------------------------------------------------------------ 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 5 sequences from file SPASE_II PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 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 SPASE_II.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: LSPA_ECOLI 164 LSPA_ENTAE 165 LSPA_HAEIN 171 LSPA_PSEFL 170 LSPA_STAAU 163 Pratt run started at Thu Feb 6 21:14:35 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 41.7005 5( 5) L-x(3)-G-A-L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 2: 41.2005 5( 5) L-x(2)-G-x(0,1)-A-L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 3: 41.2005 6( 5) L-x(2,3)-G-A-L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 4: 39.7005 6( 5) A-x(2)-L-x(2,4)-A-x(0,2)-L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 5: 37.5305 5( 5) G-A-L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 6: 29.1904 5( 5) L-x-N-x(2)-D-R-x(3)-G-x-V-x-D 7: 29.1904 5( 5) A-x(2)-N-x(2)-D-R-x(3)-G-x-V-x-D 8: 25.0203 5( 5) N-x(2)-D-R-x(3)-G-x-V-x-D 9: 24.5203 5( 5) F-N-x-A-D-x(5)-G-x(2,3)-L 10: 20.8503 5( 5) D-R-x(3)-G-x-V-x-D 11: 20.8503 5( 5) N-x-G-A-A-x(3)-L 12: 20.3503 5( 5) N-x-A-D-x(5)-G-x(2,3)-L 13: 20.3503 6( 5) N-x(0,1)-G-A-A-x(3)-L 14: 19.8503 5( 5) G-x(2)-F-x(1,2)-F-x(1,2)-A-D 15: 19.8503 5( 5) F-x(2,3)-D-x(2)-I-x(3)-A-x(3,4)-L 16: 19.8503 5( 5) L-x(5)-V-x(0,1)-I-x(0,1)-D-x(3)-K 17: 19.3503 5( 5) A-x-S-x(0,1)-L-x(0,2)-A-x(3)-G 18: 16.6802 5( 5) R-x(3)-G-x-V-x-D 19: 16.6802 7( 5) G-A-A-x(3)-L 20: 16.1802 5( 5) L-x(0,1)-I-x(2)-A-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 77.2049 5( 5) N-x-G-A-A-[FW]-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] B 2: 76.7049 6( 5) N-x(0,1)-G-A-A-[FW]-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] C 3: 69.6038 5( 5) G-A-A-x-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] D 4: 68.6775 5( 5) L-[ILV]-[FIL]-[AG]-G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] E 5: 64.9543 5( 5) L-[FIV]-[AIL]-G-x(0,1)-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] F 6: 61.3252 5( 5) A-x-[AS]-L-x(2,4)-A-x(0,2)-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] G 7: 60.3773 5( 5) L-x-[ALV]-[LV]-x(2)-V-x(0,1)-I-x(0,1)-D-x-[GLV]-[ST]-K-x(2)-[FIV]-x-[GQT]-x-[FLM]-x-[ILM]-x-[DEQ]-[QST]-[FIV]-x-[LV]-[FIL]-P H 8: 59.6461 6( 5) L-x(2,3)-G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] I 9: 58.0786 5( 5) G-x-[AD]-F-x(1,2)-F-x(1,2)-A-D-x-[GS]-[GL]-x(4)-[FIL]-[FL]-[AI]-[GILV]-[IL]-A-[ILV]-[AGLV]-x-[CDS]-[AGTV] J 10: 55.9761 5( 5) G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] K 11: 51.8060 5( 5) A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] L 12: 47.6360 5( 5) L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] M 13: 45.0357 5( 5) F-N-[FIL]-A-D-x-[AS]-[IL]-[CT]-[IV]-G-x(2,3)-L-[AILV]-[ILV] N 14: 40.8656 5( 5) N-[FIL]-A-D-x-[AS]-[IL]-[CT]-[IV]-G-x(2,3)-L-[AILV]-[ILV] O 15: 40.2958 5( 5) N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] P 16: 33.2486 5( 5) D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Q 17: 29.0786 5( 5) R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] R 18: 28.9594 5( 5) F-x(2,3)-D-x-[AP]-I-x(2)-[GI]-A-x(3,4)-L-[DET] S 19: 26.3442 5( 5) L-x(0,1)-I-[AGI]-[GIL]-A-L-[AGLV]-x(3)-[ADS] T 20: 25.7610 5( 5) A-[FI]-S-x(0,1)-L-x(0,2)-A-[DG]-x(2)-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 77.2049 5( 5) N-x-G-A-A-[FW]-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] Occurences: 5(5) LSPA_ECOLI : 53- 84: lhyar NyGAAFSFLADsgGWqrwFfAGIAIGISvILA vmmyr LSPA_ENTAE : 53- 84: lhyar NyGAAFSFLADsgGWqrwFfAGIAVGICvVLA vlmyr LSPA_HAEIN : 50- 81: ltyvr NyGAAFSFLADhsGWqqyFfILLALAISgMLV yflak LSPA_PSEFL : 55- 86: wtlay NtGAAFSFLADggGWqrwLfAVIAVVVSaVLV vwlkr LSPA_STAAU : 52- 83: itshr NnGAAWGILSGkmTFffiItIIILIALVyFFI kdaqy B 2: 76.7049 6( 5) N-x(0,1)-G-A-A-[FW]-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] Occurences: 6(5) LSPA_ECOLI : 53- 84: lhyar NyGAAFSFLADsgGWqrwFfAGIAIGISvILA vmmyr LSPA_ENTAE : 53- 84: lhyar NyGAAFSFLADsgGWqrwFfAGIAVGICvVLA vlmyr LSPA_HAEIN : 50- 81: ltyvr NyGAAFSFLADhsGWqqyFfILLALAISgMLV yflak LSPA_PSEFL : 55- 86: wtlay NtGAAFSFLADggGWqrwLfAVIAVVVSaVLV vwlkr LSPA_STAAU : 52- 83: itshr NnGAAWGILSGkmTFffiItIIILIALVyFFI kdaqy LSPA_STAAU : 53- 83: tshrn N-GAAWGILSGkmTFffiItIIILIALVyFFI kdaqy C 3: 69.6038 5( 5) G-A-A-x-[GS]-[FI]-L-[AS]-[DG]-x(2)-[GT]-[FW]-x(3)-[FIL]-x-[AI]-[GILV]-[IL]-[AL]-[ILV]-[AGV]-[ILV]-[CSV]-x-[FIMV]-[FL]-[AIV] Occurences: 5(5) LSPA_ECOLI : 55- 84: yarny GAAfSFLADsgGWqrwFfAGIAIGISvILA vmmyr LSPA_ENTAE : 55- 84: yarny GAAfSFLADsgGWqrwFfAGIAVGICvVLA vlmyr LSPA_HAEIN : 52- 81: yvrny GAAfSFLADhsGWqqyFfILLALAISgMLV yflak LSPA_PSEFL : 57- 86: laynt GAAfSFLADggGWqrwLfAVIAVVVSaVLV vwlkr LSPA_STAAU : 54- 83: shrnn GAAwGILSGkmTFffiItIIILIALVyFFI kdaqy D 4: 68.6775 5( 5) L-[ILV]-[FIL]-[AG]-G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 103- 125: niaya LIIGGALGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 103- 125: niaya LIIGGALGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 100- 122: nsaya LIIGGALANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 105- 127: aiala LVLGGALGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 98- 120: qvais LLFAGALGNFiDRIltGeVVDFI dtnif E 5: 64.9543 5( 5) L-[FIV]-[AIL]-G-x(0,1)-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 103- 125: niaya LIIGgALGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 103- 125: niaya LIIGgALGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 100- 122: nsaya LIIGgALANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 105- 127: aiala LVLGgALGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 99- 120: vaisl LFAG-ALGNFiDRIltGeVVDFI dtnif F 6: 61.3252 5( 5) A-x-[AS]-L-x(2,4)-A-x(0,2)-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 100- 125: klnni AyALiiggA--LGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 100- 125: klnni AyALiiggA--LGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 97- 122: kiqns AyALiiggA--LANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 102- 127: twlai AlALvlggA--LGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 95- 120: lfmqv AiSLlfagA--LGNFiDRIltGeVVDFI dtnif LSPA_STAAU : 95- 120: lfmqv AiSLlf--AgaLGNFiDRIltGeVVDFI dtnif G 7: 60.3773 5( 5) L-x-[ALV]-[LV]-x(2)-V-x(0,1)-I-x(0,1)-D-x-[GLV]-[ST]-K-x(2)-[FIV]-x-[GQT]-x-[FLM]-x-[ILM]-x-[DEQ]-[QST]-[FIV]-x-[LV]-[FIL]-P Occurences: 5(5) LSPA_ECOLI : 13- 44: tglrw LwLVvvVlIiDlGSKylIlQnFaLgDTVpLFP slnlh LSPA_ENTAE : 13- 44: tglrw LwVVvaVlIiDlGSKflIlQnFaLgETVsLFP slnlh LSPA_HAEIN : 12- 41: lsflw LsAVafV-I-DlLTKyiVvQkFdLyESVnVLP vfnlt LSPA_PSEFL : 16- 45: lgwlv LsLLvlV-I-DqVSKahFeGsLeMfQQIvVIP dyfsw LSPA_STAAU : 12- 42: igtsi LiAVfvV-IfDqVTKyiIaTtMkIgDSFeVIP hflni H 8: 59.6461 6( 5) L-x(2,3)-G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 6(5) LSPA_ECOLI : 103- 125: niaya LiigGALGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 103- 125: niaya LiigGALGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 100- 122: nsaya LiigGALANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 105- 127: aiala LvlgGALGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 98- 120: qvais LlfaGALGNFiDRIltGeVVDFI dtnif LSPA_STAAU : 99- 120: vaisl Lfa-GALGNFiDRIltGeVVDFI dtnif I 9: 58.0786 5( 5) G-x-[AD]-F-x(1,2)-F-x(1,2)-A-D-x-[GS]-[GL]-x(4)-[FIL]-[FL]-[AI]-[GILV]-[IL]-A-[ILV]-[AGLV]-x-[CDS]-[AGTV] Occurences: 5(5) LSPA_ECOLI : 55- 81: yarny GaAFs-Fl-ADsGGwqrwFFAGIAIGiSV ilavm LSPA_ENTAE : 55- 81: yarny GaAFs-Fl-ADsGGwqrwFFAGIAVGiCV vlavl LSPA_HAEIN : 52- 78: yvrny GaAFs-Fl-ADhSGwqqyFFILLALAiSG mlvyf LSPA_PSEFL : 57- 83: laynt GaAFs-Fl-ADgGGwqrwLFAVIAVVvSA vlvvw LSPA_STAAU : 126- 154: dtnif GyDFpiFniADsSLtigvILIIIALLkDT snkkd J 10: 55.9761 5( 5) G-A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 107- 125: aliig GALGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 107- 125: aliig GALGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 104- 122: aliig GALANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 109- 127: alvlg GALGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 102- 120: sllfa GALGNFiDRIltGeVVDFI dtnif K 11: 51.8060 5( 5) A-L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 108- 125: liigg ALGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 108- 125: liigg ALGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 105- 122: liigg ALANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 110- 127: lvlgg ALGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 103- 120: llfag ALGNFiDRIltGeVVDFI dtnif L 12: 47.6360 5( 5) L-[AG]-N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 109- 125: iigga LGNLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 109- 125: iigga LGNLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 106- 122: iigga LANMvDRAynGfVVDFF dfywd LSPA_PSEFL : 111- 127: vlgga LGNLyDRIalGhVIDFI lvhwq LSPA_STAAU : 104- 120: lfaga LGNFiDRIltGeVVDFI dtnif M 13: 45.0357 5( 5) F-N-[FIL]-A-D-x-[AS]-[IL]-[CT]-[IV]-G-x(2,3)-L-[AILV]-[ILV] Occurences: 5(5) LSPA_ECOLI : 137- 152: whfat FNLADtAICVGaa-LIV legfl LSPA_ENTAE : 137- 152: whfat FNLADsAICIGaa-LIV legfl LSPA_HAEIN : 134- 149: yhypv FNIADiAICIGag-LLV ldafk LSPA_HAEIN : 134- 150: yhypv FNIADiAICIGaglLVL dafks LSPA_PSEFL : 140- 156: hyfpa FNFADsAITVGaimLAL dmfks LSPA_STAAU : 132- 147: ydfpi FNIADsSLTIGvi-LII iallk N 14: 40.8656 5( 5) N-[FIL]-A-D-x-[AS]-[IL]-[CT]-[IV]-G-x(2,3)-L-[AILV]-[ILV] Occurences: 5(5) LSPA_ECOLI : 138- 152: hfatf NLADtAICVGaa-LIV legfl LSPA_ENTAE : 138- 152: hfatf NLADsAICIGaa-LIV legfl LSPA_HAEIN : 135- 149: hypvf NIADiAICIGag-LLV ldafk LSPA_HAEIN : 135- 150: hypvf NIADiAICIGaglLVL dafks LSPA_PSEFL : 141- 156: yfpaf NFADsAITVGaimLAL dmfks LSPA_STAAU : 133- 147: dfpif NIADsSLTIGvi-LII iallk O 15: 40.2958 5( 5) N-[FLM]-x-D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 111- 125: ggalg NLfDRLwhGfVVDMI dfyvg LSPA_ENTAE : 111- 125: ggalg NLfDRLwhGfVVDMI dfyvg LSPA_HAEIN : 108- 122: ggala NMvDRAynGfVVDFF dfywd LSPA_PSEFL : 113- 127: ggalg NLyDRIalGhVIDFI lvhwq LSPA_STAAU : 106- 120: agalg NFiDRIltGeVVDFI dtnif P 16: 33.2486 5( 5) D-R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 114- 125: lgnlf DRLwhGfVVDMI dfyvg LSPA_ENTAE : 114- 125: lgnlf DRLwhGfVVDMI dfyvg LSPA_HAEIN : 111- 122: lanmv DRAynGfVVDFF dfywd LSPA_PSEFL : 116- 127: lgnly DRIalGhVIDFI lvhwq LSPA_STAAU : 109- 120: lgnfi DRIltGeVVDFI dtnif Q 17: 29.0786 5( 5) R-[AIL]-x(2)-G-x-V-[IV]-D-[FM]-[FI] Occurences: 5(5) LSPA_ECOLI : 115- 125: gnlfd RLwhGfVVDMI dfyvg LSPA_ENTAE : 115- 125: gnlfd RLwhGfVVDMI dfyvg LSPA_HAEIN : 112- 122: anmvd RAynGfVVDFF dfywd LSPA_PSEFL : 117- 127: gnlyd RIalGhVIDFI lvhwq LSPA_STAAU : 110- 120: gnfid RIltGeVVDFI dtnif R 18: 28.9594 5( 5) F-x(2,3)-D-x-[AP]-I-x(2)-[GI]-A-x(3,4)-L-[DET] Occurences: 5(5) LSPA_ECOLI : 137- 154: whfat FnlaDtAIcvGAalivLE gflps LSPA_ENTAE : 137- 154: whfat FnlaDsAIciGAalivLE gflps LSPA_HAEIN : 134- 151: yhypv FniaDiAIciGAgllvLD afkse LSPA_PSEFL : 140- 157: hyfpa FnfaDsAItvGAimlaLD mfksk LSPA_STAAU : 125- 140: idtni Fgy-DfPIfnIAdss-LT igvil S 19: 26.3442 5( 5) L-x(0,1)-I-[AGI]-[GIL]-A-L-[AGLV]-x(3)-[ADS] Occurences: 5(5) LSPA_ECOLI : 103- 114: niaya LiIGGALGnlfD rlwhg LSPA_ENTAE : 103- 114: niaya LiIGGALGnlfD rlwhg LSPA_HAEIN : 100- 111: nsaya LiIGGALAnmvD rayng LSPA_PSEFL : 99- 110: rddtw LaIALALVlggA lgnly LSPA_STAAU : 145- 155: tigvi L-IIIALLkdtS nkkdk T 20: 25.7610 5( 5) A-[FI]-S-x(0,1)-L-x(0,2)-A-[DG]-x(2)-G Occurences: 5(5) LSPA_ECOLI : 57- 66: rnyga AFSfL--ADsgG wqrwf LSPA_ENTAE : 57- 66: rnyga AFSfL--ADsgG wqrwf LSPA_HAEIN : 54- 63: rnyga AFSfL--ADhsG wqqyf LSPA_PSEFL : 59- 68: yntga AFSfL--ADggG wqrwl LSPA_STAAU : 95- 105: lfmqv AISlLf-AGalG nfidr LSPA_STAAU : 95- 105: lfmqv AIS-LlfAGalG nfidr Number of patterns evaluated by Pratt:2768 Total running time: 0 seconds