------------------------------------------------------------ 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 8 sequences from file LUM_BINDING PATTERN CONSERVATION: CM: min Nr of Seqs to Match 8 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 LUM_BINDING.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: LUXP_PHOLE 186 LUXP_PHOPO 189 LUXY_VIBFI 194 RISA_BACSU 215 RISA_ECOLI 213 RISA_HAEIN 204 RISA_PHOLE 218 RISA_YEAST 238 Pratt run started at Thu Feb 6 20:12:04 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.8503 8( 8) N-G-x(0,1)-C-x(1,2)-T-V 2: 19.8503 8( 8) M-F-x-G-I-x(2,4)-G 3: 16.6802 13( 8) G-x(2)-V-N-x-E 4: 15.6802 8( 8) G-x(0,1)-C-x(1,2)-T-V 5: 15.6802 8( 8) F-x-G-I-x(2,4)-G 6: 14.6802 8( 8) S-x(1,3)-N-x(3)-L-x(1,3)-V 7: 14.6802 11( 8) I-x(1,3)-G-x(1,3)-S-x(2)-I 8: 12.5102 15( 8) V-N-x-E 9: 12.5102 9( 8) G-I-x(4)-G 10: 12.5102 8( 8) G-x(3)-I-x(2)-I 11: 12.0102 9( 8) G-x(1,2)-S-L 12: 12.0102 9( 8) G-x(0,1)-S-L 13: 12.0102 9( 8) G-x(3)-I-x(2,3)-I 14: 12.0102 8( 8) D-x-I-x(3,4)-G 15: 12.0102 16( 8) G-x(1,2)-L-T 16: 12.0102 16( 8) G-x(2,3)-L-T 17: 12.0102 11( 8) G-x(1,2)-V-x-G 18: 12.0102 10( 8) C-x(1,2)-T-V 19: 11.5102 16( 8) V-x(0,2)-N-x-E 20: 11.5102 12( 8) N-x(3)-L-x(1,3)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 33.2219 8( 8) N-G-x(0,1)-C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] B 2: 29.0518 8( 8) G-x(0,1)-C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] C 3: 25.3818 9( 8) C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] D 4: 23.1781 8( 8) G-x(1,2)-L-T-[GIV]-[NT]-x(4)-[ADN]-x-[FIV] E 5: 23.1781 8( 8) G-x(2,3)-L-T-[GIV]-[NT]-x(4)-[ADN]-x-[FIV] F 6: 22.0926 8( 8) M-F-x-G-I-x(2,4)-G-x-[AGIV] G 7: 21.5478 11( 8) G-[DQST]-x-V-N-[ILV]-E H 8: 18.5190 8( 8) G-x(1,2)-S-L-x-[GIV]-x(4)-[DENPQT]-x(4)-[GILV] I 9: 18.5190 8( 8) G-x(0,1)-S-L-x-[GIV]-x(4)-[DENPQT]-x(4)-[GILV] J 10: 18.2865 8( 8) N-[GV]-x(2)-L-x-V-[STV] K 11: 17.9225 8( 8) F-x-G-I-x(2,4)-G-x-[AGIV] L 12: 17.3487 8( 8) S-x(1,3)-N-[GIV]-x(2)-L-x(1,3)-V M 13: 16.8464 8( 8) D-x-I-x(3,4)-G-x-[CSV]-x-[DPST] N 14: 16.8143 10( 8) G-x(1,2)-V-[DEQS]-G-x-[AGV] O 15: 15.7350 8( 8) G-I-x(4)-G-x-[IV] P 16: 15.6802 8( 8) N-G-x(0,1)-C-x(1,2)-T Q 17: 15.1859 8( 8) G-x(3)-I-x(2)-I-x(4)-[DGN] R 18: 15.1720 15( 8) V-N-[ILV]-E S 19: 14.6859 9( 8) G-x(3)-I-x(2,3)-I-x(4)-[DGN] T 20: 14.6802 11( 8) I-x(1,3)-G-x(1,3)-S-x(2)-I Best patterns with alignements: fitness hits(seqs) Pattern A 1: 33.2219 8( 8) N-G-x(0,1)-C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] Occurences: 8(8) LUXP_PHOLE : 45- 63: tvmlv NG-CslTVVrIlgDmvyfDI dqalg LUXP_PHOPO : 45- 63: tvmlv NG-CsvTVVrItgDvvyfDI dqain LUXY_VIBFI : 45- 63: ssimf NG-CflTVTsVnsNivwfDI fekea RISA_BACSU : 44- 62: dsiav NGiCl-TVTdFtkNqftvDV mpetv RISA_ECOLI : 45- 63: asvah NGcCl-TVTeIngNhvsfDL mketl RISA_ECOLI : 45- 63: asvah NG-CclTVTeIngNhvsfDL mketl RISA_HAEIN : 45- 63: asian NGvCl-TVTeIngDlvsfDL mqetl RISA_PHOLE : 45- 63: dsiat NGvCl-TVSkLlpSgytaDL slety RISA_YEAST : 51- 69: dsiav NGvCl-TVTeFnnDsfkvGI speti B 2: 29.0518 8( 8) G-x(0,1)-C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] Occurences: 8(8) LUXP_PHOLE : 46- 63: vmlvn G-CslTVVrIlgDmvyfDI dqalg LUXP_PHOPO : 46- 63: vmlvn G-CsvTVVrItgDvvyfDI dqain LUXY_VIBFI : 46- 63: simfn G-CflTVTsVnsNivwfDI fekea RISA_BACSU : 45- 62: siavn GiCl-TVTdFtkNqftvDV mpetv RISA_ECOLI : 46- 63: svahn GcCl-TVTeIngNhvsfDL mketl RISA_ECOLI : 46- 63: svahn G-CclTVTeIngNhvsfDL mketl RISA_HAEIN : 46- 63: siann GvCl-TVTeIngDlvsfDL mqetl RISA_PHOLE : 46- 63: siatn GvCl-TVSkLlpSgytaDL slety RISA_YEAST : 52- 69: siavn GvCl-TVTeFnnDsfkvGI speti C 3: 25.3818 9( 8) C-x(1,2)-T-V-[STV]-x-[FILV]-x(2)-[DNS]-x(4)-[DG]-[ILV] Occurences: 9(8) LUXP_PHOLE : 47- 63: mlvng CslTVVrIlgDmvyfDI dqalg LUXP_PHOPO : 47- 63: mlvng CsvTVVrItgDvvyfDI dqain LUXY_VIBFI : 47- 63: imfng CflTVTsVnsNivwfDI fekea RISA_BACSU : 47- 62: avngi Cl-TVTdFtkNqftvDV mpetv RISA_ECOLI : 47- 63: vahng CclTVTeIngNhvsfDL mketl RISA_ECOLI : 48- 63: ahngc Cl-TVTeIngNhvsfDL mketl RISA_HAEIN : 48- 63: anngv Cl-TVTeIngDlvsfDL mqetl RISA_PHOLE : 48- 63: atngv Cl-TVSkLlpSgytaDL slety RISA_YEAST : 54- 69: avngv Cl-TVTeFnnDsfkvGI speti D 4: 23.1781 8( 8) G-x(1,2)-L-T-[GIV]-[NT]-x(4)-[ADN]-x-[FIV] Occurences: 8(8) LUXP_PHOLE : 96- 108: evvgr Gg-LTGNikgtAlV aaiee LUXP_PHOPO : 96- 108: sllgk Ga-LTGNikgvAtV dnite LUXY_VIBFI : 46- 59: simfn GcfLTVTsvnsNiV wfdif RISA_BACSU : 45- 58: siavn GicLTVTdftkNqF tvdvm RISA_ECOLI : 46- 59: svahn GccLTVTeingNhV sfdlm RISA_HAEIN : 46- 59: siann GvcLTVTeingDlV sfdlm RISA_PHOLE : 143- 156: svtid GisLTINavyqNvI kltiv RISA_YEAST : 52- 65: siavn GvcLTVTefnnDsF kvgis E 5: 23.1781 8( 8) G-x(2,3)-L-T-[GIV]-[NT]-x(4)-[ADN]-x-[FIV] Occurences: 8(8) LUXP_PHOLE : 94- 108: fgevv GrggLTGNikgtAlV aaiee LUXP_PHOPO : 94- 108: fgsll GkgaLTGNikgvAtV dnite LUXY_VIBFI : 46- 59: simfn Gcf-LTVTsvnsNiV wfdif RISA_BACSU : 45- 58: siavn Gic-LTVTdftkNqF tvdvm RISA_ECOLI : 46- 59: svahn Gcc-LTVTeingNhV sfdlm RISA_HAEIN : 46- 59: siann Gvc-LTVTeingDlV sfdlm RISA_PHOLE : 143- 156: svtid Gis-LTINavyqNvI kltiv RISA_YEAST : 52- 65: siavn Gvc-LTVTefnnDsF kvgis F 6: 22.0926 8( 8) M-F-x-G-I-x(2,4)-G-x-[AGIV] Occurences: 8(8) LUXP_PHOLE : 1- 10: MFrGIvq--GrG virsi LUXP_PHOLE : 1- 12: MFrGIvqgrGvI rsisk LUXP_PHOPO : 1- 10: MFkGIvq--GvG iikki LUXP_PHOPO : 1- 12: MFkGIvqgvGiI kkisk LUXY_VIBFI : 1- 10: MFkGIve--GiG iieki LUXY_VIBFI : 1- 12: MFkGIvegiGiI ekidi RISA_BACSU : 1- 12: MFtGIieetGtI esmkk RISA_ECOLI : 1- 10: MFtGIvq--GtA klvsi RISA_HAEIN : 1- 10: MFtGIvq--GtA pihsi RISA_PHOLE : 1- 12: MFtGIiesiGnI gaiir RISA_YEAST : 1- 12: MFtGIvecmGtV lennp G 7: 21.5478 11( 8) G-[DQST]-x-V-N-[ILV]-E Occurences: 11(8) LUXP_PHOLE : 78- 84: dglke GDqVNLE ihpkf LUXP_PHOPO : 175- 181: gtlet GSeVNVE tlnvs LUXY_VIBFI : 177- 183: kwrkk GDkVNVE lsnki RISA_BACSU : 78- 84: ndltk GSkVNLE ramaa RISA_BACSU : 175- 181: sekti GSkVNIE cdmig RISA_ECOLI : 79- 85: gdlkv GDwVNVE raakf RISA_HAEIN : 79- 85: gtvkv GDyVNIE ramqm RISA_HAEIN : 177- 183: grrkv GDiVNIE idpqt RISA_PHOLE : 79- 85: hsyri GQeVNLE kamlp RISA_YEAST : 85- 91: aswiq GTqVNLE ravsq RISA_YEAST : 187- 193: plkki GDeVNIE vdltg H 8: 18.5190 8( 8) G-x(1,2)-S-L-x-[GIV]-x(4)-[DENPQT]-x(4)-[GILV] Occurences: 8(8) LUXP_PHOLE : 142- 157: digid Gi-SLpItdmsDsiitL nysrd LUXP_PHOPO : 88- 104: levrp GfgSLlGkgalTgnikG vatvd LUXY_VIBFI : 144- 159: yiavd Gi-SLtIdtikNnqffI slplk RISA_BACSU : 142- 157: sitvd Gv-SLtIfgltEdtvtI sliph RISA_ECOLI : 144- 159: figid Gi-SLtVgevtPtrfcV hlipe RISA_HAEIN : 144- 159: fvavd Gi-SLtIgevrDtqfcV nlipe RISA_PHOLE : 143- 158: svtid Gi-SLtInavyQnvikL tivph RISA_YEAST : 150- 165: ficid Gt-SLtIikvdPlsqgG afyis I 9: 18.5190 8( 8) G-x(0,1)-S-L-x-[GIV]-x(4)-[DENPQT]-x(4)-[GILV] Occurences: 8(8) LUXP_PHOLE : 142- 157: digid GiSLpItdmsDsiitL nysrd LUXP_PHOPO : 90- 104: vrpgf G-SLlGkgalTgnikG vatvd LUXY_VIBFI : 144- 159: yiavd GiSLtIdtikNnqffI slplk RISA_BACSU : 142- 157: sitvd GvSLtIfgltEdtvtI sliph RISA_ECOLI : 144- 159: figid GiSLtVgevtPtrfcV hlipe RISA_HAEIN : 144- 159: fvavd GiSLtIgevrDtqfcV nlipe RISA_PHOLE : 143- 158: svtid GiSLtInavyQnvikL tivph RISA_YEAST : 150- 165: ficid GtSLtIikvdPlsqgG afyis J 10: 18.2865 8( 8) N-[GV]-x(2)-L-x-V-[STV] Occurences: 8(8) LUXP_PHOLE : 45- 52: tvmlv NGcsLtVV rilgd LUXP_PHOPO : 179- 186: tgsev NVetLnVS new LUXY_VIBFI : 45- 52: ssimf NGcfLtVT svnsn RISA_BACSU : 44- 51: dsiav NGicLtVT dftkn RISA_ECOLI : 45- 52: asvah NGccLtVT eingn RISA_HAEIN : 45- 52: asian NGvcLtVT eingd RISA_PHOLE : 45- 52: dsiat NGvcLtVS kllps RISA_YEAST : 51- 58: dsiav NGvcLtVT efnnd K 11: 17.9225 8( 8) F-x-G-I-x(2,4)-G-x-[AGIV] Occurences: 8(8) LUXP_PHOLE : 2- 10: m FrGIvq--GrG virsi LUXP_PHOLE : 2- 12: m FrGIvqgrGvI rsisk LUXP_PHOPO : 2- 10: m FkGIvq--GvG iikki LUXP_PHOPO : 2- 12: m FkGIvqgvGiI kkisk LUXY_VIBFI : 2- 10: m FkGIve--GiG iieki LUXY_VIBFI : 2- 12: m FkGIvegiGiI ekidi RISA_BACSU : 2- 12: m FtGIieetGtI esmkk RISA_ECOLI : 2- 10: m FtGIvq--GtA klvsi RISA_HAEIN : 2- 10: m FtGIvq--GtA pihsi RISA_PHOLE : 2- 12: m FtGIiesiGnI gaiir RISA_YEAST : 2- 12: m FtGIvecmGtV lennp L 12: 17.3487 8( 8) S-x(1,3)-N-[GIV]-x(2)-L-x(1,3)-V Occurences: 8(8) LUXP_PHOLE : 166- 176: rdlla St--NIasLakdV kvnve LUXP_PHOPO : 176- 185: tletg Sev-NVetLn--V snew LUXY_VIBFI : 41- 51: ikkes SimfNGcfLt--V tsvns RISA_BACSU : 40- 50: vhlgd SiavNGicLt--V tdftk RISA_ECOLI : 41- 51: letga SvahNGccLt--V teing RISA_HAEIN : 41- 51: leiga SianNGvcLt--V teing RISA_PHOLE : 41- 51: vnigd SiatNGvcLt--V skllp RISA_YEAST : 47- 57: chvgd SiavNGvcLt--V tefnn M 13: 16.8464 8( 8) D-x-I-x(3,4)-G-x-[CSV]-x-[DPST] Occurences: 8(8) LUXP_PHOLE : 136- 146: nltvk DdIgid-GiSlP itdms LUXP_PHOPO : 136- 146: nisse DhIgin-GvSnS ieevs LUXY_VIBFI : 138- 148: flidk DyIavd-GiSlT idtik RISA_BACSU : 39- 49: dvhlg DsIavn-GiClT vtdft RISA_ECOLI : 143- 154: gfigi DgIsltvGeVtP trfcv RISA_HAEIN : 143- 154: gfvav DgIsltiGeVrD tqfcv RISA_PHOLE : 40- 50: dvnig DsIatn-GvClT vskll RISA_YEAST : 46- 56: dchvg DsIavn-GvClT vtefn N 14: 16.8143 10( 8) G-x(1,2)-V-[DEQS]-G-x-[AGV] Occurences: 10(8) LUXP_PHOLE : 4- 10: mfr Gi-VQGrG virsi LUXP_PHOPO : 4- 10: mfk Gi-VQGvG iikki LUXY_VIBFI : 4- 10: mfk Gi-VEGiG iieki RISA_BACSU : 95- 102: ngrfg GhfVSGhV dgtae RISA_BACSU : 100- 106: ghfvs Gh-VDGtA eitri RISA_ECOLI : 4- 10: mft Gi-VQGtA klvsi RISA_HAEIN : 4- 10: mft Gi-VQGtA pihsi RISA_PHOLE : 96- 103: ttrlg GhlVSGhV dgvge RISA_PHOLE : 101- 107: ghlvs Gh-VDGvG evief RISA_YEAST : 102- 109: dvrfg GhyVQGhV dtvan O 15: 15.7350 8( 8) G-I-x(4)-G-x-[IV] Occurences: 8(8) LUXP_PHOLE : 4- 12: mfr GIvqgrGvI rsisk LUXP_PHOPO : 4- 12: mfk GIvqgvGiI kkisk LUXY_VIBFI : 4- 12: mfk GIvegiGiI ekidi RISA_BACSU : 4- 12: mft GIieetGtI esmkk RISA_ECOLI : 144- 152: figid GIsltvGeV tptrf RISA_HAEIN : 144- 152: fvavd GIsltiGeV rdtqf RISA_PHOLE : 4- 12: mft GIiesiGnI gaiir RISA_YEAST : 4- 12: mft GIvecmGtV lennp P 16: 15.6802 8( 8) N-G-x(0,1)-C-x(1,2)-T Occurences: 8(8) LUXP_PHOLE : 45- 50: tvmlv NG-CslT vvril LUXP_PHOPO : 45- 50: tvmlv NG-CsvT vvrit LUXY_VIBFI : 45- 50: ssimf NG-CflT vtsvn RISA_BACSU : 44- 49: dsiav NGiCl-T vtdft RISA_ECOLI : 45- 50: asvah NGcCl-T vtein RISA_ECOLI : 45- 50: asvah NG-CclT vtein RISA_HAEIN : 45- 50: asian NGvCl-T vtein RISA_PHOLE : 45- 50: dsiat NGvCl-T vskll RISA_YEAST : 51- 56: dsiav NGvCl-T vtefn Q 17: 15.1859 8( 8) G-x(3)-I-x(2)-I-x(4)-[DGN] Occurences: 8(8) LUXP_PHOLE : 8- 20: rgivq GrgvIrsIskseD sqrhg LUXP_PHOPO : 8- 20: kgivq GvgiIkkIskndD tqrhg LUXY_VIBFI : 8- 20: kgive GigiIekIdiytD ldkya RISA_BACSU : 104- 116: sghvd GtaeItrIeeksN avyyd RISA_ECOLI : 138- 150: yilyk GfigIdgIsltvG evtpt RISA_HAEIN : 8- 20: tgivq GtapIhsIkekaN frtqv RISA_PHOLE : 137- 149: ylsek GsvtIdgIsltiN avyqn RISA_YEAST : 165- 177: plsqg GafyIsmIkhtqD nvimp R 18: 15.1720 15( 8) V-N-[ILV]-E Occurences: 15(8) LUXP_PHOLE : 81- 84: kegdq VNLE ihpkf LUXP_PHOLE : 178- 181: akdvk VNVE ilnew LUXP_PHOPO : 81- 84: evgnk VNLE vrpgf LUXP_PHOPO : 178- 181: etgse VNVE tlnvs LUXY_VIBFI : 180- 183: kkgdk VNVE lsnki RISA_BACSU : 81- 84: tkgsk VNLE ramaa RISA_BACSU : 178- 181: tigsk VNIE cdmig RISA_ECOLI : 82- 85: kvgdw VNVE raakf RISA_ECOLI : 180- 183: klgar VNIE idpqt RISA_HAEIN : 82- 85: kvgdy VNIE ramqm RISA_HAEIN : 180- 183: kvgdi VNIE idpqt RISA_PHOLE : 82- 85: rigqe VNLE kamlp RISA_PHOLE : 179- 182: nidkk VNVE idmma RISA_YEAST : 88- 91: iqgtq VNLE ravsq RISA_YEAST : 190- 193: kigde VNIE vdltg S 19: 14.6859 9( 8) G-x(3)-I-x(2,3)-I-x(4)-[DGN] Occurences: 9(8) LUXP_PHOLE : 8- 20: rgivq GrgvIrs-IskseD sqrhg LUXP_PHOLE : 139- 152: vkddi GidgIslpItdmsD siitl LUXP_PHOPO : 8- 20: kgivq GvgiIkk-IskndD tqrhg LUXY_VIBFI : 8- 20: kgive GigiIek-IdiytD ldkya RISA_BACSU : 104- 116: sghvd GtaeItr-IeeksN avyyd RISA_ECOLI : 138- 150: yilyk GfigIdg-IsltvG evtpt RISA_HAEIN : 8- 20: tgivq GtapIhs-IkekaN frtqv RISA_PHOLE : 137- 149: ylsek GsvtIdg-IsltiN avyqn RISA_YEAST : 165- 177: plsqg GafyIsm-IkhtqD nvimp T 20: 14.6802 11( 8) I-x(1,3)-G-x(1,3)-S-x(2)-I Occurences: 11(8) LUXP_PHOLE : 138- 147: tvkdd IgidGi--SlpI tdmsd LUXP_PHOLE : 140- 147: kddig Id--Gi--SlpI tdmsd LUXP_PHOPO : 138- 147: ssedh IginGv--SnsI eevsn LUXP_PHOPO : 140- 147: edhig In--Gv--SnsI eevsn LUXY_VIBFI : 140- 149: idkdy IavdGi--SltI dtikn RISA_BACSU : 138- 147: vlkgs ItvdGv--SltI fglte RISA_ECOLI : 94- 103: kfsde Ig--GhlmSghI mttae RISA_HAEIN : 94- 103: qmgte Ig--GhllSghI yctak RISA_PHOLE : 141- 148: kgsvt Id--Gi--SltI navyq RISA_YEAST : 146- 155: vekgf IcidGt--SltI ikvdp RISA_YEAST : 148- 155: kgfic Id--Gt--SltI ikvdp Number of patterns evaluated by Pratt:2040 Total running time: 1 seconds