------------------------------------------------------------ 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 THYMID_PHOSPHORYLASE 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 THYMID_PHOSPHORYLASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PDP_BACSU 434 TYPH_ECOLI 440 TYPH_HUMAN 482 TYPH_LACCA 23 Pratt run started at Thu Feb 6 21:26:55 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.1802 4( 4) V-K-x-G-x(3,4)-F 2: 15.6802 4( 4) G-x(2)-A-x(0,1)-F-x(3,4)-E 3: 15.6802 4( 4) M-x(3,4)-G-x(4,5)-G-x(4)-L 4: 15.1802 4( 4) G-x(1,2)-G-R-x(0,2)-A 5: 15.1802 4( 4) M-x(3,4)-G-x(4)-G-x(0,2)-G 6: 12.0102 5( 4) G-R-x(0,1)-L 7: 12.0102 5( 4) G-x(1,2)-L-x(4)-I 8: 12.0102 5( 4) G-R-x(1,2)-G 9: 12.0102 4( 4) G-x(2)-G-x(1,2)-L 10: 12.0102 4( 4) G-x(2,3)-G-x-L 11: 12.0102 5( 4) E-x(4)-G-x(1,2)-A 12: 12.0102 4( 4) I-x(4)-R-x(3,4)-A 13: 12.0102 4( 4) G-x(3,4)-G-x(2)-G 14: 12.0102 4( 4) I-x(5)-G-x(2,3)-G 15: 12.0102 4( 4) K-x-G-x(3,4)-F 16: 12.0102 4( 4) K-x(1,2)-G-x(3)-F 17: 12.0102 4( 4) K-x(2,3)-I-x(2)-F 18: 11.5102 4( 4) A-x(0,1)-F-x(3,4)-E 19: 11.5102 9( 4) L-x(0,2)-A-x-R 20: 11.5102 4( 4) L-x(0,2)-A-x(2)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 37.8227 4( 4) M-x(3,4)-G-x(4,5)-G-x-[IL]-[DG]-[KR]-L-[AE]-x(3)-[GI]-[FY]-x-[ILV] B 2: 37.8063 4( 4) M-x(3,4)-G-[IL]-[GN]-[EH]-x-G-x(0,2)-G-x-[IL]-[AD]-x(2)-[ER]-x(3)-[GL] C 3: 26.3677 4( 4) I-[GQS]-x(4)-G-x(2,3)-G-x-[IL]-[ADP]-x(2)-[EQR]-x(3)-[GL] D 4: 21.1099 4( 4) G-x(3,4)-G-[HR]-x-G-x(2)-[AIL]-x-[KR] E 5: 20.4722 5( 4) G-x(1,2)-L-[AST]-x(2)-[DER]-I-x(2)-[FL] F 6: 18.7742 4( 4) V-K-x-G-x(3,4)-F-x(4)-[EQR] G 7: 18.2655 4( 4) G-x-[AGL]-A-x(0,1)-F-x(3,4)-E H 8: 17.8998 5( 4) G-R-x(0,1)-L-[AGS]-x(3)-[GI] I 9: 17.7724 5( 4) G-R-x(1,2)-G-[HR]-x-[AGL] J 10: 17.4036 4( 4) G-x(1,2)-G-R-x(0,2)-A-x-[DEKR] K 11: 17.2661 4( 4) K-x(1,2)-G-x-[AGN]-x-F-x(4)-[EQR] L 12: 17.2337 4( 4) G-x(2)-G-x(1,2)-L-[ADT]-x(2)-[DER] M 13: 17.2337 4( 4) G-x(2,3)-G-x-L-[ADT]-x(2)-[DER] N 14: 16.8969 4( 4) L-x(0,2)-A-x-R-[DR]-x(2)-[AEGT] O 15: 15.2387 4( 4) K-x(2,3)-I-x-[EG]-F P 16: 14.6042 4( 4) K-x-G-x(3,4)-F-x(4)-[EQR] Q 17: 12.0102 5( 4) E-x(4)-G-x(1,2)-A R 18: 12.0102 4( 4) I-x(4)-R-x(3,4)-A S 19: 12.0102 4( 4) I-x(5)-G-x(2,3)-G T 20: 12.0102 4( 4) K-x-G-x(3,4)-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 37.8227 4( 4) M-x(3,4)-G-x(4,5)-G-x-[IL]-[DG]-[KR]-L-[AE]-x(3)-[GI]-[FY]-x-[ILV] Occurences: 4(4) PDP_BACSU : 110- 133: vpvak Msgr-GlghtgGtIDKLEaimGFhV eltkd TYPH_ECOLI : 111- 135: ggyip MisgrGlghtgGtLDKLEsipGFdI fpddn TYPH_HUMAN : 142- 166: gckvp MisgrGlghtgGtLDKLEsipGFnV iqspe TYPH_LACCA : 1- 23: Mvki-Ginef-GrIGRLAfrrIYeL B 2: 37.8063 4( 4) M-x(3,4)-G-[IL]-[GN]-[EH]-x-G-x(0,2)-G-x-[IL]-[AD]-x(2)-[ER]-x(3)-[GL] Occurences: 4(4) PDP_BACSU : 110- 130: vpvak Msgr-GLGHtG--GtIDklEaimG fhvel TYPH_ECOLI : 111- 132: ggyip MisgrGLGHtG--GtLDklEsipG fdifp TYPH_HUMAN : 142- 163: gckvp MisgrGLGHtG--GtLDklEsipG fnviq TYPH_LACCA : 1- 23: Mvki-GINEfGriGrLAfrRiyeL C 3: 26.3677 4( 4) I-[GQS]-x(4)-G-x(2,3)-G-x-[IL]-[ADP]-x(2)-[EQR]-x(3)-[GL] Occurences: 4(4) PDP_BACSU : 21- 41: lttee IQffvnGytdGsIPdyQasaL amaif TYPH_ECOLI : 112- 132: gyipm ISgrglGhtgGtLDklEsipG fdifp TYPH_HUMAN : 143- 163: ckvpm ISgrglGhtgGtLDklEsipG fnviq TYPH_LACCA : 4- 23: mvk IGinefGri-GrLAfrRiyeL D 4: 21.1099 4( 4) G-x(3,4)-G-[HR]-x-G-x(2)-[AIL]-x-[KR] Occurences: 4(4) PDP_BACSU : 112- 124: vakms Grgl-GHtGgtIdK leaim TYPH_ECOLI : 114- 126: ipmis Grgl-GHtGgtLdK lesip TYPH_HUMAN : 145- 157: vpmis Grgl-GHtGgtLdK lesip TYPH_LACCA : 5- 18: mvki GinefGRiGrlAfR riyel E 5: 20.4722 5( 4) G-x(1,2)-L-[AST]-x(2)-[DER]-I-x(2)-[FL] Occurences: 5(4) PDP_BACSU : 13- 24: ikkqn GkeLTteEIqfF vngyt TYPH_ECOLI : 14- 25: rkkrd GhaLSdeEIrfF ingir TYPH_HUMAN : 46- 57: rmkrd GgrLSeaDIrgF vaavv TYPH_HUMAN : 47- 57: mkrdg Gr-LSeaDIrgF vaavv TYPH_LACCA : 13- 23: efgri Gr-LAfrRIyeL F 6: 18.7742 4( 4) V-K-x-G-x(3,4)-F-x(4)-[EQR] Occurences: 4(4) PDP_BACSU : 201- 213: aivld VKtGaga-FmkteE daael TYPH_ECOLI : 203- 215: alvmd VKvGsga-FmptyE lseal TYPH_HUMAN : 234- 247: alvvd VKfGgaavFpnqeQ arela TYPH_LACCA : 2- 14: m VKiGine-FgrigR lafrr G 7: 18.2655 4( 4) G-x-[AGL]-A-x(0,1)-F-x(3,4)-E Occurences: 4(4) PDP_BACSU : 204- 212: ldvkt GaGA-Fmkt-E edaae PDP_BACSU : 204- 213: ldvkt GaGA-FmkteE daael TYPH_ECOLI : 206- 215: mdvkv GsGA-FmptyE lseal TYPH_HUMAN : 237- 246: vdvkf GgAAvFpnq-E qarel TYPH_LACCA : 13- 22: efgri GrLA-FrriyE l H 8: 17.8998 5( 4) G-R-x(0,1)-L-[AGS]-x(3)-[GI] Occurences: 5(4) PDP_BACSU : 112- 120: vakms GRgLGhtgG tidkl TYPH_ECOLI : 114- 122: ipmis GRgLGhtgG tldkl TYPH_HUMAN : 47- 54: mkrdg GR-LSeadI rgfva TYPH_HUMAN : 145- 153: vpmis GRgLGhtgG tldkl TYPH_LACCA : 13- 20: efgri GR-LAfrrI yel I 9: 17.7724 5( 4) G-R-x(1,2)-G-[HR]-x-[AGL] Occurences: 5(4) PDP_BACSU : 112- 119: vakms GRglGHtG gtidk TYPH_ECOLI : 114- 121: ipmis GRglGHtG gtldk TYPH_HUMAN : 145- 152: vpmis GRglGHtG gtldk TYPH_HUMAN : 278- 285: mdkpl GRcvGHaL eveea TYPH_LACCA : 10- 16: ginef GRi-GRlA frriy J 10: 17.4036 4( 4) G-x(1,2)-G-R-x(0,2)-A-x-[DEKR] Occurences: 4(4) PDP_BACSU : 363- 369: aamll Ga-GR--AtK edeid TYPH_ECOLI : 367- 375: avvam Gg-GRrqAsD tidys TYPH_HUMAN : 405- 413: vlhel Ga-GRsrAgE plrlg TYPH_LACCA : 10- 18: ginef GriGRl-AfR riyel K 11: 17.2661 4( 4) K-x(1,2)-G-x-[AGN]-x-F-x(4)-[EQR] Occurences: 4(4) PDP_BACSU : 202- 213: ivldv Kt-GaGaFmkteE daael TYPH_ECOLI : 204- 215: lvmdv Kv-GsGaFmptyE lseal TYPH_HUMAN : 235- 247: lvvdv KfgGaAvFpnqeQ arela TYPH_LACCA : 3- 14: mv Ki-GiNeFgrigR lafrr L 12: 17.2337 4( 4) G-x(2)-G-x(1,2)-L-[ADT]-x(2)-[DER] Occurences: 4(4) PDP_BACSU : 153- 162: kvavi GqsGn-LTpaD kklya TYPH_ECOLI : 118- 128: sgrgl GhtGgtLDklE sipgf TYPH_HUMAN : 149- 159: sgrgl GhtGgtLDklE sipgf TYPH_LACCA : 10- 19: ginef GriGr-LAfrR iyel M 13: 17.2337 4( 4) G-x(2,3)-G-x-L-[ADT]-x(2)-[DER] Occurences: 4(4) PDP_BACSU : 153- 162: kvavi Gqs-GnLTpaD kklya TYPH_ECOLI : 118- 128: sgrgl GhtgGtLDklE sipgf TYPH_HUMAN : 149- 159: sgrgl GhtgGtLDklE sipgf TYPH_LACCA : 10- 19: ginef Gri-GrLAfrR iyel N 14: 16.8969 4( 4) L-x(0,2)-A-x-R-[DR]-x(2)-[AEGT] Occurences: 4(4) PDP_BACSU : 165- 173: padkk Ly-AlRDvtG tvnsi TYPH_ECOLI : 59- 68: pervs LtmAmRDsgT vldwk TYPH_HUMAN : 198- 206: padgi Ly-AaRDvtA tvdsl TYPH_LACCA : 15- 22: grigr L--AfRRiyE l O 15: 15.2387 4( 4) K-x(2,3)-I-x-[EG]-F Occurences: 4(4) PDP_BACSU : 124- 131: ggtid KleaImGF hvelt TYPH_ECOLI : 126- 133: ggtld KlesIpGF difpd TYPH_HUMAN : 157- 164: ggtld KlesIpGF nviqs TYPH_LACCA : 3- 9: mv Kig-InEF grigr P 16: 14.6042 4( 4) K-x-G-x(3,4)-F-x(4)-[EQR] Occurences: 4(4) PDP_BACSU : 202- 213: ivldv KtGaga-FmkteE daael TYPH_ECOLI : 204- 215: lvmdv KvGsga-FmptyE lseal TYPH_HUMAN : 235- 247: lvvdv KfGgaavFpnqeQ arela TYPH_LACCA : 3- 14: mv KiGine-FgrigR lafrr Q 17: 12.0102 5( 4) E-x(4)-G-x(1,2)-A Occurences: 5(4) PDP_BACSU : 299- 306: rakle EvmknGk-A lekfk TYPH_ECOLI : 282- 290: malcv EmlisGklA kddae TYPH_HUMAN : 51- 59: ggrls EadirGfvA avvng TYPH_HUMAN : 413- 421: rsrag EplrlGvgA ellvd TYPH_LACCA : 8- 16: kigin EfgriGrlA frriy R 18: 12.0102 4( 4) I-x(4)-R-x(3,4)-A Occurences: 4(4) PDP_BACSU : 141- 150: tkdef IklvnRdkv-A vigqs TYPH_ECOLI : 7- 16: flaqe IirkkRdgh-A lsdee TYPH_HUMAN : 197- 206: vpadg IlyaaRdvt-A tvdsl TYPH_LACCA : 6- 16: mvkig InefgRigrlA frriy S 19: 12.0102 4( 4) I-x(5)-G-x(2,3)-G Occurences: 4(4) PDP_BACSU : 21- 31: lttee IqffvnGytdG sipdy TYPH_ECOLI : 112- 121: gyipm IsgrglGht-G gtldk TYPH_ECOLI : 112- 122: gyipm IsgrglGhtgG tldkl TYPH_HUMAN : 143- 152: ckvpm IsgrglGht-G gtldk TYPH_HUMAN : 143- 153: ckvpm IsgrglGhtgG tldkl TYPH_LACCA : 4- 13: mvk IginefGri-G rlafr T 20: 12.0102 4( 4) K-x-G-x(3,4)-F Occurences: 4(4) PDP_BACSU : 202- 208: ivldv KtGaga-F mktee TYPH_ECOLI : 204- 210: lvmdv KvGsga-F mptye TYPH_HUMAN : 235- 242: lvvdv KfGgaavF pnqeq TYPH_LACCA : 3- 9: mv KiGine-F grigr Number of patterns evaluated by Pratt:477 Total running time: 1 seconds