------------------------------------------------------------ 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 14 sequences from file SECE_SEC61G PATTERN CONSERVATION: CM: min Nr of Seqs to Match 14 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 SECE_SEC61G.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: S61G_CANFA 68 S61G_ORYSA 69 S61G_SULSO 65 S61G_YEAST 80 SECE_BACLI 59 SECE_BACSU 59 SECE_ECOLI 127 SECE_HAEIN 106 SECE_STACA 65 SECE_STRGR 86 SECE_STRVG 84 SECE_SYNY3 81 SECE_THEMA 65 SECE_THETH 60 Pratt run started at Thu Feb 6 21:11:46 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 27( 14) V-x(3,4)-I 2: 7.3401 25( 14) V-x(0,2)-F 3: 7.3401 25( 14) V-x(2,4)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.8401 27( 14) V-x(3,4)-I B 2: 7.3401 25( 14) V-x(0,2)-F C 3: 7.3401 25( 14) V-x(2,4)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.8401 27( 14) V-x(3,4)-I Occurences: 27(14) S61G_CANFA : 15- 19: psrqf Vkds-I rlvkr S61G_CANFA : 54- 59: figff VklihI pinni S61G_ORYSA : 54- 59: fvgff VklifI pinni S61G_SULSO : 48- 52: llvma Vvgl-I ayivq S61G_YEAST : 51- 56: eytki VkavgI gliav S61G_YEAST : 54- 59: kivka VgiglI avgii SECE_BACLI : 32- 37: rytit VittvI ffaif SECE_BACLI : 36- 41: tvitt ViffaI ffali SECE_BACSU : 32- 37: rytit VistvI ffvif SECE_BACSU : 36- 41: tvist ViffvI ffall SECE_ECOLI : 48- 52: lrala Vvil-I aaagg SECE_ECOLI : 79- 83: earte Vrkv-I wptrq SECE_ECOLI : 103- 107: aavta Vmsl-I lwgld SECE_HAEIN : 24- 29: slpir VigmaI alvia SECE_HAEIN : 32- 36: maial Viaf-I laait SECE_HAEIN : 90- 94: lffwa Vdsi-I vtvin SECE_STACA : 43- 48: ivivt VvfflI ffyal SECE_STACA : 44- 48: vivtv Vffl-I ffyal SECE_STRGR : 63- 67: vvivf Vvvm-I glvtv SECE_STRVG : 59- 63: ttlvi Vfvv-I mirlv SECE_STRVG : 61- 65: lvivf Vvim-I rlvtv SECE_SYNY3 : 52- 57: sesva VilmvI lvstv SECE_SYNY3 : 59- 63: lmvil Vstv-I yfvdq SECE_THEMA : 32- 36: ltsfg Vvlv-I lavts SECE_THEMA : 46- 50: svyff Vldf-I fsgvv SECE_THEMA : 54- 58: fifsg Vvsa-I fkalg SECE_THETH : 51- 56: glydt VfrflI gllr B 2: 7.3401 25( 14) V-x(0,2)-F Occurences: 25(14) S61G_CANFA : 4- 7: mdq VmqF vepsr S61G_ORYSA : 46- 49: aigfv VmgF vgffv S61G_ORYSA : 50- 52: vvmgf Vg-F fvkli S61G_ORYSA : 50- 53: vvmgf VgfF vklif S61G_SULSO : 3- 4: mk V--F simki S61G_YEAST : 26- 28: lveap Ve-F vregt SECE_BACLI : 36- 38: tvitt Vi-F faiff SECE_BACLI : 36- 39: tvitt VifF aiffa SECE_BACSU : 36- 38: tvist Vi-F fviff SECE_BACSU : 36- 39: tvist VifF viffa SECE_BACSU : 40- 42: tviff Vi-F falld SECE_BACSU : 40- 43: tviff VifF alldt SECE_ECOLI : 69- 71: kgkat Va-F arear SECE_ECOLI : 119- 121: ilvrl Vs-F itglr SECE_HAEIN : 32- 35: maial ViaF ilaai SECE_HAEIN : 97- 100: siivt VinF ltdlr SECE_STACA : 43- 45: ivivt Vv-F fliff SECE_STACA : 43- 46: ivivt VvfF liffy SECE_STACA : 44- 45: vivtv V--F fliff SECE_STACA : 44- 46: vivtv Vf-F liffy SECE_STRGR : 59- 62: tytsv VivF vvvmi SECE_STRGR : 61- 62: tsvvi V--F vvvmi SECE_STRGR : 84- 85: rvvky V--F g SECE_STRVG : 57- 60: tyttl VivF vvimi SECE_STRVG : 59- 60: ttlvi V--F vvimi SECE_STRVG : 70- 73: irlvt VidF gfeka SECE_STRVG : 82- 83: kaikf V--F g SECE_SYNY3 : 62- 65: ilvst ViyF vdqif SECE_THEMA : 42- 44: lavts Vy-F fvldf SECE_THEMA : 42- 45: lavts VyfF vldfi SECE_THEMA : 46- 49: svyff VldF ifsgv SECE_THETH : 51- 52: glydt V--F rflig SECE_THETH : 51- 54: glydt VfrF ligll C 3: 7.3401 25( 14) V-x(2,4)-T Occurences: 25(14) S61G_CANFA : 22- 26: dsirl Vkrc-T kpdrk S61G_ORYSA : 36- 40: keftk Vaar-T aigfv S61G_SULSO : 56- 59: liayi Vql--T tslii S61G_SULSO : 56- 60: liayi Vqlt-T sliir S61G_YEAST : 29- 33: apvef Vreg-T qflak SECE_BACLI : 32- 35: rytit Vit--T viffa SECE_BACSU : 32- 35: rytit Vis--T viffv SECE_ECOLI : 58- 62: aaagg Vall-T tkgka SECE_ECOLI : 58- 63: aaagg ValltT kgkat SECE_ECOLI : 82- 86: tevrk Viwp-T rqetl SECE_ECOLI : 97- 101: httli Vaav-T avmsl SECE_ECOLI : 119- 123: ilvrl Vsfi-T glrf SECE_HAEIN : 61- 65: teark Vvwp-T raear SECE_HAEIN : 62- 65: earkv Vwp--T raear SECE_HAEIN : 76- 80: qttli Vigv-T miasl SECE_HAEIN : 97- 102: siivt VinflT dlrf SECE_STACA : 39- 42: kytti Viv--T vvffl SECE_STRGR : 44- 48: aelrk Vvwp-T rsqlt SECE_STRGR : 45- 48: elrkv Vwp--T rsqlt SECE_STRVG : 42- 46: aelpk Vvwp-T rnqlt SECE_STRVG : 43- 46: elpkv Vwp--T rnqlt SECE_SYNY3 : 7- 12: vkkea VrtdsT ednsv SECE_SYNY3 : 56- 61: avilm VilvsT viyfv SECE_THEMA : 35- 40: fgvvl VilavT svyff SECE_THETH : 19- 23: aelar Vtwp-T reqvv SECE_THETH : 27- 31: ptreq Vveg-T qaill SECE_THETH : 28- 31: treqv Veg--T qaill Number of patterns evaluated by Pratt:5 Total running time: 0 seconds