------------------------------------------------------------ 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_L46E 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_L46E.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL39_RAT 50 RL46_HALMA 49 RL46_SULSO 50 RL46_YEAST 50 Pratt run started at Thu Feb 6 21:06:01 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.1904 5( 4) K-x(3,4)-K-x(3,4)-K-x(4)-N-x(3)-P-x-W-x(4)-T 2: 25.0203 4( 4) N-x(2)-R-R-x-W-R-R 3: 24.5203 4( 4) R-x(3,4)-R-R-x-W-R-R 4: 20.8503 4( 4) R-R-x-W-R-R 5: 20.8503 4( 4) K-x(4)-N-x(3)-P-x-W-x(4)-T 6: 16.6802 4( 4) R-x-W-R-R 7: 16.6802 4( 4) N-x(3)-P-x-W-x(4)-T 8: 15.1802 4( 4) R-x(1,2)-P-x(1,3)-W-x(4)-T 9: 14.6802 4( 4) N-x(3)-R-x(1,3)-W-x(3,5)-K 10: 14.6802 5( 4) K-x(4)-K-x(0,2)-K-x(0,2)-R 11: 14.6802 5( 4) K-x(2,4)-K-x(2)-K-x(0,2)-R 12: 12.5102 4( 4) W-R-R 13: 12.5102 5( 4) R-x(3)-R-R 14: 12.5102 4( 4) P-x-W-x(4)-T 15: 12.0102 4( 4) R-x(0,1)-N-x-K 16: 12.0102 4( 4) R-x(3)-R-x(2,3)-K 17: 12.0102 5( 4) S-x(2,3)-K-x(4)-K 18: 11.5102 5( 4) N-x(1,2)-R-x(2,3)-W 19: 11.5102 5( 4) K-x(1,2)-R-x(2,3)-K 20: 11.5102 5( 4) K-x(4)-K-x(2,4)-N Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 86.7628 5( 4) K-x(3,4)-K-x(3,4)-K-x(3)-[QR]-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] B 2: 86.1589 4( 4) K-x(2)-[LM]-[AG]-K-x(2,4)-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] C 3: 79.4227 4( 4) K-x(3)-[QR]-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] D 4: 72.0818 4( 4) N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] E 5: 62.0306 4( 4) P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] F 6: 61.4181 4( 4) R-x(1,2)-P-x(1,3)-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] G 7: 28.2146 4( 4) N-x(2)-R-R-x-W-R-R-[NT] H 8: 27.7146 4( 4) R-x(3,4)-R-R-x-W-R-R-[NT] I 9: 24.0446 4( 4) R-R-x-W-R-R-[NT] J 10: 23.5446 4( 4) N-x(1,2)-R-x(2)-W-R-R-[NT] K 11: 19.8745 4( 4) R-x-W-R-R-[NT] L 12: 17.8994 4( 4) N-x(2)-[RS]-R-x(1,3)-W-x(3,5)-K M 13: 17.2891 5( 4) K-x(3)-[AGT]-K-x(0,2)-K-x(0,2)-R N 14: 15.7045 4( 4) W-R-R-[NT] O 15: 14.6881 4( 4) S-x(2,3)-K-x(3)-[AGI]-K P 16: 14.6802 5( 4) K-x(2,4)-K-x(2)-K-x(0,2)-R Q 17: 14.6017 4( 4) R-[ENR]-x(2)-R-x(2,3)-K R 18: 12.5102 5( 4) R-x(3)-R-R S 19: 12.0102 4( 4) R-x(0,1)-N-x-K T 20: 11.5102 5( 4) N-x(1,2)-R-x(2,3)-W Best patterns with alignements: fitness hits(seqs) Pattern A 1: 86.7628 5( 4) K-x(3,4)-K-x(3,4)-K-x(3)-[QR]-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 5(4) RL39_RAT : 4- 46: ssh KtfriKrflaKkqkQNRpIPQWIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 3- 45: gk KskatKkrlaKldnQNSrVPAWVmLKTDreVQrNhkRRhWRRN dtde RL46_HALMA : 5- 45: gkks Katk-Krla-KldnQNSrVPAWVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 4- 46: skh KslgkKlrlgKalkRNSpIPAWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 4- 46: aaq KsfriKqkmaKakkQNRpLPQWIrLRTNntIRyNakRRnWRRT kmni B 2: 86.1589 4( 4) K-x(2)-[LM]-[AG]-K-x(2,4)-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 9- 46: ktfri KrfLAKkqkqNRpIPQWIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 8- 45: kskat KkrLAKldnqNSrVPAWVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 9- 46: kslgk KlrLGKalkrNSpIPAWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 9- 46: ksfri KqkMAKakkqNRpLPQWIrLRTNntIRyNakRRnWRRT kmni C 3: 79.4227 4( 4) K-x(3)-[QR]-N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 14- 46: krfla KkqkQNRpIPQWIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 13- 45: kkrla KldnQNSrVPAWVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 14- 46: klrlg KalkRNSpIPAWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 14- 46: kqkma KakkQNRpLPQWIrLRTNntIRyNakRRnWRRT kmni D 4: 72.0818 4( 4) N-[RS]-x-[ILV]-P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 19- 46: kkqkq NRpIPQWIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 18- 45: kldnq NSrVPAWVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 19- 46: kalkr NSpIPAWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 19- 46: kakkq NRpLPQWIrLRTNntIRyNakRRnWRRT kmni E 5: 62.0306 4( 4) P-[AQ]-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 23- 46: qnrpi PQWIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 22- 45: qnsrv PAWVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 23- 46: rnspi PAWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 23- 46: qnrpl PQWIrLRTNntIRyNakRRnWRRT kmni F 6: 61.4181 4( 4) R-x(1,2)-P-x(1,3)-W-[IV]-x-[ILM]-[KR]-T-[DGNQ]-x(2)-[IV]-[QR]-x-N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 20- 46: kqkqn RpiPq--WIrMKTGnkIRyNskRRhWRRT klgl RL46_HALMA : 20- 45: dnqns Rv-Pa--WVmLKTDreVQrNhkRRhWRRN dtde RL46_SULSO : 18- 46: gkalk RnsPipaWViIKTQaeIRfNplRRnWRRN nlkv RL46_YEAST : 20- 46: akkqn RplPq--WIrLRTNntIRyNakRRnWRRT kmni G 7: 28.2146 4( 4) N-x(2)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 37- 46: nkiry NskRRhWRRT klgl RL46_HALMA : 36- 45: revqr NhkRRhWRRN dtde RL46_SULSO : 37- 46: aeirf NplRRnWRRN nlkv RL46_YEAST : 37- 46: ntiry NakRRnWRRT kmni H 8: 27.7146 4( 4) R-x(3,4)-R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 35- 46: tgnki RynskRRhWRRT klgl RL46_HALMA : 35- 45: drevq Rnhk-RRhWRRN dtde RL46_SULSO : 35- 46: tqaei RfnplRRnWRRN nlkv RL46_YEAST : 35- 46: tnnti RynakRRnWRRT kmni I 9: 24.0446 4( 4) R-R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 40- 46: rynsk RRhWRRT klgl RL46_HALMA : 39- 45: qrnhk RRhWRRN dtde RL46_SULSO : 40- 46: rfnpl RRnWRRN nlkv RL46_YEAST : 40- 46: rynak RRnWRRT kmni J 10: 23.5446 4( 4) N-x(1,2)-R-x(2)-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 37- 46: nkiry NskRrhWRRT klgl RL46_HALMA : 36- 45: revqr NhkRrhWRRN dtde RL46_SULSO : 37- 46: aeirf NplRrnWRRN nlkv RL46_YEAST : 37- 46: ntiry NakRrnWRRT kmni K 11: 19.8745 4( 4) R-x-W-R-R-[NT] Occurences: 4(4) RL39_RAT : 41- 46: ynskr RhWRRT klgl RL46_HALMA : 40- 45: rnhkr RhWRRN dtde RL46_SULSO : 41- 46: fnplr RnWRRN nlkv RL46_YEAST : 41- 46: ynakr RnWRRT kmni L 12: 17.8994 4( 4) N-x(2)-[RS]-R-x(1,3)-W-x(3,5)-K Occurences: 4(4) RL39_RAT : 37- 47: nkiry NskRRh--Wrrt--K lgl RL46_HALMA : 16- 28: lakld NqnSRvpaWvml--K tdrev RL46_SULSO : 37- 49: aeirf NplRRn--WrrnnlK v RL46_YEAST : 37- 47: ntiry NakRRn--Wrrt--K mni M 13: 17.2891 5( 4) K-x(3)-[AGT]-K-x(0,2)-K-x(0,2)-R Occurences: 5(4) RL39_RAT : 9- 20: ktfri KrflAKkqKqnR pipqw RL46_HALMA : 3- 10: gk KskaTK--K--R lakld RL46_SULSO : 9- 18: kslgk KlrlGKalK--R nspip RL46_YEAST : 9- 20: ksfri KqkmAKakKqnR plpqw RL46_YEAST : 11- 20: frikq KmakAK--KqnR plpqw N 14: 15.7045 4( 4) W-R-R-[NT] Occurences: 4(4) RL39_RAT : 43- 46: skrrh WRRT klgl RL46_HALMA : 42- 45: hkrrh WRRN dtde RL46_SULSO : 43- 46: plrrn WRRN nlkv RL46_YEAST : 43- 46: akrrn WRRT kmni O 15: 14.6881 4( 4) S-x(2,3)-K-x(3)-[AGI]-K Occurences: 4(4) RL39_RAT : 1- 9: Ssh-KtfrIK rflak RL46_HALMA : 4- 13: gkk SkatKkrlAK ldnqn RL46_SULSO : 5- 14: skhk SlgkKlrlGK alkrn RL46_YEAST : 5- 14: aaqk SfriKqkmAK akkqn P 16: 14.6802 5( 4) K-x(2,4)-K-x(2)-K-x(0,2)-R Occurences: 5(4) RL39_RAT : 9- 20: ktfri KrflaKkqKqnR pipqw RL46_HALMA : 2- 10: g Kks--KatKk-R lakld RL46_SULSO : 9- 18: kslgk KlrlgKalK--R nspip RL46_YEAST : 9- 20: ksfri KqkmaKakKqnR plpqw RL46_YEAST : 11- 20: frikq Kma--KakKqnR plpqw Q 17: 14.6017 4( 4) R-[ENR]-x(2)-R-x(2,3)-K Occurences: 4(4) RL39_RAT : 40- 47: rynsk RRhwRrt-K lgl RL46_HALMA : 31- 38: mlktd REvqRnh-K rrhwr RL46_SULSO : 41- 49: fnplr RNwrRnnlK v RL46_YEAST : 40- 47: rynak RRnwRrt-K mni R 18: 12.5102 5( 4) R-x(3)-R-R Occurences: 5(4) RL39_RAT : 40- 45: rynsk RrhwRR tklgl RL46_HALMA : 35- 40: drevq RnhkRR hwrrn RL46_HALMA : 39- 44: qrnhk RrhwRR ndtde RL46_SULSO : 40- 45: rfnpl RrnwRR nnlkv RL46_YEAST : 40- 45: rynak RrnwRR tkmni S 19: 12.0102 4( 4) R-x(0,1)-N-x-K Occurences: 4(4) RL39_RAT : 35- 39: tgnki RyNsK rrhwr RL46_HALMA : 35- 38: drevq R-NhK rrhwr RL46_SULSO : 45- 49: rrnwr RnNlK v RL46_YEAST : 35- 39: tnnti RyNaK rrnwr T 20: 11.5102 5( 4) N-x(1,2)-R-x(2,3)-W Occurences: 5(4) RL39_RAT : 37- 43: nkiry NskRrh-W rrtkl RL46_HALMA : 18- 24: kldnq Ns-RvpaW vmlkt RL46_HALMA : 36- 42: revqr NhkRrh-W rrndt RL46_SULSO : 37- 43: aeirf NplRrn-W rrnnl RL46_YEAST : 37- 43: ntiry NakRrn-W rrtkm Number of patterns evaluated by Pratt:242 Total running time: 0 seconds