------------------------------------------------------------ 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 29 sequences from file TIM PATTERN CONSERVATION: CM: min Nr of Seqs to Match 29 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 TIM.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: TPI1_GIALA 257 TPI2_GIALA 257 TPIC_SECCE 298 TPIS_BACME 251 TPIS_BACST 253 TPIS_BACSU 252 TPIS_CHICK 247 TPIS_COPJA 253 TPIS_CORGL 259 TPIS_CULTA 246 TPIS_DROME 247 TPIS_ECOLI 255 TPIS_EMENI 249 TPIS_HAEIN 263 TPIS_HORVU 9 TPIS_HUMAN 248 TPIS_LATCH 247 TPIS_MACMU 248 TPIS_MAIZE 252 TPIS_MORSP 269 TPIS_MOUSE 248 TPIS_MYCLE 261 TPIS_NICPL 10 TPIS_PLAFA 248 TPIS_RABIT 248 TPIS_SCHPO 249 TPIS_SECCE 253 TPIS_TRYBB 250 TPIS_YEAST 247 Pratt run started at Thu Feb 6 21:26:57 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 83( 29) G-G 2: 8.3401 69( 29) V-G 3: 7.8401 68( 29) G-x(0,1)-N Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 13.2841 44( 29) V-G-[ADEGNQ]-[AN] B 2: 10.9905 78( 29) G-G-[ANS] C 3: 7.8401 68( 29) G-x(0,1)-N Best patterns with alignements: fitness hits(seqs) Pattern A 1: 13.2841 44( 29) V-G-[ADEGNQ]-[AN] Occurences: 44(29) TPI1_GIALA : 236- 239: idgfl VGGA slkpe TPI2_GIALA : 236- 239: idgfl VGGA slkpe TPIC_SECCE : 51- 54: sgkff VGGN wkcng TPIC_SECCE : 274- 277: idgfl VGGA slkgp TPIS_BACME : 233- 236: idgal VGGA slead TPIS_BACST : 233- 236: idgpl VGGA slepa TPIS_BACSU : 232- 235: idgal VGGA slepq TPIS_CHICK : 7- 10: prkff VGGN wkmng TPIS_CHICK : 230- 233: vdgfl VGGA slkpe TPIS_COPJA : 7- 10: grkff VGGN wkcng TPIS_COPJA : 232- 235: idgfl VGGA slkpe TPIS_CORGL : 238- 241: vdggl VGGA sldge TPIS_CULTA : 6- 9: grkfc VGGN wkmng TPIS_CULTA : 229- 232: idgfl VGGA slkpe TPIS_DROME : 7- 10: srkfc VGGN wkmng TPIS_DROME : 230- 233: idgfl VGGA slkpe TPIS_ECOLI : 232- 235: idgal VGGA slkad TPIS_EMENI : 7- 10: prkff VGGN fkmng TPIS_EMENI : 232- 235: idgfl VGGA slkpa TPIS_HAEIN : 241- 244: idgal VGGA slkap TPIS_HORVU : 6- 9: axkff VGGN TPIS_HUMAN : 8- 11: srkff VGGN wkmng TPIS_HUMAN : 231- 234: vdgfl VGGA slkpe TPIS_LATCH : 7- 10: prkff VGGN wkmng TPIS_LATCH : 230- 233: vdgfl VGGA slkpe TPIS_MACMU : 8- 11: srkff VGGN wkmng TPIS_MACMU : 231- 234: vdgfl VGGA slkpe TPIS_MAIZE : 6- 9: grkff VGGN wkcng TPIS_MAIZE : 231- 234: vdgfl VGGA slkpe TPIS_MORSP : 247- 250: idgal VGGA slkad TPIS_MOUSE : 8- 11: trkff VGGN wkmng TPIS_MOUSE : 231- 234: vdgfl VGGA slkpe TPIS_MYCLE : 238- 241: vdggl VGGA sldga TPIS_NICPL : 6- 9: grtff VGGN w TPIS_PLAFA : 231- 234: idgfl VGNA slkes TPIS_RABIT : 8- 11: srkff VGGN wkmng TPIS_RABIT : 231- 234: vdgfl VGGA slkpe TPIS_SCHPO : 6- 9: arkff VGGN fkmng TPIS_SCHPO : 230- 233: idgfl VGGA slkpe TPIS_SECCE : 7- 10: grkff VGGN wkcng TPIS_SECCE : 232- 235: vdgfl VGGA slkpe TPIS_TRYBB : 233- 236: vngfl VGGA slkpe TPIS_YEAST : 6- 9: artff VGGN fklng TPIS_YEAST : 230- 233: vdgfl VGGA slkpe B 2: 10.9905 78( 29) G-G-[ANS] Occurences: 78(29) TPI1_GIALA : 9- 11: rrpfi GGN fkcng TPI1_GIALA : 214- 216: iriiy GGS angsn TPI1_GIALA : 237- 239: dgflv GGA slkpe TPI2_GIALA : 9- 11: rrpfi GGN fkcng TPI2_GIALA : 214- 216: iriiy GGS angsn TPI2_GIALA : 237- 239: dgflv GGA slkpe TPIC_SECCE : 52- 54: gkffv GGN wkcng TPIC_SECCE : 114- 116: twigk GGA ftgei TPIC_SECCE : 252- 254: vriiy GGS vnaan TPIC_SECCE : 275- 277: dgflv GGA slkgp TPIS_BACME : 211- 213: vriqy GGS vkpan TPIS_BACME : 234- 236: dgalv GGA slead TPIS_BACST : 211- 213: iriqy GGS vkpdn TPIS_BACST : 234- 236: dgplv GGA slepa TPIS_BACSU : 210- 212: lriqy GGS vkpan TPIS_BACSU : 233- 235: dgalv GGA slepq TPIS_CHICK : 8- 10: rkffv GGN wkmng TPIS_CHICK : 208- 210: triiy GGS vtggn TPIS_CHICK : 213- 215: ggsvt GGN ckela TPIS_CHICK : 231- 233: dgflv GGA slkpe TPIS_COPJA : 8- 10: rkffv GGN wkcng TPIS_COPJA : 72- 74: cwvkk GGA ftgev TPIS_COPJA : 210- 212: vriiy GGS vngan TPIS_COPJA : 233- 235: dgflv GGA slkpe TPIS_CORGL : 216- 218: lrily GGS vkaet TPIS_CORGL : 239- 241: dgglv GGA sldge TPIS_CULTA : 7- 9: rkfcv GGN wkmng TPIS_CULTA : 207- 209: iriqy GGS vtaan TPIS_CULTA : 230- 232: dgflv GGA slkpe TPIS_DROME : 8- 10: rkfcv GGN wkmng TPIS_DROME : 208- 210: lriqy GGS vtaan TPIS_DROME : 231- 233: dgflv GGA slkpe TPIS_ECOLI : 210- 212: viiqy GGS vnasn TPIS_ECOLI : 233- 235: dgalv GGA slkad TPIS_EMENI : 8- 10: rkffv GGN fkmng TPIS_EMENI : 210- 212: triiy GGS vsekn TPIS_EMENI : 233- 235: dgflv GGA slkpa TPIS_HAEIN : 219- 221: viiqy GGS vndan TPIS_HAEIN : 242- 244: dgalv GGA slkap TPIS_HORVU : 7- 9: xkffv GGN TPIS_HUMAN : 9- 11: rkffv GGN wkmng TPIS_HUMAN : 209- 211: triiy GGS vtgat TPIS_HUMAN : 232- 234: dgflv GGA slkpe TPIS_LATCH : 8- 10: rkffv GGN wkmng TPIS_LATCH : 208- 210: vriiy GGS vtgat TPIS_LATCH : 231- 233: dgflv GGA slkpe TPIS_MACMU : 9- 11: rkffv GGN wkmng TPIS_MACMU : 209- 211: triiy GGS vtgat TPIS_MACMU : 232- 234: dgflv GGA slkpe TPIS_MAIZE : 7- 9: rkffv GGN wkcng TPIS_MAIZE : 71- 73: cwvkk GGA ftgev TPIS_MAIZE : 209- 211: triiy GGS vtaan TPIS_MAIZE : 232- 234: dgflv GGA slkpe TPIS_MORSP : 225- 227: mtvly GGS vnadn TPIS_MORSP : 248- 250: dgalv GGA slkad TPIS_MOUSE : 9- 11: rkffv GGN wkmng TPIS_MOUSE : 209- 211: triiy GGS vtgat TPIS_MOUSE : 232- 234: dgflv GGA slkpe TPIS_MYCLE : 216- 218: vrvly GGS lnakn TPIS_MYCLE : 239- 241: dgglv GGA sldga TPIS_NICPL : 7- 9: rtffv GGN w TPIS_PLAFA : 209- 211: irily GGS vnten TPIS_RABIT : 9- 11: rkffv GGN wkmng TPIS_RABIT : 209- 211: triiy GGS vtgat TPIS_RABIT : 232- 234: dgflv GGA slkpe TPIS_SCHPO : 7- 9: rkffv GGN fkmng TPIS_SCHPO : 208- 210: lrviy GGS vtggn TPIS_SCHPO : 213- 215: ggsvt GGN ckefl TPIS_SCHPO : 231- 233: dgflv GGA slkpe TPIS_SECCE : 8- 10: rkffv GGN wkcng TPIS_SECCE : 72- 74: cwvkk GGA ftgev TPIS_SECCE : 210- 212: triiy GGS vtgas TPIS_SECCE : 233- 235: dgflv GGA slkpe TPIS_TRYBB : 211- 213: lrily GGS vngkn TPIS_TRYBB : 234- 236: ngflv GGA slkpe TPIS_YEAST : 7- 9: rtffv GGN fklng TPIS_YEAST : 208- 210: lrily GGS angsn TPIS_YEAST : 231- 233: dgflv GGA slkpe C 3: 7.8401 68( 29) G-x(0,1)-N Occurences: 68(29) TPI1_GIALA : 9- 11: rrpfi GgN fkcng TPI1_GIALA : 10- 11: rpfig G-N fkcng TPI1_GIALA : 71- 72: nvyle G-N gawtg TPI1_GIALA : 219- 221: ggsan GsN ceklg TPI2_GIALA : 9- 11: rrpfi GgN fkcng TPI2_GIALA : 10- 11: rpfig G-N fkcng TPI2_GIALA : 71- 72: nvyle G-N gawtg TPI2_GIALA : 219- 221: ggsan GsN ceklg TPIC_SECCE : 52- 54: gkffv GgN wkcng TPIC_SECCE : 53- 54: kffvg G-N wkcng TPIS_BACME : 8- 9: kpiia G-N wkmnk TPIS_BACME : 87- 89: aladl GvN yvilg TPIS_BACME : 182- 184: sstae GaN evcay TPIS_BACST : 8- 9: kpiia G-N wkmhk TPIS_BACSU : 8- 9: kpiia G-N wkmnk TPIS_CHICK : 8- 10: rkffv GgN wkmng TPIS_CHICK : 9- 10: kffvg G-N wkmng TPIS_CHICK : 213- 215: ggsvt GgN ckela TPIS_CHICK : 214- 215: gsvtg G-N ckela TPIS_COPJA : 8- 10: rkffv GgN wkcng TPIS_COPJA : 9- 10: kffvg G-N wkcng TPIS_COPJA : 215- 217: ggsvn GaN skela TPIS_CORGL : 9- 10: kplia G-N wkmnl TPIS_CULTA : 7- 9: rkfcv GgN wkmng TPIS_CULTA : 8- 9: kfcvg G-N wkmng TPIS_DROME : 8- 10: rkfcv GgN wkmng TPIS_DROME : 9- 10: kfcvg G-N wkmng TPIS_DROME : 62- 64: elgla GqN aykva TPIS_ECOLI : 8- 9: hplvm G-N wklng TPIS_EMENI : 8- 10: rkffv GgN fkmng TPIS_EMENI : 9- 10: kffvg G-N fkmng TPIS_EMENI : 15- 16: nfkmn G-N aestt TPIS_HAEIN : 9- 10: rplvm G-N wklng TPIS_HORVU : 7- 9: xkffv GgN TPIS_HORVU : 8- 9: kffvg G-N TPIS_HUMAN : 9- 11: rkffv GgN wkmng TPIS_HUMAN : 10- 11: kffvg G-N wkmng TPIS_LATCH : 8- 10: rkffv GgN wkmng TPIS_LATCH : 9- 10: kffvg G-N wkmng TPIS_MACMU : 9- 11: rkffv GgN wkmng TPIS_MACMU : 10- 11: kffvg G-N wkmng TPIS_MAIZE : 7- 9: rkffv GgN wkcng TPIS_MAIZE : 8- 9: kffvg G-N wkcng TPIS_MORSP : 7- 8: qawvi G-N wkqnp TPIS_MOUSE : 9- 11: rkffv GgN wkmng TPIS_MOUSE : 10- 11: kffvg G-N wkmng TPIS_MYCLE : 9- 10: kslia G-N wkmnl TPIS_MYCLE : 165- 166: speqi G-N vvivy TPIS_NICPL : 7- 9: rtffv GgN w TPIS_NICPL : 8- 9: tffvg G-N w TPIS_PLAFA : 70- 71: nvskf G-N gsytg TPIS_PLAFA : 232- 233: dgflv G-N aslke TPIS_RABIT : 9- 11: rkffv GgN wkmng TPIS_RABIT : 10- 11: kffvg G-N wkmng TPIS_SCHPO : 7- 9: rkffv GgN fkmng TPIS_SCHPO : 8- 9: kffvg G-N fkmng TPIS_SCHPO : 25- 27: ktiie GlN ttkln TPIS_SCHPO : 75- 77: ngayt GeN saqsl TPIS_SCHPO : 213- 215: ggsvt GgN ckefl TPIS_SCHPO : 214- 215: gsvtg G-N ckefl TPIS_SECCE : 8- 10: rkffv GgN wkcng TPIS_SECCE : 9- 10: kffvg G-N wkcng TPIS_TRYBB : 87- 89: ilkdf GvN wivlg TPIS_TRYBB : 216- 218: ggsvn GkN artly TPIS_YEAST : 7- 9: rtffv GgN fklng TPIS_YEAST : 8- 9: tffvg G-N fklng TPIS_YEAST : 75- 77: sgaft GeN svdqi TPIS_YEAST : 213- 215: ggsan GsN avtfk Number of patterns evaluated by Pratt:11 Total running time: 1 seconds