------------------------------------------------------------ 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 T2SP_N 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 T2SP_N.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: GSPN_AERHY 252 GSPN_AERSA 47 GSPN_ERWCA 248 GSPN_KLEPN 252 GSPN_VIBCH 251 Pratt run started at Thu Feb 6 21:21:31 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.1802 6( 5) L-x(1,2)-Q-G-x-L 2: 15.6802 5( 5) L-x(0,1)-Q-x(2)-G-x(4,5)-P 3: 15.6802 5( 5) L-x(3,4)-G-x-G-x(2,3)-P 4: 15.6802 5( 5) L-x(1,2)-L-x(2)-P-x(3,4)-R 5: 15.6802 5( 5) R-x(4,5)-Q-G-x(1,2)-L 6: 15.6802 7( 5) Q-x(1,2)-R-x(4,5)-Q-G 7: 15.1802 5( 5) Q-x(2,4)-G-x-G-x(2,3)-P 8: 15.1802 6( 5) L-x(2,3)-L-x-Q-x(3,5)-Q 9: 15.1802 5( 5) R-x(2,3)-F-x(1,3)-G-x-L 10: 14.6802 8( 5) L-x(0,2)-Q-x(3,5)-Q-x(4)-G 11: 12.5102 7( 5) Q-G-R 12: 12.5102 6( 5) L-x(2)-Q-G 13: 12.5102 5( 5) D-x(5)-P-x(4)-G 14: 12.5102 7( 5) L-x(5)-Q-x(4)-L 15: 12.5102 7( 5) L-x(2)-G-x(2)-L 16: 12.5102 9( 5) G-x-L-x(2)-G 17: 12.5102 8( 5) Q-G-x-L 18: 12.5102 6( 5) L-x-Q-G 19: 12.0102 5( 5) R-x-Q-x(0,1)-G 20: 12.0102 5( 5) R-x(1,2)-Q-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 41.1431 5( 5) G-[ST]-L-x-[PQ]-G-[EPQS]-x(4)-[EQRS]-x(2)-[GQT]-x(2)-[LP]-x(2)-[GLV]-x(2)-[DEN]-x(3)-[RS]-x(2)-[LM] B 2: 28.6712 5( 5) L-x(2,3)-L-x-Q-x(3,5)-Q-[GL]-[RS]-x(3)-[NQRS]-x(2)-[GLP]-x-[GILP] C 3: 25.4597 5( 5) L-x(2)-[ANP]-x(2)-Q-[ADGT]-x(3)-L-x(2)-[PQST]-[GV]-x-[GIL] D 4: 24.9175 5( 5) D-x-[AQ]-x-[KR]-x-P-x(3)-[AQ]-G-[EQR] E 5: 21.6838 7( 5) L-x(0,2)-Q-x(3,5)-Q-x(4)-G-x(3)-[AGLP]-x-[GLP]-[DENR] F 6: 21.4912 5( 5) L-x(1,2)-L-[AGP]-x-P-x(3,4)-R-x-[PQ] G 7: 21.3147 5( 5) L-[FW]-Q-G-[EQST]-[AL] H 8: 20.9228 5( 5) L-x(0,1)-Q-[LPV]-[DNS]-G-x(4,5)-P I 9: 20.2505 5( 5) L-x(2)-G-[LP]-x-L-[APT]-[ADEGS] J 10: 19.6158 5( 5) Q-G-x-L-x(2)-[ADGN]-[GLPV]-[EKR] K 11: 17.8924 6( 5) Q-x(1,2)-R-x(4,5)-Q-G-[EQRS] L 12: 16.1802 6( 5) L-x(1,2)-Q-G-x-L M 13: 15.7968 5( 5) L-x(2)-Q-G-x-[IL] N 14: 15.7276 5( 5) Q-G-R-x-[LP] O 15: 15.6802 5( 5) L-x(3,4)-G-x-G-x(2,3)-P P 16: 15.6802 5( 5) R-x(4,5)-Q-G-x(1,2)-L Q 17: 15.1802 5( 5) Q-x(2,4)-G-x-G-x(2,3)-P R 18: 15.1802 5( 5) R-x(2,3)-F-x(1,3)-G-x-L S 19: 12.5102 7( 5) Q-G-R T 20: 12.5102 6( 5) L-x(2)-Q-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 41.1431 5( 5) G-[ST]-L-x-[PQ]-G-[EPQS]-x(4)-[EQRS]-x(2)-[GQT]-x(2)-[LP]-x(2)-[GLV]-x(2)-[DEN]-x(3)-[RS]-x(2)-[LM] Occurences: 5(5) GSPN_AERHY : 216- 246: qylfq GTLkPGPelpdQmkQglPflGqpDgqgRfpL ryqgr GSPN_AERSA : 11- 41: qylfq GSLkPGPelpeEmkQglPflGqpDgqgRfpL ryqgr GSPN_ERWCA : 46- 76: vaeaa GTLwQGSlqrfSwrTltLddVhwNitfSdfM paldi GSPN_KLEPN : 43- 73: laqts GTLwQGEahqaSwrGveLayLrwEfgfStwL pgwhi GSPN_VIBCH : 45- 75: ltgie GTLwQGQaaqvRwqGmsLgdLnwDlhlSalL lgqle B 2: 28.6712 5( 5) L-x(2,3)-L-x-Q-x(3,5)-Q-[GL]-[RS]-x(3)-[NQRS]-x(2)-[GLP]-x-[GILP] Occurences: 5(5) GSPN_AERHY : 232- 252: qmkqg Lpf-LgQpdg--QGRfplRyqGrI GSPN_AERSA : 27- 47: emkqg Lpf-LgQpdg--QGRfplRyqGrI GSPN_ERWCA : 182- 205: cqqga LeanLrQtsshlQLSgkgSvtPkG eyrft GSPN_KLEPN : 181- 202: tpaga LavaLtQdsh--QLSltgQgvLtP dgryt GSPN_VIBCH : 231- 251: slkeq Lsw-LpQpdg--QGRypfNqqGqL C 3: 25.4597 5( 5) L-x(2)-[ANP]-x(2)-Q-[ADGT]-x(3)-L-x(2)-[PQST]-[GV]-x-[GIL] Occurences: 5(5) GSPN_AERHY : 235- 252: qglpf LgqPdgQGrfpLryQGrI GSPN_AERSA : 30- 47: qglpf LgqPdgQGrfpLryQGrI GSPN_ERWCA : 182- 199: cqqga LeaNlrQTsshLqlSGkG svtpk GSPN_KLEPN : 181- 198: tpaga LavAltQDshqLslTGqG vltpd GSPN_VIBCH : 113- 130: addfl LslPaaQAitwLplPVpL maqgq D 4: 24.9175 5( 5) D-x-[AQ]-x-[KR]-x-P-x(3)-[AQ]-G-[EQR] Occurences: 5(5) GSPN_AERHY : 239- 251: flgqp DgQgRfPlryQGR i GSPN_AERSA : 34- 46: flgqp DgQgRfPlryQGR i GSPN_ERWCA : 80- 92: fmpal DiAfKnPegiAGR giirg GSPN_KLEPN : 233- 245: qngrk DeQgRiPwrwQGE wlsee GSPN_VIBCH : 238- 250: wlpqp DgQgRyPfnqQGQ l E 5: 21.6838 7( 5) L-x(0,2)-Q-x(3,5)-Q-x(4)-G-x(3)-[AGLP]-x-[GLP]-[DENR] Occurences: 7(5) GSPN_AERHY : 204- 223: qvlgk LelQpnr--QylfqGtlkPgPE lpdqm GSPN_AERHY : 206- 223: lgkle L--Qpnr--QylfqGtlkPgPE lpdqm GSPN_AERSA : 1- 18: L--Qanr--QylfqGslkPgPE lpeem GSPN_ERWCA : 186- 206: alean Lr-QtsshlQlsgkGsvtPkGE yrftg GSPN_KLEPN : 45- 64: qtsgt Lw-Qgeah-QaswrGvelAyLR wefgf GSPN_KLEPN : 185- 203: alava Lt-Qdsh--QlsltGqgvLtPD grytf GSPN_VIBCH : 47- 66: giegt Lw-Qgqaa-QvrwqGmslGdLN wdlhl F 6: 21.4912 5( 5) L-x(1,2)-L-[AGP]-x-P-x(3,4)-R-x-[PQ] Occurences: 5(5) GSPN_AERHY : 232- 245: qmkqg LpfLGqPdgqgRfP lryqg GSPN_AERSA : 27- 40: emkqg LpfLGqPdgqgRfP lryqg GSPN_ERWCA : 166- 178: tplgg Lv-LAtPqatlRcQ qgale GSPN_KLEPN : 116- 127: lisqr La-LGmPlea-RgQ laltl GSPN_VIBCH : 231- 244: slkeq LswLPqPdgqgRyP fnqqg G 7: 21.3147 5( 5) L-[FW]-Q-G-[EQST]-[AL] Occurences: 5(5) GSPN_AERHY : 213- 218: pnrqy LFQGTL kpgpe GSPN_AERSA : 8- 13: anrqy LFQGSL kpgpe GSPN_ERWCA : 48- 53: eaagt LWQGSL qrfsw GSPN_KLEPN : 45- 50: qtsgt LWQGEA hqasw GSPN_VIBCH : 47- 52: giegt LWQGQA aqvrw H 8: 20.9228 5( 5) L-x(0,1)-Q-[LPV]-[DNS]-G-x(4,5)-P Occurences: 5(5) GSPN_AERHY : 235- 245: qglpf LgQPDGqgrf-P lryqg GSPN_AERSA : 30- 40: qglpf LgQPDGqgrf-P lryqg GSPN_ERWCA : 193- 203: qtssh L-QLSGkgsvtP kgeyr GSPN_KLEPN : 166- 177: aglle LaQVNGklsctP agala GSPN_VIBCH : 234- 244: eqlsw LpQPDGqgry-P fnqqg I 9: 20.2505 5( 5) L-x(2)-G-[LP]-x-L-[APT]-[ADEGS] Occurences: 5(5) GSPN_AERHY : 218- 226: lfqgt LkpGPeLPD qmkqg GSPN_AERSA : 13- 21: lfqgs LkpGPeLPE emkqg GSPN_ERWCA : 15- 23: gvalv LayGLfLAS yapar GSPN_KLEPN : 5- 13: mknr LtiGLlLAA iylfw GSPN_VIBCH : 34- 42: lsplp LpeGLeLTG iegtl J 10: 19.6158 5( 5) Q-G-x-L-x(2)-[ADGN]-[GLPV]-[EKR] Occurences: 5(5) GSPN_AERHY : 215- 223: rqylf QGtLkpGPE lpdqm GSPN_AERSA : 10- 18: rqylf QGsLkpGPE lpeem GSPN_ERWCA : 179- 187: tlrcq QGaLeaNLR qtssh GSPN_KLEPN : 197- 205: lsltg QGvLtpDGR ytfng GSPN_VIBCH : 133- 141: vplma QGqLemAVK qyrfg K 11: 17.8924 6( 5) Q-x(1,2)-R-x(4,5)-Q-G-[EQRS] Occurences: 6(5) GSPN_AERHY : 241- 251: gqpdg Qg-RfplryQGR i GSPN_AERSA : 2- 12: l QanRqylf-QGS lkpgp GSPN_AERSA : 36- 46: gqpdg Qg-RfplryQGR i GSPN_ERWCA : 236- 246: gkane QgaRtlnf-QGR ll GSPN_KLEPN : 235- 245: grkde Qg-RipwrwQGE wlsee GSPN_VIBCH : 240- 250: pqpdg Qg-RypfnqQGQ l L 12: 16.1802 6( 5) L-x(1,2)-Q-G-x-L Occurences: 6(5) GSPN_AERHY : 213- 218: pnrqy Lf-QGtL kpgpe GSPN_AERSA : 8- 13: anrqy Lf-QGsL kpgpe GSPN_ERWCA : 48- 53: eaagt Lw-QGsL qrfsw GSPN_ERWCA : 241- 247: qgart LnfQGrL l GSPN_KLEPN : 194- 200: shqls LtgQGvL tpdgr GSPN_VIBCH : 130- 136: plpvp LmaQGqL emavk M 13: 15.7968 5( 5) L-x(2)-Q-G-x-[IL] Occurences: 5(5) GSPN_AERHY : 246- 252: qgrfp LryQGrI GSPN_AERSA : 41- 47: qgrfp LryQGrI GSPN_ERWCA : 241- 247: qgart LnfQGrL l GSPN_KLEPN : 194- 200: shqls LtgQGvL tpdgr GSPN_VIBCH : 130- 136: plpvp LmaQGqL emavk N 14: 15.7276 5( 5) Q-G-R-x-[LP] Occurences: 5(5) GSPN_AERHY : 241- 245: gqpdg QGRfP lryqg GSPN_AERSA : 36- 40: gqpdg QGRfP lryqg GSPN_ERWCA : 244- 248: rtlnf QGRlL GSPN_KLEPN : 235- 239: grkde QGRiP wrwqg GSPN_VIBCH : 240- 244: pqpdg QGRyP fnqqg O 15: 15.6802 5( 5) L-x(3,4)-G-x-G-x(2,3)-P Occurences: 5(5) GSPN_AERHY : 235- 245: qglpf LgqpdGqGrf-P lryqg GSPN_AERSA : 30- 40: qglpf LgqpdGqGrf-P lryqg GSPN_ERWCA : 193- 203: qtssh Lqls-GkGsvtP kgeyr GSPN_KLEPN : 192- 202: qdshq Lslt-GqGvltP dgryt GSPN_VIBCH : 234- 244: eqlsw LpqpdGqGry-P fnqqg P 16: 15.6802 5( 5) R-x(4,5)-Q-G-x(1,2)-L Occurences: 5(5) GSPN_AERHY : 210- 218: elqpn Rqylf-QGt-L kpgpe GSPN_AERSA : 5- 13: lqan Rqylf-QGs-L kpgpe GSPN_ERWCA : 239- 247: neqga Rtlnf-QGr-L l GSPN_ERWCA : 239- 248: neqga Rtlnf-QGrlL GSPN_KLEPN : 237- 247: kdeqg RipwrwQGewL seekk GSPN_VIBCH : 242- 251: pdgqg RypfnqQGq-L Q 17: 15.1802 5( 5) Q-x(2,4)-G-x-G-x(2,3)-P Occurences: 5(5) GSPN_AERHY : 237- 245: lpflg Qpd--GqGrf-P lryqg GSPN_AERSA : 32- 40: lpflg Qpd--GqGrf-P lryqg GSPN_ERWCA : 194- 203: tsshl Qls--GkGsvtP kgeyr GSPN_KLEPN : 191- 202: tqdsh QlsltGqGvltP dgryt GSPN_VIBCH : 236- 244: lswlp Qpd--GqGry-P fnqqg R 18: 15.1802 5( 5) R-x(2,3)-F-x(1,3)-G-x-L Occurences: 5(5) GSPN_AERHY : 210- 218: elqpn RqylFq--GtL kpgpe GSPN_AERSA : 5- 13: lqan RqylFq--GsL kpgpe GSPN_ERWCA : 239- 247: neqga RtlnFq--GrL l GSPN_KLEPN : 205- 212: ltpdg Ryt-Fn--GtL qprqa GSPN_VIBCH : 242- 251: pdgqg Ryp-FnqqGqL S 19: 12.5102 7( 5) Q-G-R Occurences: 7(5) GSPN_AERHY : 241- 243: gqpdg QGR fplry GSPN_AERHY : 249- 251: fplry QGR i GSPN_AERSA : 36- 38: gqpdg QGR fplry GSPN_AERSA : 44- 46: fplry QGR i GSPN_ERWCA : 244- 246: rtlnf QGR ll GSPN_KLEPN : 235- 237: grkde QGR ipwrw GSPN_VIBCH : 240- 242: pqpdg QGR ypfnq T 20: 12.5102 6( 5) L-x(2)-Q-G Occurences: 6(5) GSPN_AERHY : 92- 96: gdrsg LngQG vvgwn GSPN_AERHY : 246- 250: qgrfp LryQG ri GSPN_AERSA : 41- 45: qgrfp LryQG ri GSPN_ERWCA : 241- 245: qgart LnfQG rll GSPN_KLEPN : 194- 198: shqls LtgQG vltpd GSPN_VIBCH : 130- 134: plpvp LmaQG qlema Number of patterns evaluated by Pratt:1023 Total running time: 0 seconds