------------------------------------------------------------ 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 19 sequences from file GAMMA_THIONIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 19 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 GAMMA_THIONIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: 10KD_VIGUN 75 AFP1_ARATH 27 AFP1_BRANA 44 AFP1_BRARA 27 AFP1_SINAL 25 AFP2_BRANA 23 AFP2_BRARA 27 AFP2_RAPSA 36 AFP2_SINAL 26 ASF1_HELAN 161 P322_SOLTU 74 SIA1_SORBI 47 SIA2_SORBI 48 SIA3_SORBI 47 SRP_SOYBN 74 THG1_WHEAT 47 THG2_WHEAT 47 THGF_TOBAC 105 THG_HORVU 47 Pratt run started at Thu Feb 6 19:31:21 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 32( 19) C-x(5)-C 2: 8.3401 33( 19) G-x-C 3: 7.8401 20( 19) C-x(3,4)-S 4: 7.8401 35( 19) K-x(1,2)-C 5: 7.3401 23( 19) A-x(0,2)-C 6: 7.3401 33( 19) C-x(0,2)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 11.5166 19( 19) C-x-[CN]-x(3)-C B 2: 10.0224 23( 19) C-x(0,2)-R-x-[ACS] C 3: 8.3401 33( 19) G-x-C D 4: 7.8401 20( 19) C-x(3,4)-S E 5: 7.8401 35( 19) K-x(1,2)-C F 6: 7.3401 23( 19) A-x(0,2)-C Best patterns with alignements: fitness hits(seqs) Pattern A 1: 11.5166 19( 19) C-x-[CN]-x(3)-C Occurences: 19(19) 10KD_VIGUN : 69- 75: rddvr CwCtrnC AFP1_ARATH : 15- 21: twsgv CgNsnaC knqci AFP1_BRANA : 15- 21: twsgv CgNnnaC knqci AFP1_BRARA : 15- 21: twsgv CgNnnaC knqci AFP1_SINAL : 15- 21: twsgv CgNnnaC knqc AFP2_BRANA : 15- 21: twsgv CgNnnaC kn AFP2_BRARA : 15- 21: txsgv CgNnnaC knqci AFP2_RAPSA : 15- 21: twsgv CgNnnaC knqci AFP2_SINAL : 15- 21: twsgv CgNnnaC rnqci ASF1_HELAN : 59- 65: eakhm CfCyfdC dpqkn P322_SOLTU : 68- 74: gfrrr CfCtkpC SIA1_SORBI : 41- 47: chlry CrCqkaC SIA2_SORBI : 41- 47: gvmrq CkCirqC w SIA3_SORBI : 41- 47: gvirq CkCirqC SRP_SOYBN : 68- 74: krsrr CfCtriC THG1_WHEAT : 41- 47: gpfrr CkCirqC THG2_WHEAT : 41- 47: gpfrr CkCirqC THGF_TOBAC : 66- 72: kllrr ClCtkpC vfdek THG_HORVU : 41- 47: gplrr CkCmrrC B 2: 10.0224 23( 19) C-x(0,2)-R-x-[ACS] Occurences: 23(19) 10KD_VIGUN : 71- 75: dvrcw Ct-RnC AFP1_ARATH : 4- 8: qkl Ce-RpS gtwsg AFP1_BRANA : 4- 8: qkl Ce-RpS gtwsg AFP1_BRARA : 4- 8: qkl Ce-RpS gtwsg AFP1_SINAL : 4- 8: qkl Ce-RpS gtwsg AFP2_BRANA : 4- 8: qkl Ce-RpS gtwsg AFP2_BRARA : 4- 8: qkl Ce-RpS gtxsg AFP2_RAPSA : 4- 8: qkl Cq-RpS gtwsg AFP2_SINAL : 4- 8: qkl Cq-RpS gtwsg ASF1_HELAN : 50- 55: akhga ChqReA khmcf P322_SOLTU : 41- 45: rfkgp Ct-RdS ncasv SIA1_SORBI : 36- 41: wtagy ChlRyC rcqka SIA2_SORBI : 43- 47: mrqck Ci-RqC w SIA3_SORBI : 3- 7: rv Cr-RrS agfkg SIA3_SORBI : 3- 8: rv CrrRsA gfkgl SIA3_SORBI : 43- 47: irqck Ci-RqC SRP_SOYBN : 70- 74: srrcf Ct-RiC THG1_WHEAT : 3- 7: ki Cr-RrS agfkg THG1_WHEAT : 3- 8: ki CrrRsA gfkgp THG1_WHEAT : 43- 47: frrck Ci-RqC THG2_WHEAT : 3- 8: kv CrqRsA gfkgp THG2_WHEAT : 43- 47: frrck Ci-RqC THGF_TOBAC : 45- 48: itkpp C--RkA cisek THG_HORVU : 3- 7: ri Cr-RrS agfkg THG_HORVU : 3- 8: ri CrrRsA gfkgp THG_HORVU : 43- 47: lrrck Cm-RrC C 3: 8.3401 33( 19) G-x-C Occurences: 33(19) 10KD_VIGUN : 8- 10: kksia GlC flflv 10KD_VIGUN : 40- 42: vdtyr GpC fttgs 10KD_VIGUN : 46- 48: pcftt GsC ddhck 10KD_VIGUN : 61- 63: ehlls GrC rddvr AFP1_ARATH : 13- 15: sgtws GvC gnsna AFP1_BRANA : 13- 15: sgtws GvC gnnna AFP1_BRANA : 34- 36: ekarh GsC nyvfp AFP1_BRARA : 13- 15: sgtws GvC gnnna AFP1_SINAL : 13- 15: sgtws GvC gnnna AFP2_BRANA : 13- 15: sgtws GvC gnnna AFP2_BRARA : 13- 15: sgtxs GvC gnnna AFP2_RAPSA : 13- 15: sgtws GvC gnnna AFP2_RAPSA : 34- 36: ekarh GsC AFP2_SINAL : 13- 15: sgtws GvC gnnna ASF1_HELAN : 27- 29: sktwf GnC kdtdk ASF1_HELAN : 48- 50: egakh GaC hqrea P322_SOLTU : 39- 41: shrfk GpC trdsn P322_SOLTU : 59- 61: erfsg GnC hgfrr SIA1_SORBI : 34- 36: ggwta GyC hlryc SIA2_SORBI : 12- 14: sagfk GlC mrdqn SIA2_SORBI : 32- 34: egwgg GnC dgvmr SIA3_SORBI : 12- 14: sagfk GlC msdhn SIA3_SORBI : 32- 34: egwgg GnC dgvir SRP_SOYBN : 40- 42: shgfh GlC nrdhn SRP_SOYBN : 60- 62: egfsg GrC krsrr THG1_WHEAT : 12- 14: sagfk GpC msnkn THG1_WHEAT : 32- 34: egwgg GnC dgpfr THG2_WHEAT : 12- 14: sagfk GpC vsdkn THG2_WHEAT : 32- 34: egwgg GnC dgpfr THGF_TOBAC : 37- 39: sntfp GiC itkpp THGF_TOBAC : 57- 59: ekftd GhC skllr THG_HORVU : 12- 14: sagfk GpC vsnkn THG_HORVU : 32- 34: egwgg GnC dgplr D 4: 7.8401 20( 19) C-x(3,4)-S Occurences: 20(19) 10KD_VIGUN : 42- 47: tyrgp CfttgS cddhc AFP1_ARATH : 4- 8: qkl Cerp-S gtwsg AFP1_BRANA : 4- 8: qkl Cerp-S gtwsg AFP1_BRARA : 4- 8: qkl Cerp-S gtwsg AFP1_SINAL : 4- 8: qkl Cerp-S gtwsg AFP2_BRANA : 4- 8: qkl Cerp-S gtwsg AFP2_BRARA : 4- 8: qkl Cerp-S gtxsg AFP2_RAPSA : 4- 8: qkl Cqrp-S gtwsg AFP2_SINAL : 4- 8: qkl Cqrp-S gtwsg ASF1_HELAN : 18- 22: vngki Cekp-S ktwfg P322_SOLTU : 30- 34: aearh Cesl-S hrfkg P322_SOLTU : 41- 45: rfkgp Ctrd-S ncasv SIA1_SORBI : 3- 7: rv Cmgk-S qhhsf SIA2_SORBI : 3- 7: rv Cmgk-S agfkg SIA3_SORBI : 3- 7: rv Crrr-S agfkg SRP_SOYBN : 31- 35: tegrv Cesq-S hgfhg THG1_WHEAT : 3- 7: ki Crrr-S agfkg THG2_WHEAT : 3- 7: kv Crqr-S agfkg THGF_TOBAC : 28- 32: vqare Ckte-S ntfpg THG_HORVU : 3- 7: ri Crrr-S agfkg E 5: 7.8401 35( 19) K-x(1,2)-C Occurences: 35(19) 10KD_VIGUN : 29- 31: vqsea Kt-C enlvd AFP1_ARATH : 2- 4: q Kl-C erpsg AFP1_ARATH : 22- 25: nsnac KnqC in AFP1_BRANA : 2- 4: q Kl-C erpsg AFP1_BRANA : 22- 25: nnnac KnqC inlek AFP1_BRARA : 2- 4: q Kl-C erpsg AFP1_BRARA : 22- 25: nnnac KnqC in AFP1_SINAL : 2- 4: q Kl-C erpsg AFP1_SINAL : 22- 25: nnnac KnqC AFP2_BRANA : 2- 4: q Kl-C erpsg AFP2_BRARA : 2- 4: q Kl-C erpsg AFP2_BRARA : 22- 25: nnnac KnqC ir AFP2_RAPSA : 2- 4: q Kl-C qrpsg AFP2_RAPSA : 22- 25: nnnac KnqC irlek AFP2_SINAL : 2- 4: q Kl-C qrpsg ASF1_HELAN : 16- 18: atvng Ki-C ekpsk ASF1_HELAN : 37- 39: tdkcd Kr-C idweg ASF1_HELAN : 56- 59: hqrea KhmC fcyfd P322_SOLTU : 38- 41: lshrf KgpC trdsn P322_SOLTU : 72- 74: rcfct Kp-C SIA1_SORBI : 45- 47: ycrcq Ka-C SIA2_SORBI : 11- 14: ksagf KglC mrdqn SIA3_SORBI : 11- 14: rsagf KglC msdhn SRP_SOYBN : 5- 7: memr Ks-C gfffl THG1_WHEAT : 1- 3: Ki-C rrrsa THG1_WHEAT : 11- 14: rsagf KgpC msnkn THG1_WHEAT : 18- 20: pcmsn Kn-C aqvcq THG2_WHEAT : 1- 3: Kv-C rqrsa THG2_WHEAT : 11- 14: rsagf KgpC vsdkn THG2_WHEAT : 18- 20: pcvsd Kn-C aqvcl THGF_TOBAC : 42- 45: gicit KppC rkaci THGF_TOBAC : 47- 49: kppcr Ka-C isekf THGF_TOBAC : 70- 72: rclct Kp-C vfdek THG_HORVU : 11- 14: rsagf KgpC vsnkn THG_HORVU : 18- 20: pcvsn Kn-C aqvcm F 6: 7.3401 23( 19) A-x(0,2)-C Occurences: 23(19) 10KD_VIGUN : 7- 10: ekksi AglC flflv 10KD_VIGUN : 28- 31: vvqse AktC enlvd AFP1_ARATH : 20- 21: cgnsn A--C knqci AFP1_BRANA : 20- 21: cgnnn A--C knqci AFP1_BRARA : 20- 21: cgnnn A--C knqci AFP1_SINAL : 20- 21: cgnnn A--C knqc AFP2_BRANA : 20- 21: cgnnn A--C kn AFP2_BRARA : 20- 21: cgnnn A--C knqci AFP2_RAPSA : 20- 21: cgnnn A--C knqci AFP2_SINAL : 20- 21: cgnnn A--C rnqci ASF1_HELAN : 49- 50: gakhg A--C hqrea P322_SOLTU : 27- 30: mriae ArhC eslsh P322_SOLTU : 48- 51: rdsnc AsvC eterf SIA1_SORBI : 33- 36: eggwt AgyC hlryc SIA1_SORBI : 46- 47: crcqk A--C SIA2_SORBI : 21- 24: rdqnc AqvC lqegw SIA3_SORBI : 21- 24: sdhnc AqvC lqegw SRP_SOYBN : 49- 52: rdhnc AlvC rnegf THG1_WHEAT : 21- 24: snknc AqvC qqegw THG2_WHEAT : 21- 24: sdknc AqvC lqegw THGF_TOBAC : 25- 28: ayevq AreC ktesn THGF_TOBAC : 48- 49: ppcrk A--C isekf THG_HORVU : 21- 24: snknc AqvC mqegw Number of patterns evaluated by Pratt:7 Total running time: 0 seconds