------------------------------------------------------------ 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 5 sequences from file YEDF PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 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 YEDF.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: Y242_HAEIN 73 YEDF_ECOLI 77 YEED_ECOLI 75 YHHP_ECOLI 81 YHHP_HAEIN 79 Pratt run started at Thu Feb 6 21:36:07 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.5102 5( 5) C-P-x-P 2: 11.0102 6( 5) P-x(2,4)-L-x(2,3)-K 3: 10.5102 5( 5) L-x(1,3)-E-x(1,3)-V 4: 10.5102 7( 5) L-x(1,3)-K-x(2,4)-L 5: 10.5102 6( 5) P-x(1,3)-L-x(1,3)-K 6: 8.3401 7( 5) E-x(5)-A 7: 8.3401 6( 5) L-I 8: 8.3401 7( 5) L-D 9: 8.3401 5( 5) I-P 10: 8.3401 6( 5) P-x-P 11: 7.8401 10( 5) E-x(1,2)-V 12: 7.8401 7( 5) E-x(3,4)-L 13: 7.8401 6( 5) L-x(0,1)-V 14: 7.8401 9( 5) E-x(4,5)-A 15: 7.8401 11( 5) L-x(1,2)-A 16: 7.8401 9( 5) L-x(2,3)-E 17: 7.8401 7( 5) L-x(1,2)-I 18: 7.8401 6( 5) E-x(0,1)-L 19: 7.8401 8( 5) D-x(1,2)-L 20: 7.8401 10( 5) L-x(3,4)-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 77.7222 5( 5) C-P-x-P-[ALV]-[ILMV]-x-[ATV]-x(2)-[ANT]-[ILMV]-x(2)-[LM]-x(2)-[GN]-[DE]-x-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] B 2: 73.5522 5( 5) P-x-P-[ALV]-[ILMV]-x-[ATV]-x(2)-[ANT]-[ILMV]-x(2)-[LM]-x(2)-[GN]-[DE]-x-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] C 3: 46.2241 5( 5) E-x(0,1)-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] D 4: 43.8310 5( 5) L-D-x(2)-[DGNQT]-x(3)-[LP]-x-[LP]-x-[ILMV]-x-[ASTV]-x(2)-[AENT]-x(3)-[ILM]-x(2)-[EG]-[DE]-x(3)-[AIV]-x(2)-[DE]-x(3)-[AST]-x-[ENR] E 5: 21.8996 7( 5) L-x(3,4)-D-x-[ANPT]-[ADQT]-[AEST]-x(3)-I-[LP] F 6: 18.5288 5( 5) I-P-x(2)-[ACS]-x(3)-[ADEG]-x(4)-[ADQ]-x-[ENQ] G 7: 17.9236 6( 5) L-x(1,2)-A-[DKR]-x(2)-[AGL]-x-[ENT]-x(4)-[DGQS] H 8: 15.8790 5( 5) E-x(5)-A-x-[ADE]-[ANPT]-x(2)-[AQT] I 9: 15.3790 5( 5) E-x(4,5)-A-x-[ADE]-[ANPT]-x(2)-[AQT] J 10: 13.1721 6( 5) P-x(1,3)-L-x(1,3)-K-[AGN] K 11: 12.9044 5( 5) D-x(1,2)-L-x-[ILM]-x(2)-[DENP] L 12: 12.7027 7( 5) L-x(1,2)-I-x(4)-[APST]-[AQT] M 13: 11.0102 6( 5) P-x(2,4)-L-x(2,3)-K N 14: 10.5102 5( 5) L-x(1,3)-E-x(1,3)-V O 15: 10.5102 7( 5) L-x(1,3)-K-x(2,4)-L P 16: 8.3401 6( 5) L-I Q 17: 7.8401 10( 5) E-x(1,2)-V R 18: 7.8401 7( 5) E-x(3,4)-L S 19: 7.8401 6( 5) L-x(0,1)-V T 20: 7.8401 9( 5) L-x(2,3)-E Best patterns with alignments: fitness hits(seqs) Pattern A 1: 77.7222 5( 5) C-P-x-P-[ALV]-[ILMV]-x-[ATV]-x(2)-[ANT]-[ILMV]-x(2)-[LM]-x(2)-[GN]-[DE]-x-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] Occurrences: 5(5) Y242_HAEIN : 12- 58: ltalr CPiPLLsAkkALknLdkNDeLmLilNlESAvENFSifAeenSvALvE qyyas YEDF_ECOLI : 17- 63: mvgep CPyPAVaTleAMpqLkkGEiLeVvsDcPQSiNNIPldArnhGyTVlD iqqdg YEED_ECOLI : 13- 59: vvtqv CPfPLIeAkaALaeMvsGDeLvIefDcTQAtEAIPqwAaeeGhAItD yqqig YHHP_ECOLI : 19- 65: alglr CPePVMmVrkTVrnMqpGEtLlIiaDdPATtRDIPgfCtfmEhELvA ketdg YHHP_HAEIN : 17- 63: tlglr CPePVMlVrkNIrhLndGEiLlIiaDdPATtRDIPsfCqfmDhTLlQ cevek B 2: 73.5522 5( 5) P-x-P-[ALV]-[ILMV]-x-[ATV]-x(2)-[ANT]-[ILMV]-x(2)-[LM]-x(2)-[GN]-[DE]-x-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] Occurrences: 5(5) Y242_HAEIN : 13- 58: talrc PiPLLsAkkALknLdkNDeLmLilNlESAvENFSifAeenSvALvE qyyas YEDF_ECOLI : 18- 63: vgepc PyPAVaTleAMpqLkkGEiLeVvsDcPQSiNNIPldArnhGyTVlD iqqdg YEED_ECOLI : 14- 59: vtqvc PfPLIeAkaALaeMvsGDeLvIefDcTQAtEAIPqwAaeeGhAItD yqqig YHHP_ECOLI : 20- 65: lglrc PePVMmVrkTVrnMqpGEtLlIiaDdPATtRDIPgfCtfmEhELvA ketdg YHHP_HAEIN : 18- 63: lglrc PePVMlVrkNIrhLndGEiLlIiaDdPATtRDIPsfCqfmDhTLlQ cevek C 3: 46.2241 5( 5) E-x(0,1)-L-x-[ILV]-x(2)-[DN]-x-[EPT]-[AQS]-[AST]-x-[ENR]-[ADN]-[FI]-[PS]-x(2)-[AC]-x(3)-[DEGS]-x-[AET]-[ILV]-x-[ADEQ] Occurrences: 5(5) Y242_HAEIN : 31- 58: ldknd E-LmLilNlESAvENFSifAeenSvALvE qyyas YEDF_ECOLI : 35- 63: qlkkg EiLeVvsDcPQSiNNIPldArnhGyTVlD iqqdg YEED_ECOLI : 32- 59: mvsgd E-LvIefDcTQAtEAIPqwAaeeGhAItD yqqig YHHP_ECOLI : 37- 65: nmqpg EtLlIiaDdPATtRDIPgfCtfmEhELvA ketdg YHHP_HAEIN : 35- 63: hlndg EiLlIiaDdPATtRDIPsfCqfmDhTLlQ cevek D 4: 43.8310 5( 5) L-D-x(2)-[DGNQT]-x(3)-[LP]-x-[LP]-x-[ILMV]-x-[ASTV]-x(2)-[AENT]-x(3)-[ILM]-x(2)-[EG]-[DE]-x(3)-[AIV]-x(2)-[DE]-x(3)-[AST]-x-[ENR] Occurrences: 5(5) Y242_HAEIN : 26- 64: kalkn LDknDelmLiLnLeSavEnfsIfaEEnsvAlvEqyyAsE kefiv YEDF_ECOLI : 10- 48: vpdyr LDmvGepcPyPaVaTleAmpqLkkGEileVvsDcpqSiN nipld YEED_ECOLI : 6- 44: mvikk LDvvTqvcPfPlIeAkaAlaeMvsGDelvIefDctqAtE aipqw YHHP_ECOLI : 12- 50: spdht LDalGlrcPePvMmVrkTvrnMqpGEtllIiaDdpaTtR dipgf YHHP_HAEIN : 10- 48: svtqt LDtlGlrcPePvMlVrkNirhLndGEillIiaDdpaTtR dipsf E 5: 21.8996 7( 5) L-x(3,4)-D-x-[ANPT]-[ADQT]-[AEST]-x(3)-I-[LP] Occurrences: 7(5) Y242_HAEIN : 23- 36: sakka Lknl-DkNDElmlIL nlesa YEDF_ECOLI : 37- 51: kkgei LevvsDcPQSinnIP ldarn YEED_ECOLI : 33- 47: vsgde LviefDcTQAteaIP qwaae YHHP_ECOLI : 39- 53: qpget LliiaDdPATtrdIP gfctf YHHP_ECOLI : 40- 53: pgetl Liia-DdPATtrdIP gfctf YHHP_HAEIN : 37- 51: ndgei LliiaDdPATtrdIP sfcqf YHHP_HAEIN : 38- 51: dgeil Liia-DdPATtrdIP sfcqf F 6: 18.5288 5( 5) I-P-x(2)-[ACS]-x(3)-[ADEG]-x(4)-[ADQ]-x-[ENQ] Occurrences: 5(5) Y242_HAEIN : 14- 29: alrcp IPllSakkAlknlDkN delml YEDF_ECOLI : 50- 65: qsinn IPldArnhGytvlDiQ qdgpt YEED_ECOLI : 46- 61: qatea IPqwAaeeGhaitDyQ qigda YHHP_ECOLI : 52- 67: attrd IPgfCtfmEhelvAkE tdglp YHHP_HAEIN : 50- 65: attrd IPsfCqfmDhtllQcE vekpp G 7: 17.9236 6( 5) L-x(1,2)-A-[DKR]-x(2)-[AGL]-x-[ENT]-x(4)-[DGQS] Occurrences: 6(5) Y242_HAEIN : 16- 30: rcpip LlsAKkaLkNldknD elmli Y242_HAEIN : 17- 30: cpipl Ls-AKkaLkNldknD elmli YEDF_ECOLI : 52- 65: innip Ld-ARnhGyTvldiQ qdgpt YEED_ECOLI : 17- 31: vcpfp LieAKaaLaEmvsgD elvie YHHP_ECOLI : 40- 54: pgetl LiiADdpAtTrdipG fctfm YHHP_HAEIN : 38- 52: dgeil LiiADdpAtTrdipS fcqfm H 8: 15.8790 5( 5) E-x(5)-A-x-[ADE]-[ANPT]-x(2)-[AQT] Occurrences: 5(5) Y242_HAEIN : 43- 55: lesav EnfsifAeENsvA lveqy YEDF_ECOLI : 15- 27: ldmvg EpcpypAvATleA mpqlk YEED_ECOLI : 36- 48: delvi EfdctqAtEAipQ waaee YHHP_ECOLI : 37- 49: nmqpg EtlliiAdDPatT rdipg YHHP_HAEIN : 35- 47: hlndg EilliiAdDPatT rdips I 9: 15.3790 5( 5) E-x(4,5)-A-x-[ADE]-[ANPT]-x(2)-[AQT] Occurrences: 5(5) Y242_HAEIN : 43- 55: lesav EnfsifAeENsvA lveqy YEDF_ECOLI : 15- 27: ldmvg EpcpypAvATleA mpqlk YEED_ECOLI : 36- 48: delvi EfdctqAtEAipQ waaee YHHP_ECOLI : 37- 49: nmqpg EtlliiAdDPatT rdipg YHHP_HAEIN : 35- 47: hlndg EilliiAdDPatT rdips J 10: 13.1721 6( 5) P-x(1,3)-L-x(1,3)-K-[AGN] Occurrences: 6(5) Y242_HAEIN : 13- 22: talrc PiplLsakKA lknld Y242_HAEIN : 15- 22: lrcpi Pl--LsakKA lknld YEDF_ECOLI : 29- 34: tleam Pq--Lk--KG eilev YEED_ECOLI : 14- 22: vtqvc Pfp-LieaKA alaem YHHP_ECOLI : 72- 80: etdgl PyryLir-KG g YHHP_HAEIN : 20- 27: lrcpe Pvm-Lvr-KN irhln K 11: 12.9044 5( 5) D-x(1,2)-L-x-[ILM]-x(2)-[DENP] Occurrences: 5(5) Y242_HAEIN : 30- 37: nldkn De-LmLilN lesav YEDF_ECOLI : 7- 15: knivp DyrLdMvgE pcpyp YEED_ECOLI : 31- 38: emvsg De-LvIefD ctqat YHHP_ECOLI : 13- 20: pdhtl Da-LgLrcP epvmm YHHP_HAEIN : 11- 18: vtqtl Dt-LgLrcP epvml L 12: 12.7027 7( 5) L-x(1,2)-I-x(4)-[APST]-[AQT] Occurrences: 7(5) Y242_HAEIN : 32- 41: dknde LmlIlnleSA venfs YEDF_ECOLI : 62- 70: hgytv Ld-IqqdgPT iryli YEED_ECOLI : 33- 41: vsgde Lv-IefdcTQ ateai YHHP_ECOLI : 39- 47: qpget Ll-IiaddPA ttrdi YHHP_ECOLI : 39- 48: qpget LliIaddpAT trdip YHHP_ECOLI : 40- 48: pgetl Li-IaddpAT trdip YHHP_HAEIN : 37- 45: ndgei Ll-IiaddPA ttrdi YHHP_HAEIN : 37- 46: ndgei LliIaddpAT trdip YHHP_HAEIN : 38- 46: dgeil Li-IaddpAT trdip M 13: 11.0102 6( 5) P-x(2,4)-L-x(2,3)-K Occurrences: 6(5) Y242_HAEIN : 13- 20: talrc Pipl-Lsa-K kalkn Y242_HAEIN : 13- 20: talrc Pip--LlsaK kalkn Y242_HAEIN : 13- 21: talrc Pipl-LsakK alknl YEDF_ECOLI : 69- 77: iqqdg PtiryLiq-K YEED_ECOLI : 14- 21: vtqvc Pfp--LieaK aalae YHHP_ECOLI : 72- 79: etdgl Pyry-Lir-K gg YHHP_HAEIN : 18- 26: lglrc PepvmLvr-K nirhl YHHP_HAEIN : 20- 26: lrcpe Pvm--Lvr-K nirhl N 14: 10.5102 5( 5) L-x(1,3)-E-x(1,3)-V Occurrences: 5(5) Y242_HAEIN : 36- 42: elmli Lnl-Esa-V enfsi YEDF_ECOLI : 31- 39: eampq LkkgEileV vsdcp YEED_ECOLI : 24- 28: eakaa La--Em--V sgdel YHHP_ECOLI : 17- 23: ldalg LrcpEp--V mmvrk YHHP_HAEIN : 15- 21: ldtlg LrcpEp--V mlvrk O 15: 10.5102 7( 5) L-x(1,3)-K-x(2,4)-L Occurrences: 7(5) Y242_HAEIN : 16- 23: rcpip LlsaKka--L knldk Y242_HAEIN : 17- 23: cpipl Lsa-Kka--L knldk Y242_HAEIN : 17- 26: cpipl LsakKalknL dknde Y242_HAEIN : 26- 32: kalkn Ld--Knde-L mliln YEDF_ECOLI : 31- 37: eampq Lk--Kgei-L evvsd YEED_ECOLI : 17- 24: vcpfp LieaKaa--L aemvs YHHP_ECOLI : 63- 71: fmehe Lva-KetdgL pyryl YHHP_HAEIN : 23- 31: pepvm Lvr-KnirhL ndgei P 16: 8.3401 6( 5) L-I Occurrences: 6(5) Y242_HAEIN : 34- 35: ndelm LI lnles YEDF_ECOLI : 74- 75: ptiry LI qk YEED_ECOLI : 17- 18: vcpfp LI eakaa YHHP_ECOLI : 40- 41: pgetl LI iaddp YHHP_ECOLI : 76- 77: lpyry LI rkgg YHHP_HAEIN : 38- 39: dgeil LI iaddp Q 17: 7.8401 10( 5) E-x(1,2)-V Occurrences: 10(5) Y242_HAEIN : 39- 42: lilnl EsaV enfsi Y242_HAEIN : 51- 54: sifae EnsV alveq Y242_HAEIN : 66- 69: yasek EfiV ilkk YEDF_ECOLI : 38- 40: kgeil Ev-V sdcpq YEED_ECOLI : 26- 28: kaala Em-V sgdel YEED_ECOLI : 32- 34: mvsgd El-V iefdc YHHP_ECOLI : 21- 23: glrcp Ep-V mmvrk YHHP_ECOLI : 62- 64: tfmeh El-V aketd YHHP_HAEIN : 3- 6: ms EisV tqtld YHHP_HAEIN : 19- 21: glrcp Ep-V mlvrk R 18: 7.8401 7( 5) E-x(3,4)-L Occurrences: 7(5) Y242_HAEIN : 31- 36: ldknd ElmliL nlesa Y242_HAEIN : 51- 56: sifae EnsvaL veqyy Y242_HAEIN : 66- 71: yasek EfiviL kk YEDF_ECOLI : 26- 31: avatl EampqL kkgei YEED_ECOLI : 19- 24: pfpli EakaaL aemvs YHHP_ECOLI : 67- 71: elvak Etdg-L pyryl YHHP_HAEIN : 19- 23: glrcp Epvm-L vrkni S 19: 7.8401 6( 5) L-x(0,1)-V Occurrences: 6(5) Y242_HAEIN : 56- 57: ensva L-V eqyya YEDF_ECOLI : 37- 39: kkgei LeV vsdcp YEED_ECOLI : 6- 8: mvikk LdV vtqvc YEED_ECOLI : 33- 34: vsgde L-V iefdc YHHP_ECOLI : 63- 64: fmehe L-V aketd YHHP_HAEIN : 23- 24: pepvm L-V rknir T 20: 7.8401 9( 5) L-x(2,3)-E Occurrences: 9(5) Y242_HAEIN : 36- 39: elmli Lnl-E saven YEDF_ECOLI : 31- 35: eampq LkkgE ilevv YEED_ECOLI : 33- 36: vsgde Lvi-E fdctq YHHP_ECOLI : 17- 21: ldalg LrcpE pvmmv YHHP_ECOLI : 63- 67: fmehe LvakE tdglp YHHP_HAEIN : 15- 19: ldtlg LrcpE pvmlv YHHP_HAEIN : 31- 35: knirh LndgE illii YHHP_HAEIN : 61- 65: fmdht LlqcE vekpp YHHP_HAEIN : 62- 65: mdhtl Lqc-E vekpp Number of patterns evaluated by Pratt:95 Total running time: 1 seconds