------------------------------------------------------------ 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 RIBOSOMAL_L30E_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 RIBOSOMAL_L30E_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: RL30_HUMAN 114 RL30_LEIMA 104 RL3E_KLULA 104 RL3E_METVA 105 RL3E_SULAC 104 RL3E_THECE 101 RL3E_YEAST 104 YBXF_BACSU 82 Pratt run started at Thu Feb 6 21:05:56 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.5102 8( 8) L-G-x(3)-G 2: 11.5102 8( 8) G-x(1,2)-V-x(0,1)-G 3: 11.5102 9( 8) K-x-G-x(0,2)-K 4: 11.5102 10( 8) L-x(4)-G-x(2,4)-V 5: 11.0102 10( 8) K-x(1,2)-G-x(0,2)-K 6: 11.0102 12( 8) S-x(3,4)-L-x(0,2)-G 7: 11.0102 8( 8) D-x(1,3)-D-x(0,1)-I 8: 11.0102 10( 8) G-x(1,2)-K-x(1,3)-V 9: 10.5102 13( 8) V-x(3,5)-K-x(3,5)-K 10: 10.5102 19( 8) L-x(2,4)-G-x(0,2)-K 11: 10.5102 12( 8) V-x(0,2)-L-x(0,2)-G 12: 10.5102 11( 8) K-x(3,5)-K-x(2,4)-K 13: 8.3401 12( 8) G-x(2)-V 14: 8.3401 19( 8) G-K 15: 8.3401 11( 8) G-x(3)-G 16: 8.3401 14( 8) K-L 17: 8.3401 11( 8) G-x-S 18: 8.3401 13( 8) S-x(4)-L 19: 8.3401 12( 8) L-x(4)-V 20: 8.3401 13( 8) K-x(5)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 28.5379 8( 8) L-G-x-[AIL]-x-G-x(4)-[ATV]-[ACGS]-[ATV]-[ILV]-x-[IV] B 2: 26.2247 8( 8) K-x-G-x(0,2)-K-x(2)-[ILV]-[GIV]-x(2)-[DNQST]-x(4)-[ILV]-x-[DEQS]-[DGS] C 3: 25.7247 8( 8) K-x(1,2)-G-x(0,2)-K-x(2)-[ILV]-[GIV]-x(2)-[DNQST]-x(4)-[ILV]-x-[DEQS]-[DGS] D 4: 23.5120 8( 8) G-x-[AILV]-x-G-x(4)-[ASTV]-[ACGS]-[ATV]-[ILV]-x-[IV] E 5: 17.7323 10( 8) G-K-x(3)-[GIV]-x(3)-[ACST]-[AILV]-x(2)-[AILV] F 6: 17.2968 8( 8) L-[GV]-x(3)-G-x(2,4)-V-x-[AGV] G 7: 13.5958 9( 8) G-x(1,2)-K-x(1,3)-V-x(4)-[NQR] H 8: 12.7509 8( 8) K-x(3,5)-K-x(2,4)-K-x-[GILV] I 9: 12.4422 8( 8) L-x(4)-V-x(3)-[DEQST]-x(2)-[GNST] J 10: 11.5102 8( 8) G-x(1,2)-V-x(0,1)-G K 11: 11.0102 12( 8) S-x(3,4)-L-x(0,2)-G L 12: 11.0102 8( 8) D-x(1,3)-D-x(0,1)-I M 13: 10.9463 11( 8) K-x-[GST]-x(3)-L N 14: 10.7348 10( 8) G-x-S-x(2)-[ILMV] O 15: 10.5961 10( 8) S-x(4)-L-[AEGQ] P 16: 10.5102 13( 8) V-x(3,5)-K-x(3,5)-K Q 17: 10.5102 19( 8) L-x(2,4)-G-x(0,2)-K R 18: 10.5102 12( 8) V-x(0,2)-L-x(0,2)-G S 19: 10.2489 10( 8) K-L-[AGILV] T 20: 8.3401 12( 8) G-x(2)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 28.5379 8( 8) L-G-x-[AIL]-x-G-x(4)-[ATV]-[ACGS]-[ATV]-[ILV]-x-[IV] Occurences: 8(8) RL30_HUMAN : 80- 95: gnnie LGtAcGkyyrVCTLaI idpgd RL30_LEIMA : 79- 94: gnnld LGtAcGkpfrTCVLsV tnvgd RL3E_KLULA : 76- 91: ggnne LGtAvGklfrVGVVtI ldagd RL3E_METVA : 76- 91: vtsie LGaIcGkpfpVSALlV lepgn RL3E_SULAC : 72- 87: gsgye LGtLcGkpfmVSVIgI vdege RL3E_THECE : 71- 86: gtsve LGtLlGrphtVSALaV vdpge RL3E_YEAST : 76- 91: ggnne LGtAvGklfrVGVVsI leagd YBXF_BACSU : 65- 80: esmkk LGkAcGievgAAAVaI il B 2: 26.2247 8( 8) K-x-G-x(0,2)-K-x(2)-[ILV]-[GIV]-x(2)-[DNQST]-x(4)-[ILV]-x-[DEQS]-[DGS] Occurences: 8(8) RL30_HUMAN : 22- 40: lqlvm KsG--KyvLGykQtlkmIrQG kaklv RL30_LEIMA : 21- 39: lqlvm KsG--KyvLGtqQalttLrQG rsklv RL3E_KLULA : 18- 36: lalvv KsG--KysLGykStvksLrQG kakli RL3E_METVA : 34- 54: aikni KhGegKlvIIagNcakdVkED ifyyt RL3E_SULAC : 30- 50: tlkll KtGkvKgvVVssTlrqdLkDD imtfs RL3E_THECE : 29- 49: siqya KmGgaKliIVarNarpdIkED ieyya RL3E_YEAST : 18- 36: lalvi KsG--KytLGykStvksLrQG kskli YBXF_BACSU : 24- 44: tvkal KrGsvKevVVakDadpiLtSS vvsla C 3: 25.7247 8( 8) K-x(1,2)-G-x(0,2)-K-x(2)-[ILV]-[GIV]-x(2)-[DNQST]-x(4)-[ILV]-x-[DEQS]-[DGS] Occurences: 8(8) RL30_HUMAN : 22- 40: lqlvm Ks-G--KyvLGykQtlkmIrQG kaklv RL30_LEIMA : 21- 39: lqlvm Ks-G--KyvLGtqQalttLrQG rsklv RL3E_KLULA : 18- 36: lalvv Ks-G--KysLGykStvksLrQG kakli RL3E_METVA : 34- 54: aikni Kh-GegKlvIIagNcakdVkED ifyyt RL3E_SULAC : 30- 50: tlkll Kt-GkvKgvVVssTlrqdLkDD imtfs RL3E_THECE : 29- 49: siqya KmgGa-KliIVarNarpdIkED ieyya RL3E_THECE : 29- 49: siqya Km-GgaKliIVarNarpdIkED ieyya RL3E_YEAST : 18- 36: lalvi Ks-G--KytLGykStvksLrQG kskli YBXF_BACSU : 24- 44: tvkal Kr-GsvKevVVakDadpiLtSS vvsla D 4: 23.5120 8( 8) G-x-[AILV]-x-G-x(4)-[ASTV]-[ACGS]-[ATV]-[ILV]-x-[IV] Occurences: 8(8) RL30_HUMAN : 81- 95: nniel GtAcGkyyrVCTLaI idpgd RL30_LEIMA : 80- 94: nnldl GtAcGkpfrTCVLsV tnvgd RL3E_KLULA : 77- 91: gnnel GtAvGklfrVGVVtI ldagd RL3E_METVA : 77- 91: tsiel GaIcGkpfpVSALlV lepgn RL3E_SULAC : 73- 87: sgyel GtLcGkpfmVSVIgI vdege RL3E_THECE : 72- 86: tsvel GtLlGrphtVSALaV vdpge RL3E_YEAST : 77- 91: gnnel GtAvGklfrVGVVsI leagd YBXF_BACSU : 66- 80: smkkl GkAcGievgAAAVaI il E 5: 17.7323 10( 8) G-K-x(3)-[GIV]-x(3)-[ACST]-[AILV]-x(2)-[AILV] Occurences: 10(8) RL30_HUMAN : 24- 37: lvmks GKyvlGykqTLkmI rqgka RL30_LEIMA : 23- 36: lvmks GKyvlGtqqALttL rqgrs RL3E_KLULA : 20- 33: lvvks GKyslGyksTVksL rqgka RL3E_KLULA : 81- 94: lgtav GKlfrVgvvTIldA gdsdi RL3E_METVA : 38- 51: ikhge GKlviIagnCAkdV kedif RL3E_SULAC : 16- 29: tllrs GKvilGtrkTLklL ktgkv RL3E_THECE : 15- 28: kaqdt GKivmGarkSIqyA kmgga RL3E_YEAST : 20- 33: lviks GKytlGyksTVksL rqgks RL3E_YEAST : 81- 94: lgtav GKlfrVgvvSIleA gdsdi YBXF_BACSU : 66- 79: smkkl GKacgIevgAAavA iil F 6: 17.2968 8( 8) L-[GV]-x(3)-G-x(2,4)-V-x-[AGV] Occurences: 8(8) RL30_HUMAN : 19- 29: nsrlq LVmksGky--VlG ykqtl RL30_LEIMA : 18- 28: naklq LVmksGky--VlG tqqal RL3E_KLULA : 76- 88: ggnne LGtavGklfrVgV vtild RL3E_METVA : 76- 88: vtsie LGaicGkpfpVsA llvle RL3E_SULAC : 72- 84: gsgye LGtlcGkpfmVsV igivd RL3E_THECE : 71- 83: gtsve LGtllGrphtVsA lavvd RL3E_YEAST : 76- 88: ggnne LGtavGklfrVgV vsile YBXF_BACSU : 65- 75: esmkk LGkacGie--VgA aavai G 7: 13.5958 9( 8) G-x(1,2)-K-x(1,3)-V-x(4)-[NQR] Occurences: 9(8) RL30_HUMAN : 40- 50: kmirq GkaKl--VilanN cpalr RL30_LEIMA : 39- 49: ttlrq GrsKl--VvianN cppir RL3E_KLULA : 25- 35: gkysl Gy-Kst-VkslrQ gkakl RL3E_METVA : 36- 46: knikh GegKl--ViiagN cakdv RL3E_SULAC : 32- 44: kllkt GkvKgvvVsstlR qdlkd RL3E_THECE : 31- 43: qyakm GgaKliiVarnaR pdike RL3E_THECE : 32- 43: yakmg Ga-KliiVarnaR pdike RL3E_YEAST : 25- 35: gkytl Gy-Kst-VkslrQ gkskl YBXF_BACSU : 15- 25: ksiii Gt-Kqt-VkalkR gsvke H 8: 12.7509 8( 8) K-x(3,5)-K-x(2,4)-K-x-[GILV] Occurences: 8(8) RL30_HUMAN : 25- 37: vmksg KyvlgyKqtl-KmI rqgka RL30_LEIMA : 15- 26: ntina KlqlvmKsg--KyV lgtqq RL3E_KLULA : 21- 33: vvksg KyslgyKstv-KsL rqgka RL3E_METVA : 27- 36: vvlgt Kqai--Kni--KhG egklv RL3E_SULAC : 24- 37: ilgtr KtlkllKtgkvKgV vvsst RL3E_THECE : 23- 36: vmgar KsiqyaKmggaKlI ivarn RL3E_YEAST : 21- 33: viksg KytlgyKstv-KsL rqgks YBXF_BACSU : 17- 26: iiigt Kqtv--Kal--KrG svkev I 9: 12.4422 8( 8) L-x(4)-V-x(3)-[DEQST]-x(2)-[GNST] Occurences: 8(8) RL30_HUMAN : 65- 77: eyyam LaktgVhhySgnN ielgt RL30_LEIMA : 92- 104: frtcv LsvtnVgdsDiaT RL3E_KLULA : 61- 73: eyyam LsktkVyyfQggN nelgt RL3E_METVA : 61- 73: fyytk LsetpVythQvtS ielga RL3E_SULAC : 13- 25: elktl LrsgkVilgTrkT lkllk RL3E_THECE : 56- 68: eyyar LsgipVyefEgtS velgt RL3E_YEAST : 61- 73: eyyam LsktkVyyfQggN nelgt YBXF_BACSU : 41- 53: dadpi LtssvVslaEdqG isvsm J 10: 11.5102 8( 8) G-x(1,2)-V-x(0,1)-G Occurences: 8(8) RL30_HUMAN : 24- 29: lvmks GkyVlG ykqtl RL30_LEIMA : 23- 28: lvmks GkyVlG tqqal RL3E_KLULA : 77- 81: gnnel GtaV-G klfrv RL3E_METVA : 20- 25: vavdt GnvVlG tkqai RL3E_SULAC : 32- 36: kllkt Gk-VkG vvvss RL3E_THECE : 15- 20: kaqdt GkiVmG arksi RL3E_YEAST : 77- 81: gnnel GtaV-G klfrv YBXF_BACSU : 70- 74: lgkac GieV-G aaava K 11: 11.0102 12( 8) S-x(3,4)-L-x(0,2)-G Occurences: 12(8) RL30_HUMAN : 23- 29: qlvmk SgkyvL--G ykqtl RL30_LEIMA : 22- 28: qlvmk SgkyvL--G tqqal RL30_LEIMA : 73- 80: pihhy Sgnn-LdlG tacgk RL3E_KLULA : 19- 25: alvvk SgkysL--G ykstv RL3E_KLULA : 28- 36: slgyk StvksLrqG kakli RL3E_METVA : 87- 95: kpfpv SallvLepG nsail RL3E_SULAC : 15- 21: ktllr SgkviL--G trktl RL3E_SULAC : 68- 73: ylykg Sgye-L--G tlcgk RL3E_THECE : 92- 98: vdpge SrilaL--G gke RL3E_THECE : 92- 99: vdpge SrilaLg-G ke RL3E_YEAST : 19- 25: alvik SgkytL--G ykstv RL3E_YEAST : 28- 36: tlgyk StvksLrqG kskli YBXF_BACSU : 61- 66: vsmve Smkk-L--G kacgi L 12: 11.0102 8( 8) D-x(1,3)-D-x(0,1)-I Occurences: 8(8) RL30_HUMAN : 100- 103: iidpg Ds--D-I irsmp RL30_HUMAN : 100- 104: iidpg Ds--DiI rsmpe RL30_LEIMA : 99- 102: vtnvg Ds--D-I at RL3E_KLULA : 96- 99: ildag Ds--D-I ltala RL3E_METVA : 50- 55: gncak DvkeD-I fyytk RL3E_SULAC : 46- 51: stlrq DlkdD-I mtfsk RL3E_SULAC : 46- 51: stlrq Dlk-DdI mtfsk RL3E_THECE : 45- 50: rnarp DikeD-I eyyar RL3E_YEAST : 96- 99: ileag Ds--D-I lttla YBXF_BACSU : 36- 40: vvvak Da--DpI ltssv M 13: 10.9463 11( 8) K-x-[GST]-x(3)-L Occurences: 11(8) RL30_HUMAN : 4- 10: vaa KkTkksL esins RL30_HUMAN : 22- 28: lqlvm KsGkyvL gykqt RL30_LEIMA : 21- 27: lqlvm KsGkyvL gtqqa RL3E_KLULA : 18- 24: lalvv KsGkysL gykst RL3E_KLULA : 27- 33: yslgy KsTvksL rqgka RL3E_METVA : 34- 40: aikni KhGegkL viiag RL3E_SULAC : 66- 72: piyly KgSgyeL gtlcg RL3E_THECE : 29- 35: siqya KmGgakL iivar RL3E_YEAST : 18- 24: lalvi KsGkytL gykst RL3E_YEAST : 27- 33: ytlgy KsTvksL rqgks YBXF_BACSU : 17- 23: iiigt KqTvkaL krgsv N 14: 10.7348 10( 8) G-x-S-x(2)-[ILMV] Occurences: 10(8) RL30_HUMAN : 99- 104: aiidp GdSdiI rsmpe RL30_LEIMA : 39- 44: ttlrq GrSklV viann RL3E_KLULA : 95- 100: tilda GdSdiL tala RL3E_METVA : 95- 100: lvlep GnSaiL ninne RL3E_SULAC : 91- 96: givde GeSkiL efike RL3E_THECE : 66- 71: vyefe GtSveL gtllg RL3E_THECE : 90- 95: avvdp GeSriL alggk RL3E_YEAST : 36- 41: kslrq GkSklI iiaan RL3E_YEAST : 95- 100: silea GdSdiL ttla YBXF_BACSU : 53- 58: laedq GiSvsM vesmk O 15: 10.5961 10( 8) S-x(4)-L-[AEGQ] Occurences: 10(8) RL30_HUMAN : 12- 18: kksle SinsrLQ lvmks RL30_HUMAN : 23- 29: qlvmk SgkyvLG ykqtl RL30_LEIMA : 22- 28: qlvmk SgkyvLG tqqal RL3E_KLULA : 19- 25: alvvk SgkysLG ykstv RL3E_METVA : 87- 93: kpfpv SallvLE pgnsa RL3E_SULAC : 15- 21: ktllr SgkviLG trktl RL3E_THECE : 92- 98: vdpge SrilaLG gke RL3E_YEAST : 8- 14: vksqe SinqkLA lviks RL3E_YEAST : 19- 25: alvik SgkytLG ykstv YBXF_BACSU : 43- 49: dpilt SsvvsLA edqgi P 16: 10.5102 13( 8) V-x(3,5)-K-x(3,5)-K Occurences: 13(8) RL30_HUMAN : 20- 31: srlql Vmksg-KyvlgyK qtlkm RL30_HUMAN : 27- 35: ksgky Vlgy--Kqtl--K mirqg RL30_LEIMA : 9- 21: ktksk VntinaKlqlvmK sgkyv RL3E_KLULA : 16- 27: qklal Vvksg-KyslgyK stvks RL3E_KLULA : 17- 27: klalv Vksg--KyslgyK stvks RL3E_METVA : 22- 31: vdtgn Vvlgt-Kqai--K nikhg RL3E_METVA : 23- 31: dtgnv Vlgt--Kqai--K nikhg RL3E_SULAC : 18- 30: lrsgk VilgtrKtlkllK tgkvk RL3E_SULAC : 88- 100: svigi VdegesKilefiK evkq RL3E_THECE : 18- 29: dtgki Vmgar-KsiqyaK mggak RL3E_YEAST : 16- 27: qklal Viksg-KytlgyK stvks YBXF_BACSU : 20- 29: gtkqt Vkal--Krgsv-K evvva YBXF_BACSU : 59- 67: isvsm Vesm--Kklg--K acgie Q 17: 10.5102 19( 8) L-x(2,4)-G-x(0,2)-K Occurences: 19(8) RL30_HUMAN : 19- 25: nsrlq LvmksG--K yvlgy RL30_HUMAN : 80- 86: gnnie LgtacG--K yyrvc RL30_LEIMA : 18- 24: naklq LvmksG--K yvlgt RL30_LEIMA : 36- 42: qaltt Lrq--GrsK lvvia RL30_LEIMA : 79- 85: gnnld LgtacG--K pfrtc RL3E_KLULA : 15- 21: nqkla LvvksG--K yslgy RL3E_KLULA : 33- 37: stvks Lrq--G--K aklii RL3E_KLULA : 33- 39: stvks Lrq--GkaK liiia RL3E_KLULA : 76- 82: ggnne LgtavG--K lfrvg RL3E_METVA : 76- 82: vtsie LgaicG--K pfpvs RL3E_SULAC : 12- 17: gelkt Llrs-G--K vilgt RL3E_SULAC : 13- 17: elktl Lrs--G--K vilgt RL3E_SULAC : 28- 33: rktlk Llkt-G--K vkgvv RL3E_SULAC : 28- 35: rktlk Llkt-GkvK gvvvs RL3E_SULAC : 29- 33: ktlkl Lkt--G--K vkgvv RL3E_SULAC : 29- 35: ktlkl Lkt--GkvK gvvvs RL3E_SULAC : 72- 78: gsgye LgtlcG--K pfmvs RL3E_THECE : 95- 100: gesri Lalg-G--K e RL3E_THECE : 95- 100: gesri Lal--Gg-K e RL3E_YEAST : 15- 21: nqkla LviksG--K ytlgy RL3E_YEAST : 33- 37: stvks Lrq--G--K sklii RL3E_YEAST : 33- 39: stvks Lrq--GksK liiia RL3E_YEAST : 76- 82: ggnne LgtavG--K lfrvg YBXF_BACSU : 23- 29: qtvka Lkr--GsvK evvva R 18: 10.5102 12( 8) V-x(0,2)-L-x(0,2)-G Occurences: 12(8) RL30_HUMAN : 27- 29: ksgky V--L--G ykqtl RL30_LEIMA : 26- 28: ksgky V--L--G tqqal RL3E_KLULA : 30- 36: gykst VksLrqG kakli RL3E_KLULA : 89- 95: frvgv VtiLdaG dsdil RL3E_METVA : 22- 25: vdtgn Vv-L--G tkqai RL3E_METVA : 23- 25: dtgnv V--L--G tkqai RL3E_METVA : 91- 95: vsall V--LepG nsail RL3E_SULAC : 18- 21: lrsgk Vi-L--G trktl RL3E_THECE : 69- 72: fegts Ve-L--G tllgr RL3E_YEAST : 30- 36: gykst VksLrqG kskli RL3E_YEAST : 89- 95: frvgv VsiLeaG dsdil YBXF_BACSU : 20- 26: gtkqt VkaLkrG svkev S 19: 10.2489 10( 8) K-L-[AGILV] Occurences: 10(8) RL30_HUMAN : 43- 45: rqgka KLV ilann RL30_LEIMA : 42- 44: rqgrs KLV viann RL3E_KLULA : 12- 14: eninq KLA lvvks RL3E_KLULA : 39- 41: rqgka KLI iiaan RL3E_METVA : 39- 41: khgeg KLV iiagn RL3E_SULAC : 27- 29: trktl KLL ktgkv RL3E_THECE : 34- 36: kmgga KLI ivarn RL3E_YEAST : 12- 14: esinq KLA lviks RL3E_YEAST : 39- 41: rqgks KLI iiaan YBXF_BACSU : 64- 66: vesmk KLG kacgi T 20: 8.3401 12( 8) G-x(2)-V Occurences: 12(8) RL30_HUMAN : 24- 27: lvmks GkyV lgykq RL30_LEIMA : 23- 26: lvmks GkyV lgtqq RL3E_KLULA : 77- 80: gnnel GtaV gklfr RL3E_METVA : 20- 23: vavdt GnvV lgtkq RL3E_METVA : 38- 41: ikhge GklV iiagn RL3E_SULAC : 36- 39: tgkvk GvvV sstlr RL3E_THECE : 15- 18: kaqdt GkiV mgark RL3E_THECE : 58- 61: yarls GipV yefeg RL3E_THECE : 66- 69: vyefe GtsV elgtl RL3E_YEAST : 77- 80: gnnel GtaV gklfr YBXF_BACSU : 53- 56: laedq GisV smves YBXF_BACSU : 70- 73: lgkac GieV gaaav Number of patterns evaluated by Pratt:261 Total running time: 1 seconds