------------------------------------------------------------ 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 DEHYDROQUINASE_I 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 DEHYDROQUINASE_I.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ARO1_EMENI 1603 ARO1_YEAST 1588 AROD_BACSU 255 AROD_ECOLI 252 AROD_SALTI 252 EBSD_ENTFA 253 Pratt run started at Thu Feb 6 19:17:45 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.0203 6( 6) P-x(0,1)-I-x(3,4)-M-x(3)-G-x(2)-S-R 2: 20.3503 6( 6) A-x(0,1)-A-P-G-Q 3: 20.3503 8( 6) I-x(3,4)-M-x(3)-G-x(2)-S-R 4: 20.3503 6( 6) M-x(3)-Y-A-x(2)-P-x(1,2)-T 5: 19.8503 6( 6) S-x(4,5)-G-x(4,5)-A-x(4)-Q-x(5)-L 6: 19.3503 6( 6) S-x(3,4)-G-x(1,3)-I-x(4)-G-x(5)-A 7: 18.8503 6( 6) L-x-T-x(1,3)-R-x(4)-G-x(1,3)-E 8: 16.6802 6( 6) A-P-G-Q 9: 16.6802 6( 6) A-S-A-x(5)-V 10: 16.1802 6( 6) I-x(4)-G-x(2,3)-F-x(2)-A 11: 16.1802 6( 6) I-x(3,4)-G-x(3)-G-x(4)-F 12: 16.1802 6( 6) Y-A-x(2)-P-x(1,2)-T 13: 16.1802 6( 6) T-L-L-x(0,1)-A 14: 16.1802 7( 6) L-x(1,2)-L-x(2)-A-T 15: 16.1802 6( 6) Q-x(5)-I-x-K-x(3,4)-M 16: 16.1802 8( 6) K-x(4,5)-G-x(3)-P-K 17: 15.6802 8( 6) L-x(0,1)-T-x-L-x(1,2)-A 18: 15.6802 6( 6) D-x(4)-L-T-x(1,3)-L 19: 15.6802 6( 6) V-x(2)-L-x(2,4)-V-x(3)-L 20: 15.6802 6( 6) Q-x(4,5)-D-L-x(3,4)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 55.2328 6( 6) S-x(3,4)-G-x(1,3)-I-[DS]-x-[LPV]-x-G-x(2)-[FL]-[GI]-[GS]-A-x(3)-[GP]-x(4)-[AIV]-[DS]-[AIL]-x(4)-[APST]-[LV]-x(3)-[ER] B 2: 53.2143 6( 6) P-x(0,1)-I-x(3,4)-M-[AGT]-x(2)-G-x-[IL]-S-R-[ILV]-x-[GN]-[EGNQ]-[FLV]-[FLM]-[GT]-[PS]-[AV] C 3: 51.3769 6( 6) M-x-[AEQT]-x-Y-A-x(2)-P-x(1,2)-T-[LM]-x-[LM]-[AGV]-x(4)-I-S-x-[LPV]-x-[GIV]-[DEQ]-[LMV] D 4: 49.5443 8( 6) I-x(3,4)-M-[AGT]-x(2)-G-x-[IL]-S-R-[ILV]-x-[GN]-[EGNQ]-[FLV]-[FLM]-[GT]-[PS]-[AV] E 5: 46.5111 6( 6) S-x(4,5)-G-x(4,5)-A-x-[AV]-[PS]-[GS]-Q-x(2)-[SV]-[NQS]-x-L-x-[CNST]-x-[LP]-x(3)-[EH]-x-[ANV] F 6: 44.9701 6( 6) Y-A-x(2)-P-x(1,2)-T-[LM]-x-[LM]-[AGV]-x(4)-I-S-x-[LPV]-x-[GIV]-[DEQ]-[LMV] G 7: 43.9308 6( 6) Q-x(3)-[AT]-x-I-x-K-x(3,4)-M-[GP]-[EGNQ]-x(3)-[DK]-x-[FL]-x-[ILV]-[FLV]-[ADGST]-x-[PT]-x-[EGST] H 8: 39.3066 6( 6) I-x(3,4)-G-x(3)-G-[DS]-x(2)-[GQT]-F-[GV]-[AS]-[ADGSV]-x(3)-[RS]-x-[IPV]-x(4)-[TV] I 9: 37.3972 6( 6) A-x(0,1)-A-P-G-Q-[IL]-[APST]-[AV]-[ANQST]-x-[IL]-[NR] J 10: 33.7272 6( 6) A-P-G-Q-[IL]-[APST]-[AV]-[ANQST]-x-[IL]-[NR] K 11: 30.0040 6( 6) L-x-T-x(1,3)-R-[EST]-x(2)-[EN]-G-x(1,3)-E-x(3)-[ST]-[AEST] L 12: 26.2028 6( 6) K-x(4,5)-G-[AEGT]-[GI]-x-P-K-x-[FILV]-x(2)-[FILV] M 13: 24.1126 6( 6) I-x(4)-G-x(2,3)-F-x-[GNS]-A-x(3)-[GIP]-x(4)-[ALV] N 14: 19.2698 6( 6) A-S-A-x(5)-V-x(3)-[DER] O 15: 18.7791 7( 6) L-x(1,2)-L-x(2)-A-T-x-[EST] P 16: 17.9194 6( 6) D-x(3)-[AILV]-L-T-x(1,3)-L Q 17: 16.1802 6( 6) T-L-L-x(0,1)-A R 18: 16.1802 6( 6) Q-x(5)-I-x-K-x(3,4)-M S 19: 16.1802 8( 6) K-x(4,5)-G-x(3)-P-K T 20: 15.6802 8( 6) L-x(0,1)-T-x-L-x(1,2)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 55.2328 6( 6) S-x(3,4)-G-x(1,3)-I-[DS]-x-[LPV]-x-G-x(2)-[FL]-[GI]-[GS]-A-x(3)-[GP]-x(4)-[AIV]-[DS]-[AIL]-x(4)-[APST]-[LV]-x(3)-[ER] Occurences: 6(6) ARO1_EMENI : 147- 187: lamvd Ssig-GktaIDtPlGknLIGAiwqPtkiyIDLefleTLpvrE fingm ARO1_YEAST : 142- 182: lamvd Ssig-GktaIDtPlGknFIGAfwqPkfvlVDIkwleTLakrE fingm AROD_BACSU : 204- 243: piitm SmaatGl--ISrLsGevFGSActfGageeASApgqiPVselR svldi AROD_ECOLI : 204- 243: piitm SmaktGv--ISrLaGevFGSAatfGavkkASApgqiSVndlR tvlti AROD_SALTI : 204- 243: pvitm SmakeGv--ISrLaGevFGSAatfGavkqASApgqiAVndlR svlmi EBSD_ENTFA : 204- 243: pivtm SmgqlGm--ISrVtGqlFGSAltfGsaqqASApgqlSVqvlR nylkt B 2: 53.2143 6( 6) P-x(0,1)-I-x(3,4)-M-[AGT]-x(2)-G-x-[IL]-S-R-[ILV]-x-[GN]-[EGNQ]-[FLV]-[FLM]-[GT]-[PS]-[AV] Occurences: 6(6) ARO1_EMENI : 1236- 1259: eahdv PlIain-MGdqGqLSRIlNGFMTPV shpsl ARO1_YEAST : 1252- 1275: thknk PlIavn-MTskGsISRVlNNVLTPV tsdll AROD_BACSU : 199- 222: iyadr PiItms-MAatGlISRLsGEVFGSA ctfga AROD_BACSU : 199- 222: iyadr P-IitmsMAatGlISRLsGEVFGSA ctfga AROD_ECOLI : 199- 222: qyadr PiItms-MAktGvISRLaGEVFGSA atfga AROD_ECOLI : 199- 222: qyadr P-IitmsMAktGvISRLaGEVFGSA atfga AROD_SALTI : 199- 222: hyadr PvItms-MAkeGvISRLaGEVFGSA atfga EBSD_ENTFA : 199- 222: hyasv P-IvtmsMGqlGmISRVtGQLFGSA ltfgs C 3: 51.3769 6( 6) M-x-[AEQT]-x-Y-A-x(2)-P-x(1,2)-T-[LM]-x-[LM]-[AGV]-x(4)-I-S-x-[LPV]-x-[GIV]-[DEQ]-[LMV] Occurences: 6(6) ARO1_EMENI : 577- 603: vssll McApYAkePv-TLrLVggkpISqPyIDM ttamm ARO1_YEAST : 589- 615: vssil McApYAeePv-TLaLVggkpISkLyVDM tikmm AROD_BACSU : 191- 218: datyt MkTiYAdrPiiTMsMAatglISrLsGEV fgsac AROD_ECOLI : 191- 218: aatle MqEqYAdrPiiTMsMAktgvISrLaGEV fgsaa AROD_SALTI : 191- 218: tatle MqQhYAdrPviTMsMAkegvISrLaGEV fgsaa EBSD_ENTFA : 191- 218: satne MyThYAsvPivTMsMGqlgmISrVtGQL fgsal D 4: 49.5443 8( 6) I-x(3,4)-M-[AGT]-x(2)-G-x-[IL]-S-R-[ILV]-x-[GN]-[EGNQ]-[FLV]-[FLM]-[GT]-[PS]-[AV] Occurences: 8(6) ARO1_EMENI : 1238- 1259: hdvpl Iain-MGdqGqLSRIlNGFMTPV shpsl ARO1_YEAST : 1254- 1275: knkpl Iavn-MTskGsISRVlNNVLTPV tsdll AROD_BACSU : 200- 222: yadrp IitmsMAatGlISRLsGEVFGSA ctfga AROD_BACSU : 201- 222: adrpi Itms-MAatGlISRLsGEVFGSA ctfga AROD_ECOLI : 200- 222: yadrp IitmsMAktGvISRLaGEVFGSA atfga AROD_ECOLI : 201- 222: adrpi Itms-MAktGvISRLaGEVFGSA atfga AROD_SALTI : 201- 222: adrpv Itms-MAkeGvISRLaGEVFGSA atfga EBSD_ENTFA : 200- 222: yasvp IvtmsMGqlGmISRVtGQLFGSA ltfgs E 5: 46.5111 6( 6) S-x(4,5)-G-x(4,5)-A-x-[AV]-[PS]-[GS]-Q-x(2)-[SV]-[NQS]-x-L-x-[CNST]-x-[LP]-x(3)-[EH]-x-[ANV] Occurences: 6(6) ARO1_EMENI : 553- 586: lkiaa SggfagGninlaAkVSSQyvSSlLmCaPyakEpV tlrlv ARO1_YEAST : 566- 598: kvytd Svfkg-GrielaAtVSSQyvSSiLmCaPyaeEpV tlalv AROD_BACSU : 221- 252: gevfg Sactf-Gagee-AsAPGQipVSeLrSvLdilHkN trg AROD_ECOLI : 221- 252: gevfg Saatf-Gavkk-AsAPGQisVNdLrTvLtilHqA AROD_SALTI : 221- 252: gevfg Saatf-Gavkq-AsAPGQiaVNdLrSvLmilHnA EBSD_ENTFA : 221- 252: gqlfg Saltf-Gsaqq-AsAPGQlsVQvLrNyLktfEqN k F 6: 44.9701 6( 6) Y-A-x(2)-P-x(1,2)-T-[LM]-x-[LM]-[AGV]-x(4)-I-S-x-[LPV]-x-[GIV]-[DEQ]-[LMV] Occurences: 6(6) ARO1_EMENI : 581- 603: lmcap YAkePv-TLrLVggkpISqPyIDM ttamm ARO1_YEAST : 593- 615: lmcap YAeePv-TLaLVggkpISkLyVDM tikmm AROD_BACSU : 195- 218: tmkti YAdrPiiTMsMAatglISrLsGEV fgsac AROD_ECOLI : 195- 218: emqeq YAdrPiiTMsMAktgvISrLaGEV fgsaa AROD_SALTI : 195- 218: emqqh YAdrPviTMsMAkegvISrLaGEV fgsaa EBSD_ENTFA : 195- 218: emyth YAsvPivTMsMGqlgmISrVtGQL fgsal G 7: 43.9308 6( 6) Q-x(3)-[AT]-x-I-x-K-x(3,4)-M-[GP]-[EGNQ]-x(3)-[DK]-x-[FL]-x-[ILV]-[FLV]-[ADGST]-x-[PT]-x-[EGST] Occurences: 6(6) ARO1_EMENI : 1272- 1301: kaapg QlsaTeIrKglslMGEikpKkFaIFGsPiS qsapq ARO1_YEAST : 1288- 1317: saapg QltvAqInKmytsMGGiepKeLfVVGkPiG hsrsp AROD_BACSU : 162- 190: rlrkm QdlgAhIpKmav-MPNdtgDlLtLLDaTyT mktiy AROD_ECOLI : 162- 190: rlrkm QsfdAdIpKial-MPQstsDvLtLLAaTlE mqeqy AROD_SALTI : 162- 190: rlrkm QalgAdIpKiav-MPQskhDvLtLLTaTlE mqqhy EBSD_ENTFA : 162- 190: rlrqm QmrqAdIcKiav-MPQdatDvLtLLSaTnE mythy H 8: 39.3066 6( 6) I-x(3,4)-G-x(3)-G-[DS]-x(2)-[GQT]-F-[GV]-[AS]-[ADGSV]-x(3)-[RS]-x-[IPV]-x(4)-[TV] Occurences: 6(6) ARO1_EMENI : 110- 137: rdtvv Ialg-GgviGDltGFVAStymRgVryvqV pttll ARO1_YEAST : 375- 403: kkkvv IlesiGkcyGDsaQFVSDedlRfIltdeT lvypf AROD_BACSU : 211- 239: aatgl IsrlsGevfGSacTFGAGeeaSaPgqipV selrs AROD_ECOLI : 211- 239: aktgv IsrlaGevfGSaaTFGAVkkaSaPgqisV ndlrt AROD_SALTI : 211- 239: akegv IsrlaGevfGSaaTFGAVkqaSaPgqiaV ndlrs EBSD_ENTFA : 211- 239: gqlgm IsrvtGqlfGSalTFGSAqqaSaPgqlsV qvlrn I 9: 37.3972 6( 6) A-x(0,1)-A-P-G-Q-[IL]-[APST]-[AV]-[ANQST]-x-[IL]-[NR] Occurences: 6(6) ARO1_EMENI : 1268- 1279: slpfk A-APGQLSATeIR kglsl ARO1_YEAST : 1284- 1295: llpns A-APGQLTVAqIN kmyts AROD_BACSU : 231- 243: gagee AsAPGQIPVSeLR svldi AROD_ECOLI : 231- 243: gavkk AsAPGQISVNdLR tvlti AROD_SALTI : 231- 243: gavkq AsAPGQIAVNdLR svlmi EBSD_ENTFA : 231- 243: gsaqq AsAPGQLSVQvLR nylkt J 10: 33.7272 6( 6) A-P-G-Q-[IL]-[APST]-[AV]-[ANQST]-x-[IL]-[NR] Occurences: 6(6) ARO1_EMENI : 1269- 1279: lpfka APGQLSATeIR kglsl ARO1_YEAST : 1285- 1295: lpnsa APGQLTVAqIN kmyts AROD_BACSU : 233- 243: geeas APGQIPVSeLR svldi AROD_ECOLI : 233- 243: vkkas APGQISVNdLR tvlti AROD_SALTI : 233- 243: vkqas APGQIAVNdLR svlmi EBSD_ENTFA : 233- 243: aqqas APGQLSVQvLR nylkt K 11: 30.0040 6( 6) L-x-T-x(1,3)-R-[EST]-x(2)-[EN]-G-x(1,3)-E-x(3)-[ST]-[AEST] Occurences: 6(6) ARO1_EMENI : 180- 199: idlef LeTlpvREfiNGma-EvikTA aisse ARO1_YEAST : 175- 194: vdikw LeTlakREfiNGma-EvikTA ciwna AROD_BACSU : 78- 96: edklf LfTf--RThkEGgsmEmdeSS ylall AROD_ECOLI : 78- 94: pekpl LfTf--RSakEGg--EqaiST eayia AROD_SALTI : 78- 94: pdipl LfTf--RSakEGg--EqtiTT qhylt EBSD_ENTFA : 78- 94: gqkpl LlTf--RTqkEGg--EmafSE enyfa L 12: 26.2028 6( 6) K-x(4,5)-G-[AEGT]-[GI]-x-P-K-x-[FILV]-x(2)-[FILV] Occurences: 6(6) ARO1_EMENI : 1280- 1296: ateir KglslmGEIkPKkFaiF gspis ARO1_YEAST : 1296- 1312: vaqin KmytsmGGIePKeLfvV gkpig AROD_BACSU : 7- 22: nvlti Kgvsi-GEGmPKiIipL mgkte AROD_ECOLI : 7- 22: ktvtv Kdlvi-GTGaPKiIvsL makdi AROD_SALTI : 7- 22: ktvtv Knlii-GEGmPKiIvsL mgrdi EBSD_ENTFA : 7- 22: kpviv Knvri-GEGnPKiVvpI vapta M 13: 24.1126 6( 6) I-x(4)-G-x(2,3)-F-x-[GNS]-A-x(3)-[GIP]-x(4)-[ALV] Occurences: 6(6) ARO1_EMENI : 910- 931: mtipd IiktrGwqgFrNAeleIlkrtL kersr ARO1_YEAST : 150- 170: ggkta IdtplGkn-FiGAfwqPkfvlV dikwl AROD_BACSU : 211- 231: aatgl IsrlsGev-FgSActfGageeA sapgq AROD_ECOLI : 211- 231: aktgv IsrlaGev-FgSAatfGavkkA sapgq AROD_SALTI : 211- 231: akegv IsrlaGev-FgSAatfGavkqA sapgq EBSD_ENTFA : 211- 231: gqlgm IsrvtGql-FgSAltfGsaqqA sapgq N 14: 19.2698 6( 6) A-S-A-x(5)-V-x(3)-[DER] Occurences: 6(6) ARO1_EMENI : 245- 257: karil ASArhkayVvsaD eregg ARO1_YEAST : 909- 921: iskwc ASAlgyklVdldE lfeqq AROD_BACSU : 231- 243: gagee ASApgqipVselR svldi AROD_ECOLI : 231- 243: gavkk ASApgqisVndlR tvlti AROD_SALTI : 231- 243: gavkq ASApgqiaVndlR svlmi EBSD_ENTFA : 231- 243: gsaqq ASApgqlsVqvlR nylkt O 15: 18.7791 7( 6) L-x(1,2)-L-x(2)-A-T-x-[EST] Occurences: 7(6) ARO1_EMENI : 450- 459: vmlna LerLgaATfS weeeg ARO1_YEAST : 1122- 1131: fvskq LsiLrkATdS ipiif AROD_BACSU : 181- 190: ndtgd LltLldATyT mktiy AROD_BACSU : 182- 190: dtgdl Lt-LldATyT mktiy AROD_ECOLI : 182- 190: stsdv Lt-LlaATlE mqeqy AROD_SALTI : 182- 190: skhdv Lt-LltATlE mqqhy EBSD_ENTFA : 182- 190: datdv Lt-LlsATnE mythy P 16: 17.9194 6( 6) D-x(3)-[AILV]-L-T-x(1,3)-L Occurences: 6(6) ARO1_EMENI : 525- 535: qrpig DlvdALTanvL plnts ARO1_YEAST : 394- 404: fvsde DlrfILTdetL vypfk AROD_BACSU : 177- 185: avmpn DtgdLLTl--L datyt AROD_ECOLI : 241- 249: qisvn DlrtVLTi--L hqa AROD_SALTI : 180- 189: pqskh DvltLLTat-L emqqh EBSD_ENTFA : 177- 185: avmpq DatdVLTl--L satne Q 17: 16.1802 6( 6) T-L-L-x(0,1)-A Occurences: 6(6) ARO1_EMENI : 140- 143: vqvpt TLL-A mvdss ARO1_YEAST : 1528- 1532: aafvp TLLeA aykps AROD_BACSU : 183- 187: tgdll TLLdA tytmk AROD_ECOLI : 183- 186: tsdvl TLL-A atlem AROD_ECOLI : 183- 187: tsdvl TLLaA tlemq AROD_SALTI : 183- 187: khdvl TLLtA tlemq EBSD_ENTFA : 183- 187: atdvl TLLsA tnemy R 18: 16.1802 6( 6) Q-x(5)-I-x-K-x(3,4)-M Occurences: 6(6) ARO1_EMENI : 1272- 1285: kaapg QlsateIrKglslM geikp ARO1_YEAST : 1288- 1301: saapg QltvaqInKmytsM ggiep AROD_BACSU : 162- 174: rlrkm QdlgahIpKmav-M pndtg AROD_ECOLI : 162- 174: rlrkm QsfdadIpKial-M pqsts AROD_SALTI : 162- 174: rlrkm QalgadIpKiav-M pqskh EBSD_ENTFA : 162- 174: rlrqm QmrqadIcKiav-M pqdat S 19: 16.1802 8( 6) K-x(4,5)-G-x(3)-P-K Occurences: 8(6) ARO1_EMENI : 1280- 1291: ateir KglslmGeikPK kfaif ARO1_YEAST : 1296- 1307: vaqin KmytsmGgiePK elfvv AROD_BACSU : 7- 17: nvlti Kgvsi-GegmPK iiipl AROD_BACSU : 160- 170: isrlr Kmqdl-GahiPK mavmp AROD_ECOLI : 7- 17: ktvtv Kdlvi-GtgaPK iivsl AROD_SALTI : 7- 17: ktvtv Knlii-GegmPK iivsl AROD_SALTI : 160- 170: vsrlr Kmqal-GadiPK iavmp EBSD_ENTFA : 7- 17: kpviv Knvri-GegnPK ivvpi T 20: 15.6802 8( 6) L-x(0,1)-T-x-L-x(1,2)-A Occurences: 8(6) ARO1_EMENI : 325- 332: laayg LpTsLkdA rirkl ARO1_YEAST : 506- 511: tasrf L-TsLa-A lvnst AROD_BACSU : 181- 187: ndtgd LlTlLd-A tytmk AROD_BACSU : 182- 187: dtgdl L-TlLd-A tytmk AROD_ECOLI : 182- 187: stsdv L-TlLa-A tlemq AROD_ECOLI : 246- 252: dlrtv L-TiLhqA AROD_SALTI : 182- 187: skhdv L-TlLt-A tlemq EBSD_ENTFA : 182- 187: datdv L-TlLs-A tnemy Number of patterns evaluated by Pratt:13572 Total running time: 10 seconds