------------------------------------------------------------ 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 COMPLEX1_75K_3 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 COMPLEX1_75K_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: HOXU_ALCEU 233 HOXU_NOCOP 33 NQO3_PARDE 672 NUAM_BOVIN 727 NUAM_HUMAN 727 NUAM_NEUCR 744 Pratt run started at Thu Feb 6 19:08:51 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 27.6904 6( 6) E-x(3)-T-x(2,3)-D-V-x(4)-G-x(2)-I-x(1,3)-T 2: 24.0203 8( 6) E-x(2,3)-T-x(2,3)-D-V-x(4)-G-x(2)-I 3: 23.5203 6( 6) T-x(2,3)-D-V-x(4)-G-x(2)-I-x(1,3)-T 4: 20.8503 6( 6) I-x(3)-T-x(3)-E-x(2)-R-x-L 5: 19.8503 6( 6) A-x-E-x(0,1)-G-V-x(3,4)-L 6: 19.3503 6( 6) L-x(1,3)-A-x-E-x(1,2)-G-x(3)-P 7: 16.6802 6( 6) T-x(3)-E-x(2)-R-x-L 8: 16.1802 6( 6) A-x(2)-G-V-x(3,4)-L 9: 16.1802 6( 6) G-x(3)-T-x(0,1)-E-x(5)-V 10: 16.1802 6( 6) G-x(3,4)-T-E-x(5)-V 11: 16.1802 6( 6) I-x(0,1)-G-x(5)-E-x(4)-L 12: 15.6802 6( 6) E-x(0,1)-G-V-x(3,4)-L 13: 15.6802 9( 6) A-x(0,1)-E-x(1,2)-G-x(3)-P 14: 15.6802 8( 6) A-x(0,1)-E-x(0,1)-G-V 15: 15.6802 6( 6) D-x(5)-G-x(2)-I-x(1,3)-T 16: 15.6802 6( 6) T-x(3)-R-x(5)-A-x(3,5)-G 17: 15.6802 10( 6) T-x(1,3)-E-x(2)-R-x-L 18: 15.6802 8( 6) T-x(2,3)-E-x(1,2)-R-x-L 19: 15.1802 7( 6) A-x(0,2)-G-V-x(3,4)-L 20: 15.1802 6( 6) A-x-E-x(1,2)-G-x(0,2)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 47.4511 6( 6) I-x-[GIV]-x-T-x-[GT]-x-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] B 2: 47.0725 6( 6) G-x-[ACT]-x-T-x(0,1)-E-[EK]-[AGS]-x(3)-V-[DN]-[TV]-[AE]-[AG]-[ER]-x-[GQ]-x(4)-[AT] C 3: 44.3877 6( 6) G-x(3,4)-T-E-[EK]-[AGS]-x(3)-V-[DN]-[TV]-[AE]-[AG]-[ER]-x-[GQ]-x(4)-[AT] D 4: 41.6597 6( 6) I-x(0,1)-G-x(2)-[LV]-[DPST]-x-E-[AE]-x(2)-[AST]-L-x-[DQ]-[ALV]-x-[AEN]-x(2)-[DG]-[GSV] E 5: 40.6125 6( 6) T-x-[GT]-x-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] F 6: 39.9757 6( 6) E-x(2)-[KR]-T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T G 7: 36.4121 10( 6) T-x(1,3)-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] H 8: 36.4121 8( 6) T-x(2,3)-E-x(1,2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] I 9: 33.9465 6( 6) T-[ER]-x(2)-R-x(2)-[NSTV]-[DE]-[IV]-A-x(3,5)-G-x(2)-[GI]-x-[GT] J 10: 33.0575 8( 6) E-x(2,3)-T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I K 11: 32.5575 6( 6) T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T L 12: 28.8875 6( 6) D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T M 13: 28.6893 6( 6) L-x(1,3)-A-[AC]-E-x(1,2)-G-[IMV]-x-[IV]-P N 14: 22.0228 6( 6) A-[ER]-[AEN]-G-V-x(3,4)-L O 15: 21.7013 8( 6) A-x(0,1)-E-x(1,2)-G-[IMV]-x-[IV]-P P 16: 19.8503 6( 6) A-x-E-x(0,1)-G-V-x(3,4)-L Q 17: 18.8977 8( 6) A-x(0,1)-E-x(0,1)-G-V-x(4)-[LP] R 18: 17.8625 6( 6) A-[ACS]-E-x(1,2)-G-x(0,2)-V S 19: 15.7583 2( 2) E-x(2)-[KR]-T-x(2)-D T 20: 15.6802 6( 6) E-x(0,1)-G-V-x(3,4)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 47.4511 6( 6) I-x-[GIV]-x-T-x-[GT]-x-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] Occurences: 6(6) HOXU_ALCEU : 6- 32: siqit IdGkTlTtEegRtLVDvaAEnGvyiPT lcylk HOXU_NOCOP : 6- 32: sieie IdGvTvTtEesRtLVDvaAEaGvyiPT l NQO3_PARDE : 242- 268: algss IrIdTkGrEvmRiLPRnhDGvNeewIS dktrf NUAM_BOVIN : 261- 287: avgsn IvVsTrTgEvmRiLPRmhEDiNeewIS dktrf NUAM_HUMAN : 261- 287: avgsn IvVsTrTgEvmRiLPRmhEDiNeewIS dktrf NUAM_NEUCR : 267- 293: glgsn IrVdTrGlEvmRiLPRlnDEvNeewIN dktrf B 2: 47.0725 6( 6) G-x-[ACT]-x-T-x(0,1)-E-[EK]-[AGS]-x(3)-V-[DN]-[TV]-[AE]-[AG]-[ER]-x-[GQ]-x(4)-[AT] Occurences: 6(6) HOXU_ALCEU : 8- 32: qitid GkTlTtEEGrtlVDVAAEnGvyipT lcylk HOXU_NOCOP : 8- 32: eieid GvTvTtEESrtlVDVAAEaGvyipT l NQO3_PARDE : 542- 565: diilp GaCyT-EESglfVNTEGRpQlamrA nfapg NUAM_BOVIN : 586- 609: dvilp GaAyT-EKSatyVNTEGRaQqtkvA vtppg NUAM_HUMAN : 586- 609: dvilp GaAyT-EKSatyVNTEGRaQqtkvA vtppg NUAM_NEUCR : 590- 613: divlp GaAyT-EKAgtyVNTEGRvQmtraA tglpg C 3: 44.3877 6( 6) G-x(3,4)-T-E-[EK]-[AGS]-x(3)-V-[DN]-[TV]-[AE]-[AG]-[ER]-x-[GQ]-x(4)-[AT] Occurences: 6(6) HOXU_ALCEU : 8- 32: qitid GktltTEEGrtlVDVAAEnGvyipT lcylk HOXU_NOCOP : 8- 32: eieid GvtvtTEESrtlVDVAAEaGvyipT l NQO3_PARDE : 542- 565: diilp Gacy-TEESglfVNTEGRpQlamrA nfapg NUAM_BOVIN : 586- 609: dvilp Gaay-TEKSatyVNTEGRaQqtkvA vtppg NUAM_HUMAN : 586- 609: dvilp Gaay-TEKSatyVNTEGRaQqtkvA vtppg NUAM_NEUCR : 590- 613: divlp Gaay-TEKAgtyVNTEGRvQmtraA tglpg D 4: 41.6597 6( 6) I-x(0,1)-G-x(2)-[LV]-[DPST]-x-E-[AE]-x(2)-[AST]-L-x-[DQ]-[ALV]-x-[AEN]-x(2)-[DG]-[GSV] Occurences: 6(6) HOXU_ALCEU : 6- 28: siqit IdGktLTtEEgrTLvDVaAenGV yiptl HOXU_NOCOP : 6- 28: sieie IdGvtVTtEEsrTLvDVaAeaGV yiptl NQO3_PARDE : 319- 340: kiagl I-GdlVPaEAafSLkQLvEglGG kvecr NUAM_BOVIN : 341- 363: ndvaa IaGglVDaEAliALkDLlNrvDS dtlct NUAM_HUMAN : 341- 363: kdvaa IaGglVDaEAlvALkDLlNrvDS dtlct NUAM_NEUCR : 40- 62: evelt IdGkkVSiEAgsALiQAcEkaGV tipry E 5: 40.6125 6( 6) T-x-[GT]-x-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] Occurences: 6(6) HOXU_ALCEU : 10- 32: tidgk TlTtEegRtLVDvaAEnGvyiPT lcylk HOXU_NOCOP : 10- 32: eidgv TvTtEesRtLVDvaAEaGvyiPT l NQO3_PARDE : 246- 268: sirid TkGrEvmRiLPRnhDGvNeewIS dktrf NUAM_BOVIN : 265- 287: nivvs TrTgEvmRiLPRmhEDiNeewIS dktrf NUAM_HUMAN : 265- 287: nivvs TrTgEvmRiLPRmhEDiNeewIS dktrf NUAM_NEUCR : 271- 293: nirvd TrGlEvmRiLPRlnDEvNeewIN dktrf F 6: 39.9757 6( 6) E-x(2)-[KR]-T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T Occurences: 6(6) HOXU_ALCEU : 14- 32: ktltt EegRTlv-DVaAEnGVyIp--T lcylk HOXU_NOCOP : 14- 32: vtvtt EesRTlv-DVaAEaGVyIp--T l NQO3_PARDE : 225- 246: tarpw EltKTesiDVmDAlGSsIridT kgrev NUAM_BOVIN : 244- 265: tarpw EtrKTesiDVmDAvGSnIvvsT rtgev NUAM_HUMAN : 244- 265: tarpw EtrKTesiDVmDAvGSnIvvsT rtgev NUAM_NEUCR : 250- 271: rarpw ElkKTesiDVlDGlGSnIrvdT rglev G 7: 36.4121 10( 6) T-x(1,3)-E-x(2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] Occurences: 10(6) HOXU_ALCEU : 10- 32: tidgk TlttEegRtLVDvaAEnGvyiPT lcylk HOXU_ALCEU : 12- 32: dgktl Tt--EegRtLVDvaAEnGvyiPT lcylk HOXU_NOCOP : 10- 32: eidgv TvttEesRtLVDvaAEaGvyiPT l HOXU_NOCOP : 12- 32: dgvtv Tt--EesRtLVDvaAEaGvyiPT l NQO3_PARDE : 246- 268: sirid TkgrEvmRiLPRnhDGvNeewIS dktrf NUAM_BOVIN : 265- 287: nivvs TrtgEvmRiLPRmhEDiNeewIS dktrf NUAM_BOVIN : 267- 287: vvstr Tg--EvmRiLPRmhEDiNeewIS dktrf NUAM_HUMAN : 265- 287: nivvs TrtgEvmRiLPRmhEDiNeewIS dktrf NUAM_HUMAN : 267- 287: vvstr Tg--EvmRiLPRmhEDiNeewIS dktrf NUAM_NEUCR : 271- 293: nirvd TrglEvmRiLPRlnDEvNeewIN dktrf H 8: 36.4121 8( 6) T-x(2,3)-E-x(1,2)-R-x-L-[PV]-[DR]-x(2)-[ADE]-[DEG]-x-[GN]-x(3)-[IP]-[NST] Occurences: 8(6) HOXU_ALCEU : 10- 32: tidgk TlttEegRtLVDvaAEnGvyiPT lcylk HOXU_ALCEU : 12- 32: dgktl Tte-Eg-RtLVDvaAEnGvyiPT lcylk HOXU_NOCOP : 10- 32: eidgv TvttEesRtLVDvaAEaGvyiPT l HOXU_NOCOP : 12- 32: dgvtv Tte-Es-RtLVDvaAEaGvyiPT l NQO3_PARDE : 246- 268: sirid TkgrEvmRiLPRnhDGvNeewIS dktrf NUAM_BOVIN : 265- 287: nivvs TrtgEvmRiLPRmhEDiNeewIS dktrf NUAM_HUMAN : 265- 287: nivvs TrtgEvmRiLPRmhEDiNeewIS dktrf NUAM_NEUCR : 271- 293: nirvd TrglEvmRiLPRlnDEvNeewIN dktrf I 9: 33.9465 6( 6) T-[ER]-x(2)-R-x(2)-[NSTV]-[DE]-[IV]-A-x(3,5)-G-x(2)-[GI]-x-[GT] Occurences: 6(6) HOXU_ALCEU : 13- 32: gktlt TEegRtlVDVAaen--GvyIpT lcylk HOXU_NOCOP : 13- 32: gvtvt TEesRtlVDVAaea--GvyIpT l NQO3_PARDE : 161- 182: rcisc TRcvRftTEVAgitqmGqtGrG edsei NUAM_BOVIN : 180- 201: rciqc TRciRfaSEIAgvddlGttGrG ndmqv NUAM_HUMAN : 180- 201: rciqc TRciRfaSEIAgvddlGttGrG ndmqv NUAM_NEUCR : 186- 207: rciqc TRcvRfaNDIAgapelGstGrG ndlqi J 10: 33.0575 8( 6) E-x(2,3)-T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I Occurences: 8(6) HOXU_ALCEU : 14- 30: ktltt EegrTlv-DVaAEnGVyI ptlcy HOXU_ALCEU : 15- 30: tltte Egr-Tlv-DVaAEnGVyI ptlcy HOXU_NOCOP : 14- 30: vtvtt EesrTlv-DVaAEaGVyI ptl HOXU_NOCOP : 15- 30: tvtte Esr-Tlv-DVaAEaGVyI ptl NQO3_PARDE : 225- 242: tarpw EltkTesiDVmDAlGSsI ridtk NUAM_BOVIN : 244- 261: tarpw EtrkTesiDVmDAvGSnI vvstr NUAM_HUMAN : 244- 261: tarpw EtrkTesiDVmDAvGSnI vvstr NUAM_NEUCR : 250- 267: rarpw ElkkTesiDVlDGlGSnI rvdtr K 11: 32.5575 6( 6) T-x(2,3)-D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T Occurences: 6(6) HOXU_ALCEU : 18- 32: teegr Tlv-DVaAEnGVyIp--T lcylk HOXU_NOCOP : 18- 32: teesr Tlv-DVaAEaGVyIp--T l NQO3_PARDE : 229- 246: weltk TesiDVmDAlGSsIridT kgrev NUAM_BOVIN : 248- 265: wetrk TesiDVmDAvGSnIvvsT rtgev NUAM_HUMAN : 248- 265: wetrk TesiDVmDAvGSnIvvsT rtgev NUAM_NEUCR : 254- 271: welkk TesiDVlDGlGSnIrvdT rglev L 12: 28.8875 6( 6) D-V-x-[AD]-[AEG]-x-G-[SV]-x-I-x(1,3)-T Occurences: 6(6) HOXU_ALCEU : 21- 32: grtlv DVaAEnGVyIp--T lcylk HOXU_NOCOP : 21- 32: srtlv DVaAEaGVyIp--T l NQO3_PARDE : 233- 246: ktesi DVmDAlGSsIridT kgrev NUAM_BOVIN : 252- 265: ktesi DVmDAvGSnIvvsT rtgev NUAM_HUMAN : 252- 265: ktesi DVmDAvGSnIvvsT rtgev NUAM_NEUCR : 258- 271: ktesi DVlDGlGSnIrvdT rglev M 13: 28.6893 6( 6) L-x(1,3)-A-[AC]-E-x(1,2)-G-[IMV]-x-[IV]-P Occurences: 6(6) HOXU_ALCEU : 19- 31: eegrt LvdvAAEn-GVyIP tlcyl HOXU_NOCOP : 19- 31: eesrt LvdvAAEa-GVyIP tl NQO3_PARDE : 21- 33: dpnmt Liq-ACEmaGIeVP rfcyh NUAM_BOVIN : 50- 61: pgttv Lq--ACEkvGMqIP rfcyh NUAM_HUMAN : 50- 61: pgttv Lq--ACEkvGMqIP rfcyh NUAM_NEUCR : 53- 65: eagsa Liq-ACEkaGVtIP rycyh N 14: 22.0228 6( 6) A-[ER]-[AEN]-G-V-x(3,4)-L Occurences: 6(6) HOXU_ALCEU : 24- 33: lvdva AENGVyiptL cylkd HOXU_NOCOP : 24- 33: lvdva AEAGVyiptL NQO3_PARDE : 93- 101: pmvkk AREGVmef-L linhp NQO3_PARDE : 93- 102: pmvkk AREGVmeflL inhpl NUAM_BOVIN : 112- 120: ektkk AREGVmef-L lanhp NUAM_BOVIN : 112- 121: ektkk AREGVmeflL anhpl NUAM_HUMAN : 112- 120: ekskk AREGVmef-L lanhp NUAM_HUMAN : 112- 121: ekskk AREGVmeflL anhpl NUAM_NEUCR : 116- 124: plthk AREGVmef-L panhp O 15: 21.7013 8( 6) A-x(0,1)-E-x(1,2)-G-[IMV]-x-[IV]-P Occurences: 8(6) HOXU_ALCEU : 23- 31: tlvdv AaEn-GVyIP tlcyl HOXU_ALCEU : 24- 31: lvdva A-En-GVyIP tlcyl HOXU_NOCOP : 23- 31: tlvdv AaEa-GVyIP tl HOXU_NOCOP : 24- 31: lvdva A-Ea-GVyIP tl NQO3_PARDE : 24- 33: mtliq AcEmaGIeVP rfcyh NUAM_BOVIN : 52- 61: ttvlq AcEkvGMqIP rfcyh NUAM_HUMAN : 52- 61: ttvlq AcEkvGMqIP rfcyh NUAM_NEUCR : 56- 65: saliq AcEkaGVtIP rycyh P 16: 19.8503 6( 6) A-x-E-x(0,1)-G-V-x(3,4)-L Occurences: 6(6) HOXU_ALCEU : 23- 33: tlvdv AaEnGVyiptL cylkd HOXU_NOCOP : 23- 33: tlvdv AaEaGVyiptL NQO3_PARDE : 93- 101: pmvkk ArE-GVmef-L linhp NQO3_PARDE : 93- 102: pmvkk ArE-GVmeflL inhpl NUAM_BOVIN : 112- 120: ektkk ArE-GVmef-L lanhp NUAM_BOVIN : 112- 121: ektkk ArE-GVmeflL anhpl NUAM_HUMAN : 112- 120: ekskk ArE-GVmef-L lanhp NUAM_HUMAN : 112- 121: ekskk ArE-GVmeflL anhpl NUAM_NEUCR : 116- 124: plthk ArE-GVmef-L panhp Q 17: 18.8977 8( 6) A-x(0,1)-E-x(0,1)-G-V-x(4)-[LP] Occurences: 8(6) HOXU_ALCEU : 23- 33: tlvdv AaEnGVyiptL cylkd HOXU_ALCEU : 24- 33: lvdva A-EnGVyiptL cylkd HOXU_NOCOP : 23- 33: tlvdv AaEaGVyiptL HOXU_NOCOP : 24- 33: lvdva A-EaGVyiptL NQO3_PARDE : 93- 102: pmvkk ArE-GVmeflL inhpl NUAM_BOVIN : 112- 121: ektkk ArE-GVmeflL anhpl NUAM_HUMAN : 112- 121: ekskk ArE-GVmeflL anhpl NUAM_NEUCR : 116- 125: plthk ArE-GVmeflP anhpl R 18: 17.8625 6( 6) A-[ACS]-E-x(1,2)-G-x(0,2)-V Occurences: 6(6) HOXU_ALCEU : 23- 28: tlvdv AAEn-G--V yiptl HOXU_NOCOP : 23- 28: tlvdv AAEa-G--V yiptl NQO3_PARDE : 24- 32: mtliq ACEmaGieV prfcy NUAM_BOVIN : 186- 192: rcirf ASEiaG--V ddlgt NUAM_HUMAN : 186- 192: rcirf ASEiaG--V ddlgt NUAM_NEUCR : 56- 62: saliq ACEkaG--V tipry S 19: 15.7583 2( 2) E-x(2)-[KR]-T-x(2)-D Occurences: 2(2) HOXU_ALCEU : 14- 21: ktltt EegRTlvD vaaen HOXU_NOCOP : 14- 21: vtvtt EesRTlvD vaaea T 20: 15.6802 6( 6) E-x(0,1)-G-V-x(3,4)-L Occurences: 6(6) HOXU_ALCEU : 25- 33: vdvaa EnGVyiptL cylkd HOXU_NOCOP : 25- 33: vdvaa EaGVyiptL NQO3_PARDE : 95- 101: vkkar E-GVmef-L linhp NQO3_PARDE : 95- 102: vkkar E-GVmeflL inhpl NUAM_BOVIN : 114- 120: tkkar E-GVmef-L lanhp NUAM_BOVIN : 114- 121: tkkar E-GVmeflL anhpl NUAM_HUMAN : 114- 120: skkar E-GVmef-L lanhp NUAM_HUMAN : 114- 121: skkar E-GVmeflL anhpl NUAM_NEUCR : 118- 124: thkar E-GVmef-L panhp Number of patterns evaluated by Pratt:2055 Total running time: 2 seconds