------------------------------------------------------------ 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 AA_TRANSFER_CLASS_3 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 46 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 AA_TRANSFER_CLASS_3.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ARGD_BACST 149 ARGD_BACSU 385 ARGD_ECOLI 406 ARGD_RHOCA 71 ARGD_SALTY 17 ARGD_YEAST 423 BIOA_BACSH 455 BIOA_BREFL 423 BIOA_CITFR 5 BIOA_ECOLI 429 BIOA_HAEIN 430 BIOA_MYCLE 436 BIOA_SALTY 5 BIOA_SERMA 425 DGDA_BURCE 432 GABT_ECOLI 426 GABT_HUMAN 472 GABT_MYCLE 446 GABT_PIG 500 GATA_EMENI 498 GATA_YEAST 471 GSA_ARATH 474 GSA_BACSU 430 GSA_ECOLI 426 GSA_HORVU 469 GSA_MYCLE 446 GSA_PROFR 441 GSA_SALTY 426 GSA_SOYBN 466 GSA_SYNP6 432 GSA_TOBAC 478 GSA_XANCH 429 OAPT_PSEPU 449 OAT_BACSU 401 OAT_ECOLI 429 OAT_HUMAN 439 OAT_MOUSE 439 OAT_PLAFA 414 OAT_RAT 439 OAT_VIGAC 426 OAT_YEAST 423 Y949_HAEIN 454 YHXA_BACSU 99 YKAB_BACFI 445 Pratt run started at Thu Feb 6 18:27:30 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.3401 127( 44) T-x(0,2)-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.3401 127( 44) T-x(0,2)-D Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.3401 127( 44) T-x(0,2)-D Occurences: 127(44) ARGD_BACST : 24- 25: egtvv T--D vngkq ARGD_BACSU : 30- 33: dqngk TylD fiqgi ARGD_BACSU : 133- 136: agmaa TgqD kiktg ARGD_BACSU : 362- 364: apltv Tk-D eiaea ARGD_ECOLI : 12- 14: aitra Tf-D evilp ARGD_ECOLI : 235- 237: cgmgr Tg-D lfaym ARGD_ECOLI : 247- 249: mhygv Tp-D iltsa ARGD_RHOCA : 26- 28: gswlw Ta-D gsryl ARGD_SALTY : 12- 14: aitra Tf-D evi ARGD_YEAST : 201- 204: qsyie TkkD eiagl ARGD_YEAST : 322- 325: nyvld TiaD eaflk ARGD_YEAST : 401- 404: fvpal TieD eliee BIOA_BACSH : 147- 148: rflal T--D ayhge BIOA_BACSH : 247- 250: lrelc TqyD vhlia BIOA_BACSH : 299- 302: lsvvm TtnD vyqaf BIOA_BACSH : 300- 302: svvmt Tn-D vyqaf BIOA_BACSH : 431- 432: ppyii T--D demqf BIOA_BACSH : 431- 433: ppyii Td-D emqfm BIOA_BACSH : 441- 444: qfmiq TtkD tivqf BIOA_BACSH : 442- 444: fmiqt Tk-D tivqf BIOA_BREFL : 29- 32: rnrlv TntD gvflt BIOA_BREFL : 31- 32: rlvtn T--D gvflt BIOA_BREFL : 37- 40: dgvfl TleD gstvi BIOA_BREFL : 43- 46: ledgs TviD amssw BIOA_BREFL : 287- 288: aatvc T--D kvaql BIOA_CITFR : 2- 4: m Tt-D d BIOA_CITFR : 2- 5: m TtdD BIOA_CITFR : 3- 4: mt T--D d BIOA_CITFR : 3- 5: mt Td-D BIOA_ECOLI : 2- 4: m Tt-D dlafd BIOA_ECOLI : 2- 5: m TtdD lafdq BIOA_ECOLI : 3- 4: mt T--D dlafd BIOA_ECOLI : 3- 5: mt Td-D lafdq BIOA_HAEIN : 40- 43: dgvmi TlkD grrli BIOA_HAEIN : 86- 88: mfggf Th-D pavel BIOA_MYCLE : 181- 182: mhslw T--D ilarq BIOA_MYCLE : 300- 302: aatlc Tt-D iahai BIOA_MYCLE : 301- 302: atlct T--D iahai BIOA_SALTY : 2- 4: m Tt-D d BIOA_SALTY : 2- 5: m TtdD BIOA_SALTY : 3- 4: mt T--D d BIOA_SALTY : 3- 5: mt Td-D BIOA_SERMA : 4- 7: msv TasD lafdq DGDA_BURCE : 263- 265: qrdgv Tp-D iltls GABT_ECOLI : 404- 407: ilvpl TieD aqirq GABT_HUMAN : 416- 418: fcsfd Tp-D dsirn GABT_HUMAN : 416- 419: fcsfd TpdD sirnk GABT_MYCLE : 201- 202: nkdla T--D gklag GABT_MYCLE : 247- 250: egfla TllD wcrkn GABT_MYCLE : 355- 356: ierli T--D rllrl GABT_MYCLE : 426- 429: llppl TisD ellae GABT_PIG : 444- 446: fcsfd Tp-D esirn GATA_EMENI : 347- 350: hwnle TppD mvtfs GATA_EMENI : 411- 413: entaa Tg-D ylysg GATA_YEAST : 58- 59: lgnyi T--D vdgnt GATA_YEAST : 58- 61: lgnyi TdvD gntyl GATA_YEAST : 64- 67: dvdgn TylD lyaqi GSA_ARATH : 222- 224: vpkaa Ts-D tltap GSA_ARATH : 276- 278: glrql Tk-D ngvll GSA_ARATH : 306- 308: eyfgi Tp-D lttlg GSA_ARATH : 456- 459: tslah TpeD iqlti GSA_BACSU : 70- 72: lilgh Tn-D rvves GSA_BACSU : 260- 262: gyfgv Tp-D ltclg GSA_BACSU : 409- 410: lstah T--D edien GSA_BACSU : 409- 412: lstah TdeD ienti GSA_ECOLI : 105- 107: telvp Tm-D mvrmv GSA_ECOLI : 130- 133: largf TgrD kiikf GSA_ECOLI : 180- 183: ytltc TynD lasvr GSA_ECOLI : 323- 325: pgvhe Tl-D elttr GSA_ECOLI : 360- 361: fgiff T--D aesvt GSA_ECOLI : 415- 417: edinn Ti-D aarrv GSA_HORVU : 271- 274: alrev TkqD gallv GSA_HORVU : 301- 303: eyfgi Tp-D vttlg GSA_HORVU : 451- 454: tslah TtqD iektv GSA_HORVU : 452- 454: slaht Tq-D iektv GSA_MYCLE : 4- 5: mgs T--D qatap GSA_MYCLE : 59- 60: rgcwl T--D adgrr GSA_MYCLE : 59- 62: rgcwl TdaD grryv GSA_MYCLE : 336- 338: davya Tl-D rnadr GSA_MYCLE : 353- 354: lseal T--D agvph GSA_MYCLE : 378- 379: seapv T--D fasac GSA_PROFR : 262- 264: akegw Tp-D lftfg GSA_PROFR : 331- 333: srlda Ta-D rvsam GSA_PROFR : 364- 365: fsvfl T--D apvtd GSA_PROFR : 369- 370: tdapv T--D fasas GSA_PROFR : 408- 411: awfcs TalD dddle GSA_SALTY : 105- 107: tnlvp Tm-D mvrmv GSA_SALTY : 130- 133: largf TgrD kiikf GSA_SALTY : 180- 183: htltc TynD ltsvr GSA_SALTY : 323- 325: pgihe Tl-D elttr GSA_SALTY : 360- 361: fgiff T--D aesvt GSA_SALTY : 415- 417: ddinn Ti-D aarrv GSA_SOYBN : 36- 37: sidpk T--D nkltl GSA_SOYBN : 298- 300: eyfgi Tp-D ittlg GSA_SOYBN : 448- 450: tslah Ts-D dikkt GSA_SOYBN : 448- 451: tslah TsdD ikkti GSA_SYNP6 : 137- 140: vvray TgrD kiikf GSA_SYNP6 : 264- 266: ekfgv Tp-D lttlg GSA_SYNP6 : 414- 417: tslah TeeD idatl GSA_TOBAC : 226- 228: gpkaa Ts-D tltap GSA_TOBAC : 310- 312: eyfgi Tp-D lttlg GSA_TOBAC : 460- 463: tslah TseD iqktv GSA_XANCH : 259- 261: ahygv Tp-D lttfg GSA_XANCH : 362- 363: fglff T--D dvves GSA_XANCH : 362- 364: fglff Td-D vvesy GSA_XANCH : 373- 376: syaqa TacD itsfn OAPT_PSEPU : 81- 83: akqls Tl-D yspgf OAPT_PSEPU : 103- 104: laeki T--D ltpgn OAPT_PSEPU : 116- 117: nhvff T--D sgsec OAPT_PSEPU : 280- 282: dsfgv Tp-D lmcia OAT_BACSU : 369- 371: llcke Th-D tvirf OAT_ECOLI : 45- 48: agsln TlvD tqgqe OAT_ECOLI : 198- 200: neckk Tg-D dvaav OAT_ECOLI : 198- 201: neckk TgdD vaavi OAT_HUMAN : 39- 41: vqgpp Ts-D difer OAT_HUMAN : 39- 42: vqgpp TsdD ifere OAT_HUMAN : 189- 190: aisss T--D ptsyd OAT_HUMAN : 192- 195: sstdp TsyD gfgpf OAT_HUMAN : 385- 387: ivike Tk-D wdawk OAT_HUMAN : 407- 410: llakp ThgD iirfa OAT_MOUSE : 189- 190: aisss T--D ptsyd OAT_MOUSE : 192- 195: sstdp TsyD gfgpf OAT_MOUSE : 385- 387: ivire Tk-D cdawk OAT_MOUSE : 407- 410: llakp ThgD iirla OAT_PLAFA : 159- 160: cvsas T--D kkckn OAT_RAT : 189- 190: avsss T--D ptsyd OAT_RAT : 192- 195: sstdp TsyD gfgpf OAT_RAT : 385- 387: ivire Tk-D cdawk OAT_RAT : 407- 410: llakp ThgD iirla OAT_VIGAC : 116- 117: srafy T--D vlgey OAT_VIGAC : 188- 189: aisas T--D pmsyd OAT_VIGAC : 319- 322: qpglh TamD vmdpr OAT_VIGAC : 398- 401: nlckp ThgD iirfa OAT_VIGAC : 414- 415: ghhrg T--D prmcq OAT_YEAST : 156- 157: aisls T--D yedsk OAT_YEAST : 373- 376: kangk TawD lcllm OAT_YEAST : 391- 393: llakp Th-D hiirl Y949_HAEIN : 48- 49: qgcwv T--D vegne Y949_HAEIN : 90- 92: glplh Tl-D lttpl YHXA_BACSU : 81- 84: ppfcl TeeD lsfiv YKAB_BACFI : 272- 274: qtfgv Tp-D imaia YKAB_BACFI : 323- 325: saala Tl-D vlkee Number of patterns evaluated by Pratt:2 Total running time: 2 seconds