------------------------------------------------------------ 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 16 sequences from file COMPLEX1_30K PATTERN CONSERVATION: CM: min Nr of Seqs to Match 16 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 COMPLEX1_30K.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: NQO5_PARDE 206 NUGC_MAIZE 159 NUGC_MARPO 169 NUGC_ORYSA 159 NUGC_SOYBN 97 NUGC_SYNY3 157 NUGC_TOBAC 158 NUGM_BOVIN 266 NUGM_CANMA 276 NUGM_DICDI 209 NUGM_MARPO 212 NUGM_NEUCR 283 NUGM_PARPR 209 NUGM_PARTE 209 NUGM_SOLTU 17 NUOC_ECOLI 183 Pratt run started at Thu Feb 6 19:08:45 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 41( 16) L-x-K 2: 7.8401 24( 16) E-x(0,1)-T 3: 7.8401 31( 16) E-x(1,2)-L 4: 7.8401 38( 16) S-x(3,4)-L 5: 7.3401 28( 16) T-x(0,2)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 8.3401 41( 16) L-x-K B 2: 7.8401 24( 16) E-x(0,1)-T C 3: 7.8401 31( 16) E-x(1,2)-L D 4: 7.8401 38( 16) S-x(3,4)-L E 5: 7.3401 28( 16) T-x(0,2)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 8.3401 41( 16) L-x-K Occurences: 41(16) NQO5_PARDE : 147- 149: frghp LrK dfptt NUGC_MAIZE : 10- 12: wlsnw LvK hdvvh NUGC_MAIZE : 143- 145: wigwp LrK dyitp NUGC_MARPO : 20- 22: rlsiw LiK hnlkh NUGC_MARPO : 102- 104: ikifi LrK npkip NUGC_MARPO : 153- 155: wlgwp LrK dyivp NUGC_ORYSA : 10- 12: wlsnw LvK hevvh NUGC_ORYSA : 143- 145: wigwp LrK dyitp NUGC_SOYBN : 9- 11: rlssw LvK hglsh NUGC_SYNY3 : 70- 72: vsfyh LvK ltedt NUGC_SYNY3 : 141- 143: wvgwp LrK dyisp NUGC_TOBAC : 9- 11: rlsaw LvK hglih NUGC_TOBAC : 142- 144: wigwp LrK dyiap NUGM_BOVIN : 71- 73: yvaei LpK yvqqv NUGM_CANMA : 6- 8: misrt LlK rtvpa NUGM_CANMA : 66- 68: vqiee LhK fgtyi NUGM_CANMA : 77- 79: yimsc LpK yiqqf NUGM_CANMA : 205- 207: feghp LrK dfptt NUGM_DICDI : 25- 27: lsipg LvK kimyk NUGM_DICDI : 154- 156: fvgyp LkK dfpit NUGM_MARPO : 31- 33: sliat LpK wihkc NUGM_MARPO : 159- 161: feghp LrK dfpls NUGM_NEUCR : 73- 75: skadn LhK ygswl NUGM_NEUCR : 84- 86: wlmgc LpK yiqqf NUGM_NEUCR : 212- 214: fdghp LrK dfpmt NUGM_PARPR : 76- 78: ggelf LgK sqlve NUGM_PARPR : 118- 120: sfyff LlK kritf NUGM_PARPR : 119- 121: fyffl LkK ritff NUGM_PARPR : 159- 161: fgvsy LlK kdsrn NUGM_PARPR : 160- 162: gvsyl LkK dsrnl NUGM_PARPR : 179- 181: sfnpf LkK fpstg NUGM_PARTE : 76- 78: ggelf LaK sqlve NUGM_PARTE : 118- 120: sfyff LlK kritf NUGM_PARTE : 119- 121: fyffl LkK ritff NUGM_PARTE : 159- 161: frgsn LlK kesrn NUGM_PARTE : 160- 162: rgsnl LkK esrnl NUGM_PARTE : 179- 181: sfnpf LkK fpstg NUGM_SOLTU : 14- 16: yswet LpK k NUOC_ECOLI : 64- 66: evgdf LkK lpkpy NUOC_ECOLI : 67- 69: dflkk LpK pyvml NUOC_ECOLI : 169- 171: wkghp LrK dypra B 2: 7.8401 24( 16) E-x(0,1)-T Occurences: 24(16) NQO5_PARDE : 32- 34: tqavg ElT vnatl NUGC_MAIZE : 28- 29: dhrgv E-T lqika NUGC_MARPO : 38- 39: dyqgi E-T lqirs NUGC_ORYSA : 28- 29: dhrgi E-T lqika NUGC_SOYBN : 27- 28: dyqgi E-T lqikp NUGC_SYNY3 : 75- 77: lvklt EdT rnpee NUGC_TOBAC : 27- 28: dyqgi E-T lqikp NUGM_BOVIN : 151- 153: ktytd ElT piess NUGM_CANMA : 90- 92: svwkd ElT iyvap NUGM_CANMA : 156- 157: ktyan E-T spvps NUGM_CANMA : 176- 177: nwyer E-T ydlfg NUGM_CANMA : 232- 234: iyepl ElT qawrn NUGM_DICDI : 110- 111: nngii E-T tsglf NUGM_DICDI : 110- 112: nngii EtT sglfe NUGM_MARPO : 110- 112: ltsvd EiT picsv NUGM_MARPO : 130- 131: gwwer E-T wdmfg NUGM_MARPO : 186- 188: vsepi EmT qefry NUGM_NEUCR : 97- 99: svwkd ElT iyisp NUGM_NEUCR : 121- 123: yntaa EyT qvsdi NUGM_NEUCR : 239- 241: vtepl EmT qafrn NUGM_NEUCR : 276- 277: ptpkp E-T kpeek NUGM_PARPR : 83- 85: ksqlv EaT afdlt NUGM_PARTE : 83- 85: ksqlv EaT afdlt NUGM_SOLTU : 12- 13: fkysw E-T lpkk NUOC_ECOLI : 140- 141: nwyer E-T wdlfg C 3: 7.8401 31( 16) E-x(1,2)-L Occurences: 31(16) NQO5_PARDE : 2- 4: s Ea-L sdeal NQO5_PARDE : 7- 9: ealsd Ea-L lelae NQO5_PARDE : 7- 10: ealsd EalL elaeh NQO5_PARDE : 47- 49: vigli Ef-L rndpn NQO5_PARDE : 98- 101: kvqvr EdeL vpsli NUGC_MAIZE : 28- 30: dhrgv Et-L qikag NUGC_MARPO : 38- 40: dyqgi Et-L qirse NUGC_ORYSA : 28- 30: dhrgi Et-L qikae NUGC_SOYBN : 27- 29: dyqgi Et-L qikpe NUGC_SYNY3 : 31- 34: emvqv EadL llplc NUGC_SYNY3 : 82- 85: trnpe EvrL kvflp NUGC_TOBAC : 27- 29: dyqgi Et-L qikpe NUGM_BOVIN : 69- 71: geyva Ei-L pkyvq NUGM_BOVIN : 252- 254: yrqpp Es-L kleag NUGM_CANMA : 31- 34: rlsah EedL vnvnn NUGM_CANMA : 32- 34: lsahe Ed-L vnvnn NUGM_CANMA : 64- 66: ykvqi Ee-L hkfgt NUGM_CANMA : 229- 231: krviy Ep-L eltqa NUGM_DICDI : 16- 18: kinlg Eh-L rlsip NUGM_DICDI : 43- 46: iqvek EkmL tvlky NUGM_MARPO : 44- 47: qtskh EniL ytnpn NUGM_NEUCR : 49- 51: rqfpr Ep-L pgaln NUGM_NEUCR : 236- 238: krivt Ep-L emtqa NUGM_PARPR : 37- 39: lyfff Ek-L nfsyw NUGM_PARPR : 73- 76: svlgg ElfL gksql NUGM_PARTE : 37- 39: lyfff Ek-L nfsyw NUGM_PARTE : 73- 76: svlgg ElfL aksql NUGM_SOLTU : 12- 14: fkysw Et-L pkk NUOC_ECOLI : 55- 57: vwikr Eq-L levgd NUOC_ECOLI : 55- 58: vwikr EqlL evgdf NUOC_ECOLI : 82- 84: lhgmd Er-L rthre NUOC_ECOLI : 89- 91: lrthr Eg-L paadf NUOC_ECOLI : 119- 122: kvala EndL hvptf D 4: 7.8401 38( 16) S-x(3,4)-L Occurences: 38(16) NQO5_PARDE : 5- 9: seal Sdea-L lelae NQO5_PARDE : 5- 10: seal SdealL elaeh NQO5_PARDE : 40- 45: vnatl SgvigL ieflr NQO5_PARDE : 128- 133: fgilf SghsdL rrilt NUGC_MAIZE : 39- 44: agdwd SiaviL yvygy NUGC_MAIZE : 68- 72: ggsla Svyh-L triqy NUGC_MARPO : 49- 54: sedwp SlavaL yvygf NUGC_ORYSA : 39- 44: aedwd SiaviL yvygy NUGC_ORYSA : 68- 72: ggsla Svyh-L triqy NUGC_SOYBN : 15- 19: vkhgl Shrs-L gfdyq NUGC_SOYBN : 38- 43: pedwh SiaviL yvygy NUGC_SOYBN : 67- 71: gglla Svyh-L trley NUGC_SYNY3 : 66- 70: gkslv Sfyh-L vklte NUGC_TOBAC : 67- 71: gglla Svyh-L tried NUGC_TOBAC : 114- 118: fqere Sydm-L gisyd NUGM_BOVIN : 30- 34: vagrp Svll-L pvrre NUGM_BOVIN : 81- 86: qqvqv ScfneL eicih NUGM_BOVIN : 112- 116: naqfk Slad-L tavdi NUGM_BOVIN : 207- 212: kdfpl SgyveL rydde NUGM_CANMA : 3- 7: mi Srtl-L krtvp NUGM_CANMA : 23- 27: rsftt Snvr-L sahee NUGM_CANMA : 162- 166: tspvp Svtp-L fngan NUGM_DICDI : 21- 25: ehlrl Sipg-L vkkim NUGM_DICDI : 118- 122: sglfe Ssvw-L ereiw NUGM_MARPO : 26- 31: qlffk SliatL pkwih NUGM_MARPO : 53- 57: ytnpn Slfq-L lyflk NUGM_MARPO : 53- 58: ytnpn SlfqlL yflky NUGM_MARPO : 140- 145: fgvyf SnhpdL rrilt NUGM_NEUCR : 68- 73: adkyq SkadnL hkygs NUGM_NEUCR : 169- 173: vspvp Sitp-L ydgan NUGM_PARPR : 113- 118: ivlsy SfyffL lkkri NUGM_PARPR : 141- 146: veafy SnanwL ereis NUGM_PARPR : 164- 168: llkkd Srnl-L ldygs NUGM_PARPR : 164- 169: llkkd SrnllL dygss NUGM_PARPR : 174- 179: ldygs SfnpfL kkfps NUGM_PARTE : 113- 118: vvlsy SfyffL lkkri NUGM_PARTE : 141- 146: lesfy SnanwL ereis NUGM_PARTE : 164- 168: llkke Srnl-L ldygs NUGM_PARTE : 164- 169: llkke SrnllL dygss NUGM_PARTE : 174- 179: ldygs SfnpfL kkfps NUGM_SOLTU : 10- 14: fifky Swet-L pkk NUOC_ECOLI : 97- 102: paadf SvfyhL isidr E 5: 7.3401 28( 16) T-x(0,2)-L Occurences: 28(16) NQO5_PARDE : 38- 39: ltvna T--L sgvig NQO5_PARDE : 59- 60: ncrfs T--L idita NUGC_MAIZE : 29- 30: hrgve T--L qikag NUGC_MARPO : 39- 40: yqgie T--L qirse NUGC_ORYSA : 29- 30: hrgie T--L qikae NUGC_SOYBN : 28- 29: yqgie T--L qikpe NUGC_SOYBN : 72- 74: svyhl Tr-L eydig NUGC_SYNY3 : 6- 8: mgpvs Tw-L ttngf NUGC_SYNY3 : 40- 42: llplc Ta-L yaygf NUGC_TOBAC : 28- 29: yqgie T--L qikpe NUGM_BOVIN : 100- 102: vipvl Tf-L rdhsn NUGM_BOVIN : 149- 152: rvkty TdeL tpies NUGM_CANMA : 5- 6: misr T--L lkrtv NUGM_CANMA : 5- 7: misr Tl-L krtvp NUGM_CANMA : 164- 166: pvpsv Tp-L fngan NUGM_CANMA : 177- 180: wyere TydL fgvff NUGM_DICDI : 33- 36: kimyk ThyL eiqve NUGM_DICDI : 47- 49: kekml Tv-L kylke NUGM_DICDI : 112- 115: giiet TsgL fessv NUGM_DICDI : 161- 164: kdfpi TgyL evyyd NUGM_MARPO : 30- 31: kslia T--L pkwih NUGM_NEUCR : 171- 173: pvpsi Tp-L ydgan NUGM_NEUCR : 235- 238: kkriv TepL emtqa NUGM_PARPR : 124- 127: lkkri TffL hggek NUGM_PARTE : 124- 127: lkkri TffL hggdk NUGM_SOLTU : 13- 14: kyswe T--L pkk NUOC_ECOLI : 6- 8: mvnnm Td-L taqep NUOC_ECOLI : 128- 130: hvptf Tk-L fpnan NUOC_ECOLI : 141- 144: wyere TwdL fgitf Number of patterns evaluated by Pratt:10 Total running time: 0 seconds