------------------------------------------------------------ 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_L31 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_L31.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_BACSU 66 RL31_ECOLI 70 RL31_HAEIN 70 RL31_MYCLE 84 Pratt run started at Thu Feb 6 21:05:57 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 45.8706 4( 4) M-K-x(2)-I-H-P-x(5)-T-x(2)-C-x-C-G-N-x(5)-S 2: 41.7005 4( 4) K-x(2)-I-H-P-x(5)-T-x(2)-C-x-C-G-N-x(5)-S 3: 37.5305 4( 4) I-H-P-x(5)-T-x(2)-C-x-C-G-N-x(5)-S 4: 33.3604 4( 4) C-x(2)-C-H-P-F-x-T-G-x-Q 5: 29.1904 4( 4) C-H-P-F-x-T-G-x-Q 6: 29.1904 4( 4) P-x(5)-T-x(2)-C-x-C-G-N-x(5)-S 7: 25.0203 4( 4) H-P-F-x-T-G-x-Q 8: 25.0203 4( 4) T-x(2)-C-x-C-G-N-x(5)-S 9: 23.5203 4( 4) V-x(3)-C-x(2,3)-F-x-T-G-x(0,2)-K 10: 20.8503 4( 4) G-R-V-x-R-F 11: 20.8503 4( 4) P-F-x-T-G-x-Q 12: 20.8503 4( 4) C-x-C-G-N-x(5)-S 13: 19.3503 5( 4) C-x(2,3)-F-x-T-G-x(0,2)-K 14: 18.8503 4( 4) A-x(3,5)-C-x(0,2)-G-N-x(5)-S 15: 16.6802 4( 4) R-V-x-R-F 16: 16.6802 4( 4) F-x-T-G-x-Q 17: 16.6802 4( 4) C-G-N-x(5)-S 18: 15.6802 4( 4) C-S-x(0,1)-C-x(4,5)-T 19: 15.6802 5( 4) F-x-T-G-x(0,2)-K 20: 15.1802 4( 4) P-x(0,1)-F-x(1,3)-T-x-K Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 90.3994 4( 4) C-[GS]-x-C-H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] B 2: 83.0488 4( 4) C-H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] C 3: 78.8788 4( 4) H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] D 4: 74.7087 4( 4) P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] E 5: 70.5387 4( 4) F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] F 6: 69.2204 4( 4) M-K-x-[DGN]-I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] G 7: 65.0504 4( 4) K-x-[DGN]-I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] H 8: 58.2046 4( 4) I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] I 9: 50.2782 4( 4) V-x-[CGS]-x-C-x(2,3)-F-x-T-G-x(0,2)-K-[EQ]-[EKR]-x(2)-[ADV]-[EST]-[GI]-[CG]-[RS]-x(2)-[HR] J 10: 49.8645 4( 4) P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] K 11: 43.8816 4( 4) C-S-x(0,1)-C-x(4,5)-T-x(2)-[QT]-x(3)-[ADS]-x-[DGN]-[GL]-[DR]-V-[ACD]-x(3)-[HK]-x-[FY] L 12: 39.8543 4( 4) C-x(2)-F-[FY]-T-G-x(0,2)-K-x(2)-[DSV]-[ASV]-[ADG]-[GT]-x-[GV]-x(3)-[ENR] M 13: 39.2986 4( 4) T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] N 14: 38.0474 4( 4) P-x(0,1)-F-x(1,3)-T-[GV]-K-x(3)-[GLV]-[ADN]-[EST]-x-[EG]-x-[GV]-[ADES]-x(2)-[EN] O 15: 35.6842 4( 4) F-[FY]-T-G-x(0,2)-K-x(2)-[DSV]-[ASV]-[ADG]-[GT]-x-[GV]-x(3)-[ENR] P 16: 33.1073 4( 4) G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Q 17: 31.9427 4( 4) C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] R 18: 28.9373 4( 4) R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] S 19: 27.3493 4( 4) A-x(3,5)-C-x(0,2)-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] T 20: 25.1793 4( 4) C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 90.3994 4( 4) C-[GS]-x-C-H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 36- 63: vrvei CSeCHPFYTGRQKfASADGRVDRFNkKY glk RL31_ECOLI : 37- 64: lnldv CSkCHPFFTGKQRdVATGGRVDRFNkRF nipgs RL31_HAEIN : 37- 64: inldv CGnCHPFYTGKQRvVDTGGRVERFNsRF kipst RL31_MYCLE : 38- 65: ivvev CSqCHPFYTGKQKiLDSGGRVARFEkRY gkrkv B 2: 83.0488 4( 4) C-H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 39- 63: eicse CHPFYTGRQKfASADGRVDRFNkKY glk RL31_ECOLI : 40- 64: dvcsk CHPFFTGKQRdVATGGRVDRFNkRF nipgs RL31_HAEIN : 40- 64: dvcgn CHPFYTGKQRvVDTGGRVERFNsRF kipst RL31_MYCLE : 41- 65: evcsq CHPFYTGKQKiLDSGGRVARFEkRY gkrkv C 3: 78.8788 4( 4) H-P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 40- 63: icsec HPFYTGRQKfASADGRVDRFNkKY glk RL31_ECOLI : 41- 64: vcskc HPFFTGKQRdVATGGRVDRFNkRF nipgs RL31_HAEIN : 41- 64: vcgnc HPFYTGKQRvVDTGGRVERFNsRF kipst RL31_MYCLE : 42- 65: vcsqc HPFYTGKQKiLDSGGRVARFEkRY gkrkv D 4: 74.7087 4( 4) P-F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 41- 63: csech PFYTGRQKfASADGRVDRFNkKY glk RL31_ECOLI : 42- 64: cskch PFFTGKQRdVATGGRVDRFNkRF nipgs RL31_HAEIN : 42- 64: cgnch PFYTGKQRvVDTGGRVERFNsRF kipst RL31_MYCLE : 43- 65: csqch PFYTGKQKiLDSGGRVARFEkRY gkrkv E 5: 70.5387 4( 4) F-[FY]-T-G-[KR]-Q-[KR]-x-[ALV]-[ADS]-[AST]-[DG]-G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 42- 63: sechp FYTGRQKfASADGRVDRFNkKY glk RL31_ECOLI : 43- 64: skchp FFTGKQRdVATGGRVDRFNkRF nipgs RL31_HAEIN : 43- 64: gnchp FYTGKQRvVDTGGRVERFNsRF kipst RL31_MYCLE : 44- 65: sqchp FYTGKQKiLDSGGRVARFEkRY gkrkv F 6: 69.2204 4( 4) M-K-x-[DGN]-I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 1- 31: MKaGIHPnFkKaTVkCACGNeFetgSVkeeV rveic RL31_ECOLI : 1- 31: MKkDIHPkYeEiTAsCSCGNvMkirSTvghD lnldv RL31_HAEIN : 1- 31: MKqGIHPeYkEiTAtCSCGNvIktrSTlgkD inldv RL31_MYCLE : 1- 31: MKaNIHPaYaEtTVvCGCGNtFqtrSTkpgG rivve G 7: 65.0504 4( 4) K-x-[DGN]-I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 2- 31: m KaGIHPnFkKaTVkCACGNeFetgSVkeeV rveic RL31_ECOLI : 2- 31: m KkDIHPkYeEiTAsCSCGNvMkirSTvghD lnldv RL31_HAEIN : 2- 31: m KqGIHPeYkEiTAtCSCGNvIktrSTlgkD inldv RL31_MYCLE : 2- 31: m KaNIHPaYaEtTVvCGCGNtFqtrSTkpgG rivve H 8: 58.2046 4( 4) I-H-P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 5- 31: mkag IHPnFkKaTVkCACGNeFetgSVkeeV rveic RL31_ECOLI : 5- 31: mkkd IHPkYeEiTAsCSCGNvMkirSTvghD lnldv RL31_HAEIN : 5- 31: mkqg IHPeYkEiTAtCSCGNvIktrSTlgkD inldv RL31_MYCLE : 5- 31: mkan IHPaYaEtTVvCGCGNtFqtrSTkpgG rivve I 9: 50.2782 4( 4) V-x-[CGS]-x-C-x(2,3)-F-x-T-G-x(0,2)-K-[EQ]-[EKR]-x(2)-[ADV]-[EST]-[GI]-[CG]-[RS]-x(2)-[HR] Occurences: 4(4) RL31_BACSU : 14- 40: fkkat VkCaCgneFeTGsvKEEvrVEICSecH pfytg RL31_ECOLI : 36- 59: dlnld VcSkChp-FfTG--KQRdvATGGRvdR fnkrf RL31_HAEIN : 36- 59: dinld VcGnChp-FyTG--KQRvvDTGGRveR fnsrf RL31_MYCLE : 37- 60: rivve VcSqChp-FyTG--KQKilDSGGRvaR fekry J 10: 49.8645 4( 4) P-x-[FY]-x-[EK]-x-T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 7- 31: kagih PnFkKaTVkCACGNeFetgSVkeeV rveic RL31_ECOLI : 7- 31: kkdih PkYeEiTAsCSCGNvMkirSTvghD lnldv RL31_HAEIN : 7- 31: kqgih PeYkEiTAtCSCGNvIktrSTlgkD inldv RL31_MYCLE : 7- 31: kanih PaYaEtTVvCGCGNtFqtrSTkpgG rivve K 11: 43.8816 4( 4) C-S-x(0,1)-C-x(4,5)-T-x(2)-[QT]-x(3)-[ADS]-x-[DGN]-[GL]-[DR]-V-[ACD]-x(3)-[HK]-x-[FY] Occurences: 4(4) RL31_BACSU : 36- 63: vrvei CSeChpfy-TgrQkfaSaDGRVDrfnKkY glk RL31_ECOLI : 37- 64: lnldv CSkChpff-TgkQrdvAtGGRVDrfnKrF nipgs RL31_HAEIN : 16- 43: eitat CS-CgnvikTrsTlgkDiNLDVCgncHpF ytgkq RL31_MYCLE : 38- 65: ivvev CSqChpfy-TgkQkilDsGGRVArfeKrY gkrkv L 12: 39.8543 4( 4) C-x(2)-F-[FY]-T-G-x(0,2)-K-x(2)-[DSV]-[ASV]-[ADG]-[GT]-x-[GV]-x(3)-[ENR] Occurences: 4(4) RL31_BACSU : 39- 60: eicse ChpFYTGrqKfaSADGrVdrfN kkygl RL31_ECOLI : 40- 59: dvcsk ChpFFTG--KqrDVATgGrvdR fnkrf RL31_HAEIN : 40- 59: dvcgn ChpFYTG--KqrVVDTgGrveR fnsrf RL31_MYCLE : 41- 62: evcsq ChpFYTGkqKilDSGGrVarfE krygk M 13: 39.2986 4( 4) T-[AV]-x-C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 13- 31: nfkka TVkCACGNeFetgSVkeeV rveic RL31_ECOLI : 13- 31: kyeei TAsCSCGNvMkirSTvghD lnldv RL31_HAEIN : 13- 31: eykei TAtCSCGNvIktrSTlgkD inldv RL31_MYCLE : 13- 31: ayaet TVvCGCGNtFqtrSTkpgG rivve N 14: 38.0474 4( 4) P-x(0,1)-F-x(1,3)-T-[GV]-K-x(3)-[GLV]-[ADN]-[EST]-x-[EG]-x-[GV]-[ADES]-x(2)-[EN] Occurences: 4(4) RL31_BACSU : 7- 29: kagih PnFkkaTVKcacGNEfEtGSvkE evrve RL31_ECOLI : 42- 61: cskch P-Ff--TGKqrdVATgGrVDrfN krfni RL31_HAEIN : 42- 61: cgnch P-Fy--TGKqrvVDTgGrVErfN srfki RL31_MYCLE : 43- 62: csqch P-Fy--TGKqkiLDSgGrVArfE krygk O 15: 35.6842 4( 4) F-[FY]-T-G-x(0,2)-K-x(2)-[DSV]-[ASV]-[ADG]-[GT]-x-[GV]-x(3)-[ENR] Occurences: 4(4) RL31_BACSU : 42- 60: sechp FYTGrqKfaSADGrVdrfN kkygl RL31_ECOLI : 43- 59: skchp FFTG--KqrDVATgGrvdR fnkrf RL31_HAEIN : 43- 59: gnchp FYTG--KqrVVDTgGrveR fnsrf RL31_MYCLE : 44- 62: sqchp FYTGkqKilDSGGrVarfE krygk P 16: 33.1073 4( 4) G-R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 54- 63: fasad GRVDRFNkKY glk RL31_ECOLI : 55- 64: dvatg GRVDRFNkRF nipgs RL31_HAEIN : 55- 64: vvdtg GRVERFNsRF kipst RL31_MYCLE : 56- 65: ildsg GRVARFEkRY gkrkv Q 17: 31.9427 4( 4) C-[AGS]-C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 16- 31: katvk CACGNeFetgSVkeeV rveic RL31_ECOLI : 16- 31: eitas CSCGNvMkirSTvghD lnldv RL31_HAEIN : 16- 31: eitat CSCGNvIktrSTlgkD inldv RL31_MYCLE : 16- 31: ettvv CGCGNtFqtrSTkpgG rivve R 18: 28.9373 4( 4) R-V-[ADE]-R-F-[EN]-x-[KR]-[FY] Occurences: 4(4) RL31_BACSU : 55- 63: asadg RVDRFNkKY glk RL31_ECOLI : 56- 64: vatgg RVDRFNkRF nipgs RL31_HAEIN : 56- 64: vdtgg RVERFNsRF kipst RL31_MYCLE : 57- 65: ldsgg RVARFEkRY gkrkv S 19: 27.3493 4( 4) A-x(3,5)-C-x(0,2)-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 12- 31: pnfkk AtvkcaC--GNeFetgSVkeeV rveic RL31_BACSU : 12- 31: pnfkk Atvk--CacGNeFetgSVkeeV rveic RL31_ECOLI : 14- 31: yeeit Ascs--C--GNvMkirSTvghD lnldv RL31_HAEIN : 14- 31: ykeit Atcs--C--GNvIktrSTlgkD inldv RL31_MYCLE : 10- 31: ihpay AettvvCgcGNtFqtrSTkpgG rivve T 20: 25.1793 4( 4) C-G-N-x-[FIM]-x(3)-S-[TV]-x(3)-[DGV] Occurences: 4(4) RL31_BACSU : 18- 31: tvkca CGNeFetgSVkeeV rveic RL31_ECOLI : 18- 31: tascs CGNvMkirSTvghD lnldv RL31_HAEIN : 18- 31: tatcs CGNvIktrSTlgkD inldv RL31_MYCLE : 18- 31: tvvcg CGNtFqtrSTkpgG rivve Number of patterns evaluated by Pratt:611 Total running time: 0 seconds