------------------------------------------------------------ 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 16 sequences from file RIBOSOMAL_L33 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 16 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 RIBOSOMAL_L33.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL33_BACLI 49 RL33_BACST 49 RL33_BACSU 49 RL33_CYAPA 64 RL33_ECOLI 54 RL33_EPIVI 66 RL33_HAEIN 56 RL33_LACLA 48 RL33_MAIZE 65 RL33_MARPO 64 RL33_ORYSA 65 RL33_PINTH 67 RL33_SPIOL 50 RL33_THEMA 49 RL33_THETH 54 RL33_TOBAC 65 Pratt run started at Thu Feb 6 21:05:58 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 25( 16) E-x(2)-K 2: 8.3401 17( 16) Y-x(4)-N 3: 7.8401 28( 16) T-x(1,2)-K 4: 7.8401 30( 16) E-x(0,1)-K 5: 7.8401 36( 16) K-x(0,1)-K 6: 7.8401 18( 16) Y-x(3,4)-K 7: 7.3401 25( 16) R-x(0,2)-V 8: 7.3401 33( 16) T-x(1,3)-K Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 18.5228 16( 16) Y-x(3,4)-K-[DNS]-x(2)-[ANST]-x-[ALP]-x(3)-[EK] B 2: 13.7321 16( 16) Y-x-[NPST]-x(2)-N-x(2)-[NT] C 3: 11.5246 16( 16) E-x(2)-K-[FY] D 4: 9.4973 24( 16) K-x(0,1)-K-x-[ACDNTV] E 5: 7.8401 28( 16) T-x(1,2)-K F 6: 7.8401 30( 16) E-x(0,1)-K G 7: 7.3401 25( 16) R-x(0,2)-V H 8: 7.3401 33( 16) T-x(1,3)-K Best patterns with alignements: fitness hits(seqs) Pattern A 1: 18.5228 16( 16) Y-x(3,4)-K-[DNS]-x(2)-[ANST]-x-[ALP]-x(3)-[EK] Occurences: 16(16) RL33_BACLI : 17- 31: cgsrn Yttm-KSsaAlAerlE vkkyc RL33_BACST : 17- 31: cgern Yits-KNkrNnPerlE lkkyc RL33_BACSU : 17- 31: cgnrn Yttm-KSsaSaAerlE vkkyc RL33_CYAPA : 32- 46: ggvsr Yatk-KNrrNtPnrlE lnkfc RL33_ECOLI : 20- 34: gtghf Yttt-KNkrTkPeklE lkkfd RL33_EPIVI : 33- 47: tgisr Yitq-KNrrNtPnrlE lrkfc RL33_HAEIN : 22- 36: etghf Yttd-KNkrNmPekmE ikkfd RL33_LACLA : 17- 31: cgnkn Yiss-KNkaThPekvE tmkfc RL33_MAIZE : 32- 46: tgisr Ystq-KNrhNtPgqlE lrkfc RL33_MARPO : 31- 45: kgisr Yttq-KNrrNtPirlE lkkfc RL33_ORYSA : 32- 46: agisr Ystq-KNrhNtPgqlE lrkfc RL33_PINTH : 32- 46: pgisr Yttr-KNrrNtPirlE snkfc RL33_SPIOL : 32- 46: rgvsr Yitq-KNrhNtPcrlE lkkf RL33_THEMA : 18- 33: gnkny YttrnKDkrAkLelrK ycpkc RL33_THETH : 21- 35: ckrrn Yate-KNkrNtPnklE lrkyc RL33_TOBAC : 32- 46: rgisr Yitq-KNrhNtPnrlE lkkfc B 2: 13.7321 16( 16) Y-x-[NPST]-x(2)-N-x(2)-[NT] Occurences: 16(16) RL33_BACLI : 35- 43: levkk YcNncNshT vhlet RL33_BACST : 17- 25: cgern YiTskNkrN nperl RL33_BACSU : 35- 43: levkk YcStcNshT ahlet RL33_CYAPA : 32- 40: ggvsr YaTkkNrrN tpnrl RL33_ECOLI : 20- 28: gtghf YtTtkNkrT kpekl RL33_EPIVI : 33- 41: tgisr YiTqkNrrN tpnrl RL33_HAEIN : 22- 30: etghf YtTdkNkrN mpekm RL33_LACLA : 17- 25: cgnkn YiSskNkaT hpekv RL33_MAIZE : 32- 40: tgisr YsTqkNrhN tpgql RL33_MARPO : 31- 39: kgisr YtTqkNrrN tpirl RL33_ORYSA : 32- 40: agisr YsTqkNrhN tpgql RL33_PINTH : 32- 40: pgisr YtTrkNrrN tpirl RL33_SPIOL : 32- 40: rgvsr YiTqkNrhN tpcrl RL33_THEMA : 34- 42: lelrk YcPkcNahT ihtet RL33_THETH : 21- 29: ckrrn YaTekNkrN tpnkl RL33_TOBAC : 32- 40: rgisr YiTqkNrhN tpnrl C 3: 11.5246 16( 16) E-x(2)-K-[FY] Occurences: 16(16) RL33_BACLI : 31- 35: laerl EvkKY cnncn RL33_BACST : 31- 35: nperl ElkKY cprdr RL33_BACSU : 31- 35: aaerl EvkKY cstcn RL33_CYAPA : 46- 50: tpnrl ElnKF cpyck RL33_ECOLI : 34- 38: kpekl ElkKF dpvvr RL33_EPIVI : 47- 51: tpnrl ElrKF cpycy RL33_HAEIN : 36- 40: mpekm EikKF dpvvr RL33_LACLA : 31- 35: hpekv EtmKF cpker RL33_MAIZE : 46- 50: tpgql ElrKF crycr RL33_MARPO : 45- 49: tpirl ElkKF ccycn RL33_ORYSA : 46- 50: tpgql ElrKF crycr RL33_PINTH : 46- 50: tpirl EsnKF cpycy RL33_SPIOL : 46- 50: tpcrl ElkKF RL33_THEMA : 30- 34: krakl ElrKY cpkcn RL33_THETH : 35- 39: tpnkl ElrKY cpwcr RL33_TOBAC : 46- 50: tpnrl ElkKF cpycy D 4: 9.4973 24( 16) K-x(0,1)-K-x-[ACDNTV] Occurences: 24(16) RL33_BACLI : 2- 5: m K-KkV tlack RL33_BACLI : 2- 6: m KkKvT lackn RL33_BACLI : 3- 6: mk K-KvT lackn RL33_BACLI : 33- 36: erlev K-KyC nncns RL33_BACST : 21- 25: nyits KnKrN nperl RL33_BACST : 33- 36: erlel K-KyC prdrk RL33_BACSU : 3- 6: mr K-KiT lackt RL33_BACSU : 33- 36: erlev K-KyC stcns RL33_CYAPA : 55- 58: fcpyc K-KhV lhrei RL33_ECOLI : 7- 11: kgire KiKlV ssagt RL33_ECOLI : 24- 28: fyttt KnKrT kpekl RL33_ECOLI : 36- 39: eklel K-KfD pvvrq RL33_EPIVI : 3- 7: ma KsKdA rvavi RL33_HAEIN : 26- 30: fyttd KnKrN mpekm RL33_HAEIN : 38- 41: ekmei K-KfD pvvrk RL33_LACLA : 21- 25: nyiss KnKaT hpekv RL33_MAIZE : 2- 6: a KgKdV rirvi RL33_MARPO : 47- 50: irlel K-KfC cycnk RL33_ORYSA : 2- 6: a KgKdV rirvi RL33_PINTH : 64- 67: ihgei K-KrD RL33_SPIOL : 2- 6: a KgKdV rvkvi RL33_THEMA : 23- 27: yttrn KdKrA klelr RL33_THETH : 25- 29: nyate KnKrN tpnkl RL33_TOBAC : 2- 6: a KgKdV rvtvi RL33_TOBAC : 48- 51: nrlel K-KfC pycyk E 5: 7.8401 28( 16) T-x(1,2)-K Occurences: 28(16) RL33_BACLI : 18- 21: gsrny TtmK ssaal RL33_BACLI : 19- 21: srnyt Tm-K ssaal RL33_BACST : 19- 21: ernyi Ts-K nkrnn RL33_BACSU : 18- 21: gnrny TtmK ssasa RL33_BACSU : 19- 21: nrnyt Tm-K ssasa RL33_CYAPA : 34- 36: vsrya Tk-K nrrnt RL33_ECOLI : 21- 24: tghfy TttK nkrtk RL33_ECOLI : 22- 24: ghfyt Tt-K nkrtk RL33_ECOLI : 23- 26: hfytt TknK rtkpe RL33_EPIVI : 35- 37: isryi Tq-K nrrnt RL33_HAEIN : 23- 26: tghfy TtdK nkrnm RL33_HAEIN : 24- 26: ghfyt Td-K nkrnm RL33_LACLA : 32- 34: pekve Tm-K fcpke RL33_MAIZE : 22- 24: cvrkg Tn-K estgi RL33_MAIZE : 34- 36: isrys Tq-K nrhnt RL33_MARPO : 32- 35: gisry TtqK nrrnt RL33_MARPO : 33- 35: isryt Tq-K nrrnt RL33_MARPO : 57- 60: ycnkh TihK eikk RL33_ORYSA : 34- 36: isrys Tq-K nrhnt RL33_PINTH : 33- 36: gisry TtrK nrrnt RL33_PINTH : 34- 36: isryt Tr-K nrrnt RL33_SPIOL : 34- 36: vsryi Tq-K nrhnt RL33_THEMA : 20- 23: knyyt TrnK dkrak RL33_THEMA : 45- 48: ahtih TetK a RL33_THETH : 14- 17: lllec TecK rrnya RL33_THETH : 23- 25: rrnya Te-K nkrnt RL33_THETH : 30- 33: knkrn TpnK lelrk RL33_TOBAC : 34- 36: isryi Tq-K nrhnt F 6: 7.8401 30( 16) E-x(0,1)-K Occurences: 30(16) RL33_BACLI : 31- 33: laerl EvK kycnn RL33_BACLI : 47- 49: htvhl EtK RL33_BACST : 31- 33: nperl ElK kycpr RL33_BACST : 47- 49: vtlhr EtK RL33_BACSU : 31- 33: aaerl EvK kycst RL33_BACSU : 47- 49: htahl EtK RL33_CYAPA : 62- 64: hvlhr EiK RL33_ECOLI : 6- 7: akgir E-K iklvs RL33_ECOLI : 31- 32: krtkp E-K lelkk RL33_ECOLI : 34- 36: kpekl ElK kfdpv RL33_ECOLI : 50- 52: hviyk EaK ik RL33_EPIVI : 63- 65: hmihg EiK k RL33_HAEIN : 8- 9: akgar E-K irlvs RL33_HAEIN : 33- 34: krnmp E-K meikk RL33_HAEIN : 36- 38: mpekm EiK kfdpv RL33_HAEIN : 52- 54: hviyk EaK ik RL33_LACLA : 28- 29: kathp E-K vetmk RL33_MAIZE : 62- 64: htthn EiK k RL33_MARPO : 22- 23: caqnd E-K rkkgi RL33_MARPO : 45- 47: tpirl ElK kfccy RL33_MARPO : 61- 63: htihk EiK k RL33_ORYSA : 62- 64: htiha EiK k RL33_PINTH : 62- 64: htihg EiK krd RL33_SPIOL : 46- 48: tpcrl ElK kf RL33_THEMA : 46- 48: htiht EtK a RL33_THETH : 15- 17: llect EcK rrnya RL33_THETH : 24- 25: rnyat E-K nkrnt RL33_THETH : 51- 53: htvhr EvK i RL33_TOBAC : 46- 48: tpnrl ElK kfcpy RL33_TOBAC : 62- 64: htihg EiK k G 7: 7.3401 25( 16) R-x(0,2)-V Occurences: 25(16) RL33_BACLI : 29- 32: aalae RleV kkycn RL33_BACST : 2- 3: m R--V nitla RL33_BACST : 40- 42: ycprd Rk-V tlhre RL33_BACSU : 29- 32: asaae RleV kkycs RL33_CYAPA : 8- 11: rakgv RilV tlect RL33_ECOLI : 43- 46: fdpvv RqhV iykea RL33_EPIVI : 8- 9: kskda R--V avile RL33_EPIVI : 8- 11: kskda RvaV ilect RL33_EPIVI : 20- 23: ctsci RnsV nkvlt RL33_HAEIN : 11- 13: areki Rl-V staet RL33_HAEIN : 45- 48: fdpvv RkhV iykea RL33_LACLA : 2- 3: m R--V kitli RL33_LACLA : 40- 42: fcpke Ri-V tlhre RL33_MAIZE : 7- 10: kgkdv RirV ileci RL33_MAIZE : 9- 10: kdvri R--V ileci RL33_MARPO : 7- 8: kskdi R--V tinle RL33_ORYSA : 7- 10: kgkdv RirV ilqcv RL33_ORYSA : 9- 10: kdvri R--V ilqcv RL33_PINTH : 7- 8: ksgdi R--V title RL33_SPIOL : 7- 8: kgkdv R--V kvile RL33_SPIOL : 7- 10: kgkdv RvkV ilect RL33_SPIOL : 19- 22: ctgcv RksV nkgsr RL33_SPIOL : 27- 29: vnkgs Rg-V sryit RL33_THEMA : 2- 3: m R--V kvalk RL33_THEMA : 2- 5: m RvkV alkcs RL33_THETH : 50- 52: khtvh Re-V ki RL33_TOBAC : 7- 8: kgkdv R--V tvile RL33_TOBAC : 7- 10: kgkdv RvtV ilect RL33_TOBAC : 19- 22: ctscv RnsV dkvsr H 8: 7.3401 33( 16) T-x(1,3)-K Occurences: 33(16) RL33_BACLI : 6- 10: mkkkv TlacK ncgsr RL33_BACLI : 18- 21: gsrny Ttm-K ssaal RL33_BACLI : 19- 21: srnyt Tm--K ssaal RL33_BACST : 19- 21: ernyi Ts--K nkrnn RL33_BACST : 19- 23: ernyi TsknK rnnpe RL33_BACSU : 6- 10: mrkki TlacK tcgnr RL33_BACSU : 18- 21: gnrny Ttm-K ssasa RL33_BACSU : 19- 21: nrnyt Tm--K ssasa RL33_CYAPA : 34- 36: vsrya Tk--K nrrnt RL33_ECOLI : 21- 24: tghfy Ttt-K nkrtk RL33_ECOLI : 22- 24: ghfyt Tt--K nkrtk RL33_ECOLI : 22- 26: ghfyt TtknK rtkpe RL33_ECOLI : 23- 26: hfytt Tkn-K rtkpe RL33_ECOLI : 28- 32: tknkr TkpeK lelkk RL33_EPIVI : 35- 37: isryi Tq--K nrrnt RL33_HAEIN : 23- 26: tghfy Ttd-K nkrnm RL33_HAEIN : 24- 26: ghfyt Td--K nkrnm RL33_HAEIN : 24- 28: ghfyt TdknK rnmpe RL33_LACLA : 25- 29: sknka ThpeK vetmk RL33_LACLA : 32- 34: pekve Tm--K fcpke RL33_MAIZE : 22- 24: cvrkg Tn--K estgi RL33_MAIZE : 34- 36: isrys Tq--K nrhnt RL33_MARPO : 32- 35: gisry Ttq-K nrrnt RL33_MARPO : 33- 35: isryt Tq--K nrrnt RL33_MARPO : 57- 60: ycnkh Tih-K eikk RL33_ORYSA : 34- 36: isrys Tq--K nrhnt RL33_PINTH : 33- 36: gisry Ttr-K nrrnt RL33_PINTH : 34- 36: isryt Tr--K nrrnt RL33_SPIOL : 34- 36: vsryi Tq--K nrhnt RL33_THEMA : 19- 23: nknyy TtrnK dkrak RL33_THEMA : 20- 23: knyyt Trn-K dkrak RL33_THEMA : 45- 48: ahtih Tet-K a RL33_THETH : 14- 17: lllec Tec-K rrnya RL33_THETH : 23- 25: rrnya Te--K nkrnt RL33_THETH : 23- 27: rrnya TeknK rntpn RL33_THETH : 30- 33: knkrn Tpn-K lelrk RL33_TOBAC : 34- 36: isryi Tq--K nrhnt Number of patterns evaluated by Pratt:10 Total running time: 0 seconds