------------------------------------------------------------ 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 4 sequences from file PYRIDOX_OXIDASE PATTERN CONSERVATION: CM: min Nr of Seqs to Match 4 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 PYRIDOX_OXIDASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PDX3_YEAST 228 PDXH_ECOLI 217 PDXH_HAEIN 229 PDXH_MYXXA 270 Pratt run started at Thu Feb 6 20:56:36 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 48.5406 4( 4) W-x(5)-R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 2: 45.3706 4( 4) E-x(3,4)-Y-F-x(2)-R-x(3)-S-x(2)-G-A-W-x-S-x-Q-S 3: 44.3706 4( 4) R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 4: 41.7005 4( 4) Y-F-x(2)-R-x(3)-S-x(2)-G-A-W-x-S-x-Q-S 5: 40.2005 4( 4) L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 6: 37.5305 4( 4) F-x(2)-R-x(3)-S-x(2)-G-A-W-x-S-x-Q-S 7: 36.0305 4( 4) H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 8: 33.3604 4( 4) R-x(3)-S-x(2)-G-A-W-x-S-x-Q-S 9: 32.3604 7( 4) R-x(1,3)-S-x(2)-G-A-W-x-S-x-Q-S 10: 31.8604 4( 4) D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 11: 29.1904 4( 4) S-x(2)-G-A-W-x-S-x-Q-S 12: 29.1904 4( 4) P-x(5)-F-x-W-x(2)-L-x(2)-Q-V-x(3)-G 13: 25.0203 4( 4) G-A-W-x-S-x-Q-S 14: 25.0203 4( 4) F-x-W-x(2)-L-x(2)-Q-V-x(3)-G 15: 24.0203 4( 4) R-x(1,2)-L-L-x(0,1)-K-x(5)-G-x(5)-N 16: 24.0203 4( 4) G-x(4)-R-x(2)-L-x-K-x(5)-G-x(0,2)-F 17: 23.5203 4( 4) Y-x(0,1)-R-x(0,2)-E-x(3)-W-x(4)-L-x-P 18: 23.5203 4( 4) P-x-P-x(2)-W-x(0,1)-G-x(3)-V-x(2,4)-E 19: 23.5203 4( 4) G-x(3,4)-R-x(2)-L-x-K-x(5)-G-x(0,2)-F 20: 20.8503 4( 4) A-W-x-S-x-Q-S Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 118.3506 4( 4) P-x-[AV]-[AS]-[IL]-x-F-x-W-x-[DEPT]-L-[ENQ]-[ER]-Q-V-x-[IV]-x-G-x-[ATV]-x-[HKR]-[ILV]-[NPST]-x(2)-[EQT]-[ASV]-x(2)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q B 2: 116.8825 4( 4) F-x-W-x-[DEPT]-L-[ENQ]-[ER]-Q-V-x-[IV]-x-G-x-[ATV]-x-[HKR]-[ILV]-[NPST]-x(2)-[EQT]-[ASV]-x(2)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT] C 3: 75.7900 4( 4) E-x(3,4)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] D 4: 72.1199 4( 4) Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] E 5: 67.9499 4( 4) F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] F 6: 62.9925 4( 4) W-x-[AG]-x-[EP]-x-R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P G 7: 60.6044 4( 4) R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] H 8: 55.4722 4( 4) R-x(1,2)-L-L-x(0,1)-K-[DEH]-x-[DN]-x(2)-G-[FM]-[TV]-[FI]-[FY]-[ST]-N-x(2)-[ST]-[RS]-[KR] I 9: 53.7463 7( 4) R-x(1,3)-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] J 10: 52.4822 4( 4) R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P K 11: 50.5763 4( 4) S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] L 12: 48.3122 4( 4) L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P M 13: 47.0883 4( 4) G-x(4)-R-[IMV]-[LV]-L-[FL]-K-[DEH]-x-[DN]-x(2)-G-x(0,2)-F-x(4)-[EGN]-x(4)-[HKR]-x-[AGI] N 14: 46.5883 4( 4) G-x(3,4)-R-[IMV]-[LV]-L-[FL]-K-[DEH]-x-[DN]-x(2)-G-x(0,2)-F-x(4)-[EGN]-x(4)-[HKR]-x-[AGI] O 15: 44.1421 4( 4) H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P P 16: 43.1814 4( 4) G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Q 17: 39.9721 4( 4) D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P R 18: 39.0113 4( 4) A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] S 19: 31.6320 4( 4) Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P T 20: 28.7227 4( 4) P-x-P-[DPS]-[FHY]-W-x(0,1)-G-x(3)-V-x(2,4)-E Best patterns with alignements: fitness hits(seqs) Pattern A 1: 118.3506 4( 4) P-x-[AV]-[AS]-[IL]-x-F-x-W-x-[DEPT]-L-[ENQ]-[ER]-Q-V-x-[IV]-x-G-x-[ATV]-x-[HKR]-[ILV]-[NPST]-x(2)-[EQT]-[ASV]-x(2)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q Occurences: 4(4) PDX3_YEAST : 104- 153: diatn PnAAIvFfWkDLQRQVrVeGiTeHVNreTSerYFkTRPrGSkIGAWASrQ sdvik PDXH_ECOLI : 96- 145: qienn PrVSLlFpWhTLERQVmViGkAeRLStlEVmkYFhSRPrDSqIGAWVSkQ ssris PDXH_HAEIN : 109- 158: ciehn PyVALtFfWpELERQVrIeGkAvKIPaeQSdkYFaTRPyTSrIGAWASeQ savis PDXH_MYXXA : 149- 198: earah PyAALcFyWqPLNEQVrVeGrVeRVTdaEAdaYFqSRArGSqVGAWASlQ sqpla B 2: 116.8825 4( 4) F-x-W-x-[DEPT]-L-[ENQ]-[ER]-Q-V-x-[IV]-x-G-x-[ATV]-x-[HKR]-[ILV]-[NPST]-x(2)-[EQT]-[ASV]-x(2)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT] Occurences: 4(4) PDX3_YEAST : 110- 159: naaiv FfWkDLQRQVrVeGiTeHVNreTSerYFkTRPrGSkIGAWASrQSDvIkN reeld PDXH_ECOLI : 102- 151: rvsll FpWhTLERQVmViGkAeRLStlEVmkYFhSRPrDSqIGAWVSkQSSrIsA rgile PDXH_HAEIN : 115- 164: yvalt FfWpELERQVrIeGkAvKIPaeQSdkYFaTRPyTSrIGAWASeQSAvIsN yksll PDXH_MYXXA : 155- 204: yaalc FyWqPLNEQVrVeGrVeRVTdaEAdaYFqSRArGSqVGAWASlQSQpLaT reele C 3: 75.7900 4( 4) E-x(3,4)-Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 131- 165: ehvnr EtserYFkTRPrGSkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 124- 157: rlstl Evmk-YFhSRPrDSqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 136- 170: vkipa EqsdkYFaTRPyTSrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 177- 210: rvtda Eada-YFqSRArGSqVGAWASlQSQpLaTreeLeA rvaev D 4: 72.1199 4( 4) Y-F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 136- 165: etser YFkTRPrGSkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 128- 157: levmk YFhSRPrDSqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 141- 170: eqsdk YFaTRPyTSrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 181- 210: aeada YFqSRArGSqVGAWASlQSQpLaTreeLeA rvaev E 5: 67.9499 4( 4) F-x-[ST]-R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 137- 165: tsery FkTRPrGSkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 129- 157: evmky FhSRPrDSqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 142- 170: qsdky FaTRPyTSrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 182- 210: eaday FqSRArGSqVGAWASlQSQpLaTreeLeA rvaev F 6: 62.9925 4( 4) W-x-[AG]-x-[EP]-x-R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 199- 228: leief WqGrPsRLHDRfvYrRktENDPWkvvrLaP PDXH_ECOLI : 190- 217: eqief WqGgEhRLHDRflYqR--ENDAWkidrLaP PDXH_HAEIN : 202- 229: etvef WqGrPsRLHDRirY-Rk-ESDNWirerLsP PDXH_MYXXA : 243- 270: drief WhAqEsRLHDRhvYlR--EDGGWrtqmLyP G 7: 60.6044 4( 4) R-[AP]-x-[DGT]-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 140- 165: ryfkt RPrGSkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 132- 157: kyfhs RPrDSqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 145- 170: kyfat RPyTSrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 185- 210: ayfqs RArGSqVGAWASlQSQpLaTreeLeA rvaev H 8: 55.4722 4( 4) R-x(1,2)-L-L-x(0,1)-K-[DEH]-x-[DN]-x(2)-G-[FM]-[TV]-[FI]-[FY]-[ST]-N-x(2)-[ST]-[RS]-[KR] Occurences: 4(4) PDX3_YEAST : 73- 95: grvss Ri-LLfKElDhrGFTIYSNwgTSR kahdi PDXH_ECOLI : 66- 88: gqpyq RivLL-KHyDekGMVFYTNlgSRK ahqie PDXH_HAEIN : 79- 101: grpns RmvLL-KEvNeqGFVFFTNylSRK ggcie PDXH_MYXXA : 119- 141: grpsa RvvLL-KDfDarGFVFYTNheSRK grear I 9: 53.7463 7( 4) R-x(1,3)-S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 7(4) PDX3_YEAST : 140- 165: ryfkt RprgSkIGAWASrQSDvIkNreeLdE ltqkn PDX3_YEAST : 142- 165: fktrp Rg--SkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 132- 157: kyfhs RprdSqIGAWVSkQSSrIsArgiLeS kflel PDXH_ECOLI : 134- 157: fhsrp Rd--SqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 145- 170: kyfat RpytSrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 185- 210: ayfqs RargSqVGAWASlQSQpLaTreeLeA rvaev PDXH_MYXXA : 187- 210: fqsra Rg--SqVGAWASlQSQpLaTreeLeA rvaev J 10: 52.4822 4( 4) R-L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 205- 228: qgrps RLHDRfvYrRktENDPWkvvrLaP PDXH_ECOLI : 196- 217: qggeh RLHDRflYqR--ENDAWkidrLaP PDXH_HAEIN : 208- 229: qgrps RLHDRirY-Rk-ESDNWirerLsP PDXH_MYXXA : 249- 270: haqes RLHDRhvYlR--EDGGWrtqmLyP K 11: 50.5763 4( 4) S-x-[IV]-G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 144- 165: trprg SkIGAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 136- 157: srprd SqIGAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 149- 170: trpyt SrIGAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 189- 210: srarg SqVGAWASlQSQpLaTreeLeA rvaev L 12: 48.3122 4( 4) L-H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 206- 228: grpsr LHDRfvYrRktENDPWkvvrLaP PDXH_ECOLI : 197- 217: ggehr LHDRflYqR--ENDAWkidrLaP PDXH_HAEIN : 209- 229: grpsr LHDRirY-Rk-ESDNWirerLsP PDXH_MYXXA : 250- 270: aqesr LHDRhvYlR--EDGGWrtqmLyP M 13: 47.0883 4( 4) G-x(4)-R-[IMV]-[LV]-L-[FL]-K-[DEH]-x-[DN]-x(2)-G-x(0,2)-F-x(4)-[EGN]-x(4)-[HKR]-x-[AGI] Occurences: 4(4) PDX3_YEAST : 68- 97: aelps GrvssRILLFKElDhrG--FtiysNwgtsRkA hdiat PDXH_ECOLI : 61- 92: tvdeh GqpyqRIVLLKHyDekGmvFytnlGsrkaHqI ennpr PDXH_HAEIN : 74- 103: tvdeq GrpnsRMVLLKEvNeqG--FvfftNylsrKgG ciehn PDXH_MYXXA : 114- 145: tvgdd GrpsaRVVLLKDfDarGfvFytnhEsrkgReA rahpy N 14: 46.5883 4( 4) G-x(3,4)-R-[IMV]-[LV]-L-[FL]-K-[DEH]-x-[DN]-x(2)-G-x(0,2)-F-x(4)-[EGN]-x(4)-[HKR]-x-[AGI] Occurences: 4(4) PDX3_YEAST : 68- 97: aelps GrvssRILLFKElDhrG--FtiysNwgtsRkA hdiat PDXH_ECOLI : 61- 92: tvdeh GqpyqRIVLLKHyDekGmvFytnlGsrkaHqI ennpr PDXH_HAEIN : 74- 103: tvdeq GrpnsRMVLLKEvNeqG--FvfftNylsrKgG ciehn PDXH_MYXXA : 114- 145: tvgdd GrpsaRVVLLKDfDarGfvFytnhEsrkgReA rahpy O 15: 44.1421 4( 4) H-D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 207- 228: rpsrl HDRfvYrRktENDPWkvvrLaP PDXH_ECOLI : 198- 217: gehrl HDRflYqR--ENDAWkidrLaP PDXH_HAEIN : 210- 229: rpsrl HDRirY-Rk-ESDNWirerLsP PDXH_MYXXA : 251- 270: qesrl HDRhvYlR--EDGGWrtqmLyP P 16: 43.1814 4( 4) G-A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 147- 165: rgski GAWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 139- 157: rdsqi GAWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 152- 170: ytsri GAWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 192- 210: rgsqv GAWASlQSQpLaTreeLeA rvaev Q 17: 39.9721 4( 4) D-R-x(2)-Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 208- 228: psrlh DRfvYrRktENDPWkvvrLaP PDXH_ECOLI : 199- 217: ehrlh DRflYqR--ENDAWkidrLaP PDXH_HAEIN : 211- 229: psrlh DRirY-Rk-ESDNWirerLsP PDXH_MYXXA : 252- 270: esrlh DRhvYlR--EDGGWrtqmLyP R 18: 39.0113 4( 4) A-W-[AV]-S-x-Q-S-[ADQS]-x-[IL]-x-[ANT]-x(3)-L-x-[AES] Occurences: 4(4) PDX3_YEAST : 148- 165: gskig AWASrQSDvIkNreeLdE ltqkn PDXH_ECOLI : 140- 157: dsqig AWVSkQSSrIsArgiLeS kflel PDXH_HAEIN : 153- 170: tsrig AWASeQSAvIsNyksLlA kaalv PDXH_MYXXA : 193- 210: gsqvg AWASlQSQpLaTreeLeA rvaev S 19: 31.6320 4( 4) Y-x(0,1)-R-x(0,2)-E-[DNS]-[DG]-[AGNP]-W-x(4)-L-x-P Occurences: 4(4) PDX3_YEAST : 212- 228: hdrfv YrRktENDPWkvvrLaP PDXH_ECOLI : 203- 217: hdrfl YqR--ENDAWkidrLaP PDXH_HAEIN : 215- 229: hdrir Y-Rk-ESDNWirerLsP PDXH_MYXXA : 256- 270: hdrhv YlR--EDGGWrtqmLyP T 20: 28.7227 4( 4) P-x-P-[DPS]-[FHY]-W-x(0,1)-G-x(3)-V-x(2,4)-E Occurences: 4(4) PDX3_YEAST : 181- 195: daedi PcPDYWgGlriVpl--E iefwq PDX3_YEAST : 181- 197: daedi PcPDYWgGlriVpleiE fwqgr PDXH_ECOLI : 172- 185: qqgev PlPSFW-GgfrVsl--E qiefw PDXH_HAEIN : 184- 197: hplnv PrPDYW-GgylVvp--E tvefw PDXH_HAEIN : 184- 200: hplnv PrPDYWgGylvVpetvE fwqgr PDXH_MYXXA : 225- 241: agqpv PrPPHWsGfrvVpdriE fwhaq Number of patterns evaluated by Pratt:4471 Total running time: 1 seconds