------------------------------------------------------------ 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 23 sequences from file RIBOSOMAL_S10 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 23 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_S10.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RS10_BACSU 28 RS10_CRYPH 102 RS10_CYAPA 105 RS10_DESMO 65 RS10_ECOLI 103 RS10_HAEIN 118 RS10_HALMA 99 RS10_METVA 91 RS10_MYCCA 102 RS10_MYCLE 101 RS10_PYRWO 102 RS10_SULAC 102 RS10_SULSO 102 RS10_THEAC 104 RS10_THEMA 102 RS10_THETH 32 RS20_HUMAN 119 RS20_ORYSA 117 RS22_XENLA 119 RSU2_YEAST 121 RT10_ARATH 241 RT10_MARPO 102 RT10_PROWI 107 Pratt run started at Thu Feb 6 21:06:05 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 48( 23) I-x-I 2: 7.8401 52( 23) K-x(2,3)-D 3: 7.8401 53( 23) K-x(0,1)-R 4: 7.3401 30( 23) I-x(0,2)-V 5: 7.3401 74( 23) R-x(0,2)-I Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 8.3401 48( 23) I-x-I B 2: 7.8401 52( 23) K-x(2,3)-D C 3: 7.8401 53( 23) K-x(0,1)-R D 4: 7.3401 30( 23) I-x(0,2)-V E 5: 7.3401 74( 23) R-x(0,2)-I Best patterns with alignements: fitness hits(seqs) Pattern A 1: 8.3401 48( 23) I-x-I Occurences: 48(23) RS10_BACSU : 5- 7: akqk IrI rlkay RS10_CRYPH : 6- 8: mqkqk IrI rlkgy RS10_CRYPH : 74- 76: ihkrv IdI yepns RS10_CRYPH : 96- 98: dlpag IdI diki RS10_CRYPH : 98- 100: pagid IdI ki RS10_CRYPH : 100- 102: gidid IkI RS10_CYAPA : 9- 11: nqqlk IrI qlrsy RS10_DESMO : 4- 6: mvk IkI wstnv RS10_ECOLI : 6- 8: mqnqr IrI rlkaf RS10_HAEIN : 21- 23: mqnqr IrI rlkaf RS10_HALMA : 73- 75: vhkrl IdI dader RS10_HALMA : 96- 98: pndvs IeI r RS10_METVA : 73- 75: vhkrv IdI eader RS10_MYCCA : 49- 51: tekqv ItI lravh RS10_MYCCA : 98- 100: psgvd IeI kl RS10_MYCLE : 6- 8: magqk IrI rlkay RS10_MYCLE : 74- 76: thkrl IdI ldptp RS10_PYRWO : 6- 8: mqkar IkI astnv RS10_PYRWO : 45- 47: lptkr IrI ttrks RS10_PYRWO : 73- 75: vhkrl IdI eader RS10_PYRWO : 96- 98: pedvt IeI elis RS10_SULAC : 74- 76: vhkri IdI aader RS10_SULAC : 97- 99: pddvy IeI eli RS10_SULSO : 74- 76: vhkrl IdI aader RS10_SULSO : 97- 99: pedvy IeI qli RS10_THEAC : 90- 92: rqlmr IpI pdgvq RS10_THEAC : 98- 100: pdgvq IeI qiks RS10_THEAC : 100- 102: gvqie IqI ks RS10_THEMA : 6- 8: mpgqk IrI klkay RS10_THEMA : 74- 76: vhkrl IdI idpsp RS10_THETH : 3- 5: pk IrI klrgf RS20_HUMAN : 20- 22: vaihr IrI tltsr RS20_HUMAN : 104- 106: kqits IsI epgve RS20_ORYSA : 18- 20: evqhr IrI tlssk RS20_ORYSA : 102- 104: kqits ItI epgve RS22_XENLA : 20- 22: vaihr IrI tltsr RS22_XENLA : 104- 106: kqits IsI epgve RSU2_YEAST : 20- 22: qqqqi IkI ritlt RSU2_YEAST : 22- 24: qqiik IrI tltst RSU2_YEAST : 106- 108: kritq ItI epgvd RT10_ARATH : 61- 63: irarn IhI rseps RT10_ARATH : 96- 98: ikkak IkI spdnv RT10_ARATH : 130- 132: ikgtk IcI airsf RT10_ARATH : 132- 134: gtkic IaI rsfvn RT10_MARPO : 5- 7: mtak IcI viksf RT10_MARPO : 7- 9: takic IvI ksfen RT10_PROWI : 79- 81: isftn IdI lhafl RT10_PROWI : 99- 101: vvgvq IhI svkyh B 2: 7.8401 52( 23) K-x(2,3)-D Occurences: 52(23) RS10_BACSU : 10- 13: irirl Kay-D hrilb RS10_CRYPH : 71- 75: etrih KrviD iyepn RS10_CYAPA : 33- 36: iieaa Krt-D atavg RS10_CYAPA : 85- 88: ylpss Kti-D tltrl RS10_DESMO : 12- 15: wstnv Kvl-D dfvgk RS10_DESMO : 12- 16: wstnv KvldD fvgki RS10_DESMO : 20- 23: ddfvg Kit-D ivkkt RS10_ECOLI : 11- 14: irirl Kaf-D hrlid RS10_ECOLI : 59- 63: sphvn KdarD qyeir RS10_ECOLI : 82- 85: vepte Ktv-D almrl RS10_HAEIN : 26- 29: irirl Kaf-D hrlid RS10_HAEIN : 74- 78: sphvn KdarD qyeir RS10_HAEIN : 86- 90: eirth KrlvD ivept RS10_HAEIN : 97- 100: vepte Ktv-D almrl RS10_HALMA : 51- 54: evpsr Ksp-D gegta RS10_HALMA : 70- 74: emrvh KrliD idade RS10_METVA : 29- 33: kaiae KtgvD magpi RS10_METVA : 51- 54: kittr Kst-D gegss RS10_METVA : 70- 74: tmrvh KrviD ieade RS10_MYCCA : 11- 14: mrikl Kgy-D haivd RS10_MYCCA : 57- 60: lravh Kyk-D sreqf RS10_MYCLE : 11- 14: irirl Kay-D heaid RS10_MYCLE : 57- 60: irsph Kyk-D srehf RS10_MYCLE : 71- 75: emrth KrliD ildpt RS10_MYCLE : 82- 85: ldptp Ktv-D almri RS10_PYRWO : 51- 54: rittr Ksp-D gegsa RS10_PYRWO : 70- 74: elrvh KrliD ieade RS10_SULAC : 71- 75: emkvh KriiD iaade RS10_SULSO : 71- 75: emrvh KrliD iaade RS10_THEAC : 53- 56: vvpvr Ksp-D gegtn RS10_THEAC : 72- 76: emrih KrliD vdade RS10_THEMA : 11- 14: irikl Kay-D helld RS10_THEMA : 57- 60: lrspm Khk-D srehf RS10_THEMA : 71- 75: ekrvh KrliD iidps RS10_THEMA : 82- 85: idpsp Kti-D almri RS10_THETH : 13- 16: rgfdh Ktl-D asaqk RS20_HUMAN : 34- 38: vksle KvcaD lirga RS20_HUMAN : 75- 78: cgegs Ktw-D rfqmr RS20_HUMAN : 86- 90: qmrih KrliD lhsps RS20_ORYSA : 32- 36: vknle KvcgD lvkga RS20_ORYSA : 39- 43: cgdlv KgakD kslkv RS20_ORYSA : 84- 88: emrvh KrviD lvssa RS22_XENLA : 8- 12: fkdpg KapvD qevai RS22_XENLA : 34- 38: vksle KvcaD lirga RS22_XENLA : 75- 78: cgegs Ktw-D rfqmr RS22_XENLA : 86- 90: qmrih KrliD lhsps RSU2_YEAST : 88- 92: emrih KryiD leapv RT10_ARATH : 97- 101: kkaki KispD nvrpl RT10_ARATH : 221- 225: lqfhc KtrlD mtqvl RT10_MARPO : 77- 80: klnwl Klh-D llgvq RT10_PROWI : 9- 12: vqlkl Ksf-D pvyin RT10_PROWI : 57- 61: sphih KksrD qfqik RT10_PROWI : 58- 61: phihk Ksr-D qfqik C 3: 7.8401 53( 23) K-x(0,1)-R Occurences: 53(23) RS10_BACSU : 4- 6: akq KiR irlka RS10_CRYPH : 5- 7: mqkq KiR irlkg RS10_CRYPH : 71- 72: etrih K-R vidiy RS10_CYAPA : 8- 10: snqql KiR iqlrs RS10_CYAPA : 33- 34: iieaa K-R tdata RS10_DESMO : 41- 42: iplpt K-R mkirt RS10_DESMO : 44- 46: ptkrm KiR tmklp RS10_ECOLI : 30- 31: iveta K-R tgaqv RS10_ECOLI : 46- 48: plptr KeR ftvli RS10_HAEIN : 45- 46: iveta K-R tgaqv RS10_HAEIN : 61- 63: plptr KeR ftvli RS10_HAEIN : 86- 87: eirth K-R lvdiv RS10_HALMA : 70- 71: emrvh K-R lidid RS10_METVA : 3- 5: mq KaR iklss RS10_METVA : 70- 71: tmrvh K-R vidie RS10_MYCCA : 5- 7: maen KmR iklkg RS10_MYCCA : 35- 37: egtga KvR gpipl RS10_MYCCA : 71- 72: emrth K-R lleil RS10_MYCCA : 88- 89: tmdvl K-R vqlps RS10_MYCLE : 5- 7: magq KiR irlka RS10_MYCLE : 71- 72: emrth K-R lidil RS10_PYRWO : 3- 5: mq KaR ikias RS10_PYRWO : 43- 44: iplpt K-R iritt RS10_PYRWO : 70- 71: elrvh K-R lidie RS10_SULAC : 4- 6: mpt KaR irlws RS10_SULAC : 71- 72: emkvh K-R iidia RS10_SULSO : 4- 6: mpt KaR irlws RS10_SULSO : 71- 72: emrvh K-R lidia RS10_THEAC : 5- 7: mvsy KaR islsg RS10_THEAC : 45- 46: mplpt K-R lvvpv RS10_THEAC : 72- 73: emrih K-R lidvd RS10_THEMA : 5- 7: mpgq KiR iklka RS10_THEMA : 67- 68: rehfe K-R vhkrl RS10_THEMA : 71- 72: ekrvh K-R lidii RS10_THETH : 2- 4: p KiR iklrg RS10_THETH : 6- 8: pkiri KlR gfdhk RS20_HUMAN : 86- 87: qmrih K-R lidlh RS20_ORYSA : 84- 85: emrvh K-R vidlv RS22_XENLA : 86- 87: qmrih K-R lidlh RSU2_YEAST : 21- 23: qqqii KiR itlts RSU2_YEAST : 88- 89: emrih K-R yidle RSU2_YEAST : 101- 102: pvqiv K-R itqit RT10_ARATH : 85- 87: yatvt KdR kneik RT10_ARATH : 174- 176: phvdk KsR eqfem RT10_ARATH : 184- 186: femrf KkR flvik RT10_ARATH : 185- 186: emrfk K-R flvik RT10_ARATH : 205- 206: klfwl K-R yrilg RT10_ARATH : 221- 223: lqfhc KtR ldmtq RT10_MARPO : 46- 48: phidk KsR eqfem RT10_MARPO : 68- 70: eteth KlR eklnw RT10_PROWI : 58- 60: phihk KsR dqfqi RT10_PROWI : 66- 67: dqfqi K-R ykrsm RT10_PROWI : 69- 70: qikry K-R smiis D 4: 7.3401 30( 23) I-x(0,2)-V Occurences: 30(23) RS10_BACSU : 24- 25: zsazk I--V zta RS10_CRYPH : 48- 51: ptrrk IycV lrsph RS10_CYAPA : 51- 54: ptkkk IycV lrsph RS10_CYAPA : 70- 72: rehfe Ir-V hrrii RS10_DESMO : 24- 25: gkitd I--V kktgv RS10_ECOLI : 25- 26: qatae I--V etakr RS10_ECOLI : 76- 77: lrlvd I--V eptek RS10_HAEIN : 40- 41: qstae I--V etakr RS10_HAEIN : 91- 92: krlvd I--V eptek RS10_HALMA : 88- 90: rqlmr Iq-V pndvs RS10_METVA : 85- 88: rtmkh ImkV kns RS10_MYCCA : 17- 18: gydha I--V dqsit RS10_MYCLE : 25- 26: asark I--V etvvr RS10_PYRWO : 88- 90: rqimr Ir-V pedvt RS10_SULAC : 33- 35: aqktg Iq-V sgpip RS10_SULSO : 27- 28: tqirg I--V ektgi RS10_THEAC : 75- 77: ihkrl Id-V dader RS10_THEMA : 25- 26: esakk I--V evaks RS10_THEMA : 25- 28: esakk IveV akstn RS10_THETH : 22- 23: asaqk I--V eaarr RS20_HUMAN : 97- 98: hspse I--V kqits RS20_ORYSA : 87- 90: vhkrv IdlV ssadv RS22_XENLA : 97- 98: hspse I--V kqits RSU2_YEAST : 41- 42: nvssn I--V knaeq RSU2_YEAST : 99- 100: eapvq I--V kritq RT10_ARATH : 2- 5: m IagV lprss RT10_ARATH : 70- 71: sepsm I--V pagia RT10_MARPO : 5- 8: mtak IciV iksfe RT10_MARPO : 7- 8: takic I--V iksfe RT10_PROWI : 47- 49: skikk It-V irsph RT10_PROWI : 101- 103: gvqih Is-V kyhs E 5: 7.3401 74( 23) R-x(0,2)-I Occurences: 74(23) RS10_BACSU : 6- 7: akqki R--I rlkay RS10_BACSU : 15- 16: kaydh R--I lbzsa RS10_CRYPH : 7- 8: qkqki R--I rlkgy RS10_CRYPH : 45- 48: iplpt RrkI ycvlr RS10_CRYPH : 46- 48: plptr Rk-I ycvlr RS10_CRYPH : 68- 69: ehfet R--I hkrvi RS10_CRYPH : 72- 74: trihk Rv-I diyep RS10_CYAPA : 10- 11: qqlki R--I qlrsy RS10_CYAPA : 74- 76: eirvh Rr-I idlyl RS10_CYAPA : 74- 77: eirvh RriI dlylp RS10_CYAPA : 75- 76: irvhr R--I idlyl RS10_CYAPA : 75- 77: irvhr Ri-I dlylp RS10_DESMO : 42- 45: plptk RmkI rtmkl RS10_ECOLI : 5- 6: mqnq R--I rirlk RS10_ECOLI : 5- 8: mqnq RirI rlkaf RS10_ECOLI : 7- 8: qnqri R--I rlkaf RS10_ECOLI : 16- 18: kafdh Rl-I dqata RS10_ECOLI : 37- 40: tgaqv RgpI plptr RS10_HAEIN : 20- 21: lmqnq R--I rirlk RS10_HAEIN : 20- 23: lmqnq RirI rlkaf RS10_HAEIN : 22- 23: qnqri R--I rlkaf RS10_HAEIN : 31- 33: kafdh Rl-I dqsta RS10_HAEIN : 52- 55: tgaqv RgpI plptr RS10_HALMA : 24- 26: icadv Re-I anktg RS10_HALMA : 71- 73: mrvhk Rl-I didad RS10_HALMA : 87- 88: lrqlm R--I qvpnd RS10_METVA : 5- 6: mqka R--I klsst RS10_METVA : 71- 73: mrvhk Rv-I diead RS10_MYCCA : 7- 8: aenkm R--I klkgy RS10_MYCCA : 37- 40: tgakv RgpI plpte RS10_MYCLE : 7- 8: agqki R--I rlkay RS10_MYCLE : 23- 25: idasa Rk-I vetvv RS10_MYCLE : 72- 74: mrthk Rl-I dildp RS10_MYCLE : 89- 90: vdalm R--I dlpas RS10_PYRWO : 5- 6: mqka R--I kiast RS10_PYRWO : 5- 8: mqka RikI astnv RS10_PYRWO : 44- 45: plptk R--I rittr RS10_PYRWO : 44- 47: plptk RirI ttrks RS10_PYRWO : 46- 47: ptkri R--I ttrks RS10_PYRWO : 71- 73: lrvhk Rl-I diead RS10_PYRWO : 83- 85: deram Rq-I mrirv RS10_PYRWO : 87- 88: mrqim R--I rvped RS10_SULAC : 6- 7: mptka R--I rlwss RS10_SULAC : 72- 73: mkvhk R--I idiaa RS10_SULAC : 72- 74: mkvhk Ri-I diaad RS10_SULSO : 6- 7: mptka R--I rlwst RS10_SULSO : 25- 27: vitqi Rg-I vektg RS10_SULSO : 36- 39: tgiem RgpI plpts RS10_SULSO : 72- 74: mrvhk Rl-I diaad RS10_THEAC : 7- 8: vsyka R--I slsgt RS10_THEAC : 69- 70: dhwem R--I hkrli RS10_THEAC : 73- 75: mrihk Rl-I dvdad RS10_THEAC : 89- 90: lrqlm R--I pipdg RS10_THEAC : 89- 92: lrqlm RipI pdgvq RS10_THEMA : 7- 8: pgqki R--I klkay RS10_THEMA : 72- 74: krvhk Rl-I diidp RS10_THEMA : 89- 90: idalm R--I nlpag RS10_THETH : 4- 5: pki R--I klrgf RS20_HUMAN : 19- 20: evaih R--I ritlt RS20_HUMAN : 19- 22: evaih RirI tltsr RS20_HUMAN : 21- 22: aihri R--I tltsr RS20_HUMAN : 62- 63: ptktl R--I ttrkt RS20_HUMAN : 83- 84: drfqm R--I hkrli RS20_HUMAN : 87- 89: mrihk Rl-I dlhsp RS20_ORYSA : 17- 18: qevqh R--I ritls RS20_ORYSA : 17- 20: qevqh RirI tlssk RS20_ORYSA : 19- 20: vqhri R--I tlssk RS20_ORYSA : 85- 87: mrvhk Rv-I dlvss RS22_XENLA : 19- 20: evaih R--I ritlt RS22_XENLA : 19- 22: evaih RirI tltsr RS22_XENLA : 21- 22: aihri R--I tltsr RS22_XENLA : 62- 63: ptktl R--I ttrkt RS22_XENLA : 83- 84: drfqm R--I hkrli RS22_XENLA : 87- 89: mrihk Rl-I dlhsp RSU2_YEAST : 23- 24: qiiki R--I tltst RSU2_YEAST : 85- 86: etyem R--I hkryi RSU2_YEAST : 89- 91: mrihk Ry-I dleap RSU2_YEAST : 102- 103: vqivk R--I tqiti RT10_ARATH : 59- 61: fgira Rn-I hirse RT10_ARATH : 108- 111: vrpls RkeI alqke RT10_ARATH : 206- 209: lfwlk RyrI lgaqy RT10_ARATH : 208- 209: wlkry R--I lgaqy RT10_MARPO : 24- 26: lllnt Rk-I glpkk RT10_MARPO : 54- 55: eqfem R--I hkqll RT10_PROWI : 70- 73: ikryk RsmI isftn Number of patterns evaluated by Pratt:7 Total running time: 0 seconds