------------------------------------------------------------ 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 17 sequences from file GLUTAREDOXIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 17 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 GLUTAREDOXIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: GLR1_ECOLI 85 GLR2_ECOLI 18 GLR3_ECOLI 82 GLRX_BOVIN 105 GLRX_HAEIN 87 GLRX_HUMAN 105 GLRX_METTH 83 GLRX_PIG 105 GLRX_RABIT 106 GLRX_VACCC 108 GLRX_VARV 108 GLRX_YEAST 108 THIO_BPT4 87 YBM4_YEAST 203 YCD5_YEAST 110 YMA9_YEAST 489 YRUB_CLOPA 75 Pratt run started at Thu Feb 6 19:35:40 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.3401 32( 17) L-x(3,5)-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.3401 32( 17) L-x(3,5)-D Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.3401 32( 17) L-x(3,5)-D Occurences: 32(17) GLR1_ECOLI : 24- 29: dlaek Lsner-D dfqyq GLR1_ECOLI : 24- 30: dlaek LsnerdD fqyqy GLR2_ECOLI : 3- 7: mk Lyiy--D hcpyc GLR3_ECOLI : 68- 72: ggcdd Lyal--D arggl GLRX_BOVIN : 41- 46: pfkqg Llefv-D itaag GLRX_BOVIN : 42- 46: fkqgl Lefv--D itaag GLRX_HAEIN : 24- 30: nlaek LkgevaD fdyry GLRX_HUMAN : 41- 46: pikqg Llefv-D itatn GLRX_HUMAN : 42- 46: ikqgl Lefv--D itatn GLRX_METTH : 75- 81: pgree LfeaisD ei GLRX_PIG : 41- 46: pfkeg Llefv-D itats GLRX_PIG : 42- 46: fkegl Lefv--D itats GLRX_RABIT : 41- 46: pfkqg Llefv-D itats GLRX_RABIT : 42- 46: fkqgl Lefv--D itats GLRX_VACCC : 86- 90: ggysd Llei--D nmdal GLRX_VACCC : 87- 93: gysdl LeidnmD algdi GLRX_VARV : 86- 90: ggysd Llei--D nmdal GLRX_VARV : 87- 93: gysdl LeidnmD algdi GLRX_YEAST : 48- 53: pkska Lvlel-D emsng THIO_BPT4 : 52- 58: kiael LtklgrD tqigl YBM4_YEAST : 46- 50: hhpds Lvtf--D nsgna YBM4_YEAST : 174- 178: teiae Lhkn--D ellds YCD5_YEAST : 49- 55: prskv LvlqlnD mkega YCD5_YEAST : 51- 55: skvlv Lqln--D mkega YMA9_YEAST : 139- 143: pfytp Lqdf--D eswtr YMA9_YEAST : 151- 156: wtrde Likiv-D glplh YMA9_YEAST : 158- 162: kivdg Lplh--D tfden YMA9_YEAST : 160- 165: vdglp Lhdtf-D enlee YMA9_YEAST : 168- 173: tfden Leefe-D vpign YMA9_YEAST : 255- 259: rknyh Lpsd--D lkytl YMA9_YEAST : 469- 473: reair Lsle--D qdnrk YMA9_YEAST : 469- 475: reair LsledqD nrkks YMA9_YEAST : 471- 475: airls Ledq--D nrkks YRUB_CLOPA : 20- 26: ktkey LkskniD fvdvn Number of patterns evaluated by Pratt:1 Total running time: 0 seconds