------------------------------------------------------------ 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 8 sequences from file COMPLEX1_75K_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 8 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 COMPLEX1_75K_1.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HOXU_ALCEU 233 HOXU_NOCOP 33 NQO3_PARDE 672 NUAM_BOVIN 727 NUAM_HUMAN 727 NUAM_NEUCR 744 NUOG_ECOLI 819 NUOG_SALTY 611 Pratt run started at Thu Feb 6 19:08:48 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 18.8503 8( 8) E-x(3)-T-x(2,4)-D-x(0,2)-V-x(4)-G 2: 15.6802 8( 8) I-x(3)-T-x(3,5)-E-x(4)-L 3: 15.1802 8( 8) L-x(1,3)-D-x-A-x(0,1)-A 4: 15.1802 10( 8) L-x(1,3)-A-x(3,4)-G-x(2)-I 5: 15.1802 9( 8) T-x(3,5)-E-x(2)-R-x(1,2)-L 6: 15.1802 8( 8) I-x(3)-T-x(3,5)-E-x(2,3)-R 7: 15.1802 8( 8) I-x(2,3)-T-x(3,5)-E-x(4)-L 8: 14.6802 8( 8) V-x(4)-G-x(0,2)-I-x(1,3)-T 9: 14.6802 8( 8) T-x(2,4)-D-x(0,2)-V-x(4)-G 10: 14.6802 10( 8) S-x(2,4)-V-x(3,5)-A-x-A 11: 12.5102 10( 8) D-x-A-A 12: 12.5102 8( 8) L-x-D-x(5)-G 13: 12.5102 8( 8) T-x(3)-E-x(4)-L 14: 12.5102 10( 8) G-x(2)-V-x(5)-R 15: 12.0102 8( 8) E-x(0,1)-G-x(5)-L 16: 12.0102 8( 8) A-E-x(0,1)-A 17: 12.0102 16( 8) V-x(2)-E-x(0,1)-G 18: 12.0102 12( 8) V-x(1,2)-E-x-G 19: 12.0102 15( 8) D-V-x(3,4)-G 20: 12.0102 16( 8) R-x(1,2)-L-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 26.7490 8( 8) E-x(3)-T-x(2,4)-D-x(0,2)-V-x-[ADE]-[AEG]-x-G-[NSV] B 2: 22.5789 8( 8) T-x(2,4)-D-x(0,2)-V-x-[ADE]-[AEG]-x-G-[NSV] C 3: 20.9501 8( 8) I-x(3)-T-x(3,5)-E-x(4)-L-[GPV]-x(3)-[ADE] D 4: 20.5928 8( 8) I-x-[AGIV]-x-T-x(3,5)-E-x(2,3)-R-x-[GL] E 5: 20.4501 8( 8) I-x(2,3)-T-x(3,5)-E-x(4)-L-[GPV]-x(3)-[ADE] F 6: 18.4013 10( 8) L-x(1,3)-A-x(3,4)-G-x(2)-I-[AP] G 7: 17.8902 10( 8) V-x(2)-E-x(0,1)-G-x(3)-[LP]-[AQT] H 8: 17.8007 8( 8) T-x(3,5)-E-x(2)-R-x(1,2)-L-[APV] I 9: 17.3102 8( 8) V-x(2)-[AEG]-x-G-x(0,2)-I-x(1,3)-T J 10: 16.9302 8( 8) T-x(3)-E-x(4)-L-x-[DERS]-x(3)-[DEGT] K 11: 16.8181 11( 8) D-V-x(3,4)-G-[ASTV]-x-[IPV] L 12: 15.1802 8( 8) L-x(1,3)-D-x-A-x(0,1)-A M 13: 15.1145 8( 8) L-x-D-x-[AST]-x(3)-G N 14: 14.7102 9( 8) G-x(2)-V-x(4)-[APST]-R O 15: 14.6802 8( 8) E-x(3)-T-x(2,4)-D-x(0,2)-V P 16: 14.6802 10( 8) S-x(2,4)-V-x(3,5)-A-x-A Q 17: 14.6607 14( 8) R-x(1,2)-L-V-[DEG] R 18: 14.2646 8( 8) A-E-x(0,1)-A-x(3)-[AILP] S 19: 14.2646 10( 8) V-x(1,2)-E-x-G-x(3)-[AILP] T 20: 12.5102 10( 8) D-x-A-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 26.7490 8( 8) E-x(3)-T-x(2,4)-D-x(0,2)-V-x-[ADE]-[AEG]-x-G-[NSV] Occurences: 8(8) HOXU_ALCEU : 14- 28: ktltt EegrTlv--D--VaAEnGV yiptl HOXU_NOCOP : 14- 28: vtvtt EesrTlv--D--VaAEaGV yiptl NQO3_PARDE : 225- 240: tarpw EltkTesi-D--VmDAlGS sirid NUAM_BOVIN : 244- 259: tarpw EtrkTesi-D--VmDAvGS nivvs NUAM_HUMAN : 244- 259: tarpw EtrkTesi-D--VmDAvGS nivvs NUAM_NEUCR : 250- 265: rarpw ElkkTesi-D--VlDGlGS nirvd NUOG_ECOLI : 92- 110: resvv EwlmTnhphDcpVcEEgGN chlqd NUOG_SALTY : 92- 110: resvv EwlmTnhphDcpVcEEgGN chlqd B 2: 22.5789 8( 8) T-x(2,4)-D-x(0,2)-V-x-[ADE]-[AEG]-x-G-[NSV] Occurences: 8(8) HOXU_ALCEU : 18- 28: teegr Tlv--D--VaAEnGV yiptl HOXU_NOCOP : 18- 28: teesr Tlv--D--VaAEaGV yiptl NQO3_PARDE : 229- 240: weltk Tesi-D--VmDAlGS sirid NUAM_BOVIN : 248- 259: wetrk Tesi-D--VmDAvGS nivvs NUAM_HUMAN : 248- 259: wetrk Tesi-D--VmDAvGS nivvs NUAM_NEUCR : 254- 265: welkk Tesi-D--VlDGlGS nirvd NUOG_ECOLI : 96- 110: vewlm TnhphDcpVcEEgGN chlqd NUOG_SALTY : 96- 110: vewlm TnhphDcpVcEEgGN chlqd C 3: 20.9501 8( 8) I-x(3)-T-x(3,5)-E-x(4)-L-[GPV]-x(3)-[ADE] Occurences: 8(8) HOXU_ALCEU : 6- 24: siqit IdgkTltt--EegrtLVdvaA engvy HOXU_NOCOP : 6- 24: sieie IdgvTvtt--EesrtLVdvaA eagvy NQO3_PARDE : 242- 260: algss IridTkgr--EvmriLPrnhD gvnee NUAM_BOVIN : 261- 279: avgsn IvvsTrtg--EvmriLPrmhE dinee NUAM_HUMAN : 261- 279: avgsn IvvsTrtg--EvmriLPrmhE dinee NUAM_NEUCR : 267- 285: glgsn IrvdTrgl--EvmriLPrlnD evnee NUOG_ECOLI : 440- 460: trldd IaawTyrapvEdqarLGfaiA haldn NUOG_SALTY : 441- 461: trldd IaawTyrapvEdqarLGfaiA haldn D 4: 20.5928 8( 8) I-x-[AGIV]-x-T-x(3,5)-E-x(2,3)-R-x-[GL] Occurences: 8(8) HOXU_ALCEU : 6- 19: siqit IdGkTltt--Eeg-RtL vdvaa HOXU_NOCOP : 6- 19: sieie IdGvTvtt--Ees-RtL vdvaa NQO3_PARDE : 242- 255: algss IrIdTkgr--Evm-RiL prnhd NUAM_BOVIN : 261- 274: avgsn IvVsTrtg--Evm-RiL prmhe NUAM_HUMAN : 261- 274: avgsn IvVsTrtg--Evm-RiL prmhe NUAM_NEUCR : 267- 280: glgsn IrVdTrgl--Evm-RiL prlnd NUOG_ECOLI : 440- 456: trldd IaAwTyrapvEdqaRlG faiah NUOG_SALTY : 441- 457: trldd IaAwTyrapvEdqaRlG faiah E 5: 20.4501 8( 8) I-x(2,3)-T-x(3,5)-E-x(4)-L-[GPV]-x(3)-[ADE] Occurences: 8(8) HOXU_ALCEU : 6- 24: siqit IdgkTltt--EegrtLVdvaA engvy HOXU_NOCOP : 6- 24: sieie IdgvTvtt--EesrtLVdvaA eagvy NQO3_PARDE : 242- 260: algss IridTkgr--EvmriLPrnhD gvnee NUAM_BOVIN : 261- 279: avgsn IvvsTrtg--EvmriLPrmhE dinee NUAM_HUMAN : 261- 279: avgsn IvvsTrtg--EvmriLPrmhE dinee NUAM_NEUCR : 267- 285: glgsn IrvdTrgl--EvmriLPrlnD evnee NUOG_ECOLI : 440- 460: trldd IaawTyrapvEdqarLGfaiA haldn NUOG_SALTY : 441- 461: trldd IaawTyrapvEdqarLGfaiA haldn F 6: 18.4013 10( 8) L-x(1,3)-A-x(3,4)-G-x(2)-I-[AP] Occurences: 10(8) HOXU_ALCEU : 19- 31: eegrt LvdvAaen-GvyIP tlcyl HOXU_NOCOP : 19- 31: eesrt LvdvAaea-GvyIP tl NQO3_PARDE : 303- 316: swpea LeaaAramkGkkIA gligd NUAM_BOVIN : 50- 61: pgttv Lq--AcekvGmqIP rfcyh NUAM_HUMAN : 50- 61: pgttv Lq--AcekvGmqIP rfcyh NUAM_NEUCR : 53- 65: eagsa Liq-AcekaGvtIP rycyh NUOG_ECOLI : 18- 30: ngadn Lle-AclslGldIP yfcwh NUOG_ECOLI : 19- 30: gadnl Le--AclslGldIP yfcwh NUOG_SALTY : 18- 30: ngadn Llq-AclslGldIP yfcwh NUOG_SALTY : 19- 30: gadnl Lq--AclslGldIP yfcwh G 7: 17.8902 10( 8) V-x(2)-E-x(0,1)-G-x(3)-[LP]-[AQT] Occurences: 10(8) HOXU_ALCEU : 22- 32: rtlvd VaaEnGvyiPT lcylk HOXU_NOCOP : 22- 32: rtlvd VaaEaGvyiPT l NQO3_PARDE : 553- 562: esglf VntE-GrpqLA mranf NUAM_BOVIN : 41- 51: vdgqs VmvEpGttvLQ acekv NUAM_HUMAN : 41- 51: vdgqs VmvEpGttvLQ acekv NUAM_NEUCR : 313- 322: ltipl VrrE-GkfePA swdqa NUOG_ECOLI : 104- 114: phdcp VceEgGnchLQ dmtvm NUOG_ECOLI : 354- 364: qlalk VlrEgGiytPA lreie NUOG_SALTY : 104- 114: phdcp VceEgGnchLQ dmtvm NUOG_SALTY : 354- 364: qlalk VlrEgGiytPA lreie H 8: 17.8007 8( 8) T-x(3,5)-E-x(2)-R-x(1,2)-L-[APV] Occurences: 8(8) HOXU_ALCEU : 10- 20: tidgk Tltt--EegRt-LV dvaae HOXU_NOCOP : 10- 20: eidgv Tvtt--EesRt-LV dvaae NQO3_PARDE : 246- 256: sirid Tkgr--EvmRi-LP rnhdg NUAM_BOVIN : 265- 275: nivvs Trtg--EvmRi-LP rmhed NUAM_HUMAN : 265- 275: nivvs Trtg--EvmRi-LP rmhed NUAM_NEUCR : 271- 281: nirvd Trgl--EvmRi-LP rlnde NUOG_ECOLI : 338- 351: eenfy TgiahgEqeRlqLA lkvlr NUOG_SALTY : 338- 351: aenfy TgiargEqeRlqLA lkvlr I 9: 17.3102 8( 8) V-x(2)-[AEG]-x-G-x(0,2)-I-x(1,3)-T Occurences: 8(8) HOXU_ALCEU : 22- 32: rtlvd VaaEnGvyIp--T lcylk HOXU_NOCOP : 22- 32: rtlvd VaaEaGvyIp--T l NQO3_PARDE : 234- 246: tesid VmdAlGssIridT kgrev NUAM_BOVIN : 253- 265: tesid VmdAvGsnIvvsT rtgev NUAM_HUMAN : 253- 265: tesid VmdAvGsnIvvsT rtgev NUAM_NEUCR : 259- 271: tesid VldGlGsnIrvdT rglev NUOG_ECOLI : 354- 362: qlalk VlrEgG--Iy--T palre NUOG_SALTY : 354- 362: qlalk VlrEgG--Iy--T palre J 10: 16.9302 8( 8) T-x(3)-E-x(4)-L-x-[DERS]-x(3)-[DEGT] Occurences: 8(8) HOXU_ALCEU : 10- 25: tidgk TlttEegrtLvDvaaE ngvyi HOXU_NOCOP : 10- 25: eidgv TvttEesrtLvDvaaE agvyi NQO3_PARDE : 246- 261: sirid TkgrEvmriLpRnhdG vneew NUAM_BOVIN : 265- 280: nivvs TrtgEvmriLpRmheD ineew NUAM_HUMAN : 265- 280: nivvs TrtgEvmriLpRmheD ineew NUAM_NEUCR : 271- 286: nirvd TrglEvmriLpRlndE vneew NUOG_ECOLI : 641- 656: yydsk TvmlEtwrwLhSlhsT llsre NUOG_SALTY : 187- 202: rpedg TlesEfsgnLvEicpT gvftd K 11: 16.8181 11( 8) D-V-x(3,4)-G-[ASTV]-x-[IPV] Occurences: 11(8) HOXU_ALCEU : 21- 30: grtlv DVaaenGVyI ptlcy HOXU_NOCOP : 21- 30: srtlv DVaaeaGVyI ptl NQO3_PARDE : 233- 242: ktesi DVmdalGSsI ridtk NUAM_BOVIN : 252- 261: ktesi DVmdavGSnI vvstr NUAM_BOVIN : 398- 407: gveea DVvllvGTnP rfeap NUAM_HUMAN : 252- 261: ktesi DVmdavGSnI vvstr NUAM_HUMAN : 398- 407: gveea DVvllvGTnP rfeap NUAM_NEUCR : 258- 267: ktesi DVldglGSnI rvdtr NUAM_NEUCR : 407- 416: giesa DVillvGTnP rheaa NUOG_ECOLI : 380- 388: lvlge DVtqt-GArV lavrq NUOG_SALTY : 380- 388: lvlge DVtqt-GArV alavr L 12: 15.1802 8( 8) L-x(1,3)-D-x-A-x(0,1)-A Occurences: 8(8) HOXU_ALCEU : 19- 24: eegrt Lv--DvA-A engvy HOXU_NOCOP : 19- 24: eesrt Lv--DvA-A eagvy NQO3_PARDE : 120- 126: ggecd Lq--DqAmA ygvdf NUAM_BOVIN : 481- 488: lgssa LqrnDgA-A ilaav NUAM_HUMAN : 481- 488: lgssa LqrnDgA-A ilaav NUAM_NEUCR : 454- 460: fefeh Lgt-DhA-A lqkal NUOG_ECOLI : 437- 442: vddtr Ld--DiA-A wtyra NUOG_SALTY : 438- 443: vddtr Ld--DiA-A wtyra M 13: 15.1145 8( 8) L-x-D-x-[AST]-x(3)-G Occurences: 8(8) HOXU_ALCEU : 19- 27: eegrt LvDvAaenG vyipt HOXU_NOCOP : 19- 27: eesrt LvDvAaeaG vyipt NQO3_PARDE : 120- 128: ggecd LqDqAmayG vdfsr NUAM_BOVIN : 139- 147: ggecd LqDqSmmfG sdrsr NUAM_HUMAN : 139- 147: ggecd LqDqSmmfG ndrsr NUAM_NEUCR : 143- 151: ggecd LqDqSmryG rdrgr NUOG_ECOLI : 113- 121: ggnch LqDmTvmtG hsfrr NUOG_SALTY : 113- 121: ggnch LqDmTvmtG hsfrr N 14: 14.7102 9( 8) G-x(2)-V-x(4)-[APST]-R Occurences: 9(8) HOXU_ALCEU : 111- 120: qlqav GyeVdmmvSR fpyrf HOXU_NOCOP : 8- 17: eieid GvtVtteeSR tlvdv NQO3_PARDE : 147- 156: edlnl GplVethmTR cisct NQO3_PARDE : 248- 257: ridtk GreVmrilPR nhdgv NUAM_BOVIN : 166- 175: edkni GplVktimTR ciqct NUAM_HUMAN : 166- 175: edkni GplVktimTR ciqct NUAM_NEUCR : 273- 282: rvdtr GleVmrilPR lndev NUOG_ECOLI : 378- 387: avlvl GedVtqtgAR vlavr NUOG_SALTY : 378- 387: avlvl GedVtqtgAR valav O 15: 14.6802 8( 8) E-x(3)-T-x(2,4)-D-x(0,2)-V Occurences: 8(8) HOXU_ALCEU : 14- 22: ktltt EegrTlv--D--V aaeng HOXU_NOCOP : 14- 22: vtvtt EesrTlv--D--V aaeag NQO3_PARDE : 225- 234: tarpw EltkTesi-D--V mdalg NUAM_BOVIN : 244- 253: tarpw EtrkTesi-D--V mdavg NUAM_HUMAN : 244- 253: tarpw EtrkTesi-D--V mdavg NUAM_NEUCR : 250- 259: rarpw ElkkTesi-D--V ldglg NUOG_ECOLI : 92- 104: resvv EwlmTnhphDcpV ceegg NUOG_SALTY : 92- 104: resvv EwlmTnhphDcpV ceegg P 16: 14.6802 10( 8) S-x(2,4)-V-x(3,5)-A-x-A Occurences: 10(8) HOXU_ALCEU : 49- 59: tcrvc Svk--Vngnv-AaA ctvrv HOXU_NOCOP : 16- 26: vttee Srtl-Vdva--AeA gvyip NQO3_PARDE : 442- 452: tkarp Sivi-Vgqg--AiA rrdge NUAM_BOVIN : 16- 27: vglsk SskgcVrtt--AtA asnli NUAM_BOVIN : 17- 27: glsks Skgc-Vrtt--AtA asnli NUAM_HUMAN : 16- 27: vglsk SpkgcVrtt--AtA asnli NUAM_NEUCR : 672- 685: llqql SkvqlVeqnqgAtA tnepl NUOG_ECOLI : 479- 489: epelq Skid-Vivq--AlA gakkp NUOG_ECOLI : 479- 491: epelq Skid-VivqalAgA kkpli NUOG_ECOLI : 574- 585: lhrha Sair-Vnaal-AkA plvmv NUOG_SALTY : 575- 586: lhrha Satr-Vnaal-AkA plvmv Q 17: 14.6607 14( 8) R-x(1,2)-L-V-[DEG] Occurences: 14(8) HOXU_ALCEU : 17- 21: tteeg Rt-LVD vaaen HOXU_ALCEU : 81- 86: elvdm RkaLVE flfae HOXU_NOCOP : 17- 21: ttees Rt-LVD vaaea NQO3_PARDE : 48- 53: iagnc RmcLVE vvggp NQO3_PARDE : 599- 604: slagl RrkLVE avphl NQO3_PARDE : 600- 604: laglr Rk-LVE avphl NUAM_BOVIN : 7- 12: lripv RkaLVG lskss NUAM_BOVIN : 76- 81: vagnc RmcLVE iekap NUAM_HUMAN : 7- 12: lripv RraLVG lsksp NUAM_HUMAN : 8- 12: ripvr Ra-LVG lsksp NUAM_HUMAN : 76- 81: vagnc RmcLVE iekap NUAM_NEUCR : 80- 85: iagnc RmcLVE vekvp NUOG_ECOLI : 328- 332: snfal Re-LVG eenfy NUOG_SALTY : 328- 332: snfal Re-LVG aenfy R 18: 14.2646 8( 8) A-E-x(0,1)-A-x(3)-[AILP] Occurences: 8(8) HOXU_ALCEU : 179- 186: rieid AElAnamP peqvk HOXU_NOCOP : 24- 30: lvdva AE-AgvyI ptl NQO3_PARDE : 325- 331: gdlvp AE-AafsL kqlve NUAM_BOVIN : 348- 354: gglvd AE-AliaL kdlln NUAM_HUMAN : 348- 354: gglvd AE-AlvaL kdlln NUAM_NEUCR : 541- 548: ftvps AEiAqtkP kfvwl NUOG_ECOLI : 294- 301: fitln AEqAmqgA adilr NUOG_SALTY : 294- 301: fitln AEqAmqgA adilr S 19: 14.2646 10( 8) V-x(1,2)-E-x-G-x(3)-[AILP] Occurences: 10(8) HOXU_ALCEU : 22- 31: rtlvd VaaEnGvyiP tlcyl HOXU_NOCOP : 22- 31: rtlvd VaaEaGvyiP tl NQO3_PARDE : 492- 500: mdvga Vt-EgGllaA idgae NUAM_BOVIN : 41- 50: vdgqs VmvEpGttvL qacek NUAM_HUMAN : 41- 50: vdgqs VmvEpGttvL qacek NUAM_NEUCR : 45- 54: idgkk VsiEaGsalI qacek NUOG_ECOLI : 104- 113: phdcp VceEgGnchL qdmtv NUOG_ECOLI : 354- 363: qlalk VlrEgGiytP alrei NUOG_SALTY : 104- 113: phdcp VceEgGnchL qdmtv NUOG_SALTY : 354- 363: qlalk VlrEgGiytP alrei T 20: 12.5102 10( 8) D-x-A-A Occurences: 10(8) HOXU_ALCEU : 21- 24: grtlv DvAA engvy HOXU_NOCOP : 21- 24: srtlv DvAA eagvy NQO3_PARDE : 421- 424: ahvgt DrAA lesls NUAM_BOVIN : 337- 340: sfqgn DvAA iaggl NUAM_BOVIN : 485- 488: alqrn DgAA ilaav NUAM_HUMAN : 337- 340: sfqgk DvAA iaggl NUAM_HUMAN : 485- 488: alqrn DgAA ilaav NUAM_NEUCR : 457- 460: ehlgt DhAA lqkal NUOG_ECOLI : 439- 442: dtrld DiAA wtyra NUOG_SALTY : 440- 443: dtrld DiAA wtyra Number of patterns evaluated by Pratt:1618 Total running time: 2 seconds