------------------------------------------------------------ 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 3 sequences from file ALKYLBASE_DNA_GLYCOS PATTERN CONSERVATION: CM: min Nr of Seqs to Match 3 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 ALKYLBASE_DNA_GLYCOS.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: 3MG2_ECOLI 282 3MGA_BACSU 303 MAG_YEAST 296 Pratt run started at Thu Feb 6 18:35:21 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.1904 3( 3) L-x(4,5)-G-I-G-x-W-x-A-x(3,4)-L 2: 24.5203 3( 3) G-I-G-x-W-x-A-x(3,4)-L 3: 20.3503 3( 3) I-G-x-W-x-A-x(3,4)-L 4: 20.3503 3( 3) A-x(3)-L-x(5)-I-x(4,5)-A-x-Y 5: 20.3503 3( 3) I-x(0,1)-P-x(2)-A-x(3)-L-x(3)-L 6: 19.8503 3( 3) V-F-x-P-x(3,4)-I-x(1,2)-R 7: 19.8503 3( 3) D-x-F-x(0,2)-L-x(4)-L-x(2)-Q 8: 19.8503 3( 3) K-x(1,2)-L-x(5)-I-x(4,5)-A-x-Y 9: 19.8503 3( 3) P-x(1,2)-A-x(3)-L-x(3)-L-x(0,1)-R 10: 19.8503 3( 3) A-x(5)-K-x(2)-G-x(1,2)-P-x(2,3)-A 11: 19.8503 3( 3) A-x(5)-R-V-x(0,2)-L-Y 12: 19.8503 3( 3) A-x(3)-L-x(2,3)-A-R-x(4,5)-L 13: 19.8503 3( 3) G-x(2)-P-x(1,2)-A-x(3)-L-x(4,5)-R 14: 19.3503 4( 3) K-x(1,3)-V-F-x-P-x(3,4)-I 15: 19.3503 3( 3) E-x-A-x(0,1)-K-x(1,3)-L-x(3)-P 16: 19.3503 3( 3) M-x(2)-K-x(1,2)-E-x(1,3)-L-I 17: 19.3503 3( 3) A-x(3)-L-x(3)-L-x(0,1)-R-x(2,4)-A 18: 19.3503 4( 3) A-x(4,5)-R-V-x(0,2)-L-Y 19: 19.3503 3( 3) I-x(3,4)-A-x(3)-L-x(3,5)-R-x(5)-P 20: 18.8503 3( 3) G-x(1,3)-K-x(1,3)-V-F-x-P Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 54.4081 3( 3) D-x-F-x(0,2)-L-[ACP]-x-[DGT]-x-L-x(2)-Q-x(2)-[GLP]-[AGQ]-x-[AT]-x-[AS]-x(3)-[QR]-x-[AV]-[ES]-x-[FWY]-x-[DGP]-x(2)-[EPS] B 2: 49.3933 3( 3) A-x(3)-L-x(5)-I-x(4,5)-A-[NV]-Y-[FV]-x(2)-[KR]-x(2)-[DQR]-x(3)-[ALV]-F-[GLP]-x-[DK]-D C 3: 48.8933 3( 3) K-x(1,2)-L-x(5)-I-x(4,5)-A-[NV]-Y-[FV]-x(2)-[KR]-x(2)-[DQR]-x(3)-[ALV]-F-[GLP]-x-[DK]-D D 4: 44.3096 3( 3) A-x(3)-L-x(2)-[CGP]-L-x(0,1)-R-x(2,4)-A-x(4)-[ADG]-x-[AG]-x-[GIL]-x-[GS]-x(2)-[ILP]-x(4)-[EGN]-x(3)-[EQT]-x(2)-[EKR] E 5: 43.5489 3( 3) G-[IL]-[EG]-P-x(1,2)-A-x(3)-L-x(4,5)-R-[FLM]-x-[DTV]-x(2)-[CP]-x-[DP]-x-[GIV]-[GIV] F 6: 39.4242 3( 3) P-x(1,2)-A-x(3)-L-x(2)-[CGP]-L-x(0,1)-R-x-[DEP]-[ATV]-x(4)-[AD]-x-[AGV]-[AGI]-[AL] G 7: 36.5246 3( 3) M-x-[FL]-K-x(1,2)-E-x(1,3)-L-I-[HK]-[AIL]-x-[AGN]-[AIV]-x(3)-[AGT] H 8: 35.8179 3( 3) G-x(1,3)-K-x(1,3)-V-F-[ALP]-P-x-[DE]-x-[GIL]-[AI]-x(4)-[PST]-x(3)-[DPS] I 9: 34.6698 3( 3) V-F-[ALP]-P-x(3,4)-I-x(1,2)-R-x(2)-[GPS]-x(2)-[LP]-[AS]-[DQ] J 10: 34.1886 4( 3) K-x(1,3)-V-F-[ALP]-P-x(3,4)-I-x-[QR]-x(2)-[PS]-x(3)-[APS]-[AD] K 11: 33.5551 3( 3) E-x-A-x(0,1)-K-x(1,3)-L-x(3)-P-[AGL]-x(4)-[GPT]-x(3)-[FI]-[AG]-x(2)-[DEG] L 12: 31.3658 3( 3) L-x(4,5)-G-I-G-x-W-[ST]-A-x(3,4)-L M 13: 30.4992 3( 3) I-x(3,4)-A-x(3)-L-x(3,5)-R-x-[DGP]-x(3)-P-x-[CD]-x-[DGV]-[AGI] N 14: 27.7938 3( 3) A-x(2)-[ENQ]-[AIL]-[AIL]-K-x(2)-G-x(1,2)-P-x(2,3)-A O 15: 27.7300 3( 3) A-x(3)-L-x(2,3)-A-R-x(4,5)-L-x-[DGV]-x-[GPV]-x-[ALP] P 16: 27.6957 3( 3) G-I-G-x-W-[ST]-A-x(3,4)-L Q 17: 23.5257 3( 3) I-G-x-W-[ST]-A-x(3,4)-L R 18: 23.0744 3( 3) I-x(0,1)-P-x(2)-A-x(3)-L-x(2)-[CGN]-L S 19: 22.4778 3( 3) A-[AET]-x(4)-R-V-x(0,2)-L-Y T 20: 19.3503 4( 3) K-x(1,3)-V-F-x-P-x(3,4)-I Best patterns with alignements: fitness hits(seqs) Pattern A 1: 54.4081 3( 3) D-x-F-x(0,2)-L-[ACP]-x-[DGT]-x-L-x(2)-Q-x(2)-[GLP]-[AGQ]-x-[AT]-x-[AS]-x(3)-[QR]-x-[AV]-[ES]-x-[FWY]-x-[DGP]-x(2)-[EPS] Occurences: 3(3) 3MG2_ECOLI : 232- 265: gwqak DvF--LPdDyLikQrfPGmTpAqirRyAErWkPwrS yallh 3MGA_BACSU : 129- 164: vigip DlFeaLCwGvLgqQinLAfAySlkkQfVEaFgDsiE wngkk MAG_YEAST : 82- 117: pntle DyFirLAsTiLsqQisGQaAeSikaRvVSlYgGafP dykil B 2: 49.3933 3( 3) A-x(3)-L-x(5)-I-x(4,5)-A-[NV]-Y-[FV]-x(2)-[KR]-x(2)-[DQR]-x(3)-[ALV]-F-[GLP]-x-[DK]-D Occurences: 3(3) 3MG2_ECOLI : 205- 238: gdveq AmktLqtfpgIgrwt-ANYFalRgwQakdVFLpDD ylikq 3MGA_BACSU : 225- 258: mnfkd AeknLikirgIgpwt-ANYVlmRclRfptAFPiDD vglih MAG_YEAST : 136- 170: kcaei AkcgLskrkmIyleslAVYFteKykDiekLFGqKD ndeev C 3: 48.8933 3( 3) K-x(1,2)-L-x(5)-I-x(4,5)-A-[NV]-Y-[FV]-x(2)-[KR]-x(2)-[DQR]-x(3)-[ALV]-F-[GLP]-x-[DK]-D Occurences: 3(3) 3MG2_ECOLI : 207- 238: veqam Kt-LqtfpgIgrwt-ANYFalRgwQakdVFLpDD ylikq 3MGA_BACSU : 227- 258: fkdae Kn-LikirgIgpwt-ANYVlmRclRfptAFPiDD vglih MAG_YEAST : 137- 170: caeia KcgLskrkmIyleslAVYFteKykDiekLFGqKD ndeev D 4: 44.3096 3( 3) A-x(3)-L-x(2)-[CGP]-L-x(0,1)-R-x(2,4)-A-x(4)-[ADG]-x-[AG]-x-[GIL]-x-[GS]-x(2)-[ILP]-x(4)-[EGN]-x(3)-[EQT]-x(2)-[EKR] Occurences: 3(3) 3MG2_ECOLI : 168- 207: aadpq AlkaLgmPLkRae--AlihlAnAaLeGtlPmtipGdveQamK tlqtf 3MGA_BACSU : 240- 279: igpwt AnyvLmrCL-Rfpt-AfpidDvGlIhSikIlrnmNrkpTkdE ileis MAG_YEAST : 191- 232: igpws AkmfLisGLkRmdvfApedlGiArGfSkyLsdkpElekElmR erkvv E 5: 43.5489 3( 3) G-[IL]-[EG]-P-x(1,2)-A-x(3)-L-x(4,5)-R-[FLM]-x-[DTV]-x(2)-[CP]-x-[DP]-x-[GIV]-[GIV] Occurences: 3(3) 3MG2_ECOLI : 66- 91: inlsa GLEPv-AaecLakms-RLfDlqCnPqIV ngalg 3MGA_BACSU : 234- 260: likir GIGPwtAnyvLmrcl-RFpTafPiDdVG lihsi MAG_YEAST : 185- 212: vtnvk GIGPwsAkmfLisglkRMdVfaPeDlGI argfs F 6: 39.4242 3( 3) P-x(1,2)-A-x(3)-L-x(2)-[CGP]-L-x(0,1)-R-x-[DEP]-[ATV]-x(4)-[AD]-x-[AGV]-[AGI]-[AL] Occurences: 3(3) 3MG2_ECOLI : 166- 190: laaad Pq-AlkaLgmPLkRaEAlihlAnAAL egtlp 3MGA_BACSU : 237- 261: irgig PwtAnyvLmrCL-RfPTafpiDdVGL ihsik MAG_YEAST : 188- 213: vkgig PwsAkmfLisGLkRmDVfapeDlGIA rgfsk G 7: 36.5246 3( 3) M-x-[FL]-K-x(1,2)-E-x(1,3)-L-I-[HK]-[AIL]-x-[AGN]-[AIV]-x(3)-[AGT] Occurences: 3(3) 3MG2_ECOLI : 174- 192: lkalg MpLKraEa--LIHLaNAaleG tlpmt 3MGA_BACSU : 220- 239: eklmk MnFKdaEkn-LIKIrGIgpwT anyvl MAG_YEAST : 1- 20: MkLKr-EydeLIKAdAVkeiA kelgs H 8: 35.8179 3( 3) G-x(1,3)-K-x(1,3)-V-F-[ALP]-P-x-[DE]-x-[GIL]-[AI]-x(4)-[PST]-x(3)-[DPS] Occurences: 3(3) 3MG2_ECOLI : 227- 250: yfalr GwqaKd--VFLPdDyLIkqrfPgmtP aqirr 3MGA_BACSU : 167- 189: siewn Gk--Kyw-VFPPyErIArltpTdlaD ikmtv MAG_YEAST : 198- 221: mflis Gl--KrmdVFAPeDlGIargfSkylS dkpel I 9: 34.6698 3( 3) V-F-[ALP]-P-x(3,4)-I-x(1,2)-R-x(2)-[GPS]-x(2)-[LP]-[AS]-[DQ] Occurences: 3(3) 3MG2_ECOLI : 233- 252: wqakd VFLPddylIkqRfpGmtPAQ irrya 3MGA_BACSU : 172- 189: gkkyw VFPPyer-Ia-RltPtdLAD ikmtv MAG_YEAST : 204- 222: lkrmd VFAPedlgIa-RgfSkyLSD kpele J 10: 34.1886 4( 3) K-x(1,3)-V-F-[ALP]-P-x(3,4)-I-x-[QR]-x(2)-[PS]-x(3)-[APS]-[AD] Occurences: 4(3) 3MG2_ECOLI : 231- 251: rgwqa Kd--VFLPddylIkQrfPgmtPA qirry 3MGA_BACSU : 168- 189: iewng KkywVFPPyer-IaRltPtdlAD ikmtv 3MGA_BACSU : 169- 189: ewngk Kyw-VFPPyer-IaRltPtdlAD ikmtv MAG_YEAST : 200- 222: lisgl KrmdVFAPedlgIaRgfSkylSD kpele K 11: 33.5551 3( 3) E-x-A-x(0,1)-K-x(1,3)-L-x(3)-P-[AGL]-x(4)-[GPT]-x(3)-[FI]-[AG]-x(2)-[DEG] Occurences: 3(3) 3MG2_ECOLI : 203- 227: ipgdv EqAmKt--LqtfPGigrwTanyFAlrG wqakd 3MGA_BACSU : 104- 129: ltpfy EmA-KadpLlkmPArkfyGlrvIGipD lfeal MAG_YEAST : 18- 41: adavk EiA-Ke--LgsrPLevalPekyIArhE ekfnm L 12: 31.3658 3( 3) L-x(4,5)-G-I-G-x-W-[ST]-A-x(3,4)-L Occurences: 3(3) 3MG2_ECOLI : 209- 225: qamkt Lqtfp-GIGrWTAnyfaL rgwqa 3MGA_BACSU : 229- 244: daekn Likir-GIGpWTAnyv-L mrclr MAG_YEAST : 179- 195: evies LvtnvkGIGpWSAkmf-L isglk M 13: 30.4992 3( 3) I-x(3,4)-A-x(3)-L-x(3,5)-R-x-[DGP]-x(3)-P-x-[CD]-x-[DGV]-[AGI] Occurences: 3(3) 3MG2_ECOLI : 90- 113: qcnpq Ivng-AlgrLgaa--RpGlrlPgCvDA feqgv 3MGA_BACSU : 235- 260: ikirg IgpwtAnyvLmrcl-RfPtafPiDdVG lihsi MAG_YEAST : 186- 212: tnvkg IgpwsAkmfLisglkRmDvfaPeDlGI argfs N 14: 27.7938 3( 3) A-x(2)-[ENQ]-[AIL]-[AIL]-K-x(2)-G-x(1,2)-P-x(2,3)-A Occurences: 3(3) 3MG2_ECOLI : 164- 179: qrlaa AdpQALKalGm-PlkrA ealih 3MGA_BACSU : 225- 240: mnfkd AekNLIKirGigPwt-A nyvlm MAG_YEAST : 15- 31: likad AvkEIAKelGsrPlevA lpeky O 15: 27.7300 3( 3) A-x(3)-L-x(2,3)-A-R-x(4,5)-L-x-[DGV]-x-[GPV]-x-[ALP] Occurences: 3(3) 3MG2_ECOLI : 94- 113: qivng AlgrLga-ARpglr-LpGcVdA feqgv 3MGA_BACSU : 108- 128: yemak AdplLkmpARkfyg-LrViGiP dlfea MAG_YEAST : 206- 226: rmdvf ApedLgi-ARgfskyLsDkPeL ekelm P 16: 27.6957 3( 3) G-I-G-x-W-[ST]-A-x(3,4)-L Occurences: 3(3) 3MG2_ECOLI : 214- 225: lqtfp GIGrWTAnyfaL rgwqa 3MGA_BACSU : 234- 244: likir GIGpWTAnyv-L mrclr MAG_YEAST : 185- 195: vtnvk GIGpWSAkmf-L isglk Q 17: 23.5257 3( 3) I-G-x-W-[ST]-A-x(3,4)-L Occurences: 3(3) 3MG2_ECOLI : 215- 225: qtfpg IGrWTAnyfaL rgwqa 3MGA_BACSU : 235- 244: ikirg IGpWTAnyv-L mrclr MAG_YEAST : 186- 195: tnvkg IGpWSAkmf-L isglk R 18: 23.0744 3( 3) I-x(0,1)-P-x(2)-A-x(3)-L-x(2)-[CGN]-L Occurences: 3(3) 3MG2_ECOLI : 51- 63: gvvta I-PdiArhtLhiNL sagle 3MGA_BACSU : 235- 248: ikirg IgPwtAnyvLmrCL rfpta MAG_YEAST : 186- 199: tnvkg IgPwsAkmfLisGL krmdv S 19: 22.4778 3( 3) A-[AET]-x(4)-R-V-x(0,2)-L-Y Occurences: 3(3) 3MG2_ECOLI : 131- 142: vsvam AAkltaRVaqLY gerld 3MGA_BACSU : 294- 303: ewqsy ATfylwRV--LY MAG_YEAST : 101- 112: isgqa AEsikaRVvsLY ggafp T 20: 19.3503 4( 3) K-x(1,3)-V-F-x-P-x(3,4)-I Occurences: 4(3) 3MG2_ECOLI : 231- 241: rgwqa Kd--VFlPddylI kqrfp 3MGA_BACSU : 168- 179: iewng KkywVFpPyer-I arltp 3MGA_BACSU : 169- 179: ewngk Kyw-VFpPyer-I arltp MAG_YEAST : 200- 212: lisgl KrmdVFaPedlgI argfs Number of patterns evaluated by Pratt:7898 Total running time: 2 seconds