------------------------------------------------------------ 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 7 sequences from file SDH_CYT_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 SDH_CYT_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: C560_BOVIN 132 C560_MARPO 137 CYT1_CAEBR 184 CYT1_CAEEL 182 DHSC_ECOLI 129 DHSC_RICPR 124 SDH3_YEAST 198 Pratt run started at Thu Feb 6 21:11:45 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.5102 7( 7) H-x(5)-R-x(4)-D 2: 12.5102 7( 7) L-x-W-x-L 3: 12.5102 7( 7) S-x(2)-H-R 4: 12.0102 7( 7) L-T-x(1,2)-L 5: 12.0102 7( 7) G-x(1,2)-R-x(4)-D 6: 12.0102 8( 7) V-x(2)-L-x(3,4)-L 7: 12.0102 8( 7) L-x(4)-G-x(2,3)-L 8: 12.0102 9( 7) I-x(5)-G-x(2,3)-L 9: 11.5102 13( 7) L-x(0,1)-T-x(1,2)-L 10: 11.5102 10( 7) V-x(4)-L-x(0,2)-L 11: 11.5102 8( 7) G-x(0,1)-I-x(2,3)-L 12: 11.5102 9( 7) H-x(2,3)-G-x(0,1)-I 13: 11.5102 10( 7) I-x(3,4)-L-x(3,4)-S 14: 11.5102 7( 7) I-x(4,5)-L-x(3,4)-S 15: 11.5102 10( 7) L-x(1,3)-L-S 16: 11.5102 8( 7) L-x(2)-V-x(0,2)-S 17: 11.5102 7( 7) I-x(0,1)-H-x(2,3)-G 18: 11.5102 7( 7) L-x(2,3)-H-x(2,3)-G 19: 11.5102 8( 7) T-x(1,3)-S-x(2)-H 20: 11.0102 9( 7) L-x(0,1)-L-x(0,2)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 33.3449 7( 7) H-x(2)-[GNV]-[AG]-[IV]-R-[FH]-[LM]-x(2)-D-x-[AG]-x(3)-[DENST] B 2: 25.8357 8( 7) T-x(1,3)-S-x-[FL]-H-[QR]-x-[GST]-[GLV]-[ACV] C 3: 23.7963 7( 7) G-x(1,2)-R-[FH]-[LM]-x(2)-D-x-[AG]-x(3)-[DENST] D 4: 18.8559 7( 7) S-x(2)-H-R-x-[ST]-[GL] E 5: 17.3828 7( 7) I-x-[FH]-x(2)-[NSTV]-G-x(2,3)-L F 6: 16.3492 7( 7) G-x(0,1)-I-x(2,3)-L-x(2)-[ADT]-x(3)-[AEGS] G 7: 14.1756 7( 7) I-x(0,1)-H-x(2,3)-G-[AIV] H 8: 14.1088 9( 7) L-x(0,1)-T-x(1,2)-L-x-[GSV] I 9: 14.1052 8( 7) H-x(2,3)-G-x(0,1)-I-x-[FHY] J 10: 12.5102 7( 7) L-x-W-x-L K 11: 12.0102 7( 7) L-T-x(1,2)-L L 12: 12.0102 8( 7) V-x(2)-L-x(3,4)-L M 13: 12.0102 8( 7) L-x(4)-G-x(2,3)-L N 14: 11.5102 10( 7) V-x(4)-L-x(0,2)-L O 15: 11.5102 10( 7) I-x(3,4)-L-x(3,4)-S P 16: 11.5102 7( 7) I-x(4,5)-L-x(3,4)-S Q 17: 11.5102 10( 7) L-x(1,3)-L-S R 18: 11.5102 8( 7) L-x(2)-V-x(0,2)-S S 19: 11.5102 7( 7) L-x(2,3)-H-x(2,3)-G T 20: 11.5102 8( 7) T-x(1,3)-S-x(2)-H Best patterns with alignements: fitness hits(seqs) Pattern A 1: 33.3449 7( 7) H-x(2)-[GNV]-[AG]-[IV]-R-[FH]-[LM]-x(2)-D-x-[AG]-x(3)-[DENST] Occurences: 7(7) C560_BOVIN : 90- 107: fplmy HtwNGIRHLmwDlGkglT isqlh C560_MARPO : 85- 102: lalcy HmsNGVRHLlwDlGfflE lskvy CYT1_CAEBR : 129- 146: fpiif HtlNGIRFLgfDlAkgvD nigqv CYT1_CAEEL : 129- 146: fpiif HtlNGIRFLgfDlAkgvN nvgqi DHSC_ECOLI : 84- 101: talay HvvVGIRHMmmDfGyleE tfeag DHSC_RICPR : 83- 100: yswcy HlcNGIRHLfwDiGygfS ikavn SDH3_YEAST : 156- 173: ylfai HygGAIRHLiwDtAkelT lkgvy B 2: 25.8357 8( 7) T-x(1,3)-S-x-[FL]-H-[QR]-x-[GST]-[GLV]-[ACV] Occurences: 8(7) C560_BOVIN : 107- 117: lgkgl Ti--SqLHQsGVA vlvlt C560_MARPO : 19- 31: ykpql TstfSiFHRiSGA flatm C560_MARPO : 21- 31: pqlts Tf--SiFHRiSGA flatm CYT1_CAEBR : 66- 78: yqpql TwmlSgFHRiSGC vmagt CYT1_CAEEL : 66- 78: yqpql TwmlSgFHRiSGC vmagt DHSC_ECOLI : 23- 35: irfpi TaiaSiLHRvSGV itfva DHSC_RICPR : 28- 38: pqiss Tl--SiLHRmTGV alffv SDH3_YEAST : 89- 101: yqpql TwylSsLHRiSLV lmglg C 3: 23.7963 7( 7) G-x(1,2)-R-[FH]-[LM]-x(2)-D-x-[AG]-x(3)-[DENST] Occurences: 7(7) C560_BOVIN : 94- 107: yhtwn Gi-RHLmwDlGkglT isqlh C560_MARPO : 89- 102: yhmsn Gv-RHLlwDlGfflE lskvy CYT1_CAEBR : 133- 146: fhtln Gi-RFLgfDlAkgvD nigqv CYT1_CAEEL : 133- 146: fhtln Gi-RFLgfDlAkgvN nvgqi DHSC_ECOLI : 88- 101: yhvvv Gi-RHMmmDfGyleE tfeag DHSC_RICPR : 87- 100: yhlcn Gi-RHLfwDiGygfS ikavn SDH3_YEAST : 159- 173: aihyg GaiRHLiwDtAkelT lkgvy D 4: 18.8559 7( 7) S-x(2)-H-R-x-[ST]-[GL] Occurences: 7(7) C560_BOVIN : 31- 38: lpmam SicHRgTG ialsa C560_MARPO : 23- 30: ltstf SifHRiSG aflat CYT1_CAEBR : 70- 77: ltwml SgfHRiSG cvmag CYT1_CAEEL : 70- 77: ltwml SgfHRiSG cvmag DHSC_ECOLI : 27- 34: itaia SilHRvSG vitfv DHSC_RICPR : 30- 37: isstl SilHRmTG valff SDH3_YEAST : 93- 100: ltwyl SslHRiSL vlmgl E 5: 17.3828 7( 7) I-x-[FH]-x(2)-[NSTV]-G-x(2,3)-L Occurences: 7(7) C560_BOVIN : 32- 41: pmams IcHrgTGia-L sagvs C560_MARPO : 24- 33: tstfs IfHriSGaf-L atmvl CYT1_CAEBR : 127- 137: iafpi IfHtlNGirfL gfdla CYT1_CAEEL : 127- 137: iafpi IfHtlNGirfL gfdla DHSC_ECOLI : 36- 45: rvsgv ItFvaVGil-L wllgt DHSC_RICPR : 31- 40: sstls IlHrmTGva-L ffvvs SDH3_YEAST : 112- 122: fylft IlFgvSGllgL gltte F 6: 16.3492 7( 7) G-x(0,1)-I-x(2,3)-L-x(2)-[ADT]-x(3)-[AEGS] Occurences: 7(7) C560_BOVIN : 94- 105: yhtwn G-Irh-LmwDlgkG ltisq C560_MARPO : 110- 121: kvyts G-Iim-LfcAaflA llnii CYT1_CAEBR : 133- 144: fhtln G-Irf-LgfDlakG vdnig CYT1_CAEEL : 133- 144: fhtln G-Irf-LgfDlakG vnnvg DHSC_ECOLI : 42- 54: tfvav G-IllwLlgTslsS pegfe DHSC_RICPR : 87- 98: yhlcn G-Irh-LfwDigyG fsika SDH3_YEAST : 159- 171: aihyg GaIrh-LiwDtakE ltlkg G 7: 14.1756 7( 7) I-x(0,1)-H-x(2,3)-G-[AIV] Occurences: 7(7) C560_BOVIN : 32- 39: pmams IcHrgtGI alsag C560_MARPO : 24- 31: tstfs IfHrisGA flatm CYT1_CAEBR : 127- 134: iafpi IfHtlnGI rflgf CYT1_CAEEL : 127- 134: iafpi IfHtlnGI rflgf DHSC_ECOLI : 28- 35: taias IlHrvsGV itfva DHSC_RICPR : 31- 38: sstls IlHrmtGV alffv SDH3_YEAST : 155- 160: aylfa I-Hyg-GA irhli H 8: 14.1088 9( 7) L-x(0,1)-T-x(1,2)-L-x-[GSV] Occurences: 9(7) C560_BOVIN : 121- 126: vavlv L-Tv-LsS vglaa C560_MARPO : 33- 40: isgaf LaTmvLfS ilffk CYT1_CAEBR : 65- 71: iyqpq L-TwmLsG fhris CYT1_CAEEL : 65- 71: vyqpq L-TwmLsG fhris DHSC_ECOLI : 48- 54: illwl LgTs-LsS pegfe DHSC_RICPR : 117- 124: vvcsi LlTmlLwV DHSC_RICPR : 118- 124: vcsil L-TmlLwV SDH3_YEAST : 88- 94: iyqpq L-TwyLsS lhris SDH3_YEAST : 109- 115: glgfy LfTi-LfG vsgll I 9: 14.1052 8( 7) H-x(2,3)-G-x(0,1)-I-x-[FHY] Occurences: 8(7) C560_BOVIN : 90- 97: fplmy HtwnG-IrH lmwdl C560_MARPO : 129- 137: niirq HwsnGqIpY CYT1_CAEBR : 129- 136: fpiif HtlnG-IrF lgfdl CYT1_CAEEL : 129- 136: fpiif HtlnG-IrF lgfdl DHSC_ECOLI : 30- 38: iasil HrvsGvItF vavgi DHSC_ECOLI : 84- 91: talay HvvvG-IrH mmmdf DHSC_RICPR : 83- 90: yswcy HlcnG-IrH lfwdi SDH3_YEAST : 156- 163: ylfai Hyg-GaIrH liwdt J 10: 12.5102 7( 7) L-x-W-x-L Occurences: 7(7) C560_BOVIN : 98- 102: ngirh LmWdL gkglt C560_MARPO : 93- 97: ngvrh LlWdL gffle CYT1_CAEBR : 65- 69: iyqpq LtWmL sgfhr CYT1_CAEEL : 65- 69: vyqpq LtWmL sgfhr DHSC_ECOLI : 44- 48: vavgi LlWlL gtsls DHSC_RICPR : 47- 51: fvvsi LvWwL ilsky SDH3_YEAST : 88- 92: iyqpq LtWyL sslhr K 11: 12.0102 7( 7) L-T-x(1,2)-L Occurences: 7(7) C560_BOVIN : 121- 124: vavlv LTv-L ssvgl C560_MARPO : 63- 67: qyfff LTfyL nwfii CYT1_CAEBR : 65- 69: iyqpq LTwmL sgfhr CYT1_CAEEL : 65- 69: vyqpq LTwmL sgfhr DHSC_ECOLI : 78- 81: imwgi LTa-L ayhvv DHSC_RICPR : 118- 121: vcsil LTm-L lwv DHSC_RICPR : 118- 122: vcsil LTmlL wv SDH3_YEAST : 88- 92: iyqpq LTwyL sslhr L 12: 12.0102 8( 7) V-x(2)-L-x(3,4)-L Occurences: 8(7) C560_BOVIN : 116- 124: lhqsg VavLvltvL ssvgl C560_MARPO : 90- 97: hmsng VrhLlwd-L gffle CYT1_CAEBR : 86- 94: agtll VggLgfavL pldft CYT1_CAEEL : 158- 165: ksgyl VsgLsai-L alaiv DHSC_ECOLI : 41- 48: itfva VgiLlwl-L gtsls DHSC_ECOLI : 119- 127: fvitv VlsLlagvL vw DHSC_RICPR : 44- 51: alffv VsiLvww-L ilsky SDH3_YEAST : 116- 124: tilfg VsgLlglgL ttekv M 13: 12.0102 8( 7) L-x(4)-G-x(2,3)-L Occurences: 8(7) C560_BOVIN : 98- 106: ngirh LmwdlGkg-L tisql C560_MARPO : 42- 51: vlfsi LffkiGdlsL tfyhf C560_MARPO : 93- 101: ngvrh LlwdlGff-L elskv CYT1_CAEBR : 85- 94: magtl LvgglGfavL pldft CYT1_CAEEL : 85- 94: magtl LvggiGfavL pfdft DHSC_ECOLI : 44- 52: vavgi LlwllGts-L sspeg DHSC_RICPR : 32- 40: stlsi LhrmtGva-L ffvvs SDH3_YEAST : 113- 122: ylfti LfgvsGllgL gltte N 14: 11.5102 10( 7) V-x(4)-L-x(0,2)-L Occurences: 10(7) C560_BOVIN : 45- 53: alsag VslfgLsaL lvpgs C560_BOVIN : 116- 124: lhqsg VavlvLtvL ssvgl C560_MARPO : 75- 82: fiisl VnftlLa-L cyhms CYT1_CAEBR : 79- 85: risgc VmagtL--L vgglg CYT1_CAEEL : 79- 85: risgc VmagtL--L vggig DHSC_ECOLI : 39- 45: gvitf VavgiL--L wllgt DHSC_ECOLI : 39- 47: gvitf VavgiLlwL lgtsl DHSC_ECOLI : 115- 122: akisf VitvvLs-L lagvl DHSC_ECOLI : 115- 123: akisf VitvvLslL agvlv DHSC_RICPR : 112- 118: tgwcv VvcsiL--L tmllw DHSC_RICPR : 113- 121: gwcvv VcsilLtmL lwv SDH3_YEAST : 190- 196: igfta VlgtyL--L tl SDH3_YEAST : 190- 198: igfta VlgtyLltL O 15: 11.5102 10( 7) I-x(3,4)-L-x(3,4)-S Occurences: 10(7) C560_BOVIN : 21- 31: sphis IygwsLpmamS ichrg C560_MARPO : 13- 23: sphlt IykpqLtstfS ifhri CYT1_CAEBR : 8- 16: nipts Ilcr-Lgar-S aisrs CYT1_CAEBR : 60- 70: aphlt IyqpqLtwmlS gfhri CYT1_CAEEL : 8- 16: nipta Ilcr-Lgar-S sisrs CYT1_CAEEL : 8- 17: nipta Ilcr-LgarsS isrsf DHSC_ECOLI : 25- 33: fpita Iasi-Lhrv-S gvitf DHSC_ECOLI : 43- 51: fvavg Illw-Llgt-S lsspe DHSC_ECOLI : 43- 53: fvavg IllwlLgtslS spegf DHSC_RICPR : 68- 77: lascc IikicLvaf-S yswcy DHSC_RICPR : 69- 77: ascci Ikic-Lvaf-S yswcy SDH3_YEAST : 83- 93: sphlt IyqpqLtwylS slhri P 16: 11.5102 7( 7) I-x(4,5)-L-x(3,4)-S Occurences: 7(7) C560_BOVIN : 21- 31: sphis Iygws-LpmamS ichrg C560_MARPO : 13- 23: sphlt Iykpq-LtstfS ifhri CYT1_CAEBR : 60- 70: aphlt Iyqpq-LtwmlS gfhri CYT1_CAEEL : 151- 162: nnvgq IyksgyLvsglS ailal DHSC_ECOLI : 43- 53: fvavg Illwl-LgtslS spegf DHSC_RICPR : 68- 77: lascc Iikic-Lvaf-S yswcy SDH3_YEAST : 83- 93: sphlt Iyqpq-LtwylS slhri Q 17: 11.5102 10( 7) L-x(1,3)-L-S Occurences: 10(7) C560_BOVIN : 11- 16: skntt LnrpLS phisi C560_BOVIN : 47- 51: sagvs Lfg-LS allvp C560_BOVIN : 121- 125: vavlv Ltv-LS svgla C560_MARPO : 101- 104: dlgff Le--LS kvyts CYT1_CAEBR : 65- 70: iyqpq LtwmLS gfhri CYT1_CAEEL : 65- 70: vyqpq LtwmLS gfhri CYT1_CAEEL : 157- 162: yksgy LvsgLS ailal DHSC_ECOLI : 48- 53: illwl LgtsLS spegf DHSC_RICPR : 51- 54: ilvww Li--LS kydnn SDH3_YEAST : 88- 93: iyqpq LtwyLS slhri R 18: 11.5102 8( 7) L-x(2)-V-x(0,2)-S Occurences: 8(7) C560_BOVIN : 63- 68: sfesh LefVk-S lclgp C560_MARPO : 103- 109: gffle LskVytS giiml CYT1_CAEBR : 167- 173: savia LaiVinS cqnks CYT1_CAEEL : 167- 173: saila LaiVfnS cqnks DHSC_ECOLI : 29- 33: aiasi LhrV--S gvitf DHSC_RICPR : 40- 45: mtgva LffVv-S ilvww SDH3_YEAST : 49- 54: lstsp LknVa-S emntk SDH3_YEAST : 113- 117: ylfti LfgV--S gllgl S 19: 11.5102 7( 7) L-x(2,3)-H-x(2,3)-G Occurences: 7(7) C560_BOVIN : 87- 94: alvfp Lmy-HtwnG irhlm C560_MARPO : 82- 89: ftlla Lcy-HmsnG vrhll CYT1_CAEBR : 69- 77: qltwm LsgfHrisG cvmag CYT1_CAEEL : 69- 77: qltwm LsgfHrisG cvmag DHSC_ECOLI : 81- 88: gilta Lay-HvvvG irhmm DHSC_RICPR : 29- 37: qisst LsilHrmtG valff SDH3_YEAST : 152- 159: gsfay LfaiHyg-G airhl T 20: 11.5102 8( 7) T-x(1,3)-S-x(2)-H Occurences: 8(7) C560_BOVIN : 107- 112: lgkgl Ti--SqlH qsgva C560_MARPO : 19- 26: ykpql TstfSifH risga C560_MARPO : 21- 26: pqlts Tf--SifH risga CYT1_CAEBR : 66- 73: yqpql TwmlSgfH risgc CYT1_CAEEL : 66- 73: yqpql TwmlSgfH risgc DHSC_ECOLI : 23- 30: irfpi TaiaSilH rvsgv DHSC_RICPR : 28- 33: pqiss Tl--SilH rmtgv SDH3_YEAST : 89- 96: yqpql TwylSslH rislv Number of patterns evaluated by Pratt:671 Total running time: 1 seconds