------------------------------------------------------------ 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 5 sequences from file OX2_COVAL_FAD PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 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 OX2_COVAL_FAD.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: FAS5_RHOFA 438 GGLO_RAT 439 HDNO_ARTOX 458 MCRA_STRLA 447 RETO_ESCCA 538 Pratt run started at Thu Feb 6 20:26:40 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.3503 5( 5) L-x(4,5)-G-x(4)-V-x(3)-G-x(4)-G 2: 19.8503 5( 5) L-x(4,5)-G-x(3,4)-V-x(3)-G-x(4)-G 3: 16.6802 6( 5) G-x(4)-V-x(3)-G-x(4)-G 4: 16.1802 7( 5) G-x(3,4)-V-x(3)-G-x(4)-G 5: 15.6802 5( 5) L-x(3,4)-L-x(2,3)-L-x(3)-L 6: 15.6802 8( 5) V-x(1,2)-G-x(0,1)-G-x(4)-G 7: 15.6802 6( 5) A-x(2,3)-G-x(0,1)-G-x(4)-G 8: 15.6802 5( 5) F-x-A-x-R-x(1,3)-G 9: 15.6802 6( 5) V-x(0,1)-G-x-G-x(3,4)-G 10: 15.6802 7( 5) V-x(0,1)-G-x(1,2)-G-x(4)-G 11: 15.6802 5( 5) V-x(3)-G-x(4)-G-x(1,3)-G 12: 15.6802 5( 5) V-x(4)-L-x(4)-G-x(1,3)-L 13: 15.1802 6( 5) L-x(1,2)-T-A-x(0,2)-G 14: 15.1802 5( 5) L-x(0,2)-L-x(2,3)-A-D 15: 15.1802 6( 5) L-x(1,3)-L-x(4)-E-x(2,3)-P 16: 15.1802 5( 5) L-L-x(0,2)-S-x(1,2)-L 17: 15.1802 5( 5) L-x(0,2)-L-x(0,1)-S-x-L 18: 15.1802 6( 5) A-x(0,2)-G-x(1,2)-L-x(3)-L 19: 15.1802 5( 5) G-x(0,2)-L-x(0,1)-A-x(2)-N 20: 15.1802 5( 5) V-x(2,3)-A-x(3)-G-x(1,3)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 31.9816 5( 5) V-[GI]-x(2)-G-x(4)-G-x(1,3)-G-[FILM]-x-[AGST]-x(3)-[DGV]-x-[AL]-[AST] B 2: 25.8048 5( 5) F-x-A-[AIV]-R-x(1,3)-G-x(4)-[GIV]-[ALV]-x(2)-[AGTV] C 3: 23.8687 5( 5) L-x(1,2)-T-A-x(0,2)-G-x(2)-[AILP]-x(3)-[ADEST]-[DGS]-x(2)-[AILPV] D 4: 23.5506 5( 5) L-x(4,5)-G-x(4)-V-[GT]-x(2)-G-x(4)-G E 5: 23.0506 5( 5) L-x(4,5)-G-x(3,4)-V-[GT]-x(2)-G-x(4)-G F 6: 22.6838 5( 5) V-x(0,1)-G-[AGST]-G-x(3,4)-G-x(3)-[AEG]-x(2)-[AGSV] G 7: 20.5720 5( 5) V-x(4)-L-x(2)-[ANT]-[DGNV]-G-x(1,3)-L H 8: 19.8806 5( 5) G-x(4)-V-[GT]-x(2)-G-x(4)-G I 9: 19.3806 6( 5) G-x(3,4)-V-[GT]-x(2)-G-x(4)-G J 10: 19.2634 5( 5) L-L-x(0,2)-S-x(1,2)-L-[DPQT]-x(2)-[AGNSV] K 11: 17.5646 7( 5) V-x(1,2)-G-x(0,1)-G-x(2)-[NPQST]-x-G L 12: 17.0913 5( 5) L-x(0,2)-L-x(0,1)-S-x-L-x(3)-[AEGNS] M 13: 15.6802 5( 5) L-x(3,4)-L-x(2,3)-L-x(3)-L N 14: 15.6802 6( 5) A-x(2,3)-G-x(0,1)-G-x(4)-G O 15: 15.6802 7( 5) V-x(0,1)-G-x(1,2)-G-x(4)-G P 16: 15.1802 5( 5) L-x(0,2)-L-x(2,3)-A-D Q 17: 15.1802 6( 5) L-x(1,3)-L-x(4)-E-x(2,3)-P R 18: 15.1802 5( 5) L-L-x(0,2)-S-x(1,2)-L S 19: 15.1802 5( 5) L-x(0,2)-L-x(0,1)-S-x-L T 20: 15.1802 6( 5) A-x(0,2)-G-x(1,2)-L-x(3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 31.9816 5( 5) V-[GI]-x(2)-G-x(4)-G-x(1,3)-G-[FILM]-x-[AGST]-x(3)-[DGV]-x-[AL]-[AST] Occurences: 5(5) FAS5_RHOFA : 129- 150: ggtls VGgfGgsshGf--GLqTdnvDsLA vvtgs GGLO_RAT : 120- 143: vtvag VIgsGthntGikhGIlAtqvVaLT lmtad HDNO_ARTOX : 132- 154: gmhpk VGfcGlalnGgv-GFlTpkyGlAS dnilg MCRA_STRLA : 122- 144: gsspn VGavGylvgGga-GLlGrrfGyAA dhvrr RETO_ESCCA : 169- 191: gwcpt VGtgGhisgGgf-GMmSrkyGlAA dnvvd B 2: 25.8048 5( 5) F-x-A-[AIV]-R-x(1,3)-G-x(4)-[GIV]-[ALV]-x(2)-[AGTV] Occurences: 5(5) FAS5_RHOFA : 170- 187: snsel FdAVRgglGqfgvIVnaT irlta GGLO_RAT : 163- 180: rnadv FqAARvhlGclgiILtvT lqcvp HDNO_ARTOX : 181- 197: erpel FwAVRga-GpnfgVVteV evqly MCRA_STRLA : 171- 186: tdpdl FwAVRg--GkdnfGLvvG mevdl RETO_ESCCA : 217- 233: mgedv FwAIRgg-GggvwGAiyA wkikl C 3: 23.8687 5( 5) L-x(1,2)-T-A-x(0,2)-G-x(2)-[AILP]-x(3)-[ADEST]-[DGS]-x(2)-[AILPV] Occurences: 5(5) FAS5_RHOFA : 363- 380: fmlav Lr-TAspGaeArmiASnrL lyeqa GGLO_RAT : 144- 160: vvalt Lm-TAd-GevLecsESrnA dvfqa HDNO_ARTOX : 162- 178: ilgat Lv-TAt-GdvIycsDDerP elfwa MCRA_STRLA : 104- 122: rwrkv LehTAphGlaPlngSSpnV gavgy RETO_ESCCA : 159- 175: esssk LgfTA--GwcPtvgTGghI sgggf D 4: 23.5506 5( 5) L-x(4,5)-G-x(4)-V-[GT]-x(2)-G-x(4)-G Occurences: 5(5) FAS5_RHOFA : 119- 138: vltdy Lgttv-GgtlsVGgfGgsshG fglqt GGLO_RAT : 104- 124: ldehg LamsnlGavsdVTvaGvigsG thntg HDNO_ARTOX : 122- 141: aakfg Laavt-GmhpkVGfcGlalnG gvgfl MCRA_STRLA : 112- 131: taphg Lapln-GsspnVGavGylvgG gagll RETO_ESCCA : 159- 178: esssk Lgfta-GwcptVGtgGhisgG gfgmm E 5: 23.0506 5( 5) L-x(4,5)-G-x(3,4)-V-[GT]-x(2)-G-x(4)-G Occurences: 5(5) FAS5_RHOFA : 119- 138: vltdy LgttvgGtls-VGgfGgsshG fglqt FAS5_RHOFA : 119- 138: vltdy Lgttv-GgtlsVGgfGgsshG fglqt GGLO_RAT : 104- 124: ldehg LamsnlGavsdVTvaGvigsG thntg HDNO_ARTOX : 122- 141: aakfg Laavt-GmhpkVGfcGlalnG gvgfl MCRA_STRLA : 112- 131: taphg Lapln-GsspnVGavGylvgG gagll RETO_ESCCA : 159- 178: esssk Lgfta-GwcptVGtgGhisgG gfgmm F 6: 22.6838 5( 5) V-x(0,1)-G-[AGST]-G-x(3,4)-G-x(3)-[AEG]-x(2)-[AGSV] Occurences: 5(5) FAS5_RHOFA : 55- 71: nlsla VrGSGhstyGqcqAdgG vvldm GGLO_RAT : 120- 136: vtvag ViGSGthntGikhGilA tqvva HDNO_ARTOX : 184- 199: elfwa VrGAGpnf-GvvtEveV qlyel MCRA_STRLA : 129- 144: avgyl V-GGGagllGrrfGyaA dhvrr RETO_ESCCA : 169- 184: gwcpt V-GTGghisGggfGmmS rkygl G 7: 20.5720 5( 5) V-x(4)-L-x(2)-[ANT]-[DGNV]-G-x(1,3)-L Occurences: 5(5) FAS5_RHOFA : 114- 127: qqtpp VltdyLgtTVGgt-L svggf GGLO_RAT : 139- 152: ilatq VvaltLmtADGev-L ecses HDNO_ARTOX : 132- 146: gmhpk VgfcgLalNGGvgfL tpkyg MCRA_STRLA : 147- 159: yaadh VrrlrLvtADGr--L rdvta RETO_ESCCA : 194- 207: laadn VvdaiLidANGai-L drqam H 8: 19.8806 5( 5) G-x(4)-V-[GT]-x(2)-G-x(4)-G Occurences: 5(5) FAS5_RHOFA : 124- 138: lgttv GgtlsVGgfGgsshG fglqt GGLO_RAT : 110- 124: amsnl GavsdVTvaGvigsG thntg HDNO_ARTOX : 127- 141: laavt GmhpkVGfcGlalnG gvgfl MCRA_STRLA : 117- 131: lapln GsspnVGavGylvgG gagll RETO_ESCCA : 164- 178: lgfta GwcptVGtgGhisgG gfgmm I 9: 19.3806 6( 5) G-x(3,4)-V-[GT]-x(2)-G-x(4)-G Occurences: 6(5) FAS5_RHOFA : 124- 138: lgttv GgtlsVGgfGgsshG fglqt FAS5_RHOFA : 125- 138: gttvg Gtls-VGgfGgsshG fglqt GGLO_RAT : 110- 124: amsnl GavsdVTvaGvigsG thntg HDNO_ARTOX : 127- 141: laavt GmhpkVGfcGlalnG gvgfl MCRA_STRLA : 117- 131: lapln GsspnVGavGylvgG gagll RETO_ESCCA : 164- 178: lgfta GwcptVGtgGhisgG gfgmm J 10: 19.2634 5( 5) L-L-x(0,2)-S-x(1,2)-L-[DPQT]-x(2)-[AGNSV] Occurences: 5(5) FAS5_RHOFA : 259- 267: pddda LL--Ss-LQydS caeyn GGLO_RAT : 258- 269: yllef LLwtStyLPclV gwinr HDNO_ARTOX : 225- 234: selag LLt-Sl-LDalN emadh MCRA_STRLA : 311- 319: ydrnv LL--Sd-LTddA vdiiv RETO_ESCCA : 27- 35: lggnd LL--Sc-LTfnG vrnht K 11: 17.5646 7( 5) V-x(1,2)-G-x(0,1)-G-x(2)-[NPQST]-x-G Occurences: 7(5) FAS5_RHOFA : 55- 64: nlsla Vr-GsGhsTyG qcqad FAS5_RHOFA : 129- 138: ggtls Vg-GfGgsShG fglqt FAS5_RHOFA : 173- 181: elfda Vr-G-GlgQfG vivna GGLO_RAT : 120- 129: vtvag Vi-GsGthNtG ikhgi HDNO_ARTOX : 66- 75: gleis VrsG-GhnPnG yatnd MCRA_STRLA : 174- 182: dlfwa Vr-G-GkdNfG lvvgm RETO_ESCCA : 169- 178: gwcpt VgtG-GhiSgG gfgmm L 12: 17.0913 5( 5) L-x(0,2)-L-x(0,1)-S-x-L-x(3)-[AEGNS] Occurences: 5(5) FAS5_RHOFA : 259- 267: pddda L--L-SsLqydS caeyn GGLO_RAT : 202- 213: tlkev LdnLdShLkrsE yfrfl HDNO_ARTOX : 225- 234: selag L--LtSlLdalN emadh MCRA_STRLA : 311- 319: ydrnv L--L-SdLtddA vdiiv RETO_ESCCA : 27- 35: lggnd L--L-ScLtfnG vrnht M 13: 15.6802 5( 5) L-x(3,4)-L-x(2,3)-L-x(3)-L Occurences: 5(5) FAS5_RHOFA : 202- 215: vrqyk LqysnLgvfLgdqL ramsn GGLO_RAT : 198- 209: sfpst Lkev-Ldn-LdshL krsey HDNO_ARTOX : 222- 233: psvse Lagl-Lts-LldaL nemad MCRA_STRLA : 268- 279: adgeh Lvrp-Lre-LgpiL ldtvr RETO_ESCCA : 11- 22: piffs Lsif-Lsl-LncaL ggndl N 14: 15.6802 6( 5) A-x(2,3)-G-x(0,1)-G-x(4)-G Occurences: 6(5) FAS5_RHOFA : 54- 64: rnlsl Avr-GsGhstyG qcqad FAS5_RHOFA : 172- 181: selfd Avr-G-GlgqfG vivna GGLO_RAT : 118- 129: sdvtv AgviGsGthntG ikhgi HDNO_ARTOX : 102- 111: tagsr Ari-G-GgvisG dlvke MCRA_STRLA : 173- 182: pdlfw Avr-G-GkdnfG lvvgm RETO_ESCCA : 219- 229: edvfw AirgG-GggvwG aiyaw RETO_ESCCA : 219- 229: edvfw Air-GgGggvwG aiyaw O 15: 15.6802 7( 5) V-x(0,1)-G-x(1,2)-G-x(4)-G Occurences: 7(5) FAS5_RHOFA : 55- 64: nlsla VrGs-GhstyG qcqad FAS5_RHOFA : 129- 138: ggtls VgGf-GgsshG fglqt FAS5_RHOFA : 129- 138: ggtls V-GgfGgsshG fglqt GGLO_RAT : 120- 129: vtvag ViGs-GthntG ikhgi HDNO_ARTOX : 132- 141: gmhpk V-GfcGlalnG gvgfl MCRA_STRLA : 122- 131: gsspn V-GavGylvgG gagll MCRA_STRLA : 129- 137: avgyl V-Gg-GagllG rrfgy RETO_ESCCA : 169- 177: gwcpt V-Gt-GghisG ggfgm RETO_ESCCA : 169- 178: gwcpt V-GtgGhisgG gfgmm P 16: 15.1802 5( 5) L-x(0,2)-L-x(2,3)-A-D Occurences: 5(5) FAS5_RHOFA : 306- 311: hpwas L--Lip-AD kieqf GGLO_RAT : 142- 148: tqvva Lt-Lmt-AD gevle HDNO_ARTOX : 230- 238: lltsl LdaLnemAD hiyps MCRA_STRLA : 150- 156: dhvrr Lr-Lvt-AD grlrd RETO_ESCCA : 279- 286: eedft LsvLgg-AD ekqvw Q 17: 15.1802 6( 5) L-x(1,3)-L-x(4)-E-x(2,3)-P Occurences: 6(5) FAS5_RHOFA : 289- 300: madqe Ld--LrhtgEwfyP hpwas GGLO_RAT : 319- 330: ktkea Lle-LkamlEah-P kvvah GGLO_RAT : 320- 330: tkeal Le--LkamlEah-P kvvah HDNO_ARTOX : 5- 18: mssk LatpLsiqgEviyP ddsgf MCRA_STRLA : 20- 30: yddar Lg--LnraaEsr-P ayvve RETO_ESCCA : 434- 446: kktef Ldw-LekvyEfmkP fvskn R 18: 15.1802 5( 5) L-L-x(0,2)-S-x(1,2)-L Occurences: 5(5) FAS5_RHOFA : 259- 263: pddda LL--Ss-L qydsc GGLO_RAT : 258- 265: yllef LLwtStyL pclvg HDNO_ARTOX : 225- 230: selag LLt-Sl-L dalne MCRA_STRLA : 311- 315: ydrnv LL--Sd-L tddav RETO_ESCCA : 27- 31: lggnd LL--Sc-L tfngv S 19: 15.1802 5( 5) L-x(0,2)-L-x(0,1)-S-x-L Occurences: 5(5) FAS5_RHOFA : 259- 263: pddda L--L-SsL qydsc GGLO_RAT : 202- 209: tlkev LdnLdShL krsey HDNO_ARTOX : 225- 230: selag L--LtSlL dalne MCRA_STRLA : 311- 315: ydrnv L--L-SdL tddav RETO_ESCCA : 27- 31: lggnd L--L-ScL tfngv T 20: 15.1802 6( 5) A-x(0,2)-G-x(1,2)-L-x(3)-L Occurences: 6(5) FAS5_RHOFA : 234- 242: rirvd Ad-Gh-LryrL dlaky GGLO_RAT : 88- 95: qitve A--Gi-LladL hpqld GGLO_RAT : 249- 258: wfwdy Ai-GfyLlefL lwtst HDNO_ARTOX : 223- 230: svsel A--Gl-LtslL dalne MCRA_STRLA : 263- 272: ysgep Ad-GehLvrpL relgp RETO_ESCCA : 21- 31: sllnc AlgGndLlscL tfngv Number of patterns evaluated by Pratt:12712 Total running time: 5 seconds