------------------------------------------------------------ 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 24 sequences from file CEREAL_TRYP_AMYL_INH PATTERN CONSERVATION: CM: min Nr of Seqs to Match 24 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 CEREAL_TRYP_AMYL_INH.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: IA01_WHEAT 145 IA02_WHEAT 145 IA03_WHEAT 168 IA16_WHEAT 143 IA17_WHEAT 27 IAA1_HORVU 20 IAA1_WHEAT 124 IAA2_WHEAT 123 IAA3_WHEAT 44 IAA5_WHEAT 124 IAAA_HORVU 145 IAAB_HORVU 149 IAAC_HORVU 35 IAAD_HORVU 171 IAAE_HORVU 144 IAAI_HORVU 152 IAAT_ELECO 122 IAA_HORVU 147 ITRF_MAIZE 155 RA05_ORYSA 157 RA14_ORYSA 165 RA17_ORYSA 162 RAG1_ORYSA 95 RAG2_ORYSA 166 Pratt run started at Thu Feb 6 19:05:31 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 46( 24) P-x(2,3)-C 2: 7.3401 86( 24) P-x(1,3)-C 3: 7.3401 35( 24) C-x(1,3)-P Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.8401 46( 24) P-x(2,3)-C B 2: 7.3401 86( 24) P-x(1,3)-C C 3: 7.3401 35( 24) C-x(1,3)-P Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.8401 46( 24) P-x(2,3)-C Occurences: 46(24) IA01_WHEAT : 40- 44: glpin PlegC reyva IA01_WHEAT : 70- 74: epgnt PrdrC ckely IA02_WHEAT : 40- 44: glpsn PlegC reyva IA02_WHEAT : 70- 74: epgnt PrdrC ckely IA02_WHEAT : 126- 129: kvlvt Pgh-C nvmtv IA03_WHEAT : 145- 148: rllva Pgq-C nlati IA16_WHEAT : 40- 44: stlit PlpsC rdyve IA16_WHEAT : 76- 79: elani Pqq-C rcqal IA16_WHEAT : 120- 123: rilvt Pgy-C nlttv IA17_WHEAT : 14- 18: stlix PlpxC rnyvx IAA1_HORVU : 2- 6: s PgewC wpgmg IAA1_HORVU : 16- 20: gypvy PfpxC IAA1_WHEAT : 3- 6: sg Pwm-C ypgqa IAA2_WHEAT : 3- 7: sg PwswC npatg IAA2_WHEAT : 95- 98: taasv Pev-C kvpip IAA3_WHEAT : 3- 6: sg Pwm-C ypgya IAA5_WHEAT : 3- 6: sg Pwm-C ypgqa IAAA_HORVU : 40- 44: glpsn PlegC reyva IAAA_HORVU : 70- 74: epgdt PkdrC cqeld IAAA_HORVU : 82- 85: eldea Pqh-C rceav IAAA_HORVU : 126- 129: kvlvt Pgq-C nvltv IAAB_HORVU : 40- 44: atpit PlpsC rdyve IAAB_HORVU : 76- 79: elani Pqq-C rcqal IAAB_HORVU : 120- 123: rilvt Pgf-C nlttv IAAC_HORVU : 16- 20: glpvn PlqgC rfyva IAAD_HORVU : 94- 97: elaei Pqq-C rceal IAAD_HORVU : 148- 151: rllva Pgq-C nlati IAAE_HORVU : 39- 43: alphn PlraC rtyvv IAAE_HORVU : 75- 78: elsai Pay-C rceal IAAE_HORVU : 123- 126: anlvt Pqe-C nlgti IAAI_HORVU : 33- 37: sdnsg PwmwC dpemg IAAI_HORVU : 47- 51: ghkvs PltrC ralvk IAAI_HORVU : 126- 129: lvagv Pal-C nvpip IAAT_ELECO : 16- 20: aiphn PldsC rwyva IAAT_ELECO : 52- 55: qleai Pay-C rceav IAA_HORVU : 43- 47: dfphn PlatC htyvi IAA_HORVU : 78- 81: elaav Pdh-C rceal ITRF_MAIZE : 44- 48: aiphn PlpsC rwyvt ITRF_MAIZE : 80- 83: eladi Pay-C rctal RA05_ORYSA : 134- 137: aaasl Paf-C nvdip RA14_ORYSA : 137- 140: aaasl Paf-C nvdip RA17_ORYSA : 35- 39: hqvys PgeqC rpgis RA17_ORYSA : 134- 137: aaasl Paf-C nvdip RA17_ORYSA : 145- 149: dipng PggvC ywlgy RAG1_ORYSA : 35- 39: hqvys PgeqC rpgis RAG2_ORYSA : 138- 141: aaasl Paf-C nvdip B 2: 7.3401 86( 24) P-x(1,3)-C Occurences: 86(24) IA01_WHEAT : 28- 30: atatg Py--C yagmg IA01_WHEAT : 40- 44: glpin PlegC reyva IA01_WHEAT : 70- 74: epgnt PrdrC ckely IA01_WHEAT : 109- 111: vlkdl Pg--C prepq IA01_WHEAT : 138- 140: tvhna Py--C lgldi IA02_WHEAT : 28- 30: aaatg Py--C ypgmg IA02_WHEAT : 40- 44: glpsn PlegC reyva IA02_WHEAT : 70- 74: epgnt PrdrC ckely IA02_WHEAT : 109- 111: vlkdl Pg--C prepq IA02_WHEAT : 126- 129: kvlvt Pgh-C nvmtv IA02_WHEAT : 138- 140: tvhnt Py--C lgldi IA03_WHEAT : 41- 43: rtnll Ph--C rdyvl IA03_WHEAT : 128- 130: glidl Pg--C premq IA03_WHEAT : 145- 148: rllva Pgq-C nlati IA16_WHEAT : 40- 44: stlit PlpsC rdyve IA16_WHEAT : 42- 44: litpl Ps--C rdyve IA16_WHEAT : 76- 79: elani Pqq-C rcqal IA16_WHEAT : 103- 105: glmel Pg--C prevq IA16_WHEAT : 120- 123: rilvt Pgy-C nlttv IA16_WHEAT : 132- 134: tvhnt Py--C lamee IA17_WHEAT : 14- 18: stlix PlpxC rnyvx IA17_WHEAT : 16- 18: lixpl Px--C rnyvx IAA1_HORVU : 2- 6: s PgewC wpgmg IAA1_HORVU : 16- 20: gypvy PfpxC IAA1_HORVU : 18- 20: pvypf Px--C IAA1_WHEAT : 3- 6: sg Pwm-C ypgqa IAA1_WHEAT : 18- 20: qvpal Pa--C rpllr IAA1_WHEAT : 81- 83: gtgaf Pr--C rrevv IAA2_WHEAT : 3- 7: sg PwswC npatg IAA2_WHEAT : 80- 82: gkevl Pg--C rkevm IAA2_WHEAT : 95- 98: taasv Pev-C kvpip IAA3_WHEAT : 3- 6: sg Pwm-C ypgya IAA3_WHEAT : 18- 20: kvpal Pg--C rpvll IAA5_WHEAT : 3- 6: sg Pwm-C ypgqa IAA5_WHEAT : 18- 20: qvpal Pg--C rpllk IAA5_WHEAT : 52- 54: disew Pr--C galys IAA5_WHEAT : 81- 83: gtgaf Ps--C rrevv IAAA_HORVU : 40- 44: glpsn PlegC reyva IAAA_HORVU : 70- 74: epgdt PkdrC cqeld IAAA_HORVU : 82- 85: eldea Pqh-C rceav IAAA_HORVU : 109- 111: vlkdl Pg--C pkepq IAAA_HORVU : 126- 129: kvlvt Pgq-C nvltv IAAA_HORVU : 138- 140: tvhna Py--C lgldi IAAB_HORVU : 40- 44: atpit PlpsC rdyve IAAB_HORVU : 42- 44: pitpl Ps--C rdyve IAAB_HORVU : 76- 79: elani Pqq-C rcqal IAAB_HORVU : 103- 105: glmel Pg--C prevq IAAB_HORVU : 120- 123: rilvt Pgf-C nlttv IAAB_HORVU : 132- 134: tvhnt Py--C lamde IAAC_HORVU : 16- 20: glpvn PlqgC rfyva IAAD_HORVU : 94- 97: elaei Pqq-C rceal IAAD_HORVU : 131- 133: glmdl Pg--C premq IAAD_HORVU : 148- 151: rllva Pgq-C nlati IAAE_HORVU : 39- 43: alphn PlraC rtyvv IAAE_HORVU : 75- 78: elsai Pay-C rceal IAAE_HORVU : 106- 108: yfkds Pn--C prerq IAAE_HORVU : 123- 126: anlvt Pqe-C nlgti IAAI_HORVU : 33- 37: sdnsg PwmwC dpemg IAAI_HORVU : 47- 51: ghkvs PltrC ralvk IAAI_HORVU : 111- 113: peevf Pg--C qkdvm IAAI_HORVU : 126- 129: lvagv Pal-C nvpip IAAT_ELECO : 16- 20: aiphn PldsC rwyva IAAT_ELECO : 52- 55: qleai Pay-C rceav IAAT_ELECO : 83- 85: llqdl Pg--C prqvq IAAT_ELECO : 112- 114: tihgg Pf--C lsllg IAA_HORVU : 43- 47: dfphn PlatC htyvi IAA_HORVU : 78- 81: elaav Pdh-C rceal ITRF_MAIZE : 44- 48: aiphn PlpsC rwyvt ITRF_MAIZE : 46- 48: phnpl Ps--C rwyvt ITRF_MAIZE : 80- 83: eladi Pay-C rctal ITRF_MAIZE : 112- 114: rledl Pg--C prevq RA05_ORYSA : 53- 55: pmysl Pr--C ralvk RA05_ORYSA : 134- 137: aaasl Paf-C nvdip RA14_ORYSA : 53- 55: pmysl Pr--C ravvk RA14_ORYSA : 122- 124: maevf Pg--C rrgdl RA14_ORYSA : 137- 140: aaasl Paf-C nvdip RA17_ORYSA : 35- 39: hqvys PgeqC rpgis RA17_ORYSA : 51- 53: ptysl Pq--C rtlvr RA17_ORYSA : 119- 121: maevf Pg--C rrgdl RA17_ORYSA : 134- 137: aaasl Paf-C nvdip RA17_ORYSA : 145- 149: dipng PggvC ywlgy RAG1_ORYSA : 35- 39: hqvys PgeqC rpgis RAG1_ORYSA : 51- 53: ptysl Pq--C rtlvr RAG2_ORYSA : 53- 55: pmysl Pr--C ravvk RAG2_ORYSA : 123- 125: maevf Pg--C rrgdl RAG2_ORYSA : 138- 141: aaasl Paf-C nvdip C 3: 7.3401 35( 24) C-x(1,3)-P Occurences: 35(24) IA01_WHEAT : 111- 115: kdlpg CpreP qrdfa IA02_WHEAT : 30- 32: atgpy Cy--P gmglp IA02_WHEAT : 111- 115: kdlpg CpreP qrdfa IA03_WHEAT : 29- 31: sasgs Cv--P gvafr IA16_WHEAT : 30- 32: igned Ct--P wmstl IA17_WHEAT : 4- 6: ned Ct--P wtstl IAA1_HORVU : 6- 8: spgew Cw--P gmgyp IAA1_WHEAT : 6- 8: sgpwm Cy--P gqafq IAA1_WHEAT : 20- 22: palpa Cr--P llrlq IAA1_WHEAT : 99- 102: sitav Crl-P ivvda IAA2_WHEAT : 7- 9: gpwsw Cn--P atgyk IAA2_WHEAT : 98- 101: svpev Ckv-P ipnps IAA3_WHEAT : 6- 8: sgpwm Cy--P gyafk IAA3_WHEAT : 20- 22: palpg Cr--P vlllq IAA5_WHEAT : 6- 8: sgpwm Cy--P gqafq IAA5_WHEAT : 20- 22: palpg Cr--P llklq IAA5_WHEAT : 99- 102: sitav Crl-P ivvda IAAA_HORVU : 111- 115: kdlpg CpkeP qrdfa IAAB_HORVU : 30- 32: vgsed Ct--P wtatp IAAC_HORVU : 29- 33: vaxqt CgavP ll IAAD_HORVU : 32- 34: aaatd Cs--P gvafp IAAE_HORVU : 29- 31: sfgds Ca--P gdalp IAAE_HORVU : 52- 56: vvsqi ChqgP rllts IAAI_HORVU : 37- 39: gpwmw Cd--P emghk IAAI_HORVU : 129- 132: gvpal Cnv-P ipnea IAAT_ELECO : 6- 8: svgts Ci--P gmaip IAAT_ELECO : 29- 33: vakra CgvgP rlatq IAA_HORVU : 56- 60: vikrv CgrgP srpml ITRF_MAIZE : 34- 36: sagts Cv--P gwaip ITRF_MAIZE : 57- 61: vtsrt CgigP rlpwp RA05_ORYSA : 41- 43: ytrar Cq--P gmgyp RA14_ORYSA : 41- 43: slger Cq--P gmgyp RA17_ORYSA : 39- 41: spgeq Cr--P gisyp RAG1_ORYSA : 39- 41: spgeq Cr--P gisyp RAG2_ORYSA : 41- 43: slger Cq--P gmgyp Number of patterns evaluated by Pratt:6 Total running time: 0 seconds