------------------------------------------------------------ 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 GLYCOPHORIN_A 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 GLYCOPHORIN_A.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: GLPA_HUMAN 150 GLPB_HUMAN 91 GLP_CANFA 52 GLP_HORSE 120 GLP_MACFU 144 GLP_MOUSE 168 GLP_PIG 133 Pratt run started at Thu Feb 6 19:35:53 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.0102 11( 7) T-x(3,4)-S-x(2)-T 2: 11.5102 16( 7) T-x(3,4)-S-x(1,2)-T 3: 11.5102 8( 7) T-x(3)-S-x(2,4)-T 4: 11.5102 7( 7) A-G-x(1,3)-I 5: 11.5102 9( 7) T-x(1,2)-A-x(2,3)-S 6: 11.5102 7( 7) S-x(4,5)-T-x(1,2)-A 7: 11.0102 12( 7) T-x(2,4)-T-x(4,5)-S 8: 11.0102 10( 7) S-x(2,3)-T-x(1,3)-T 9: 11.0102 11( 7) S-x(1,2)-T-x(0,2)-S 10: 11.0102 12( 7) S-x(2,4)-T-x(1,2)-S 11: 11.0102 11( 7) I-x(1,2)-T-x(2,4)-S 12: 11.0102 7( 7) G-x(1,3)-I-x(1,2)-T 13: 11.0102 9( 7) L-x(1,3)-A-x(2,3)-I 14: 11.0102 10( 7) S-x(3,4)-T-x(1,3)-A 15: 11.0102 8( 7) S-x(3,5)-T-x(1,2)-A 16: 11.0102 14( 7) I-x(0,2)-I-x(2,3)-I 17: 11.0102 8( 7) T-x(0,1)-I-x(0,2)-I 18: 10.5102 14( 7) S-x(0,2)-T-x(2,4)-S 19: 10.5102 21( 7) S-x(0,2)-S-x(2,4)-T 20: 8.3401 7( 7) G-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 15.9322 7( 7) T-[AEST]-[DEGT]-x-S-x(2,4)-T B 2: 15.7930 9( 7) S-x(3,4)-T-x(1,3)-A-x(3)-[EST]-x(3)-[EPST] C 3: 13.6980 7( 7) T-x(1,2)-A-x(2,3)-S-x(4)-[GSTV] D 4: 13.6165 9( 7) S-x(1,2)-T-x(0,2)-S-x(4)-[PQT] E 5: 13.2455 10( 7) T-x(2,4)-T-x(4,5)-S-[AGQS] F 6: 13.1387 12( 7) T-x(3,4)-S-x(1,2)-T-x-[ADGPST] G 7: 12.4069 13( 7) S-x(0,2)-T-x(2,4)-S-[AGNSV] H 8: 12.0102 11( 7) T-x(3,4)-S-x(2)-T I 9: 11.5102 7( 7) A-G-x(1,3)-I J 10: 11.5102 7( 7) S-x(4,5)-T-x(1,2)-A K 11: 11.0102 10( 7) S-x(2,3)-T-x(1,3)-T L 12: 11.0102 12( 7) S-x(2,4)-T-x(1,2)-S M 13: 11.0102 11( 7) I-x(1,2)-T-x(2,4)-S N 14: 11.0102 7( 7) G-x(1,3)-I-x(1,2)-T O 15: 11.0102 9( 7) L-x(1,3)-A-x(2,3)-I P 16: 11.0102 8( 7) S-x(3,5)-T-x(1,2)-A Q 17: 11.0102 14( 7) I-x(0,2)-I-x(2,3)-I R 18: 11.0102 8( 7) T-x(0,1)-I-x(0,2)-I S 19: 10.5102 21( 7) S-x(0,2)-S-x(2,4)-T T 20: 8.3401 7( 7) G-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 15.9322 7( 7) T-[AEST]-[DEGT]-x-S-x(2,4)-T Occurences: 7(7) GLPA_HUMAN : 29- 36: gvamh TSTsSsv--T ksyis GLPB_HUMAN : 29- 36: evamh TSTsSsv--T ksyis GLP_CANFA : 24- 31: agfis TEDpSfn--T pstre GLP_HORSE : 13- 20: ppiag TSDlSti--T saatp GLP_MACFU : 44- 51: sahev TTEfSgr--T hyppe GLP_MOUSE : 10- 17: taavt TSGhSlt--T tfhip GLP_MOUSE : 10- 18: taavt TSGhSltt-T fhips GLP_PIG : 109- 118: igten TADpSelqdT edppl B 2: 15.7930 9( 7) S-x(3,4)-T-x(1,3)-A-x(3)-[EST]-x(3)-[EPST] Occurences: 9(7) GLPA_HUMAN : 18- 34: aivsi SasstTgv-AmhtStssS vtksy GLPA_HUMAN : 18- 34: aivsi Sass-TtgvAmhtStssS vtksy GLPB_HUMAN : 18- 34: eivsi SalstTev-AmhtStssS vtksy GLPB_HUMAN : 18- 34: eivsi Sals-TtevAmhtStssS vtksy GLP_CANFA : 12- 27: iphqi SsklpTq--AgfiStedP sfntp GLP_CANFA : 13- 27: phqis Sklp-Tq--AgfiStedP sfntp GLP_HORSE : 14- 30: piagt Sdls-TitsAatpTfttE qdgre GLP_MACFU : 31- 48: ndkht SdshpTptsAhevTtefS grthy GLP_MACFU : 33- 48: khtsd ShptpTs--AhevTtefS grthy GLP_MOUSE : 60- 75: npnqh SatmsTp--AihvStyhT aptev GLP_PIG : 101- 118: pkpqd SpdigTentAdpsElqdT edppl C 3: 13.6980 7( 7) T-x(1,2)-A-x(2,3)-S-x(4)-[GSTV] Occurences: 7(7) GLPA_HUMAN : 23- 35: sasst TgvAmhtStsssV tksyi GLPB_HUMAN : 23- 35: salst TevAmhtStsssV tksyi GLP_CANFA : 17- 28: ssklp Tq-AgfiStedpS fntps GLP_HORSE : 2- 12: q Ti-Atg-SppiaG tsdls GLP_MACFU : 4- 16: sst TvpAthtSssslG peqyv GLP_MOUSE : 5- 16: mtes Ta-AvttSghslT ttfhi GLP_PIG : 21- 33: nvsna TvtAgkpSatspG vmtik D 4: 13.6165 9( 7) S-x(1,2)-T-x(0,2)-S-x(4)-[PQT] Occurences: 9(7) GLPA_HUMAN : 33- 43: htsts SsvTk-SyissQ tndth GLPA_HUMAN : 34- 43: tstss Sv-Tk-SyissQ tndth GLPB_HUMAN : 33- 43: htsts SsvTk-SyissQ tnget GLPB_HUMAN : 34- 43: tstss Sv-Tk-SyissQ tnget GLP_CANFA : 28- 38: stedp SfnTp-StredP sgtmy GLP_HORSE : 17- 26: gtsdl StiT--SaatpT ftteq GLP_MACFU : 33- 44: khtsd ShpTptSahevT tefsg GLP_MOUSE : 132- 143: isyci SrmTkkSsvdiQ spegg GLP_PIG : 28- 36: tagkp Sa-T--SpgvmT ikntt E 5: 13.2455 10( 7) T-x(2,4)-T-x(4,5)-S-[AGQS] Occurences: 10(7) GLPA_HUMAN : 31- 42: amhts TsssvTksyi-SS qtndt GLPA_HUMAN : 31- 43: amhts TsssvTksyisSQ tndth GLPB_HUMAN : 31- 42: amhts TsssvTksyi-SS qtnge GLPB_HUMAN : 31- 43: amhts TsssvTksyisSQ tnget GLP_CANFA : 31- 40: dpsfn Tps--Tredp-SG tmyqh GLP_HORSE : 109- 120: detsl Tsve-TdypgdSQ GLP_MACFU : 3- 14: ss TtvpaThtss-SS lgpeq GLP_MACFU : 4- 14: sst Tvpa-Thtss-SS lgpeq GLP_MOUSE : 2- 12: m Tes--TaavttSG hsltt GLP_MOUSE : 72- 82: aihvs Tyh--TaptevSA afeeq GLP_PIG : 1- 12: TetpvTgeqg-SA tpgnv GLP_PIG : 3- 12: te Tpv--Tgeqg-SA tpgnv F 6: 13.1387 12( 7) T-x(3,4)-S-x(1,2)-T-x-[ADGPST] Occurences: 12(7) GLPA_HUMAN : 29- 38: gvamh TstssSv-TkS yissq GLPA_HUMAN : 29- 38: gvamh Tsts-SsvTkS yissq GLPA_HUMAN : 36- 46: tsssv TksyiSsqTnD thkrd GLPB_HUMAN : 29- 38: evamh TstssSv-TkS yissq GLPB_HUMAN : 29- 38: evamh Tsts-SsvTkS yissq GLPB_HUMAN : 36- 46: tsssv TksyiSsqTnG etgql GLP_CANFA : 24- 33: agfis Tedp-SfnTpS tredp GLP_HORSE : 13- 22: ppiag Tsdl-StiTsA atptf GLP_MACFU : 128- 137: edpee TdelnSf-TkP nqern GLP_MOUSE : 9- 18: staav TtsghSl-TtT fhips GLP_MOUSE : 10- 18: taavt Tsgh-Sl-TtT fhips GLP_PIG : 6- 15: tetpv TgeqgSa-TpG nvsna GLP_PIG : 13- 23: eqgsa TpgnvSnaTvT agkps GLP_PIG : 23- 32: snatv TagkpSa-TsP gvmti G 7: 12.4069 13( 7) S-x(0,2)-T-x(2,4)-S-[AGNSV] Occurences: 13(7) GLPA_HUMAN : 30- 35: vamht S--Tss--SV tksyi GLPA_HUMAN : 33- 42: htsts SsvTksyiSS qtndt GLPA_HUMAN : 34- 42: tstss Sv-TksyiSS qtndt GLPA_HUMAN : 130- 139: vkplp SpdTdvplSS veien GLPB_HUMAN : 30- 35: vamht S--Tss--SV tksyi GLPB_HUMAN : 33- 42: htsts SsvTksyiSS qtnge GLPB_HUMAN : 34- 42: tstss Sv-TksyiSS qtnge GLP_CANFA : 33- 40: sfntp S--TredpSG tmyqh GLP_HORSE : 17- 22: gtsdl S--Tit--SA atptf GLP_HORSE : 89- 94: vpppa S--Tvp--SA dappp GLP_MACFU : 33- 40: khtsd ShpTpt--SA hevtt GLP_MOUSE : 132- 139: isyci SrmTkk--SS vdiqs GLP_MOUSE : 132- 140: isyci SrmTkks-SV diqsp GLP_PIG : 11- 19: tgeqg Sa-TpgnvSN atvta H 8: 12.0102 11( 7) T-x(3,4)-S-x(2)-T Occurences: 11(7) GLPA_HUMAN : 29- 36: gvamh Tsts-SsvT ksyis GLPA_HUMAN : 36- 44: tsssv TksyiSsqT ndthk GLPB_HUMAN : 29- 36: evamh Tsts-SsvT ksyis GLPB_HUMAN : 36- 44: tsssv TksyiSsqT ngetg GLP_CANFA : 24- 31: agfis Tedp-SfnT pstre GLP_HORSE : 13- 20: ppiag Tsdl-StiT saatp GLP_HORSE : 106- 113: sedde Tslt-SveT dypgd GLP_MACFU : 44- 51: sahev Ttef-SgrT hyppe GLP_MOUSE : 9- 17: staav TtsghSltT tfhip GLP_MOUSE : 10- 17: taavt Tsgh-SltT tfhip GLP_PIG : 13- 21: eqgsa TpgnvSnaT vtagk I 9: 11.5102 7( 7) A-G-x(1,3)-I Occurences: 7(7) GLPA_HUMAN : 101- 104: ifgvm AGv--I gtill GLPB_HUMAN : 72- 75: ilcvm AGi--I gtill GLP_CANFA : 19- 22: klptq AGf--I stedp GLP_HORSE : 60- 63: ilgvm AGi--I giill GLP_HORSE : 60- 65: ilgvm AGiigI illla GLP_MACFU : 81- 84: ifgvm AGv--I gtilf GLP_MOUSE : 118- 121: ilgvm AGi--I gtill GLP_PIG : 72- 77: ifavm AGlllI iflia J 10: 11.5102 7( 7) S-x(4,5)-T-x(1,2)-A Occurences: 7(7) GLPA_HUMAN : 18- 26: aivsi Sasst-TgvA mhtst GLPB_HUMAN : 18- 26: eivsi Salst-TevA mhtst GLP_CANFA : 12- 19: iphqi Ssklp-Tq-A gfist GLP_HORSE : 14- 22: piagt SdlstiTs-A atptf GLP_HORSE : 14- 23: piagt SdlstiTsaA tptft GLP_MACFU : 33- 40: khtsd Shptp-Ts-A hevtt GLP_MOUSE : 60- 67: npnqh Satms-Tp-A ihvst GLP_PIG : 125- 132: dpplt Sveie-Tp-A s K 11: 11.0102 10( 7) S-x(2,3)-T-x(1,3)-T Occurences: 10(7) GLPA_HUMAN : 41- 47: tksyi Ssq-Tnd-T hkrdt GLPB_HUMAN : 41- 48: tksyi Ssq-TngeT gqlvh GLP_CANFA : 28- 34: stedp Sfn-Tps-T redps GLP_HORSE : 14- 20: piagt SdlsTi--T saatp GLP_HORSE : 17- 24: gtsdl Sti-TsaaT ptftt GLP_HORSE : 21- 26: lstit Saa-Tp--T ftteq GLP_HORSE : 21- 28: lstit Saa-TptfT teqdg GLP_MACFU : 1- 8: Sst-TvpaT htsss GLP_MACFU : 33- 38: khtsd Shp-Tp--T sahev GLP_MOUSE : 71- 78: paihv StyhTap-T evsaa GLP_PIG : 18- 23: tpgnv Sna-Tv--T agkps L 12: 11.0102 12( 7) S-x(2,4)-T-x(1,2)-S Occurences: 12(7) GLPA_HUMAN : 32- 38: mhtst Sssv-Tk-S yissq GLPA_HUMAN : 33- 38: htsts Ssv--Tk-S yissq GLPB_HUMAN : 32- 38: mhtst Sssv-Tk-S yissq GLPB_HUMAN : 33- 38: htsts Ssv--Tk-S yissq GLP_CANFA : 28- 33: stedp Sfn--Tp-S tredp GLP_HORSE : 14- 21: piagt Sdls-TitS aatpt GLP_MACFU : 25- 33: yvssq SndkhTsdS hptpt GLP_MACFU : 31- 39: ndkht SdshpTptS ahevt GLP_MACFU : 33- 39: khtsd Shp--TptS ahevt GLP_MOUSE : 4- 11: mte StaavTt-S ghslt GLP_MOUSE : 132- 138: isyci Srm--TkkS svdiq GLP_PIG : 125- 133: dpplt SveieTpaS M 13: 11.0102 11( 7) I-x(1,2)-T-x(2,4)-S Occurences: 11(7) GLPA_HUMAN : 104- 111: vmagv Ig-TilliS ygirr GLPB_HUMAN : 74- 82: cvmag IigTilliS ytirr GLPB_HUMAN : 75- 82: vmagi Ig-TilliS ytirr GLP_CANFA : 22- 28: tqagf Is-Tedp-S fntps GLP_HORSE : 10- 17: tgspp IagTsdl-S titsa GLP_MACFU : 84- 91: vmagv Ig-TilfiS ygsrr GLP_MOUSE : 44- 51: dsllq It-TpvvaS tvgnp GLP_MOUSE : 120- 128: gvmag IigTilliS ycisr GLP_MOUSE : 121- 128: vmagi Ig-TilliS ycisr GLP_MOUSE : 157- 165: vplss IeqTpneeS snv GLP_PIG : 128- 133: ltsve Ie-Tpa--S N 14: 11.0102 7( 7) G-x(1,3)-I-x(1,2)-T Occurences: 7(7) GLPA_HUMAN : 102- 106: fgvma Gv--Ig-T illis GLPB_HUMAN : 73- 77: lcvma Gi--Ig-T illis GLP_CANFA : 20- 24: lptqa Gf--Is-T edpsf GLP_HORSE : 6- 13: qtiat GsppIagT sdlst GLP_MACFU : 82- 86: fgvma Gv--Ig-T ilfis GLP_MOUSE : 119- 123: lgvma Gi--Ig-T illis GLP_PIG : 33- 40: satsp GvmtIknT tavvq O 15: 11.0102 9( 7) L-x(1,3)-A-x(2,3)-I Occurences: 9(7) GLPA_HUMAN : 9- 17: kiifv LllsAivsI sasst GLPA_HUMAN : 10- 17: iifvl Lls-AivsI sasst GLPA_HUMAN : 11- 17: ifvll Ls--AivsI sasst GLPB_HUMAN : 68- 75: iilii LcvmAgi-I gtill GLP_CANFA : 15- 22: qissk LptqAgf-I stedp GLP_HORSE : 56- 63: itvii LgvmAgi-I giill GLP_MACFU : 70- 76: hefse Lvi-Ali-I fgvma GLP_MOUSE : 114- 121: milii LgvmAgi-I gtill GLP_PIG : 80- 85: lliif Li--Ayl-I rrmik P 16: 11.0102 8( 7) S-x(3,5)-T-x(1,2)-A Occurences: 8(7) GLPA_HUMAN : 18- 26: aivsi Sasst-TgvA mhtst GLPB_HUMAN : 18- 26: eivsi Salst-TevA mhtst GLP_CANFA : 12- 19: iphqi Ssklp-Tq-A gfist GLP_CANFA : 13- 19: phqis Sklp--Tq-A gfist GLP_HORSE : 14- 22: piagt SdlstiTs-A atptf GLP_HORSE : 14- 23: piagt SdlstiTsaA tptft GLP_MACFU : 33- 40: khtsd Shptp-Ts-A hevtt GLP_MOUSE : 60- 67: npnqh Satms-Tp-A ihvst GLP_PIG : 125- 132: dpplt Sveie-Tp-A s Q 17: 11.0102 14( 7) I-x(0,2)-I-x(2,3)-I Occurences: 14(7) GLPA_HUMAN : 104- 110: vmagv IgtIll-I sygir GLPA_HUMAN : 107- 114: gvigt IllIsygI rrlik GLPB_HUMAN : 63- 67: papvv I--Ili-I lcvma GLPB_HUMAN : 74- 78: cvmag I--Igt-I llisy GLPB_HUMAN : 75- 81: vmagi IgtIll-I sytir GLPB_HUMAN : 78- 85: giigt IllIsytI rrlik GLP_CANFA : 6- 11: edvte I--IphqI ssklp GLP_HORSE : 62- 66: gvmag I--Igi-I lllay GLP_MACFU : 84- 90: vmagv IgtIlf-I sygsr GLP_MOUSE : 120- 124: gvmag I--Igt-I llisy GLP_MOUSE : 121- 127: vmagi IgtIll-I sycis GLP_MOUSE : 124- 131: giigt IllIsycI srmtk GLP_PIG : 77- 81: aglll I--Ifl-I aylir GLP_PIG : 78- 85: gllli IflIaylI rrmik R 18: 11.0102 8( 7) T-x(0,1)-I-x(0,2)-I Occurences: 8(7) GLPA_HUMAN : 93- 96: sepei TlI--I fgvma GLPA_HUMAN : 106- 110: agvig T-IllI sygir GLPB_HUMAN : 77- 81: agiig T-IllI sytir GLP_CANFA : 4- 7: edv TeI--I phqis GLP_HORSE : 52- 55: sqpvi TvI--I lgvma GLP_MACFU : 86- 90: agvig T-IlfI sygsr GLP_MOUSE : 123- 127: agiig T-IllI sycis GLP_PIG : 64- 67: shaei TgI--I favma S 19: 10.5102 21( 7) S-x(0,2)-S-x(2,4)-T Occurences: 21(7) GLPA_HUMAN : 16- 22: lsaiv Si-Sass-T tgvam GLPA_HUMAN : 16- 23: lsaiv Si-SasstT gvamh GLPA_HUMAN : 18- 23: aivsi Sa-Sst--T gvamh GLPA_HUMAN : 30- 36: vamht StsSsv--T ksyis GLPA_HUMAN : 30- 36: vamht St-Sssv-T ksyis GLPA_HUMAN : 32- 36: mhtst S--Ssv--T ksyis GLPA_HUMAN : 38- 44: ssvtk SyiSsq--T ndthk GLPA_HUMAN : 41- 47: tksyi S--SqtndT hkrdt GLPA_HUMAN : 63- 69: rahev SeiSvr--T vyppe GLPB_HUMAN : 16- 22: lseiv Si-Sals-T tevam GLPB_HUMAN : 16- 23: lseiv Si-SalstT evamh GLPB_HUMAN : 30- 36: vamht StsSsv--T ksyis GLPB_HUMAN : 30- 36: vamht St-Sssv-T ksyis GLPB_HUMAN : 32- 36: mhtst S--Ssv--T ksyis GLPB_HUMAN : 38- 44: ssvtk SyiSsq--T ngetg GLP_CANFA : 12- 17: iphqi S--Sklp-T qagfi GLP_HORSE : 14- 20: piagt SdlSti--T saatp GLP_HORSE : 107- 113: eddet SltSve--T dypgd GLP_MACFU : 22- 30: peqyv SsqSndkhT sdshp GLP_MACFU : 23- 30: eqyvs Sq-SndkhT sdshp GLP_MACFU : 31- 36: ndkht Sd-Shp--T ptsah GLP_MACFU : 31- 38: ndkht Sd-ShptpT sahev GLP_MOUSE : 11- 17: aavtt SghSlt--T tfhip GLP_MOUSE : 11- 18: aavtt SghSltt-T fhips GLP_MOUSE : 38- 45: pslsg Sd-SllqiT tpvva GLP_MOUSE : 155- 160: nsvpl S--Sieq-T pnees GLP_PIG : 28- 36: tagkp SatSpgvmT ikntt T 20: 8.3401 7( 7) G-T Occurences: 7(7) GLPA_HUMAN : 105- 106: magvi GT illis GLPB_HUMAN : 76- 77: magii GT illis GLP_CANFA : 40- 41: redps GT myqhl GLP_HORSE : 12- 13: sppia GT sdlst GLP_MACFU : 85- 86: magvi GT ilfis GLP_MOUSE : 122- 123: magii GT illis GLP_PIG : 105- 106: dspdi GT entad Number of patterns evaluated by Pratt:163 Total running time: 0 seconds