------------------------------------------------------------ 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 DEHYDROQUINASE_II 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 DEHYDROQUINASE_II.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: 3DHQ_EMENI 153 3DHQ_NEUCR 173 AROD_ACTPL 154 AROD_AMYME 20 AROD_HAEIN 149 AROD_MYCTU 147 AROD_STRCO 34 Pratt run started at Thu Feb 6 19:17:55 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 37.5305 7( 7) N-G-P-N-L-x(2)-L-G-x-R-x-P 2: 36.5305 7( 7) N-G-P-N-L-x(2)-L-G-x-R-x(0,2)-E 3: 33.3604 7( 7) G-P-N-L-x(2)-L-G-x-R-x-P 4: 32.3604 7( 7) G-P-N-L-x(2)-L-G-x-R-x(0,2)-E 5: 29.1904 7( 7) P-N-L-x(2)-L-G-x-R-x-P 6: 28.1904 7( 7) P-N-L-x(2)-L-G-x-R-x(0,2)-E 7: 24.0203 7( 7) N-L-x(2)-L-G-x-R-x(0,2)-E 8: 20.8503 7( 7) L-x(2)-L-G-x-R-x-P 9: 19.8503 7( 7) L-x(2)-L-G-x-R-x(0,2)-E 10: 19.3503 13( 7) L-x(3,5)-N-x(3)-L-G-x(0,1)-R 11: 16.1802 10( 7) L-x(0,1)-G-x-R-x-P 12: 15.6802 7( 7) L-G-x-R-x(0,2)-E 13: 12.5102 7( 7) G-x-R-x-P 14: 12.0102 11( 7) L-G-x(0,1)-R 15: 11.5102 7( 7) G-x-R-x(0,2)-E 16: 11.5102 10( 7) L-N-x(0,2)-G 17: 11.5102 9( 7) L-x(0,1)-N-x(0,1)-G 18: 11.5102 9( 7) L-x(1,2)-G-x(1,2)-L 19: 11.5102 8( 7) L-x(0,1)-G-x(1,2)-L 20: 11.5102 10( 7) L-x(2,3)-P-x(0,1)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 43.9855 7( 7) N-G-P-N-L-[GN]-x-L-G-x-R-[EQ]-P B 2: 42.9916 7( 7) N-G-P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] C 3: 39.8155 7( 7) G-P-N-L-[GN]-x-L-G-x-R-[EQ]-P D 4: 38.8215 7( 7) G-P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] E 5: 35.6454 7( 7) P-N-L-[GN]-x-L-G-x-R-[EQ]-P F 6: 34.6515 7( 7) P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] G 7: 30.4814 7( 7) N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] H 8: 28.4127 13( 7) L-x(3,5)-N-[GL]-[GNP]-x-L-G-x(0,1)-R-x-[GP] I 9: 26.3114 7( 7) L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] J 10: 24.0322 7( 7) L-x(2)-L-G-x-R-[EQ]-P K 11: 23.6882 9( 7) L-x(2,3)-P-x(0,1)-L-x(2)-[LV]-x(2)-[RS]-[ENQ]-[PV] L 12: 19.3622 10( 7) L-x(0,1)-G-x-R-[EQ]-P M 13: 19.3622 7( 7) L-G-x(0,1)-R-[EQ]-P N 14: 18.8682 7( 7) L-G-x-R-x(0,2)-E-[IP] O 15: 17.3481 9( 7) L-x(1,2)-G-x(1,2)-L-[GNT]-x(2)-[GS] P 16: 16.4458 8( 7) L-x(0,1)-G-x(1,2)-L-[GNQT]-x(2)-[EGQ] Q 17: 15.6921 7( 7) G-x-R-[EQ]-P R 18: 14.7344 9( 7) L-x(0,1)-N-x(0,1)-G-[GP] S 19: 14.6982 7( 7) G-x-R-x(0,2)-E-[IP] T 20: 13.7213 8( 7) L-N-x(0,2)-G-[AGPT] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 43.9855 7( 7) N-G-P-N-L-[GN]-x-L-G-x-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 9- 21: silli NGPNLNlLGtREP hiygs 3DHQ_NEUCR : 11- 23: hilli NGPNLNlLGtREP qiygs AROD_ACTPL : 8- 20: killl NGPNLNmLGkREP hiygs AROD_AMYME : 7- 19: kvfvl NGPNLGrLGkREP a AROD_HAEIN : 11- 23: rilll NGPNLNmLGaREP khygs AROD_MYCTU : 10- 22: ivnvi NGPNLGrLGrREP avygg AROD_STRCO : 13- 25: pimil NGPNLNlLGqRQP eiygs B 2: 42.9916 7( 7) N-G-P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 9- 21: silli NGPNLNlLGtR--EP hiygs 3DHQ_NEUCR : 11- 23: hilli NGPNLNlLGtR--EP qiygs AROD_ACTPL : 8- 20: killl NGPNLNmLGkR--EP hiygs AROD_AMYME : 7- 19: kvfvl NGPNLGrLGkR--EP a AROD_HAEIN : 11- 23: rilll NGPNLNmLGaR--EP khygs AROD_MYCTU : 10- 22: ivnvi NGPNLGrLGrR--EP avygg AROD_STRCO : 13- 27: pimil NGPNLNlLGqRqpEI ygsdx C 3: 39.8155 7( 7) G-P-N-L-[GN]-x-L-G-x-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 10- 21: illin GPNLNlLGtREP hiygs 3DHQ_NEUCR : 12- 23: illin GPNLNlLGtREP qiygs AROD_ACTPL : 9- 20: illln GPNLNmLGkREP hiygs AROD_AMYME : 8- 19: vfvln GPNLGrLGkREP a AROD_HAEIN : 12- 23: illln GPNLNmLGaREP khygs AROD_MYCTU : 11- 22: vnvin GPNLGrLGrREP avygg AROD_STRCO : 14- 25: imiln GPNLNlLGqRQP eiygs D 4: 38.8215 7( 7) G-P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 10- 21: illin GPNLNlLGtR--EP hiygs 3DHQ_NEUCR : 12- 23: illin GPNLNlLGtR--EP qiygs AROD_ACTPL : 9- 20: illln GPNLNmLGkR--EP hiygs AROD_AMYME : 8- 19: vfvln GPNLGrLGkR--EP a AROD_HAEIN : 12- 23: illln GPNLNmLGaR--EP khygs AROD_MYCTU : 11- 22: vnvin GPNLGrLGrR--EP avygg AROD_STRCO : 14- 27: imiln GPNLNlLGqRqpEI ygsdx E 5: 35.6454 7( 7) P-N-L-[GN]-x-L-G-x-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 11- 21: lling PNLNlLGtREP hiygs 3DHQ_NEUCR : 13- 23: lling PNLNlLGtREP qiygs AROD_ACTPL : 10- 20: lllng PNLNmLGkREP hiygs AROD_AMYME : 9- 19: fvlng PNLGrLGkREP a AROD_HAEIN : 13- 23: lllng PNLNmLGaREP khygs AROD_MYCTU : 12- 22: nving PNLGrLGrREP avygg AROD_STRCO : 15- 25: milng PNLNlLGqRQP eiygs F 6: 34.6515 7( 7) P-N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 11- 21: lling PNLNlLGtR--EP hiygs 3DHQ_NEUCR : 13- 23: lling PNLNlLGtR--EP qiygs AROD_ACTPL : 10- 20: lllng PNLNmLGkR--EP hiygs AROD_AMYME : 9- 19: fvlng PNLGrLGkR--EP a AROD_HAEIN : 13- 23: lllng PNLNmLGaR--EP khygs AROD_MYCTU : 12- 22: nving PNLGrLGrR--EP avygg AROD_STRCO : 15- 27: milng PNLNlLGqRqpEI ygsdx G 7: 30.4814 7( 7) N-L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 12- 21: lingp NLNlLGtR--EP hiygs 3DHQ_NEUCR : 14- 23: lingp NLNlLGtR--EP qiygs AROD_ACTPL : 11- 20: llngp NLNmLGkR--EP hiygs AROD_AMYME : 10- 19: vlngp NLGrLGkR--EP a AROD_HAEIN : 14- 23: llngp NLNmLGaR--EP khygs AROD_MYCTU : 13- 22: vingp NLGrLGrR--EP avygg AROD_STRCO : 16- 27: ilngp NLNlLGqRqpEI ygsdx H 8: 28.4127 13( 7) L-x(3,5)-N-[GL]-[GNP]-x-L-G-x(0,1)-R-x-[GP] Occurences: 13(7) 3DHQ_EMENI : 6- 21: meksi LlingpNLNlLGtReP hiygs 3DHQ_EMENI : 7- 21: eksil Lingp-NLNlLGtReP hiygs 3DHQ_NEUCR : 8- 23: sprhi LlingpNLNlLGtReP qiygs 3DHQ_NEUCR : 9- 23: prhil Lingp-NLNlLGtReP qiygs AROD_ACTPL : 5- 20: mkki LllngpNLNmLGkReP hiygs AROD_ACTPL : 6- 20: mkkil Llngp-NLNmLGkReP hiygs AROD_ACTPL : 7- 20: kkill Lngp--NLNmLGkReP hiygs AROD_AMYME : 6- 19: mkvfv Lngp--NLGrLGkReP a AROD_HAEIN : 8- 23: qthri LllngpNLNmLGaReP khygs AROD_HAEIN : 9- 23: thril Llngp-NLNmLGaReP khygs AROD_HAEIN : 10- 23: hrill Lngp--NLNmLGaReP khygs AROD_MYCTU : 4- 18: mse LivnviNGPnLG-RlG rrepa AROD_STRCO : 12- 25: apimi Lngp--NLNlLGqRqP eiygs I 9: 26.3114 7( 7) L-[GN]-x-L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 13- 21: ingpn LNlLGtR--EP hiygs 3DHQ_NEUCR : 15- 23: ingpn LNlLGtR--EP qiygs AROD_ACTPL : 12- 20: lngpn LNmLGkR--EP hiygs AROD_AMYME : 11- 19: lngpn LGrLGkR--EP a AROD_HAEIN : 15- 23: lngpn LNmLGaR--EP khygs AROD_MYCTU : 14- 22: ingpn LGrLGrR--EP avygg AROD_STRCO : 17- 27: lngpn LNlLGqRqpEI ygsdx J 10: 24.0322 7( 7) L-x(2)-L-G-x-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 13- 21: ingpn LnlLGtREP hiygs 3DHQ_NEUCR : 15- 23: ingpn LnlLGtREP qiygs AROD_ACTPL : 12- 20: lngpn LnmLGkREP hiygs AROD_AMYME : 11- 19: lngpn LgrLGkREP a AROD_HAEIN : 15- 23: lngpn LnmLGaREP khygs AROD_MYCTU : 14- 22: ingpn LgrLGrREP avygg AROD_STRCO : 17- 25: lngpn LnlLGqRQP eiygs K 11: 23.6882 9( 7) L-x(2,3)-P-x(0,1)-L-x(2)-[LV]-x(2)-[RS]-[ENQ]-[PV] Occurences: 9(7) 3DHQ_EMENI : 7- 21: eksil LingPnLnlLgtREP hiygs 3DHQ_NEUCR : 9- 23: prhil LingPnLnlLgtREP qiygs AROD_ACTPL : 6- 20: mkkil LlngPnLnmLgkREP hiygs AROD_ACTPL : 7- 20: kkill Lng-PnLnmLgkREP hiygs AROD_AMYME : 6- 19: mkvfv Lng-PnLgrLgkREP a AROD_HAEIN : 9- 23: thril LlngPnLnmLgaREP khygs AROD_HAEIN : 10- 23: hrill Lng-PnLnmLgaREP khygs AROD_MYCTU : 94- 106: dacae Lsa-P-LieVhiSNV haree AROD_STRCO : 12- 25: apimi Lng-PnLnlLgqRQP eiygs L 12: 19.3622 10( 7) L-x(0,1)-G-x-R-[EQ]-P Occurences: 10(7) 3DHQ_EMENI : 15- 21: gpnln LlGtREP hiygs 3DHQ_EMENI : 16- 21: pnlnl L-GtREP hiygs 3DHQ_NEUCR : 17- 23: gpnln LlGtREP qiygs 3DHQ_NEUCR : 18- 23: pnlnl L-GtREP qiygs AROD_ACTPL : 15- 20: pnlnm L-GkREP hiygs AROD_AMYME : 14- 19: pnlgr L-GkREP a AROD_HAEIN : 18- 23: pnlnm L-GaREP khygs AROD_MYCTU : 17- 22: pnlgr L-GrREP avygg AROD_STRCO : 19- 25: gpnln LlGqRQP eiygs AROD_STRCO : 20- 25: pnlnl L-GqRQP eiygs M 13: 19.3622 7( 7) L-G-x(0,1)-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 16- 21: pnlnl LGtREP hiygs 3DHQ_NEUCR : 18- 23: pnlnl LGtREP qiygs AROD_ACTPL : 15- 20: pnlnm LGkREP hiygs AROD_AMYME : 14- 19: pnlgr LGkREP a AROD_HAEIN : 18- 23: pnlnm LGaREP khygs AROD_MYCTU : 17- 22: pnlgr LGrREP avygg AROD_STRCO : 20- 25: pnlnl LGqRQP eiygs N 14: 18.8682 7( 7) L-G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 16- 21: pnlnl LGtR--EP hiygs 3DHQ_NEUCR : 18- 23: pnlnl LGtR--EP qiygs AROD_ACTPL : 15- 20: pnlnm LGkR--EP hiygs AROD_AMYME : 14- 19: pnlgr LGkR--EP a AROD_HAEIN : 18- 23: pnlnm LGaR--EP khygs AROD_MYCTU : 17- 22: pnlgr LGrR--EP avygg AROD_STRCO : 20- 27: pnlnl LGqRqpEI ygsdx O 15: 17.3481 9( 7) L-x(1,2)-G-x(1,2)-L-[GNT]-x(2)-[GS] Occurences: 9(7) 3DHQ_EMENI : 7- 17: eksil LinGpnLNllG treph 3DHQ_NEUCR : 9- 19: prhil LinGpnLNllG trepq AROD_ACTPL : 6- 16: mkkil LlnGpnLNmlG kreph AROD_ACTPL : 7- 16: kkill Ln-GpnLNmlG kreph AROD_AMYME : 6- 15: mkvfv Ln-GpnLGrlG krepa AROD_HAEIN : 9- 19: thril LlnGpnLNmlG arepk AROD_HAEIN : 10- 19: hrill Ln-GpnLNmlG arepk AROD_MYCTU : 75- 84: aepvi LnaGg-LThtS valrd AROD_STRCO : 12- 21: apimi Ln-GpnLNllG qrqpe P 16: 16.4458 8( 7) L-x(0,1)-G-x(1,2)-L-[GNQT]-x(2)-[EGQ] Occurences: 8(7) 3DHQ_EMENI : 43- 51: ghaas L-GasLQtfQ snheg 3DHQ_NEUCR : 45- 53: tlass L-GlrLTtfQ snheg AROD_ACTPL : 7- 16: kkill LnGpnLNmlG kreph AROD_AMYME : 6- 15: mkvfv LnGpnLGrlG krepa AROD_AMYME : 11- 18: lngpn L-Gr-LGkrE pa AROD_HAEIN : 10- 19: hrill LnGpnLNmlG arepk AROD_MYCTU : 14- 21: ingpn L-Gr-LGrrE pavyg AROD_STRCO : 12- 21: apimi LnGpnLNllG qrqpe Q 17: 15.6921 7( 7) G-x-R-[EQ]-P Occurences: 7(7) 3DHQ_EMENI : 17- 21: nlnll GtREP hiygs 3DHQ_NEUCR : 19- 23: nlnll GtREP qiygs AROD_ACTPL : 16- 20: nlnml GkREP hiygs AROD_AMYME : 15- 19: nlgrl GkREP a AROD_HAEIN : 19- 23: nlnml GaREP khygs AROD_MYCTU : 18- 22: nlgrl GrREP avygg AROD_STRCO : 21- 25: nlnll GqRQP eiygs R 18: 14.7344 9( 7) L-x(0,1)-N-x(0,1)-G-[GP] Occurences: 9(7) 3DHQ_EMENI : 7- 11: eksil LiN-GP nlnll 3DHQ_NEUCR : 9- 13: prhil LiN-GP nlnll AROD_ACTPL : 6- 10: mkkil LlN-GP nlnml AROD_ACTPL : 7- 10: kkill L-N-GP nlnml AROD_AMYME : 6- 9: mkvfv L-N-GP nlgrl AROD_HAEIN : 9- 13: thril LlN-GP nlnml AROD_HAEIN : 10- 13: hrill L-N-GP nlnml AROD_MYCTU : 75- 79: aepvi L-NaGG lthts AROD_STRCO : 12- 15: apimi L-N-GP nlnll S 19: 14.6982 7( 7) G-x-R-x(0,2)-E-[IP] Occurences: 7(7) 3DHQ_EMENI : 17- 21: nlnll GtR--EP hiygs 3DHQ_NEUCR : 19- 23: nlnll GtR--EP qiygs AROD_ACTPL : 16- 20: nlnml GkR--EP hiygs AROD_AMYME : 15- 19: nlgrl GkR--EP a AROD_HAEIN : 19- 23: nlnml GaR--EP khygs AROD_MYCTU : 18- 22: nlgrl GrR--EP avygg AROD_STRCO : 21- 27: nlnll GqRqpEI ygsdx T 20: 13.7213 8( 7) L-N-x(0,2)-G-[AGPT] Occurences: 8(7) 3DHQ_EMENI : 13- 18: ingpn LNllGT rephi 3DHQ_NEUCR : 15- 20: ingpn LNllGT repqi AROD_ACTPL : 7- 10: kkill LN--GP nlnml AROD_AMYME : 6- 9: mkvfv LN--GP nlgrl AROD_HAEIN : 10- 13: hrill LN--GP nlnml AROD_HAEIN : 15- 20: lngpn LNmlGA repkh AROD_MYCTU : 75- 79: aepvi LNa-GG lthts AROD_STRCO : 12- 15: apimi LN--GP nlnll Number of patterns evaluated by Pratt:126 Total running time: 0 seconds