------------------------------------------------------------ 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 MOCF_BIOSYNTHESIS_2 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 MOCF_BIOSYNTHESIS_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CIN_DROME 601 GEPH_RAT 736 MOEA_ECOLI 411 MOEA_HAEIN 404 Pratt run started at Thu Feb 6 20:17:35 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 49.0406 4( 4) D-x(0,1)-V-I-x(1,2)-S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 2: 49.0406 4( 4) D-x(0,1)-V-x(0,1)-I-x-S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 3: 45.3706 4( 4) V-I-x(1,2)-S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 4: 45.3706 5( 4) V-x(0,1)-I-x-S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 5: 44.8706 4( 4) L-P-G-N-P-V-S-A-x(2)-T-x(2,3)-L-x(2,3)-P 6: 44.8706 5( 4) F-x(1,2)-L-P-G-N-P-V-S-A-x(2)-T-x(2,3)-L 7: 41.7005 4( 4) I-x-S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 8: 40.7005 4( 4) P-G-N-P-V-S-A-x(2)-T-x(2,3)-L-x(2,3)-P 9: 37.5305 4( 4) S-G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 10: 36.5305 4( 4) G-N-P-V-S-A-x(2)-T-x(2,3)-L-x(2,3)-P 11: 33.3604 4( 4) G-G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 12: 32.3604 4( 4) N-P-V-S-A-x(2)-T-x(2,3)-L-x(2,3)-P 13: 29.1904 4( 4) G-V-S-x-G-x(2)-D-x(2)-K-x(2)-L 14: 29.1904 4( 4) P-x-F-x(2)-S-x(2)-D-G-Y-A 15: 28.1904 4( 4) P-V-S-A-x(2)-T-x(2,3)-L-x(2,3)-P 16: 28.1904 4( 4) T-G-A-x(2)-P-x(5)-V-x(1,2)-Q-x(0,1)-E 17: 27.6904 4( 4) K-x(2,3)-V-x(1,3)-S-T-G-x-E-L 18: 25.0203 4( 4) V-x(3)-S-T-G-x-E-L 19: 25.0203 4( 4) F-x(2)-S-x(2)-D-G-Y-A 20: 24.5203 5( 4) G-N-x(0,1)-V-S-A-x(2)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 74.7419 4( 4) V-[AG]-[ILV]-[FLMV]-S-T-G-[DNS]-E-L-x(2)-[PV]-x(2)-[DPQ]-L-x-[DPS]-G-x-I-x-D-[ST]-N-x(3)-[LV]-x(3)-[IL] B 2: 74.7219 4( 4) P-[GPS]-F-x-[AN]-S-[AIV]-x-D-G-Y-A-[MV]-[KR]-x-[AST]-[DG]-x(2)-[GQS]-[DGST]-x(2)-[ILV]-x-[GV]-x(3)-[AS]-x-[ADE]-[GQS]-[NPQ]-[NPT] C 3: 71.0723 5( 4) F-x(1,2)-L-P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-[FV]-x-[LPV]-[LP]-[AIL]-[AIL]-[KR]-x(2)-[AGQ]-[GNQ] D 4: 70.1430 4( 4) D-x(0,1)-V-x(0,1)-I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] E 5: 69.1942 4( 4) K-x(2,3)-V-x(1,3)-S-T-G-[DNS]-E-L-x(2)-[PV]-x(2)-[DPQ]-L-x-[DPS]-G-x-I-x-D-[ST]-N-x(3)-[LV]-x(3)-[IL] F 6: 67.9306 4( 4) F-x-[AN]-S-[AIV]-x-D-G-Y-A-[MV]-[KR]-x-[AST]-[DG]-x(2)-[GQS]-[DGST]-x(2)-[ILV]-x-[GV]-x(3)-[AS]-x-[ADE]-[GQS]-[NPQ]-[NPT] G 7: 67.4976 4( 4) D-x(0,1)-V-I-x(1,2)-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] H 8: 66.4730 5( 4) V-x(0,1)-I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] I 9: 63.8275 4( 4) V-I-x(1,2)-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] J 10: 63.4085 4( 4) T-G-A-x-[ILV]-P-x-[EG]-[ACT]-[DE]-[AC]-V-x(1,2)-Q-x(0,1)-E-[DQ]-[TV]-x(3)-[DEQR]-x-[DGS]-x(4)-[AES]-[ES]-[LV] K 11: 62.8029 4( 4) I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] L 12: 61.3403 4( 4) L-P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G M 13: 57.1703 4( 4) P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G N 14: 55.9874 4( 4) S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] O 15: 53.0002 4( 4) G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G P 16: 51.8174 4( 4) G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Q 17: 51.6140 4( 4) G-N-x(0,1)-V-S-A-x-[LV]-T-x(3)-[FL]-[AV]-x-P-[AL]-[IL]-x(3)-[AQS]-G R 18: 48.8302 4( 4) N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G S 19: 47.6473 4( 4) G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] T 20: 44.6601 4( 4) P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 74.7419 4( 4) V-[AG]-[ILV]-[FLMV]-S-T-G-[DNS]-E-L-x(2)-[PV]-x(2)-[DPQ]-L-x-[DPS]-G-x-I-x-D-[ST]-N-x(3)-[LV]-x(3)-[IL] Occurences: 4(4) CIN_DROME : 365- 398: lskpk VAIVSTGSELcsPrnQLtPGkIfDSNttmLtelL vyfgf GEPH_RAT : 501- 534: nkfpv VAVMSTGNELlnPedDLlPGkIrDSNrstLlatI qehgy MOEA_ECOLI : 180- 213: irkvr VALFSTGDELqlPgqPLgDGqIyDTNrlaVhlmL eqlgc MOEA_HAEIN : 175- 208: yrqlk VGVLSTGDELveVgkPLqSGqIyDTNrftVkllL eklhc B 2: 74.7219 4( 4) P-[GPS]-F-x-[AN]-S-[AIV]-x-D-G-Y-A-[MV]-[KR]-x-[AST]-[DG]-x(2)-[GQS]-[DGST]-x(2)-[ILV]-x-[GV]-x(3)-[AS]-x-[ADE]-[GQS]-[NPQ]-[NPT] Occurences: 4(4) CIN_DROME : 232- 266: apvni PPFrASIkDGYAMKsTGfsGTkrVlGciaAgDSPN slpla GEPH_RAT : 366- 400: akdnl PPFpASVkDGYAVRaADgpGDrfIiGesqAgEQPT qtvmp MOEA_ECOLI : 51- 85: spldv PGFdNSAmDGYAVRlADiaSGqpLpVagkSfAGQP yhgew MOEA_HAEIN : 45- 79: spinv PSFdNSAmDGYAVRlSDlqQSltLsVagkSfAGNP fqeew C 3: 71.0723 5( 4) F-x(1,2)-L-P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-[FV]-x-[LPV]-[LP]-[AIL]-[AIL]-[KR]-x(2)-[AGQ]-[GNQ] Occurences: 5(4) CIN_DROME : 480- 507: rkdky FfgLPGNPVSAfVTfh-LFaLPAIRfaAG wdrck CIN_DROME : 481- 507: kdkyf Fg-LPGNPVSAfVTfh-LFaLPAIRfaAG wdrck GEPH_RAT : 622- 648: vrkii Fa-LPGNPVSAvVTcn-LFvVPALRkmQG ildpr MOEA_ECOLI : 294- 322: lsnsw FcgLPGNPVSAtLTfyqLVqPLLAKlsGN tasgl MOEA_HAEIN : 289- 317: lenaw FcgLPGNPVSAlVTfyqLVqPLIAKlqGQ kqwkk D 4: 70.1430 4( 4) D-x(0,1)-V-x(0,1)-I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 430- 451: lfevv DfV-ICSGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 566- 587: gisra D-ViITSGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 245- 266: adsqa DvV-ISSGGVSVGEaDYtKTILE elgei MOEA_ECOLI : 245- 266: adsqa D-VvISSGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 240- 261: aqsqa DlV-ITSGGVSVGEaDFtKAVLE kvgqv E 5: 69.1942 4( 4) K-x(2,3)-V-x(1,3)-S-T-G-[DNS]-E-L-x(2)-[PV]-x(2)-[DPQ]-L-x-[DPS]-G-x-I-x-D-[ST]-N-x(3)-[LV]-x(3)-[IL] Occurences: 4(4) CIN_DROME : 362- 398: rlils Kpk-VaivSTGSELcsPrnQLtPGkIfDSNttmLtelL vyfgf GEPH_RAT : 497- 534: evevn KfpvVavmSTGNELlnPedDLlPGkIrDSNrstLlatI qehgy MOEA_ECOLI : 177- 213: vpvir Kvr-ValfSTGDELqlPgqPLgDGqIyDTNrlaVhlmL eqlgc MOEA_HAEIN : 174- 208: cyrql Kvg-Vl--STGDELveVgkPLqSGqIyDTNrftVkllL eklhc F 6: 67.9306 4( 4) F-x-[AN]-S-[AIV]-x-D-G-Y-A-[MV]-[KR]-x-[AST]-[DG]-x(2)-[GQS]-[DGST]-x(2)-[ILV]-x-[GV]-x(3)-[AS]-x-[ADE]-[GQS]-[NPQ]-[NPT] Occurences: 4(4) CIN_DROME : 234- 266: vnipp FrASIkDGYAMKsTGfsGTkrVlGciaAgDSPN slpla GEPH_RAT : 368- 400: dnlpp FpASVkDGYAVRaADgpGDrfIiGesqAgEQPT qtvmp MOEA_ECOLI : 53- 85: ldvpg FdNSAmDGYAVRlADiaSGqpLpVagkSfAGQP yhgew MOEA_HAEIN : 47- 79: invps FdNSAmDGYAVRlSDlqQSltLsVagkSfAGNP fqeew G 7: 67.4976 4( 4) D-x(0,1)-V-I-x(1,2)-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 430- 451: lfevv DfVIc-SGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 566- 587: gisra D-VIitSGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 245- 266: adsqa DvVIs-SGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 240- 261: aqsqa DlVIt-SGGVSVGEaDFtKAVLE kvgqv H 8: 66.4730 5( 4) V-x(0,1)-I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 5(4) CIN_DROME : 432- 451: evvdf V-ICSGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 567- 587: israd ViITSGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 246- 266: dsqad VvISSGGVSVGEaDYtKTILE elgei MOEA_ECOLI : 247- 266: sqadv V-ISSGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 242- 261: sqadl V-ITSGGVSVGEaDFtKAVLE kvgqv I 9: 63.8275 4( 4) V-I-x(1,2)-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 432- 451: evvdf VIc-SGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 567- 587: israd VIitSGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 247- 266: sqadv VIs-SGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 242- 261: sqadl VIt-SGGVSVGEaDFtKAVLE kvgqv J 10: 63.4085 4( 4) T-G-A-x-[ILV]-P-x-[EG]-[ACT]-[DE]-[AC]-V-x(1,2)-Q-x(0,1)-E-[DQ]-[TV]-x(3)-[DEQR]-x-[DGS]-x(4)-[AES]-[ES]-[LV] Occurences: 4(4) CIN_DROME : 280- 310: cykin TGApLPlEADCVv-QvEDTkllQlDkngqESL vdilv GEPH_RAT : 413- 443: vmrvt TGApIPcGADAVv-QvEDTeliReSddgtEEL evril MOEA_ECOLI : 100- 130: cirim TGApVPeGCEAVvmQ-EQTeqmDnGvrftAEV rsgqn MOEA_HAEIN : 94- 124: avrim TGAmIPeGTDAVimQ-EQVtlnEdGtitfSEL pkpnq K 11: 62.8029 4( 4) I-[CST]-S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 433- 451: vvdfv ICSGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 569- 587: radvi ITSGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 248- 266: qadvv ISSGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 243- 261: qadlv ITSGGVSVGEaDFtKAVLE kvgqv L 12: 61.3403 4( 4) L-P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 483- 507: kyffg LPGNPVSAfVTfh-LfalPAIrfaAG wdrck GEPH_RAT : 624- 648: kiifa LPGNPVSAvVTcn-LfvvPALrkmQG ildpr MOEA_ECOLI : 297- 321: swfcg LPGNPVSAtLTfyqLvq-PLLaklSG ntasg MOEA_HAEIN : 292- 316: awfcg LPGNPVSAlVTfyqLvq-PLIaklQG qkqwk M 13: 57.1703 4( 4) P-G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 484- 507: yffgl PGNPVSAfVTfh-LfalPAIrfaAG wdrck GEPH_RAT : 625- 648: iifal PGNPVSAvVTcn-LfvvPALrkmQG ildpr MOEA_ECOLI : 298- 321: wfcgl PGNPVSAtLTfyqLvq-PLLaklSG ntasg MOEA_HAEIN : 293- 316: wfcgl PGNPVSAlVTfyqLvq-PLIaklQG qkqwk N 14: 55.9874 4( 4) S-G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 435- 451: dfvic SGGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 571- 587: dviit SGGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 250- 266: dvvis SGGVSVGEaDYtKTILE elgei MOEA_HAEIN : 245- 261: dlvit SGGVSVGEaDFtKAVLE kvgqv O 15: 53.0002 4( 4) G-N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 485- 507: ffglp GNPVSAfVTfh-LfalPAIrfaAG wdrck GEPH_RAT : 626- 648: ifalp GNPVSAvVTcn-LfvvPALrkmQG ildpr MOEA_ECOLI : 299- 321: fcglp GNPVSAtLTfyqLvq-PLLaklSG ntasg MOEA_HAEIN : 294- 316: fcglp GNPVSAlVTfyqLvq-PLIaklQG qkqwk P 16: 51.8174 4( 4) G-G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 436- 451: fvics GGVSMGDkDFvKSVLE dlqfr GEPH_RAT : 572- 587: viits GGVSMGEkDYlKQVLD idlha MOEA_ECOLI : 251- 266: vviss GGVSVGEaDYtKTILE elgei MOEA_HAEIN : 246- 261: lvits GGVSVGEaDFtKAVLE kvgqv Q 17: 51.6140 4( 4) G-N-x(0,1)-V-S-A-x-[LV]-T-x(3)-[FL]-[AV]-x-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 485- 507: ffglp GNpVSAfVTfhlFAlPAIrfaAG wdrck GEPH_RAT : 626- 648: ifalp GNpVSAvVTcnlFVvPALrkmQG ildpr MOEA_ECOLI : 299- 321: fcglp GNpVSAtLTfyqLVqPLLaklSG ntasg MOEA_HAEIN : 294- 316: fcglp GNpVSAlVTfyqLVqPLIaklQG qkqwk R 18: 48.8302 4( 4) N-P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 486- 507: fglpg NPVSAfVTfh-LfalPAIrfaAG wdrck GEPH_RAT : 627- 648: falpg NPVSAvVTcn-LfvvPALrkmQG ildpr MOEA_ECOLI : 300- 321: cglpg NPVSAtLTfyqLvq-PLLaklSG ntasg MOEA_HAEIN : 295- 316: cglpg NPVSAlVTfyqLvq-PLIaklQG qkqwk S 19: 47.6473 4( 4) G-V-S-[MV]-G-[DE]-x-D-[FY]-x-K-[AQST]-[IV]-L-[DE] Occurences: 4(4) CIN_DROME : 437- 451: vicsg GVSMGDkDFvKSVLE dlqfr GEPH_RAT : 573- 587: iitsg GVSMGEkDYlKQVLD idlha MOEA_ECOLI : 252- 266: vissg GVSVGEaDYtKTILE elgei MOEA_HAEIN : 247- 261: vitsg GVSVGEaDFtKAVLE kvgqv T 20: 44.6601 4( 4) P-V-S-A-x-[LV]-T-x(2,3)-L-x(2,3)-P-[AL]-[IL]-x(3)-[AQS]-G Occurences: 4(4) CIN_DROME : 487- 507: glpgn PVSAfVTfh-LfalPAIrfaAG wdrck GEPH_RAT : 628- 648: alpgn PVSAvVTcn-LfvvPALrkmQG ildpr MOEA_ECOLI : 301- 321: glpgn PVSAtLTfyqLvq-PLLaklSG ntasg MOEA_HAEIN : 296- 316: glpgn PVSAlVTfyqLvq-PLIaklQG qkqwk Number of patterns evaluated by Pratt:29759 Total running time: 11 seconds