------------------------------------------------------------ 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 14 sequences from file RIBOSOMAL_S16 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 14 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_S16.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RS16_BACSU 89 RS16_ECOLI 82 RS16_GALSU 77 RS16_GINBI 12 RS16_HAEIN 82 RS16_HORVU 85 RS16_MAIZE 85 RS16_ORYSA 62 RS16_SALTY 82 RS16_SINAL 88 RS16_SPIOL 25 RS16_THETH 28 RS16_TOBAC 85 RS24_NEUCR 107 Pratt run started at Thu Feb 6 21:06:07 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.6802 14( 14) R-L-x-R-x-G 2: 12.5102 14( 14) L-x-R-x-G 3: 11.5102 23( 14) L-x(1,3)-R-x-G 4: 11.5102 17( 14) V-x(3)-L-x(3,5)-G 5: 10.5102 17( 14) V-x(1,3)-L-x(0,2)-R 6: 8.3401 27( 14) R-x-G 7: 8.3401 21( 14) K-x-R 8: 7.8401 18( 14) G-x(0,1)-K 9: 7.8401 35( 14) K-x(0,1)-R 10: 7.8401 35( 14) L-x(0,1)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 16.6802 14( 14) R-L-x-R-x-G B 2: 13.6803 16( 14) V-x(1,3)-L-x(0,2)-R-x-[AG] C 3: 13.6329 17( 14) K-x-R-[ALP]-x(3)-[GIV] D 4: 13.1329 20( 14) K-x(0,1)-R-[ALP]-x(3)-[GIV] E 5: 12.5102 14( 14) L-x-R-x-G F 6: 11.5102 23( 14) L-x(1,3)-R-x-G G 7: 11.5102 17( 14) V-x(3)-L-x(3,5)-G H 8: 10.9814 18( 14) R-x-G-[QRS] I 9: 9.8817 16( 14) L-x(0,1)-R-[FILMV] J 10: 7.8401 18( 14) G-x(0,1)-K Best patterns with alignements: fitness hits(seqs) Pattern A 1: 16.6802 14( 14) R-L-x-R-x-G Occurences: 14(14) RS16_BACSU : 5- 10: avki RLkRmG akksp RS16_ECOLI : 5- 10: mvti RLaRhG akkrp RS16_GALSU : 5- 10: mlki RLkRcG rkkqt RS16_GINBI : 5- 10: mvkl RLkRcG rk RS16_HAEIN : 5- 10: mvti RLsRgG akkrp RS16_HORVU : 5- 10: mvkl RLkRcG rkqqa RS16_MAIZE : 5- 10: mvkl RLkRcG rkqqa RS16_ORYSA : 5- 10: mlkl RLkRcG rkqrf RS16_SALTY : 5- 10: mvti RLaRhG akkrp RS16_SINAL : 5- 10: mvkl RLkRcG rkqra RS16_SPIOL : 5- 10: mvkl RLkRcG rkqra RS16_THETH : 5- 10: mvki RLaRfG skhnp RS16_TOBAC : 5- 10: mvkl RLkRcG rkqra RS24_NEUCR : 6- 11: mvlkl RLaRfG rtnap B 2: 13.6803 16( 14) V-x(1,3)-L-x(0,2)-R-x-[AG] Occurences: 16(14) RS16_BACSU : 2- 10: a VkirLk-RmG akksp RS16_ECOLI : 2- 10: m VtirLa-RhG akkrp RS16_GALSU : 21- 30: sfkiv VmnnLdkRdG qaiee RS16_GINBI : 2- 10: m VklrLk-RcG rk RS16_HAEIN : 2- 10: m VtirLs-RgG akkrp RS16_HORVU : 2- 10: m VklrLk-RcG rkqqa RS16_HORVU : 67- 74: qptrt VydiL--RkA effke RS16_MAIZE : 2- 10: m VklrLk-RcG rkqqa RS16_MAIZE : 67- 74: qptrt VydiL--RkA effkd RS16_ORYSA : 44- 51: qptrt VsdiL--RkA effke RS16_SALTY : 2- 10: m VtirLa-RhG akkrp RS16_SINAL : 2- 10: m VklrLk-RcG rkqra RS16_SPIOL : 2- 10: m VklrLk-RcG rkqra RS16_THETH : 2- 10: m VkirLa-RfG skhnp RS16_TOBAC : 2- 10: m VklrLk-RcG rkqra RS24_NEUCR : 2- 8: m Vlk-L--RlA rfgrt C 3: 13.6329 17( 14) K-x-R-[ALP]-x(3)-[GIV] Occurences: 17(14) RS16_BACSU : 3- 10: av KiRLkrmG akksp RS16_ECOLI : 12- 19: arhga KkRPfyqV vvads RS16_GALSU : 3- 10: ml KiRLkrcG rkkqt RS16_GINBI : 3- 10: mv KlRLkrcG rk RS16_HAEIN : 12- 19: srgga KkRPfyqI vvads RS16_HORVU : 3- 10: mv KlRLkrcG rkqqa RS16_MAIZE : 3- 10: mv KlRLkrcG rkqqa RS16_ORYSA : 3- 10: ml KlRLkrcG rkqrf RS16_SALTY : 12- 19: arhga KkRPfyqV vvtds RS16_SINAL : 3- 10: mv KlRLkrcG rkqra RS16_SINAL : 12- 19: krcgr KqRAvyrI vaidv RS16_SPIOL : 3- 10: mv KlRLkrcG rkqra RS16_SPIOL : 12- 19: krcgr KqRAvyrI vaidv RS16_THETH : 3- 10: mv KiRLarfG skhnp RS16_TOBAC : 3- 10: mv KlRLkrcG rkqra RS16_TOBAC : 12- 19: krcgr KqRAvyrI vaidv RS24_NEUCR : 4- 11: mvl KlRLarfG rtnap D 4: 13.1329 20( 14) K-x(0,1)-R-[ALP]-x(3)-[GIV] Occurences: 20(14) RS16_BACSU : 3- 10: av KiRLkrmG akksp RS16_ECOLI : 12- 19: arhga KkRPfyqV vvads RS16_ECOLI : 13- 19: rhgak K-RPfyqV vvads RS16_GALSU : 3- 10: ml KiRLkrcG rkkqt RS16_GINBI : 3- 10: mv KlRLkrcG rk RS16_HAEIN : 12- 19: srgga KkRPfyqI vvads RS16_HAEIN : 13- 19: rggak K-RPfyqI vvads RS16_HORVU : 3- 10: mv KlRLkrcG rkqqa RS16_MAIZE : 3- 10: mv KlRLkrcG rkqqa RS16_ORYSA : 3- 10: ml KlRLkrcG rkqrf RS16_SALTY : 12- 19: arhga KkRPfyqV vvtds RS16_SALTY : 13- 19: rhgak K-RPfyqV vvtds RS16_SINAL : 3- 10: mv KlRLkrcG rkqra RS16_SINAL : 12- 19: krcgr KqRAvyrI vaidv RS16_SPIOL : 3- 10: mv KlRLkrcG rkqra RS16_SPIOL : 12- 19: krcgr KqRAvyrI vaidv RS16_THETH : 3- 10: mv KiRLarfG skhnp RS16_TOBAC : 3- 10: mv KlRLkrcG rkqra RS16_TOBAC : 12- 19: krcgr KqRAvyrI vaidv RS24_NEUCR : 4- 11: mvl KlRLarfG rtnap E 5: 12.5102 14( 14) L-x-R-x-G Occurences: 14(14) RS16_BACSU : 6- 10: avkir LkRmG akksp RS16_ECOLI : 6- 10: mvtir LaRhG akkrp RS16_GALSU : 6- 10: mlkir LkRcG rkkqt RS16_GINBI : 6- 10: mvklr LkRcG rk RS16_HAEIN : 6- 10: mvtir LsRgG akkrp RS16_HORVU : 6- 10: mvklr LkRcG rkqqa RS16_MAIZE : 6- 10: mvklr LkRcG rkqqa RS16_ORYSA : 6- 10: mlklr LkRcG rkqrf RS16_SALTY : 6- 10: mvtir LaRhG akkrp RS16_SINAL : 6- 10: mvklr LkRcG rkqra RS16_SPIOL : 6- 10: mvklr LkRcG rkqra RS16_THETH : 6- 10: mvkir LaRfG skhnp RS16_TOBAC : 6- 10: mvklr LkRcG rkqra RS24_NEUCR : 7- 11: vlklr LaRfG rtnap F 6: 11.5102 23( 14) L-x(1,3)-R-x-G Occurences: 23(14) RS16_BACSU : 6- 10: avkir Lk--RmG akksp RS16_ECOLI : 6- 10: mvtir La--RhG akkrp RS16_GALSU : 6- 10: mlkir Lk--RcG rkkqt RS16_GALSU : 25- 30: vvmnn Ldk-RdG qaiee RS16_GINBI : 4- 10: mvk LrlkRcG rk RS16_GINBI : 6- 10: mvklr Lk--RcG rk RS16_HAEIN : 6- 10: mvtir Ls--RgG akkrp RS16_HORVU : 4- 10: mvk LrlkRcG rkqqa RS16_HORVU : 6- 10: mvklr Lk--RcG rkqqa RS16_MAIZE : 4- 10: mvk LrlkRcG rkqqa RS16_MAIZE : 6- 10: mvklr Lk--RcG rkqqa RS16_ORYSA : 4- 10: mlk LrlkRcG rkqrf RS16_ORYSA : 6- 10: mlklr Lk--RcG rkqrf RS16_SALTY : 6- 10: mvtir La--RhG akkrp RS16_SINAL : 4- 10: mvk LrlkRcG rkqra RS16_SINAL : 6- 10: mvklr Lk--RcG rkqra RS16_SPIOL : 4- 10: mvk LrlkRcG rkqra RS16_SPIOL : 6- 10: mvklr Lk--RcG rkqra RS16_THETH : 6- 10: mvkir La--RfG skhnp RS16_TOBAC : 4- 10: mvk LrlkRcG rkqra RS16_TOBAC : 6- 10: mvklr Lk--RcG rkqra RS24_NEUCR : 5- 11: mvlk LrlaRfG rtnap RS24_NEUCR : 7- 11: vlklr La--RfG rtnap G 7: 11.5102 17( 14) V-x(3)-L-x(3,5)-G Occurences: 17(14) RS16_BACSU : 2- 10: a VkirLkrm--G akksp RS16_ECOLI : 2- 10: m VtirLarh--G akkrp RS16_GALSU : 21- 30: sfkiv VmnnLdkrd-G qaiee RS16_GINBI : 2- 10: m VklrLkrc--G rk RS16_HAEIN : 2- 10: m VtirLsrg--G akkrp RS16_HORVU : 2- 10: m VklrLkrc--G rkqqa RS16_HORVU : 50- 60: qtcln VpaiLyflekG aqptr RS16_MAIZE : 2- 10: m VklrLkrc--G rkqqa RS16_MAIZE : 50- 60: qtcln VpaiLyflekG aqptr RS16_ORYSA : 27- 37: qtcln VpaiLyflekG aqptr RS16_SALTY : 2- 10: m VtirLarh--G akkrp RS16_SINAL : 2- 10: m VklrLkrc--G rkqra RS16_SPIOL : 2- 10: m VklrLkrc--G rkqra RS16_THETH : 2- 10: m VkirLarf--G skhnp RS16_TOBAC : 2- 10: m VklrLkrc--G rkqra RS16_TOBAC : 50- 60: qtyln VpaiLyflekG aqptg RS24_NEUCR : 80- 88: qptdt VwrlLslv--G ildpk H 8: 10.9814 18( 14) R-x-G-[QRS] Occurences: 18(14) RS16_BACSU : 28- 31: dsrsp RdGR fietv RS16_ECOLI : 28- 31: dsrna RnGR fierv RS16_GALSU : 8- 11: kirlk RcGR kkqts RS16_GALSU : 28- 31: nnldk RdGQ aieel RS16_GINBI : 8- 11: klrlk RcGR k RS16_HAEIN : 28- 31: dsrsp RdGR fierv RS16_HORVU : 8- 11: klrlk RcGR kqqav RS16_HORVU : 28- 31: dvrsr ReGR dlrkv RS16_MAIZE : 8- 11: klrlk RcGR kqqai RS16_MAIZE : 28- 31: dvrsr ReGR dlrkv RS16_ORYSA : 8- 11: klrlk RcGR kqrfy RS16_SALTY : 28- 31: dsrna RnGR fierv RS16_SINAL : 8- 11: klrlk RcGR kqrav RS16_SINAL : 28- 31: dvrsr ReGR dlrkv RS16_SPIOL : 8- 11: klrlk RcGR kqrav RS16_THETH : 8- 11: kirla RfGS khnph RS16_TOBAC : 8- 11: klrlk RcGR kqrav RS24_NEUCR : 9- 12: klrla RfGR tnapf I 9: 9.8817 16( 14) L-x(0,1)-R-[FILMV] Occurences: 16(14) RS16_BACSU : 6- 9: avkir LkRM gakks RS16_ECOLI : 54- 57: gtrld LdRI ahwvg RS16_GALSU : 57- 59: kinhy L-RL gakpt RS16_GINBI : 4- 6: mvk L-RL krcgr RS16_HAEIN : 50- 52: gnaer L-RI nlerv RS16_HAEIN : 54- 57: rlrin LeRV nhwva RS16_HORVU : 4- 6: mvk L-RL krcgr RS16_MAIZE : 4- 6: mvk L-RL krcgr RS16_ORYSA : 4- 6: mlk L-RL krcgr RS16_SALTY : 54- 57: gtrld LdRI ahwvg RS16_SINAL : 4- 6: mvk L-RL krcgr RS16_SPIOL : 4- 6: mvk L-RL krcgr RS16_THETH : 6- 9: mvkir LaRF gskhn RS16_TOBAC : 4- 6: mvk L-RL krcgr RS24_NEUCR : 5- 7: mvlk L-RL arfgr RS24_NEUCR : 7- 10: vlklr LaRF grtna J 10: 7.8401 18( 14) G-x(0,1)-K Occurences: 18(14) RS16_BACSU : 10- 12: rlkrm GaK kspfy RS16_BACSU : 62- 64: kwlqt GaK psdtv RS16_BACSU : 88- 89: hnakq G-K RS16_ECOLI : 10- 12: rlarh GaK krpfy RS16_GALSU : 10- 12: rlkrc GrK kqtsf RS16_GALSU : 60- 62: hylrl GaK ptktv RS16_GINBI : 10- 12: rlkrc GrK RS16_HAEIN : 10- 12: rlsrg GaK krpfy RS16_HORVU : 10- 12: rlkrc GrK qqavy RS16_MAIZE : 10- 12: rlkrc GrK qqaiy RS16_ORYSA : 10- 12: rlkrc GrK qrfyd RS16_SALTY : 10- 12: rlarh GaK krpfy RS16_SINAL : 10- 12: rlkrc GrK qravy RS16_SPIOL : 10- 12: rlkrc GrK qravy RS16_THETH : 10- 12: rlarf GsK hnphy RS16_TOBAC : 10- 12: rlkrc GrK qravy RS16_TOBAC : 30- 31: rsrre G-K dlrkv RS24_NEUCR : 53- 54: tydtt G-K lhkdi Number of patterns evaluated by Pratt:37 Total running time: 1 seconds