------------------------------------------------------------ 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 6 sequences from file TNASE PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 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 TNASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: NUC_SHIFL 174 NUC_STAAU 231 NUC_STAHY 169 NUC_STAIN 168 PAB4_ECOLI 281 YFI3_ECOLI 153 Pratt run started at Thu Feb 6 21:27:10 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.8503 6( 6) D-x-Y-G-R-x-L 2: 16.6802 6( 6) Y-G-R-x-L 3: 16.6802 6( 6) R-x(4)-D-x-P-E 4: 16.6802 6( 6) D-G-D-T 5: 16.1802 7( 6) D-x(0,1)-Y-G-R 6: 16.1802 6( 6) R-L-x(2,3)-D-x(2)-E 7: 15.6802 6( 6) L-x(3,5)-D-x-P-E 8: 15.1802 11( 6) R-x(0,2)-L-x(2,3)-D-x(2)-E 9: 15.1802 6( 6) V-x-R-x(2,4)-D-x(1,2)-T 10: 12.5102 7( 6) G-R-x-L 11: 12.5102 7( 6) Y-G-R 12: 12.5102 6( 6) D-x-P-E 13: 12.5102 6( 6) G-D-T 14: 12.5102 8( 6) R-x(4)-D-T 15: 12.5102 8( 6) D-x(2)-G-R 16: 12.0102 7( 6) R-x(4)-D-x(1,2)-P 17: 12.0102 6( 6) R-x(2,3)-A-x-V 18: 12.0102 6( 6) R-x-L-x(1,2)-V 19: 12.0102 7( 6) R-x(1,2)-L-x(2)-V 20: 12.0102 7( 6) R-x(0,1)-L-x(2)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 46.0035 6( 6) R-[ILV]-[IL]-x-[GV]-D-T-[IP]-x-[TV]-x(2)-[DNPS]-x(4)-[ENQR]-x(4)-[ADEGN]-[AIV]-[DS]-[ANT]-x-[ET] B 2: 40.8992 6( 6) D-[KR]-Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] C 3: 37.1511 6( 6) D-x(0,1)-Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] D 4: 33.7922 6( 6) R-[LM]-[AILV]-x-[IV]-D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] E 5: 33.4810 6( 6) Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] F 6: 30.5941 6( 6) R-[LM]-[AILV]-x-[IV]-D-x-P-E-x(3)-[ADP]-x(4)-[AEQS] G 7: 29.3110 6( 6) G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] H 8: 23.7612 6( 6) L-x(3,5)-D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] I 9: 22.5669 6( 6) D-G-D-T-[IV]-x-[ILV] J 10: 21.0301 6( 6) V-x-R-x(2,4)-D-x(1,2)-T-[IV]-x(4)-[DNS] K 11: 20.5911 6( 6) D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] L 12: 19.5033 6( 6) R-x(0,1)-L-[AGL]-x-V-x(2)-[GNP]-x-[EGQT] M 13: 19.3644 6( 6) R-L-x(2,3)-D-x-[PQ]-E N 14: 18.3969 6( 6) G-D-T-[IV]-x-[ILV] O 15: 16.4972 6( 6) R-x-L-x(1,2)-V-x(2)-[AGNP]-x-[EGQT] P 16: 15.1803 6( 6) R-x(1,2)-L-[AG]-x-V Q 17: 15.1802 11( 6) R-x(0,2)-L-x(2,3)-D-x(2)-E R 18: 12.5102 7( 6) Y-G-R S 19: 12.5102 8( 6) D-x(2)-G-R T 20: 12.0102 6( 6) R-x(2,3)-A-x-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 46.0035 6( 6) R-[ILV]-[IL]-x-[GV]-D-T-[IP]-x-[TV]-x(2)-[DNPS]-x(4)-[ENQR]-x(4)-[ADEGN]-[AIV]-[DS]-[ANT]-x-[ET] Occurences: 6(6) NUC_SHIFL : 33- 60: rgevv RILdGDTIdVlvNrqtiRvrlaDIDApE sgqaf NUC_STAAU : 117- 144: qpmtf RLLlVDTPeTkhPkkgvEkygpEASAfT kkmve NUC_STAHY : 46- 73: tykvi RVIdGDTIiVdkDgkqqNlrmiGVDTpE tvkpn NUC_STAIN : 64- 91: qderv RLIgVDTPeTvkPntpvQpygkAASNfT kkhlt PAB4_ECOLI : 138- 165: rgevv RIIdGDTIdVlvDkqpvRvrlvDIDApE krqaf YFI3_ECOLI : 27- 54: hgrvv RVLdGDTIeVmdSrkavRirlvNIDApE kkqdy B 2: 40.8992 6( 6) D-[KR]-Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] Occurences: 6(6) NUC_SHIFL : 90- 107: tekev DRYGRtLGvVYAPlqypG gqtql NUC_STAAU : 165- 182: kgqrt DKYGRgLAyIYADgkmvN ealvr NUC_STAHY : 111- 128: dkqek DRYGRtLAyVWLGkemfN eklak NUC_STAIN : 110- 127: drepk DKYGRtLAyVWLGdemfN vklak PAB4_ECOLI : 195- 212: dekdt DRYGRtLGtVWVNmelaS rppqp YFI3_ECOLI : 84- 101: tyfqr DRYGRiLGqVYAPdgmnV nqfmv C 3: 37.1511 6( 6) D-x(0,1)-Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] Occurences: 6(6) NUC_SHIFL : 90- 107: tekev DrYGRtLGvVYAPlqypG gqtql NUC_STAAU : 165- 182: kgqrt DkYGRgLAyIYADgkmvN ealvr NUC_STAHY : 111- 128: dkqek DrYGRtLAyVWLGkemfN eklak NUC_STAIN : 110- 127: drepk DkYGRtLAyVWLGdemfN vklak PAB4_ECOLI : 195- 212: dekdt DrYGRtLGtVWVNmelaS rppqp YFI3_ECOLI : 84- 101: tyfqr DrYGRiLGqVYAPdgmnV nqfmv D 4: 33.7922 6( 6) R-[LM]-[AILV]-x-[IV]-D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] Occurences: 6(6) NUC_SHIFL : 52- 69: qtirv RLAdIDAPEsgqAfgsrA rqrla NUC_STAAU : 117- 134: qpmtf RLLlVDTPEtkhPkkgvE kygpe NUC_STAHY : 65- 82: kqqnl RMIgVDTPEtvkPntpvQ pygke NUC_STAIN : 64- 81: qderv RLIgVDTPEtvkPntpvQ pygka PAB4_ECOLI : 157- 174: qpvrv RLVdIDAPEkrqAfgerA rqala YFI3_ECOLI : 46- 63: kavri RLVnIDAPEkkqDygrwS tdmmk E 5: 33.4810 6( 6) Y-G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] Occurences: 6(6) NUC_SHIFL : 92- 107: kevdr YGRtLGvVYAPlqypG gqtql NUC_STAAU : 167- 182: qrtdk YGRgLAyIYADgkmvN ealvr NUC_STAHY : 113- 128: qekdr YGRtLAyVWLGkemfN eklak NUC_STAIN : 112- 127: epkdk YGRtLAyVWLGdemfN vklak PAB4_ECOLI : 197- 212: kdtdr YGRtLGtVWVNmelaS rppqp YFI3_ECOLI : 86- 101: fqrdr YGRiLGqVYAPdgmnV nqfmv F 6: 30.5941 6( 6) R-[LM]-[AILV]-x-[IV]-D-x-P-E-x(3)-[ADP]-x(4)-[AEQS] Occurences: 6(6) NUC_SHIFL : 52- 69: qtirv RLAdIDaPEsgqAfgsrA rqrla NUC_STAAU : 117- 134: qpmtf RLLlVDtPEtkhPkkgvE kygpe NUC_STAHY : 65- 82: kqqnl RMIgVDtPEtvkPntpvQ pygke NUC_STAIN : 64- 81: qderv RLIgVDtPEtvkPntpvQ pygka PAB4_ECOLI : 157- 174: qpvrv RLVdIDaPEkrqAfgerA rqala YFI3_ECOLI : 46- 63: kavri RLVnIDaPEkkqDygrwS tdmmk G 7: 29.3110 6( 6) G-R-x-L-[AG]-x-[IV]-[WY]-[ALV]-[DGNP]-x(4)-[GNSV] Occurences: 6(6) NUC_SHIFL : 93- 107: evdry GRtLGvVYAPlqypG gqtql NUC_STAAU : 168- 182: rtdky GRgLAyIYADgkmvN ealvr NUC_STAHY : 114- 128: ekdry GRtLAyVWLGkemfN eklak NUC_STAIN : 113- 127: pkdky GRtLAyVWLGdemfN vklak PAB4_ECOLI : 198- 212: dtdry GRtLGtVWVNmelaS rppqp YFI3_ECOLI : 87- 101: qrdry GRiLGqVYAPdgmnV nqfmv H 8: 23.7612 6( 6) L-x(3,5)-D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] Occurences: 6(6) NUC_SHIFL : 53- 69: tirvr Ladi--DAPEsgqAfgsrA rqrla NUC_STAAU : 118- 134: pmtfr Lllv--DTPEtkhPkkgvE kygpe NUC_STAHY : 64- 82: gkqqn LrmigvDTPEtvkPntpvQ pygke NUC_STAIN : 65- 81: dervr Ligv--DTPEtvkPntpvQ pygka PAB4_ECOLI : 158- 174: pvrvr Lvdi--DAPEkrqAfgerA rqala YFI3_ECOLI : 47- 63: avrir Lvni--DAPEkkqDygrwS tdmmk I 9: 22.5669 6( 6) D-G-D-T-[IV]-x-[ILV] Occurences: 6(6) NUC_SHIFL : 36- 42: vvril DGDTIdV lvnrq NUC_STAAU : 101- 107: likai DGDTVkL mykgq NUC_STAHY : 49- 55: virvi DGDTIiV dkdgk NUC_STAIN : 48- 54: vkrvi DGDTIiI dkdgq PAB4_ECOLI : 141- 147: vvrii DGDTIdV lvdkq YFI3_ECOLI : 30- 36: vvrvl DGDTIeV mdsrk J 10: 21.0301 6( 6) V-x-R-x(2,4)-D-x(1,2)-T-[IV]-x(4)-[DNS] Occurences: 6(6) NUC_SHIFL : 31- 45: dfrge VvRil--DgdTIdvlvN rqtir NUC_STAAU : 70- 85: qtdng VnRsgseDp-TVysatS tkklh NUC_STAHY : 44- 58: eqtyk ViRvi--DgdTIivdkD gkqqn NUC_STAIN : 43- 57: gesyl VkRvi--DgdTIiidkD gqder PAB4_ECOLI : 136- 150: elrge VvRii--DgdTIdvlvD kqpvr YFI3_ECOLI : 25- 39: dihgr VvRvl--DgdTIevmdS rkavr K 11: 20.5911 6( 6) D-[AT]-P-E-x(3)-[ADP]-x(4)-[AEQS] Occurences: 6(6) NUC_SHIFL : 57- 69: rladi DAPEsgqAfgsrA rqrla NUC_STAAU : 122- 134: rlllv DTPEtkhPkkgvE kygpe NUC_STAHY : 70- 82: rmigv DTPEtvkPntpvQ pygke NUC_STAIN : 69- 81: rligv DTPEtvkPntpvQ pygka PAB4_ECOLI : 162- 174: rlvdi DAPEkrqAfgerA rqala YFI3_ECOLI : 51- 63: rlvni DAPEkkqDygrwS tdmmk L 12: 19.5033 6( 6) R-x(0,1)-L-[AGL]-x-V-x(2)-[GNP]-x-[EGQT] Occurences: 6(6) NUC_SHIFL : 94- 104: vdryg RtLGvVyaPlQ ypggq NUC_STAAU : 117- 126: qpmtf R-LLlVdtPeT khpkk NUC_STAHY : 115- 125: kdryg RtLAyVwlGkE mfnek NUC_STAIN : 114- 124: kdkyg RtLAyVwlGdE mfnvk PAB4_ECOLI : 199- 209: tdryg RtLGtVwvNmE lasrp YFI3_ECOLI : 88- 98: rdryg RiLGqVyaPdG mnvnq M 13: 19.3644 6( 6) R-L-x(2,3)-D-x-[PQ]-E Occurences: 6(6) NUC_SHIFL : 52- 60: qtirv RLadiDaPE sgqaf NUC_STAAU : 117- 125: qpmtf RLllvDtPE tkhpk NUC_STAHY : 102- 109: tnqkv RLey-DkQE kdryg NUC_STAIN : 64- 72: qderv RLigvDtPE tvkpn PAB4_ECOLI : 157- 165: qpvrv RLvdiDaPE krqaf YFI3_ECOLI : 46- 54: kavri RLvniDaPE kkqdy N 14: 18.3969 6( 6) G-D-T-[IV]-x-[ILV] Occurences: 6(6) NUC_SHIFL : 37- 42: vrild GDTIdV lvnrq NUC_STAAU : 102- 107: ikaid GDTVkL mykgq NUC_STAHY : 50- 55: irvid GDTIiV dkdgk NUC_STAIN : 49- 54: krvid GDTIiI dkdgq PAB4_ECOLI : 142- 147: vriid GDTIdV lvdkq YFI3_ECOLI : 31- 36: vrvld GDTIeV mdsrk O 15: 16.4972 6( 6) R-x-L-x(1,2)-V-x(2)-[AGNP]-x-[EGQT] Occurences: 6(6) NUC_SHIFL : 94- 104: vdryg RtLgvVyaPlQ ypggq NUC_STAAU : 117- 126: qpmtf RlLl-VdtPeT khpkk NUC_STAHY : 115- 125: kdryg RtLayVwlGkE mfnek NUC_STAIN : 114- 124: kdkyg RtLayVwlGdE mfnvk PAB4_ECOLI : 199- 209: tdryg RtLgtVwvNmE lasrp YFI3_ECOLI : 88- 98: rdryg RiLgqVyaPdG mnvnq P 16: 15.1803 6( 6) R-x(1,2)-L-[AG]-x-V Occurences: 6(6) NUC_SHIFL : 94- 99: vdryg Rt-LGvV yaplq NUC_STAAU : 187- 193: nealv RqgLAkV ayvyk NUC_STAHY : 115- 120: kdryg Rt-LAyV wlgke NUC_STAIN : 114- 119: kdkyg Rt-LAyV wlgde PAB4_ECOLI : 199- 204: tdryg Rt-LGtV wvnme YFI3_ECOLI : 88- 93: rdryg Ri-LGqV yapdg Q 17: 15.1802 11( 6) R-x(0,2)-L-x(2,3)-D-x(2)-E Occurences: 11(6) NUC_SHIFL : 50- 60: nrqti RvrLadiDapE sgqaf NUC_SHIFL : 52- 60: qtirv R--LadiDapE sgqaf NUC_STAAU : 117- 125: qpmtf Rl-Llv-DtpE tkhpk NUC_STAAU : 117- 125: qpmtf R--LllvDtpE tkhpk NUC_STAHY : 102- 109: tnqkv R--Ley-DkqE kdryg NUC_STAIN : 62- 72: dgqde RvrLigvDtpE tvkpn NUC_STAIN : 64- 72: qderv R--LigvDtpE tvkpn PAB4_ECOLI : 155- 165: dkqpv RvrLvdiDapE krqaf PAB4_ECOLI : 157- 165: qpvrv R--LvdiDapE krqaf YFI3_ECOLI : 27- 35: hgrvv Rv-Ldg-DtiE vmdsr YFI3_ECOLI : 44- 54: srkav RirLvniDapE kkqdy YFI3_ECOLI : 46- 54: kavri R--LvniDapE kkqdy R 18: 12.5102 7( 6) Y-G-R Occurences: 7(6) NUC_SHIFL : 92- 94: kevdr YGR tlgvv NUC_STAAU : 167- 169: qrtdk YGR glayi NUC_STAHY : 113- 115: qekdr YGR tlayv NUC_STAIN : 112- 114: epkdk YGR tlayv PAB4_ECOLI : 197- 199: kdtdr YGR tlgtv YFI3_ECOLI : 59- 61: ekkqd YGR wstdm YFI3_ECOLI : 86- 88: fqrdr YGR ilgqv S 19: 12.5102 8( 6) D-x(2)-G-R Occurences: 8(6) NUC_SHIFL : 90- 94: tekev DryGR tlgvv NUC_STAAU : 165- 169: kgqrt DkyGR glayi NUC_STAHY : 111- 115: dkqek DryGR tlayv NUC_STAIN : 110- 114: drepk DkyGR tlayv PAB4_ECOLI : 14- 18: gytqf DqgGR deggq PAB4_ECOLI : 195- 199: dekdt DryGR tlgtv YFI3_ECOLI : 20- 24: pvlca DihGR vvrvl YFI3_ECOLI : 84- 88: tyfqr DryGR ilgqv T 20: 12.0102 6( 6) R-x(2,3)-A-x-V Occurences: 6(6) NUC_SHIFL : 9- 15: alaal RavaAaV vlivs NUC_STAAU : 187- 193: nealv RqglAkV ayvyk NUC_STAHY : 115- 120: kdryg Rtl-AyV wlgke NUC_STAIN : 114- 119: kdkyg Rtl-AyV wlgde PAB4_ECOLI : 67- 73: parpg RvpfAgV rlagg YFI3_ECOLI : 107- 113: nqfmv RagaAwV yeqyn Number of patterns evaluated by Pratt:1268 Total running time: 1 seconds