------------------------------------------------------------ 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 RIBOSOMAL_S6 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 RIBOSOMAL_S6.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RS6_BACSU 95 RS6_ECOLI 135 RS6_HAEIN 125 RS6_MYCLE 96 RS6_THETH 101 Pratt run started at Thu Feb 6 21:06:29 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.1904 5( 5) G-x(0,1)-R-R-x(0,1)-L-A-Y-x-I 2: 25.0203 5( 5) G-x-R-x-L-A-Y-x-I 3: 24.5203 6( 5) R-R-x(0,1)-L-A-Y-x-I 4: 20.3503 8( 5) R-x(0,1)-L-A-Y-x-I 5: 19.8503 5( 5) M-R-x-Y-E-x(0,2)-V 6: 16.6802 5( 5) L-A-Y-x-I 7: 15.6802 9( 5) R-x(0,1)-L-A-x(1,2)-I 8: 15.6802 5( 5) D-x(1,2)-G-x(2,3)-L-x-Y 9: 15.6802 5( 5) R-x-Y-E-x(0,2)-V 10: 12.5102 6( 5) R-x(3)-Y-x-I 11: 12.5102 5( 5) A-Y-x-I 12: 12.0102 6( 5) L-A-x(1,2)-I 13: 11.5102 8( 5) A-x(0,1)-V-x(0,1)-E 14: 11.5102 6( 5) Y-E-x(0,2)-I 15: 11.5102 5( 5) V-x(1,2)-R-x(2,3)-V 16: 11.5102 5( 5) E-x(4)-A-x(0,2)-E 17: 11.5102 5( 5) Y-E-x(0,2)-V 18: 11.0102 5( 5) E-x(0,1)-D-x(0,2)-R 19: 11.0102 6( 5) E-x(2,3)-R-x(0,2)-L 20: 11.0102 8( 5) E-x(2,4)-R-x(0,1)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 68.7768 5( 5) G-x-R-[QR]-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] B 2: 68.7760 5( 5) G-x(0,1)-R-R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] C 3: 65.1059 6( 5) R-R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] D 4: 64.6067 5( 5) R-[QR]-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] E 5: 60.9359 8( 5) R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] F 6: 57.2658 5( 5) L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] G 7: 53.0958 5( 5) A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] H 8: 53.0957 8( 5) R-x(0,1)-L-A-x(1,2)-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] I 9: 49.4256 5( 5) L-A-x(1,2)-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] J 10: 32.0047 5( 5) D-x(1,2)-G-x(2,3)-L-x-Y-[EPQ]-[IV]-[ENS]-x(3)-[DEK]-x(4)-[ILV]-x-[DNR] K 11: 19.8503 5( 5) M-R-x-Y-E-x(0,2)-V L 12: 19.3791 6( 5) A-x(0,1)-V-x(0,1)-E-x-[DSV]-x(4)-[AIL]-x-[DER] M 13: 18.9511 5( 5) E-x(4)-A-x(0,2)-E-x(3)-[ANSV]-x(2)-[DET]-x(2)-[AEG] N 14: 18.5302 5( 5) E-x(2,4)-R-x(0,1)-L-[AES]-x(3)-[ADNS]-x-[ILV] O 15: 17.0802 5( 5) V-x(1,2)-R-x(2,3)-V-[ILMV]-x-[ST] P 16: 16.7575 5( 5) Y-E-x(0,2)-I-[NSV]-x(4)-[GLP] Q 17: 16.4257 5( 5) E-x(2,3)-R-x(0,2)-L-[AS]-x(3)-[ADNS] R 18: 15.6802 5( 5) G-x(0,1)-R-R-x(0,1)-L S 19: 15.6802 5( 5) R-x-Y-E-x(0,2)-V T 20: 13.6848 5( 5) E-x(0,1)-D-x(0,2)-R-x(3)-[AIL] Best patterns with alignements: fitness hits(seqs) Pattern A 1: 68.7768 5( 5) G-x-R-[QR]-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 44- 76: gtkdw GkRRLAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 43- 75: rledw GrRQLAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 43- 75: rledw GrRQLAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 44- 76: kvdiw GrRRLAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 44- 76: kveel GlRRLAYPIAKdpqGyFlwyQVemPeDrVNDLA relri B 2: 68.7760 5( 5) G-x(0,1)-R-R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 44- 76: gtkdw GkRR-LAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 43- 75: rledw G-RRqLAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 43- 75: rledw G-RRqLAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 44- 76: kvdiw GrRR-LAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_MYCLE : 44- 76: kvdiw G-RRrLAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 44- 76: kveel GlRR-LAYPIAKdpqGyFlwyQVemPeDrVNDLA relri C 3: 65.1059 6( 5) R-R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 6(5) RS6_BACSU : 46- 76: kdwgk RR-LAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 44- 75: ledwg RRqLAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 44- 75: ledwg RRqLAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 45- 76: vdiwg RRrLAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_MYCLE : 46- 76: diwgr RR-LAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 46- 76: eelgl RR-LAYPIAKdpqGyFlwyQVemPeDrVNDLA relri D 4: 64.6067 5( 5) R-[QR]-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 46- 76: kdwgk RRLAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 45- 75: edwgr RQLAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 45- 75: edwgr RQLAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 46- 76: diwgr RRLAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 46- 76: eelgl RRLAYPIAKdpqGyFlwyQVemPeDrVNDLA relri E 5: 60.9359 8( 5) R-x(0,1)-L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 8(5) RS6_BACSU : 46- 76: kdwgk RrLAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_BACSU : 47- 76: dwgkr R-LAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 45- 75: edwgr RqLAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 45- 75: edwgr RqLAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 46- 76: diwgr RrLAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_MYCLE : 47- 76: iwgrr R-LAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 46- 76: eelgl RrLAYPIAKdpqGyFlwyQVemPeDrVNDLA relri RS6_THETH : 47- 76: elglr R-LAYPIAKdpqGyFlwyQVemPeDrVNDLA relri F 6: 57.2658 5( 5) L-A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 48- 76: wgkrr LAYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 47- 75: wgrrq LAYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 47- 75: wgrrq LAYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 48- 76: wgrrr LAYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 48- 76: lglrr LAYPIAKdpqGyFlwyQVemPeDrVNDLA relri G 7: 53.0958 5( 5) A-Y-[EP]-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 49- 76: gkrrl AYEINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 48- 75: grrql AYPINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 48- 75: grrql AYPINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 49- 76: grrrl AYEISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 49- 76: glrrl AYPIAKdpqGyFlwyQVemPeDrVNDLA relri H 8: 53.0957 8( 5) R-x(0,1)-L-A-x(1,2)-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 8(5) RS6_BACSU : 46- 76: kdwgk RrLAyeINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_BACSU : 47- 76: dwgkr R-LAyeINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 45- 75: edwgr RqLAypINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 45- 75: edwgr RqLAypINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 46- 76: diwgr RrLAyeISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_MYCLE : 47- 76: iwgrr R-LAyeISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 46- 76: eelgl RrLAypIAKdpqGyFlwyQVemPeDrVNDLA relri RS6_THETH : 47- 76: elglr R-LAypIAKdpqGyFlwyQVemPeDrVNDLA relri I 9: 49.4256 5( 5) L-A-x(1,2)-I-[ANS]-[DK]-x(3)-[AG]-x-[FY]-x(3)-[DNQ]-[LV]-x(2)-[ADP]-x-[ADEQ]-x-[IV]-[DNQS]-[DE]-[FL]-[ADE] Occurences: 5(5) RS6_BACSU : 48- 76: wgkrr LAyeINDfrdGfYqivNVqsDaAaVQEFD rlaki RS6_ECOLI : 47- 75: wgrrq LAypINKlhkAhYvlmNVeaPqEvIDELE ttfrf RS6_HAEIN : 47- 75: wgrrq LAypINKlhkAhYvlmNVeaPqQvIDELE ttfry RS6_MYCLE : 48- 76: wgrrr LAyeISKhaeGiYvviDLkaApAtVSELD rqlsl RS6_THETH : 48- 76: lglrr LAypIAKdpqGyFlwyQVemPeDrVNDLA relri J 10: 32.0047 5( 5) D-x(1,2)-G-x(2,3)-L-x-Y-[EPQ]-[IV]-[ENS]-x(3)-[DEK]-x(4)-[ILV]-x-[DNR] Occurences: 5(5) RS6_BACSU : 42- 64: itgtk Dw-GkrrLaYEINdfrDgfyqIvN vqsda RS6_ECOLI : 41- 63: ihrle Dw-GrrqLaYPINklhKahyvLmN veapq RS6_HAEIN : 41- 63: vhrle Dw-GrrqLaYPINklhKahyvLmN veapq RS6_MYCLE : 41- 64: aidkv DiwGrrrLaYEISkhaEgiyvViD lkaap RS6_THETH : 55- 77: ypiak DpqGyf-LwYQVEmpeDrvndLaR elrir K 11: 19.8503 5( 5) M-R-x-Y-E-x(0,2)-V Occurences: 5(5) RS6_BACSU : 1- 6: MRkYE--V myiir RS6_ECOLI : 1- 7: MRhYEi-V fmvhp RS6_HAEIN : 1- 7: MRhYEi-V fmvhp RS6_MYCLE : 1- 8: MRpYEimV ildpt RS6_THETH : 1- 6: MRrYE--V nivln L 12: 19.3791 6( 5) A-x(0,1)-V-x(0,1)-E-x-[DSV]-x(4)-[AIL]-x-[DER] Occurences: 6(5) RS6_BACSU : 70- 83: vqsda AaVqEfDrlakIsD diirh RS6_BACSU : 71- 83: qsdaa A-VqEfDrlakIsD diirh RS6_ECOLI : 95- 107: mrtkh A-VtEaSpmvkAkD errer RS6_HAEIN : 95- 107: ihtkh A-VtEaSpmkaAkE erkpl RS6_MYCLE : 70- 83: lkaap AtVsElDrqlsLnE svlrt RS6_THETH : 35- 47: lenyg ArV-EkVeelgLrR laypi M 13: 18.9511 5( 5) E-x(4)-A-x(0,2)-E-x(3)-[ANSV]-x(2)-[DET]-x(2)-[AEG] Occurences: 5(5) RS6_BACSU : 16- 34: rpnid EeskkAviErfnNvlTsnG aeitg RS6_ECOLI : 119- 135: ddfan EtaddA--EagdSeeEeeE RS6_HAEIN : 108- 124: kaake ErkplA--EvenNdfEdaE e RS6_MYCLE : 51- 67: rrlay EiskhA--EgiyVviDlkA apatv RS6_THETH : 24- 41: lalek EiiqrAl-EnygArvEkvE elglr N 14: 18.5302 5( 5) E-x(2,4)-R-x(0,1)-L-[AES]-x(3)-[ADNS]-x-[ILV] Occurences: 5(5) RS6_BACSU : 74- 85: aaavq Efd--R-LAkisDdI irhiv RS6_ECOLI : 40- 54: kihrl EdwgrRqLAypiNkL hkahy RS6_HAEIN : 40- 54: qvhrl EdwgrRqLAypiNkL hkahy RS6_MYCLE : 74- 86: patvs Eld--RqLSlneSvL rtkvm RS6_THETH : 24- 37: lalek Eiiq-RaLEnygArV ekvee O 15: 17.0802 5( 5) V-x(1,2)-R-x(2,3)-V-[ILMV]-x-[ST] Occurences: 5(5) RS6_BACSU : 22- 32: eskka VieRfnnVLtS ngaei RS6_ECOLI : 84- 92: rfnda Vi-Rsm-VMrT khavt RS6_HAEIN : 84- 92: rynda Vl-Rsl-VIhT khavt RS6_MYCLE : 85- 93: slnes Vl-Rtk-VMrT dkh RS6_THETH : 85- 93: rirdn Vr-Rvm-VVkS qepfl P 16: 16.7575 5( 5) Y-E-x(0,2)-I-[NSV]-x(4)-[GLP] Occurences: 5(5) RS6_BACSU : 50- 58: krrla YE--INdfrdG fyqiv RS6_ECOLI : 4- 12: mrh YE--IVfmvhP dqseq RS6_HAEIN : 4- 12: mrh YE--IVfmvhP dqseq RS6_MYCLE : 50- 58: rrrla YE--ISkhaeG iyvvi RS6_THETH : 4- 14: mrr YEvnIVlnpnL dqsql Q 17: 16.4257 5( 5) E-x(2,3)-R-x(0,2)-L-[AS]-x(3)-[ADNS] Occurences: 5(5) RS6_BACSU : 74- 83: aaavq Efd-R--LAkisD diirh RS6_ECOLI : 40- 52: kihrl EdwgRrqLAypiN klhka RS6_HAEIN : 40- 52: qvhrl EdwgRrqLAypiN klhka RS6_MYCLE : 74- 84: patvs Eld-Rq-LSlneS vlrtk RS6_THETH : 42- 53: vekve ElglRr-LAypiA kdpqg R 18: 15.6802 5( 5) G-x(0,1)-R-R-x(0,1)-L Occurences: 5(5) RS6_BACSU : 44- 48: gtkdw GkRR-L ayein RS6_ECOLI : 43- 47: rledw G-RRqL aypin RS6_HAEIN : 43- 47: rledw G-RRqL aypin RS6_MYCLE : 44- 48: kvdiw GrRR-L ayeis RS6_MYCLE : 44- 48: kvdiw G-RRrL ayeis RS6_THETH : 44- 48: kveel GlRR-L aypia S 19: 15.6802 5( 5) R-x-Y-E-x(0,2)-V Occurences: 5(5) RS6_BACSU : 2- 6: m RkYE--V myiir RS6_ECOLI : 2- 7: m RhYEi-V fmvhp RS6_HAEIN : 2- 7: m RhYEi-V fmvhp RS6_MYCLE : 2- 8: m RpYEimV ildpt RS6_THETH : 2- 6: m RrYE--V nivln T 20: 13.6848 5( 5) E-x(0,1)-D-x(0,2)-R-x(3)-[AIL] Occurences: 5(5) RS6_BACSU : 74- 81: aaavq EfD--RlakI sddii RS6_ECOLI : 40- 48: kihrl E-DwgRrqlA ypink RS6_HAEIN : 40- 48: qvhrl E-DwgRrqlA ypink RS6_MYCLE : 74- 81: patvs ElD--RqlsL nesvl RS6_THETH : 69- 75: qvemp E-D--RvndL arelr Number of patterns evaluated by Pratt:562 Total running time: 0 seconds