------------------------------------------------------------ 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 7 sequences from file ETF_ALPHA PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 ETF_ALPHA.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ETFA_HUMAN 333 ETFA_PARDE 307 ETFA_RAT 289 FIXB_AZOCA 369 FIXB_BRAJA 45 FIXB_ECOLI 277 FIXB_RHIME 353 Pratt run started at Thu Feb 6 19:27:20 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.1802 8( 7) A-x-A-x(3,5)-A-x(2,3)-E 2: 15.1802 9( 7) A-x(2)-G-x(2,4)-A-x(0,1)-A 3: 15.1802 7( 7) A-x(2)-A-x(1,2)-A-x(3,5)-A 4: 15.1802 7( 7) T-x(3,4)-A-x-A-x(1,3)-A 5: 12.5102 8( 7) A-G-x(2)-A 6: 12.0102 10( 7) V-x-V-x(3,4)-G 7: 12.0102 16( 7) V-x(0,1)-V-x(4)-G 8: 12.0102 10( 7) V-x(2,3)-L-x(2)-G 9: 12.0102 11( 7) A-x-K-x(0,1)-L 10: 12.0102 11( 7) A-x(1,2)-K-x-L 11: 12.0102 8( 7) G-A-x(3,4)-L 12: 12.0102 7( 7) G-x(0,1)-A-x(3)-L 13: 12.0102 7( 7) G-x-G-x(1,2)-K 14: 12.0102 7( 7) G-x(2)-A-x(2,3)-E 15: 12.0102 9( 7) G-x(2,3)-A-A 16: 12.0102 10( 7) G-x(3)-A-x(2,3)-L 17: 12.0102 10( 7) G-x(3,4)-A-x(3)-L 18: 12.0102 11( 7) G-x(0,1)-G-x-G 19: 12.0102 9( 7) G-x(2)-R-x(1,2)-A 20: 12.0102 7( 7) V-x(3)-A-x(4,5)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 20.5056 7( 7) G-[KR]-x-[ALV]-A-x(2,3)-L-x(3)-[FLV] B 2: 19.7338 7( 7) A-x-[AGILP]-A-x(1,2)-A-x(3,5)-A-[AEG] C 3: 19.5150 7( 7) G-[AEQ]-[EGS]-R-x(1,2)-A-[ADTV] D 4: 17.8613 7( 7) G-x(3,4)-A-x(3)-L-[AP]-[AEG] E 5: 17.7776 7( 7) A-x-[ALV]-G-x(2,4)-A-x(0,1)-A F 6: 17.3981 7( 7) T-x(3,4)-A-[DGPS]-A-x(1,3)-A G 7: 15.1802 8( 7) A-x-A-x(3,5)-A-x(2,3)-E H 8: 14.6088 9( 7) V-x(0,1)-V-x(4)-G-x-[GSV] I 9: 14.2670 7( 7) V-x(3)-A-x(4,5)-A-x(3)-[ACDV] J 10: 14.2131 7( 7) G-A-x(3,4)-L-[ALPV] K 11: 14.2126 10( 7) A-x(1,2)-K-x-L-[AGLP] L 12: 13.9212 7( 7) G-x-G-x(1,2)-K-x-[AEGNS] M 13: 13.9135 8( 7) V-x(2,3)-L-x(2)-G-[AEQST] N 14: 12.5102 8( 7) A-G-x(2)-A O 15: 12.0102 10( 7) V-x-V-x(3,4)-G P 16: 12.0102 11( 7) A-x-K-x(0,1)-L Q 17: 12.0102 7( 7) G-x(0,1)-A-x(3)-L R 18: 12.0102 7( 7) G-x(2)-A-x(2,3)-E S 19: 12.0102 9( 7) G-x(2,3)-A-A T 20: 12.0102 10( 7) G-x(3)-A-x(2,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 20.5056 7( 7) G-[KR]-x-[ALV]-A-x(2,3)-L-x(3)-[FLV] Occurences: 7(7) ETFA_HUMAN : 267- 278: qvgqt GKiVApe-LyiaV gisga ETFA_PARDE : 244- 255: qvgqt GKvVApe-LyvaV gisga ETFA_RAT : 267- 278: qvgqt GKiVApe-LyiaV gisga FIXB_AZOCA : 54- 65: elmga GRkLAdk-LkveL aaivl FIXB_BRAJA : 14- 26: mpaga GRgAAkkeLpehF ksykh FIXB_ECOLI : 56- 67: pntrr GKlLAak-LgyrL kaavs FIXB_RHIME : 37- 48: ellge GRkLAdk-LgvhL agvvi B 2: 19.7338 7( 7) A-x-[AGILP]-A-x(1,2)-A-x(3,5)-A-[AEG] Occurences: 7(7) ETFA_HUMAN : 244- 255: dqlha AvGAsrAavd--AG fvpnd ETFA_PARDE : 48- 60: aaeea AkIAgvAkvlv-AE dalyg ETFA_RAT : 244- 255: dqlha AvGAsrAavd--AG fvpnd FIXB_AZOCA : 7- 17: septk ApAAs-Agtr--AA tkkel FIXB_BRAJA : 8- 18: kvskt AmPAg-Agrg--AA kkelp FIXB_ECOLI : 184- 197: eqlck AiGAelAcsrpvAE nekwm FIXB_RHIME : 219- 230: cdsti AnLAy-Advvv-AG glglg C 3: 19.5150 7( 7) G-[AEQ]-[EGS]-R-x(1,2)-A-[ADTV] Occurences: 7(7) ETFA_HUMAN : 246- 252: lhaav GASRa-AV dagfv ETFA_PARDE : 223- 229: lgaav GASRa-AV dsgya ETFA_RAT : 246- 252: lhaav GASRa-AV dagfv FIXB_AZOCA : 52- 59: swelm GAGRklAD klkve FIXB_BRAJA : 12- 18: tampa GAGRg-AA kkelp FIXB_ECOLI : 98- 104: gglai GEERi-AT pyavl FIXB_RHIME : 35- 42: siell GEGRklAD klgvh D 4: 17.8613 7( 7) G-x(3,4)-A-x(3)-L-[AP]-[AEG] Occurences: 7(7) ETFA_HUMAN : 279- 289: lyiav Gisg-AiqhLAG mkdsk ETFA_PARDE : 256- 266: lyvav Gisg-AiqhLAG mkdsk ETFA_RAT : 279- 289: lyiav Gisg-AiqhLAG FIXB_AZOCA : 339- 350: dfahv GivtdAirlLPA lteaf FIXB_BRAJA : 14- 24: mpaga Grga-AkkeLPE hfksy FIXB_ECOLI : 259- 270: qyady GivgdAvkiLPA ltaal FIXB_RHIME : 323- 334: dfahl GvvadAisfLPA ltevf E 5: 17.7776 7( 7) A-x-[ALV]-G-x(2,4)-A-x(0,1)-A Occurences: 7(7) ETFA_HUMAN : 243- 251: adqlh AaVGasr-A-A vdagf ETFA_PARDE : 220- 228: adklg AaVGasr-A-A vdsgy ETFA_RAT : 243- 251: adqlh AaVGasr-A-A vdagf FIXB_AZOCA : 10- 17: tkapa AsAGtr--A-A tkkel FIXB_BRAJA : 11- 18: ktamp AgAGrg--A-A kkelp FIXB_ECOLI : 61- 70: gklla AkLGyrlkA-A vsnda FIXB_RHIME : 320- 328: pifdf AhLGvv--AdA isflp F 6: 17.3981 7( 7) T-x(3,4)-A-[DGPS]-A-x(1,3)-A Occurences: 7(7) ETFA_HUMAN : 106- 114: kqfny Thic-AGAs--A fgknl ETFA_PARDE : 32- 40: algdv Tvlc-AGAs--A kaaae ETFA_PARDE : 32- 42: algdv Tvlc-AGAsakA aaeea ETFA_RAT : 106- 114: kqfsy Thiv-AGAs--A fgknl FIXB_AZOCA : 5- 16: msep TkapaASAgtrA atkke FIXB_BRAJA : 7- 17: skvsk Tamp-AGAgrgA akkel FIXB_ECOLI : 131- 140: hceth TvewqAPAv--A itrta FIXB_RHIME : 61- 70: pggqg TanaiADAf--A ygadl G 7: 15.1802 8( 7) A-x-A-x(3,5)-A-x(2,3)-E Occurences: 8(7) ETFA_HUMAN : 175- 186: gtsfd AaAtsggsAss-E kasst ETFA_PARDE : 36- 45: vtvlc AgAsak--Aaa-E eaaki ETFA_PARDE : 36- 46: vtvlc AgAsaka-Aae-E aakia ETFA_PARDE : 36- 46: vtvlc AgAsak--AaaeE aakia ETFA_RAT : 175- 186: gtsfe AaAasggsAss-E kapss ETFA_RAT : 176- 186: tsfea AaAsggs-Ass-E kapss FIXB_AZOCA : 10- 21: tkapa AsAgtra-AtkkE lpehf FIXB_BRAJA : 11- 21: ktamp AgAgrga-Akk-E lpehf FIXB_BRAJA : 11- 21: ktamp AgAgrg--AakkE lpehf FIXB_ECOLI : 176- 188: skeni AlAeqlckAigaE lacsr FIXB_RHIME : 326- 337: hlgvv AdAisflpAlt-E vftkr H 8: 14.6088 9( 7) V-x(0,1)-V-x(4)-G-x-[GSV] Occurences: 9(7) ETFA_HUMAN : 163- 172: kcdek VkVfsvrGtS fdaaa ETFA_PARDE : 195- 203: tsarr V-VsggrGlG skesf ETFA_RAT : 163- 172: kcdek VkVfsvrGtS feaaa FIXB_AZOCA : 242- 251: layad VvVagglGlG spenf FIXB_AZOCA : 243- 251: ayadv V-VagglGlG spenf FIXB_BRAJA : 34- 43: ykhvw VfVelerGqV hp FIXB_ECOLI : 162- 170: dkarl V-VsvgrGiG skeni FIXB_RHIME : 226- 235: layad VvVagglGlG avqnl FIXB_RHIME : 227- 235: ayadv V-VagglGlG avqnl I 9: 14.2670 7( 7) V-x(3)-A-x(4,5)-A-x(3)-[ACDV] Occurences: 7(7) ETFA_HUMAN : 70- 83: qdlck VagiAkvlv-AqhdV ykgll ETFA_PARDE : 8- 21: lllge VtngAlnrd-AtakA vaavk ETFA_RAT : 70- 83: qdlck VagvAkvlv-AqhdA ykgll FIXB_AZOCA : 259- 272: enfql VrhvAgvlg-AeygC srplv FIXB_BRAJA : 4- 17: msk VsktAmpag-AgrgA akkel FIXB_ECOLI : 233- 247: qiqhm VganAsqtifAinkD knapi FIXB_RHIME : 324- 338: fahlg VvadAisflpAlteV ftkrl J 10: 14.2131 7( 7) G-A-x(3,4)-L-[ALPV] Occurences: 7(7) ETFA_HUMAN : 282- 288: avgis GAiqh-LA gmkds ETFA_PARDE : 259- 265: avgis GAiqh-LA gmkds ETFA_RAT : 282- 288: avgis GAiqh-LA g FIXB_AZOCA : 52- 58: swelm GAgrk-LA dklkv FIXB_BRAJA : 16- 23: agagr GAakkeLP ehfks FIXB_ECOLI : 43- 50: tirqh GAdglvLL pntrr FIXB_RHIME : 72- 79: dafay GAdlsyLV espll K 11: 14.2126 10( 7) A-x(1,2)-K-x-L-[AGLP] Occurences: 10(7) ETFA_HUMAN : 114- 120: cagas AfgKnLL prvaa ETFA_PARDE : 23- 29: takav AavKaLG dvtvl ETFA_PARDE : 24- 29: akava Av-KaLG dvtvl ETFA_RAT : 83- 88: vaqhd Ay-KgLL peelt ETFA_RAT : 114- 120: vagas AfgKnLL prvaa FIXB_AZOCA : 17- 23: agtra AtkKeLP ehfka FIXB_BRAJA : 17- 23: gagrg AakKeLP ehfks FIXB_BRAJA : 18- 23: agrga Ak-KeLP ehfks FIXB_ECOLI : 264- 269: givgd Av-KiLP altaa FIXB_RHIME : 204- 209: leeei At-KvLA ffsdc L 12: 13.9212 7( 7) G-x-G-x(1,2)-K-x-[AEGNS] Occurences: 7(7) ETFA_HUMAN : 222- 228: vvvsg GrGl-KsG enfkl ETFA_PARDE : 201- 207: vsggr GlGs-KeS faiie ETFA_RAT : 222- 228: vvvsg GrGl-KsG enfkl FIXB_AZOCA : 52- 58: swelm GaGr-KlA dklkv FIXB_BRAJA : 14- 21: mpaga GrGaaKkE lpehf FIXB_ECOLI : 168- 174: vsvgr GiGs-KeN ialae FIXB_RHIME : 35- 41: siell GeGr-KlA dklgv M 13: 13.9135 8( 7) V-x(2,3)-L-x(2)-G-[AEQST] Occurences: 8(7) ETFA_HUMAN : 51- 58: rlgge Vsc-LvaGT kcdkv ETFA_PARDE : 31- 38: kalgd Vtv-LcaGA sakaa ETFA_RAT : 51- 58: rlgge Vsc-LvaGT kcdkv FIXB_AZOCA : 244- 252: yadvv VaggLglGS penfq FIXB_BRAJA : 34- 42: ykhvw VfveLerGQ vhp FIXB_ECOLI : 91- 99: tvkhm VyggLaiGE eriat FIXB_RHIME : 17- 25: yrnvw VfieLehGQ vhpvs FIXB_RHIME : 228- 236: yadvv VaggLglGA vqnlq N 14: 12.5102 8( 7) A-G-x(2)-A Occurences: 8(7) ETFA_HUMAN : 110- 114: ythic AGasA fgknl ETFA_PARDE : 36- 40: vtvlc AGasA kaaae ETFA_RAT : 110- 114: ythiv AGasA fgknl FIXB_AZOCA : 12- 16: apaas AGtrA atkke FIXB_AZOCA : 136- 140: lgrdl AGsvA ttllt FIXB_BRAJA : 13- 17: ampag AGrgA akkel FIXB_ECOLI : 32- 36: miedy AGvmA dtirq FIXB_RHIME : 120- 124: lgrdl AGsvA ttlkt O 15: 12.0102 10( 7) V-x-V-x(3,4)-G Occurences: 10(7) ETFA_HUMAN : 163- 170: kcdek VkVfsvrG tsfda ETFA_HUMAN : 217- 224: ltgak VvVsggrG lksge ETFA_PARDE : 31- 37: kalgd VtVlca-G asaka ETFA_PARDE : 253- 259: apely VaVgis-G aiqhl ETFA_RAT : 163- 170: kcdek VkVfsvrG tsfea ETFA_RAT : 217- 224: ltgak VvVsggrG lksge FIXB_AZOCA : 242- 249: layad VvVagglG lgspe FIXB_BRAJA : 34- 41: ykhvw VfVelerG qvhp FIXB_ECOLI : 163- 170: karlv VsVgrgiG skeni FIXB_RHIME : 226- 233: layad VvVagglG lgavq P 16: 12.0102 11( 7) A-x-K-x(0,1)-L Occurences: 11(7) ETFA_HUMAN : 124- 127: llprv AaK-L evapi ETFA_PARDE : 24- 28: akava AvKaL gdvtv ETFA_PARDE : 215- 218: iieel AdK-L gaavg ETFA_RAT : 83- 87: vaqhd AyKgL lpeel ETFA_RAT : 124- 127: llprv AaK-L nvapv FIXB_AZOCA : 58- 61: agrkl AdK-L kvela FIXB_BRAJA : 18- 22: agrga AkKeL pehfk FIXB_ECOLI : 60- 63: rgkll AaK-L gyrlk FIXB_ECOLI : 264- 268: givgd AvKiL palta FIXB_RHIME : 41- 44: egrkl AdK-L gvhla FIXB_RHIME : 204- 208: leeei AtKvL affsd Q 17: 12.0102 7( 7) G-x(0,1)-A-x(3)-L Occurences: 7(7) ETFA_HUMAN : 282- 287: avgis G-AiqhL agmkd ETFA_PARDE : 259- 264: avgis G-AiqhL agmkd ETFA_RAT : 282- 287: avgis G-AiqhL ag FIXB_AZOCA : 52- 57: swelm G-AgrkL adklk FIXB_BRAJA : 16- 22: agagr GaAkkeL pehfk FIXB_ECOLI : 262- 268: dygiv GdAvkiL palta FIXB_RHIME : 235- 240: gglgl G-AvqnL qllkd R 18: 12.0102 7( 7) G-x(2)-A-x(2,3)-E Occurences: 7(7) ETFA_HUMAN : 180- 186: aaats GgsAss-E kasst ETFA_PARDE : 157- 164: daage GgtApvtE taaaa ETFA_RAT : 180- 186: aaaas GgsAss-E kapss FIXB_AZOCA : 146- 153: ttllt GltAdctE ldvda FIXB_BRAJA : 14- 21: mpaga GrgAakkE lpehf FIXB_ECOLI : 93- 99: khmvy GglAig-E eriat FIXB_ECOLI : 93- 100: khmvy GglAigeE riatp FIXB_RHIME : 130- 137: ttlkt GltAdctE lnvds S 19: 12.0102 9( 7) G-x(2,3)-A-A Occurences: 9(7) ETFA_HUMAN : 246- 251: lhaav GasrAA vdagf ETFA_PARDE : 223- 228: lgaav GasrAA vdsgy ETFA_RAT : 246- 251: lhaav GasrAA vdagf FIXB_AZOCA : 13- 17: paasa Gtr-AA tkkel FIXB_AZOCA : 160- 164: dvdad Gsl-AA trptf FIXB_BRAJA : 14- 18: mpaga Grg-AA kkelp FIXB_ECOLI : 56- 61: pntrr GkllAA klgyr FIXB_ECOLI : 114- 119: ltiss GtfdAA qpdax FIXB_RHIME : 144- 148: nvdsd Gsl-AA trptf T 20: 12.0102 10( 7) G-x(3)-A-x(2,3)-L Occurences: 10(7) ETFA_HUMAN : 267- 274: qvgqt GkivApe-L yiavg ETFA_HUMAN : 279- 287: lyiav GisgAiqhL agmkd ETFA_PARDE : 244- 251: qvgqt GkvvApe-L yvavg ETFA_PARDE : 256- 264: lyvav GisgAiqhL agmkd ETFA_RAT : 267- 274: qvgqt GkivApe-L yiavg ETFA_RAT : 279- 287: lyiav GisgAiqhL ag FIXB_AZOCA : 54- 61: elmga GrklAdk-L kvela FIXB_BRAJA : 14- 22: mpaga GrgaAkkeL pehfk FIXB_ECOLI : 56- 63: pntrr GkllAak-L gyrlk FIXB_RHIME : 37- 44: ellge GrklAdk-L gvhla Number of patterns evaluated by Pratt:782 Total running time: 0 seconds