLpwsV kilrr NUOF_SALTY : 359- 365: ctpcr DgLpwsV kilra Q 17: 12.0102 8( 7) D-x(4)-V-x(3,4)-G Occurences: 8(7) HOXF_ALCEU : 21- 31: rtrli DilwdVqheyG hipda HOXF_NOCOP : 20- 30: rtrli DilwdVqhlyG hipde NQO1_PARDE : 307- 317: aimdy DgmrdVrssfG tacmi NUBM_BOVIN : 192- 202: cgsgy DfdvfVvrgaG ayicg NUBM_BOVIN : 312- 321: vtggw DnllaVipg-G sstpl NUBM_NEUCR : 324- 333: vrggw DnllaVipg-G sstpi NUOF_ECOLI : 166- 176: mgtgf DfelfVhtgaG ryicg NUOF_SALTY : 166- 176: mgtgf DfelfVhtgaG ryicg R 18: 12.0102 8( 7) D-x(4,5)-V-x(4)-G Occurences: 8(7) HOXF_ALCEU : 21- 31: rtrli Dilwd-VqheyG hipda HOXF_ALCEU : 489- 500: leivr DhmqffVeescG icvpc HOXF_NOCOP : 20- 30: rtrli Dilwd-VqhlyG hipde NQO1_PARDE : 307- 317: aimdy Dgmrd-VrssfG tacmi NUBM_BOVIN : 192- 202: cgsgy Dfdvf-VvrgaG ayicg NUBM_NEUCR : 32- 43: fatvq DgsanpVrhygG lkdqd NUOF_ECOLI : 166- 176: mgtgf Dfelf-VhtgaG ryicg NUOF_SALTY : 166- 176: mgtgf Dfelf-VhtgaG ryicg S 19: 12.0102 7( 7) L-x-D-x(4,5)-V Occurences: 7(7) HOXF_ALCEU : 19- 26: sdrtr LiDilwd-V qheyg HOXF_NOCOP : 18- 25: sertr LiDilwd-V qhlyg NQO1_PARDE : 379- 386: eeidm LfDvtkq-V eghti NUBM_BOVIN : 427- 435: htica LgDgaawpV qglir NUBM_NEUCR : 311- 319: ipmre LiDkhcggV rggwd NUOF_ECOLI : 17- 24: pltwr LrDdkqp-V wldey NUOF_SALTY : 17- 24: pltwr LrDdkqp-V wldey T 20: 12.0102 12( 7) G-x(2,3)-T-x-L Occurences: 12(7) HOXF_ALCEU : 224- 229: grgga Gfs-TgL kwrlc HOXF_NOCOP : 12- 18: ilern GserTrL idilw NQO1_PARDE : 174- 179: gayic Gee-TaL lesle NUBM_BOVIN : 92- 97: grgga Gfp-TgL kwsfm NUBM_BOVIN : 207- 212: gayic Gee-TaL iesie NUBM_BOVIN : 320- 326: lavip GgssTpL ipksv NUBM_BOVIN : 321- 326: avipg Gss-TpL ipksv NUBM_NEUCR : 219- 224: gayvc Gee-TsL iesle NUOF_ECOLI : 66- 71: grgga Gfs-TgL kwslm NUOF_ECOLI : 181- 186: gryic Gee-TaL insle NUOF_SALTY : 66- 71: grgga Gfs-TgL kwslm NUOF_SALTY : 181- 186: gryic Gee-TaL insle Number of patterns evaluated by Pratt:1165 Total running time: 1 seconds