------------------------------------------------------------ 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 CRF 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 CRF.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CRF1_CATCO 162 CRF2_CATCO 162 CRF_HUMAN 196 CRF_PIG 41 CRF_RAT 187 CRF_SHEEP 190 DIU1_MANSE 138 DIU2_MANSE 30 DIUH_ACHDO 46 DIUH_LOCMI 46 DIUH_MUSDO 44 DIUH_PERAM 46 SAUV_PHYSA 40 UR1_CATCO 41 UR1_CYPCA 145 UR1_PLAFE 60 Pratt run started at Thu Feb 6 19:11:56 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 11.0102 17( 16) P-x(1,3)-D-x(0,1)-L 2: 10.5102 38( 16) L-x(0,2)-R-x(1,3)-E 3: 8.3401 38( 16) R-x(2)-L 4: 7.8401 53( 16) L-x(0,1)-R 5: 7.8401 20( 16) N-x(2,3)-L 6: 7.8401 23( 16) D-x(0,1)-L 7: 7.3401 34( 16) N-x(1,3)-L 8: 7.3401 58( 16) R-x(2,4)-E Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 12.6224 17( 16) R-x(2)-L-[DENQST]-x-[AIV] B 2: 11.0102 17( 16) P-x(1,3)-D-x(0,1)-L C 3: 10.5102 38( 16) L-x(0,2)-R-x(1,3)-E D 4: 7.8401 53( 16) L-x(0,1)-R E 5: 7.8401 20( 16) N-x(2,3)-L F 6: 7.8401 23( 16) D-x(0,1)-L G 7: 7.3401 34( 16) N-x(1,3)-L H 8: 7.3401 58( 16) R-x(2,4)-E Best patterns with alignements: fitness hits(seqs) Pattern A 1: 12.6224 17( 16) R-x(2)-L-[DENQST]-x-[AIV] Occurences: 17(16) CRF1_CATCO : 135- 141: tfhll RevLEmA raeql CRF2_CATCO : 135- 141: tfhll RevLEmA raeql CRF_HUMAN : 169- 175: tfhll RevLEmA raeql CRF_PIG : 16- 22: tfhll RevLEmA raeql CRF_RAT : 160- 166: tfhll RevLEmA raeql CRF_SHEEP : 182- 188: qahsn RklLDiA gk DIU1_MANSE : 115- 121: raaan RnfLNdI gkrgl DIU2_MANSE : 24- 30: vaqnn RnfLNrV DIUH_ACHDO : 40- 46: riqqn RqlLTsI DIUH_LOCMI : 19- 25: dvlrq RllLEiA rrrlr DIUH_MUSDO : 17- 23: dvlrq RllLEiA rrqmk DIUH_PERAM : 19- 25: dvlrq RllLEiA rrrmr DIUH_PERAM : 40- 46: qiqan ReiLQtI SAUV_PHYSA : 34- 40: qaann RllLDtI UR1_CATCO : 35- 41: qagln RkyLDeV UR1_CYPCA : 137- 143: qagln RkyLDeV gk UR1_PLAFE : 54- 60: qaqin RnlLDeV B 2: 11.0102 17( 16) P-x(1,3)-D-x(0,1)-L Occurences: 17(16) CRF1_CATCO : 124- 129: rseep PislD-L tfhll CRF2_CATCO : 124- 129: rseep PislD-L tfhll CRF_HUMAN : 158- 163: rseep PislD-L tfhll CRF_PIG : 5- 10: seep PislD-L tfhll CRF_RAT : 149- 154: rseep PislD-L tfhll CRF_SHEEP : 152- 157: rsqep PislD-L tfhll DIU1_MANSE : 27- 30: apdsa Pm--D-L vqids DIU2_MANSE : 6- 11: sfsvn Pav-DiL qhrym DIUH_ACHDO : 11- 15: lsiva Pl--DvL rqrlm DIUH_LOCMI : 12- 16: lsivn Pm--DvL rqrll DIUH_MUSDO : 10- 14: lsivn Pl--DvL rqrll DIUH_PERAM : 12- 16: lsivn Pl--DvL rqrll SAUV_PHYSA : 4- 9: qgp PisiD-L slell UR1_CATCO : 5- 10: nddp PisiD-L tfhll UR1_CYPCA : 26- 29: lstcr Pr--D-L slmns UR1_CYPCA : 107- 112: rnddp PisiD-L tfhll UR1_PLAFE : 24- 29: rsedp PmsiD-L tfhml C 3: 10.5102 38( 16) L-x(0,2)-R-x(1,3)-E Occurences: 38(16) CRF1_CATCO : 46- 51: qsapv La-Rlg-E eyfir CRF1_CATCO : 46- 52: qsapv La-RlgeE yfirl CRF1_CATCO : 87- 93: alqlq LtqRll-E gkvgn CRF1_CATCO : 133- 139: dltfh Ll-RevlE marae CRF1_CATCO : 134- 139: ltfhl L--RevlE marae CRF2_CATCO : 46- 51: qspav La-Rmg-E eyfir CRF2_CATCO : 46- 52: qspav La-RmgeE yfirl CRF2_CATCO : 87- 93: alqlq LtqRvl-E gkvgn CRF2_CATCO : 133- 139: dltfh Ll-RevlE marae CRF2_CATCO : 134- 139: ltfhl L--RevlE marae CRF_HUMAN : 65- 70: qarpv Ll-Rmg-E eyflr CRF_HUMAN : 65- 71: qarpv Ll-RmgeE yflrl CRF_HUMAN : 66- 70: arpvl L--Rmg-E eyflr CRF_HUMAN : 66- 71: arpvl L--RmgeE yflrl CRF_HUMAN : 167- 173: dltfh Ll-RevlE marae CRF_HUMAN : 168- 173: ltfhl L--RevlE marae CRF_PIG : 14- 20: dltfh Ll-RevlE marae CRF_PIG : 15- 20: ltfhl L--RevlE marae CRF_RAT : 56- 61: qpqpi Li-Rmg-E eyflr CRF_RAT : 56- 62: qpqpi Li-RmgeE yflrl CRF_RAT : 123- 129: dsste LaeRga-E dalgg CRF_RAT : 158- 164: dltfh Ll-RevlE marae CRF_RAT : 159- 164: ltfhl L--RevlE marae CRF_SHEEP : 62- 67: qalpt Ll-Rvg-E eyflr CRF_SHEEP : 62- 68: qalpt Ll-RvgeE yflrl CRF_SHEEP : 63- 67: alptl L--Rvg-E eyflr CRF_SHEEP : 63- 68: alptl L--RvgeE yflrl CRF_SHEEP : 134- 139: gtena LgsRq--E apaar CRF_SHEEP : 161- 167: dltfh Ll-RevlE mtkad CRF_SHEEP : 162- 167: ltfhl L--RevlE mtkad DIU1_MANSE : 50- 57: yavss LegRygaE apwly DIU2_MANSE : 11- 17: pavdi LqhRym-E kvaqn DIUH_ACHDO : 15- 22: apldv LrqRlmnE lnrrr DIUH_ACHDO : 23- 30: rlmne LnrRrmrE lqgsr DIUH_LOCMI : 16- 23: npmdv LrqRlllE iarrr DIUH_LOCMI : 29- 33: iarrr L--Rda-E eqika DIUH_LOCMI : 29- 34: iarrr L--RdaeE qikan DIUH_MUSDO : 14- 21: npldv LrqRlllE iarrq DIUH_PERAM : 16- 23: npldv LrqRlllE iarrr SAUV_PHYSA : 13- 19: dlsle Ll-RkmiE iekqe SAUV_PHYSA : 14- 19: lslel L--RkmiE iekqe UR1_CATCO : 14- 20: dltfh Ll-RnmiE marie UR1_CATCO : 15- 20: ltfhl L--RnmiE marie UR1_CYPCA : 116- 122: dltfh Ll-RnmiE marne UR1_CYPCA : 117- 122: ltfhl L--RnmiE marne UR1_PLAFE : 18- 21: lgdni L--Rs--E dppms D 4: 7.8401 53( 16) L-x(0,1)-R Occurences: 53(16) CRF1_CATCO : 46- 48: qsapv LaR lgeey CRF1_CATCO : 65- 66: ryqns L-R sspdt CRF1_CATCO : 108- 109: dgnya L-R aldse CRF1_CATCO : 133- 135: dltfh LlR evlem CRF1_CATCO : 134- 135: ltfhl L-R evlem CRF2_CATCO : 46- 48: qspav LaR mgeey CRF2_CATCO : 108- 109: dgnya L-R aldse CRF2_CATCO : 133- 135: dltfh LlR evlem CRF2_CATCO : 134- 135: ltfhl L-R evlem CRF_HUMAN : 26- 28: pcral LsR gpvpg CRF_HUMAN : 65- 67: qarpv LlR mgeey CRF_HUMAN : 66- 67: arpvl L-R mgeey CRF_HUMAN : 74- 75: geeyf L-R lgnln CRF_HUMAN : 121- 123: lqqll LpR rslds CRF_HUMAN : 167- 169: dltfh LlR evlem CRF_HUMAN : 168- 169: ltfhl L-R evlem CRF_PIG : 14- 16: dltfh LlR evlem CRF_PIG : 15- 16: ltfhl L-R evlem CRF_RAT : 3- 4: mr L-R llvsa CRF_RAT : 26- 28: pcral LsR gsvsg CRF_RAT : 56- 58: qpqpi LiR mgeey CRF_RAT : 65- 66: geeyf L-R lgnln CRF_RAT : 70- 72: lrlgn LnR spaar CRF_RAT : 139- 141: ghqga LeR errse CRF_RAT : 158- 160: dltfh LlR evlem CRF_RAT : 159- 160: ltfhl L-R evlem CRF_SHEEP : 26- 28: pcral LsR gpipg CRF_SHEEP : 62- 64: qalpt LlR vgeey CRF_SHEEP : 63- 64: alptl L-R vgeey CRF_SHEEP : 71- 72: geeyf L-R lgnld CRF_SHEEP : 161- 163: dltfh LlR evlem CRF_SHEEP : 162- 163: ltfhl L-R evlem DIU1_MANSE : 94- 95: lpmsv L-R qklsl DIU1_MANSE : 109- 110: rkvha L-R aaanr DIU2_MANSE : 27- 29: nnrnf LnR v DIUH_ACHDO : 15- 16: apldv L-R qrlmn DIUH_ACHDO : 23- 25: rlmne LnR rrmre DIUH_LOCMI : 16- 17: npmdv L-R qrlll DIUH_LOCMI : 29- 30: iarrr L-R daeeq DIUH_MUSDO : 14- 15: npldv L-R qrlll DIUH_MUSDO : 36- 38: trqve LnR ailkn DIUH_PERAM : 16- 17: npldv L-R qrlll SAUV_PHYSA : 13- 15: dlsle LlR kmiei SAUV_PHYSA : 14- 15: lslel L-R kmiei UR1_CATCO : 14- 16: dltfh LlR nmiem UR1_CATCO : 15- 16: ltfhl L-R nmiem UR1_CATCO : 33- 35: reqag LnR kylde UR1_CYPCA : 61- 63: kllqy LqR nlgaq UR1_CYPCA : 116- 118: dltfh LlR nmiem UR1_CYPCA : 117- 118: ltfhl L-R nmiem UR1_CYPCA : 135- 137: reqag LnR kylde UR1_PLAFE : 18- 19: lgdni L-R sedpp UR1_PLAFE : 34- 35: ltfhm L-R nmihm E 5: 7.8401 20( 16) N-x(2,3)-L Occurences: 20(16) CRF1_CATCO : 105- 108: grwdg Nya-L ralds CRF2_CATCO : 105- 108: grwdg Nya-L ralds CRF_HUMAN : 187- 190: qqahs Nrk-L meiig CRF_PIG : 34- 37: qqahs Nrk-L menf CRF_RAT : 81- 85: arlsp NstpL tagrg CRF_RAT : 178- 181: qqahs Nrk-L meiig CRF_SHEEP : 181- 184: qqahs Nrk-L ldiag CRF_SHEEP : 181- 185: qqahs NrklL diagk DIU1_MANSE : 114- 118: lraaa NrnfL ndigk DIU2_MANSE : 23- 27: kvaqn NrnfL nrv DIUH_ACHDO : 39- 42: sriqq Nrq-L ltsi DIUH_ACHDO : 39- 43: sriqq NrqlL tsi DIUH_LOCMI : 39- 43: eqika NkdfL qqi DIUH_MUSDO : 1- 5: NkpsL sivnp DIUH_MUSDO : 37- 41: rqvel NraiL knv DIUH_PERAM : 39- 43: dqiqa NreiL qti SAUV_PHYSA : 32- 35: kqqaa Nnr-L lldti SAUV_PHYSA : 32- 36: kqqaa NnrlL ldti SAUV_PHYSA : 33- 36: qqaan Nrl-L ldti SAUV_PHYSA : 33- 37: qqaan NrllL dti UR1_CATCO : 34- 38: eqagl NrkyL dev UR1_CYPCA : 33- 36: dlslm Nsq-L ddvll UR1_CYPCA : 136- 140: eqagl NrkyL devgk UR1_PLAFE : 53- 56: eqaqi Nrn-L ldev UR1_PLAFE : 53- 57: eqaqi NrnlL dev F 6: 7.8401 23( 16) D-x(0,1)-L Occurences: 23(16) CRF1_CATCO : 128- 129: ppisl D-L tfhll CRF2_CATCO : 128- 129: ppisl D-L tfhll CRF_HUMAN : 162- 163: ppisl D-L tfhll CRF_PIG : 9- 10: ppisl D-L tfhll CRF_RAT : 130- 132: ergae DaL gghqg CRF_RAT : 153- 154: ppisl D-L tfhll CRF_SHEEP : 156- 157: ppisl D-L tfhll CRF_SHEEP : 172- 174: emtka DqL aqqah DIU1_MANSE : 29- 30: dsapm D-L vqids DIU1_MANSE : 88- 89: pslsi D-L pmsvl DIU2_MANSE : 9- 11: vnpav DiL qhrym DIUH_ACHDO : 13- 15: ivapl DvL rqrlm DIUH_LOCMI : 14- 16: ivnpm DvL rqrll DIUH_LOCMI : 41- 43: ikank DfL qqi DIUH_MUSDO : 12- 14: ivnpl DvL rqrll DIUH_PERAM : 14- 16: ivnpl DvL rqrll SAUV_PHYSA : 8- 9: ppisi D-L slell UR1_CATCO : 9- 10: ppisi D-L tfhll UR1_CYPCA : 28- 29: tcrpr D-L slmns UR1_CYPCA : 38- 40: nsqld DvL lngag UR1_CYPCA : 111- 112: ppisi D-L tfhll UR1_PLAFE : 11- 12: dsaas D-L lgdni UR1_PLAFE : 11- 13: dsaas DlL gdnil UR1_PLAFE : 28- 29: ppmsi D-L tfhml G 7: 7.3401 34( 16) N-x(1,3)-L Occurences: 34(16) CRF1_CATCO : 4- 6: mkl Nf--L vttva CRF1_CATCO : 63- 65: gnryq Ns--L rsspd CRF1_CATCO : 105- 108: grwdg Nya-L ralds CRF2_CATCO : 4- 6: mrl Nf--L vttma CRF2_CATCO : 105- 108: grwdg Nya-L ralds CRF_HUMAN : 139- 141: ergar Na--L gghqe CRF_HUMAN : 187- 190: qqahs Nrk-L meiig CRF_PIG : 34- 37: qqahs Nrk-L menf CRF_RAT : 42- 44: apqpl Nf--L qpeqp CRF_RAT : 81- 85: arlsp NstpL tagrg CRF_RAT : 178- 181: qqahs Nrk-L meiig CRF_SHEEP : 132- 134: krgte Na--L gsrqe CRF_SHEEP : 181- 184: qqahs Nrk-L ldiag CRF_SHEEP : 181- 185: qqahs NrklL diagk DIU1_MANSE : 114- 118: lraaa NrnfL ndigk DIU1_MANSE : 116- 118: aaanr Nf--L ndigk DIU2_MANSE : 23- 27: kvaqn NrnfL nrv DIU2_MANSE : 25- 27: aqnnr Nf--L nrv DIUH_ACHDO : 21- 23: rqrlm Ne--L nrrrm DIUH_ACHDO : 39- 42: sriqq Nrq-L ltsi DIUH_ACHDO : 39- 43: sriqq NrqlL tsi DIUH_LOCMI : 39- 43: eqika NkdfL qqi DIUH_MUSDO : 1- 5: NkpsL sivnp DIUH_MUSDO : 9- 11: slsiv Np--L dvlrq DIUH_MUSDO : 37- 41: rqvel NraiL knv DIUH_PERAM : 11- 13: slsiv Np--L dvlrq DIUH_PERAM : 39- 43: dqiqa NreiL qti SAUV_PHYSA : 32- 35: kqqaa Nnr-L lldti SAUV_PHYSA : 32- 36: kqqaa NnrlL ldti SAUV_PHYSA : 33- 35: qqaan Nr--L lldti SAUV_PHYSA : 33- 36: qqaan Nrl-L ldti SAUV_PHYSA : 33- 37: qqaan NrllL dti UR1_CATCO : 34- 38: eqagl NrkyL dev UR1_CYPCA : 33- 36: dlslm Nsq-L ddvll UR1_CYPCA : 91- 93: sphed Ns--L eelte UR1_CYPCA : 136- 140: eqagl NrkyL devgk UR1_PLAFE : 16- 18: dllgd Ni--L rsedp UR1_PLAFE : 53- 56: eqaqi Nrn-L ldev UR1_PLAFE : 53- 57: eqaqi NrnlL dev UR1_PLAFE : 55- 57: aqinr Nl--L dev H 8: 7.3401 58( 16) R-x(2,4)-E Occurences: 58(16) CRF1_CATCO : 48- 51: apvla Rlg--E eyfir CRF1_CATCO : 48- 52: apvla Rlge-E yfirl CRF1_CATCO : 90- 93: lqltq Rll--E gkvgn CRF1_CATCO : 109- 114: gnyal RaldsE ererr CRF1_CATCO : 116- 121: ldsee RerrsE eppis CRF1_CATCO : 118- 121: seere Rrs--E eppis CRF1_CATCO : 118- 122: seere Rrse-E ppisl CRF1_CATCO : 119- 122: eerer Rse--E ppisl CRF1_CATCO : 135- 139: tfhll Revl-E marae CRF1_CATCO : 154- 158: qahsn Rkmm-E ifgk CRF2_CATCO : 48- 51: pavla Rmg--E eyfir CRF2_CATCO : 48- 52: pavla Rmge-E yfirl CRF2_CATCO : 90- 93: lqltq Rvl--E gkvgn CRF2_CATCO : 109- 114: gnyal RaldsE ererr CRF2_CATCO : 116- 121: ldsee RerrsE eppis CRF2_CATCO : 118- 121: seere Rrs--E eppis CRF2_CATCO : 118- 122: seere Rrse-E ppisl CRF2_CATCO : 119- 122: eerer Rse--E ppisl CRF2_CATCO : 135- 139: tfhll Revl-E marae CRF2_CATCO : 154- 158: qahsn Rkmm-E ifgk CRF_HUMAN : 67- 70: rpvll Rmg--E eyflr CRF_HUMAN : 67- 71: rpvll Rmge-E yflrl CRF_HUMAN : 101- 105: ggsgs Rpsp-E qatan CRF_HUMAN : 150- 155: qeape RerrsE eppis CRF_HUMAN : 152- 155: apere Rrs--E eppis CRF_HUMAN : 152- 156: apere Rrse-E ppisl CRF_HUMAN : 153- 156: perer Rse--E ppisl CRF_HUMAN : 169- 173: tfhll Revl-E marae CRF_HUMAN : 188- 192: qahsn Rklm-E iigk CRF_PIG : 16- 20: tfhll Revl-E marae CRF_PIG : 35- 39: qahsn Rklm-E nf CRF_RAT : 58- 61: qpili Rmg--E eyflr CRF_RAT : 58- 62: qpili Rmge-E yflrl CRF_RAT : 126- 129: telae Rga--E dalgg CRF_RAT : 141- 146: qgale RerrsE eppis CRF_RAT : 143- 146: alere Rrs--E eppis CRF_RAT : 143- 147: alere Rrse-E ppisl CRF_RAT : 144- 147: lerer Rse--E ppisl CRF_RAT : 160- 164: tfhll Revl-E marae CRF_RAT : 179- 183: qahsn Rklm-E iigk CRF_SHEEP : 64- 67: lptll Rvg--E eyflr CRF_SHEEP : 64- 68: lptll Rvge-E yflrl CRF_SHEEP : 128- 131: agpak Rgt--E nalgs CRF_SHEEP : 146- 150: paark Rrsq-E ppisl CRF_SHEEP : 147- 150: aarkr Rsq--E ppisl CRF_SHEEP : 163- 167: tfhll Revl-E mtkad DIU1_MANSE : 53- 57: ssleg Ryga-E apwly DIU2_MANSE : 14- 17: dilqh Rym--E kvaqn DIUH_ACHDO : 18- 22: dvlrq Rlmn-E lnrrr DIUH_ACHDO : 25- 30: mneln RrrmrE lqgsr DIUH_ACHDO : 26- 30: nelnr Rrmr-E lqgsr DIUH_ACHDO : 27- 30: elnrr Rmr--E lqgsr DIUH_LOCMI : 19- 23: dvlrq Rlll-E iarrr DIUH_LOCMI : 28- 33: eiarr RlrdaE eqika DIUH_LOCMI : 30- 33: arrrl Rda--E eqika DIUH_LOCMI : 30- 34: arrrl Rdae-E qikan DIUH_MUSDO : 17- 21: dvlrq Rlll-E iarrq DIUH_MUSDO : 24- 29: lleia RrqmkE ntrqv DIUH_MUSDO : 25- 29: leiar Rqmk-E ntrqv DIUH_MUSDO : 32- 35: mkent Rqv--E lnrai DIUH_PERAM : 19- 23: dvlrq Rlll-E iarrr SAUV_PHYSA : 15- 19: slell Rkmi-E iekqe UR1_CATCO : 16- 20: tfhll Rnmi-E marie UR1_CATCO : 23- 27: miema Rien-E reqag UR1_CATCO : 35- 40: qagln RkyldE v UR1_CYPCA : 118- 122: tfhll Rnmi-E marne UR1_CYPCA : 137- 142: qagln RkyldE vgk UR1_PLAFE : 54- 59: qaqin RnlldE v Number of patterns evaluated by Pratt:13 Total running time: 1 seconds