------------------------------------------------------------ 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 11 sequences from file TRANSALDOLASE_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 11 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 TRANSALDOLASE_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ORFU_BACSU 186 TAL1_HUMAN 336 TAL1_KLULA 333 TAL1_PICJA 9 TAL1_YEAST 334 TAL3_PICJA 9 TALA_CARMA 65 TALA_ECOLI 40 TALB_ECOLI 316 TALB_HAEIN 316 TALC_ECOLI 220 Pratt run started at Thu Feb 6 21:28:45 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.3401 64( 11) L-x(0,2)-L 2: 7.3401 41( 11) T-x(1,3)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.3401 64( 11) L-x(0,2)-L B 2: 7.3401 41( 11) T-x(1,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.3401 64( 11) L-x(0,2)-L Occurences: 64(11) ORFU_BACSU : 19- 22: reane LgiL agvtt ORFU_BACSU : 98- 101: kavra LtgL giktn ORFU_BACSU : 117- 118: nanqa L--L aarag ORFU_BACSU : 131- 134: yvspf LgrL ddigh ORFU_BACSU : 142- 144: ighng Ld-L isevk TAL1_HUMAN : 15- 18: rmesa LdqL kqftt TAL1_HUMAN : 48- 50: ttnps Li-L aaaqm TAL1_HUMAN : 87- 90: naidk LfvL fgaei TAL1_HUMAN : 125- 128: ararr LieL ykeag TAL1_HUMAN : 140- 143: skdri LikL sstwe TAL1_HUMAN : 168- 169: hcnmt L--L fsfaq TAL1_HUMAN : 258- 259: tispk L--L gellq TAL1_HUMAN : 259- 262: ispkl LgeL lqdna TAL1_HUMAN : 262- 263: kllge L--L qdnak TAL1_KLULA : 14- 17: kfans LeaL katgt TAL1_KLULA : 48- 50: ttnps Li-L aaakq TAL1_KLULA : 87- 88: iavdk L--L vefgt TAL1_KLULA : 166- 168: dihvn Lt-L lfsfa TAL1_KLULA : 166- 169: dihvn LtlL fsfaq TAL1_KLULA : 168- 169: hvnlt L--L fsfaq TAL1_KLULA : 258- 259: tispk L--L dells TAL1_KLULA : 259- 262: ispkl LdeL lssde TAL1_KLULA : 262- 263: kllde L--L ssdep TAL1_KLULA : 323- 326: adivt LfdL ikaki TAL1_PICJA : 8- 9: ihcbt L--L TAL1_YEAST : 15- 18: vanns LeqL kasgt TAL1_YEAST : 49- 51: ttnps Li-L aaakq TAL1_YEAST : 88- 89: navdr L--L vefgk TAL1_YEAST : 167- 169: gihcn Lt-L lfsfv TAL1_YEAST : 167- 170: gihcn LtlL fsfvq TAL1_YEAST : 169- 170: hcnlt L--L fsfvq TAL1_YEAST : 259- 260: tispa L--L dklmn TAL1_YEAST : 260- 263: ispal LdkL mnste TAL1_YEAST : 324- 327: adivt LfdL iekkv TAL3_PICJA : 8- 9: ihcnt L--L TALA_CARMA : 13- 15: ttnps Li-L qakiy TALA_ECOLI : 4- 7: tgk LqqL rqytt TALB_ECOLI : 4- 7: tdk LtsL rqytt TALB_ECOLI : 37- 39: ttnps Li-L naaqi TALB_ECOLI : 82- 85: avnig LeiL klvpg TALB_ECOLI : 85- 87: iglei Lk-L vpgri TALB_ECOLI : 114- 117: akakr LikL yndag TALB_ECOLI : 129- 132: sndri LikL astwq TALB_ECOLI : 154- 156: gincn Lt-L lfsfa TALB_ECOLI : 154- 157: gincn LtlL fsfaq TALB_ECOLI : 156- 157: ncnlt L--L fsfaq TALB_ECOLI : 233- 235: nigei Le-L agcdr TALB_ECOLI : 247- 248: tiapa L--L kelae TALB_ECOLI : 248- 251: iapal LkeL aeseg TALB_ECOLI : 315- 316: kmigd L--L TALB_HAEIN : 4- 7: ttq LdsL rnmtv TALB_HAEIN : 37- 39: ttnps Li-L sasal TALB_HAEIN : 82- 85: avnig LeiL kivpg TALB_HAEIN : 114- 117: ekark LiaL ynaag TALB_HAEIN : 154- 156: gincn Lt-L lfsea TALB_HAEIN : 154- 157: gincn LtlL fseaq TALB_HAEIN : 156- 157: ncnlt L--L fseaq TALB_HAEIN : 247- 248: tiapa L--L kelqe TALB_HAEIN : 248- 251: iapal LkeL qenst TALC_ECOLI : 3- 5: me Ly-L dtanv TALC_ECOLI : 43- 46: siwev LprL qkaig TALC_ECOLI : 118- 119: saaqg L--L aalag TALC_ECOLI : 119- 122: aaqgl LaaL agaky TALC_ECOLI : 149- 152: rtvqe LqtL lemha TALC_ECOLI : 152- 153: qelqt L--L emhap TALC_ECOLI : 174- 177: tprqa LdcL lagce TALC_ECOLI : 177- 178: qaldc L--L agces TALC_ECOLI : 186- 188: cesit Lp-L dvaqq B 2: 7.3401 41( 11) T-x(1,3)-L Occurences: 41(11) ORFU_BACSU : 27- 31: lagvt TnpsL vakea ORFU_BACSU : 88- 92: vkipm TsdgL kavra ORFU_BACSU : 99- 101: avral Tg--L giktn ORFU_BACSU : 105- 109: glgik TnvtL ifnan ORFU_BACSU : 173- 177: hpqhv TeaaL rgaht TAL1_HUMAN : 44- 48: pqdat TnpsL ilaaa TAL1_HUMAN : 167- 169: ihcnm Tl--L fsfaq TAL1_KLULA : 44- 48: pqdat TnpsL ilaaa TAL1_KLULA : 93- 96: lvefg Tai-L kvvpg TAL1_KLULA : 167- 169: ihvnl Tl--L fsfaq TAL1_KLULA : 306- 309: edama Tek-L segir TAL1_KLULA : 322- 326: sadiv TlfdL ikaki TAL1_PICJA : 7- 9: gihcb Tl--L TAL1_YEAST : 45- 49: pqdst TnpsL ilaaa TAL1_YEAST : 58- 62: aakqp TyakL idvav TAL1_YEAST : 168- 170: ihcnl Tl--L fsfvq TAL1_YEAST : 307- 310: edama Tek-L segir TAL1_YEAST : 323- 327: sadiv TlfdL iekkv TAL3_PICJA : 7- 9: gihcn Tl--L TALA_CARMA : 9- 13: ptdat TnpsL ilqak TALA_ECOLI : 1- 4: Tgk-L qqlrq TALA_ECOLI : 33- 37: pxdat TdpxL ixd TALB_ECOLI : 1- 4: Tdk-L tslrq TALB_ECOLI : 5- 7: tdkl Ts--L rqytt TALB_ECOLI : 33- 37: pqdat TnpsL ilnaa TALB_ECOLI : 73- 76: qivda Tdk-L avnig TALB_ECOLI : 155- 157: incnl Tl--L fsfaq TALB_HAEIN : 1- 4: Ttq-L dslrn TALB_HAEIN : 2- 4: t Tq--L dslrn TALB_HAEIN : 33- 37: pqdat TnpsL ilsas TALB_HAEIN : 155- 157: incnl Tl--L fseaq TALB_HAEIN : 233- 235: nvgei Te--L agcdr TALB_HAEIN : 256- 258: lqens Ta--L vrkle TALB_HAEIN : 310- 312: qekle Tm--L sakl TALC_ECOLI : 89- 93: vkipv TsegL aaiki TALC_ECOLI : 105- 107: kkegi Tt--L gtavy TALC_ECOLI : 145- 149: gdgir TvqeL qtlle TALC_ECOLI : 151- 153: vqelq Tl--L emhap TALC_ECOLI : 185- 188: gcesi Tlp-L dvaqq TALC_ECOLI : 217- 220: naafg Tth-L TALC_ECOLI : 218- 220: aafgt Th--L Number of patterns evaluated by Pratt:2 Total running time: 0 seconds