------------------------------------------------------------ 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 12 sequences from file OSTEONECTIN_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 12 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 OSTEONECTIN_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: QR1_COTJA 676 SC1_RAT 634 SPRC_BOVIN 304 SPRC_CAEEL 264 SPRC_CHICK 298 SPRC_HUMAN 303 SPRC_MOUSE 302 SPRC_MUSVI 26 SPRC_PIG 35 SPRC_RABIT 10 SPRC_RAT 301 SPRC_XENLA 300 Pratt run started at Thu Feb 6 20:26:36 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 25( 12) A-L 2: 7.8401 72( 12) L-x(1,2)-E 3: 7.8401 45( 12) E-x(0,1)-A 4: 7.8401 51( 12) A-x(2,3)-E 5: 7.8401 40( 12) A-x(4,5)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 10.9669 17( 12) A-L-[AGP] B 2: 10.0456 29( 12) A-x(2,3)-E-x(2)-[AGPV] C 3: 9.7421 31( 12) E-x(0,1)-A-x(3)-[ADEGT] D 4: 7.8401 72( 12) L-x(1,2)-E E 5: 7.8401 40( 12) A-x(4,5)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 10.9669 17( 12) A-L-[AGP] Occurences: 17(12) QR1_COTJA : 158- 160: espvd ALG lvrer QR1_COTJA : 440- 442: nstgk ALP dlcrn SC1_RAT : 10- 12: lllly ALG iaaav SPRC_BOVIN : 15- 17: clagr ALA apqqe SPRC_BOVIN : 23- 25: apqqe ALP detev SPRC_CAEEL : 4- 6: mry ALA aclll SPRC_CHICK : 15- 17: clagk ALA apqea SPRC_CHICK : 22- 24: aapqe ALA detev SPRC_HUMAN : 15- 17: clagr ALA apqqe SPRC_HUMAN : 23- 25: apqqe ALP detev SPRC_MOUSE : 15- 17: clagr ALA apqqt SPRC_MUSVI : 5- 7: dkyi ALG ewagc SPRC_PIG : 6- 8: apqqe ALP detev SPRC_RABIT : 6- 8: apqqe ALP de SPRC_RAT : 15- 17: clagr ALA apqte SPRC_XENLA : 15- 17: clagk ALA apqqd SPRC_XENLA : 23- 25: apqqd ALP eeeev B 2: 10.0456 29( 12) A-x(2,3)-E-x(2)-[AGPV] Occurences: 29(12) QR1_COTJA : 149- 156: magqw AlrgEspV dalgl SC1_RAT : 49- 56: vpaea AadiEkhP nhkae SC1_RAT : 50- 56: paeaa Adi-EkhP nhkae SC1_RAT : 65- 72: aekps AlnsEeeA heqst SC1_RAT : 261- 267: egdsn Aeg-EdkA agske SC1_RAT : 268- 275: gedka AgskEhlP htewq SC1_RAT : 378- 385: gdnqg AkkaEssP naeps SPRC_BOVIN : 18- 25: grala ApqqEalP detev SPRC_BOVIN : 23- 30: apqqe AlpdEteV veetv SPRC_BOVIN : 36- 43: veetv AevaEvpV ganpv SPRC_BOVIN : 59- 66: efddg AeetEeeV vaenp SPRC_BOVIN : 283- 289: ndkyi Ald-EwaG cfgik SPRC_CAEEL : 147- 154: teehm AqfpErmA dwlfq SPRC_CHICK : 17- 24: agkal AapqEalA detev SPRC_CHICK : 18- 24: gkala Apq-EalA detev SPRC_CHICK : 22- 29: aapqe AladEteV iedlt SPRC_HUMAN : 18- 25: grala ApqqEalP detev SPRC_HUMAN : 23- 30: apqqe AlpdEteV veetv SPRC_HUMAN : 36- 43: veetv AevtEvsV ganpv SPRC_HUMAN : 59- 66: efddg AeetEeeV vaenp SPRC_HUMAN : 282- 288: ndkyi Ald-EwaG cfgik SPRC_MOUSE : 281- 287: ndkyi Ale-EwaG cfgik SPRC_MUSVI : 5- 11: dkyi Alg-EwaG cfgik SPRC_PIG : 1- 8: ApqqEalP detev SPRC_PIG : 6- 13: apqqe AlpdEteV veetv SPRC_RABIT : 1- 8: ApqqEalP de SPRC_RAT : 23- 29: apqte Aae-EmvA eetvv SPRC_RAT : 280- 286: ndkyi Ale-EwaG cfgik SPRC_XENLA : 23- 30: apqqd AlpeEeeV iedvp C 3: 9.7421 31( 12) E-x(0,1)-A-x(3)-[ADEGT] Occurences: 31(12) QR1_COTJA : 187- 193: ngsee EeAgeeE deewg QR1_COTJA : 188- 193: gseee E-AgeeE deewg QR1_COTJA : 334- 339: gnvwr E-AvyeE eermq QR1_COTJA : 431- 437: gsyhe EsArnsT gkalp QR1_COTJA : 624- 630: slths ElAplrA slvpm SC1_RAT : 37- 43: tlptl EdAtvpT vpaea SC1_RAT : 47- 53: ptvpa EaAadiE khpnh SC1_RAT : 124- 130: qkrlp EnAdfpA tvstp SC1_RAT : 300- 306: kdtde EkAvstE ptdaa SC1_RAT : 582- 588: ilths ElAplrA slvpm SPRC_BOVIN : 22- 27: aapqq E-AlpdE tevve SPRC_BOVIN : 252- 258: ylsht ElAplrA plipm SPRC_BOVIN : 286- 292: yiald EwAgcfG ikekd SPRC_CAEEL : 181- 186: eells E-AendD ekkhv SPRC_CHICK : 21- 26: laapq E-AladE tevie SPRC_CHICK : 202- 207: nekrl E-AgdhT vella SPRC_CHICK : 246- 252: ylsht ElAplrA plipm SPRC_CHICK : 266- 271: ttrff E-AcdlD fdkyi SPRC_CHICK : 280- 286: yiale EwAscfG ikeqd SPRC_HUMAN : 22- 27: aapqq E-AlpdE tevve SPRC_HUMAN : 251- 257: ylsht ElAplrA plipm SPRC_HUMAN : 285- 291: yiald EwAgcfG ikqkd SPRC_MOUSE : 250- 256: ylsht ElAplrA plipm SPRC_MOUSE : 284- 290: yiale EwAgcfG ikeqd SPRC_MUSVI : 8- 14: yialg EwAgcfG ikekd SPRC_PIG : 5- 10: apqq E-AlpdE tevve SPRC_RABIT : 5- 10: apqq E-AlpdE SPRC_RAT : 249- 255: ylsht ElAplrA plipm SPRC_RAT : 283- 289: yiale EwAgcfG ikeqd SPRC_XENLA : 54- 59: vgefd E-AineE eeeep SPRC_XENLA : 282- 288: yiale EwAkcfG ikeqd D 4: 7.8401 72( 12) L-x(1,2)-E Occurences: 72(12) QR1_COTJA : 150- 153: agqwa LrgE spvda QR1_COTJA : 161- 164: vdalg LvrE rntwk QR1_COTJA : 177- 179: kntvg Ld-E nnngs QR1_COTJA : 261- 264: esqek LykE gklpl QR1_COTJA : 561- 563: dtsaf Lt-E kqrnk QR1_COTJA : 574- 576: vkkiy Ln-E krlvs QR1_COTJA : 656- 658: dklit Lk-E wchcf SC1_RAT : 66- 69: ekpsa LnsE eeahe SC1_RAT : 89- 92: sfevd LkdE edgdg SC1_RAT : 110- 112: ertld Lq-E gtsep SC1_RAT : 122- 124: pqqkr Lp-E nadfp SC1_RAT : 232- 234: qsedi Lq-E ssqpt SC1_RAT : 344- 347: psqef LeaE rmhsl SC1_RAT : 508- 510: nilmq Ly-E pnpkh SC1_RAT : 519- 521: khggy Ln-E kqrsk SC1_RAT : 532- 534: vkkiy Ld-E krlla SC1_RAT : 614- 616: dkhit Lk-E wghcf SPRC_BOVIN : 24- 27: pqqea LpdE tevve SPRC_BOVIN : 85- 87: gkvce Ld-E nntpm SPRC_BOVIN : 156- 159: yippc LdsE ltefp SPRC_BOVIN : 160- 162: cldse Lt-E fplrm SPRC_BOVIN : 178- 180: nvlvt Ly-E rdedn SPRC_BOVIN : 187- 190: dednn LltE kqklr SPRC_BOVIN : 188- 190: ednnl Lt-E kqklr SPRC_BOVIN : 284- 286: dkyia Ld-E wagcf SPRC_CAEEL : 30- 32: iadde Lg-E lldni SPRC_CAEEL : 105- 108: tslcd LyrE rclck SPRC_CAEEL : 132- 134: vhley Lg-E ckkld SPRC_CAEEL : 138- 140: geckk Ld-E cteeh SPRC_CAEEL : 173- 176: relhk LewE ellse SPRC_CAEEL : 178- 181: lewee LlsE aendd SPRC_CAEEL : 179- 181: eweel Ls-E aendd SPRC_CAEEL : 255- 257: gkclg Lk-E geiqe SPRC_CHICK : 23- 26: apqea LadE tevie SPRC_CHICK : 33- 36: evied LttE gpvga SPRC_CHICK : 151- 154: fipac LdtE ltefp SPRC_CHICK : 155- 157: cldte Lt-E fplrm SPRC_CHICK : 173- 175: nvlit Ly-E rdedn SPRC_CHICK : 182- 185: dednn LltE kqklk SPRC_CHICK : 183- 185: ednnl Lt-E kqklk SPRC_CHICK : 278- 280: dkyia Le-E wascf SPRC_HUMAN : 24- 27: pqqea LpdE tevve SPRC_HUMAN : 85- 87: gkvce Ld-E nntpm SPRC_HUMAN : 156- 159: yippc LdsE ltefp SPRC_HUMAN : 160- 162: cldse Lt-E fplrm SPRC_HUMAN : 178- 180: nvlvt Ly-E rdedn SPRC_HUMAN : 187- 190: dednn LltE kqklr SPRC_HUMAN : 188- 190: ednnl Lt-E kqklr SPRC_HUMAN : 283- 285: dkyia Ld-E wagcf SPRC_MOUSE : 84- 86: gkvce Ld-E sntpm SPRC_MOUSE : 155- 158: yiapc LdsE ltefp SPRC_MOUSE : 159- 161: cldse Lt-E fplrm SPRC_MOUSE : 177- 179: nvlvt Ly-E rdegn SPRC_MOUSE : 186- 189: degnn LltE kqklr SPRC_MOUSE : 187- 189: egnnl Lt-E kqklr SPRC_MOUSE : 282- 284: dkyia Le-E wagcf SPRC_MUSVI : 6- 8: dkyia Lg-E wagcf SPRC_PIG : 7- 10: pqqea LpdE tevve SPRC_RABIT : 7- 10: pqqea LpdE SPRC_RAT : 154- 157: yiapc LdsE ltefp SPRC_RAT : 158- 160: cldse Lt-E fplrm SPRC_RAT : 176- 178: nvlvt Ly-E rdegn SPRC_RAT : 185- 188: degnn LltE kqklr SPRC_RAT : 186- 188: egnnl Lt-E kqklr SPRC_RAT : 281- 283: dkyia Le-E wagcf SPRC_XENLA : 24- 26: pqqda Lp-E eeevi SPRC_XENLA : 24- 27: pqqda LpeE eevie SPRC_XENLA : 153- 156: yiapc LdnE lsefp SPRC_XENLA : 157- 159: cldne Ls-E fplri SPRC_XENLA : 175- 177: nvlvs Ly-E rdenn SPRC_XENLA : 184- 187: dennn LlnE kqklr SPRC_XENLA : 185- 187: ennnl Ln-E kqklr SPRC_XENLA : 280- 282: dkyia Le-E wakcf E 5: 7.8401 40( 12) A-x(4,5)-A Occurences: 40(12) QR1_COTJA : 28- 34: nyqfg AhgqktA ekhky SC1_RAT : 10- 15: lllly Algia-A avptt SC1_RAT : 10- 16: lllly AlgiaaA vpttf SC1_RAT : 60- 65: hpnhk Aekps-A lnsee SC1_RAT : 261- 267: egdsn AegedkA agske SC1_RAT : 372- 378: enrse AgdnqgA kkaes SC1_RAT : 381- 387: qgakk AesspnA epsde SC1_RAT : 435- 441: etcpp AkildqA cgtdn SC1_RAT : 478- 484: ldyfg AcksipA ctdfe SPRC_BOVIN : 12- 17: fllcl Agral-A apqqe SPRC_BOVIN : 12- 18: fllcl AgralaA pqqea SPRC_BOVIN : 17- 23: agral AapqqeA lpdet SPRC_BOVIN : 18- 23: grala Apqqe-A lpdet SPRC_BOVIN : 39- 45: tvaev AevpvgA npvqv SPRC_BOVIN : 283- 288: ndkyi Aldew-A gcfgi SPRC_CAEEL : 7- 13: ryala AcllllA assfv SPRC_CAEEL : 14- 20: lllla AssfvdA kkkki SPRC_CAEEL : 20- 26: ssfvd AkkkkiA ddelg SPRC_CHICK : 12- 17: fflcl Agkal-A apqea SPRC_CHICK : 12- 18: fflcl AgkalaA pqeal SPRC_CHICK : 17- 22: agkal Aapqe-A ladet SPRC_CHICK : 18- 24: gkala ApqealA detev SPRC_CHICK : 277- 282: fdkyi Aleew-A scfgi SPRC_HUMAN : 12- 17: fllcl Agral-A apqqe SPRC_HUMAN : 12- 18: fllcl AgralaA pqqea SPRC_HUMAN : 17- 23: agral AapqqeA lpdet SPRC_HUMAN : 18- 23: grala Apqqe-A lpdet SPRC_HUMAN : 282- 287: ndkyi Aldew-A gcfgi SPRC_MOUSE : 12- 17: fllcl Agral-A apqqt SPRC_MOUSE : 12- 18: fllcl AgralaA pqqte SPRC_MOUSE : 281- 286: ndkyi Aleew-A gcfgi SPRC_MUSVI : 5- 10: dkyi Algew-A gcfgi SPRC_PIG : 1- 6: Apqqe-A lpdet SPRC_PIG : 19- 25: veetv AevpvgA npvqx SPRC_RABIT : 1- 6: Apqqe-A lpde SPRC_RAT : 12- 17: fllcl Agral-A apqte SPRC_RAT : 12- 18: fllcl AgralaA pqtea SPRC_RAT : 17- 23: agral AapqteA aeemv SPRC_RAT : 18- 23: grala Apqte-A aeemv SPRC_RAT : 18- 24: grala ApqteaA eemva SPRC_RAT : 23- 29: apqte AaeemvA eetvv SPRC_RAT : 24- 29: pqtea Aeemv-A eetvv SPRC_RAT : 280- 285: ndkyi Aleew-A gcfgi SPRC_XENLA : 12- 17: fvlcl Agkal-A apqqd SPRC_XENLA : 12- 18: fvlcl AgkalaA pqqda SPRC_XENLA : 17- 23: agkal AapqqdA lpeee SPRC_XENLA : 18- 23: gkala Apqqd-A lpeee SPRC_XENLA : 279- 284: ddkyi Aleew-A kcfgi Number of patterns evaluated by Pratt:9 Total running time: 0 seconds