------------------------------------------------------------ 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 7 sequences from file ENTEROTOXIN_H_STABLE PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 ENTEROTOXIN_H_STABLE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HST2_ECOLI 18 HST4_ECOLI 72 HSTH_ECOLI 72 HSTP_ECOLI 72 HST_VIBCH 78 HST_YEREN 71 HST_YERKR 66 Pratt run started at Thu Feb 6 19:26:10 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 37.5305 7( 7) C-C-x(2)-C-C-x-P-A-C-x-G-C 2: 33.3604 7( 7) C-x(2)-C-C-x-P-A-C-x-G-C 3: 29.1904 7( 7) C-C-x-P-A-C-x-G-C 4: 25.0203 7( 7) C-x-P-A-C-x-G-C 5: 20.8503 7( 7) P-A-C-x-G-C 6: 16.6802 7( 7) A-C-x-G-C 7: 14.6802 11( 7) C-x(0,2)-A-x(0,2)-G-C 8: 11.5102 11( 7) A-x(0,2)-G-C 9: 11.0102 11( 7) N-x(2,3)-C-x(0,2)-C 10: 8.3401 9( 7) C-N 11: 8.3401 7( 7) G-C 12: 7.8401 7( 7) F-x(4,5)-L 13: 7.3401 11( 7) C-x(1,3)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 43.3629 7( 7) C-C-[DE]-[ILV]-C-C-x-P-A-C-x-G-C B 2: 39.1928 7( 7) C-[DE]-[ILV]-C-C-x-P-A-C-x-G-C C 3: 29.1904 7( 7) C-C-x-P-A-C-x-G-C D 4: 25.0203 7( 7) C-x-P-A-C-x-G-C E 5: 20.8503 7( 7) P-A-C-x-G-C F 6: 16.6802 7( 7) A-C-x-G-C G 7: 15.4414 7( 7) F-x(4,5)-L-x(3)-[GIP]-x(2)-[AGQS]-[DGQ] H 8: 14.6802 11( 7) C-x(0,2)-A-x(0,2)-G-C I 9: 11.5102 11( 7) A-x(0,2)-G-C J 10: 11.0102 11( 7) N-x(2,3)-C-x(0,2)-C K 11: 8.3401 9( 7) C-N L 12: 8.3401 7( 7) G-C M 13: 7.3401 11( 7) C-x(1,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 43.3629 7( 7) C-C-[DE]-[ILV]-C-C-x-P-A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 5- 17: ntfy CCELCCyPACaGC n HST4_ECOLI : 59- 71: nssny CCELCCnPACtGC y HSTH_ECOLI : 59- 71: nssny CCELCCnPACtGC y HSTP_ECOLI : 59- 71: nntfy CCELCCnPACaGC y HST_VIBCH : 64- 76: gnlid CCEICCnPACfGC ln HST_YEREN : 59- 71: ssdwd CCDVCCnPACaGC HST_YERKR : 54- 66: ppsdw CCEVCCnPACaGC B 2: 39.1928 7( 7) C-[DE]-[ILV]-C-C-x-P-A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 6- 17: ntfyc CELCCyPACaGC n HST4_ECOLI : 60- 71: ssnyc CELCCnPACtGC y HSTH_ECOLI : 60- 71: ssnyc CELCCnPACtGC y HSTP_ECOLI : 60- 71: ntfyc CELCCnPACaGC y HST_VIBCH : 65- 76: nlidc CEICCnPACfGC ln HST_YEREN : 60- 71: sdwdc CDVCCnPACaGC HST_YERKR : 55- 66: psdwc CEVCCnPACaGC C 3: 29.1904 7( 7) C-C-x-P-A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 9- 17: yccel CCyPACaGC n HST4_ECOLI : 63- 71: yccel CCnPACtGC y HSTH_ECOLI : 63- 71: yccel CCnPACtGC y HSTP_ECOLI : 63- 71: yccel CCnPACaGC y HST_VIBCH : 68- 76: dccei CCnPACfGC ln HST_YEREN : 63- 71: dccdv CCnPACaGC HST_YERKR : 58- 66: wccev CCnPACaGC D 4: 25.0203 7( 7) C-x-P-A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 10- 17: ccelc CyPACaGC n HST4_ECOLI : 64- 71: ccelc CnPACtGC y HSTH_ECOLI : 64- 71: ccelc CnPACtGC y HSTP_ECOLI : 64- 71: ccelc CnPACaGC y HST_VIBCH : 69- 76: cceic CnPACfGC ln HST_YEREN : 64- 71: ccdvc CnPACaGC HST_YERKR : 59- 66: ccevc CnPACaGC E 5: 20.8503 7( 7) P-A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 12- 17: elccy PACaGC n HST4_ECOLI : 66- 71: elccn PACtGC y HSTH_ECOLI : 66- 71: elccn PACtGC y HSTP_ECOLI : 66- 71: elccn PACaGC y HST_VIBCH : 71- 76: eiccn PACfGC ln HST_YEREN : 66- 71: dvccn PACaGC HST_YERKR : 61- 66: evccn PACaGC F 6: 16.6802 7( 7) A-C-x-G-C Occurences: 7(7) HST2_ECOLI : 13- 17: lccyp ACaGC n HST4_ECOLI : 67- 71: lccnp ACtGC y HSTH_ECOLI : 67- 71: lccnp ACtGC y HSTP_ECOLI : 67- 71: lccnp ACaGC y HST_VIBCH : 72- 76: iccnp ACfGC ln HST_YEREN : 67- 71: vccnp ACaGC HST_YERKR : 62- 66: vccnp ACaGC G 7: 15.4414 7( 7) F-x(4,5)-L-x(3)-[GIP]-x(2)-[AGQS]-[DGQ] Occurences: 7(7) HST2_ECOLI : 3- 16: nt Fycce-LccyPacAG cn HST4_ECOLI : 7- 21: kksil FiflsvLsfsPfaQD akpve HSTH_ECOLI : 7- 21: kksil FiflsvLsfsPfpQD akpve HSTP_ECOLI : 57- 70: nmnnt Fycce-LccnPacAG cy HST_VIBCH : 5- 19: mrnl FialmlLfssIafSQ tvenn HST_YEREN : 6- 20: mkkiv FvlvlmLssfGafGQ etvsg HST_YERKR : 6- 20: mkkiv FvlvlmLssfGtfGQ etasr H 8: 14.6802 11( 7) C-x(0,2)-A-x(0,2)-G-C Occurences: 11(7) HST2_ECOLI : 10- 17: ccelc CypAcaGC n HST2_ECOLI : 14- 17: ccypa C--A--GC n HST4_ECOLI : 64- 71: ccelc CnpActGC y HSTH_ECOLI : 64- 71: ccelc CnpActGC y HSTP_ECOLI : 64- 71: ccelc CnpAcaGC y HSTP_ECOLI : 68- 71: ccnpa C--A--GC y HST_VIBCH : 69- 76: cceic CnpAcfGC ln HST_YEREN : 64- 71: ccdvc CnpAcaGC HST_YEREN : 68- 71: ccnpa C--A--GC HST_YERKR : 59- 66: ccevc CnpAcaGC HST_YERKR : 63- 66: ccnpa C--A--GC I 9: 11.5102 11( 7) A-x(0,2)-G-C Occurences: 11(7) HST2_ECOLI : 13- 17: lccyp AcaGC n HST2_ECOLI : 15- 17: cypac A--GC n HST4_ECOLI : 67- 71: lccnp ActGC y HSTH_ECOLI : 67- 71: lccnp ActGC y HSTP_ECOLI : 67- 71: lccnp AcaGC y HSTP_ECOLI : 69- 71: cnpac A--GC y HST_VIBCH : 72- 76: iccnp AcfGC ln HST_YEREN : 67- 71: vccnp AcaGC HST_YEREN : 69- 71: cnpac A--GC HST_YERKR : 62- 66: vccnp AcaGC HST_YERKR : 64- 66: cnpac A--GC J 10: 11.0102 11( 7) N-x(2,3)-C-x(0,2)-C Occurences: 11(7) HST2_ECOLI : 1- 6: NtfyC--C elccy HST4_ECOLI : 57- 63: smnss Nyc-CelC cnpac HST4_ECOLI : 65- 71: celcc Npa-CtgC y HSTH_ECOLI : 57- 63: smnss Nyc-CelC cnpac HSTH_ECOLI : 65- 71: celcc Npa-CtgC y HSTP_ECOLI : 55- 60: senmn NtfyC--C elccn HSTP_ECOLI : 65- 71: celcc Npa-CagC y HST_VIBCH : 60- 65: vdeng NlidC--C eiccn HST_VIBCH : 70- 76: ceicc Npa-CfgC ln HST_YEREN : 65- 71: cdvcc Npa-CagC HST_YERKR : 60- 66: cevcc Npa-CagC K 11: 8.3401 9( 7) C-N Occurences: 9(7) HST2_ECOLI : 17- 18: pacag CN HST4_ECOLI : 39- 40: leskk CN iakks HST4_ECOLI : 64- 65: ccelc CN pactg HSTH_ECOLI : 39- 40: leskk CN iakks HSTH_ECOLI : 64- 65: ccelc CN pactg HSTP_ECOLI : 64- 65: ccelc CN pacag HST_VIBCH : 69- 70: cceic CN pacfg HST_YEREN : 64- 65: ccdvc CN pacag HST_YERKR : 59- 60: ccevc CN pacag L 12: 8.3401 7( 7) G-C Occurences: 7(7) HST2_ECOLI : 16- 17: ypaca GC n HST4_ECOLI : 70- 71: npact GC y HSTH_ECOLI : 70- 71: npact GC y HSTP_ECOLI : 70- 71: npaca GC y HST_VIBCH : 75- 76: npacf GC ln HST_YEREN : 70- 71: npaca GC HST_YERKR : 65- 66: npaca GC M 13: 7.3401 11( 7) C-x(1,3)-L Occurences: 11(7) HST2_ECOLI : 5- 8: ntfy Cce-L ccypa HST2_ECOLI : 6- 8: ntfyc Ce--L ccypa HST4_ECOLI : 59- 62: nssny Cce-L ccnpa HST4_ECOLI : 60- 62: ssnyc Ce--L ccnpa HSTH_ECOLI : 59- 62: nssny Cce-L ccnpa HSTH_ECOLI : 60- 62: ssnyc Ce--L ccnpa HSTP_ECOLI : 59- 62: nntfy Cce-L ccnpa HSTP_ECOLI : 60- 62: ntfyc Ce--L ccnpa HST_VIBCH : 73- 77: ccnpa CfgcL n HST_YEREN : 44- 48: vykqa CdppL ppaev HST_YERKR : 44- 48: vnkka CdteL ppsdw Number of patterns evaluated by Pratt:138 Total running time: 0 seconds