------------------------------------------------------------ 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 9 sequences from file TRANSGLUTAMINASES PATTERN CONSERVATION: CM: min Nr of Seqs to Match 9 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 TRANSGLUTAMINASES.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: 42_HUMAN 690 F13A_BOVIN 37 F13A_HUMAN 731 TGLC_CAVCU 690 TGLC_HUMAN 687 TGLC_MOUSE 685 TGLK_HUMAN 817 TGLK_RABIT 382 TGLK_RAT 824 Pratt run started at Thu Feb 6 21:28:51 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.1802 11( 9) V-x(0,1)-L-x(1,3)-G-x(3)-R 2: 15.1802 13( 9) T-x(1,2)-L-x(1,3)-G-x(3)-R 3: 14.6802 9( 9) T-x(2)-L-x(2,4)-L-x(0,2)-V 4: 12.5102 9( 9) E-x(3)-P-x(3)-L 5: 12.0102 10( 9) L-x(0,1)-G-x(3)-R 6: 12.0102 10( 9) V-E-x(4,5)-V 7: 12.0102 14( 9) V-x-L-x(2,3)-L 8: 12.0102 17( 9) T-V-x(0,1)-L 9: 12.0102 9( 9) P-x(4)-L-x(3,4)-V 10: 12.0102 11( 9) S-S-x(4,5)-G 11: 11.5102 11( 9) G-x(0,1)-L-x(2,3)-R 12: 11.5102 10( 9) L-x(0,2)-Q-G 13: 11.5102 12( 9) E-x(0,1)-Q-x(2,3)-V 14: 11.5102 9( 9) E-x(1,3)-Q-x-L 15: 11.5102 11( 9) E-x(2,3)-G-x(0,1)-L 16: 11.5102 14( 9) P-x(3,4)-L-x(2,3)-L 17: 11.5102 13( 9) P-x(2)-V-x(3,5)-G 18: 11.5102 15( 9) D-x(1,2)-P-x(1,2)-E 19: 11.5102 13( 9) D-x(1,2)-T-x(1,2)-E 20: 11.5102 18( 9) D-x(3,4)-V-x(0,1)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 23.7123 12( 9) T-x(1,2)-L-x(1,3)-G-[IL]-[APV]-[APT]-R B 2: 22.7268 9( 9) T-V-x(0,1)-L-x-[ACG]-[ALV]-[GV]-[ILPV] C 3: 20.5423 9( 9) L-x(0,1)-G-[IL]-[APV]-[APT]-R D 4: 19.6351 9( 9) V-x(0,1)-L-x(1,3)-G-[AILV]-x-[ADPT]-R E 5: 17.2556 10( 9) L-x(0,1)-G-x-[APV]-[APT]-R F 6: 16.9451 10( 9) P-[ACPV]-x-V-x(3,5)-G-x-[LV] G 7: 16.3560 10( 9) D-x(1,2)-T-x(1,2)-E-x-[QST]-[DEGS] H 8: 14.6802 9( 9) T-x(2)-L-x(2,4)-L-x(0,2)-V I 9: 14.6406 9( 9) P-x(3)-[EGT]-L-x(3,4)-V J 10: 14.6352 10( 9) L-x(0,1)-G-x(2)-[APT]-R K 11: 13.7530 11( 9) D-x(3,4)-V-x(0,1)-L-[AGQT] L 12: 13.7514 12( 9) D-x(1,2)-P-x(1,2)-E-x(3)-[AGIL] M 13: 13.4128 12( 9) P-x(3,4)-L-x(2,3)-L-[DGNTV] N 14: 13.3888 9( 9) E-x(1,3)-Q-[AGLPV]-L O 15: 12.5102 9( 9) E-x(3)-P-x(3)-L P 16: 12.0102 10( 9) L-x(0,1)-G-x(3)-R Q 17: 12.0102 10( 9) V-E-x(4,5)-V R 18: 12.0102 14( 9) V-x-L-x(2,3)-L S 19: 12.0102 11( 9) S-S-x(4,5)-G T 20: 11.5102 11( 9) G-x(0,1)-L-x(2,3)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 23.7123 12( 9) T-x(1,2)-L-x(1,3)-G-[IL]-[APV]-[APT]-R Occurences: 12(9) 42_HUMAN : 276- 286: aavac Tv-LrclGIPAR vvttf F13A_BOVIN : 28- 37: eddpp TveLq--GLVPR F13A_HUMAN : 323- 333: agvfn Tf-LrclGIPAR ivtny TGLC_CAVCU : 285- 295: aavac Tv-LrclGIPTR vvtnf TGLC_HUMAN : 286- 296: aavac Tv-LrclGIPTR vvtny TGLC_MOUSE : 286- 296: aavac Tv-LrclGIPTR vvtny TGLK_HUMAN : 385- 396: fagvt TtgLrclGLATR tvtnf TGLK_HUMAN : 386- 396: agvtt Tg-LrclGLATR tvtnf TGLK_RABIT : 38- 49: fagvt TtvLrclGLATR tvtnf TGLK_RABIT : 39- 49: agvtt Tv-LrclGLATR tvtnf TGLK_RAT : 393- 404: fagvt TtvLrclGLATR tvtnf TGLK_RAT : 394- 404: agvtt Tv-LrclGLATR tvtnf B 2: 22.7268 9( 9) T-V-x(0,1)-L-x-[ACG]-[ALV]-[GV]-[ILPV] Occurences: 9(9) 42_HUMAN : 276- 283: aavac TV-LrCLGI parvv F13A_BOVIN : 28- 36: eddpp TVeLqGLVP r F13A_HUMAN : 28- 36: eddlp TVeLqGVVP rgvnl TGLC_CAVCU : 285- 292: aavac TV-LrCLGI ptrvv TGLC_HUMAN : 286- 293: aavac TV-LrCLGI ptrvv TGLC_MOUSE : 286- 293: aavac TV-LrCLGI ptrvv TGLK_HUMAN : 696- 703: pdlsl TV-LgAAVV gqece TGLK_RABIT : 39- 46: agvtt TV-LrCLGL atrtv TGLK_RAT : 394- 401: agvtt TV-LrCLGL atrtv C 3: 20.5423 9( 9) L-x(0,1)-G-[IL]-[APV]-[APT]-R Occurences: 9(9) 42_HUMAN : 281- 286: tvlrc L-GIPAR vvttf F13A_BOVIN : 31- 37: pptve LqGLVPR F13A_HUMAN : 328- 333: tflrc L-GIPAR ivtny TGLC_CAVCU : 290- 295: tvlrc L-GIPTR vvtnf TGLC_HUMAN : 291- 296: tvlrc L-GIPTR vvtny TGLC_MOUSE : 291- 296: tvlrc L-GIPTR vvtny TGLK_HUMAN : 391- 396: tglrc L-GLATR tvtnf TGLK_RABIT : 44- 49: tvlrc L-GLATR tvtnf TGLK_RAT : 399- 404: tvlrc L-GLATR tvtnf D 4: 19.6351 9( 9) V-x(0,1)-L-x(1,3)-G-[AILV]-x-[ADPT]-R Occurences: 9(9) 42_HUMAN : 277- 286: avact V-LrclGIpAR vvttf F13A_BOVIN : 29- 37: ddppt VeLq--GLvPR F13A_HUMAN : 29- 37: ddlpt VeLq--GVvPR gvnlq TGLC_CAVCU : 286- 295: avact V-LrclGIpTR vvtnf TGLC_HUMAN : 287- 296: avact V-LrclGIpTR vvtny TGLC_MOUSE : 287- 296: avact V-LrclGIpTR vvtny TGLK_HUMAN : 636- 645: etkke VeLap-GAwDR vtmpv TGLK_RABIT : 40- 49: gvttt V-LrclGLaTR tvtnf TGLK_RAT : 395- 404: gvttt V-LrclGLaTR tvtnf E 5: 17.2556 10( 9) L-x(0,1)-G-x-[APV]-[APT]-R Occurences: 10(9) 42_HUMAN : 281- 286: tvlrc L-GiPAR vvttf F13A_BOVIN : 31- 37: pptve LqGlVPR F13A_HUMAN : 31- 37: lptve LqGvVPR gvnlq F13A_HUMAN : 328- 333: tflrc L-GiPAR ivtny TGLC_CAVCU : 290- 295: tvlrc L-GiPTR vvtnf TGLC_HUMAN : 291- 296: tvlrc L-GiPTR vvtny TGLC_MOUSE : 291- 296: tvlrc L-GiPTR vvtny TGLK_HUMAN : 391- 396: tglrc L-GlATR tvtnf TGLK_RABIT : 44- 49: tvlrc L-GlATR tvtnf TGLK_RAT : 399- 404: tvlrc L-GlATR tvtnf F 6: 16.9451 10( 9) P-[ACPV]-x-V-x(3,5)-G-x-[LV] Occurences: 10(9) 42_HUMAN : 207- 217: ekwsq PVhVarvl-GaL lhflk F13A_BOVIN : 26- 35: aaedd PPtVelq--GlV pr F13A_HUMAN : 411- 422: myrcg PAsVqaikhGhV cfqfd TGLC_CAVCU : 373- 384: tyccg PVpVraikeGhL nvkyd TGLC_HUMAN : 217- 228: srrss PVyVgrvgsGmV ncndd TGLC_HUMAN : 373- 384: tyccg PVpVraikeGdL stkyd TGLC_MOUSE : 373- 384: tyccg PVsVraikeGdL stkyd TGLK_HUMAN : 474- 485: ifccg PCsVesiknGlV ymkyd TGLK_RABIT : 127- 138: ifccg PCsVesvknGlV ymkyd TGLK_RAT : 482- 493: ifccg PCsVesiknGlV ymkyd G 7: 16.3560 10( 9) D-x(1,2)-T-x(1,2)-E-x-[QST]-[DEGS] Occurences: 10(9) 42_HUMAN : 400- 407: wkcce Dg-Tl-ElTD sntky F13A_BOVIN : 25- 33: naaed DppTv-ElQG lvpr F13A_HUMAN : 25- 33: naaed DlpTv-ElQG vvprg F13A_HUMAN : 396- 404: gwqav Ds-TpqEnSD gmyrc TGLC_CAVCU : 358- 366: gvqal Dp-TpqEkSE gtycc TGLC_HUMAN : 358- 366: gwqal Dp-TpqEkSE gtycc TGLC_MOUSE : 358- 366: gwqal Dp-TpqEkSE gtycc TGLK_HUMAN : 459- 467: gwqvv Da-TpqEtSS gifcc TGLK_RABIT : 112- 120: gwqvv Da-TpqEtSS gifcc TGLK_RAT : 467- 475: gwqvv Da-TpqEtSS gifcc H 8: 14.6802 9( 9) T-x(2)-L-x(2,4)-L-x(0,2)-V Occurences: 9(9) 42_HUMAN : 22- 32: neehh TkaLssrrLf-V rrgqp F13A_BOVIN : 28- 35: eddpp TveLqg--L--V pr F13A_HUMAN : 653- 663: vtvqf TnpLket-LrnV wvhld TGLC_CAVCU : 22- 31: grdhr TadLcrerL--V lrrgq TGLC_HUMAN : 23- 32: grdhh TadLcrekL--V vrrgq TGLC_HUMAN : 23- 33: grdhh TadLcrekLv-V rrgqp TGLC_MOUSE : 23- 33: grdhh TadLcqekLl-V rrgqr TGLK_HUMAN : 609- 618: sssrr TvkLhly-Ls-V tfytg TGLK_RABIT : 262- 271: sssrr TvkLhly-Ls-V tfytg TGLK_RAT : 617- 626: gssrr TvkLhly-Lc-V tyytg I 9: 14.6406 9( 9) P-x(3)-[EGT]-L-x(3,4)-V Occurences: 9(9) 42_HUMAN : 655- 665: kfqft PthvGLqrltV evdcn F13A_BOVIN : 26- 35: aaedd PptvELqgl-V pr F13A_HUMAN : 655- 665: vqftn PlkeTLrnvwV hldgp TGLC_CAVCU : 659- 668: rvdll PtevGLhkl-V vnfec TGLC_CAVCU : 659- 669: rvdll PtevGLhklvV nfecd TGLC_HUMAN : 656- 665: rmdlv PlhmGLhkl-V vnfes TGLC_HUMAN : 656- 666: rmdlv PlhmGLhklvV nfesd TGLC_MOUSE : 654- 663: rvdls PtdiGLhkl-V vnfqc TGLC_MOUSE : 654- 664: rvdls PtdiGLhklvV nfqcd TGLK_HUMAN : 716- 725: ivfkn PlpvTLtnv-V frleg TGLK_RABIT : 369- 378: ivfrn PlpiTLtnv-V frle TGLK_RAT : 724- 733: ivfkn PlpiTLtnv-V frleg J 10: 14.6352 10( 9) L-x(0,1)-G-x(2)-[APT]-R Occurences: 10(9) 42_HUMAN : 281- 286: tvlrc L-GipAR vvttf F13A_BOVIN : 31- 37: pptve LqGlvPR F13A_HUMAN : 31- 37: lptve LqGvvPR gvnlq F13A_HUMAN : 328- 333: tflrc L-GipAR ivtny TGLC_CAVCU : 290- 295: tvlrc L-GipTR vvtnf TGLC_HUMAN : 291- 296: tvlrc L-GipTR vvtny TGLC_MOUSE : 291- 296: tvlrc L-GipTR vvtny TGLK_HUMAN : 391- 396: tglrc L-GlaTR tvtnf TGLK_RABIT : 44- 49: tvlrc L-GlaTR tvtnf TGLK_RAT : 399- 404: tvlrc L-GlaTR tvtnf K 11: 13.7530 11( 9) D-x(3,4)-V-x(0,1)-L-[AGQT] Occurences: 11(9) 42_HUMAN : 264- 271: grpvy DgqawV-LA avact F13A_BOVIN : 24- 32: snaae DdpptVeLQ glvpr F13A_BOVIN : 25- 32: naaed Dppt-VeLQ glvpr F13A_HUMAN : 24- 32: snaae DdlptVeLQ gvvpr F13A_HUMAN : 25- 32: naaed Dlpt-VeLQ gvvpr TGLC_CAVCU : 231- 237: mvncn Ddqg-V-LQ grwdn TGLC_HUMAN : 232- 239: mvncn Ddqg-VlLG rwdnn TGLC_MOUSE : 232- 239: mvncn Ddqg-VlLG rwdnn TGLK_HUMAN : 692- 699: rlrtp DlsltV-LG aavvg TGLK_RABIT : 246- 254: avmgq DltvsVvLT nrsss TGLK_RAT : 601- 609: avmgq DltvsVvLT nrgss L 12: 13.7514 12( 9) D-x(1,2)-P-x(1,2)-E-x(3)-[AGIL] Occurences: 12(9) 42_HUMAN : 614- 622: lqnsl Da-Pm-EdcvI silgr F13A_BOVIN : 24- 34: snaae DdpPtvElqgL vpr F13A_BOVIN : 25- 34: naaed Dp-PtvElqgL vpr F13A_HUMAN : 396- 405: gwqav DstPq-EnsdG myrcg TGLC_CAVCU : 358- 367: gvqal DptPq-EkseG tyccg TGLC_HUMAN : 346- 356: wmtrp DlqPgyEgwqA ldptp TGLC_HUMAN : 358- 367: gwqal DptPq-EkseG tyccg TGLC_MOUSE : 346- 356: wmtrp DlqPgyEgwqA ldptp TGLC_MOUSE : 358- 367: gwqal DptPq-EkseG tyccg TGLK_HUMAN : 459- 468: gwqvv DatPq-EtssG ifccg TGLK_RABIT : 112- 121: gwqvv DatPq-EtssG ifccg TGLK_RAT : 467- 476: gwqvv DatPq-EtssG ifccg M 13: 13.4128 12( 9) P-x(3,4)-L-x(2,3)-L-[DGNTV] Occurences: 12(9) 42_HUMAN : 655- 664: kfqft PthvgLqr-LT vevdc F13A_BOVIN : 26- 35: aaedd PptveLqg-LV pr F13A_BOVIN : 27- 35: aeddp Ptve-Lqg-LV pr F13A_HUMAN : 36- 46: lqgvv PrgvnLqefLN vtsvh TGLC_CAVCU : 659- 668: rvdll PtevgLhk-LV vnfec TGLC_HUMAN : 656- 665: rmdlv PlhmgLhk-LV vnfes TGLC_MOUSE : 654- 663: rvdls PtdigLhk-LV vnfqc TGLK_HUMAN : 691- 699: frlrt Pdls-Ltv-LG aavvg TGLK_HUMAN : 761- 771: fvpvr PgprqLiasLD spqls TGLK_RABIT : 344- 352: frvrt Pdls-Ltl-LG aavvg TGLK_RAT : 699- 707: frlrt Pdls-Ltl-LG aavvg TGLK_RAT : 769- 779: fvpvr PgprqLiasLD spqls N 14: 13.3888 9( 9) E-x(1,3)-Q-[AGLPV]-L Occurences: 9(9) 42_HUMAN : 598- 603: mpeka Eqy-QPL tasvs F13A_BOVIN : 30- 34: dpptv El--QGL vpr F13A_HUMAN : 593- 599: liqag EymgQLL eqasl TGLC_CAVCU : 507- 511: taesh Ec--QLL lcari TGLC_HUMAN : 352- 357: lqpgy Egw-QAL dptpq TGLC_MOUSE : 352- 357: lqpgy Egw-QAL dptpq TGLK_HUMAN : 675- 680: sghvk Esg-QVL akqht TGLK_RABIT : 328- 333: sghvk Esg-QVL akqht TGLK_RAT : 683- 688: sghvk Esg-QVL akqht O 15: 12.5102 9( 9) E-x(3)-P-x(3)-L Occurences: 9(9) 42_HUMAN : 469- 477: rppsl EtasPlylL lkaps F13A_BOVIN : 23- 31: tsnaa EddpPtveL qglvp F13A_HUMAN : 23- 31: nsnaa EddlPtveL qgvvp TGLC_CAVCU : 542- 550: ldpfs EnsiPlhiL yekyg TGLC_HUMAN : 539- 547: lepfs EksvPlciL yekyr TGLC_MOUSE : 537- 545: ldpys EnsiPlriL yekys TGLK_HUMAN : 419- 427: diyfd EnmkPlehL nhdsv TGLK_RABIT : 72- 80: diyfd EnmkPlehL nrdsv TGLK_RAT : 427- 435: diyfd EnmkPlehL nhdsv P 16: 12.0102 10( 9) L-x(0,1)-G-x(3)-R Occurences: 10(9) 42_HUMAN : 281- 286: tvlrc L-GipaR vvttf F13A_BOVIN : 31- 37: pptve LqGlvpR F13A_HUMAN : 31- 37: lptve LqGvvpR gvnlq F13A_HUMAN : 328- 333: tflrc L-GipaR ivtny TGLC_CAVCU : 290- 295: tvlrc L-GiptR vvtnf TGLC_HUMAN : 291- 296: tvlrc L-GiptR vvtny TGLC_MOUSE : 291- 296: tvlrc L-GiptR vvtny TGLK_HUMAN : 391- 396: tglrc L-GlatR tvtnf TGLK_RABIT : 44- 49: tvlrc L-GlatR tvtnf TGLK_RAT : 399- 404: tvlrc L-GlatR tvtnf Q 17: 12.0102 10( 9) V-E-x(4,5)-V Occurences: 10(9) 42_HUMAN : 201- 208: skdkq VEkwsqpV hvarv F13A_BOVIN : 29- 35: ddppt VElqgl-V pr F13A_HUMAN : 29- 35: ddlpt VElqgv-V prgvn TGLC_CAVCU : 639- 645: kdqks VEvpdp-V eageq TGLC_HUMAN : 636- 642: eeqkt VEipdp-V eagee TGLC_HUMAN : 642- 648: eipdp VEagee-V kvrmd TGLC_MOUSE : 634- 640: keqks VEvsdp-V pagdl TGLK_HUMAN : 583- 589: dvamq VEaqda-V mgqdl TGLK_RABIT : 236- 242: dvamq VEaqda-V mgqdl TGLK_RAT : 591- 597: dvamq VEaqda-V mgqdl R 18: 12.0102 14( 9) V-x-L-x(2,3)-L Occurences: 14(9) 42_HUMAN : 607- 613: pltas VsLqnsL dapme 42_HUMAN : 658- 663: ftpth VgLqr-L tvevd F13A_BOVIN : 29- 34: ddppt VeLqg-L vpr F13A_HUMAN : 39- 45: vvprg VnLqefL nvtsv F13A_HUMAN : 575- 580: ketfd VtLep-L sfkke TGLC_CAVCU : 610- 616: kliae VsLknpL pvpll TGLC_CAVCU : 662- 667: llpte VgLhk-L vvnfe TGLC_HUMAN : 542- 547: fseks VpLci-L yekyr TGLC_HUMAN : 607- 613: klvae VsLqnpL pvale TGLC_HUMAN : 655- 661: vrmdl VpLhmgL hklvv TGLC_MOUSE : 605- 611: klvae VsLknpL sdply TGLK_HUMAN : 610- 616: ssrrt VkLhlyL svtfy TGLK_RABIT : 263- 269: ssrrt VkLhlyL svtfy TGLK_RAT : 618- 624: ssrrt VkLhlyL cvtyy S 19: 12.0102 11( 9) S-S-x(4,5)-G Occurences: 11(9) 42_HUMAN : 482- 488: llkap SSlplr-G daqis F13A_BOVIN : 3- 9: se SSgtaf-G grrai F13A_BOVIN : 3- 10: se SSgtafgG rraip F13A_HUMAN : 148- 155: rlsiq SSpkcivG kfrmy TGLC_CAVCU : 79- 85: arfsl SSaveg-G twsas TGLC_HUMAN : 215- 221: dcsrr SSpvyv-G rvgsg TGLC_MOUSE : 215- 221: dcsrr SSpiyv-G rvvsd TGLK_HUMAN : 74- 81: rgrgs SSgtrrpG srgsd TGLK_HUMAN : 466- 473: tpqet SSgifccG pcsve TGLK_RABIT : 119- 126: tpqet SSgifccG pcsve TGLK_RAT : 34- 40: pepdr SSrsrr-G ggrsf TGLK_RAT : 34- 41: pepdr SSrsrrgG grsfw TGLK_RAT : 474- 481: tpqet SSgifccG pcsve T 20: 11.5102 11( 9) G-x(0,1)-L-x(2,3)-R Occurences: 11(9) 42_HUMAN : 238- 244: qatqe GaLlnkR rgsvp 42_HUMAN : 628- 632: silgr G-Lih-R ersyr F13A_BOVIN : 33- 37: tvelq G-Lvp-R F13A_HUMAN : 168- 174: vwtpy GvLrtsR npetd TGLC_CAVCU : 234- 239: cnddq GvLqg-R wdnny TGLC_HUMAN : 235- 240: cnddq GvLlg-R wdnny TGLC_MOUSE : 235- 240: cnddq GvLlg-R wdnny TGLC_MOUSE : 643- 649: dpvpa GdLvkaR vdlsp TGLK_HUMAN : 392- 396: glrcl G-Lat-R tvtnf TGLK_RABIT : 45- 49: vlrcl G-Lat-R tvtnf TGLK_RAT : 400- 404: vlrcl G-Lat-R tvtnf Number of patterns evaluated by Pratt:1193 Total running time: 1 seconds