------------------------------------------------------------ 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 8 sequences from file N4_MTASE PATTERN CONSERVATION: CM: min Nr of Seqs to Match 8 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 N4_MTASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: MTB2_BACAM 265 MTC1_CITFR 376 MTC9_CITFR 300 MTHZ_METTF 355 MTMV_MICVA 454 MTP2_PROVU 336 MTSM_SERMA 292 MTX1_XANCC 300 Pratt run started at Thu Feb 6 20:21:47 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.3503 12( 8) V-x(0,1)-T-S-P-P 2: 16.6802 8( 8) D-x-F-x-G-x(2)-T 3: 16.6802 8( 8) T-S-P-P 4: 15.6802 8( 8) D-P-x(0,2)-F-x(4)-T 5: 15.6802 9( 8) T-x(0,2)-S-P-P 6: 12.5102 8( 8) F-x-G-S 7: 12.5102 8( 8) S-P-P 8: 12.0102 10( 8) D-x(3,4)-D-x(4)-S 9: 12.0102 9( 8) L-x(0,1)-D-x(2)-I 10: 12.0102 10( 8) D-x(4)-L-x(3,4)-S 11: 11.5102 11( 8) Y-x(3,4)-E-x(2,3)-E 12: 11.5102 9( 8) P-x(0,1)-F-x(4,5)-T 13: 11.5102 9( 8) P-x(0,2)-F-x(4)-T 14: 11.5102 8( 8) P-x(3,5)-S-G 15: 11.5102 11( 8) V-x(1,3)-D-x(4)-S 16: 11.5102 8( 8) D-I-x(3,5)-P 17: 11.5102 11( 8) D-x(1,2)-F-x(3,4)-G 18: 11.5102 17( 8) E-x(1,2)-I-x(0,1)-L 19: 11.5102 10( 8) E-x(3)-L-x(0,2)-S 20: 11.5102 14( 8) L-x(0,2)-E-x(3)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 33.8404 8( 8) D-[IP]-F-x-G-[ST]-[GN]-T-[STV]-x(3)-[ACG]-x(3)-[DGNS] B 2: 26.1816 12( 8) V-x(0,1)-T-S-P-P-[FY]-x(3)-[EKR] C 3: 22.5116 8( 8) T-S-P-P-[FY]-x(3)-[EKR] D 4: 21.7121 8( 8) V-x(1,3)-D-[ILP]-x(2)-[GLV]-S-[GNQ]-x(2)-[AGNS] E 5: 21.5116 9( 8) T-x(0,2)-S-P-P-[FY]-x(3)-[EKR] F 6: 21.4778 8( 8) D-P-x(0,2)-F-x-[GT]-[PST]-x-T G 7: 20.6815 8( 8) F-x-G-S-[GN]-x(2)-[AGLP]-x(2)-[ACG] H 8: 19.5926 8( 8) D-x(1,2)-F-x(3,4)-G-[GT]-[ASTV]-x(3)-[ACG] I 9: 18.3415 8( 8) S-P-P-[FY]-x(3)-[EKR] J 10: 17.3078 8( 8) P-x(0,2)-F-x-[GT]-[PST]-x-T K 11: 15.6868 8( 8) P-x(3,5)-S-G-x(2)-[AGILP]-x(2)-[ACGS] L 12: 14.6189 10( 8) D-x(3,4)-D-x(3)-[GTV]-S M 13: 13.1594 8( 8) P-x(0,1)-F-x(4,5)-T-x-[AGILPV] N 14: 12.0102 9( 8) L-x(0,1)-D-x(2)-I O 15: 12.0102 10( 8) D-x(4)-L-x(3,4)-S P 16: 11.5102 11( 8) Y-x(3,4)-E-x(2,3)-E Q 17: 11.5102 8( 8) D-I-x(3,5)-P R 18: 11.5102 11( 8) D-x(1,2)-F-x(3,4)-G S 19: 11.5102 17( 8) E-x(1,2)-I-x(0,1)-L T 20: 11.5102 10( 8) E-x(3)-L-x(0,2)-S Best patterns with alignements: fitness hits(seqs) Pattern A 1: 33.8404 8( 8) D-[IP]-F-x-G-[ST]-[GN]-T-[STV]-x(3)-[ACG]-x(3)-[DGNS] Occurences: 8(8) MTB2_BACAM : 207- 223: gdivf DPFmGSGTTakmAalnN rkyig MTC1_CITFR : 330- 346: ndvil DPFaGSGTTakaAidlG rrfvm MTC9_CITFR : 251- 267: gdyvl DPFfGSGTVgvvCqqeD rqyvg MTHZ_METTF : 238- 254: gdwvl DPFlGTGTTmiaAacaG rnsig MTMV_MICVA : 71- 87: ikkly DPFmGSGTSlveGlahG levyg MTP2_PROVU : 271- 287: ddlvv DIFgGSNTTglvAereS rkwis MTSM_SERMA : 252- 268: ggkvl DPFfGSGTTgvvCqelD recvg MTX1_XANCC : 251- 267: gdyvl DPFfGSGTVglvCqdeN rqyvg B 2: 26.1816 12( 8) V-x(0,1)-T-S-P-P-[FY]-x(3)-[EKR] Occurences: 12(8) MTB2_BACAM : 14- 23: tidlt V-TSPPYddlR nyngy MTC1_CITFR : 135- 145: esvnl VfTSPPYynaK peyse MTC9_CITFR : 49- 58: svrci V-TSPPYwglR dygid MTHZ_METTF : 26- 36: ksinl VvTSPPYpmvE iwdrl MTHZ_METTF : 27- 36: sinlv V-TSPPYpmvE iwdrl MTMV_MICVA : 270- 280: emfdi VvTSPPYgdsK ttvay MTMV_MICVA : 271- 280: mfdiv V-TSPPYgdsK ttvay MTP2_PROVU : 50- 60: esisl VmTSPPFalqR kkeyg MTSM_SERMA : 47- 57: eifdc VvTSPPYwglR dygng MTSM_SERMA : 48- 57: ifdcv V-TSPPYwglR dygng MTX1_XANCC : 48- 58: gsvrc VvTSPPYwglR dygie MTX1_XANCC : 49- 58: svrcv V-TSPPYwglR dygie C 3: 22.5116 8( 8) T-S-P-P-[FY]-x(3)-[EKR] Occurences: 8(8) MTB2_BACAM : 15- 23: idltv TSPPYddlR nyngy MTC1_CITFR : 137- 145: vnlvf TSPPYynaK peyse MTC9_CITFR : 50- 58: vrciv TSPPYwglR dygid MTHZ_METTF : 28- 36: inlvv TSPPYpmvE iwdrl MTMV_MICVA : 272- 280: fdivv TSPPYgdsK ttvay MTP2_PROVU : 52- 60: islvm TSPPFalqR kkeyg MTSM_SERMA : 49- 57: fdcvv TSPPYwglR dygng MTX1_XANCC : 50- 58: vrcvv TSPPYwglR dygie D 4: 21.7121 8( 8) V-x(1,3)-D-[ILP]-x(2)-[GLV]-S-[GNQ]-x(2)-[AGNS] Occurences: 8(8) MTB2_BACAM : 205- 216: negdi Vf--DPfmGSGttA kmaal MTC1_CITFR : 327- 339: sfknd Vil-DPfaGSGttA kaaid MTC9_CITFR : 249- 260: kpgdy Vl--DPffGSGtvG vvcqq MTHZ_METTF : 194- 206: qwfsd Vwt-DLtgVSQrlN hknlr MTMV_MICVA : 90- 103: ahgle VygtDInpLSQmmS kaktt MTP2_PROVU : 269- 280: epddl Vv--DIfgGSNttG lvaer MTSM_SERMA : 250- 261: rpggk Vl--DPffGSGttG vvcqe MTX1_XANCC : 249- 260: epgdy Vl--DPffGSGtvG lvcqd E 5: 21.5116 9( 8) T-x(0,2)-S-P-P-[FY]-x(3)-[EKR] Occurences: 9(8) MTB2_BACAM : 13- 23: ctidl TvtSPPYddlR nyngy MTB2_BACAM : 15- 23: idltv T--SPPYddlR nyngy MTC1_CITFR : 137- 145: vnlvf T--SPPYynaK peyse MTC9_CITFR : 50- 58: vrciv T--SPPYwglR dygid MTHZ_METTF : 28- 36: inlvv T--SPPYpmvE iwdrl MTMV_MICVA : 272- 280: fdivv T--SPPYgdsK ttvay MTP2_PROVU : 52- 60: islvm T--SPPFalqR kkeyg MTSM_SERMA : 49- 57: fdcvv T--SPPYwglR dygng MTX1_XANCC : 50- 58: vrcvv T--SPPYwglR dygie F 6: 21.4778 8( 8) D-P-x(0,2)-F-x-[GT]-[PST]-x-T Occurences: 8(8) MTB2_BACAM : 207- 214: gdivf DP--FmGSgT takma MTC1_CITFR : 330- 337: ndvil DP--FaGSgT takaa MTC9_CITFR : 251- 258: gdyvl DP--FfGSgT vgvvc MTHZ_METTF : 238- 245: gdwvl DP--FlGTgT tmiaa MTMV_MICVA : 71- 78: ikkly DP--FmGSgT slveg MTP2_PROVU : 190- 199: kklie DPdkFyTPkT rpsgh MTSM_SERMA : 252- 259: ggkvl DP--FfGSgT tgvvc MTX1_XANCC : 251- 258: gdyvl DP--FfGSgT vglvc G 7: 20.6815 8( 8) F-x-G-S-[GN]-x(2)-[AGLP]-x(2)-[ACG] Occurences: 8(8) MTB2_BACAM : 209- 219: ivfdp FmGSGttAkmA alnnr MTC1_CITFR : 332- 342: vildp FaGSGttAkaA idlgr MTC9_CITFR : 253- 263: yvldp FfGSGtvGvvC qqedr MTHZ_METTF : 138- 148: nkptk FmGSGmlPpnA yvthe MTMV_MICVA : 73- 83: klydp FmGSGtsLveG lahgl MTP2_PROVU : 273- 283: lvvdi FgGSNttGlvA eresr MTSM_SERMA : 254- 264: kvldp FfGSGttGvvC qeldr MTX1_XANCC : 253- 263: yvldp FfGSGtvGlvC qdenr H 8: 19.5926 8( 8) D-x(1,2)-F-x(3,4)-G-[GT]-[ASTV]-x(3)-[ACG] Occurences: 8(8) MTB2_BACAM : 207- 219: gdivf Dp-Fmgs-GTTakmA alnnr MTC1_CITFR : 330- 342: ndvil Dp-Fags-GTTakaA idlgr MTC9_CITFR : 251- 263: gdyvl Dp-Ffgs-GTVgvvC qqedr MTHZ_METTF : 238- 250: gdwvl Dp-Flgt-GTTmiaA acagr MTMV_MICVA : 71- 83: ikkly Dp-Fmgs-GTSlveG lahgl MTP2_PROVU : 90- 104: kklkp DgsFvvdfGGAymkG vpars MTSM_SERMA : 252- 264: ggkvl Dp-Ffgs-GTTgvvC qeldr MTX1_XANCC : 251- 263: gdyvl Dp-Ffgs-GTVglvC qdenr I 9: 18.3415 8( 8) S-P-P-[FY]-x(3)-[EKR] Occurences: 8(8) MTB2_BACAM : 16- 23: dltvt SPPYddlR nyngy MTC1_CITFR : 138- 145: nlvft SPPYynaK peyse MTC9_CITFR : 51- 58: rcivt SPPYwglR dygid MTHZ_METTF : 29- 36: nlvvt SPPYpmvE iwdrl MTMV_MICVA : 273- 280: divvt SPPYgdsK ttvay MTP2_PROVU : 53- 60: slvmt SPPFalqR kkeyg MTSM_SERMA : 50- 57: dcvvt SPPYwglR dygng MTX1_XANCC : 51- 58: rcvvt SPPYwglR dygie J 10: 17.3078 8( 8) P-x(0,2)-F-x-[GT]-[PST]-x-T Occurences: 8(8) MTB2_BACAM : 208- 214: divfd P--FmGSgT takma MTC1_CITFR : 331- 337: dvild P--FaGSgT takaa MTC9_CITFR : 252- 258: dyvld P--FfGSgT vgvvc MTHZ_METTF : 239- 245: dwvld P--FlGTgT tmiaa MTMV_MICVA : 72- 78: kklyd P--FmGSgT slveg MTP2_PROVU : 191- 199: klied PdkFyTPkT rpsgh MTSM_SERMA : 253- 259: gkvld P--FfGSgT tgvvc MTX1_XANCC : 252- 258: dyvld P--FfGSgT vglvc K 11: 15.6868 8( 8) P-x(3,5)-S-G-x(2)-[AGILP]-x(2)-[ACGS] Occurences: 8(8) MTB2_BACAM : 208- 219: divfd Pfmg--SGttAkmA alnnr MTC1_CITFR : 331- 342: dvild Pfag--SGttAkaA idlgr MTC9_CITFR : 252- 263: dyvld Pffg--SGtvGvvC qqedr MTHZ_METTF : 135- 148: kqsnk PtkfmgSGmlPpnA yvthe MTMV_MICVA : 72- 83: kklyd Pfmg--SGtsLveG lahgl MTP2_PROVU : 197- 209: dkfyt Pktrp-SGhdIgkS fskdn MTSM_SERMA : 253- 264: gkvld Pffg--SGttGvvC qeldr MTX1_XANCC : 252- 263: dyvld Pffg--SGtvGlvC qdenr L 12: 14.6189 10( 8) D-x(3,4)-D-x(3)-[GTV]-S Occurences: 10(8) MTB2_BACAM : 7- 16: kenig Dcti-DltvTS ppydd MTB2_BACAM : 203- 212: wsneg Divf-DpfmGS gttak MTC1_CITFR : 326- 335: ysfkn Dvil-DpfaGS gttak MTC9_CITFR : 247- 256: stkpg Dyvl-DpffGS gtvgv MTHZ_METTF : 193- 202: nqwfs Dvwt-DltgVS qrlnh MTMV_MICVA : 264- 273: peefk Demf-DivvTS ppygd MTP2_PROVU : 266- 276: mltep DdlvvDifgGS nttgl MTP2_PROVU : 267- 276: ltepd Dlvv-DifgGS nttgl MTSM_SERMA : 40- 50: avqgl DseifDcvvTS ppywg MTX1_XANCC : 247- 256: stepg Dyvl-DpffGS gtvgl M 13: 13.1594 8( 8) P-x(0,1)-F-x(4,5)-T-x-[AGILPV] Occurences: 8(8) MTB2_BACAM : 208- 216: divfd P-Fmgsg-TtA kmaal MTC1_CITFR : 331- 339: dvild P-Fagsg-TtA kaaid MTC9_CITFR : 252- 260: dyvld P-Ffgsg-TvG vvcqq MTHZ_METTF : 239- 248: dwvld P-FlgtgtTmI aaaca MTMV_MICVA : 72- 80: kklyd P-Fmgsg-TsL vegla MTP2_PROVU : 255- 265: fpakl PeFfirmlTeP ddlvv MTSM_SERMA : 253- 261: gkvld P-Ffgsg-TtG vvcqe MTSM_SERMA : 253- 262: gkvld PfFgsgt-TgV vcqel MTSM_SERMA : 253- 262: gkvld P-FfgsgtTgV vcqel MTX1_XANCC : 252- 260: dyvld P-Ffgsg-TvG lvcqd N 14: 12.0102 9( 8) L-x(0,1)-D-x(2)-I Occurences: 9(8) MTB2_BACAM : 80- 85: elgfn LhDtmI yekds MTC1_CITFR : 266- 271: kktdk LiDwnI rnhhs MTC9_CITFR : 57- 62: ppywg LrDygI deqig MTHZ_METTF : 18- 23: admne LkDksI nlvvt MTMV_MICVA : 296- 300: lsaqw L-DlkI ddetk MTMV_MICVA : 361- 365: qfyvd L-DksI kettr MTP2_PROVU : 308- 312: safrf L-DnnI seeki MTSM_SERMA : 39- 43: eavqg L-DseI fdcvv MTX1_XANCC : 57- 62: ppywg LrDygI eeqig O 15: 12.0102 10( 8) D-x(4)-L-x(3,4)-S Occurences: 10(8) MTB2_BACAM : 7- 16: kenig DctidLtvt-S ppydd MTC1_CITFR : 129- 138: lkklp DesvnLvft-S ppyyn MTC9_CITFR : 32- 42: tlfeg DalsvLrrlpS gsvrc MTHZ_METTF : 20- 29: mnelk DksinLvvt-S ppypm MTHZ_METTF : 193- 202: nqwfs DvwtdLtgv-S qrlnh MTMV_MICVA : 6- 16: meyln DkdqhLidklS kkind MTMV_MICVA : 326- 336: niivn DvleyLnsptS ksvfn MTP2_PROVU : 172- 181: ewpks DitkvLapy-S drmkk MTSM_SERMA : 92- 102: rtlkd DgtlwLnigdS ytsgg MTX1_XANCC : 32- 42: tlfeg DaltvLrrlpS gsvrc P 16: 11.5102 11( 8) Y-x(3,4)-E-x(2,3)-E Occurences: 11(8) MTB2_BACAM : 226- 234: lnnrk Yigt-EiskE ycdia MTC1_CITFR : 142- 150: tsppy YnakpEys-E yhtyd MTC9_CITFR : 192- 201: tksek YyydwEavrE ekdsg MTC9_CITFR : 193- 201: kseky Yydw-EavrE ekdsg MTC9_CITFR : 270- 278: qedrq Yvgi-ElnpE yvdia MTHZ_METTF : 63- 71: dglrs YnlmhEel-E kvwhe MTMV_MICVA : 202- 210: nefkl YrmapEkl-E iwnpn MTP2_PROVU : 64- 71: qrkke Ygnl-Eqh-E yvdwf MTSM_SERMA : 191- 200: skgkk YyydwEsikE pasdp MTSM_SERMA : 192- 200: kgkky Yydw-EsikE pasdp MTX1_XANCC : 270- 278: denrq Yvgi-ElnpE yvtla Q 17: 11.5102 8( 8) D-I-x(3,5)-P Occurences: 8(8) MTB2_BACAM : 203- 208: wsneg DIvfd--P fmgsg MTC1_CITFR : 219- 225: yefid DIhwvk-P egagw MTC9_CITFR : 159- 165: wylrs DIvwnk-P nampe MTHZ_METTF : 319- 325: trqeq DIrlyy-P rtykk MTMV_MICVA : 268- 274: kdemf DIvvts-P pygds MTMV_MICVA : 268- 275: kdemf DIvvtspP ygdsk MTP2_PROVU : 172- 179: ewpks DItkvlaP ysdrm MTSM_SERMA : 158- 164: wylrt DIiwnk-P ncqpe MTX1_XANCC : 159- 165: wylrs DIvwnk-P nampe R 18: 11.5102 11( 8) D-x(1,2)-F-x(3,4)-G Occurences: 11(8) MTB2_BACAM : 203- 211: wsneg DivFdpfmG sgtta MTB2_BACAM : 207- 213: gdivf Dp-Fmgs-G ttakm MTC1_CITFR : 279- 286: hhske Dv-FdskiG ddyek MTC1_CITFR : 330- 336: ndvil Dp-Fags-G ttaka MTC9_CITFR : 251- 257: gdyvl Dp-Ffgs-G tvgvv MTHZ_METTF : 113- 119: hvrti Df-Ffdr-G yqvlp MTHZ_METTF : 238- 244: gdwvl Dp-Flgt-G ttmia MTMV_MICVA : 71- 77: ikkly Dp-Fmgs-G tslve MTP2_PROVU : 90- 98: kklkp DgsFvvdfG gaymk MTSM_SERMA : 252- 258: ggkvl Dp-Ffgs-G ttgvv MTX1_XANCC : 251- 257: gdyvl Dp-Ffgs-G tvglv S 19: 11.5102 17( 8) E-x(1,2)-I-x(0,1)-L Occurences: 17(8) MTB2_BACAM : 192- 196: pekla EdhI-L swsne MTC1_CITFR : 254- 257: pvpvt Ey-I-L vyrkk MTC9_CITFR : 64- 68: dygid Eq-IgL essmt MTHZ_METTF : 155- 158: vtheh Ey-I-L ifrke MTHZ_METTF : 317- 322: vttrq EqdIrL yyprt MTMV_MICVA : 54- 58: pqlak Ef-IeL tqqvk MTMV_MICVA : 128- 132: eysir EmtI-L yhegn MTMV_MICVA : 156- 161: fwfke EviIsL qlikn MTMV_MICVA : 442- 445: vtmts Ei-I-L mlkny MTP2_PROVU : 44- 49: lesfp EesIsL vmtsp MTP2_PROVU : 45- 49: esfpe Es-IsL vmtsp MTSM_SERMA : 180- 184: ptrsh Ey-IfL lskgk MTSM_SERMA : 286- 289: aslak Er-I-L rrr MTX1_XANCC : 13- 16: ppsgv Er-I-L rpepl MTX1_XANCC : 19- 23: rilrp EplI-L rgstl MTX1_XANCC : 63- 68: rdygi EeqIgL evtmp MTX1_XANCC : 64- 68: dygie Eq-IgL evtmp T 20: 11.5102 10( 8) E-x(3)-L-x(0,2)-S Occurences: 10(8) MTB2_BACAM : 192- 197: pekla EdhiL--S wsneg MTB2_BACAM : 192- 199: pekla EdhiLswS negdi MTC1_CITFR : 156- 163: yhtyd EylsLlrS vikec MTC9_CITFR : 30- 35: gatlf EgdaL--S vlrrl MTC9_CITFR : 64- 70: dygid EqigLe-S smtqf MTC9_CITFR : 64- 71: dygid EqigLesS mtqfl MTHZ_METTF : 56- 62: etlid EedgLr-S ynlmh MTHZ_METTF : 276- 281: esrin EtlkL--S neivm MTMV_MICVA : 111- 116: kttpi EpskL--S raisd MTP2_PROVU : 328- 334: rilng EsldLn-S ii MTSM_SERMA : 180- 186: ptrsh EyifLl-S kgkky MTX1_XANCC : 19- 26: rilrp EpliLrgS tlfeg Number of patterns evaluated by Pratt:3010 Total running time: 2 seconds