------------------------------------------------------------ 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 RIBOSOMAL_L24E 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 RIBOSOMAL_L24E.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL21_HALMA 66 RL24_ARATH 163 RL24_HUMAN 157 RL30_KLULA 155 RL3A_YEAST 155 RL3B_YEAST 155 Pratt run started at Thu Feb 6 21:05:52 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.5203 6( 6) E-x(4,5)-G-x(2)-I-x-P-G-x-G 2: 20.8503 6( 6) G-x(2)-I-x-P-G-x-G 3: 16.6802 6( 6) I-x-P-G-x-G 4: 15.1802 9( 6) E-x(3,4)-A-x(2)-E-x(1,3)-A 5: 15.1802 6( 6) E-x(5)-R-x(0,1)-E-x(1,3)-A 6: 15.1802 6( 6) R-x-A-x(0,1)-R-x(0,2)-E 7: 15.1802 6( 6) K-x-E-x(2,3)-A-x(1,3)-R 8: 14.6802 8( 6) E-x(3)-A-x(0,2)-E-x(1,3)-A 9: 14.6802 6( 6) R-x(4)-T-x(3,5)-R-x(3,5)-G 10: 12.5102 6( 6) W-T-x(3)-R 11: 12.5102 6( 6) D-x(5)-F-x(3)-K 12: 12.5102 6( 6) P-G-x-G 13: 12.0102 6( 6) R-x(3)-G-x(0,1)-A 14: 12.0102 6( 6) R-x(5)-A-x(2,3)-E 15: 12.0102 8( 6) A-x(2,3)-E-x(4)-A 16: 12.0102 6( 6) A-x-L-x(4,5)-R 17: 12.0102 9( 6) S-K-x(4,5)-A 18: 12.0102 7( 6) S-x-K-x(3,4)-A 19: 12.0102 6( 6) F-x(1,2)-S-K 20: 11.5102 10( 6) A-x(2,3)-E-x(0,1)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 64.7552 6( 6) E-x(4,5)-G-x-[DK]-I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] B 2: 61.0852 6( 6) G-x-[DK]-I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] C 3: 53.6943 6( 6) I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] D 4: 49.5242 6( 6) P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] E 5: 41.7372 6( 6) K-[CP]-E-x(2,3)-A-x(1,3)-R-[DE]-[AEQ]-x(3)-[AE]-x(2)-[DE]-x(2)-[KR]-x(3)-[AGV]-[AES]-x-[EKR] F 6: 30.1736 6( 6) E-x(2)-[DK]-[AT]-[ANQ]-R-x(0,1)-E-x(1,3)-A-x-[DKR]-[AE] G 7: 29.6036 6( 6) W-T-[ADV]-x(2)-R-x(4)-[EK]-[ADG]-x-[ADST]-[EQ]-[AE] H 8: 27.9871 6( 6) D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] I 9: 23.2634 6( 6) R-[DEK]-A-x(0,1)-R-x(0,2)-E-x(4)-[ADEN]-x(2)-[EK] J 10: 23.0408 6( 6) R-[NQR]-x(3)-T-x(3,5)-R-x(3,5)-G-x-[AST]-x-[DE] K 11: 22.5987 6( 6) A-x(2,3)-E-x(4)-A-x(2)-[AEQ]-[AGS]-x-[EKR]-x(3)-[AEQ] L 12: 22.0655 6( 6) R-[AGPS]-x-[ATV]-G-x(0,1)-A-[EST]-x-[ADE] M 13: 21.0571 8( 6) E-x(3,4)-A-x(2)-E-x(1,3)-A-x-[DKR]-[AE] N 14: 19.9817 6( 6) R-[DEG]-[AEQ]-x(2)-[EKR]-A-x(2,3)-E O 15: 17.9175 6( 6) A-x(2,3)-E-x(0,1)-A-x(2)-[AE]-x(2)-[EQ] P 16: 16.9036 8( 6) E-x(2)-[DEKR]-A-x(0,2)-E-x(1,3)-A Q 17: 16.8797 6( 6) S-x-K-x(3,4)-A-[ADQS]-x-[AGP] R 18: 14.2469 9( 6) S-K-x(4,5)-A-x(4)-[AEQT] S 19: 12.0102 6( 6) A-x-L-x(4,5)-R T 20: 12.0102 7( 6) S-x-K-x(3,4)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 64.7552 6( 6) E-x(4,5)-G-x-[DK]-I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] Occurences: 6(6) RL21_HALMA : 5- 38: prtr Ecdyc-GtDIePGtGtmFVHkDGatthFcSSKCeN nadlg RL24_ARATH : 6- 40: mvlkt ElcrfsGqKIyPGrGirFIRsDSqvflFlNSKCkR yfhnk RL24_HUMAN : 4- 38: mkv ElcsfsGyKIyPGhGrrYARtDGkvfqFlNAKCeS aflsk RL30_KLULA : 4- 38: mkv EidsfsGaKIyPGrGtlFVRgDSkifrFqSSKSaS lfhqr RL3A_YEAST : 4- 38: mkv EidsfsGaKIyPGrGtlFVRgDSkifrFqNSKSaS lfkqr RL3B_YEAST : 4- 38: mkv EvdsfsGaKIyPGrGtlFVRgDSkifrFqNSKSaS lfkqr B 2: 61.0852 6( 6) G-x-[DK]-I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] Occurences: 6(6) RL21_HALMA : 10- 38: ecdyc GtDIePGtGtmFVHkDGatthFcSSKCeN nadlg RL24_ARATH : 12- 40: lcrfs GqKIyPGrGirFIRsDSqvflFlNSKCkR yfhnk RL24_HUMAN : 10- 38: lcsfs GyKIyPGhGrrYARtDGkvfqFlNAKCeS aflsk RL30_KLULA : 10- 38: idsfs GaKIyPGrGtlFVRgDSkifrFqSSKSaS lfhqr RL3A_YEAST : 10- 38: idsfs GaKIyPGrGtlFVRgDSkifrFqNSKSaS lfkqr RL3B_YEAST : 10- 38: vdsfs GaKIyPGrGtlFVRgDSkifrFqNSKSaS lfkqr C 3: 53.6943 6( 6) I-x-P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] Occurences: 6(6) RL21_HALMA : 13- 38: ycgtd IePGtGtmFVHkDGatthFcSSKCeN nadlg RL24_ARATH : 15- 40: fsgqk IyPGrGirFIRsDSqvflFlNSKCkR yfhnk RL24_HUMAN : 13- 38: fsgyk IyPGhGrrYARtDGkvfqFlNAKCeS aflsk RL30_KLULA : 13- 38: fsgak IyPGrGtlFVRgDSkifrFqSSKSaS lfhqr RL3A_YEAST : 13- 38: fsgak IyPGrGtlFVRgDSkifrFqNSKSaS lfkqr RL3B_YEAST : 13- 38: fsgak IyPGrGtlFVRgDSkifrFqNSKSaS lfkqr D 4: 49.5242 6( 6) P-G-x-G-x(2)-[FY]-[AIV]-[HR]-x-D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] Occurences: 6(6) RL21_HALMA : 15- 38: gtdie PGtGtmFVHkDGatthFcSSKCeN nadlg RL24_ARATH : 17- 40: gqkiy PGrGirFIRsDSqvflFlNSKCkR yfhnk RL24_HUMAN : 15- 38: gykiy PGhGrrYARtDGkvfqFlNAKCeS aflsk RL30_KLULA : 15- 38: gakiy PGrGtlFVRgDSkifrFqSSKSaS lfhqr RL3A_YEAST : 15- 38: gakiy PGrGtlFVRgDSkifrFqNSKSaS lfkqr RL3B_YEAST : 15- 38: gakiy PGrGtlFVRgDSkifrFqNSKSaS lfkqr E 5: 41.7372 6( 6) K-[CP]-E-x(2,3)-A-x(1,3)-R-[DE]-[AEQ]-x(3)-[AE]-x(2)-[DE]-x(2)-[KR]-x(3)-[AGV]-[AES]-x-[EKR] Occurences: 6(6) RL21_HALMA : 35- 63: hfcss KCEnn-AdlgREArnlEwtDtaRgeaGEaE dea RL24_ARATH : 100- 127: kkrae KPEvrdAa--REAalrExkEriKktkVErR lrrwn RL24_HUMAN : 97- 124: akrnq KPEvrkAq--REQairAakEakKakqASkK tamaa RL30_KLULA : 97- 124: errsl KPEvrkAq--RDEkkkAdkEkkKadkAArK sekak RL3A_YEAST : 97- 124: errsl KPEvrkAn--REEklkAnkEkkKaekAArK aekak RL3B_YEAST : 97- 124: errsl KPEvrkAn--REEklkAnkEkkRaekAArK aekak F 6: 30.1736 6( 6) E-x(2)-[DK]-[AT]-[ANQ]-R-x(0,1)-E-x(1,3)-A-x-[DKR]-[AE] Occurences: 6(6) RL21_HALMA : 50- 65: earnl EwtDTARgEageAeDE a RL24_ARATH : 102- 114: raekp EvrDAAR-Ea--AlRE xkeri RL24_HUMAN : 99- 111: rnqkp EvrKAQR-Eq--AiRA akeak RL30_KLULA : 99- 114: rslkp EvrKAQRdEkkkAdKE kkkad RL3A_YEAST : 99- 114: rslkp EvrKANReEklkAnKE kkkae RL3B_YEAST : 99- 114: rslkp EvrKANReEklkAnKE kkrae G 7: 29.6036 6( 6) W-T-[ADV]-x(2)-R-x(4)-[EK]-[ADG]-x-[ADST]-[EQ]-[AE] Occurences: 6(6) RL21_HALMA : 51- 66: arnle WTDtaRgeagEAeDEA RL24_ARATH : 53- 68: pskla WTAiyRkqhkKDaAQE avkrr RL24_HUMAN : 51- 66: prqin WTVlyRrkhkKGqSEE iqkkr RL30_KLULA : 51- 66: prria WTVlyRrhhkKGiTEE varkr RL3A_YEAST : 51- 66: prria WTVlfRkhhkKGiTEE vakkr RL3B_YEAST : 51- 66: prria WTVlfRkhhkKGiTEE vakkr H 8: 27.9871 6( 6) D-[GS]-x(4)-F-x-[NS]-[AS]-K-[CS]-x-[NRS] Occurences: 6(6) RL21_HALMA : 25- 38: mfvhk DGatthFcSSKCeN nadlg RL24_ARATH : 27- 40: rfirs DSqvflFlNSKCkR yfhnk RL24_HUMAN : 25- 38: ryart DGkvfqFlNAKCeS aflsk RL30_KLULA : 25- 38: lfvrg DSkifrFqSSKSaS lfhqr RL3A_YEAST : 25- 38: lfvrg DSkifrFqNSKSaS lfkqr RL3B_YEAST : 25- 38: lfvrg DSkifrFqNSKSaS lfkqr I 9: 23.2634 6( 6) R-[DEK]-A-x(0,1)-R-x(0,2)-E-x(4)-[ADEN]-x(2)-[EK] Occurences: 6(6) RL21_HALMA : 44- 58: nadlg REA-RnlEwtdtArgE ageae RL24_ARATH : 104- 117: ekpev RDAaR--EaalrExkE rikkt RL24_HUMAN : 101- 114: qkpev RKAqR--EqairAakE akkak RL30_KLULA : 101- 115: lkpev RKAqRd-EkkkaDkeK kkadk RL3A_YEAST : 101- 114: lkpev RKAnR--EeklkAnkE kkkae RL3A_YEAST : 101- 115: lkpev RKAnRe-EklkaNkeK kkaek RL3B_YEAST : 101- 114: lkpev RKAnR--EeklkAnkE kkrae RL3B_YEAST : 101- 115: lkpev RKAnRe-EklkaNkeK kraek J 10: 23.0408 6( 6) R-[NQR]-x(3)-T-x(3,5)-R-x(3,5)-G-x-[AST]-x-[DE] Occurences: 6(6) RL21_HALMA : 47- 64: lgrea RNlewTdta--Rgea--GeAeD ea RL24_ARATH : 72- 91: qeavk RRrxxTkxpysRsiv--GaTlE viqkk RL24_HUMAN : 47- 66: skrnp RQinwTvlyr-Rkhkk-GqSeE iqkkr RL24_HUMAN : 47- 66: skrnp RQinwTvly--RrkhkkGqSeE iqkkr RL30_KLULA : 47- 66: qrknp RRiawTvlyr-Rhhkk-GiTeE varkr RL30_KLULA : 47- 66: qrknp RRiawTvly--RrhhkkGiTeE varkr RL3A_YEAST : 47- 66: qrknp RRiawTvlf--RkhhkkGiTeE vakkr RL3B_YEAST : 47- 66: qrknp RRiawTvlf--RkhhkkGiTeE vakkr K 11: 22.5987 6( 6) A-x(2,3)-E-x(4)-A-x(2)-[AEQ]-[AGS]-x-[EKR]-x(3)-[AEQ] Occurences: 6(6) RL21_HALMA : 46- 65: dlgre ArnlEwtdtArgEAgEaedE a RL24_ARATH : 98- 117: iqkkr AekpEvrdaAreAAlRexkE rikkt RL24_HUMAN : 103- 121: pevrk Aqr-EqairAakEAkKakqA skkta RL30_KLULA : 122- 141: kadka ArksEkaklAaaQGsKvskQ qakga RL3A_YEAST : 122- 141: kaeka ArkaEkaksAgtQSsKfskQ qakga RL3B_YEAST : 122- 141: raeka ArkaEkaksAgvQGsKvskQ qakga L 12: 22.0655 6( 6) R-[AGPS]-x-[ATV]-G-x(0,1)-A-[EST]-x-[ADE] Occurences: 6(6) RL21_HALMA : 56- 65: wtdta RGeAGeAEdE a RL24_ARATH : 83- 91: kxpys RSiVG-ATlE viqkk RL24_HUMAN : 80- 88: avkfq RAiTG-ASlA dimak RL30_KLULA : 80- 88: svkaq RAvVG-ASlE liker RL3A_YEAST : 80- 88: tvkaq RPiTG-ASlD liker RL3B_YEAST : 80- 88: tvkaq RPiTG-ASlD liker M 13: 21.0571 8( 6) E-x(3,4)-A-x(2)-E-x(1,3)-A-x-[DKR]-[AE] Occurences: 8(6) RL21_HALMA : 50- 65: earnl EwtdtArgEageAeDE a RL24_ARATH : 102- 114: raekp Evrd-AarEa--AlRE xkeri RL24_HUMAN : 99- 111: rnqkp Evrk-AqrEq--AiRA akeak RL30_KLULA : 107- 121: kaqrd Ekkk-AdkEkkkAdKA arkse RL3A_YEAST : 106- 121: rkanr EeklkAnkEkkkAeKA arkae RL3A_YEAST : 107- 121: kanre Eklk-AnkEkkkAeKA arkae RL3B_YEAST : 106- 121: rkanr EeklkAnkEkkrAeKA arkae RL3B_YEAST : 107- 121: kanre Eklk-AnkEkkrAeKA arkae N 14: 19.9817 6( 6) R-[DEG]-[AEQ]-x(2)-[EKR]-A-x(2,3)-E Occurences: 6(6) RL21_HALMA : 56- 65: wtdta RGEagEAed-E a RL24_ARATH : 104- 114: ekpev RDAarEAalrE xkeri RL24_HUMAN : 105- 114: vrkaq REQaiRAak-E akkak RL30_KLULA : 105- 114: vrkaq RDEkkKAdk-E kkkad RL3A_YEAST : 105- 114: vrkan REEklKAnk-E kkkae RL3B_YEAST : 105- 114: vrkan REEklKAnk-E kkrae O 15: 17.9175 6( 6) A-x(2,3)-E-x(0,1)-A-x(2)-[AE]-x(2)-[EQ] Occurences: 6(6) RL21_HALMA : 55- 65: ewtdt Arg-E-AgeAedE a RL24_ARATH : 106- 117: pevrd Aar-EaAlrExkE rikkt RL24_HUMAN : 103- 114: pevrk Aqr-EqAirAakE akkak RL30_KLULA : 122- 134: kadka ArksEkAklAaaQ gskvs RL3A_YEAST : 122- 134: kaeka ArkaEkAksAgtQ sskfs RL3B_YEAST : 122- 134: raeka ArkaEkAksAgvQ gskvs P 16: 16.9036 8( 6) E-x(2)-[DEKR]-A-x(0,2)-E-x(1,3)-A Occurences: 8(6) RL21_HALMA : 58- 66: dtarg EagEA--Ede-A RL24_ARATH : 102- 111: raekp EvrDAarEa--A lrexk RL24_HUMAN : 99- 108: rnqkp EvrKAqrEq--A iraak RL30_KLULA : 107- 118: kaqrd EkkKAdkEkkkA dkaar RL3A_YEAST : 107- 118: kanre EklKAnkEkkkA ekaar RL3A_YEAST : 114- 121: lkank EkkKA--Ek--A arkae RL3A_YEAST : 114- 122: lkank EkkKA--Eka-A rkaek RL3B_YEAST : 107- 118: kanre EklKAnkEkkrA ekaar RL3B_YEAST : 114- 121: lkank EkkRA--Ek--A arkae RL3B_YEAST : 114- 122: lkank EkkRA--Eka-A rkaek Q 17: 16.8797 6( 6) S-x-K-x(3,4)-A-[ADQS]-x-[AGP] Occurences: 6(6) RL21_HALMA : 33- 43: tthfc SsKcennADlG rearn RL24_ARATH : 144- 153: rsrli SpKlll-ASkG pkvgg RL24_HUMAN : 122- 132: kakqa SkKtamaAAkA ptkaa RL30_KLULA : 125- 135: kaark SeKaklaAAqG skvsk RL3A_YEAST : 72- 81: vakkr SrKtvk-AQrP itgas RL3B_YEAST : 72- 81: vakkr SrKtvk-AQrP itgas R 18: 14.2469 9( 6) S-K-x(4,5)-A-x(4)-[AEQT] Occurences: 9(6) RL21_HALMA : 34- 45: thfcs SKcenn-AdlgrE arnle RL24_ARATH : 49- 60: nklxp SKlawt-AiyrkQ hkkda RL24_HUMAN : 122- 134: kakqa SKktamaAakapT kaapk RL30_KLULA : 136- 148: aaaqg SKvskqqAkgafQ kvaat RL30_KLULA : 139- 151: qgskv SKqqakgAfqkvA atsr RL3A_YEAST : 136- 148: agtqs SKfskqqAkgafQ kvaat RL3A_YEAST : 139- 151: qsskf SKqqakgAfqkvA atsr RL3B_YEAST : 136- 148: agvqg SKvskqqAkgafQ kvaat RL3B_YEAST : 139- 151: qgskv SKqqakgAfqkvA atsr S 19: 12.0102 6( 6) A-x-L-x(4,5)-R Occurences: 6(6) RL21_HALMA : 40- 47: kcenn AdLgrea-R nlewt RL24_ARATH : 110- 118: daare AaLrexkeR ikktk RL24_HUMAN : 39- 47: akces AfLskrnpR qinwt RL30_KLULA : 85- 93: ravvg AsLelikeR rslkp RL3A_YEAST : 85- 93: rpitg AsLdlikeR rslkp RL3B_YEAST : 85- 93: rpitg AsLdlikeR rslkp T 20: 12.0102 7( 6) S-x-K-x(3,4)-A Occurences: 7(6) RL21_HALMA : 33- 40: tthfc SsKcennA dlgre RL24_ARATH : 144- 150: rsrli SpKlll-A skgpk RL24_HUMAN : 122- 128: kakqa SkKtam-A aakap RL24_HUMAN : 122- 129: kakqa SkKtamaA akapt RL30_KLULA : 75- 81: krtrk SvKaqr-A vvgas RL30_KLULA : 125- 131: kaark SeKakl-A aaqgs RL30_KLULA : 125- 132: kaark SeKaklaA aqgsk RL3A_YEAST : 72- 78: vakkr SrKtvk-A qrpit RL3B_YEAST : 72- 78: vakkr SrKtvk-A qrpit Number of patterns evaluated by Pratt:465 Total running time: 0 seconds