------------------------------------------------------------ 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 SUCCINYL_COA_LIGASES 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 SUCCINYL_COA_LIGASES.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ACLY_RAT 1100 SUCA_DICDI 41 SUCA_RAT 333 SUCD_ECOLI 288 SUCD_HAEIN 293 SUCD_THEFL 288 Pratt run started at Thu Feb 6 21:16:10 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.8503 6( 6) F-x(3)-L-x(2)-F-x(2)-D-x(1,3)-T 2: 16.1802 6( 6) G-x-A-x(0,1)-G-A 3: 15.6802 6( 6) A-x(2,3)-I-x(0,1)-V-P 4: 15.6802 8( 6) G-x(0,1)-A-x-A-x(1,2)-I 5: 15.6802 7( 6) L-x(0,1)-P-x-F-x(0,1)-N 6: 15.6802 6( 6) L-x(2)-F-x(2)-D-x(1,3)-T 7: 15.6802 6( 6) K-P-x-V-x(1,3)-I 8: 15.1802 6( 6) V-x(2,4)-G-x(1,2)-T-G 9: 15.1802 6( 6) L-x(3,4)-T-K-x(0,2)-V 10: 14.6802 8( 6) A-x(4)-A-x(2,4)-I-x(1,3)-V 11: 14.6802 7( 6) P-V-x(0,2)-F-x(3,5)-A 12: 14.6802 6( 6) H-x(3,5)-P-V-x(0,2)-F 13: 14.6802 6( 6) I-x(0,2)-N-x(0,2)-T-x-V 14: 12.5102 6( 6) T-x(3)-A-x-V 15: 12.5102 8( 6) V-x(2)-G-x(3)-G 16: 12.5102 6( 6) L-x(2)-P-V 17: 12.5102 7( 6) T-x(3)-V-x-I 18: 12.0102 6( 6) I-x(0,1)-V-P 19: 12.0102 6( 6) V-x(1,2)-V-P 20: 12.0102 6( 6) A-x(2)-I-x(1,2)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 36.2517 6( 6) F-x(3)-L-x(2)-F-x(2)-D-x(1,3)-T-x-[AGL]-x-[AIV]-x-[IPV]-[GIL]-x-[IV]-[GPT] B 2: 33.3167 6( 6) V-[FLMV]-x-G-[DE]-[AI]-[GT]-G-x-[ADEN]-[AE]-x(2)-[AI] C 3: 32.0816 6( 6) L-x(2)-F-x(2)-D-x(1,3)-T-x-[AGL]-x-[AIV]-x-[IPV]-[GIL]-x-[IV]-[GPT] D 4: 29.3790 7( 6) L-x(0,1)-P-[LV]-F-x(0,1)-N-x-[ADV]-x-[AET]-x(4)-[PTV]-x-[AIV] E 5: 28.2867 6( 6) L-[DGT]-x-P-V-x-[CDN]-x-[CDV]-x-[EGT]-[AGT]-x-[AEN] F 6: 25.8661 6( 6) T-[EK]-[ADGP]-x-V-x-I-x-[DEK]-x-[AGT]-x(4)-[AEQ] G 7: 25.8599 6( 6) I-x(0,2)-N-x(0,2)-T-x-V-[AIL]-x-[QT]-x(3)-[GIL]-x(2)-[AGP] H 8: 25.8466 6( 6) V-x(2,4)-G-x(1,2)-T-G-x-[ENPQ]-[AGI]-x-[FV]-x(3)-[EPQ] I 9: 24.1175 6( 6) K-P-[SV]-V-x(1,3)-I-[AGN]-x(2)-[AST] J 10: 22.6956 6( 6) H-x(3,5)-P-V-x(0,2)-F-x-[GNT]-x(2)-[DEST]-[AG] K 11: 22.6618 6( 6) G-[DH]-A-x(0,1)-G-A-x-[AI] L 12: 19.2121 7( 6) A-[AET]-x(2)-[ADENT]-A-x(2,4)-I-x(1,3)-V M 13: 18.3339 8( 6) G-x(0,1)-A-x-A-x(1,2)-I-x-[GNV] N 14: 17.7211 6( 6) T-x(2)-[NTV]-A-x-V-x(2)-[AGV] O 15: 15.6802 6( 6) A-x(2,3)-I-x(0,1)-V-P P 16: 15.1998 6( 6) G-[DH]-A-x(0,1)-G Q 17: 15.1802 6( 6) L-x(3,4)-T-K-x(0,2)-V R 18: 14.6802 7( 6) P-V-x(0,2)-F-x(3,5)-A S 19: 14.6136 6( 6) A-[DST]-x-I-x(1,2)-V T 20: 12.5102 6( 6) T-x(3)-A-x-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 36.2517 6( 6) F-x(3)-L-x(2)-F-x(2)-D-x(1,3)-T-x-[AGL]-x-[AIV]-x-[IPV]-[GIL]-x-[IV]-[GPT] Occurences: 6(6) ACLY_RAT : 184- 208: eilas FisgLfnFyeDlyfTyLeInPLvVT kdgvy SUCA_DICDI : 19- 41: viiqx FhldLpvFngDa--TgAnAtVIyVP SUCA_RAT : 223- 246: fngtn FidcLdvFlkDpa-TeGiVlIGeIG ghaee SUCD_ECOLI : 187- 210: ipgsn FidiLemFekDpq-TeAiVmIGeIG gsaee SUCD_HAEIN : 188- 211: ipgss FidiLerFqqDpe-TeAiVmIGeIG gsaee SUCD_THEFL : 187- 210: vigtt FkdlLplFneDpe-TeAvVlIGeIG gsdee B 2: 33.3167 6( 6) V-[FLMV]-x-G-[DE]-[AI]-[GT]-G-x-[ADEN]-[AE]-x(2)-[AI] Occurences: 6(6) ACLY_RAT : 713- 726: gvkmi VVlGEIGGtEEykI crgik SUCA_DICDI : 25- 38: hldlp VFnGDATGaNAtvI yvp SUCA_RAT : 240- 253: ategi VLiGEIGGhAEenA aeflk SUCD_ECOLI : 204- 217: qteai VMiGEIGGsAEeeA aayik SUCD_HAEIN : 205- 218: eteai VMiGEIGGsAEeeA aifik SUCD_THEFL : 204- 217: eteav VLiGEIGGsDEeeA aawvk C 3: 32.0816 6( 6) L-x(2)-F-x(2)-D-x(1,3)-T-x-[AGL]-x-[AIV]-x-[IPV]-[GIL]-x-[IV]-[GPT] Occurences: 6(6) ACLY_RAT : 188- 208: sfisg LfnFyeDlyfTyLeInPLvVT kdgvy SUCA_DICDI : 23- 41: xfhld LpvFngDa--TgAnAtVIyVP SUCA_RAT : 227- 246: nfidc LdvFlkDpa-TeGiVlIGeIG ghaee SUCD_ECOLI : 191- 210: nfidi LemFekDpq-TeAiVmIGeIG gsaee SUCD_HAEIN : 192- 211: sfidi LerFqqDpe-TeAiVmIGeIG gsaee SUCD_THEFL : 191- 210: tfkdl LplFneDpe-TeAvVlIGeIG gsdee D 4: 29.3790 7( 6) L-x(0,1)-P-[LV]-F-x(0,1)-N-x-[ADV]-x-[AET]-x(4)-[PTV]-x-[AIV] Occurences: 7(6) ACLY_RAT : 548- 565: ghkei LiPVFkNmAdAmkkhPeV dvlin SUCA_DICDI : 23- 38: xfhld L-PVF-NgDaTganaTvI yvp SUCA_RAT : 85- 100: kkhlg L-PVF-NtVkEakekTgA tasvi SUCD_ECOLI : 50- 65: tthlg L-PVF-NtVrEavaaTgA tasvi SUCD_HAEIN : 51- 66: tthlg L-PVF-NtVrEavenTgV tatvi SUCD_THEFL : 190- 206: ttfkd LlPLF-NeDpEteavVlI geigg SUCD_THEFL : 191- 206: tfkdl L-PLF-NeDpEteavVlI geigg E 5: 28.2867 6( 6) L-[DGT]-x-P-V-x-[CDN]-x-[CDV]-x-[EGT]-[AGT]-x-[AEN] Occurences: 6(6) ACLY_RAT : 735- 748: ikegr LTkPVvCwCiGTcA tmfss SUCA_DICDI : 21- 34: iqxfh LDlPVfNgDaTGaN atviy SUCA_RAT : 83- 96: ggkkh LGlPVfNtVkEAkE ktgat SUCD_ECOLI : 48- 61: ggtth LGlPVfNtVrEAvA atgat SUCD_HAEIN : 49- 62: ggtth LGlPVfNtVrEAvE ntgvt SUCD_THEFL : 48- 61: ggtev LGvPVyDtVkEAvA hhevd F 6: 25.8661 6( 6) T-[EK]-[ADGP]-x-V-x-I-x-[DEK]-x-[AGT]-x(4)-[AEQ] Occurences: 6(6) ACLY_RAT : 208- 223: nplvv TKDgVyIlDlAakvdA tadyi SUCA_DICDI : 2- 17: d TKPsVlInKxTkviiQ xfhld SUCA_RAT : 236- 251: lkdpa TEGiVlIgEiGghaeE naaef SUCD_ECOLI : 200- 215: ekdpq TEAiVmIgEiGgsaeE eaaay SUCD_HAEIN : 201- 216: qqdpe TEAiVmIgEiGgsaeE eaaif SUCD_THEFL : 200- 215: nedpe TEAvVlIgEiGgsdeE eaaaw G 7: 25.8599 6( 6) I-x(0,2)-N-x(0,2)-T-x-V-[AIL]-x-[QT]-x(3)-[GIL]-x(2)-[AGP] Occurences: 6(6) ACLY_RAT : 344- 360: iiggs Ia-Nf-TnVAaTfkgIvrA irdyq SUCA_DICDI : 8- 24: kpsvl I--NkxTkVIiQxfhLdlP vfngd SUCA_RAT : 39- 55: rkniy IdkN--TkVIcQgftGkqG tfhsq SUCD_ECOLI : 4- 20: sil IdkN--TkVIcQgftGsqG tfhse SUCD_HAEIN : 5- 21: mail IdkN--TkVIcQgftGgqG tfhse SUCD_THEFL : 2- 20: m IlvNreTrVLvQgitGreG qfhtk H 8: 25.8466 6( 6) V-x(2,4)-G-x(1,2)-T-G-x-[ENPQ]-[AGI]-x-[FV]-x(3)-[EPQ] Occurences: 6(6) ACLY_RAT : 390- 408: qeglr VmgevGktTGiPIhVfgtE thmta SUCA_DICDI : 25- 41: hldlp Vfn--GdaTGaNAtViyvP SUCA_RAT : 45- 61: dkntk Vicq-Gf-TGkQGtFhsqQ aleyg SUCD_ECOLI : 10- 26: dkntk Vicq-Gf-TGsQGtFhseQ aiayg SUCD_HAEIN : 11- 27: dkntk Vicq-Gf-TGgQGtFhseQ alayg SUCD_THEFL : 10- 26: nretr Vlvq-Gi-TGrEGqFhtkQ mldyg I 9: 24.1175 6( 6) K-P-[SV]-V-x(1,3)-I-[AGN]-x(2)-[AST] Occurences: 6(6) ACLY_RAT : 737- 748: egrlt KPVVcwcIGtcA tmfss SUCA_DICDI : 3- 12: dt KPSVl--INkxT kviiq SUCA_RAT : 267- 277: sgpka KPVVsf-IAgiT appgr SUCD_ECOLI : 227- 237: kehvt KPVVgy-IAgvT apkgk SUCD_HAEIN : 228- 238: kdnvt KPVVay-IAgiT apkgk SUCD_THEFL : 227- 237: kdhmk KPVVgf-IGgrS apkgk J 10: 22.6956 6( 6) H-x(3,5)-P-V-x(0,2)-F-x-[GNT]-x(2)-[DEST]-[AG] Occurences: 6(6) ACLY_RAT : 544- 558: kfywg HkeiliPV--FkNmaDA mkkhp SUCA_DICDI : 20- 32: iiqxf Hldl--PV--FnGdaTG anatv SUCA_RAT : 82- 94: kggkk Hlgl--PV--FnTvkEA kektg SUCD_ECOLI : 47- 59: kggtt Hlgl--PV--FnTvrEA vaatg SUCD_HAEIN : 48- 60: kggtt Hlgl--PV--FnTvrEA ventg SUCD_THEFL : 224- 238: awvkd Hmkk--PVvgFiGgrSA pkgkr K 11: 22.6618 6( 6) G-[DH]-A-x(0,1)-G-A-x-[AI] Occurences: 6(6) ACLY_RAT : 758- 764: sevqf GHA-GAcA nqase SUCA_DICDI : 28- 35: lpvfn GDAtGAnA tviyv SUCA_RAT : 285- 291: pgrrm GHA-GAiI aggkg SUCD_ECOLI : 245- 251: kgkrm GHA-GAiI aggkg SUCD_HAEIN : 246- 252: kgkrm GHA-GAiI sggkg SUCD_THEFL : 245- 251: kgkrm GHA-GAiI mgnvg L 12: 19.2121 7( 6) A-[AET]-x(2)-[ADENT]-A-x(2,4)-I-x(1,3)-V Occurences: 7(6) ACLY_RAT : 218- 231: yildl AAkvDAtadyIck-V kwgdi SUCA_DICDI : 30- 40: vfngd ATgaNAtv--Iy--V p SUCA_RAT : 114- 127: ppfaa AAinEAidaeIpl-V vcite SUCA_RAT : 114- 128: ppfaa AAinEAidaeIplvV citeg SUCD_ECOLI : 62- 72: reava ATgaTAsv--Iy--V papfc SUCD_ECOLI : 213- 225: eiggs AEeeAAay--IkehV tkpvv SUCD_HAEIN : 214- 226: eiggs AEeeAAif--IkdnV tkpvv SUCD_THEFL : 80- 93: paaad AAleAAhag-IpliV liteg M 13: 18.3339 8( 6) G-x(0,1)-A-x-A-x(1,2)-I-x-[GNV] Occurences: 8(6) ACLY_RAT : 416- 425: mtaiv GmAwApaIpN qppta SUCA_DICDI : 32- 40: ngdat G-AnAtvIyV p SUCA_RAT : 99- 107: akekt G-AtAsvIyV pppfa SUCA_RAT : 285- 293: pgrrm GhAgAi-IaG gkgga SUCD_ECOLI : 64- 72: avaat G-AtAsvIyV papfc SUCD_ECOLI : 245- 253: kgkrm GhAgAi-IaG gkgta SUCD_HAEIN : 246- 254: kgkrm GhAgAi-IsG gkgta SUCD_THEFL : 245- 253: kgkrm GhAgAi-ImG nvgtp N 14: 17.7211 6( 6) T-x(2)-[NTV]-A-x-V-x(2)-[AGV] Occurences: 6(6) ACLY_RAT : 409- 418: vfgte ThmTAiVgmA wapai SUCA_DICDI : 31- 40: fngda TgaNAtViyV p SUCA_RAT : 98- 107: eakek TgaTAsViyV pppfa SUCD_ECOLI : 63- 72: eavaa TgaTAsViyV papfc SUCD_HAEIN : 64- 73: eaven TgvTAtViyV pasfc SUCD_THEFL : 32- 41: mldyg TkiVAgVtpG kggte O 15: 15.6802 6( 6) A-x(2,3)-I-x(0,1)-V-P Occurences: 6(6) ACLY_RAT : 805- 811: yedlv AkgaI-VP aqevp SUCA_DICDI : 35- 41: atgan Atv-IyVP SUCA_RAT : 102- 108: ktgat Asv-IyVP ppfaa SUCD_ECOLI : 67- 73: atgat Asv-IyVP apfck SUCD_HAEIN : 68- 74: ntgvt Atv-IyVP asfck SUCD_THEFL : 67- 73: hhevd Asi-IfVP apaaa P 16: 15.1998 6( 6) G-[DH]-A-x(0,1)-G Occurences: 6(6) ACLY_RAT : 758- 761: sevqf GHA-G acanq SUCA_DICDI : 28- 32: lpvfn GDAtG anatv SUCA_RAT : 285- 288: pgrrm GHA-G aiiag SUCD_ECOLI : 245- 248: kgkrm GHA-G aiiag SUCD_HAEIN : 246- 249: kgkrm GHA-G aiisg SUCD_THEFL : 245- 248: kgkrm GHA-G aiimg Q 17: 15.1802 6( 6) L-x(3,4)-T-K-x(0,2)-V Occurences: 6(6) ACLY_RAT : 491- 500: gksat LfsrhTKaiV wgmqt SUCA_DICDI : 7- 14: tkpsv LinkxTK--V iiqxf SUCA_RAT : 63- 70: hsqqa Leyg-TKl-V ggttp SUCD_ECOLI : 3- 10: si LidknTK--V icqgf SUCD_HAEIN : 4- 11: mai LidknTK--V icqgf SUCD_THEFL : 28- 35: htkqm Ldyg-TKi-V agvtp R 18: 14.6802 7( 6) P-V-x(0,2)-F-x(3,5)-A Occurences: 7(6) ACLY_RAT : 550- 556: keili PV--Fknm--A damkk ACLY_RAT : 550- 558: keili PV--FknmadA mkkhp SUCA_DICDI : 24- 30: fhldl PV--Fngd--A tgana SUCA_RAT : 86- 94: khlgl PV--FntvkeA kektg SUCA_RAT : 268- 278: gpkak PVvsFiagitA ppgrr SUCD_ECOLI : 51- 59: thlgl PV--FntvreA vaatg SUCD_HAEIN : 52- 60: thlgl PV--FntvreA ventg SUCD_THEFL : 228- 238: dhmkk PVvgFiggrsA pkgkr S 19: 14.6136 6( 6) A-[DST]-x-I-x(1,2)-V Occurences: 6(6) ACLY_RAT : 225- 231: kvdat ADyIckV kwgdi SUCA_DICDI : 35- 40: atgan ATvIy-V p SUCA_RAT : 102- 107: ktgat ASvIy-V pppfa SUCD_ECOLI : 67- 72: atgat ASvIy-V papfc SUCD_HAEIN : 68- 73: ntgvt ATvIy-V pasfc SUCD_THEFL : 67- 72: hhevd ASiIf-V papaa T 20: 12.5102 6( 6) T-x(3)-A-x-V Occurences: 6(6) ACLY_RAT : 409- 415: vfgte ThmtAiV gmawa SUCA_DICDI : 31- 37: fngda TganAtV iyvp SUCA_RAT : 98- 104: eakek TgatAsV iyvpp SUCD_ECOLI : 63- 69: eavaa TgatAsV iyvpa SUCD_HAEIN : 64- 70: eaven TgvtAtV iyvpa SUCD_THEFL : 32- 38: mldyg TkivAgV tpgkg Number of patterns evaluated by Pratt:1081 Total running time: 1 seconds