------------------------------------------------------------ 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 26 sequences from file ALPHA_2_MACROGLOBULIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 26 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 29 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 ALPHA_2_MACROGLOBULIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: A1I3_RAT 1477 A2MG_HUMAN 1474 A2MG_MOUSE 1476 A2MG_RAT 1472 A2MH_MOUSE 1451 A2M_HOMAM 38 A2M_OCTVU 18 A2M_PACLE 32 CO3_CAVPO 1666 CO3_EPTBU 1620 CO3_HUMAN 1663 CO3_MOUSE 1663 CO3_NAJNA 1651 CO3_RABIT 726 CO3_RAT 1663 CO4A_BOVIN 77 CO4A_RAT 76 CO4_HUMAN 1741 CO4_MOUSE 1738 CO5A_BOVIN 74 CO5A_PIG 74 CO5A_RAT 76 CO5_HUMAN 1676 CO5_MOUSE 1680 OVOS_ANAPL 32 PZP_HUMAN 1482 Pratt run started at Thu Feb 6 18:35:23 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 97( 26) C-x(0,1)-E 2: 7.3401 117( 26) C-x(0,2)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 14.1921 34( 26) C-x(0,1)-E-[EQ]-[NR] B 2: 7.3401 117( 26) C-x(0,2)-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 14.1921 34( 26) C-x(0,1)-E-[EQ]-[NR] Occurences: 34(26) A1I3_RAT : 975- 979: qmpyg CgEQN mvlfa A2MG_HUMAN : 972- 976: qmpyg CgEQN mvlfa A2MG_MOUSE : 426- 430: csyfy CmEER hasak A2MG_MOUSE : 974- 978: hmpyg CgEQN mvlfa A2MG_RAT : 970- 974: kmpyg CgEQN mvlfa A2MH_MOUSE : 426- 430: cyffy CmEER yasae A2MH_MOUSE : 974- 978: hmpyg CgEQN mvlfa A2M_HOMAM : 27- 31: vmpyg CgEQN mvnfa A2M_OCTVU : 5- 9: kpsg CgEQN minfy A2M_PACLE : 16- 20: vmpyg CgEQN mvnfa CO3_CAVPO : 1015- 1019: itpsg CgEQN migmt CO3_CAVPO : 1517- 1521: kdlcr CaEEN cfiql CO3_EPTBU : 672- 675: plrls C-EER tkhih CO3_EPTBU : 970- 974: rlprg CgEQN mmyts CO3_HUMAN : 1010- 1014: vtpsg CgEQN migmt CO3_HUMAN : 1513- 1517: delcr CaEEN cfiqk CO3_MOUSE : 1010- 1014: vtpag CgEQN migmt CO3_MOUSE : 1513- 1517: semcr CaEEN cfmqq CO3_NAJNA : 999- 1003: itpsg CgEQN mitmt CO3_RABIT : 73- 77: vtgsg CgEQN miamt CO3_RABIT : 576- 580: kemcr CaEEN cfmqq CO3_RAT : 1010- 1014: vtpsg CgEQN migmt CO3_RAT : 1513- 1517: nemcr CaEEN cfmhq CO4A_BOVIN : 37- 40: pmart C-EQR aarvq CO4A_RAT : 37- 40: pmart C-EQR aarvp CO4_HUMAN : 716- 719: pmmrs C-EQR aarvq CO4_MOUSE : 714- 717: pmkrt C-EQR aarvp CO5A_BOVIN : 34- 37: nddet C-EER aaria CO5A_PIG : 34- 37: nddet C-EER aarik CO5A_RAT : 37- 40: nkyet C-EQR varvt CO5_HUMAN : 711- 714: nndet C-EQR aaris CO5_MOUSE : 715- 718: nfyet C-EER varvt OVOS_ANAPL : 27- 31: qmpfg CgEQN m PZP_HUMAN : 978- 982: qmpyg CgEQN mvlfa B 2: 7.3401 117( 26) C-x(0,2)-G Occurences: 117(26) A1I3_RAT : 269- 271: vkisl Ch-G nptfs A1I3_RAT : 595- 596: spqsl C--G lravd A1I3_RAT : 850- 852: nqdsy Cl-G angrh A1I3_RAT : 886- 887: qspgp C--G sevat A1I3_RAT : 975- 976: qmpyg C--G eqnmv A2MG_HUMAN : 251- 252: mnvsv C--G lytyg A2MG_HUMAN : 278- 280: sdasd Ch-G edsqa A2MG_HUMAN : 431- 433: kdrsp Cy-G yqwvs A2MG_HUMAN : 470- 471: shelp C--G htqtv A2MG_HUMAN : 849- 852: aphci CanG rqtvs A2MG_HUMAN : 883- 884: esqel C--G tevps A2MG_HUMAN : 921- 924: fnsll CpsG gevse A2MG_HUMAN : 972- 973: qmpyg C--G eqnmv A2MG_MOUSE : 251- 252: lsvta C--G kytyg A2MG_MOUSE : 403- 406: sidtt CisG sslhi A2MG_MOUSE : 587- 588: spqsl C--G lravd A2MG_MOUSE : 885- 886: qssep C--G sevat A2MG_MOUSE : 974- 975: hmpyg C--G eqnmv A2MG_RAT : 254- 255: mnvsv C--G iytyg A2MG_RAT : 281- 283: snpsn Cf-G eesva A2MG_RAT : 434- 436: kdsna Cy-G frwlt A2MG_RAT : 598- 599: spqsl C--G lravd A2MG_RAT : 881- 882: nskel C--G nevpv A2MG_RAT : 919- 922: fnsll CpmG aevse A2MG_RAT : 970- 971: kmpyg C--G eqnmv A2MH_MOUSE : 251- 252: lqvtv C--G kytyg A2MH_MOUSE : 587- 588: spqsl C--G lravd A2MH_MOUSE : 885- 886: qssep C--G sevat A2MH_MOUSE : 974- 975: hmpyg C--G eqnmv A2M_HOMAM : 27- 28: vmpyg C--G eqnmv A2M_OCTVU : 5- 6: kpsg C--G eqnmi A2M_PACLE : 16- 17: vmpyg C--G eqnmv CO3_CAVPO : 557- 559: dvrds Cv-G tlvvk CO3_CAVPO : 630- 633: kadig CtpG sgkdy CO3_CAVPO : 699- 702: elrrc CedG mrenp CO3_CAVPO : 1015- 1016: itpsg C--G eqnmi CO3_CAVPO : 1106- 1107: dsevl C--G avkwl CO3_CAVPO : 1540- 1543: rleka CepG vdyvy CO3_EPTBU : 593- 596: asdlg CsvG sgktg CO3_EPTBU : 628- 631: vkdpg CpnG htrrk CO3_EPTBU : 780- 782: qskgl Cv-G pslel CO3_EPTBU : 831- 832: eiqvk C--G dgict CO3_EPTBU : 831- 834: eiqvk CgdG ictda CO3_EPTBU : 970- 971: rlprg C--G eqnmm CO3_EPTBU : 1062- 1063: pvsei C--G svrwl CO3_EPTBU : 1321- 1323: vikkd Ck-G fslei CO3_EPTBU : 1420- 1422: kdekn Cv-G frlnq CO3_EPTBU : 1467- 1469: npdas Ch-G nicnc CO3_EPTBU : 1551- 1552: vipmh C--G knlnv CO3_HUMAN : 559- 561: dvkds Cv-G slvvk CO3_HUMAN : 627- 630: kadig CtpG sgkdy CO3_HUMAN : 694- 697: elrkc CedG mrenp CO3_HUMAN : 1010- 1011: vtpsg C--G eqnmi CO3_HUMAN : 1101- 1102: dsqvl C--G avkwl CO3_HUMAN : 1537- 1540: rldka CepG vdyvy CO3_MOUSE : 559- 561: dvkds Ci-G tlvvk CO3_MOUSE : 626- 629: kadig CtpG sgkny CO3_MOUSE : 694- 697: glrkc CedG mrdip CO3_MOUSE : 1010- 1011: vtpag C--G eqnmi CO3_MOUSE : 1101- 1102: dshvl C--G avkwl CO3_MOUSE : 1158- 1160: eardi Ce-G qvnsl CO3_MOUSE : 1537- 1540: rldka CepG vdyvy CO3_NAJNA : 546- 548: dvkdt Cm-G tlvvk CO3_NAJNA : 615- 618: ksdfg CtaG sgqnn CO3_NAJNA : 684- 687: glrkc CedG mhenp CO3_NAJNA : 999- 1000: itpsg C--G eqnmi CO3_NAJNA : 1091- 1092: sheii C--G gvkwl CO3_NAJNA : 1091- 1093: sheii Cg-G vkwli CO3_NAJNA : 1494- 1496: llnki Ch-G nicrc CO3_RABIT : 73- 74: vtgsg C--G eqnmi CO3_RABIT : 164- 165: dsqvl C--G avkwl CO3_RABIT : 600- 603: rldka CepG ldyvy CO3_RAT : 558- 560: dvkds Cv-G tlvvk CO3_RAT : 626- 629: kadig CtpG sgkny CO3_RAT : 694- 697: glrkc CedG mrdip CO3_RAT : 1010- 1011: vtpsg C--G eqnmi CO3_RAT : 1101- 1102: dsqvl C--G avkwl CO3_RAT : 1158- 1160: eardi Ce-G qvnsl CO3_RAT : 1537- 1540: rldka CepG vdyvy CO4A_BOVIN : 24- 27: vakrc CqdG ltrlp CO4A_RAT : 24- 27: dtkrc CqdG mtklp CO4_HUMAN : 97- 98: kdaks C--G lhqll CO4_HUMAN : 567- 569: vqaga Ce-G klels CO4_HUMAN : 635- 636: sydlg C--G pgggd CO4_HUMAN : 635- 638: sydlg CgpG ggdsa CO4_HUMAN : 703- 706: takrc CqdG vtrlp CO4_HUMAN : 876- 879: pvegl ClaG gggla CO4_HUMAN : 1010- 1011: rlprg C--G eqtmi CO4_HUMAN : 1532- 1534: ptsre Cv-G feavq CO4_HUMAN : 1587- 1590: aevcq CaeG kcprq CO4_MOUSE : 95- 96: edvrs C--G lfdlr CO4_MOUSE : 565- 567: iqsrd Ce-G klqlk CO4_MOUSE : 633- 634: synvg C--G pgggd CO4_MOUSE : 633- 636: synvg CgpG ggdda CO4_MOUSE : 701- 704: dakrc CqdG mtklp CO4_MOUSE : 874- 877: pvegl ClaG ggmma CO4_MOUSE : 1529- 1531: pttre Cv-G fgasq CO4_MOUSE : 1577- 1579: llatl Cs-G dvcqc CO4_MOUSE : 1584- 1587: gdvcq CaeG kcprl CO5A_BOVIN : 22- 25: wvkkc CydG ahrnd CO5A_PIG : 22- 25: mlkkc CydG ayrnd CO5A_RAT : 25- 28: vpkkc CydG arenk CO5_HUMAN : 567- 568: nieek C--G nqlqv CO5_HUMAN : 634- 635: ksdlg C--G agggl CO5_HUMAN : 634- 637: ksdlg CgaG gglnn CO5_HUMAN : 699- 702: vvkkc CydG acvnn CO5_HUMAN : 1520- 1522: kiqkv Ce-G aackc CO5_HUMAN : 1532- 1533: cvead C--G qmqee CO5_MOUSE : 567- 568: nieek C--G nqlqv CO5_MOUSE : 635- 636: ksdlg C--G agggh CO5_MOUSE : 635- 638: ksdlg CgaG gghdn CO5_MOUSE : 703- 706: vpkkc CydG arvnf CO5_MOUSE : 870- 873: avegi CtsG ssaas CO5_MOUSE : 1524- 1526: rlqkv Ce-G aactc OVOS_ANAPL : 27- 28: qmpfg C--G eqnm PZP_HUMAN : 250- 251: vnitv C--G eytyg PZP_HUMAN : 466- 467: agtlp C--G hteti PZP_HUMAN : 853- 856: geesy CicG serqt PZP_HUMAN : 855- 856: esyci C--G serqt PZP_HUMAN : 889- 890: qslel C--G nevve PZP_HUMAN : 927- 930: fssmt CasG anvse PZP_HUMAN : 978- 979: qmpyg C--G eqnmv PZP_HUMAN : 1358- 1360: tvpqt Cd-G hkaht Number of patterns evaluated by Pratt:2 Total running time: 2 seconds