------------------------------------------------------------ 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 4 sequences from file RIBOSOMAL_L31E PATTERN CONSERVATION: CM: min Nr of Seqs to Match 4 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_L31E.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL31_CHLRE 116 RL31_HUMAN 125 RL34_HALMA 91 RL34_YEAST 112 Pratt run started at Thu Feb 6 21:05:57 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.6904 5( 4) D-x(0,1)-V-R-x(5)-N-x-A-x-W-x(2)-G 2: 23.5203 4( 4) A-x(2)-E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R 3: 23.5203 4( 4) P-x(1,3)-A-x(2)-E-x(2,3)-K-x-A-x(3)-M 4: 20.8503 4( 4) K-x(5)-A-x(2)-E-x(4)-A-x(5)-T 5: 20.8503 4( 4) R-x(5)-N-x-A-x-W-x(2)-G 6: 20.3503 4( 4) K-x(4)-A-x(2,3)-E-x(4)-A-x(5)-T 7: 19.8503 4( 4) A-x(0,2)-A-x(2)-E-x(4)-A-x(5)-T 8: 19.8503 4( 4) A-x(1,2)-A-x(4,5)-K-x-A-x(3)-M 9: 19.3503 4( 4) R-x(2)-T-x(2,4)-K-x(0,1)-R-x(5)-F 10: 19.3503 4( 4) E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R 11: 19.3503 5( 4) A-x(0,2)-E-x(2,3)-K-x-A-x(3)-M 12: 19.3503 4( 4) A-x(4,5)-K-x-A-x(3)-M-x(3,5)-R 13: 18.8503 4( 4) H-x(4)-K-x(0,2)-A-x(5)-E-x(2,4)-A 14: 16.6802 4( 4) A-x(2)-E-x(4)-A-x(5)-T 15: 16.6802 4( 4) N-x-A-x-W-x(2)-G 16: 16.6802 4( 4) V-R-L-x(4)-N 17: 16.1802 4( 4) A-x(4)-K-x(0,1)-I-x(3)-A 18: 15.6802 6( 4) R-x-R-x(2,4)-R-x(5)-E 19: 15.6802 4( 4) E-x(3,4)-A-x(5)-T-x(3,4)-R 20: 15.6802 4( 4) P-x(3,4)-E-x(3,4)-A-x(5)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 105.3745 5( 4) D-x(0,1)-V-R-[IL]-[AD]-[PTV]-x-[IL]-N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] B 2: 97.5344 4( 4) R-[IL]-[AD]-[PTV]-x-[IL]-N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] C 3: 80.9627 4( 4) N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] D 4: 56.6963 4( 4) R-[AE]-x-T-x(2,4)-K-x(0,1)-R-[ILV]-[HR]-x-[ATV]-x-F-[EK]-[EK]-x-[AG]-[EP]-x-[AI]-[LV]-[EK]-[AE] E 5: 55.0215 4( 4) P-x(3,4)-E-x(3,4)-A-x(4)-[GN]-T-[DPS]-[DS]-x(3)-[ADV]-x(2)-[AL]-[NR]-x-[AE]-x(3)-[EKR]-[AG]-[IV]-x-[EGN]-[AV]-[EP] F 6: 54.2314 4( 4) A-[NP]-x-[AP]-x-K-x(0,1)-I-[KR]-x(2)-A-x(4)-[EG]-[ET]-[DGPS]-[DE]-[AV]-x-[ILV]-[ADE]-[APTV]-[EKR]-x-[AN] G 7: 51.6678 4( 4) P-x(1,3)-A-x(2)-E-x(2,3)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] H 8: 47.9978 4( 4) A-x(1,2)-A-x(4,5)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] I 9: 47.4978 5( 4) A-x(0,2)-E-x(2,3)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] J 10: 46.4352 4( 4) H-x(2)-[AGS]-x-K-x(0,2)-A-x(2)-[AL]-[ILV]-[KR]-E-x(2,4)-A-x(4)-[GV]-[DT]-[DEPS]-D-[AV] K 11: 44.6363 4( 4) E-x(3,4)-A-x(4)-[GN]-T-x(3,4)-R-[ILV]-x-[APTV]-x(4)-[AE]-x(4)-[GI]-[IV]-[EKR]-[AGN]-x-[EPT]-x-[ER] L 12: 38.0407 4( 4) K-x(2)-[PV]-[KR]-A-x(2,3)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] M 13: 36.8734 6( 4) R-x-R-x(2,4)-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] N 14: 35.2976 4( 4) K-x(2)-[AV]-x(2)-A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] O 15: 31.1118 4( 4) A-x(0,2)-A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] P 16: 28.9902 4( 4) V-R-L-[ADS]-x(3)-N-x-[AD]-x(4)-[GN]-x(3)-[TV] Q 17: 27.9417 4( 4) A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] R 18: 23.5203 4( 4) A-x(2)-E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R S 19: 19.3503 4( 4) E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R T 20: 19.3503 4( 4) A-x(4,5)-K-x-A-x(3)-M-x(3,5)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 105.3745 5( 4) D-x(0,1)-V-R-[IL]-[AD]-[PTV]-x-[IL]-N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] Occurences: 5(4) RL31_CHLRE : 52- 95: vmgts D-VRLDVkLNkAVWsKGikNVPtRLRIvISRrRNDDEDakEemyS fvtva RL31_HUMAN : 61- 104: emgtp D-VRIDTrLNkAVWaKGirNVPyRIRVrLSRkRNEDEDspNklyT lvtyv RL34_HALMA : 46- 90: fsvde DaVRLDPsINeAAWaRGraNTPsKIRVrAARfEEEGEAivEaetA e RL34_YEAST : 46- 90: lhmgt DdVRLAPeLNqAIWkRGvkGVEyRLRLrISRkRNEEEDakNplfS yvepv RL34_YEAST : 47- 90: hmgtd D-VRLAPeLNqAIWkRGvkGVEyRLRLrISRkRNEEEDakNplfS yvepv B 2: 97.5344 4( 4) R-[IL]-[AD]-[PTV]-x-[IL]-N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] Occurences: 4(4) RL31_CHLRE : 54- 95: gtsdv RLDVkLNkAVWsKGikNVPtRLRIvISRrRNDDEDakEemyS fvtva RL31_HUMAN : 63- 104: gtpdv RIDTrLNkAVWaKGirNVPyRIRVrLSRkRNEDEDspNklyT lvtyv RL34_HALMA : 49- 90: dedav RLDPsINeAAWaRGraNTPsKIRVrAARfEEEGEAivEaetA e RL34_YEAST : 49- 90: gtddv RLAPeLNqAIWkRGvkGVEyRLRLrISRkRNEEEDakNplfS yvepv C 3: 80.9627 4( 4) N-x-A-[AIV]-W-x-[KR]-G-x(2)-[GN]-[TV]-[EP]-x-[KR]-[IL]-R-[ILV]-x-[AIL]-[AS]-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] Occurences: 4(4) RL31_CHLRE : 60- 95: ldvkl NkAVWsKGikNVPtRLRIvISRrRNDDEDakEemyS fvtva RL31_HUMAN : 69- 104: idtrl NkAVWaKGirNVPyRIRVrLSRkRNEDEDspNklyT lvtyv RL34_HALMA : 55- 90: ldpsi NeAAWaRGraNTPsKIRVrAARfEEEGEAivEaetA e RL34_YEAST : 55- 90: lapel NqAIWkRGvkGVEyRLRLrISRkRNEEEDakNplfS yvepv D 4: 56.6963 4( 4) R-[AE]-x-T-x(2,4)-K-x(0,1)-R-[ILV]-[HR]-x-[ATV]-x-F-[EK]-[EK]-x-[AG]-[EP]-x-[AI]-[LV]-[EK]-[AE] Occurences: 4(4) RL31_CHLRE : 14- 39: keqvt REyTihlsK-RLHkTsFKKcAPkAVKE irkfa RL31_HUMAN : 23- 48: nevvt REyTinihK-RIHgVgFKKrAPrALKE irkfa RL34_HALMA : 63- 87: awarg RAnTps--KiRVRaArFEEeGEaIVEA etae RL34_YEAST : 9- 34: kdvvt REyTinlhK-RLHgVsFKKrAPrAVKE ikkfa E 5: 55.0215 4( 4) P-x(3,4)-E-x(3,4)-A-x(4)-[GN]-T-[DPS]-[DS]-x(3)-[ADV]-x(2)-[AL]-[NR]-x-[AE]-x(3)-[EKR]-[AG]-[IV]-x-[EGN]-[AV]-[EP] Occurences: 4(4) RL31_CHLRE : 34- 72: fkkca PkavkEirkfAskvmGTSDvrlDvkLNkAvwsKGIkNVP trlri RL31_HUMAN : 43- 81: fkkra PralkEirkfAmkemGTPDvriDtrLNkAvwaKGIrNVP yrirv RL34_HALMA : 52- 88: avrld Psin-Eaaw-ArgraNTPSkirVraARfEeegEAIvEAE tae RL34_YEAST : 29- 67: fkkra PravkEikkfAklhmGTDDvrlApeLNqAiwkRGVkGVE yrlrl F 6: 54.2314 4( 4) A-[NP]-x-[AP]-x-K-x(0,1)-I-[KR]-x(2)-A-x(4)-[EG]-[ET]-[DGPS]-[DE]-[AV]-x-[ILV]-[ADE]-[APTV]-[EKR]-x-[AN] Occurences: 4(4) RL31_CHLRE : 33- 60: sfkkc APkAvKeIRkfAskvmGTSDVrLDVKlN kavws RL31_HUMAN : 42- 69: gfkkr APrAlKeIRkfAmkemGTPDVrIDTRlN kavwa RL34_HALMA : 64- 90: wargr ANtPsK-IRvrAarfeEEGEAiVEAEtA e RL34_YEAST : 28- 55: sfkkr APrAvKeIKkfAklhmGTDDVrLAPElN qaiwk G 7: 51.6678 4( 4) P-x(1,3)-A-x(2)-E-x(2,3)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] Occurences: 4(4) RL31_CHLRE : 34- 62: fkkca Pk--AvkEir-KfAskvMGtsDvRLDvKLNkA vwskg RL31_HUMAN : 43- 71: fkkra Pr--AlkEir-KfAmkeMGtpDvRIDtRLNkA vwakg RL34_HALMA : 13- 44: rvvti PlrdAraEpnhKrAdkaMIliReHLAkHFSvD edavr RL34_YEAST : 29- 57: fkkra Pr--AvkEik-KfAklhMGtdDvRLApELNqA iwkrg H 8: 47.9978 4( 4) A-x(1,2)-A-x(4,5)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] Occurences: 4(4) RL31_CHLRE : 33- 62: sfkkc ApkAvkeirKfAskvMGtsDvRLDvKLNkA vwskg RL31_HUMAN : 42- 71: gfkkr AprAlkeirKfAmkeMGtpDvRIDtRLNkA vwakg RL34_HALMA : 17- 44: iplrd Ar-Aepnh-KrAdkaMIliReHLAkHFSvD edavr RL34_YEAST : 28- 57: sfkkr AprAvkeikKfAklhMGtdDvRLApELNqA iwkrg I 9: 47.4978 5( 4) A-x(0,2)-E-x(2,3)-K-x-A-x(3)-M-[GI]-x(2)-[DR]-x-[HR]-[IL]-[AD]-x-[EHKR]-[FL]-[NS]-x-[AD] Occurences: 5(4) RL31_CHLRE : 36- 62: kcapk AvkEir-KfAskvMGtsDvRLDvKLNkA vwskg RL31_HUMAN : 45- 71: krapr AlkEir-KfAmkeMGtpDvRIDtRLNkA vwakg RL34_HALMA : 17- 44: iplrd AraEpnhKrAdkaMIliReHLAkHFSvD edavr RL34_HALMA : 19- 44: lrdar A--EpnhKrAdkaMIliReHLAkHFSvD edavr RL34_YEAST : 31- 57: krapr AvkEik-KfAklhMGtdDvRLApELNqA iwkrg J 10: 46.4352 4( 4) H-x(2)-[AGS]-x-K-x(0,2)-A-x(2)-[AL]-[ILV]-[KR]-E-x(2,4)-A-x(4)-[GV]-[DT]-[DEPS]-D-[AV] Occurences: 4(4) RL31_CHLRE : 25- 53: lskrl HktSfKkcApkAVKEirkfAskvmGTSDV rldvk RL31_HUMAN : 34- 62: ihkri HgvGfKkrAprALKEirkfAmkemGTPDV ridtr RL34_HALMA : 23- 47: raepn HkrAdK--AmiLIREhl--AkhfsVDEDA vrldp RL34_YEAST : 20- 48: lhkrl HgvSfKkrAprAVKEikkfAklhmGTDDV rlape K 11: 44.6363 4( 4) E-x(3,4)-A-x(4)-[GN]-T-x(3,4)-R-[ILV]-x-[APTV]-x(4)-[AE]-x(4)-[GI]-[IV]-[EKR]-[AGN]-x-[EPT]-x-[ER] Occurences: 4(4) RL31_CHLRE : 39- 74: pkavk EirkfAskvmGTsdv-RLdVklnkAvwskGIKNvPtR lrivi RL31_HUMAN : 48- 83: pralk EirkfAmkemGTpdv-RIdTrlnkAvwakGIRNvPyR irvrl RL34_HALMA : 56- 91: dpsin Eaaw-ArgraNTpskiRVrAarfeEegeaIVEAeTaE RL34_YEAST : 34- 69: pravk EikkfAklhmGTddv-RLaPelnqAiwkrGVKGvEyR lrlri L 12: 38.0407 4( 4) K-x(2)-[PV]-[KR]-A-x(2,3)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] Occurences: 4(4) RL31_CHLRE : 31- 52: ktsfk KcaPKAvk-EiRkfAskvmGTSD vrldv RL31_HUMAN : 40- 61: gvgfk KraPRAlk-EiRkfAmkemGTPD vridt RL34_HALMA : 69- 91: antps KirVRAarfEeEgeAiveaETAE RL34_YEAST : 26- 47: gvsfk KraPRAvk-EiKkfAklhmGTDD vrlap M 13: 36.8734 6( 4) R-x-R-x(2,4)-R-x-[ER]-[EN]-[DE]-[DEG]-E-[AD]-x(2)-[EN]-x(3)-[AST] Occurences: 6(4) RL31_CHLRE : 74- 95: knvpt RlRivisRrRNDDEDakEemyS fvtva RL31_HUMAN : 83- 104: rnvpy RiRvrlsRkRNEDEDspNklyT lvtyv RL31_HUMAN : 85- 104: vpyri RvRls--RkRNEDEDspNklyT lvtyv RL34_HALMA : 71- 90: tpski RvRaa--RfEEEGEAivEaetA e RL34_YEAST : 69- 90: kgvey RlRlrisRkRNEEEDakNplfS yvepv RL34_YEAST : 71- 90: veyrl RlRis--RkRNEEEDakNplfS yvepv N 14: 35.2976 4( 4) K-x(2)-[AV]-x(2)-A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] Occurences: 4(4) RL31_CHLRE : 30- 52: hktsf KkcApkAvkEiRkfAskvmGTSD vrldv RL31_HUMAN : 39- 61: hgvgf KkrAprAlkEiRkfAmkemGTPD vridt RL34_HALMA : 69- 91: antps KirVraArfEeEgeAiveaETAE RL34_YEAST : 25- 47: hgvsf KkrAprAvkEiKkfAklhmGTDD vrlap O 15: 31.1118 4( 4) A-x(0,2)-A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] Occurences: 4(4) RL31_CHLRE : 33- 52: sfkkc ApkAvkEiRkfAskvmGTSD vrldv RL31_HUMAN : 42- 61: gfkkr AprAlkEiRkfAmkemGTPD vridt RL34_HALMA : 74- 91: kirvr A--ArfEeEgeAiveaETAE RL34_YEAST : 28- 47: sfkkr AprAvkEiKkfAklhmGTDD vrlap P 16: 28.9902 4( 4) V-R-L-[ADS]-x(3)-N-x-[AD]-x(4)-[GN]-x(3)-[TV] Occurences: 4(4) RL31_CHLRE : 53- 71: mgtsd VRLDvklNkAvwskGiknV ptrlr RL31_HUMAN : 86- 104: pyrir VRLSrkrNeDedspNklyT lvtyv RL34_HALMA : 48- 66: vdeda VRLDpsiNeAawarGranT pskir RL34_YEAST : 48- 66: mgtdd VRLApelNqAiwkrGvkgV eyrlr Q 17: 27.9417 4( 4) A-x(2)-E-x-[EKR]-x(2)-A-x(4)-[EG]-T-[ADPS]-[DE] Occurences: 4(4) RL31_CHLRE : 36- 52: kcapk AvkEiRkfAskvmGTSD vrldv RL31_HUMAN : 45- 61: krapr AlkEiRkfAmkemGTPD vridt RL34_HALMA : 75- 91: irvra ArfEeEgeAiveaETAE RL34_YEAST : 31- 47: krapr AvkEiKkfAklhmGTDD vrlap R 18: 23.5203 4( 4) A-x(2)-E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R Occurences: 4(4) RL31_CHLRE : 36- 54: kcapk AvkEir-KfAskvMgtsdvR ldvkl RL31_HUMAN : 45- 63: krapr AlkEir-KfAmkeMgtpdvR idtrl RL34_HALMA : 17- 34: iplrd AraEpnhKrAdkaMili--R ehlak RL34_YEAST : 31- 49: krapr AvkEik-KfAklhMgtddvR lapel S 19: 19.3503 4( 4) E-x(2,3)-K-x-A-x(3)-M-x(3,5)-R Occurences: 4(4) RL31_CHLRE : 39- 54: pkavk Eir-KfAskvMgtsdvR ldvkl RL31_HUMAN : 48- 63: pralk Eir-KfAmkeMgtpdvR idtrl RL34_HALMA : 20- 34: rdara EpnhKrAdkaMili--R ehlak RL34_YEAST : 34- 49: pravk Eik-KfAklhMgtddvR lapel T 20: 19.3503 4( 4) A-x(4,5)-K-x-A-x(3)-M-x(3,5)-R Occurences: 4(4) RL31_CHLRE : 36- 54: kcapk AvkeirKfAskvMgtsdvR ldvkl RL31_HUMAN : 45- 63: krapr AlkeirKfAmkeMgtpdvR idtrl RL34_HALMA : 19- 34: lrdar Aepnh-KrAdkaMili--R ehlak RL34_YEAST : 31- 49: krapr AvkeikKfAklhMgtddvR lapel Number of patterns evaluated by Pratt:944 Total running time: 1 seconds