------------------------------------------------------------ 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 MIF 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 MIF.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: DOPD_HUMAN 11 DOPD_RAT 117 MIF_BOVIN 114 MIF_CHICK 114 MIF_HUMAN 114 MIF_MOUSE 114 MIF_RAT 115 Pratt run started at Thu Feb 6 20:17:25 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.6802 7( 7) E-L-x(0,1)-T-x(1,2)-L 2: 14.6802 9( 7) L-x(0,2)-E-L-x(1,3)-L 3: 12.0102 12( 7) T-x(2)-P-x(0,1)-A 4: 12.0102 9( 7) L-x(3)-L-x(1,2)-A 5: 11.5102 8( 7) T-N-x(2,4)-A 6: 11.5102 10( 7) L-x(0,1)-T-x(1,2)-L 7: 11.5102 8( 7) L-x(1,3)-T-x(2)-P 8: 11.5102 9( 7) L-x(0,1)-E-x(0,1)-L 9: 11.5102 8( 7) G-x(0,2)-L-x(3)-L 10: 11.0102 11( 7) G-x(0,1)-L-x(1,3)-L 11: 7.8401 17( 7) P-x(0,1)-A 12: 7.8401 10( 7) L-x(1,2)-A 13: 7.8401 7( 7) N-x(1,2)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 20.9744 7( 7) L-[DET]-[QT]-[NQ]-L-x(1,2)-A B 2: 19.3489 7( 7) L-x(0,1)-E-x(0,1)-L-[DST]-x-[DNQ]-x-[ADP] C 3: 18.9013 7( 7) E-L-x(0,1)-T-x(1,2)-L-[AP] D 4: 18.5910 7( 7) G-x(0,1)-L-x(1,3)-L-[ACDT]-x-[ANQ]-x-[AGP] E 5: 18.0044 8( 7) L-x(1,3)-T-[GN]-x-P-[AP] F 6: 17.8479 7( 7) G-x(0,2)-L-[ADEST]-[DENQT]-[NQR]-L G 7: 17.3249 9( 7) L-x(0,2)-E-L-x(1,3)-L-[ADP] H 8: 15.2832 11( 7) T-[GN]-x-P-x(0,1)-A I 9: 14.7313 7( 7) L-x(0,1)-T-x(1,2)-L-[AP] J 10: 11.5102 8( 7) T-N-x(2,4)-A K 11: 7.8401 17( 7) P-x(0,1)-A L 12: 7.8401 10( 7) L-x(1,2)-A M 13: 7.8401 7( 7) N-x(1,2)-A N 14: 7.3401 1( 1) L-x(0,2)-E O 15: 7.3401 8( 7) L-x(1,3)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 20.9744 7( 7) L-[DET]-[QT]-[NQ]-L-x(1,2)-A Occurences: 7(7) DOPD_HUMAN : 5- 11: xgle LDTNLp-A DOPD_RAT : 5- 11: pfve LETNLp-A sripa MIF_BOVIN : 22- 29: gllse LTQQLaqA tgkpa MIF_CHICK : 22- 29: sllge LTQQLakA tgkpa MIF_HUMAN : 22- 29: gflse LTQQLaqA tgkpp MIF_MOUSE : 22- 29: gflse LTQQLaqA tgkpa MIF_RAT : 23- 30: gflse LTQQLaqA tgkpa B 2: 19.3489 7( 7) L-x(0,1)-E-x(0,1)-L-[DST]-x-[DNQ]-x-[ADP] Occurences: 7(7) DOPD_HUMAN : 3- 10: xg L-E-LDtNlP a DOPD_RAT : 84- 93: sffkf LtEeLSlDqD riiir MIF_BOVIN : 19- 27: vpdgl LsE-LTqQlA qatgk MIF_CHICK : 19- 27: vpdsl LgE-LTqQlA katgk MIF_HUMAN : 19- 27: vpdgf LsE-LTqQlA qatgk MIF_MOUSE : 19- 27: vpegf LsE-LTqQlA qatgk MIF_RAT : 20- 28: vpegf LsE-LTqQlA qatgk C 3: 18.9013 7( 7) E-L-x(0,1)-T-x(1,2)-L-[AP] Occurences: 7(7) DOPD_HUMAN : 4- 10: xgl ELdTn-LP a DOPD_RAT : 4- 10: pfv ELeTn-LP asrip MIF_BOVIN : 21- 27: dglls EL-TqqLA qatgk MIF_CHICK : 21- 27: dsllg EL-TqqLA katgk MIF_HUMAN : 21- 27: dgfls EL-TqqLA qatgk MIF_MOUSE : 21- 27: egfls EL-TqqLA qatgk MIF_RAT : 22- 28: egfls EL-TqqLA qatgk D 4: 18.5910 7( 7) G-x(0,1)-L-x(1,3)-L-[ACDT]-x-[ANQ]-x-[AGP] Occurences: 7(7) DOPD_HUMAN : 2- 10: x G-Le--LDtNlP a DOPD_RAT : 17- 27: sripa G-LenrLCaAtA tildk MIF_BOVIN : 17- 27: asvpd GlLse-LTqQlA qatgk MIF_BOVIN : 17- 27: asvpd G-LlseLTqQlA qatgk MIF_CHICK : 20- 31: pdsll GeLtqqLAkAtG kpaqy MIF_HUMAN : 17- 27: asvpd GfLse-LTqQlA qatgk MIF_MOUSE : 17- 27: asvpe GfLse-LTqQlA qatgk MIF_RAT : 18- 28: asvpe GfLse-LTqQlA qatgk E 5: 18.0044 8( 7) L-x(1,3)-T-[GN]-x-P-[AP] Occurences: 8(7) DOPD_HUMAN : 3- 11: xg LeldTNlPA DOPD_HUMAN : 5- 11: xgle Ld--TNlPA DOPD_RAT : 5- 11: pfve Le--TNlPA sripa MIF_BOVIN : 26- 34: eltqq LaqaTGkPA qyiav MIF_CHICK : 26- 34: eltqq LakaTGkPA qyiav MIF_HUMAN : 26- 34: eltqq LaqaTGkPP qyiav MIF_MOUSE : 26- 34: eltqq LaqaTGkPA qyiav MIF_RAT : 27- 35: eltqq LaqaTGkPA qyiav F 6: 17.8479 7( 7) G-x(0,2)-L-[ADEST]-[DENQT]-[NQR]-L Occurences: 7(7) DOPD_HUMAN : 2- 9: x GleLDTNL pa DOPD_RAT : 17- 22: sripa G--LENRL caata MIF_BOVIN : 81- 87: skllc Gl-LTERL rispd MIF_CHICK : 20- 26: pdsll Ge-LTQQL akatg MIF_HUMAN : 81- 87: skllc Gl-LAERL rispd MIF_MOUSE : 81- 87: skllc Gl-LSDRL hispd MIF_RAT : 82- 88: skllc Gl-LSDRL hispd G 7: 17.3249 9( 7) L-x(0,2)-E-L-x(1,3)-L-[ADP] Occurences: 9(7) DOPD_HUMAN : 3- 10: xg L--ELdtnLP a DOPD_RAT : 84- 91: sffkf LteELs--LD qdrii MIF_BOVIN : 18- 27: svpdg LlsELtqqLA qatgk MIF_BOVIN : 19- 27: vpdgl Ls-ELtqqLA qatgk MIF_CHICK : 18- 27: avpds LlgELtqqLA katgk MIF_CHICK : 19- 27: vpdsl Lg-ELtqqLA katgk MIF_HUMAN : 19- 27: vpdgf Ls-ELtqqLA qatgk MIF_MOUSE : 19- 27: vpegf Ls-ELtqqLA qatgk MIF_RAT : 20- 28: vpegf Ls-ELtqqLA qatgk H 8: 15.2832 11( 7) T-[GN]-x-P-x(0,1)-A Occurences: 11(7) DOPD_HUMAN : 7- 11: gleld TNlP-A DOPD_RAT : 7- 11: fvele TNlP-A sripa MIF_BOVIN : 7- 12: mfvvn TNvPrA svpdg MIF_BOVIN : 30- 34: qlaqa TGkP-A qyiav MIF_CHICK : 30- 34: qlaka TGkP-A qyiav MIF_HUMAN : 7- 12: mfivn TNvPrA svpdg MIF_MOUSE : 7- 12: mfivn TNvPrA svpeg MIF_MOUSE : 30- 34: qlaqa TGkP-A qyiav MIF_MOUSE : 52- 57: mtfsg TNdPcA lcslh MIF_RAT : 8- 13: mfivn TNvPrA svpeg MIF_RAT : 31- 35: qlaqa TGkP-A qyiav I 9: 14.7313 7( 7) L-x(0,1)-T-x(1,2)-L-[AP] Occurences: 7(7) DOPD_HUMAN : 5- 10: xgle LdTn-LP a DOPD_RAT : 5- 10: pfve LeTn-LP asrip MIF_BOVIN : 22- 27: gllse L-TqqLA qatgk MIF_CHICK : 22- 27: sllge L-TqqLA katgk MIF_HUMAN : 22- 27: gflse L-TqqLA qatgk MIF_MOUSE : 22- 27: gflse L-TqqLA qatgk MIF_RAT : 23- 28: gflse L-TqqLA qatgk J 10: 11.5102 8( 7) T-N-x(2,4)-A Occurences: 8(7) DOPD_HUMAN : 7- 11: gleld TNlp--A DOPD_RAT : 7- 11: fvele TNlp--A sripa MIF_BOVIN : 7- 12: mfvvn TNvpr-A svpdg MIF_CHICK : 7- 13: mftih TNvckdA vpdsl MIF_HUMAN : 7- 12: mfivn TNvpr-A svpdg MIF_MOUSE : 7- 12: mfivn TNvpr-A svpeg MIF_MOUSE : 52- 57: mtfsg TNdpc-A lcslh MIF_RAT : 8- 13: mfivn TNvpr-A svpeg K 11: 7.8401 17( 7) P-x(0,1)-A Occurences: 17(7) DOPD_HUMAN : 10- 11: ldtnl P-A DOPD_RAT : 10- 11: letnl P-A sripa DOPD_RAT : 15- 16: pasri P-A glenr DOPD_RAT : 55- 57: nkste PcA hllis MIF_BOVIN : 10- 12: vntnv PrA svpdg MIF_BOVIN : 33- 34: qatgk P-A qyiav MIF_BOVIN : 55- 57: ggsse PcA lcslh MIF_CHICK : 33- 34: katgk P-A qyiav MIF_CHICK : 55- 57: ggstd PcA lcsly MIF_HUMAN : 10- 12: vntnv PrA svpdg MIF_HUMAN : 55- 57: ggsse PcA lcslh MIF_MOUSE : 10- 12: vntnv PrA svpeg MIF_MOUSE : 33- 34: qatgk P-A qyiav MIF_MOUSE : 55- 57: sgtnd PcA lcslh MIF_RAT : 11- 13: vntnv PrA svpeg MIF_RAT : 34- 35: qatgk P-A qyiav MIF_RAT : 56- 58: sgtsd PcA lcslh L 12: 7.8401 10( 7) L-x(1,2)-A Occurences: 10(7) DOPD_HUMAN : 9- 11: eldtn Lp-A DOPD_RAT : 9- 11: eletn Lp-A sripa DOPD_RAT : 22- 24: glenr Lc-A atati DOPD_RAT : 22- 25: glenr LcaA tatil MIF_BOVIN : 26- 29: eltqq LaqA tgkpa MIF_CHICK : 26- 29: eltqq LakA tgkpa MIF_HUMAN : 26- 29: eltqq LaqA tgkpp MIF_HUMAN : 46- 48: vvpdq Lm-A fggss MIF_HUMAN : 82- 84: kllcg Ll-A erlri MIF_MOUSE : 26- 29: eltqq LaqA tgkpa MIF_RAT : 27- 30: eltqq LaqA tgkpa M 13: 7.8401 7( 7) N-x(1,2)-A Occurences: 7(7) DOPD_HUMAN : 8- 11: leldt NlpA DOPD_RAT : 8- 11: velet NlpA sripa MIF_BOVIN : 102- 104: nfcdm Na-A nvgwn MIF_CHICK : 102- 104: nyfdi Na-A nvgwn MIF_HUMAN : 102- 104: nyydm Na-A nvgwn MIF_MOUSE : 102- 104: nyydm Na-A nvgwn MIF_RAT : 103- 105: nyydm Na-A nvgwn N 14: 7.3401 1( 1) L-x(0,2)-E Occurences: 1(1) DOPD_RAT : 84- 87: sffkf LteE lsldq O 15: 7.3401 8( 7) L-x(1,3)-T Occurences: 8(7) DOPD_HUMAN : 3- 7: xg LeldT nlpa DOPD_HUMAN : 5- 7: xgle Ld--T nlpa DOPD_RAT : 5- 7: pfve Le--T nlpas MIF_BOVIN : 26- 30: eltqq LaqaT gkpaq MIF_CHICK : 26- 30: eltqq LakaT gkpaq MIF_HUMAN : 26- 30: eltqq LaqaT gkppq MIF_MOUSE : 26- 30: eltqq LaqaT gkpaq MIF_RAT : 27- 31: eltqq LaqaT gkpaq Number of patterns evaluated by Pratt:42 Total running time: 0 seconds