------------------------------------------------------------ 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 6 sequences from file CLAT_ADAPTOR_S PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 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 CLAT_ADAPTOR_S.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AP17_RAT 142 AP17_YEAST 147 AP19_MOUSE 158 AP19_YEAST 156 COPZ_BOVIN 177 YJC4_YEAST 194 Pratt run started at Thu Feb 6 19:08:07 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.3503 6( 6) E-x(5)-F-x(2)-V-x-E-x(1,2)-D 2: 16.6802 6( 6) Y-x(5)-L-Y-F 3: 16.1802 6( 6) F-x(2)-V-x-E-x(1,2)-D 4: 14.6802 7( 6) L-x(0,2)-Y-F-x(1,3)-V 5: 12.5102 6( 6) L-Y-F 6: 12.5102 6( 6) Y-x(3)-A-x-L 7: 12.0102 8( 6) F-x(2)-V-x(3,4)-D 8: 12.0102 6( 6) E-x(3,4)-F-N 9: 12.0102 6( 6) V-x-E-x(1,2)-D 10: 12.0102 6( 6) V-x(1,2)-E-x-D 11: 12.0102 7( 6) F-x(2)-V-x(1,2)-E 12: 12.0102 7( 6) L-x(3,4)-E-x-I 13: 12.0102 7( 6) D-x(5)-L-x(1,2)-L 14: 12.0102 6( 6) D-x-E-x(2,3)-L 15: 12.0102 7( 6) L-x(5)-G-x(2,3)-L 16: 11.5102 10( 6) L-x(0,2)-L-E 17: 11.5102 8( 6) L-x(0,1)-L-x(2,3)-E 18: 11.5102 8( 6) L-x(2)-L-x(1,3)-L 19: 11.5102 9( 6) L-x(2,3)-L-x(1,2)-L 20: 11.5102 9( 6) D-x(0,1)-E-x(2,3)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 39.8943 6( 6) E-x-[LM]-[DEN]-x(2)-F-x-[AENS]-V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] B 2: 38.3276 6( 6) V-x(1,2)-E-x-D-[ILP]-x(2)-[NV]-x(3)-[ALV]-x(4)-[DEN]-[DE]-[FIMV]-x(2)-[ACGT]-[DEG]-x(3)-[ADES]-x-[NSV] C 3: 36.0550 6( 6) Y-[KR]-[NRS]-x-[AI]-[DGST]-L-Y-F-x(4)-[DEST]-x(3)-[DNS]-[EN] D 4: 29.5671 6( 6) F-x-[AENS]-V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] E 5: 27.0948 6( 6) F-x-[AENS]-V-x-E-[IL]-[DV]-x-[GIV]-x-[NV] F 6: 23.1651 6( 6) V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] G 7: 22.7986 6( 6) F-x-[AENS]-V-x(3,4)-D-[GIL]-[GIV]-[FV] H 8: 20.6064 6( 6) Y-x(3)-A-x-L-x-[FL]-x(4)-[DET]-x(3)-[ADNS] I 9: 20.5004 6( 6) L-Y-F-x(4)-[DEST]-x(3)-[DNS]-[EN] J 10: 16.8692 7( 6) L-x(0,2)-Y-F-x(1,3)-V-x(3)-[DEPS] K 11: 14.2241 6( 6) D-[DNQS]-E-x(2,3)-L L 12: 14.2110 7( 6) L-x(2)-[DNST]-x(2)-G-x(2,3)-L M 13: 14.1720 8( 6) L-x(0,2)-L-E-x-[ILV] N 14: 12.0102 6( 6) E-x(3,4)-F-N O 15: 12.0102 7( 6) L-x(3,4)-E-x-I P 16: 12.0102 7( 6) D-x(5)-L-x(1,2)-L Q 17: 11.5102 8( 6) L-x(0,1)-L-x(2,3)-E R 18: 11.5102 8( 6) L-x(2)-L-x(1,3)-L S 19: 11.5102 9( 6) L-x(2,3)-L-x(1,2)-L T 20: 11.5102 9( 6) D-x(0,1)-E-x(2,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 39.8943 6( 6) E-x-[LM]-[DEN]-x(2)-F-x-[AENS]-V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] Occurences: 6(6) AP17_RAT : 89- 105: ihnfv EvLNeyFhNVCEl-DLVF nfykv AP17_YEAST : 94- 110: ihlfv EvLDafFgNVCEl-DIVF nfykv AP19_MOUSE : 89- 105: ihryv ElLDkyFgSVCEl-DIIF nfeka AP19_YEAST : 92- 108: ihrfv EtMDtyFgNVCEl-DIIF nfskv COPZ_BOVIN : 116- 133: krall EnMEglFlAVDEivDGGV ilesd YJC4_YEAST : 107- 123: iqtfv EsLDrcFtEVNEl-DLIF nwqtl B 2: 38.3276 6( 6) V-x(1,2)-E-x-D-[ILP]-x(2)-[NV]-x(3)-[ALV]-x(4)-[DEN]-[DE]-[FIMV]-x(2)-[ACGT]-[DEG]-x(3)-[ADES]-x-[NSV] Occurences: 6(6) AP17_RAT : 98- 127: eyfhn Vc-ElDLvfNfykVytvvDEMflAGeirEtS qtkvl AP17_YEAST : 103- 132: affgn Vc-ElDIvfNfykVymimDEMfiGGeiqEiS kdmll AP19_MOUSE : 98- 127: kyfgs Vc-ElDIifNfekAyfilDEFlmGGdvqDtS kksvl AP19_YEAST : 101- 130: tyfgn Vc-ElDIifNfskVydilNEMimCDgsiAeS srkev COPZ_BOVIN : 133- 163: ivdgg VilEsDPqqVvhrValrgEDVplTEqtvSqV lqsak YJC4_YEAST : 116- 145: rcfte Vn-ElDLifNwqtLesvlEEIvqGGmviEtN vnriv C 3: 36.0550 6( 6) Y-[KR]-[NRS]-x-[AI]-[DGST]-L-Y-F-x(4)-[DEST]-x(3)-[DNS]-[EN] Occurences: 6(6) AP17_RAT : 59- 77: nfkii YRRyAGLYFcicvDvndNN layle AP17_YEAST : 64- 82: stkli YRRyAGLYFvmgvDlldDE piylc AP19_MOUSE : 59- 77: dlkvv YKRyASLYFccaiEgqdNE litle AP19_YEAST : 61- 79: dhkvv YKRyASLYFivgmTpdvDN elltl COPZ_BOVIN : 69- 87: gltvv YKSsIDLYFyvigSsyeNE lmlmt YJC4_YEAST : 77- 95: diqii YKNyATLYFtfivDdqeSE laild D 4: 29.5671 6( 6) F-x-[AENS]-V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] Occurences: 6(6) AP17_RAT : 95- 105: vlney FhNVCEl-DLVF nfykv AP17_YEAST : 100- 110: vldaf FgNVCEl-DIVF nfykv AP19_MOUSE : 95- 105: lldky FgSVCEl-DIIF nfeka AP19_YEAST : 98- 108: tmdty FgNVCEl-DIIF nfskv COPZ_BOVIN : 122- 133: nmegl FlAVDEivDGGV ilesd YJC4_YEAST : 113- 123: sldrc FtEVNEl-DLIF nwqtl E 5: 27.0948 6( 6) F-x-[AENS]-V-x-E-[IL]-[DV]-x-[GIV]-x-[NV] Occurences: 6(6) AP17_RAT : 95- 106: vlney FhNVcELDlVfN fykvy AP17_YEAST : 100- 111: vldaf FgNVcELDiVfN fykvy AP19_MOUSE : 95- 106: lldky FgSVcELDiIfN fekay AP19_YEAST : 98- 109: tmdty FgNVcELDiIfN fskvy COPZ_BOVIN : 122- 133: nmegl FlAVdEIVdGgV ilesd YJC4_YEAST : 113- 124: sldrc FtEVnELDlIfN wqtle F 6: 23.1651 6( 6) V-[CDN]-E-x(1,2)-D-[GIL]-[GIV]-[FV] Occurences: 6(6) AP17_RAT : 98- 105: eyfhn VCEl-DLVF nfykv AP17_YEAST : 103- 110: affgn VCEl-DIVF nfykv AP19_MOUSE : 98- 105: kyfgs VCEl-DIIF nfeka AP19_YEAST : 101- 108: tyfgn VCEl-DIIF nfskv COPZ_BOVIN : 125- 133: glfla VDEivDGGV ilesd YJC4_YEAST : 116- 123: rcfte VNEl-DLIF nwqtl G 7: 22.7986 6( 6) F-x-[AENS]-V-x(3,4)-D-[GIL]-[GIV]-[FV] Occurences: 6(6) AP17_RAT : 95- 105: vlney FhNVcel-DLVF nfykv AP17_YEAST : 100- 110: vldaf FgNVcel-DIVF nfykv AP19_MOUSE : 95- 105: lldky FgSVcel-DIIF nfeka AP19_YEAST : 98- 108: tmdty FgNVcel-DIIF nfskv COPZ_BOVIN : 122- 133: nmegl FlAVdeivDGGV ilesd YJC4_YEAST : 113- 123: sldrc FtEVnel-DLIF nwqtl H 8: 20.6064 6( 6) Y-x(3)-A-x-L-x-[FL]-x(4)-[DET]-x(3)-[ADNS] Occurences: 6(6) AP17_RAT : 59- 76: nfkii YrryAgLyFcicvDvndN nlayl AP17_YEAST : 64- 81: stkli YrryAgLyFvmgvDlldD epiyl AP19_MOUSE : 59- 76: dlkvv YkryAsLyFccaiEgqdN elitl AP19_YEAST : 61- 78: dhkvv YkryAsLyFivgmTpdvD nellt COPZ_BOVIN : 11- 28: lqpsl YtvkAiLiLdndgDrlfA kyydd YJC4_YEAST : 77- 94: diqii YknyAtLyFtfivDdqeS elail I 9: 20.5004 6( 6) L-Y-F-x(4)-[DEST]-x(3)-[DNS]-[EN] Occurences: 6(6) AP17_RAT : 65- 77: rryag LYFcicvDvndNN layle AP17_YEAST : 70- 82: rryag LYFvmgvDlldDE piylc AP19_MOUSE : 65- 77: kryas LYFccaiEgqdNE litle AP19_YEAST : 67- 79: kryas LYFivgmTpdvDN elltl COPZ_BOVIN : 75- 87: kssid LYFyvigSsyeNE lmlmt YJC4_YEAST : 83- 95: knyat LYFtfivDdqeSE laild J 10: 16.8692 7( 6) L-x(0,2)-Y-F-x(1,3)-V-x(3)-[DEPS] Occurences: 7(6) AP17_RAT : 65- 75: rryag L--YFcicVdvnD nnlay AP17_RAT : 91- 102: nfvev LneYFhn-VcelD lvfnf AP17_YEAST : 70- 80: rryag L--YFvmgVdllD depiy AP19_MOUSE : 91- 102: ryvel LdkYFgs-VcelD iifnf AP19_YEAST : 67- 75: kryas L--YFi--VgmtP dvdne COPZ_BOVIN : 75- 83: kssid L--YFy--VigsS yenel YJC4_YEAST : 83- 93: knyat L--YFtfiVddqE selai K 11: 14.2241 6( 6) D-[DNQS]-E-x(2,3)-L Occurences: 6(6) AP17_RAT : 25- 31: ymqfd DDEkqkL ieevh AP17_YEAST : 80- 86: gvdll DDEpiyL chihl AP19_MOUSE : 75- 81: aiegq DNElitL elihr AP19_YEAST : 78- 84: mtpdv DNElltL eiihr COPZ_BOVIN : 56- 61: kthrt DSEia-L leglt COPZ_BOVIN : 56- 62: kthrt DSEialL egltv YJC4_YEAST : 91- 96: tfivd DQEse-L aildl L 12: 14.2110 7( 6) L-x(2)-[DNST]-x(2)-G-x(2,3)-L Occurences: 7(6) AP17_RAT : 6- 16: mirfi LiqNraGktrL akwym AP17_YEAST : 7- 17: avqfi LcfNkqGvvrL vrwfd AP19_MOUSE : 6- 16: mmrfm LlfSrqGklrL qkwyl AP19_YEAST : 8- 18: qlkyl LlvSrqGkirL kkwyt COPZ_BOVIN : 17- 26: tvkai LilDndGdr-L fakyy COPZ_BOVIN : 114- 123: vekra LleNmeGlf-L avdei YJC4_YEAST : 170- 179: skigr LtsTgfGsa-L qafaq M 13: 14.1720 8( 6) L-x(0,2)-L-E-x-[ILV] Occurences: 8(6) AP17_RAT : 78- 84: vndnn LayLEaI hnfve AP17_YEAST : 136- 140: iskdm L--LErL sildr AP19_MOUSE : 78- 84: gqdne LitLElI hryve AP19_YEAST : 81- 87: dvdne LltLEiI hrfve AP19_YEAST : 82- 87: vdnel Lt-LEiI hrfve COPZ_BOVIN : 61- 65: dseia L--LEgL tvvyk YJC4_YEAST : 30- 35: lpkqk Ll-LEqV yelis YJC4_YEAST : 31- 35: pkqkl L--LEqV yelis N 14: 12.0102 6( 6) E-x(3,4)-F-N Occurences: 6(6) AP17_RAT : 100- 106: fhnvc EldlvFN fykvy AP17_YEAST : 105- 111: fgnvc EldivFN fykvy AP19_MOUSE : 100- 106: fgsvc EldiiFN fekay AP19_YEAST : 103- 109: fgnvc EldiiFN fskvy COPZ_BOVIN : 45- 50: eqkaf Ekni-FN kthrt YJC4_YEAST : 118- 124: ftevn EldliFN wqtle O 15: 12.0102 7( 6) L-x(3,4)-E-x-I Occurences: 7(6) AP17_RAT : 78- 84: vndnn Layl-EaI hnfve AP17_YEAST : 78- 84: vmgvd Lldd-EpI ylchi AP19_MOUSE : 78- 84: gqdne Litl-ElI hryve AP19_YEAST : 81- 87: dvdne Lltl-EiI hrfve COPZ_BOVIN : 164- 171: tvsqv LqsakEqI kwsll YJC4_YEAST : 32- 39: kqkll LeqvyElI sqrns YJC4_YEAST : 128- 135: fnwqt LesvlEeI vqggm P 16: 12.0102 7( 6) D-x(5)-L-x(1,2)-L Occurences: 7(6) AP17_RAT : 72- 81: fcicv DvndnnLayL eaihn AP17_YEAST : 134- 143: qeisk DmllerLsiL drld AP19_MOUSE : 75- 83: aiegq DnelitLe-L ihryv AP19_YEAST : 76- 84: vgmtp DvdnelLt-L eiihr COPZ_BOVIN : 56- 65: kthrt DseialLegL tvvyk YJC4_YEAST : 24- 32: fytpv DlpkqkLl-L eqvye YJC4_YEAST : 90- 99: ftfiv DdqeseLaiL dliqt Q 17: 11.5102 8( 6) L-x(0,1)-L-x(2,3)-E Occurences: 8(6) AP17_RAT : 136- 142: vlkql LmLqslE AP17_YEAST : 78- 82: vmgvd L-Ldd-E piylc AP19_MOUSE : 140- 144: ieqad L-Lqe-E despr AP19_YEAST : 81- 85: dvdne L-Ltl-E iihrf COPZ_BOVIN : 114- 119: vekra L-LenmE glfla COPZ_BOVIN : 121- 127: enmeg LfLavdE ivdgg YJC4_YEAST : 57- 62: vtpps LlLsn-E nnnde YJC4_YEAST : 57- 62: vtpps L-LlsnE nnnde YJC4_YEAST : 58- 62: tppsl L-Lsn-E nnnde R 18: 11.5102 8( 6) L-x(2)-L-x(1,3)-L Occurences: 8(6) AP17_RAT : 132- 138: sqtkv LkqLlm-L qsle AP17_RAT : 135- 141: kvlkq LlmLqs-L e AP17_YEAST : 137- 143: skdml LerLsi-L drld AP17_YEAST : 140- 146: mller LsiLdr-L d AP19_MOUSE : 78- 83: gqdne LitLe--L ihryv AP19_YEAST : 4- 9: mtq LkyLl--L vsrqg COPZ_BOVIN : 94- 101: mlmtv LncLfdsL sqmlr YJC4_YEAST : 96- 101: dqese LaiLd--L iqtfv S 19: 11.5102 9( 6) L-x(2,3)-L-x(1,2)-L Occurences: 9(6) AP17_RAT : 132- 138: sqtkv LkqlLm-L qsle AP17_RAT : 132- 138: sqtkv Lkq-LlmL qsle AP17_RAT : 135- 141: kvlkq Llm-LqsL e AP17_YEAST : 136- 143: iskdm LlerLsiL drld AP17_YEAST : 137- 143: skdml Ler-LsiL drld AP17_YEAST : 140- 146: mller Lsi-LdrL d AP19_MOUSE : 78- 83: gqdne Lit-Le-L ihryv AP19_YEAST : 4- 9: mtq Lky-Ll-L vsrqg COPZ_BOVIN : 90- 97: enelm LmtvLncL fdsls YJC4_YEAST : 96- 101: dqese Lai-Ld-L iqtfv T 20: 11.5102 9( 6) D-x(0,1)-E-x(2,3)-L Occurences: 9(6) AP17_RAT : 25- 31: ymqfd DdEkqkL ieevh AP17_RAT : 26- 31: mqfdd D-EkqkL ieevh AP17_RAT : 115- 119: vytvv D-Emf-L ageir AP17_YEAST : 80- 86: gvdll DdEpiyL chihl AP17_YEAST : 81- 86: vdlld D-EpiyL chihl AP19_MOUSE : 75- 81: aiegq DnElitL elihr AP19_YEAST : 78- 84: mtpdv DnElltL eiihr COPZ_BOVIN : 56- 61: kthrt DsEia-L leglt COPZ_BOVIN : 56- 62: kthrt DsEialL egltv YJC4_YEAST : 91- 96: tfivd DqEse-L aildl Number of patterns evaluated by Pratt:876 Total running time: 0 seconds