------------------------------------------------------------ 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 4 sequences from file YKL151C_YJEF_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 4 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 YKL151C_YJEF_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: Y201_MYCLE 392 YJEF_ECOLI 515 YKP1_YEAST 337 YNH2_CAEEL 285 Pratt run started at Thu Feb 6 21:36:11 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 25.0203 4( 4) V-x-G-P-G-L-G 2: 24.5203 4( 4) V-x(1,2)-T-P-x(3)-E-x(2)-R-L 3: 20.8503 4( 4) T-P-x(3)-E-x(2)-R-L 4: 20.8503 4( 4) G-P-G-L-G 5: 20.3503 7( 4) G-x(1,2)-G-D-x(3)-G-x(5)-L 6: 20.3503 4( 4) G-x(0,1)-G-D-x(3)-G-x(5)-L 7: 19.8503 4( 4) G-x-G-D-x(3)-G-x(3,5)-L 8: 19.8503 6( 4) G-x(4,5)-T-G-A-x(3,4)-A 9: 19.8503 4( 4) G-x(3,4)-T-G-x(4,5)-A-x(3)-A 10: 19.8503 4( 4) G-G-x(2,3)-Y-x(2,3)-A-x(4)-A 11: 19.3503 7( 4) G-x(0,1)-G-x(0,2)-D-x(3)-G-x(5)-L 12: 19.3503 7( 4) G-x(1,2)-G-D-x(3)-G-x(3,5)-L 13: 19.3503 4( 4) D-x(2,4)-V-x(0,1)-I-G-x(2)-L 14: 19.3503 4( 4) L-x(1,3)-D-x(2,3)-V-x(3)-G-x-G 15: 19.3503 4( 4) G-x(4)-T-G-x(4,5)-A-x(0,2)-A 16: 18.8503 4( 4) I-G-x(2)-L-x(0,2)-G-x(2,4)-P 17: 18.8503 4( 4) L-x(0,2)-T-G-A-x(3,5)-A 18: 18.8503 5( 4) G-x(1,3)-L-x(0,2)-T-G-A 19: 16.6802 4( 4) P-x(3)-E-x(2)-R-L 20: 16.6802 4( 4) P-x(3)-D-x-D-x-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 42.1995 4( 4) V-x(1,2)-T-P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] B 2: 40.4257 4( 4) P-[FLMV]-[LV]-x-D-[AG]-D-[AG]-L-x-[FLM]-[LV]-[AST]-x(3)-[DE] C 3: 38.5294 4( 4) T-P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] D 4: 36.4217 4( 4) D-x(2,4)-V-x(0,1)-I-G-[LP]-[DG]-L-[GP]-[DQR]-[DNQS]-[DEP] E 5: 35.4707 7( 4) G-x(1,2)-G-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L F 6: 35.4707 4( 4) G-x(0,1)-G-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L G 7: 34.4707 7( 4) G-x(0,1)-G-x(0,2)-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L H 8: 34.3594 4( 4) P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] I 9: 30.8357 4( 4) V-[IV]-G-P-G-L-G-x-[DNQ] J 10: 30.1160 4( 4) L-x(1,3)-D-x(2,3)-V-[GIV]-[GIV]-x-G-x-G-x(4)-[AGIP]-x(2)-[AL] K 11: 27.8618 4( 4) G-x-G-D-[TV]-x-[AST]-G-x(3,5)-L-x(2)-[AGQS] L 12: 27.3618 7( 4) G-x(1,2)-G-D-[TV]-x-[AST]-G-x(3,5)-L-x(2)-[AGQS] M 13: 26.4648 4( 4) G-G-x(2,3)-Y-x(2,3)-A-x(4)-A-[ANSV]-[AGST]-x-[AEGS] N 14: 25.2417 4( 4) I-G-[AP]-[GL]-L-x(0,2)-G-x(2,4)-P O 15: 24.7232 4( 4) G-x(3,4)-T-G-x(4,5)-A-[ANV]-x-[ANST]-A P 16: 23.7336 4( 4) G-x(4)-T-G-x(4,5)-A-x(0,2)-A-[AGST]-x(3)-[AGTV] Q 17: 23.6407 6( 4) G-x(4,5)-T-G-A-x(3,4)-A-[ANSTV]-x-[AGNST] R 18: 23.4408 4( 4) G-P-G-L-G-x-[DNQ] S 19: 19.3503 4( 4) G-x(4)-T-G-x(4,5)-A-x(0,2)-A T 20: 18.8503 4( 4) I-G-x(2)-L-x(0,2)-G-x(2,4)-P Best patterns with alignements: fitness hits(seqs) Pattern A 1: 42.1995 4( 4) V-x(1,2)-T-P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] Occurences: 4(4) Y201_MYCLE : 290- 311: rnapt Vl-TPhASEfaRLagTpPgDdRV gacrk YJEF_ECOLI : 371- 392: krhnr Vi-TPhPGEaaRLlgCsVaEiES drlhc YKP1_YEAST : 177- 199: ypkgr VilTPnVVEfkRLcdAiGkKgDS hsemg YNH2_CAEEL : 124- 145: qmsat Vl-TPnIVEfsRLckSaLgEeDV lnvrn B 2: 40.4257 4( 4) P-[FLMV]-[LV]-x-D-[AG]-D-[AG]-L-x-[FLM]-[LV]-[AST]-x(3)-[DE] Occurences: 4(4) Y201_MYCLE : 264- 280: letdl PVLvDADGLtMLAahpD lvinr YJEF_ECOLI : 349- 365: enfrk PMLwDADALnLLAinpD krhnr YKP1_YEAST : 148- 164: hegki PLViDADGLfLVTqdsE vkeml YNH2_CAEEL : 98- 114: rnrdv PFViDGDGLwFVSehiE kfprq C 3: 38.5294 4( 4) T-P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] Occurences: 4(4) Y201_MYCLE : 292- 311: aptvl TPhASEfaRLagTpPgDdRV gacrk YJEF_ECOLI : 373- 392: hnrvi TPhPGEaaRLlgCsVaEiES drlhc YKP1_YEAST : 180- 199: grvil TPnVVEfkRLcdAiGkKgDS hsemg YNH2_CAEEL : 126- 145: satvl TPnIVEfsRLckSaLgEeDV lnvrn D 4: 36.4217 4( 4) D-x(2,4)-V-x(0,1)-I-G-[LP]-[DG]-L-[GP]-[DQR]-[DNQS]-[DEP] Occurences: 4(4) Y201_MYCLE : 137- 151: ladcg Dvtl-VdIGLDLPDSD ilglq YJEF_ECOLI : 322- 334: slewa Dvv--V-IGPGLGQQE wgkka YKP1_YEAST : 111- 126: insll DrihvVvIGPGLGRDP lmlks YNH2_CAEEL : 67- 79: klsrm Dai--V-IGPGLGRNP niwpl E 5: 35.4707 7( 4) G-x(1,2)-G-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L Occurences: 7(4) Y201_MYCLE : 355- 368: waata Gs-GDVlSGmIGaLL aaglp YJEF_ECOLI : 438- 452: agmas GgmGDVlSGiIGaLL gqkls YJEF_ECOLI : 439- 452: gmasg Gm-GDVlSGiIGaLL gqkls YKP1_YEAST : 246- 260: snkrv GgqGDTlTGaIScML afsra YKP1_YEAST : 247- 260: nkrvg Gq-GDTlTGaIScML afsra YNH2_CAEEL : 198- 212: slrrc GgqGDVtAGsLGlFL ywakk YNH2_CAEEL : 199- 212: lrrcg Gq-GDVtAGsLGlFL ywakk F 6: 35.4707 4( 4) G-x(0,1)-G-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L Occurences: 4(4) Y201_MYCLE : 355- 368: waata GsGDVlSGmIGaLL aaglp YJEF_ECOLI : 439- 452: gmasg GmGDVlSGiIGaLL gqkls YKP1_YEAST : 247- 260: nkrvg GqGDTlTGaIScML afsra YNH2_CAEEL : 199- 212: lrrcg GqGDVtAGsLGlFL ywakk G 7: 34.4707 7( 4) G-x(0,1)-G-x(0,2)-D-[TV]-x-[AST]-G-x-[IL]-[GS]-x-[FLM]-L Occurences: 7(4) Y201_MYCLE : 355- 368: waata GsG--DVlSGmIGaLL aaglp YJEF_ECOLI : 438- 452: agmas G-GmgDVlSGiIGaLL gqkls YJEF_ECOLI : 439- 452: gmasg GmG--DVlSGiIGaLL gqkls YKP1_YEAST : 246- 260: snkrv G-GqgDTlTGaIScML afsra YKP1_YEAST : 247- 260: nkrvg GqG--DTlTGaIScML afsra YNH2_CAEEL : 198- 212: slrrc G-GqgDVtAGsLGlFL ywakk YNH2_CAEEL : 199- 212: lrrcg GqG--DVtAGsLGlFL ywakk H 8: 34.3594 4( 4) P-x-[AIPV]-[GSV]-E-x(2)-R-L-x(2)-[ACST]-x-[GLPV]-x-[DEK]-x-[DER]-[SV] Occurences: 4(4) Y201_MYCLE : 293- 311: ptvlt PhASEfaRLagTpPgDdRV gacrk YJEF_ECOLI : 374- 392: nrvit PhPGEaaRLlgCsVaEiES drlhc YKP1_YEAST : 181- 199: rvilt PnVVEfkRLcdAiGkKgDS hsemg YNH2_CAEEL : 127- 145: atvlt PnIVEfsRLckSaLgEeDV lnvrn I 9: 30.8357 4( 4) V-[IV]-G-P-G-L-G-x-[DNQ] Occurences: 4(4) Y201_MYCLE : 240- 248: rvqsw VVGPGLGiD atata YJEF_ECOLI : 325- 333: wadvv VIGPGLGqQ ewgkk YKP1_YEAST : 117- 125: rihvv VIGPGLGrD plmlk YNH2_CAEEL : 70- 78: rmdai VIGPGLGrN pniwp J 10: 30.1160 4( 4) L-x(1,3)-D-x(2,3)-V-[GIV]-[GIV]-x-G-x-G-x(4)-[AGIP]-x(2)-[AL] Occurences: 4(4) Y201_MYCLE : 62- 82: saatd Lvi-Dgv-VGIsGsGplrpAaaA vfatv YJEF_ECOLI : 318- 339: sltes LewaDvv-VIGpGlGqqewGkkA lqkve YKP1_YEAST : 109- 129: kkins Ll--DrihVVViGpGlgrdPlmL ksikd YNH2_CAEEL : 63- 84: siipk LsrmDai-VIGpGlGrnpnIwpL mqelf K 11: 27.8618 4( 4) G-x-G-D-[TV]-x-[AST]-G-x(3,5)-L-x(2)-[AGQS] Occurences: 4(4) Y201_MYCLE : 355- 370: waata GsGDVlSGmiga-LlaA glpap Y201_MYCLE : 355- 371: waata GsGDVlSGmigalLaaG lpapr YJEF_ECOLI : 439- 454: gmasg GmGDVlSGiiga-LlgQ klspy YKP1_YEAST : 247- 263: nkrvg GqGDTlTGaiscmLafS ramyd YNH2_CAEEL : 199- 215: lrrcg GqGDVtAGslglfLywA kknlg L 12: 27.3618 7( 4) G-x(1,2)-G-D-[TV]-x-[AST]-G-x(3,5)-L-x(2)-[AGQS] Occurences: 7(4) Y201_MYCLE : 355- 370: waata Gs-GDVlSGmiga-LlaA glpap Y201_MYCLE : 355- 371: waata Gs-GDVlSGmigalLaaG lpapr YJEF_ECOLI : 438- 454: agmas GgmGDVlSGiiga-LlgQ klspy YJEF_ECOLI : 439- 454: gmasg Gm-GDVlSGiiga-LlgQ klspy YKP1_YEAST : 246- 263: snkrv GgqGDTlTGaiscmLafS ramyd YKP1_YEAST : 247- 263: nkrvg Gq-GDTlTGaiscmLafS ramyd YNH2_CAEEL : 198- 215: slrrc GgqGDVtAGslglfLywA kknlg YNH2_CAEEL : 199- 215: lrrcg Gq-GDVtAGslglfLywA kknlg M 13: 26.4648 4( 4) G-G-x(2,3)-Y-x(2,3)-A-x(4)-A-[ANSV]-[AGST]-x-[AEGS] Occurences: 4(4) Y201_MYCLE : 338- 355: viadp GGpv-YlnpAgqswAATaG sgdvl YJEF_ECOLI : 73- 89: ghgnn GGdg-Yvv-ArlakAVGiE vtlla YKP1_YEAST : 39- 56: rvcii GGcedYtg-ApyfsANAtA lmgcd YNH2_CAEEL : 5- 22: mgvi GGsleYtg-ApyfaASSaS rlgad N 14: 25.2417 4( 4) I-G-[AP]-[GL]-L-x(0,2)-G-x(2,4)-P Occurences: 4(4) Y201_MYCLE : 364- 375: vlsgm IGALLaaGlpa-P rprrg YJEF_ECOLI : 448- 458: vlsgi IGALL--GqklsP ydaac YKP1_YEAST : 118- 126: ihvvv IGPGL--Grd--P lmlks YNH2_CAEEL : 71- 79: mdaiv IGPGL--Grn--P niwpl O 15: 24.7232 4( 4) G-x(3,4)-T-G-x(4,5)-A-[ANV]-x-[ANST]-A Occurences: 4(4) Y201_MYCLE : 102- 118: vdlps GidvvTGvingpAVhAA ltvtf YJEF_ECOLI : 172- 187: vdips GllaeTGatpg-AViNA dhtit YKP1_YEAST : 40- 56: vciig GcedyTGapyfsANaTA lmgcd YNH2_CAEEL : 6- 21: mgvig GsleyTGapyf-AAsSA srlga P 16: 23.7336 4( 4) G-x(4)-T-G-x(4,5)-A-x(0,2)-A-[AGST]-x(3)-[AGTV] Occurences: 4(4) Y201_MYCLE : 102- 122: vdlps GidvvTGvingpAvhAAltvT fgglk YJEF_ECOLI : 268- 287: dhgta GairmTGeaalrAg-AGlvrV ltrse YKP1_YEAST : 40- 59: vciig GcedyTGapyfsAn-ATalmG cdlth YNH2_CAEEL : 6- 26: mgvig GsleyTGapyfaAssASrlgA dlihi Q 17: 23.6407 6( 4) G-x(4,5)-T-G-A-x(3,4)-A-[ANSTV]-x-[AGNST] Occurences: 6(4) Y201_MYCLE : 190- 205: sstyp GaavlcTGAava-ATsG mvrya YJEF_ECOLI : 172- 186: vdips Gllae-TGAtpg-AViN adhti YKP1_YEAST : 39- 55: rvcii GgcedyTGApyfsANaT almgc YKP1_YEAST : 40- 55: vciig Gcedy-TGApyfsANaT almgc YNH2_CAEEL : 5- 20: mgvi GgsleyTGApyf-AAsS asrlg YNH2_CAEEL : 5- 21: mgvi GgsleyTGApyfaASsA srlga YNH2_CAEEL : 6- 20: mgvig Gsley-TGApyf-AAsS asrlg YNH2_CAEEL : 6- 21: mgvig Gsley-TGApyfaASsA srlga R 18: 23.4408 4( 4) G-P-G-L-G-x-[DNQ] Occurences: 4(4) Y201_MYCLE : 242- 248: qswvv GPGLGiD atata YJEF_ECOLI : 327- 333: dvvvi GPGLGqQ ewgkk YKP1_YEAST : 119- 125: hvvvi GPGLGrD plmlk YNH2_CAEEL : 72- 78: daivi GPGLGrN pniwp S 19: 19.3503 4( 4) G-x(4)-T-G-x(4,5)-A-x(0,2)-A Occurences: 4(4) Y201_MYCLE : 102- 117: vdlps GidvvTGvingpAvhA altvt YJEF_ECOLI : 268- 282: dhgta GairmTGeaalrAg-A glvrv YKP1_YEAST : 40- 54: vciig GcedyTGapyfsAn-A talmg YNH2_CAEEL : 6- 18: mgvig GsleyTGapyf-A--A ssasr YNH2_CAEEL : 6- 21: mgvig GsleyTGapyfaAssA srlga T 20: 18.8503 4( 4) I-G-x(2)-L-x(0,2)-G-x(2,4)-P Occurences: 4(4) Y201_MYCLE : 364- 375: vlsgm IGalLaaGlpa-P rprrg YJEF_ECOLI : 448- 458: vlsgi IGalL--GqklsP ydaac YKP1_YEAST : 118- 126: ihvvv IGpgL--Grd--P lmlks YNH2_CAEEL : 71- 79: mdaiv IGpgL--Grn--P niwpl Number of patterns evaluated by Pratt:8546 Total running time: 3 seconds