------------------------------------------------------------ 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 RNA_POL_15KD 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 RNA_POL_15KD.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RPA9_YEAST 125 RPB9_DROME 129 RPB9_HUMAN 125 RPB9_YEAST 122 Pratt run started at Thu Feb 6 21:06:55 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.3503 4( 4) F-C-x(2)-C-x(3)-L-x(1,2)-P 2: 19.8503 4( 4) C-x(2)-C-x(0,1)-N-x(1,2)-M-x-Y 3: 19.3503 4( 4) E-x(2,3)-N-x(2)-L-x(3,5)-C-x(2)-C 4: 19.3503 4( 4) C-x(3,4)-Y-P-x(5)-N-x(0,2)-L 5: 18.8503 4( 4) E-N-x(2,4)-L-x(3,5)-C-x(2)-C 6: 15.6802 4( 4) T-L-x(1,2)-R-x(1,2)-D 7: 15.6802 4( 4) P-x(4,5)-E-x(0,1)-N-x(3)-L 8: 15.6802 4( 4) Y-P-x(5)-N-x(0,2)-L 9: 15.6802 4( 4) L-x(3,4)-D-x(1,2)-E-N 10: 15.6802 4( 4) C-x(0,1)-N-x(1,2)-M-x-Y 11: 15.6802 4( 4) C-x-N-x(0,2)-M-x-Y 12: 15.1802 4( 4) V-x(2,4)-F-x(0,1)-C-x(2)-C 13: 15.1802 4( 4) D-x(1,2)-E-N-x(2,4)-L 14: 15.1802 4( 4) D-x(2,3)-N-x(2,4)-L-x(5)-C 15: 15.1802 4( 4) E-x(0,2)-E-x(0,1)-N-x(3)-L 16: 15.1802 4( 4) P-x(4)-E-x(0,2)-N-x(2,3)-L 17: 14.6802 4( 4) C-x(0,2)-P-x-C-x(3,5)-E 18: 14.6802 4( 4) D-x(4)-K-x(0,2)-C-x(3,5)-E 19: 12.5102 4( 4) C-x(2)-C-x-Y 20: 12.5102 4( 4) L-x(2)-C-x(2)-C Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 53.1248 4( 4) D-x(2)-[CT]-x-K-x(0,2)-C-x(3,5)-E-[AEN]-[MV]-x-[FY]-x-[AST]-x-[QST]-x-R-x-[ADE]-[DET]-[AES]-x(4)-[FY]-x-[CT]-x-[ANST] B 2: 49.9349 4( 4) C-x(3,4)-Y-P-[KR]-[ES]-[DQ]-x-[ES]-N-x(0,2)-L-x(3)-[CT]-x-[NT]-[AC]-[DS]-x(4)-[AST]-[DGNS] C 3: 46.9344 4( 4) C-x-[DEQ]-C-x(0,1)-N-x(1,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] D 4: 46.3987 4( 4) F-C-x-[DE]-C-[GN]-[DN]-[LM]-L-x(1,2)-P-x-[AE]-[DV]-x-[EG]-[NS] E 5: 46.2648 4( 4) Y-P-[KR]-[ES]-[DQ]-x-[ES]-N-x(0,2)-L-x(3)-[CT]-x-[NT]-[AC]-[DS]-x(4)-[AST]-[DGNS] F 6: 45.3859 4( 4) L-x(3,4)-D-x(1,2)-E-N-x(2)-[AL]-[LV]-x-[AEG]-[CS]-[NR]-[NTV]-x-[CDS]-x(3)-[EK]-[AT]-x(2)-[NPS] G 7: 43.4439 4( 4) C-[GN]-N-x(0,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] H 8: 40.1708 4( 4) C-x(0,1)-N-x(1,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] I 9: 33.9654 4( 4) L-x(2)-C-x-[DNT]-C-[DGS]-x(3)-[EK]-[ANT]-[DGNP]-[NS]-[ANPS]-x-[ILV] J 10: 32.5777 4( 4) P-x(4,5)-E-x(0,1)-N-x(3)-L-x(3)-[RS]-[ANT]-[CD]-[DES]-x(2)-[EQT]-x(3)-[NST] K 11: 32.0777 4( 4) E-x(0,2)-E-x(0,1)-N-x(3)-L-x(3)-[RS]-[ANT]-[CD]-[DES]-x(2)-[EQT]-x(3)-[NST] L 12: 31.8142 4( 4) V-x(2,4)-F-x(0,1)-C-x-[DES]-C-[GNS]-x-[ILM]-[FL]-x-[NPS]-x-[ENQ] M 13: 29.5025 4( 4) C-x-[NST]-C-[DGS]-Y-x(2)-[EKR]-[AT]-[DGN]-[NS] N 14: 26.9136 4( 4) P-x(2)-[DG]-x-E-x(0,2)-N-x(2,3)-L-x(3)-[CS]-x-[DNT]-x-[DGS] O 15: 26.7774 4( 4) D-x(2,3)-N-x(2,4)-L-x-[AES]-[CN]-x-[ENT]-C-[DS] P 16: 25.2669 4( 4) D-x(1,2)-E-N-x(2,4)-L-x(2)-[ACN]-x(2)-C-[DS] Q 17: 25.1820 4( 4) E-x(2,3)-N-x(2)-L-x(3,5)-C-[RS]-[NQT]-C R 18: 24.6820 4( 4) E-N-x(2,4)-L-x(3,5)-C-[RS]-[NQT]-C S 19: 24.2075 4( 4) T-L-x(1,2)-R-x(1,2)-D-[EHR]-x-[AC]-[PQT] T 20: 18.2738 4( 4) C-x-[DEQ]-C-x(0,1)-N-x(1,2)-M Best patterns with alignements: fitness hits(seqs) Pattern A 1: 53.1248 4( 4) D-x(2)-[CT]-x-K-x(0,2)-C-x(3,5)-E-[AEN]-[MV]-x-[FY]-x-[AST]-x-[QST]-x-R-x-[ADE]-[DET]-[AES]-x(4)-[FY]-x-[CT]-x-[ANST] Occurences: 4(4) RPA9_YEAST : 78- 115: knelk DgaTiKekCpqcgnEEMnYhTlQlRsADEgatvFyTcT scgyk RPB9_DROME : 87- 120: lprte DhaCpK--Cshr--EAVfFkAqTrRaEEEmrlyYvCtN qncth RPB9_HUMAN : 83- 116: lprte DhpCqK--Cghk--EAVfFqShSaRaEDAmrlyYvCtA phcgh RPB9_YEAST : 72- 105: tlprs DreCpK--Chsr--ENVfFqSqQrRkDTSmvlfFvClS cshif B 2: 49.9349 4( 4) C-x(3,4)-Y-P-[KR]-[ES]-[DQ]-x-[ES]-N-x(0,2)-L-x(3)-[CT]-x-[NT]-[AC]-[DS]-x(4)-[AST]-[DGNS] Occurences: 4(4) RPA9_YEAST : 33- 59: vecsq Ckai-YPKSQfSN--LkvvTtTADdafpSS lrakk RPB9_DROME : 24- 53: rfcqe CnnmlYPKEDkENkiLlyaCrNCDykqkTN snciy RPB9_HUMAN : 20- 49: rfcqe CnnmlYPKEDkENriLlyaCrNCDyqqeAD nsciy RPB9_YEAST : 10- 39: rfcrd CnnmlYPREDkENnrLlfeCrTCSyveeAG splvy C 3: 46.9344 4( 4) C-x-[DEQ]-C-x(0,1)-N-x(1,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] Occurences: 4(4) RPA9_YEAST : 86- 114: tikek CpQCgNeeMnYhtlQlRSadeGaTVfyTC tscgy RPB9_DROME : 21- 47: vgirf CqEC-Nn-MlYpkeDkENkilLyACrnCD ykqkt RPB9_HUMAN : 17- 43: vgirf CqEC-Nn-MlYpkeDkENrilLyACrnCD yqqea RPB9_YEAST : 7- 33: ttfrf CrDC-Nn-MlYpreDkENnrlLfECrtCS yveea D 4: 46.3987 4( 4) F-C-x-[DE]-C-[GN]-[DN]-[LM]-L-x(1,2)-P-x-[AE]-[DV]-x-[EG]-[NS] Occurences: 4(4) RPA9_YEAST : 9- 26: vgsli FClDCGDLLenPnAVlGS nvecs RPB9_DROME : 20- 36: fvgir FCqECNNMLy-PkEDkEN killy RPB9_HUMAN : 16- 32: fvgir FCqECNNMLy-PkEDkEN rilly RPB9_YEAST : 6- 22: mttfr FCrDCNNMLy-PrEDkEN nrllf E 5: 46.2648 4( 4) Y-P-[KR]-[ES]-[DQ]-x-[ES]-N-x(0,2)-L-x(3)-[CT]-x-[NT]-[AC]-[DS]-x(4)-[AST]-[DGNS] Occurences: 4(4) RPA9_YEAST : 37- 59: qckai YPKSQfSN--LkvvTtTADdafpSS lrakk RPB9_DROME : 29- 53: cnnml YPKEDkENkiLlyaCrNCDykqkTN snciy RPB9_HUMAN : 25- 49: cnnml YPKEDkENriLlyaCrNCDyqqeAD nsciy RPB9_YEAST : 15- 39: cnnml YPREDkENnrLlfeCrTCSyveeAG splvy F 6: 45.3859 4( 4) L-x(3,4)-D-x(1,2)-E-N-x(2)-[AL]-[LV]-x-[AEG]-[CS]-[NR]-[NTV]-x-[CDS]-x(3)-[EK]-[AT]-x(2)-[NPS] Occurences: 4(4) RPA9_YEAST : 11- 38: slifc Ldcg-DllENpnAVlGSNVeCsqcKAiyP ksqfs RPB9_DROME : 28- 55: ecnnm LypkeDk-ENkiLLyACRNcDykqKTnsN ciyvn RPB9_HUMAN : 24- 51: ecnnm LypkeDk-ENriLLyACRNcDyqqEAdnS ciyvn RPB9_YEAST : 14- 41: dcnnm LypreDk-ENnrLLfECRTcSyveEAgsP lvyrh G 7: 43.4439 4( 4) C-[GN]-N-x(0,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] Occurences: 4(4) RPA9_YEAST : 89- 114: ekcpq CGNeeMnYhtlQlRSadeGaTVfyTC tscgy RPB9_DROME : 24- 47: rfcqe CNN--MlYpkeDkENkilLyACrnCD ykqkt RPB9_HUMAN : 20- 43: rfcqe CNN--MlYpkeDkENrilLyACrnCD yqqea RPB9_YEAST : 10- 33: rfcrd CNN--MlYpreDkENnrlLfECrtCS yveea H 8: 40.1708 4( 4) C-x(0,1)-N-x(1,2)-M-x-Y-x(3)-[DQ]-x-[ER]-[NS]-x(3)-[GL]-x-[AET]-[CV]-x(2)-[CT]-[CDS] Occurences: 4(4) RPA9_YEAST : 89- 114: ekcpq CgNeeMnYhtlQlRSadeGaTVfyTC tscgy RPB9_DROME : 24- 47: rfcqe C-Nn-MlYpkeDkENkilLyACrnCD ykqkt RPB9_HUMAN : 20- 43: rfcqe C-Nn-MlYpkeDkENrilLyACrnCD yqqea RPB9_YEAST : 10- 33: rfcrd C-Nn-MlYpreDkENnrlLfECrtCS yveea I 9: 33.9654 4( 4) L-x(2)-C-x-[DNT]-C-[DGS]-x(3)-[EK]-[ANT]-[DGNP]-[NS]-[ANPS]-x-[ILV] Occurences: 4(4) RPA9_YEAST : 7- 24: svvgs LifClDCGdllENPNAvL gsnve RPB9_DROME : 40- 57: enkil LyaCrNCDykqKTNSNcI yvnki RPB9_HUMAN : 36- 53: enril LyaCrNCDyqqEADNScI yvnki RPB9_YEAST : 26- 43: ennrl LfeCrTCSyveEAGSPlV yrhel J 10: 32.5777 4( 4) P-x(4,5)-E-x(0,1)-N-x(3)-L-x(3)-[RS]-[ANT]-[CD]-[DES]-x(2)-[EQT]-x(3)-[NST] Occurences: 4(4) RPA9_YEAST : 87- 113: ikekc PqcgneEmNyhtLqlrSADEgaTvfyT ctscg RPB9_DROME : 30- 54: nnmly Pkedk-E-NkilLyacRNCDykQktnS nciyv RPB9_HUMAN : 26- 50: nnmly Pkedk-E-NrilLyacRNCDyqQeadN sciyv RPB9_YEAST : 16- 40: nnmly Predk-E-NnrlLfecRTCSyvEeagS plvyr K 11: 32.0777 4( 4) E-x(0,2)-E-x(0,1)-N-x(3)-L-x(3)-[RS]-[ANT]-[CD]-[DES]-x(2)-[EQT]-x(3)-[NST] Occurences: 4(4) RPA9_YEAST : 92- 113: pqcgn E--EmNyhtLqlrSADEgaTvfyT ctscg RPB9_DROME : 32- 54: mlypk EdkE-NkilLyacRNCDykQktnS nciyv RPB9_HUMAN : 28- 50: mlypk EdkE-NrilLyacRNCDyqQeadN sciyv RPB9_YEAST : 18- 40: mlypr EdkE-NnrlLfecRTCSyvEeagS plvyr L 12: 31.8142 4( 4) V-x(2,4)-F-x(0,1)-C-x-[DES]-C-[GNS]-x-[ILM]-[FL]-x-[NPS]-x-[ENQ] Occurences: 4(4) RPA9_YEAST : 4- 21: msv VgsliF-ClDCGdLLeNpN avlgs RPB9_DROME : 16- 32: egpgf Vgir-F-CqECNnMLyPkE dkenk RPB9_HUMAN : 12- 28: yepgf Vgir-F-CqECNnMLyPkE dkenr RPB9_YEAST : 98- 114: kdtsm Vlf--FvClSCShIFtSdQ knkrt M 13: 29.5025 4( 4) C-x-[NST]-C-[DGS]-Y-x(2)-[EKR]-[AT]-[DGN]-[NS] Occurences: 4(4) RPA9_YEAST : 114- 125: tvfyt CtSCGYkfRTNN RPB9_DROME : 43- 54: illya CrNCDYkqKTNS nciyv RPB9_HUMAN : 39- 50: illya CrNCDYqqEADN sciyv RPB9_YEAST : 29- 40: rllfe CrTCSYveEAGS plvyr N 14: 26.9136 4( 4) P-x(2)-[DG]-x-E-x(0,2)-N-x(2,3)-L-x(3)-[CS]-x-[DNT]-x-[DGS] Occurences: 4(4) RPA9_YEAST : 87- 107: ikekc PqcGnEemNyhtLqlrSaDeG atvfy RPB9_DROME : 30- 47: nnmly PkeDkE--Nki-LlyaCrNcD ykqkt RPB9_HUMAN : 26- 43: nnmly PkeDkE--Nri-LlyaCrNcD yqqea RPB9_YEAST : 16- 33: nnmly PreDkE--Nnr-LlfeCrTcS yveea O 15: 26.7774 4( 4) D-x(2,3)-N-x(2,4)-L-x-[AES]-[CN]-x-[ENT]-C-[DS] Occurences: 4(4) RPA9_YEAST : 15- 31: cldcg DlleNpnavLgSNvECS qckai RPB9_DROME : 33- 47: lypke Dke-Nkil-LyACrNCD ykqkt RPB9_HUMAN : 29- 43: lypke Dke-Nril-LyACrNCD yqqea RPB9_YEAST : 19- 33: lypre DkenNrl--LfECrTCS yveea RPB9_YEAST : 19- 33: lypre Dke-Nnrl-LfECrTCS yveea P 16: 25.2669 4( 4) D-x(1,2)-E-N-x(2,4)-L-x(2)-[ACN]-x(2)-C-[DS] Occurences: 4(4) RPA9_YEAST : 15- 31: cldcg DllENpnavLgsNveCS qckai RPB9_DROME : 33- 47: lypke Dk-ENkil-LyaCrnCD ykqkt RPB9_HUMAN : 29- 43: lypke Dk-ENril-LyaCrnCD yqqea RPB9_YEAST : 19- 33: lypre Dk-ENnrl-LfeCrtCS yveea Q 17: 25.1820 4( 4) E-x(2,3)-N-x(2)-L-x(3,5)-C-[RS]-[NQT]-C Occurences: 4(4) RPA9_YEAST : 18- 33: cgdll Enp-NavLgsnveCSQC kaiyp RPB9_DROME : 32- 46: mlypk EdkeNkiLlya--CRNC dykqk RPB9_HUMAN : 28- 42: mlypk EdkeNriLlya--CRNC dyqqe RPB9_YEAST : 18- 32: mlypr EdkeNnrLlfe--CRTC syvee R 18: 24.6820 4( 4) E-N-x(2,4)-L-x(3,5)-C-[RS]-[NQT]-C Occurences: 4(4) RPA9_YEAST : 18- 33: cgdll ENpnavLgsnveCSQC kaiyp RPB9_DROME : 35- 46: pkedk ENki--Llya--CRNC dykqk RPB9_HUMAN : 31- 42: pkedk ENri--Llya--CRNC dyqqe RPB9_YEAST : 21- 32: predk ENnr--Llfe--CRTC syvee S 19: 24.2075 4( 4) T-L-x(1,2)-R-x(1,2)-D-[EHR]-x-[AC]-[PQT] Occurences: 4(4) RPA9_YEAST : 98- 109: emnyh TLqlRsaDEgAT vfytc RPB9_DROME : 81- 91: visdp TLp-RteDHaCP kcshr RPB9_HUMAN : 77- 87: vsqdp TLp-RteDHpCQ kcghk RPB9_YEAST : 67- 76: igsdp TLp-Rs-DReCP kchsr T 20: 18.2738 4( 4) C-x-[DEQ]-C-x(0,1)-N-x(1,2)-M Occurences: 4(4) RPA9_YEAST : 86- 94: tikek CpQCgNeeM nyhtl RPB9_DROME : 21- 27: vgirf CqEC-Nn-M lypke RPB9_HUMAN : 17- 23: vgirf CqEC-Nn-M lypke RPB9_YEAST : 7- 13: ttfrf CrDC-Nn-M lypre Number of patterns evaluated by Pratt:824 Total running time: 1 seconds