------------------------------------------------------------ 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 3 sequences from file AVIDIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 3 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 AVIDIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AVID_CHICK 152 EGFH_STRPU 482 STAV_STRAV 183 Pratt run started at Thu Feb 6 18:57:23 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 18.8503 3( 3) V-x(0,2)-N-x(0,2)-S-x(4)-T-G 2: 18.8503 3( 3) A-x(5)-T-G-x(3,5)-N-x(3,5)-S 3: 16.6802 3( 3) K-x(3)-V-G-x(4)-T 4: 16.1802 3( 3) G-x-E-x(3,4)-T-x-W 5: 16.1802 3( 3) G-x(3)-I-x(3)-G-x(3,4)-L 6: 16.1802 3( 3) S-T-x(3)-T-x(0,1)-G 7: 16.1802 3( 3) T-x(4,5)-T-x(4)-K-x-S 8: 16.1802 4( 3) G-x(1,2)-T-G-T 9: 15.6802 3( 3) T-x(4)-N-x(2,4)-T-x(3)-T 10: 15.6802 3( 3) D-x(2)-K-x(3)-V-x(0,2)-G 11: 15.6802 3( 3) I-x(0,1)-D-x(3,4)-A-x(5)-N 12: 15.6802 3( 3) T-x(0,1)-T-x(2,3)-T-x(5)-D 13: 15.6802 3( 3) F-T-x(0,1)-V-x(4,5)-S 14: 15.6802 3( 3) I-x(3,4)-T-x(1,2)-S-x(5)-S 15: 15.6802 3( 3) T-Y-x(2,3)-A-x(2,3)-A 16: 15.6802 4( 3) G-x(0,1)-T-x(4)-V-x(1,2)-A 17: 15.6802 3( 3) G-x(0,1)-Y-x(2)-A-x(0,1)-V 18: 15.6802 3( 3) T-x(2,3)-Y-x(2)-A-x(0,1)-V 19: 15.6802 3( 3) S-x(1,2)-G-x(5)-Y-x(1,2)-T 20: 15.6802 3( 3) N-x(0,2)-S-x(4)-T-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 74.0309 3( 3) A-x(2)-[ACP]-[GS]-[FIL]-T-G-x(3,5)-N-x(3,5)-S-[DNT]-x(2)-[ILV]-[GNT]-[AG]-[GV]-x-[CDS]-x-[ADG]-x(2)-[GNT]-[GT]-x(3)-[AQT]-[ACV]-[GPV]-[NPT]-[AN]-x-S-x(4)-[ET] B 2: 70.7090 3( 3) G-x(0,1)-Y-x-[CST]-A-x(0,1)-V-[GPT]-[AGN]-x-[EST]-[GNS]-[ERS]-x(3)-[ST]-[GNP]-x(2)-[DEG]-[CST]-[AE]-[NPS]-[ADT]-x-[CDN]-x-[NRS]-[GT]-[GQT]-[AIP]-x(4)-[TV]-[ANV] C 3: 70.7090 3( 3) T-x(2,3)-Y-x-[CST]-A-x(0,1)-V-[GPT]-[AGN]-x-[EST]-[GNS]-[ERS]-x(3)-[ST]-[GNP]-x(2)-[DEG]-[CST]-[AE]-[NPS]-[ADT]-x-[CDN]-x-[NRS]-[GT]-[GQT]-[AIP]-x(4)-[TV]-[ANV] D 4: 63.4563 3( 3) G-x(1,2)-T-G-T-[HWY]-x-[ENST]-[AT]-[DV]-x-[ADN]-[AET]-x-[ANS]-[ER]-x(3)-[QST]-[GNP]-x(2)-[DG]-[CST]-x-[DNP]-[AGT]-x-[DN]-x(2)-[GTV]-x-[AIP] E 5: 58.5516 3( 3) T-Y-x(2,3)-A-x(2,3)-A-[AET]-[PS]-x(2)-[IV]-x-[EGT]-x(4)-[GNS]-x-[DEP]-x-[PT]-x(4)-T-x-[LPV]-x(2)-[GNT]-x-[AQT]-x(4)-[FWY]-x-[EGN]-[AQS]-x(2)-[ALV] F 6: 52.7126 3( 3) I-x(3,4)-T-x(1,2)-S-x-[EPT]-[AIL]-x(2)-S-[AGP]-x(2)-[CGS]-x-[DEN]-[NS]-x(2)-[ENQ]-x-[RS]-[AST]-x-[EP]-[ACT]-x(3)-[GT]-[TV] G 7: 52.0209 3( 3) S-x(1,2)-G-x(3)-[GS]-x-Y-x(1,2)-T-x(4)-[AST]-x-[GNP]-x(4)-[ST]-[GPV]-x(2)-[GL]-x(2)-[NST]-[NTV]-x(2)-[DK]-x-[NPT]-x(2)-[GNT]-x(3)-[ATV]-x-[DNT] H 8: 45.4036 3( 3) G-x-E-x(3,4)-T-x-W-[IL]-x(2)-[NS]-x-[TV]-[NST]-[DET]-x-[GNQ]-[AD]-x(3)-[AST]-x(2)-[GV]-x(2)-[DNT] I 9: 44.6172 3( 3) K-[AS]-[NT]-x-V-G-x-[DN]-x-[FW]-T-[KR]-x-[EKR]-[PQT]-[QS]-x-[AE] J 10: 35.8627 3( 3) T-x(4,5)-T-x-[NQT]-[DEK]-[IV]-K-x-S-[ANP]-x(2)-[GI]-[DQT]-[ADE] K 11: 32.5950 3( 3) V-x(0,2)-N-x(0,2)-S-x(4)-T-G-x(4)-[AC]-x-[AGT]-[AET]-[DET]-[GSV] L 12: 32.1815 3( 3) F-T-x(0,1)-V-x(4,5)-S-x-[DST]-[AST]-x(3)-[AQT]-[CG]-x(4)-[DGN]-x(2)-[DGV] M 13: 31.6107 3( 3) I-x(0,1)-D-x(3,4)-A-[GST]-x(2)-[CGN]-x-N-[GIP]-x(3)-[ILV]-[DQR]-[GQT] N 14: 31.2311 3( 3) S-T-x(3)-T-x(0,1)-G-[AQ]-[CD]-x-[AIL]-x(2)-[GN]-[EGT] O 15: 29.4250 3( 3) N-x(0,2)-S-x(4)-T-G-x(4)-[AC]-x-[AGT]-[AET]-[DET]-[GSV] P 16: 26.8052 3( 3) G-x-[CTV]-x-I-[CDV]-x-[ANP]-G-x(3,4)-L-x-[CGT] Q 17: 26.7176 3( 3) D-x(2)-K-x-[ANT]-x-V-x(0,2)-G-x-[DNP]-x(2)-[AT]-x(2)-[EQR] R 18: 24.1504 3( 3) T-x(0,1)-T-x(2,3)-T-[AG]-x(3)-[AGI]-D-x(4)-[ENS] S 19: 21.5235 3( 3) T-x-[TV]-x(2)-N-x(2,4)-T-x(3)-T-[AGQ] T 20: 21.4538 4( 3) G-x(0,1)-T-x(2)-[DST]-[AL]-V-x(1,2)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 74.0309 3( 3) A-x(2)-[ACP]-[GS]-[FIL]-T-G-x(3,5)-N-x(3,5)-S-[DNT]-x(2)-[ILV]-[GNT]-[AG]-[GV]-x-[CDS]-x-[ADG]-x(2)-[GNT]-[GT]-x(3)-[AQT]-[ACV]-[GPV]-[NPT]-[AN]-x-S-x(4)-[ET] Occurences: 3(3) AVID_CHICK : 25- 70: apgls ArkCSLTGkwt--Ndlg--SNmtIGAVnSrGefTGtyiTAVTAtSneikE splhg EGFH_STRPU : 227- 276: ngyic AcvPGFTGsncetNidecaSDpcLNGGiCvDgvNGfvcQCPPNySgtycE islda STAV_STRAV : 36- 81: kaqvs AaeAGITGtwy--Nqlg--STfiVTAGaDgAltGTyesAVGNAeSryvlT gryds B 2: 70.7090 3( 3) G-x(0,1)-Y-x-[CST]-A-x(0,1)-V-[GPT]-[AGN]-x-[EST]-[GNS]-[ERS]-x(3)-[ST]-[GNP]-x(2)-[DEG]-[CST]-[AE]-[NPS]-[ADT]-x-[CDN]-x-[NRS]-[GT]-[GQT]-[AIP]-x(4)-[TV]-[ANV] Occurences: 3(3) AVID_CHICK : 55- 92: rgeft GtYiTA-VTAtSNEikeSPlhGTENTiNkRTQPtfgfTV nwkfs EGFH_STRPU : 223- 260: tdtin G-YiCAcVPGfTGSnceTNidECASDpClNGGIcvdgVN gfvcq STAV_STRAV : 65- 102: dgalt GtYeSA-VGNaESRyvlTGryDSAPAtDgSGTAlgwtVA wknny C 3: 70.7090 3( 3) T-x(2,3)-Y-x-[CST]-A-x(0,1)-V-[GPT]-[AGN]-x-[EST]-[GNS]-[ERS]-x(3)-[ST]-[GNP]-x(2)-[DEG]-[CST]-[AE]-[NPS]-[ADT]-x-[CDN]-x-[NRS]-[GT]-[GQT]-[AIP]-x(4)-[TV]-[ANV] Occurences: 3(3) AVID_CHICK : 54- 92: srgef Tgt-YiTA-VTAtSNEikeSPlhGTENTiNkRTQPtfgfTV nwkfs EGFH_STRPU : 220- 260: gvctd TingYiCAcVPGfTGSnceTNidECASDpClNGGIcvdgVN gfvcq STAV_STRAV : 64- 102: adgal Tgt-YeSA-VGNaESRyvlTGryDSAPAtDgSGTAlgwtVA wknny D 4: 63.4563 3( 3) G-x(1,2)-T-G-T-[HWY]-x-[ENST]-[AT]-[DV]-x-[ADN]-[AET]-x-[ANS]-[ER]-x(3)-[QST]-[GNP]-x(2)-[DG]-[CST]-x-[DNP]-[AGT]-x-[DN]-x(2)-[GTV]-x-[AIP] Occurences: 3(3) AVID_CHICK : 51- 86: avnsr GefTGTYiTAVtATsNEikeSPlhGTeNTiNkrTqP tfgft EGFH_STRPU : 117- 151: cdcqp Gy-TGTHcETDiDEcARppcQNggDCvDGvNgyVcI capgf STAV_STRAV : 61- 96: tagad GalTGTYeSAVgNAeSRyvlTGryDSaPAtDgsGtA lgwtv E 5: 58.5516 3( 3) T-Y-x(2,3)-A-x(2,3)-A-[AET]-[PS]-x(2)-[IV]-x-[EGT]-x(4)-[GNS]-x-[DEP]-x-[PT]-x(4)-T-x-[LPV]-x(2)-[GNT]-x-[AQT]-x(4)-[FWY]-x-[EGN]-[AQS]-x(2)-[ALV] Occurences: 3(3) AVID_CHICK : 56- 102: geftg TYit-Avt-ATSneIkEsplhGtEnTinkrTqPtfGfTvnwkFsESttV ftgqc EGFH_STRPU : 387- 435: lgdym TYnerAlgyAAPtvVvGyasnNyDfPsfgfTvVrdNgQsttsWtGQchL cdgee STAV_STRAV : 66- 113: galtg TYes-AvgnAESryVlTgrydSaPaTdgsgTaLgwTvAwknnYrNAhsA ttwsg F 6: 52.7126 3( 3) I-x(3,4)-T-x(1,2)-S-x-[EPT]-[AIL]-x(2)-S-[AGP]-x(2)-[CGS]-x-[DEN]-[NS]-x(2)-[ENQ]-x-[RS]-[AST]-x-[EP]-[ACT]-x(3)-[GT]-[TV] Occurences: 3(3) AVID_CHICK : 58- 92: ftgty Itav-TatSnEIkeSPlhGtENtiNkRTqPTfgfTV nwkfs EGFH_STRPU : 31- 64: icidg Ingy-Tc-ScPLgfSGdnCeNNddEcSSiPClngGT cvdlv STAV_STRAV : 9- 44: ivvaa IavslTtvSiTAsaSAdpSkDSkaQvSAaEAgitGT wynql G 7: 52.0209 3( 3) S-x(1,2)-G-x(3)-[GS]-x-Y-x(1,2)-T-x(4)-[AST]-x-[GNP]-x(4)-[ST]-[GPV]-x(2)-[GL]-x(2)-[NST]-[NTV]-x(2)-[DK]-x-[NPT]-x(2)-[GNT]-x(3)-[ATV]-x-[DNT] Occurences: 3(3) AVID_CHICK : 49- 93: igavn Sr-GeftGtYi-TavtaTsNeikeSPlhGteNTinKrTqpTfgfTvN wkfse EGFH_STRPU : 377- 421: titkt St-GmmlGdYm-TynerAlGyaapTVvvGyaSNnyDfPsfGftvVrD ngqst STAV_STRAV : 69- 115: tgtye SavGnaeSrYvlTgrydSaPatdgSGtaLgwTVawKnNyrNahsAtT wsgqy H 8: 45.4036 3( 3) G-x-E-x(3,4)-T-x-W-[IL]-x(2)-[NS]-x-[TV]-[NST]-[DET]-x-[GNQ]-[AD]-x(3)-[AST]-x(2)-[GV]-x(2)-[DNT] Occurences: 3(3) AVID_CHICK : 113- 142: fidrn GkEvlk-TmWLlrSsVNDiGDdwkAtrVgiN iftrl EGFH_STRPU : 438- 467: chlcd GeEvly-TtWIntNmVSTcQDikkSnmVgqD kwtry STAV_STRAV : 123- 153: gqyvg GaEarinTqWLltSgTTEaNAwksTlvGhdT ftkvk I 9: 44.6172 3( 3) K-[AS]-[NT]-x-V-G-x-[DN]-x-[FW]-T-[KR]-x-[EKR]-[PQT]-[QS]-x-[AE] Occurences: 3(3) AVID_CHICK : 135- 152: igddw KATrVGiNiFTRlRTQkE EGFH_STRPU : 460- 477: cqdik KSNmVGqDkWTRyEQSiA pqpda STAV_STRAV : 145- 162: eanaw KSTlVGhDtFTKvKPSaA sidaa J 10: 35.8627 3( 3) T-x(4,5)-T-x-[NQT]-[DEK]-[IV]-K-x-S-[ANP]-x(2)-[GI]-[DQT]-[ADE] Occurences: 3(3) AVID_CHICK : 59- 77: tgtyi Tavta-TsNEIKeSPlhGTE ntink EGFH_STRPU : 449- 467: ttwin Tnmvs-TcQDIKkSNmvGQD kwtry STAV_STRAV : 147- 166: nawks TlvghdTfTKVKpSAasIDA akkag K 11: 32.5950 3( 3) V-x(0,2)-N-x(0,2)-S-x(4)-T-G-x(4)-[AC]-x-[AGT]-[AET]-[DET]-[GSV] Occurences: 3(3) AVID_CHICK : 47- 65: mtiga V--N--SrgefTGtyitAvTATS neike EGFH_STRPU : 419- 441: fgftv VrdNgqSttswTGqchlCdGEEV lyttw STAV_STRAV : 71- 92: tyesa Vg-NaeSryvlTGrydsApATDG sgtal L 12: 32.1815 3( 3) F-T-x(0,1)-V-x(4,5)-S-x-[DST]-[AST]-x(3)-[AQT]-[CG]-x(4)-[DGN]-x(2)-[DGV] Occurences: 3(3) AVID_CHICK : 90- 113: qptfg FT-Vnwkf-SeSTtvfTGqcfiDrnG kevlk EGFH_STRPU : 416- 441: fpsfg FTvVrdngqStTSwtgQChlcdGeeV lyttw STAV_STRAV : 154- 179: vghdt FTkVkpsaaSiDAakkAGvnngNplD avqq M 13: 31.6107 3( 3) I-x(0,1)-D-x(3,4)-A-[GST]-x(2)-[CGN]-x-N-[GIP]-x(3)-[ILV]-[DQR]-[GQT] Occurences: 3(3) AVID_CHICK : 130- 149: ssvnd IgDdwk-ATrvGiNIftrLRT qke EGFH_STRPU : 315- 334: gqnce I-DinecASlpCqNGglcIDG iagyt STAV_STRAV : 164- 183: psaas I-DaakkAGvnNgNPldaVQQ N 14: 31.2311 3( 3) S-T-x(3)-T-x(0,1)-G-[AQ]-[CD]-x-[AIL]-x(2)-[GN]-[EGT] Occurences: 3(3) AVID_CHICK : 99- 113: wkfse STtvfT-GQCfIdrNG kevlk EGFH_STRPU : 425- 439: rdngq STtswT-GQChLcdGE evlyt STAV_STRAV : 51- 66: ynqlg STfivTaGADgAltGT yesav O 15: 29.4250 3( 3) N-x(0,2)-S-x(4)-T-G-x(4)-[AC]-x-[AGT]-[AET]-[DET]-[GSV] Occurences: 3(3) AVID_CHICK : 48- 65: tigav N--SrgefTGtyitAvTATS neike EGFH_STRPU : 422- 441: tvvrd NgqSttswTGqchlCdGEEV lyttw STAV_STRAV : 73- 92: esavg NaeSryvlTGrydsApATDG sgtal P 16: 26.8052 3( 3) G-x-[CTV]-x-I-[CDV]-x-[ANP]-G-x(3,4)-L-x-[CGT] Occurences: 3(3) AVID_CHICK : 105- 119: ttvft GqCfIDrNGkev-LkT mwllr EGFH_STRPU : 147- 161: vdgvn GyVcICaPGfdg-LnC ennid STAV_STRAV : 50- 65: wynql GsTfIVtAGadgaLtG tyesa Q 17: 26.7176 3( 3) D-x(2)-K-x-[ANT]-x-V-x(0,2)-G-x-[DNP]-x(2)-[AT]-x(2)-[EQR] Occurences: 3(3) AVID_CHICK : 132- 148: vndig DdwKaTrV--GiNifTrlR tqke EGFH_STRPU : 457- 473: vstcq DikKsNmV--GqDkwTryE qsiap STAV_STRAV : 165- 183: saasi DaaKkAgVnnGnPldAvqQ R 18: 24.1504 3( 3) T-x(0,1)-T-x(2,3)-T-[AG]-x(3)-[AGI]-D-x(4)-[ENS] Occurences: 3(3) AVID_CHICK : 100- 115: kfses T-Tvf-TGqcfIDrngkE vlktm EGFH_STRPU : 372- 389: cndqv TiTktsTGmmlGDymtyN eralg STAV_STRAV : 14- 30: iavsl T-TvsiTAsasADpskdS kaqvs S 19: 21.5235 3( 3) T-x-[TV]-x(2)-N-x(2,4)-T-x(3)-T-[AGQ] Occurences: 3(3) AVID_CHICK : 137- 150: ddwka TrVgiNif--TrlrTQ ke EGFH_STRPU : 417- 431: psfgf TvVrdNgqs-TtswTG qchlc STAV_STRAV : 42- 57: aeagi TgTwyNqlgsTfivTA gadga T 20: 21.4538 4( 3) G-x(0,1)-T-x(2)-[DST]-[AL]-V-x(1,2)-A Occurences: 4(3) AVID_CHICK : 55- 63: rgeft G-TyiTAVt-A tsnei EGFH_STRPU : 62- 71: ipcln GgTcvDLVn-A ymcvc EGFH_STRPU : 63- 71: pclng G-TcvDLVn-A ymcvc STAV_STRAV : 65- 74: dgalt G-TyeSAVgnA esryv Number of patterns evaluated by Pratt:3103 Total running time: 1 seconds