------------------------------------------------------------ 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 COX5B 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 COX5B.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: COX4_YEAST 155 COX5_DICDI 119 COXB_BOVIN 98 COXB_HUMAN 129 COXB_MOUSE 128 COXB_RAT 117 Pratt run started at Thu Feb 6 19:09:40 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 29.1904 6( 6) G-T-x(3)-P-x(4)-S-x(4)-R-x-V-x-C 2: 25.0203 6( 6) T-x(3)-P-x(4)-S-x(4)-R-x-V-x-C 3: 20.8503 6( 6) C-x(2)-C-G-x(3)-K-L 4: 20.8503 6( 6) P-x(4)-S-x(4)-R-x-V-x-C 5: 16.6802 6( 6) C-G-x(3)-K-L 6: 16.6802 6( 6) S-x(4)-R-x-V-x-C 7: 15.6802 6( 6) A-x(2,3)-G-x(4,5)-D-x(4)-T 8: 15.1802 6( 6) I-x(2)-E-x(0,2)-D-x(3,4)-V 9: 15.1802 8( 6) A-x(1,2)-G-T-x(1,3)-P 10: 15.1802 6( 6) L-x(2,4)-A-x(1,2)-G-T 11: 14.6802 7( 6) D-x(1,3)-E-x(0,2)-T-G 12: 12.5102 6( 6) G-x(3)-K-L 13: 12.5102 6( 6) R-x-V-x-C 14: 12.0102 7( 6) R-x(3)-C-x(0,1)-G 15: 12.0102 7( 6) E-x(2,3)-G-x-E 16: 12.0102 6( 6) D-x-E-x(4,5)-L 17: 12.0102 10( 6) G-x(3,4)-D-x(4)-T 18: 12.0102 10( 6) G-x(1,2)-V-x-T 19: 12.0102 10( 6) G-x(4,5)-D-x(4)-T 20: 12.0102 6( 6) G-x(2)-V-x(1,2)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 71.5453 6( 6) G-T-x-[EK]-[DS]-P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] B 2: 67.3752 6( 6) T-x-[EK]-[DS]-P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] C 3: 56.7962 6( 6) P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] D 4: 42.9445 6( 6) S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] E 5: 41.8526 6( 6) A-x(2,3)-G-x(4,5)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] F 6: 38.7745 6( 6) R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] G 7: 38.1825 10( 6) G-x(3,4)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] H 8: 38.1825 10( 6) G-x(4,5)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] I 9: 30.8046 6( 6) C-x-[DENRS]-C-G-[AQST]-x-[FY]-K-L-x(3)-[GQS] J 10: 29.9689 6( 6) L-x(2,4)-A-x(1,2)-G-T-x(2)-[DST]-[DP]-x(3)-[EP]-[ST]-[GIV] K 11: 26.7935 8( 6) A-x(1,2)-G-T-x(1,3)-P-[NTV]-x-[LV]-[DEP]-[QS] L 12: 25.8317 6( 6) E-x(2,3)-G-x-E-x(2)-[IV]-x(3)-[AT]-x(2)-[EG]-x(2)-P M 13: 24.7551 6( 6) C-G-[AQST]-x-[FY]-K-L-x(3)-[GQS] N 14: 24.3816 10( 6) G-x(1,2)-V-[LP]-T-[DG]-x(2)-[GQ]-[AET] O 15: 20.5851 6( 6) G-[AQST]-x-[FY]-K-L-x(3)-[GQS] P 16: 19.9490 6( 6) G-x-[DEG]-V-x(1,2)-T-x(3)-[DGQ]-[AST] Q 17: 17.8503 7( 6) D-x(1,3)-E-x(0,2)-T-G-[AL] R 18: 17.4209 6( 6) I-x(2)-E-x(0,2)-D-x(3,4)-V-[GILV] S 19: 17.3810 6( 6) R-x-[PV]-x-C-x(0,1)-G-[AGST] T 20: 17.3570 6( 6) D-[EGQ]-E-x(4,5)-L-x(3)-[GIV] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 71.5453 6( 6) G-T-x-[EK]-[DS]-P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] Occurences: 6(6) COX4_YEAST : 92- 123: dssrk GTmKDPiIIESyddyRyVGCtGSPAGshTImW lkptv COX5_DICDI : 56- 87: ltgaf GTlKSPvIVESifhsRiVACeGGDGEehDIlF htvae COXB_BOVIN : 41- 72: pkats GTkEDPnLVPSitnkRiVGCiCEEDNstVIwF wlhkg COXB_HUMAN : 72- 103: pkgas GTrEDPnLVPSisnkRiVGCiCEEDNtsVVwF wlhkg COXB_MOUSE : 71- 102: pkaas GTkEDPnLVPSisnkRiVGCiCEEDNctVIwF wlhkg COXB_RAT : 60- 91: pkaas GTkEDPnLVPSvsnkRiVGCiCEEDNctVIwF wlhqg B 2: 67.3752 6( 6) T-x-[EK]-[DS]-P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] Occurences: 6(6) COX4_YEAST : 93- 123: ssrkg TmKDPiIIESyddyRyVGCtGSPAGshTImW lkptv COX5_DICDI : 57- 87: tgafg TlKSPvIVESifhsRiVACeGGDGEehDIlF htvae COXB_BOVIN : 42- 72: katsg TkEDPnLVPSitnkRiVGCiCEEDNstVIwF wlhkg COXB_HUMAN : 73- 103: kgasg TrEDPnLVPSisnkRiVGCiCEEDNtsVVwF wlhkg COXB_MOUSE : 72- 102: kaasg TkEDPnLVPSisnkRiVGCiCEEDNctVIwF wlhkg COXB_RAT : 61- 91: kaasg TkEDPnLVPSvsnkRiVGCiCEEDNctVIwF wlhqg C 3: 56.7962 6( 6) P-x-[IL]-[IV]-[EP]-S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] Occurences: 6(6) COX4_YEAST : 97- 123: gtmkd PiIIESyddyRyVGCtGSPAGshTImW lkptv COX5_DICDI : 61- 87: gtlks PvIVESifhsRiVACeGGDGEehDIlF htvae COXB_BOVIN : 46- 72: gtked PnLVPSitnkRiVGCiCEEDNstVIwF wlhkg COXB_HUMAN : 77- 103: gtred PnLVPSisnkRiVGCiCEEDNtsVVwF wlhkg COXB_MOUSE : 76- 102: gtked PnLVPSisnkRiVGCiCEEDNctVIwF wlhkg COXB_RAT : 65- 91: gtked PnLVPSvsnkRiVGCiCEEDNctVIwF wlhqg D 4: 42.9445 6( 6) S-x(4)-R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] Occurences: 6(6) COX4_YEAST : 102- 123: piiie SyddyRyVGCtGSPAGshTImW lkptv COX5_DICDI : 66- 87: pvive SifhsRiVACeGGDGEehDIlF htvae COXB_BOVIN : 51- 72: pnlvp SitnkRiVGCiCEEDNstVIwF wlhkg COXB_HUMAN : 82- 103: pnlvp SisnkRiVGCiCEEDNtsVVwF wlhkg COXB_MOUSE : 81- 102: pnlvp SisnkRiVGCiCEEDNctVIwF wlhkg COXB_RAT : 70- 91: pnlvp SvsnkRiVGCiCEEDNctVIwF wlhqg E 5: 41.8526 6( 6) A-x(2,3)-G-x(4,5)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] Occurences: 6(6) COX4_YEAST : 51- 79: ligpg Ake-Gtvpt-DldqeTGLARlelLGkleGiD vfdtk COX5_DICDI : 74- 104: hsriv AcegGdgeehDilfhTVAEKkptICldcGqV fklkh COXB_BOVIN : 1- 29: Asg-Ggvpt-DeeqaTGLERevmLAarkGqD pynil COXB_HUMAN : 32- 60: amrsm Asg-Ggvpt-DeeqaTGLEReimLAakkGlD pynvl COXB_MOUSE : 31- 59: vtrsm Asg-Ggvpt-DeeqaTGLEReimIAaqkGlD pynml COXB_RAT : 20- 48: atrsm Asg-Ggvpt-DeeqaTGLEReimIAaqrGlD pynml F 6: 38.7745 6( 6) R-x-V-[AG]-C-x-[CG]-[EGS]-[DEP]-[ADG]-[EGN]-x(2)-[DTV]-[IV]-x-[FW] Occurences: 6(6) COX4_YEAST : 107- 123: syddy RyVGCtGSPAGshTImW lkptv COX5_DICDI : 71- 87: sifhs RiVACeGGDGEehDIlF htvae COXB_BOVIN : 56- 72: sitnk RiVGCiCEEDNstVIwF wlhkg COXB_HUMAN : 87- 103: sisnk RiVGCiCEEDNtsVVwF wlhkg COXB_MOUSE : 86- 102: sisnk RiVGCiCEEDNctVIwF wlhkg COXB_RAT : 75- 91: svsnk RiVGCiCEEDNctVIwF wlhqg G 7: 38.1825 10( 6) G-x(3,4)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] Occurences: 10(6) COX4_YEAST : 54- 79: pgake GtvptDldqeTGLARlelLGkleGiD vfdtk COX5_DICDI : 80- 104: ceggd Geeh-DilfhTVAEKkptICldcGqV fklkh COXB_BOVIN : 4- 29: asg GgvptDeeqaTGLERevmLAarkGqD pynil COXB_BOVIN : 5- 29: asgg Gvpt-DeeqaTGLERevmLAarkGqD pynil COXB_HUMAN : 35- 60: smasg GgvptDeeqaTGLEReimLAakkGlD pynvl COXB_HUMAN : 36- 60: masgg Gvpt-DeeqaTGLEReimLAakkGlD pynvl COXB_MOUSE : 34- 59: smasg GgvptDeeqaTGLEReimIAaqkGlD pynml COXB_MOUSE : 35- 59: masgg Gvpt-DeeqaTGLEReimIAaqkGlD pynml COXB_RAT : 23- 48: smasg GgvptDeeqaTGLEReimIAaqrGlD pynml COXB_RAT : 24- 48: masgg Gvpt-DeeqaTGLEReimIAaqrGlD pynml H 8: 38.1825 10( 6) G-x(4,5)-D-x(4)-T-[GV]-[AL]-[AE]-[KR]-x(3)-[IL]-[ACG]-x(3)-G-x-[DV] Occurences: 10(6) COX4_YEAST : 54- 79: pgake Gtvpt-DldqeTGLARlelLGkleGiD vfdtk COX5_DICDI : 78- 104: vaceg GdgeehDilfhTVAEKkptICldcGqV fklkh COXB_BOVIN : 3- 29: as GggvptDeeqaTGLERevmLAarkGqD pynil COXB_BOVIN : 4- 29: asg Ggvpt-DeeqaTGLERevmLAarkGqD pynil COXB_HUMAN : 34- 60: rsmas GggvptDeeqaTGLEReimLAakkGlD pynvl COXB_HUMAN : 35- 60: smasg Ggvpt-DeeqaTGLEReimLAakkGlD pynvl COXB_MOUSE : 33- 59: rsmas GggvptDeeqaTGLEReimIAaqkGlD pynml COXB_MOUSE : 34- 59: smasg Ggvpt-DeeqaTGLEReimIAaqkGlD pynml COXB_RAT : 22- 48: rsmas GggvptDeeqaTGLEReimIAaqrGlD pynml COXB_RAT : 23- 48: smasg Ggvpt-DeeqaTGLEReimIAaqrGlD pynml I 9: 30.8046 6( 6) C-x-[DENRS]-C-G-[AQST]-x-[FY]-K-L-x(3)-[GQS] Occurences: 6(6) COX4_YEAST : 134- 147: nevar CwECGSvYKLnpvG vpndd COX5_DICDI : 98- 111: kkpti ClDCGQvFKLkhiS segev COXB_BOVIN : 82- 95: geaqr CpSCGThYKLvphQ lah COXB_HUMAN : 113- 126: gqaqr CpRCGAhYKLvpqQ lah COXB_MOUSE : 112- 125: gesqr CpNCGThYKLvphQ mah COXB_RAT : 101- 114: gesqr CpNCGThYKLvpyQ mvh J 10: 29.9689 6( 6) L-x(2,4)-A-x(1,2)-G-T-x(2)-[DST]-[DP]-x(3)-[EP]-[ST]-[GIV] Occurences: 6(6) COX4_YEAST : 46- 65: ngpet LigpgAkeGTvpTDldqETG larle COX5_DICDI : 51- 67: fghev Ltg--Af-GTlkSPvivESI fhsri COXB_BOVIN : 34- 52: dpyni Lapk-AtsGTkeDPnlvPSI tnkri COXB_HUMAN : 65- 83: dpynv LapkgAs-GTreDPnlvPSI snkri COXB_MOUSE : 64- 82: dpynm LppkaAs-GTkeDPnlvPSI snkri COXB_MOUSE : 64- 82: dpynm Lppk-AasGTkeDPnlvPSI snkri COXB_RAT : 53- 71: dpynm LppkaAs-GTkeDPnlvPSV snkri COXB_RAT : 53- 71: dpynm Lppk-AasGTkeDPnlvPSV snkri K 11: 26.7935 8( 6) A-x(1,2)-G-T-x(1,3)-P-[NTV]-x-[LV]-[DEP]-[QS] Occurences: 8(6) COX4_YEAST : 51- 62: ligpg AkeGTv--PTdLDQ etgla COX5_DICDI : 54- 66: evltg Af-GTlksPViVES ifhsr COXB_BOVIN : 38- 51: ilapk AtsGTkedPNlVPS itnkr COXB_HUMAN : 70- 82: lapkg As-GTredPNlVPS isnkr COXB_MOUSE : 68- 81: mlppk AasGTkedPNlVPS isnkr COXB_MOUSE : 69- 81: lppka As-GTkedPNlVPS isnkr COXB_RAT : 57- 70: mlppk AasGTkedPNlVPS vsnkr COXB_RAT : 58- 70: lppka As-GTkedPNlVPS vsnkr L 12: 25.8317 6( 6) E-x(2,3)-G-x-E-x(2)-[IV]-x(3)-[AT]-x(2)-[EG]-x(2)-P Occurences: 6(6) COX4_YEAST : 39- 57: aqnla Evn-GpEtlIgpgAkeGtvP tdldq COX5_DICDI : 76- 95: rivac EggdGeEhdIlfhTvaEkkP ticld COXB_BOVIN : 11- 30: vptde EqatGlEreVmlaArkGqdP ynila COXB_HUMAN : 42- 61: vptde EqatGlEreImlaAkkGldP ynvla COXB_MOUSE : 41- 60: vptde EqatGlEreImiaAqkGldP ynmlp COXB_RAT : 30- 49: vptde EqatGlEreImiaAqrGldP ynmlp M 13: 24.7551 6( 6) C-G-[AQST]-x-[FY]-K-L-x(3)-[GQS] Occurences: 6(6) COX4_YEAST : 137- 147: arcwe CGSvYKLnpvG vpndd COX5_DICDI : 101- 111: ticld CGQvFKLkhiS segev COXB_BOVIN : 85- 95: qrcps CGThYKLvphQ lah COXB_HUMAN : 116- 126: qrcpr CGAhYKLvpqQ lah COXB_MOUSE : 115- 125: qrcpn CGThYKLvphQ mah COXB_RAT : 104- 114: qrcpn CGThYKLvpyQ mvh N 14: 24.3816 10( 6) G-x(1,2)-V-[LP]-T-[DG]-x(2)-[GQ]-[AET] Occurences: 10(6) COX4_YEAST : 54- 63: pgake Gt-VPTDldQE tglar COX5_DICDI : 47- 57: kredf GheVLTGafGT lkspv COXB_BOVIN : 3- 13: as GggVPTDeeQA tgler COXB_BOVIN : 4- 13: asg Gg-VPTDeeQA tgler COXB_HUMAN : 34- 44: rsmas GggVPTDeeQA tgler COXB_HUMAN : 35- 44: smasg Gg-VPTDeeQA tgler COXB_MOUSE : 33- 43: rsmas GggVPTDeeQA tgler COXB_MOUSE : 34- 43: smasg Gg-VPTDeeQA tgler COXB_RAT : 22- 32: rsmas GggVPTDeeQA tgler COXB_RAT : 23- 32: smasg Gg-VPTDeeQA tgler O 15: 20.5851 6( 6) G-[AQST]-x-[FY]-K-L-x(3)-[GQS] Occurences: 6(6) COX4_YEAST : 138- 147: rcwec GSvYKLnpvG vpndd COX5_DICDI : 102- 111: icldc GQvFKLkhiS segev COXB_BOVIN : 86- 95: rcpsc GThYKLvphQ lah COXB_HUMAN : 117- 126: rcprc GAhYKLvpqQ lah COXB_MOUSE : 116- 125: rcpnc GThYKLvphQ mah COXB_RAT : 105- 114: rcpnc GThYKLvpyQ mvh P 16: 19.9490 6( 6) G-x-[DEG]-V-x(1,2)-T-x(3)-[DGQ]-[AST] Occurences: 6(6) COX4_YEAST : 77- 88: lgkle GiDVfdTkplDS srkgt COX5_DICDI : 47- 57: kredf GhEVl-TgafGT lkspv COXB_BOVIN : 3- 13: as GgGVp-TdeeQA tgler COXB_HUMAN : 34- 44: rsmas GgGVp-TdeeQA tgler COXB_MOUSE : 33- 43: rsmas GgGVp-TdeeQA tgler COXB_RAT : 22- 32: rsmas GgGVp-TdeeQA tgler Q 17: 17.8503 7( 6) D-x(1,3)-E-x(0,2)-T-G-[AL] Occurences: 7(6) COX4_YEAST : 59- 66: gtvpt DldqE--TGL arlel COX4_YEAST : 61- 66: vptdl Dq--E--TGL arlel COX5_DICDI : 45- 54: nikre DfghEvlTGA fgtlk COXB_BOVIN : 9- 16: ggvpt De--EqaTGL erevm COXB_HUMAN : 40- 47: ggvpt De--EqaTGL ereim COXB_MOUSE : 39- 46: ggvpt De--EqaTGL ereim COXB_RAT : 28- 35: ggvpt De--EqaTGL ereim R 18: 17.4209 6( 6) I-x(2)-E-x(0,2)-D-x(3,4)-V-[GILV] Occurences: 6(6) COX4_YEAST : 98- 110: tmkdp IiiEsyDdyryVG ctgsp COX5_DICDI : 41- 51: fvrrn IkrE--DfgheVL tgafg COXB_BOVIN : 61- 70: rivgc IceE--Dnst-VI wfwlh COXB_HUMAN : 92- 101: rivgc IceE--Dnts-VV wfwlh COXB_MOUSE : 91- 100: rivgc IceE--Dnct-VI wfwlh COXB_RAT : 80- 89: rivgc IceE--Dnct-VI wfwlh S 19: 17.3810 6( 6) R-x-[PV]-x-C-x(0,1)-G-[AGST] Occurences: 6(6) COX4_YEAST : 107- 114: syddy RyVgCtGS pagsh COX5_DICDI : 71- 78: sifhs RiVaCeGG dgeeh COXB_BOVIN : 81- 87: kgeaq RcPsC-GT hyklv COXB_HUMAN : 112- 118: kgqaq RcPrC-GA hyklv COXB_MOUSE : 111- 117: kgesq RcPnC-GT hyklv COXB_RAT : 100- 106: qgesq RcPnC-GT hyklv T 20: 17.3570 6( 6) D-[EGQ]-E-x(4,5)-L-x(3)-[GIV] Occurences: 6(6) COX4_YEAST : 61- 73: vptdl DQEtglarLellG klegi COX5_DICDI : 79- 90: acegg DGEehdi-LfhtV aekkp COXB_BOVIN : 9- 20: ggvpt DEEqatg-LereV mlaar COXB_HUMAN : 40- 51: ggvpt DEEqatg-LereI mlaak COXB_MOUSE : 39- 50: ggvpt DEEqatg-LereI miaaq COXB_RAT : 28- 39: ggvpt DEEqatg-LereI miaaq Number of patterns evaluated by Pratt:731 Total running time: 1 seconds