------------------------------------------------------------ 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 6 sequences from file FOLYLPOLYGLU_SYNT_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 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 FOLYLPOLYGLU_SYNT_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: FOLC_BACSU 430 FOLC_ECOLI 422 FOLC_HAEIN 437 FOLC_HUMAN 545 FOLC_LACCA 428 FOLC_YEAST 430 Pratt run started at Thu Feb 6 19:29:52 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.6802 6( 6) G-T-x-G-K 2: 16.1802 6( 6) V-x(2,3)-T-x-G-K 3: 15.6802 6( 6) N-A-x(0,1)-A-x(2,3)-L 4: 15.6802 6( 6) E-x-G-x(1,2)-G-x(2,3)-D 5: 15.1802 7( 6) L-x(3)-G-x(1,3)-G-x(3,4)-S 6: 15.1802 8( 6) A-x(4,5)-A-A-x(2,4)-L 7: 15.1802 7( 6) N-x(0,1)-A-x(5)-A-x(2,4)-L 8: 15.1802 7( 6) L-x(2,3)-G-L-x(0,2)-V 9: 15.1802 11( 6) A-x(1,3)-L-x(0,1)-A-x(2)-L 10: 15.1802 6( 6) L-x(1,2)-L-x(1,3)-Q-x(4)-V 11: 15.1802 6( 6) V-x(2)-T-x(1,2)-G-x(1,3)-G 12: 14.6802 8( 6) A-x-A-x(1,3)-L-x(0,2)-A 13: 14.6802 7( 6) A-x(2)-A-x(0,2)-L-x(0,2)-A 14: 14.6802 6( 6) A-x(1,3)-V-x(3,5)-E-x(2)-L 15: 14.6802 6( 6) A-L-x(1,3)-L-x(2,4)-A 16: 14.6802 6( 6) G-x(3)-G-x(3,5)-S-x(0,2)-P 17: 14.6802 12( 6) A-x(0,2)-A-x(2)-L-x(0,2)-A 18: 12.5102 7( 6) V-x(3)-G-S 19: 12.5102 6( 6) A-x(2)-A-x(2)-L 20: 12.5102 6( 6) G-x(2)-G-x(2)-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 40.6718 6( 6) L-x(3)-G-x(1,3)-G-x(3,4)-S-x-[FHY]-[IL]-x(4)-[EQ]-[HR]-[IPV]-x(2)-[DNQ]-x(3)-[ILV]-x(2)-[AEGS]-x(2)-[TV] B 2: 31.8383 6( 6) G-[IL]-[AG]-G-x(2)-D-x-[GT]-[NS]-[IV]-[IV] C 3: 31.7235 6( 6) E-[TV]-G-x(1,2)-G-x(2,3)-D-x-[GT]-[NS]-[IV]-[IV] D 4: 27.9335 6( 6) G-T-x-G-K-[EG]-[ST]-[ATV]-[ACSV] E 5: 25.6855 6( 6) G-x(2)-[TV]-G-x(3,5)-S-x(0,2)-P-x(2)-[ILMV]-x(4)-[KR]-x(3)-[DNQT] F 6: 23.6245 6( 6) V-x(2,3)-T-x-G-K-x-[STV]-[AST]-[ACPV] G 7: 20.9929 6( 6) V-x-[GV]-T-x(1,2)-G-x(1,3)-G-x-[APT] H 8: 18.3544 6( 6) N-A-x(0,1)-A-x(2,3)-L-[AEQ] I 9: 17.9100 6( 6) V-[AIL]-x(2)-G-S-x-[HWY] J 10: 17.8502 6( 6) L-x(1,2)-L-x(1,3)-Q-x(4)-V-x(3)-[EGN] K 11: 16.9149 8( 6) A-x(0,2)-A-x-[ADNV]-L-x(0,2)-A L 12: 16.6123 6( 6) A-x(1,3)-V-x(3,5)-E-x(2)-L-[ACGPT] M 13: 15.1802 8( 6) A-x(4,5)-A-A-x(2,4)-L N 14: 15.1802 7( 6) N-x(0,1)-A-x(5)-A-x(2,4)-L O 15: 15.1802 7( 6) L-x(2,3)-G-L-x(0,2)-V P 16: 15.1802 11( 6) A-x(1,3)-L-x(0,1)-A-x(2)-L Q 17: 14.6802 8( 6) A-x-A-x(1,3)-L-x(0,2)-A R 18: 14.6802 7( 6) A-x(2)-A-x(0,2)-L-x(0,2)-A S 19: 14.6802 6( 6) A-L-x(1,3)-L-x(2,4)-A T 20: 14.6802 6( 6) G-x(3)-G-x(3,5)-S-x(0,2)-P Best patterns with alignements: fitness hits(seqs) Pattern A 1: 40.6718 6( 6) L-x(3)-G-x(1,3)-G-x(3,4)-S-x-[FHY]-[IL]-x(4)-[EQ]-[HR]-[IPV]-x(2)-[DNQ]-x(3)-[ILV]-x(2)-[AEGS]-x(2)-[TV] Occurences: 6(6) FOLC_BACSU : 63- 98: firsm LqeaGytvGtft-SpYIitfnERIsvNgipIsdEewT alvnq FOLC_ECOLI : 71- 106: tlesi LmaaGykvGvys-SpHLvrytERVrvQgqeLpeSahT asfae FOLC_HAEIN : 70- 105: lleti LlnhGlrvGvys-SpHLlrynERVriQnqdLpdEahT asfaf FOLC_HUMAN : 76- 111: fteci LrsyGlktGffs-SpHLvqvrERIriNgqpIspElfT kyfwr FOLC_LACCA : 61- 96: aiahv LeasGltvGlyt-SpFImrfnERImiDhepIpdAalV navaf FOLC_YEAST : 30- 65: dslsi LhiaGtn-GketvSkFLtsilQHPgqQrqrVliGryT tssll B 2: 31.8383 6( 6) G-[IL]-[AG]-G-x(2)-D-x-[GT]-[NS]-[IV]-[IV] Occurences: 6(6) FOLC_BACSU : 147- 158: vifet GLGGrfDsTNVV epllt FOLC_ECOLI : 148- 159: vilev GLGGrlDaTNIV dadva FOLC_HAEIN : 146- 157: vilev GLGGrlDaTNIV dshla FOLC_HUMAN : 160- 171: avvev GIGGayDcTNII rkpvv FOLC_LACCA : 145- 156: aviev GIGGdtDsTNVI tpvvs FOLC_YEAST : 134- 145: ciiet GLAGkqDpGSII agqsr C 3: 31.7235 6( 6) E-[TV]-G-x(1,2)-G-x(2,3)-D-x-[GT]-[NS]-[IV]-[IV] Occurences: 6(6) FOLC_BACSU : 145- 158: dfvif ETGlgGrf-DsTNVV epllt FOLC_BACSU : 145- 158: dfvif ETGl-GgrfDsTNVV epllt FOLC_ECOLI : 146- 159: dvvil EVGlgGrl-DaTNIV dadva FOLC_ECOLI : 146- 159: dvvil EVGl-GgrlDaTNIV dadva FOLC_HAEIN : 144- 157: dvvil EVGlgGrl-DaTNIV dshla FOLC_HAEIN : 144- 157: dvvil EVGl-GgrlDaTNIV dshla FOLC_HUMAN : 158- 171: dlavv EVGigGay-DcTNII rkpvv FOLC_HUMAN : 158- 171: dlavv EVGi-GgayDcTNII rkpvv FOLC_LACCA : 143- 156: dvavi EVGigGdt-DsTNVI tpvvs FOLC_LACCA : 143- 156: dvavi EVGi-GgdtDsTNVI tpvvs FOLC_YEAST : 132- 145: qwcii ETGlaGkq-DpGSII agqsr D 4: 27.9335 6( 6) G-T-x-G-K-[EG]-[ST]-[ATV]-[ACSV] Occurences: 6(6) FOLC_BACSU : 48- 56: afhva GTnGKGSTV afirs FOLC_ECOLI : 56- 64: vftva GTnGKGTTC rtles FOLC_HAEIN : 55- 63: vitvg GTnGKGTTC rllet FOLC_HUMAN : 61- 69: iihvt GTkGKGSTC aftec FOLC_LACCA : 46- 54: yihvt GTnGKGSAA naiah FOLC_YEAST : 34- 42: ilhia GTnGKETVS kflts E 5: 25.6855 6( 6) G-x(2)-[TV]-G-x(3,5)-S-x(0,2)-P-x(2)-[ILMV]-x(4)-[KR]-x(3)-[DNQT] Occurences: 6(6) FOLC_BACSU : 67- 88: mlqea GytVGtft--S--PyiItfneRisvN gipis FOLC_ECOLI : 75- 96: ilmaa GykVGvys--S--PhlVryteRvrvQ gqelp FOLC_HAEIN : 74- 95: illnh GlrVGvys--S--PhlLryneRvriQ nqdlp FOLC_HUMAN : 80- 101: ilrsy GlkTGffs--S--PhlVqvreRiriN gqpis FOLC_LACCA : 65- 86: vleas GltVGlyt--S--PfiMrfneRimiD hepip FOLC_YEAST : 356- 381: ivtrf GsvVGmpwiqSlePvnLlafiKnryT rnvnm F 6: 23.6245 6( 6) V-x(2,3)-T-x-G-K-x-[STV]-[AST]-[ACPV] Occurences: 6(6) FOLC_BACSU : 46- 56: irafh Vag-TnGKgSTV afirs FOLC_ECOLI : 54- 64: pfvft Vag-TnGKgTTC rtles FOLC_HAEIN : 53- 63: pyvit Vgg-TnGKgTTC rllet FOLC_HUMAN : 59- 69: lniih Vtg-TkGKgSTC aftec FOLC_LACCA : 44- 54: gryih Vtg-TnGKgSAA naiah FOLC_YEAST : 327- 338: tpltf ViaiTtGKkVSP lldpl G 7: 20.9929 6( 6) V-x-[GV]-T-x(1,2)-G-x(1,3)-G-x-[APT] Occurences: 6(6) FOLC_BACSU : 46- 55: irafh VaGTn-Gk--GsT vafir FOLC_ECOLI : 54- 63: pfvft VaGTn-Gk--GtT crtle FOLC_HAEIN : 53- 62: pyvit VgGTn-Gk--GtT crlle FOLC_HUMAN : 59- 68: lniih VtGTk-Gk--GsT cafte FOLC_LACCA : 44- 53: gryih VtGTn-Gk--GsA anaia FOLC_YEAST : 350- 362: rpqdy ViVTrfGsvvGmP wiqsl H 8: 18.3544 6( 6) N-A-x(0,1)-A-x(2,3)-L-[AEQ] Occurences: 6(6) FOLC_BACSU : 266- 273: thqrq NA-AlsiLA aewln FOLC_ECOLI : 257- 263: lvpqp NA-Ata-LA alras FOLC_HAEIN : 255- 261: qipla NA-Atv-LA avqyl FOLC_HUMAN : 263- 269: ehqrs NA-Ala-LQ lahcw FOLC_LACCA : 55- 62: kgsaa NAiAhv-LE asglt FOLC_YEAST : 304- 312: ldnan NAkAarnLA chlrt I 9: 17.9100 6( 6) V-[AIL]-x(2)-G-S-x-[HWY] Occurences: 6(6) FOLC_BACSU : 413- 420: gsnei VLitGSlY fisdi FOLC_ECOLI : 398- 405: kaedt VLvcGSfH tvahv FOLC_HAEIN : 420- 427: vkndv VLvfGSfH tvaef FOLC_HUMAN : 523- 530: aaaih VLvtGSlH lvggv FOLC_LACCA : 212- 219: vvaak VAttGSqW lrfdr FOLC_YEAST : 408- 415: ktivp VIvcGSlY ickel J 10: 17.8502 6( 6) L-x(1,2)-L-x(1,3)-Q-x(4)-V-x(3)-[EGN] Occurences: 6(6) FOLC_BACSU : 303- 316: awpgr Le-Lv--QehppVyldG ahnee FOLC_ECOLI : 132- 146: gtlsa Lw-Lfk-QaqldVvilE vglgg FOLC_HAEIN : 130- 144: stlsa Lh-Lfk-QakldVvilE vglgg FOLC_HUMAN : 383- 399: dpaal LklLqpcQfdyaVfcpN ltevs FOLC_LACCA : 106- 122: fvraa LerLqqqQadfnVtefE fital FOLC_YEAST : 340- 356: kvspl LdpLirpQdyviVtrfG svvgm K 11: 16.9149 8( 6) A-x(0,2)-A-x-[ADNV]-L-x(0,2)-A Occurences: 8(6) FOLC_BACSU : 375- 384: fdfpr AslAkDLydA seisn FOLC_ECOLI : 258- 263: vpqpn A--AtAL--A alras FOLC_ECOLI : 258- 264: vpqpn A--AtALa-A lrasg FOLC_HAEIN : 254- 261: cqipl AnaAtVL--A avqyl FOLC_HAEIN : 254- 262: cqipl AnaAtVLa-A vqylp FOLC_HAEIN : 256- 261: iplan A--AtVL--A avqyl FOLC_HAEIN : 256- 262: iplan A--AtVLa-A vqylp FOLC_HUMAN : 264- 271: hqrsn A--AlALqlA hcwlq FOLC_LACCA : 56- 63: gsaan Ai-AhVLe-A sgltv FOLC_YEAST : 305- 312: dnann AkaArNL--A chlrt FOLC_YEAST : 307- 312: annak A--ArNL--A chlrt L 12: 16.6123 6( 6) A-x(1,3)-V-x(3,5)-E-x(2)-L-[ACGPT] Occurences: 6(6) FOLC_BACSU : 227- 237: qslhd Ac--Vifn--EeaLP ageqf FOLC_ECOLI : 138- 150: wlfkq AqldVvil--EvgLG grlda FOLC_HAEIN : 136- 148: hlfkq AkldVvil--EvgLG grlda FOLC_HUMAN : 211- 222: kqgvp Aft-Vlqp--EgpLA vlrdr FOLC_LACCA : 272- 284: iaiqt Ak--VyakqtEwpLT pqnir FOLC_YEAST : 154- 167: srvcc AitnVgisd-EafLC kflsq M 13: 15.1802 8( 6) A-x(4,5)-A-A-x(2,4)-L Occurences: 8(6) FOLC_BACSU : 267- 277: hqrqn AalsilAAew--L nkeni FOLC_BACSU : 268- 277: qrqna Alsil-AAew--L nkeni FOLC_ECOLI : 304- 313: vifdv Ahnph-AAey--L tgrmk FOLC_HAEIN : 256- 266: iplan Aatvl-AAvqy-L pfdis FOLC_HUMAN : 512- 524: vahsg AsilreAAaihvL vtgsl FOLC_LACCA : 98- 109: aalvn AvafvrAAler-L qqqqa FOLC_LACCA : 344- 355: iagil Adkdy-AAmadrL taafs FOLC_YEAST : 302- 311: llldn Annak-AArn--L achlr N 14: 15.1802 7( 6) N-x(0,1)-A-x(5)-A-x(2,4)-L Occurences: 7(6) FOLC_BACSU : 266- 277: thqrq NaAlsilaAew--L nkeni FOLC_BACSU : 266- 277: thqrq N-AalsilAaew-L nkeni FOLC_BACSU : 281- 294: wlnke NiAhisdeAlrsgL vkaaw FOLC_ECOLI : 275- 286: levse N-AirdgiAsai-L pgrfq FOLC_HAEIN : 255- 266: qipla N-AatvlaAvqy-L pfdis FOLC_HUMAN : 263- 275: ehqrs NaAlalqlAhcw-L qrqdr FOLC_LACCA : 97- 109: daalv N-AvafvrAalerL qqqqa FOLC_YEAST : 301- 311: allld N-AnnakaArn--L achlr O 15: 15.1802 7( 6) L-x(2,3)-G-L-x(0,2)-V Occurences: 7(6) FOLC_BACSU : 290- 295: isdea Lrs-GL--V kaawp FOLC_ECOLI : 265- 272: talaa LrasGLe-V senai FOLC_HAEIN : 70- 77: lleti LlnhGLr-V gvyss FOLC_HAEIN : 71- 77: letil Lnh-GLr-V gvyss FOLC_HUMAN : 41- 48: amely LarsGLq-V edldr FOLC_LACCA : 61- 68: aiahv LeasGLt-V glyts FOLC_YEAST : 267- 274: iskdq Lsq-GLisV dwprs P 16: 15.1802 11( 6) A-x(1,3)-L-x(0,1)-A-x(2)-L Occurences: 11(6) FOLC_BACSU : 268- 277: qrqna AlsiLaAewL nkeni FOLC_BACSU : 375- 381: fdfpr As--L-AkdL ydase FOLC_ECOLI : 9- 17: krtpq AaspL-AswL sylen FOLC_ECOLI : 10- 17: rtpqa Asp-L-AswL sylen FOLC_ECOLI : 261- 270: pnaat AlaaLrAsgL evsen FOLC_ECOLI : 263- 270: aatal Aa--LrAsgL evsen FOLC_HAEIN : 8- 16: nmqlk AtspL-AewL sylek FOLC_HUMAN : 264- 270: hqrsn Aa--L-AlqL ahcwl FOLC_LACCA : 58- 66: aanai Ahv-LeAsgL tvgly FOLC_YEAST : 307- 315: annak AarnL-AchL rttyg FOLC_YEAST : 308- 315: nnaka Arn-L-AchL rttyg Q 17: 14.6802 8( 6) A-x-A-x(1,3)-L-x(0,2)-A Occurences: 8(6) FOLC_BACSU : 127- 134: feimt AcAf--LyfA efhkv FOLC_ECOLI : 259- 267: pqpna AtAlaaLr-A sglev FOLC_ECOLI : 261- 267: pnaat AlAa--Lr-A sglev FOLC_HAEIN : 254- 261: cqipl AnAatvL--A avqyl FOLC_HAEIN : 254- 262: cqipl AnAatvLa-A vqylp FOLC_HUMAN : 265- 271: qrsna AlAlq-L--A hcwlq FOLC_LACCA : 56- 63: gsaan AiAhv-Le-A sgltv FOLC_LACCA : 350- 357: dkdya AmAdr-Lt-A afstv FOLC_LACCA : 350- 358: dkdya AmAdr-LtaA fstvy FOLC_YEAST : 305- 312: dnann AkAarnL--A chlrt R 18: 14.6802 7( 6) A-x(2)-A-x(0,2)-L-x(0,2)-A Occurences: 7(6) FOLC_BACSU : 375- 384: fdfpr AslAkdLydA seisn FOLC_ECOLI : 258- 263: vpqpn AatA--L--A alras FOLC_ECOLI : 258- 264: vpqpn AatA--La-A lrasg FOLC_ECOLI : 261- 267: pnaat AlaA--Lr-A sglev FOLC_HAEIN : 254- 261: cqipl AnaAtvL--A avqyl FOLC_HAEIN : 254- 262: cqipl AnaAtvLa-A vqylp FOLC_HUMAN : 264- 271: hqrsn AalAlqL--A hcwlq FOLC_HUMAN : 264- 271: hqrsn AalA--LqlA hcwlq FOLC_LACCA : 349- 357: adkdy AamAdrLt-A afstv FOLC_LACCA : 349- 358: adkdy AamAdrLtaA fstvy FOLC_YEAST : 305- 312: dnann AkaArnL--A chlrt S 19: 14.6802 6( 6) A-L-x(1,3)-L-x(2,4)-A Occurences: 6(6) FOLC_BACSU : 289- 297: hisde ALrsgLvk--A awpgr FOLC_BACSU : 289- 298: hisde ALrsgLvka-A wpgrl FOLC_ECOLI : 131- 138: ygtls ALw--Lfkq-A qldvv FOLC_HAEIN : 129- 136: fstls ALh--Lfkq-A kldvv FOLC_HUMAN : 265- 271: qrsna ALa--Lql--A hcwlq FOLC_LACCA : 105- 114: afvra ALer-LqqqqA dfnvt FOLC_YEAST : 296- 302: sgkki ALl--Ldn--A nnaka T 20: 14.6802 6( 6) G-x(3)-G-x(3,5)-S-x(0,2)-P Occurences: 6(6) FOLC_BACSU : 67- 76: mlqea GytvGtft--S--P yiitf FOLC_ECOLI : 75- 84: ilmaa GykvGvys--S--P hlvry FOLC_HAEIN : 74- 83: illnh GlrvGvys--S--P hllry FOLC_HUMAN : 80- 89: ilrsy GlktGffs--S--P hlvqv FOLC_LACCA : 65- 74: vleas GltvGlyt--S--P fimrf FOLC_YEAST : 356- 369: ivtrf GsvvGmpwiqSleP vnlla Number of patterns evaluated by Pratt:10813 Total running time: 6 seconds