------------------------------------------------------------ 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 FORMATE_NITRITE_TP_2 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 FORMATE_NITRITE_TP_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: FDHC_METFO 280 FOCA_ECOLI 285 FOCA_HAEIN 284 NIRC_ECOLI 268 NIRC_SALTY 269 YHA8_YEAST 627 YWCJ_BACSU 256 Pratt run started at Thu Feb 6 19:30:06 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.8503 7( 7) G-x(1,3)-N-x(2)-V-C-x-A 2: 16.6802 8( 7) I-x(3)-L-x(5)-G-x(4)-G 3: 16.6802 7( 7) F-x(3)-G-x(2)-H-x(4)-M 4: 16.6802 7( 7) N-x(2)-V-C-x-A 5: 16.1802 8( 7) F-x(2,3)-G-x(2)-H-x(4)-M 6: 16.1802 8( 7) G-N-x(2)-G-x(2,3)-F 7: 15.6802 9( 7) L-x(0,1)-G-x-L-x(3,4)-V 8: 15.6802 7( 7) T-x(0,1)-G-x(0,1)-N-x(3)-G 9: 15.6802 7( 7) P-x(3,4)-G-N-x(2,3)-G 10: 15.6802 8( 7) L-x(3,4)-G-x(1,2)-L-F 11: 15.6802 8( 7) L-x(4)-G-x(0,2)-L-F 12: 15.6802 8( 7) L-x(4)-G-x(1,3)-L-F 13: 15.1802 7( 7) N-x(3)-G-x(4,5)-G-x(2,4)-Y 14: 15.1802 7( 7) G-x(0,2)-N-x(3)-G-x(4,5)-G 15: 15.1802 7( 7) L-x-N-x(1,2)-V-x(0,2)-L 16: 15.1802 9( 7) G-x(1,3)-L-x(2)-G-x(2,3)-F 17: 15.1802 11( 7) G-x(1,3)-L-x(1,2)-G-x(2)-F 18: 12.5102 8( 7) G-N-x(3)-G 19: 12.5102 7( 7) E-x(4)-N-M 20: 12.5102 7( 7) L-x(5)-F-x(2)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 42.5026 7( 7) F-x(3)-G-[FY]-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] B 2: 42.0026 8( 7) F-x(2,3)-G-[FY]-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] C 3: 39.3181 7( 7) F-x(3)-G-x-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] D 4: 38.2986 7( 7) G-x(1,3)-N-x-[FLM]-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] E 5: 36.1430 7( 7) F-x(3)-G-x(2)-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] F 6: 35.4214 7( 7) G-x(1,3)-N-x(2)-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] G 7: 35.1285 7( 7) N-x-[FLM]-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] H 8: 30.5089 7( 7) I-x(3)-L-[GIL]-x-[AILV]-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] I 9: 27.8326 7( 7) I-x(3)-L-x(2)-[AILV]-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] J 10: 27.6006 7( 7) G-N-x(2)-[AGS]-G-[AGILV]-[FILV]-[FILM]-x-[AG]-x(3)-[FWY] K 11: 26.7405 7( 7) G-N-[FIL]-[IV]-G-x(2,3)-F-x-[AGIL]-x-[ILMV] L 12: 25.8293 7( 7) T-x(0,1)-G-x(0,1)-N-x(3)-G-[AGILV]-[FILV]-x-[IMV]-[GV] M 13: 25.5934 7( 7) I-x(3)-L-x(3)-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] N 14: 25.3378 7( 7) L-x(4)-G-x(1,3)-L-F-x-[AGS]-x-[CTV]-[FILMV]-x-[FLMV] O 15: 24.7422 7( 7) L-x(3)-[ACTV]-G-x(0,2)-L-F-x-[AEGS]-x-[CSTV]-[ILMV] P 16: 23.2629 7( 7) P-x(3,4)-G-N-x(2,3)-G-x-[ILV]-x-[FIMV]-[AGS] Q 17: 23.0047 7( 7) I-x(3)-L-x(4)-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] R 18: 20.7635 7( 7) I-x(3)-L-x(5)-G-x(2)-[FILMV]-x-G-x-[FILMV] S 19: 20.6954 7( 7) E-x(3)-[AL]-N-M-x(3)-[APV]-[ILMV] T 20: 20.0669 7( 7) L-[ACGS]-N-x(1,2)-V-x(0,2)-L-x-[FIV] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 42.5026 7( 7) F-x(3)-G-[FY]-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] Occurences: 7(7) FDHC_METFO : 214- 234: fpima FvciGFEHVVANMffipVGiF iggvt FOCA_ECOLI : 202- 222: lpvam FvasGFEHSIANMfmipMGiV irdfa FOCA_HAEIN : 205- 225: mpigl FvasGFEHCVANMfmipMGiI tahfs NIRC_ECOLI : 190- 210: wclla FiasGYEHSIANMtlfaLSwF gnhse NIRC_SALTY : 190- 210: wclla FiasGYEHSVANMtlfaLSwF ghhsd YHA8_YEAST : 203- 223: fpiid FigiGFTHVVGDMsasfIAmL nganv YWCJ_BACSU : 194- 214: lfvfc FfisGFEHSIANMctfaISlL iehpd B 2: 42.0026 8( 7) F-x(2,3)-G-[FY]-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] Occurences: 8(7) FDHC_METFO : 214- 234: fpima FvciGFEHVVANMffipVGiF iggvt FOCA_ECOLI : 202- 222: lpvam FvasGFEHSIANMfmipMGiV irdfa FOCA_HAEIN : 205- 225: mpigl FvasGFEHCVANMfmipMGiI tahfs NIRC_ECOLI : 190- 210: wclla FiasGYEHSIANMtlfaLSwF gnhse NIRC_SALTY : 190- 210: wclla FiasGYEHSVANMtlfaLSwF ghhsd YHA8_YEAST : 203- 223: fpiid FigiGFTHVVGDMsasfIAmL nganv YWCJ_BACSU : 194- 214: lfvfc FfisGFEHSIANMctfaISlL iehpd YWCJ_BACSU : 195- 214: fvfcf Fis-GFEHSIANMctfaISlL iehpd C 3: 39.3181 7( 7) F-x(3)-G-x-[ET]-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] Occurences: 7(7) FDHC_METFO : 214- 234: fpima FvciGfEHVVANMffipVGiF iggvt FOCA_ECOLI : 202- 222: lpvam FvasGfEHSIANMfmipMGiV irdfa FOCA_HAEIN : 205- 225: mpigl FvasGfEHCVANMfmipMGiI tahfs NIRC_ECOLI : 190- 210: wclla FiasGyEHSIANMtlfaLSwF gnhse NIRC_SALTY : 190- 210: wclla FiasGyEHSVANMtlfaLSwF ghhsd YHA8_YEAST : 203- 223: fpiid FigiGfTHVVGDMsasfIAmL nganv YWCJ_BACSU : 194- 214: lfvfc FfisGfEHSIANMctfaISlL iehpd D 4: 38.2986 7( 7) G-x(1,3)-N-x-[FLM]-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] Occurences: 7(7) FDHC_METFO : 182- 199: fwrai Gc--NwLVCLAVYLavasDD vigks FOCA_ECOLI : 168- 187: eavcl GilaNlMVCLAVWMsysgRS lmdka FOCA_HAEIN : 171- 190: eafnl GilcNiMVCVAVWMsysgKT vtdka NIRC_ECOLI : 157- 176: vlffk GalcNwLVCLAIWMalrtEG aakfi NIRC_SALTY : 157- 176: vlffk GalcNwLVCLAIWMairtEG takfl YHA8_YEAST : 169- 188: qtflk GiacNfFVCLAIYLqlmaKP ihvkf YWCJ_BACSU : 160- 179: elffr GmlcNwLVCLAFFIpmslKG egakl E 5: 36.1430 7( 7) F-x(3)-G-x(2)-H-[CSV]-[IV]-[AG]-[DN]-M-x(4)-[ILMV]-[AGS]-x-[FILV] Occurences: 7(7) FDHC_METFO : 214- 234: fpima FvciGfeHVVANMffipVGiF iggvt FOCA_ECOLI : 202- 222: lpvam FvasGfeHSIANMfmipMGiV irdfa FOCA_HAEIN : 205- 225: mpigl FvasGfeHCVANMfmipMGiI tahfs NIRC_ECOLI : 190- 210: wclla FiasGyeHSIANMtlfaLSwF gnhse NIRC_SALTY : 190- 210: wclla FiasGyeHSVANMtlfaLSwF ghhsd YHA8_YEAST : 203- 223: fpiid FigiGftHVVGDMsasfIAmL nganv YWCJ_BACSU : 194- 214: lfvfc FfisGfeHSIANMctfaISlL iehpd F 6: 35.4214 7( 7) G-x(1,3)-N-x(2)-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] Occurences: 7(7) FDHC_METFO : 182- 199: fwrai Gc--NwlVCLAVYLavasDD vigks FOCA_ECOLI : 168- 187: eavcl GilaNlmVCLAVWMsysgRS lmdka FOCA_HAEIN : 171- 190: eafnl GilcNimVCVAVWMsysgKT vtdka NIRC_ECOLI : 157- 176: vlffk GalcNwlVCLAIWMalrtEG aakfi NIRC_SALTY : 157- 176: vlffk GalcNwlVCLAIWMairtEG takfl YHA8_YEAST : 169- 188: qtflk GiacNffVCLAIYLqlmaKP ihvkf YWCJ_BACSU : 160- 179: elffr GmlcNwlVCLAFFIpmslKG egakl G 7: 35.1285 7( 7) N-x-[FLM]-V-C-[LV]-A-[FIV]-[FWY]-[ILM]-x(4)-[DEKR]-[DGPST] Occurences: 7(7) FDHC_METFO : 184- 199: raigc NwLVCLAVYLavasDD vigks FOCA_ECOLI : 172- 187: lgila NlMVCLAVWMsysgRS lmdka FOCA_HAEIN : 175- 190: lgilc NiMVCVAVWMsysgKT vtdka NIRC_ECOLI : 161- 176: kgalc NwLVCLAIWMalrtEG aakfi NIRC_SALTY : 161- 176: kgalc NwLVCLAIWMairtEG takfl YHA8_YEAST : 173- 188: kgiac NfFVCLAIYLqlmaKP ihvkf YWCJ_BACSU : 164- 179: rgmlc NwLVCLAFFIpmslKG egakl H 8: 30.5089 7( 7) I-x(3)-L-[GIL]-x-[AILV]-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] Occurences: 7(7) FDHC_METFO : 249- 266: finnm IpatLGnIVGGaiFvGcI ywfty FOCA_ECOLI : 251- 268: tvmnf ItdnLIpVTIGniIgGgL lvglt FOCA_HAEIN : 254- 271: dlyhf IvknLIpVTLGniVgGaI cigvf NIRC_ECOLI : 222- 239: ytlag IghnLLwVTLGntLsGaV fmglg NIRC_SALTY : 222- 239: ytlag IghnLLwVTLGntLsGvV fmglg YHA8_YEAST : 234- 251: svgky IwklLIpASLGniVgGlF fsavv YWCJ_BACSU : 231- 248: avrnl IpvtLGnLTAGivMmGwM yytln I 9: 27.8326 7( 7) I-x(3)-L-x(2)-[AILV]-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] Occurences: 7(7) FDHC_METFO : 249- 266: finnm IpatLgnIVGGaiFvGcI ywfty FOCA_ECOLI : 251- 268: tvmnf ItdnLipVTIGniIgGgL lvglt FOCA_HAEIN : 254- 271: dlyhf IvknLipVTLGniVgGaI cigvf NIRC_ECOLI : 222- 239: ytlag IghnLlwVTLGntLsGaV fmglg NIRC_SALTY : 222- 239: ytlag IghnLlwVTLGntLsGvV fmglg YHA8_YEAST : 234- 251: svgky IwklLipASLGniVgGlF fsavv YWCJ_BACSU : 231- 248: avrnl IpvtLgnLTAGivMmGwM yytln J 10: 27.6006 7( 7) G-N-x(2)-[AGS]-G-[AGILV]-[FILV]-[FILM]-x-[AG]-x(3)-[FWY] Occurences: 7(7) FDHC_METFO : 254- 268: ipatl GNivGGAIFvGciyW ftylr FOCA_ECOLI : 261- 275: ipvti GNiiGGGLLvGltyW viylr FOCA_HAEIN : 123- 137: ivvyl GNfvGGLFIaAviwF sgqtm NIRC_ECOLI : 232- 246: lwvtl GNtlSGAVFmGlgyW yatpk NIRC_SALTY : 232- 246: lwvtl GNtlSGVVFmGlgyW yatpk YHA8_YEAST : 244- 258: ipasl GNivGGLFFsAvvpF ylhlv YWCJ_BACSU : 236- 250: ipvtl GNltAGIVMmGwmyY tlnpd K 11: 26.7405 7( 7) G-N-[FIL]-[IV]-G-x(2,3)-F-x-[AGIL]-x-[ILMV] Occurences: 7(7) FDHC_METFO : 254- 266: ipatl GNIVGgaiFvGcI ywfty FOCA_ECOLI : 120- 132: lnvyf GNLVGallFvLlM wlsge FOCA_HAEIN : 123- 134: ivvyl GNFVGgl-FiAaV iwfsg NIRC_ECOLI : 111- 122: pqtwl GNLVGsv-FvAmL yswgg NIRC_SALTY : 111- 122: pqtwl GNLVGsv-FvAlL yswgg YHA8_YEAST : 244- 256: ipasl GNIVGglfFsAvV pfylh YWCJ_BACSU : 114- 126: mssya GNLIGailFaIlI satgl L 12: 25.8293 7( 7) T-x(0,1)-G-x(0,1)-N-x(3)-G-[AGILV]-[FILV]-x-[IMV]-[GV] Occurences: 7(7) FDHC_METFO : 252- 264: nmipa TlG-NivgGAIfVG ciywf FOCA_ECOLI : 259- 271: nlipv TiG-NiigGGLlVG ltywv FOCA_HAEIN : 262- 274: nlipv TlG-NivgGAIcIG vfqry NIRC_ECOLI : 230- 242: nllwv TlG-NtlsGAVfMG lgywy NIRC_SALTY : 230- 242: nllwv TlG-NtlsGVVfMG lgywy YHA8_YEAST : 72- 84: ivnli T-GvNfamGLFyVV mmgad YWCJ_BACSU : 234- 246: nlipv TlG-NltaGIVmMG wmyyt M 13: 25.5934 7( 7) I-x(3)-L-x(3)-[STV]-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] Occurences: 7(7) FDHC_METFO : 249- 266: finnm IpatLgniVGGaiFvGcI ywfty FOCA_ECOLI : 251- 268: tvmnf ItdnLipvTIGniIgGgL lvglt FOCA_HAEIN : 254- 271: dlyhf IvknLipvTLGniVgGaI cigvf NIRC_ECOLI : 222- 239: ytlag IghnLlwvTLGntLsGaV fmglg NIRC_SALTY : 222- 239: ytlag IghnLlwvTLGntLsGvV fmglg YHA8_YEAST : 234- 251: svgky IwklLipaSLGniVgGlF fsavv YWCJ_BACSU : 231- 248: avrnl IpvtLgnlTAGivMmGwM yytln N 14: 25.3378 7( 7) L-x(4)-G-x(1,3)-L-F-x-[AGS]-x-[CTV]-[FILMV]-x-[FLMV] Occurences: 7(7) FDHC_METFO : 79- 95: pvglm LvviaGse-LFtGnCMyM pmgil FOCA_ECOLI : 81- 97: slgli LcvvcGad-LFtStVLiV vakas FOCA_HAEIN : 122- 137: wivvy LgnfvGg--LFiAaVIwF sgqtm NIRC_ECOLI : 71- 87: gialt LviiaGse-LFtGhTMfL tfgvk NIRC_SALTY : 71- 87: gialt LviiaGse-LFtGhTMfL tlgvk YHA8_YEAST : 243- 258: lipas LgnivGg--LFfSaVVpF ylhlv YWCJ_BACSU : 73- 90: fgaai LmiayGggdLFtGnTFyF tytal O 15: 24.7422 7( 7) L-x(3)-[ACTV]-G-x(0,2)-L-F-x-[AEGS]-x-[CSTV]-[ILMV] Occurences: 7(7) FDHC_METFO : 79- 93: pvglm LvviAGseLFtGnCM ympmg FOCA_ECOLI : 81- 95: slgli LcvvCGadLFtStVL ivvak FOCA_HAEIN : 122- 135: wivvy LgnfVGg-LFiAaVI wfsgq NIRC_ECOLI : 71- 85: gialt LviiAGseLFtGhTM fltfg NIRC_SALTY : 71- 85: gialt LviiAGseLFtGhTM fltlg YHA8_YEAST : 243- 256: lipas LgniVGg-LFfSaVV pfylh YWCJ_BACSU : 125- 137: ilfai LisaTG--LFeEpSV hsfli P 16: 23.2629 7( 7) P-x(3,4)-G-N-x(2,3)-G-x-[ILV]-x-[FIMV]-[AGS] Occurences: 7(7) FDHC_METFO : 250- 264: innmi Patl-GNivgGaIfVG ciywf FOCA_ECOLI : 257- 271: tdnli Pvti-GNiigGgLlVG ltywv FOCA_HAEIN : 260- 274: vknli Pvtl-GNivgGaIcIG vfqry NIRC_ECOLI : 106- 120: mwail PqtwlGNlv-GsVfVA mlysw NIRC_SALTY : 106- 120: mwail PqtwlGNlv-GsVfVA llysw YHA8_YEAST : 240- 253: wklli Pasl-GNiv-GgLfFS avvpf YWCJ_BACSU : 232- 246: vrnli Pvtl-GNltaGiVmMG wmyyt Q 17: 23.0047 7( 7) I-x(3)-L-x(4)-[AGIL]-G-x(2)-[FILMV]-x-G-x-[FILMV] Occurences: 7(7) FDHC_METFO : 249- 266: finnm IpatLgnivGGaiFvGcI ywfty FOCA_ECOLI : 251- 268: tvmnf ItdnLipvtIGniIgGgL lvglt FOCA_HAEIN : 254- 271: dlyhf IvknLipvtLGniVgGaI cigvf NIRC_ECOLI : 222- 239: ytlag IghnLlwvtLGntLsGaV fmglg NIRC_SALTY : 222- 239: ytlag IghnLlwvtLGntLsGvV fmglg YHA8_YEAST : 234- 251: svgky IwklLipasLGniVgGlF fsavv YWCJ_BACSU : 231- 248: avrnl IpvtLgnltAGivMmGwM yytln R 18: 20.7635 7( 7) I-x(3)-L-x(5)-G-x(2)-[FILMV]-x-G-x-[FILMV] Occurences: 7(7) FDHC_METFO : 249- 266: finnm IpatLgnivgGaiFvGcI ywfty FOCA_ECOLI : 251- 268: tvmnf ItdnLipvtiGniIgGgL lvglt FOCA_HAEIN : 254- 271: dlyhf IvknLipvtlGniVgGaI cigvf NIRC_ECOLI : 222- 239: ytlag IghnLlwvtlGntLsGaV fmglg NIRC_SALTY : 222- 239: ytlag IghnLlwvtlGntLsGvV fmglg YHA8_YEAST : 234- 251: svgky IwklLipaslGniVgGlF fsavv YWCJ_BACSU : 231- 248: avrnl IpvtLgnltaGivMmGwM yytln S 19: 20.6954 7( 7) E-x(3)-[AL]-N-M-x(3)-[APV]-[ILMV] Occurences: 7(7) FDHC_METFO : 220- 231: vcigf EhvvANMffiPV gifig FOCA_ECOLI : 208- 219: vasgf EhsiANMfmiPM givir FOCA_HAEIN : 211- 222: vasgf EhcvANMfmiPM giita NIRC_ECOLI : 196- 207: iasgy EhsiANMtlfAL swfgn NIRC_SALTY : 196- 207: iasgy EhsvANMtlfAL swfgh YHA8_YEAST : 282- 293: yeard EqpeLNMdsrVV riqkn YWCJ_BACSU : 200- 211: fisgf EhsiANMctfAI sllie T 20: 20.0669 7( 7) L-[ACGS]-N-x(1,2)-V-x(0,2)-L-x-[FIV] Occurences: 7(7) FDHC_METFO : 27- 35: kekap LSNliV--LsF vagay FOCA_ECOLI : 170- 179: vclgi LANlmVc-LaV wmsys FOCA_HAEIN : 122- 131: wivvy LGNf-VggLfI aaviw NIRC_ECOLI : 159- 168: ffkga LCNwlVc-LaI wmalr NIRC_SALTY : 159- 168: ffkga LCNwlVc-LaI wmair YHA8_YEAST : 243- 252: lipas LGNi-VggLfF savvp YWCJ_BACSU : 162- 171: ffrgm LCNwlVc-LaF fipms Number of patterns evaluated by Pratt:5713 Total running time: 3 seconds