------------------------------------------------------------ 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 44 sequences from file S100_CABP PATTERN CONSERVATION: CM: min Nr of Seqs to Match 44 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 S100_CABP.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CAGC_PIG 91 M126_CHICK 119 S102_BOVIN 97 S102_HUMAN 97 S103_HUMAN 101 S104_BOVIN 100 S104_HUMAN 101 S104_MOUSE 101 S104_RAT 101 S105_HUMAN 110 S106_HUMAN 90 S106_MOUSE 89 S106_RABIT 90 S106_RAT 90 S107_HUMAN 100 S108_BOVIN 41 S108_HUMAN 93 S108_MOUSE 88 S109_BOVIN 122 S109_HUMAN 114 S109_MOUSE 113 S10A_BOVIN 93 S10A_HUMAN 93 S10A_RAT 93 S10B_BOVIN 91 S10B_HUMAN 91 S10B_RAT 91 S10C_CHICK 65 S10C_HUMAN 25 S10C_PIG 99 S10C_RABIT 102 S10D_BOVIN 78 S10D_HUMAN 78 S10D_PIG 78 S10D_RAT 78 S10E_HUMAN 95 S110_CHICK 96 S110_HUMAN 96 S110_MOUSE 96 S110_PIG 95 S110_RAT 94 S110_XENLA 96 TRHY_HUMAN 1898 TRHY_RABIT 1407 Pratt run started at Thu Feb 6 21:11:29 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 107( 44) L-x(4)-D 2: 7.8401 95( 44) L-x(0,1)-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 8.3401 107( 44) L-x(4)-D B 2: 7.8401 95( 44) L-x(0,1)-D Best patterns with alignements: fitness hits(seqs) Pattern A 1: 8.3401 107( 44) L-x(4)-D Occurences: 107(44) CAGC_PIG : 44- 49: elpnt LkntkD qgtid CAGC_PIG : 60- 65: kifqn LdanqD eqvsf CAGC_PIG : 81- 86: lvtdv LitahD nihke M126_CHICK : 14- 19: gplse LekaiD viidv M126_CHICK : 71- 76: qifkd LdnnkD qqlsf M126_CHICK : 99- 104: atheh LhfceD hqqqh S102_BOVIN : 58- 63: eglkk LmgdlD ensdq S102_BOVIN : 62- 67: klmgd LdensD qqvdf S102_HUMAN : 58- 63: eglkk LmgnlD ensdq S102_HUMAN : 62- 67: klmgn LdensD qqvdf S103_HUMAN : 62- 67: kfmsv LdtnkD cevdf S104_BOVIN : 4- 9: ayp LekalD vmvst S104_BOVIN : 45- 50: elpsf LgkrtD etafq S104_BOVIN : 57- 62: tafqk LmsnlD cnkdn S104_BOVIN : 61- 66: klmsn LdcnkD nevdf S104_HUMAN : 5- 10: macp LekalD vmvst S104_HUMAN : 46- 51: elpsf LgkrtD eaafq S104_HUMAN : 58- 63: aafqk LmsnlD snrdn S104_HUMAN : 62- 67: klmsn LdsnrD nevdf S104_MOUSE : 5- 10: marp LeealD vivst S104_MOUSE : 46- 51: elpsf LgkrtD eaafq S104_MOUSE : 62- 67: kvmsn LdsnrD nevdf S104_RAT : 5- 10: marp LeealD vivst S104_RAT : 46- 51: elpsf LgrrtD eaafq S104_RAT : 58- 63: aafqk LmnnlD snrdn S104_RAT : 62- 67: klmnn LdsnrD nevdf S105_HUMAN : 73- 78: ssidd LmkslD knsdq S105_HUMAN : 77- 82: dlmks LdknsD qeidf S106_HUMAN : 56- 61: aeiar LmedlD rnkdq S106_HUMAN : 60- 65: rlmed LdrnkD qevnf S106_MOUSE : 56- 61: aeiar LmddlD rnkdq S106_MOUSE : 60- 65: rlmdd LdrnkD qevnf S106_RABIT : 56- 61: aeivk LmddlD rnkdq S106_RABIT : 60- 65: klmdd LdrnkD qevnf S106_RAT : 56- 61: aeiar LmddlD rnkdq S106_RAT : 60- 65: rlmdd LdrnkD qevnf S107_HUMAN : 75- 80: dfsef LsllgD iatdy S108_BOVIN : 5- 10: mltd LexaiD slidv S108_HUMAN : 9- 14: eleka LnsiiD vyhky S108_HUMAN : 58- 63: vwfke LdintD gavnf S108_MOUSE : 8- 13: eleka LsnliD vyhny S108_MOUSE : 53- 58: inien LfrelD insdn S108_MOUSE : 57- 62: nlfre LdinsD nainf S109_BOVIN : 62- 67: eimed LdtnvD kqlsf S109_HUMAN : 66- 71: himed LdtnaD kqlsf S109_MOUSE : 67- 72: dimed LdtnqD nqlsf S10A_BOVIN : 41- 46: llqte LsgflD aqkda S10A_BOVIN : 45- 50: elsgf LdaqkD adavd S10A_BOVIN : 61- 66: kvmke LdengD gevdf S10A_HUMAN : 41- 46: llqte LsgflD aqkdv S10A_HUMAN : 45- 50: elsgf LdaqkD vdavd S10A_HUMAN : 61- 66: kvmke LdengD gevdf S10A_RAT : 41- 46: llqte LssflD vqkda S10A_RAT : 45- 50: elssf LdvqkD adavd S10A_RAT : 61- 66: kimke LdengD gevdf S10B_BOVIN : 60- 65: kvmet LdsdgD gecdf S10B_HUMAN : 60- 65: kvmet LdndgD gecdf S10B_RAT : 60- 65: kvmet LdedgD gecdf S10C_CHICK : 52- 57: rmmkr LdinsD gqldf S10C_HUMAN : 14- 19: rmnte LaaxtD pgvld S10C_PIG : 65- 70: rmmkk LdldsD gqldf S10C_RABIT : 64- 69: rmmkk LdlnsD gqldf S10D_BOVIN : 52- 57: stlde LfeelD kngdg S10D_BOVIN : 56- 61: elfee LdkngD gevsf S10D_HUMAN : 52- 57: ntldd LfqelD kngdg S10D_HUMAN : 56- 61: dlfqe LdkngD gevsf S10D_PIG : 52- 57: rtldd LfqelD kngng S10D_RAT : 52- 57: stldn LfkelD kngdg S10D_RAT : 56- 61: nlfke LdkngD gevsy S10E_HUMAN : 45- 50: elpgf LqsgkD kdavd S10E_HUMAN : 57- 62: davdk LlkdlD angda S10E_HUMAN : 61- 66: kllkd LdangD aqvdf S110_CHICK : 42- 47: efpgf LenqrD pmald S110_CHICK : 58- 63: kimkd LdqcrD gkvgf S110_HUMAN : 42- 47: efpgf LenqkD plavd S110_HUMAN : 58- 63: kimkd LdqcrD gkvgf S110_MOUSE : 42- 47: efpgf LenqkD plavd S110_MOUSE : 58- 63: kimkd LdqcrD gkvgf S110_PIG : 42- 47: efpgf LenqkD plavd S110_PIG : 58- 63: kimkd LdqcrD gkvgf S110_RAT : 42- 47: efpgf LenqkD plavd S110_RAT : 58- 63: kimkd LdqcrD gkvgf S110_XENLA : 33- 38: mnrdd LqkllD sefse S110_XENLA : 45- 50: efsef LknqnD pmtvd TRHY_HUMAN : 5- 10: mspl LrsicD iteif TRHY_HUMAN : 45- 50: efgav LrrphD pktvd TRHY_HUMAN : 727- 732: kwqwq LeseaD arqsk TRHY_HUMAN : 867- 872: eraqq LqeeeD glqed TRHY_HUMAN : 1312- 1317: eeqpl LrqerD rkfre TRHY_HUMAN : 1364- 1369: eereq LrqdrD rkfre TRHY_HUMAN : 1616- 1621: ereqq LrhdrD rkfre TRHY_HUMAN : 1792- 1797: eqeqr LrqerD rqyra TRHY_RABIT : 5- 10: mspl LksiiD iieif TRHY_RABIT : 33- 38: lkkkd LkillD refga TRHY_RABIT : 45- 50: efgav LqrphD petvd TRHY_RABIT : 61- 66: vmlel LdrdsD glvgf TRHY_RABIT : 572- 577: reeek LqreeD ekrrr TRHY_RABIT : 734- 739: reeql LrqerD rklre TRHY_RABIT : 766- 771: ereqq LrrerD rkfre TRHY_RABIT : 882- 887: qeeqe LrqerD rklre TRHY_RABIT : 904- 909: qeeqe LrqerD rklre TRHY_RABIT : 996- 1001: reeqe LrqerD rkfre TRHY_RABIT : 1092- 1097: ereqq LrrerD rkfre TRHY_RABIT : 1138- 1143: reeql LrqerD rkfre TRHY_RABIT : 1230- 1235: qeeqe LrqerD rkfre TRHY_RABIT : 1252- 1257: reeqe LrrerD rkfre TRHY_RABIT : 1301- 1306: qeeqr LrqerD rryra B 2: 7.8401 95( 44) L-x(0,1)-D Occurences: 95(44) CAGC_PIG : 3- 5: tk LeD hlegi CAGC_PIG : 60- 61: kifqn L-D anqde M126_CHICK : 71- 72: qifkd L-D nnkdq S102_BOVIN : 62- 63: klmgd L-D ensdq S102_HUMAN : 62- 63: klmgn L-D ensdq S103_HUMAN : 62- 63: kfmsv L-D tnkdc S104_BOVIN : 8- 9: pleka L-D vmvst S104_BOVIN : 61- 62: klmsn L-D cnkdn S104_HUMAN : 9- 10: pleka L-D vmvst S104_HUMAN : 62- 63: klmsn L-D snrdn S104_MOUSE : 9- 10: pleea L-D vivst S104_MOUSE : 62- 63: kvmsn L-D snrdn S104_RAT : 9- 10: pleea L-D vivst S104_RAT : 62- 63: klmnn L-D snrdn S105_HUMAN : 77- 78: dlmks L-D knsdq S105_HUMAN : 106- 108: yndff LeD nk S106_HUMAN : 5- 6: macp L-D qaigl S106_HUMAN : 48- 50: tigsk LqD aeiar S106_HUMAN : 60- 61: rlmed L-D rnkdq S106_MOUSE : 5- 6: macp L-D qaigl S106_MOUSE : 48- 50: tigsk LqD aeiar S106_MOUSE : 56- 58: aeiar LmD dldrn S106_MOUSE : 60- 61: rlmdd L-D rnkdq S106_RABIT : 5- 6: masp L-D qaigl S106_RABIT : 48- 50: tigsk LqD aeivk S106_RABIT : 56- 58: aeivk LmD dldrn S106_RABIT : 60- 61: klmdd L-D rnkdq S106_RAT : 5- 6: macp L-D qaigl S106_RAT : 48- 50: tigak LqD aeiar S106_RAT : 56- 58: aeiar LmD dldrn S106_RAT : 60- 61: rlmdd L-D rnkdq S107_HUMAN : 54- 56: kgtny LaD vfekk S107_HUMAN : 78- 80: eflsl LgD iatdy S108_BOVIN : 2- 4: m LtD lexai S108_BOVIN : 12- 14: xaids LiD vyhky S108_HUMAN : 58- 59: vwfke L-D intdg S108_MOUSE : 11- 13: kalsn LiD vyhny S108_MOUSE : 57- 58: nlfre L-D insdn S109_BOVIN : 62- 63: eimed L-D tnvdk S109_HUMAN : 66- 67: himed L-D tnadk S109_MOUSE : 67- 68: dimed L-D tnqdn S10A_BOVIN : 45- 46: elsgf L-D aqkda S10A_BOVIN : 61- 62: kvmke L-D engdg S10A_HUMAN : 45- 46: elsgf L-D aqkdv S10A_HUMAN : 61- 62: kvmke L-D engdg S10A_RAT : 33- 35: lskke LkD llqte S10A_RAT : 45- 46: elssf L-D vqkda S10A_RAT : 61- 62: kimke L-D engdg S10B_BOVIN : 10- 12: kavva LiD vfhqy S10B_BOVIN : 60- 61: kvmet L-D sdgdg S10B_HUMAN : 10- 12: kamva LiD vfhqy S10B_HUMAN : 60- 61: kvmet L-D ndgdg S10B_RAT : 10- 12: kamva LiD vfhqy S10B_RAT : 60- 61: kvmet L-D edgdg S10C_CHICK : 52- 53: rmmkr L-D insdg S10C_CHICK : 60- 61: nsdgq L-D fqef S10C_HUMAN : 23- 24: tdpgv L-D r S10C_PIG : 58- 59: kdpgv L-D rmmkk S10C_PIG : 65- 66: rmmkk L-D ldsdg S10C_PIG : 67- 68: mkkld L-D sdgql S10C_PIG : 73- 74: dsdgq L-D fqefl S10C_RABIT : 57- 58: kdpgv L-D rmmkk S10C_RABIT : 64- 65: rmmkk L-D lnsdg S10C_RABIT : 72- 73: nsdgq L-D fqefl S10D_BOVIN : 49- 50: kgpst L-D elfee S10D_BOVIN : 56- 57: elfee L-D kngdg S10D_HUMAN : 49- 50: kgpnt L-D dlfqe S10D_HUMAN : 49- 51: kgpnt LdD lfqel S10D_HUMAN : 56- 57: dlfqe L-D kngdg S10D_PIG : 49- 50: kgprt L-D dlfqe S10D_PIG : 49- 51: kgprt LdD lfqel S10D_PIG : 56- 57: dlfqe L-D kngng S10D_RAT : 49- 50: kasst L-D nlfke S10D_RAT : 56- 57: nlfke L-D kngdg S10E_HUMAN : 58- 60: avdkl LkD ldang S10E_HUMAN : 61- 62: kllkd L-D angda S110_CHICK : 51- 52: rdpma L-D kimkd S110_CHICK : 58- 59: kimkd L-D qcrdg S110_HUMAN : 58- 59: kimkd L-D qcrdg S110_MOUSE : 58- 59: kimkd L-D qcrdg S110_PIG : 58- 59: kimkd L-D qcrdg S110_RAT : 58- 59: kimkd L-D qcrdg S110_XENLA : 36- 38: ddlqk LlD sefse S110_XENLA : 37- 38: dlqkl L-D sefse S110_XENLA : 61- 62: kimkd L-D dcrkg S110_XENLA : 61- 63: kimkd LdD crkgq TRHY_HUMAN : 60- 62: dlile LlD rdsng TRHY_HUMAN : 61- 62: lilel L-D rdsng TRHY_HUMAN : 95- 96: gqatg L-D eekra TRHY_HUMAN : 110- 112: gkesl LqD rrtee TRHY_HUMAN : 1211- 1213: eqfrq LeD sqvrd TRHY_RABIT : 36- 38: kdlki LlD refga TRHY_RABIT : 37- 38: dlkil L-D refga TRHY_RABIT : 60- 62: dvmle LlD rdsdg TRHY_RABIT : 61- 62: vmlel L-D rdsdg TRHY_RABIT : 95- 96: gqasg L-D eekrs TRHY_RABIT : 123- 125: qrrfe LrD rqfed TRHY_RABIT : 601- 603: rqeeq LrD rklre Number of patterns evaluated by Pratt:4 Total running time: 1 seconds