------------------------------------------------------------ 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 V8_SER 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 V8_SER.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ETA_STAAU 280 ETB_STAAU 277 GSEP_BACLI 316 MPR_BACSU 313 STSP_STAAU 336 Pratt run started at Thu Feb 6 21:32:32 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.8503 5( 5) T-x(2,3)-G-x(1,2)-S-G-S 2: 19.8503 6( 5) T-x(1,2)-G-x(1,2)-S-G-S 3: 19.3503 5( 5) Y-x(3,5)-G-x(1,2)-S-G-S 4: 16.1802 5( 5) G-x-S-x-S-x(2,3)-F 5: 16.1802 7( 5) G-x(1,2)-S-G-S 6: 16.1802 5( 5) G-x(4)-K-x(0,1)-T-x(2)-T 7: 15.6802 5( 5) T-x(0,1)-V-x(0,1)-G-x(2)-G 8: 15.6802 5( 5) T-x(2,3)-G-x(0,1)-N-x(2)-S 9: 15.6802 6( 5) Y-x(2,3)-T-x(2)-G-x(3,4)-S 10: 15.6802 6( 5) Y-x(3)-T-x(4)-S-x(1,3)-S 11: 15.1802 5( 5) Y-x(3,4)-T-x-G-x(3,5)-G 12: 15.1802 5( 5) G-x(5)-T-x(0,1)-N-x(3,5)-A 13: 15.1802 6( 5) G-x(2,3)-G-x(2)-T-x(0,2)-T 14: 15.1802 7( 5) T-x(0,1)-V-x(2,4)-G-x(5)-T 15: 14.6802 9( 5) G-x(0,2)-S-G-x(1,3)-F 16: 14.6802 5( 5) T-x(2,4)-T-N-x(2,4)-A 17: 14.6802 5( 5) G-x(2,4)-T-x(0,2)-T-N 18: 14.6802 5( 5) A-x(1,3)-G-x(1,3)-G-K 19: 14.6802 6( 5) G-x(0,2)-T-x(2)-T-x(1,3)-V 20: 12.5102 6( 5) S-G-S Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 45.5654 5( 5) Y-x(3)-T-x(2)-[CG]-[NQ]-S-x-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] B 2: 42.2422 5( 5) T-x(2,3)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] C 3: 42.2422 6( 5) T-x(1,2)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] D 4: 41.7422 5( 5) Y-x(3,5)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] E 5: 38.5722 7( 5) G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] F 6: 34.9021 5( 5) S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] G 7: 33.1702 5( 5) T-x(2,3)-G-x(0,1)-N-[GS]-[GST]-S-x-[IPV]-[FY]-[GN]-x(3)-[EGS] H 8: 29.4271 5( 5) G-x-S-[GS]-S-x(2,3)-F-[ENP]-x(3)-[EST]-x(2)-[GNT]-x(3)-[DGPS] I 9: 26.8220 5( 5) G-x-[LPV]-x-[DG]-K-x(0,1)-T-x-[GLV]-T-x(4)-[ASTV] J 10: 24.3774 5( 5) G-x-[DENR]-[AST]-x(2)-T-x(0,1)-N-x(3,5)-A-x(2)-[AGLV]-[ADNS] K 11: 22.2312 5( 5) G-x(0,2)-T-x-[AILV]-T-x(1,3)-V-[FLV]-x-[AGN] L 12: 22.1764 9( 5) G-x(0,2)-S-G-x(1,3)-F-x(4)-[EGS]-x(2)-[EGN]-x(3)-[GPST] M 13: 20.6885 5( 5) G-x(2,3)-G-x(2)-T-x(0,2)-T-[AN]-x(3)-[AIPV] N 14: 20.4139 5( 5) Y-x(3,4)-T-x-G-x(3,5)-G-[NQS]-[DPT] O 15: 19.4933 5( 5) A-x(1,3)-G-x(1,3)-G-K-[DNTV]-[NST] P 16: 18.3343 5( 5) T-x(0,1)-V-x(0,1)-G-x(2)-G-x(4)-[ANT] Q 17: 18.3031 6( 5) Y-x(2,3)-T-x(2)-G-x(3,4)-S-[GPV] R 18: 17.8674 5( 5) G-x-[LPV]-x-[DG]-K-x(0,1)-T S 19: 17.8600 5( 5) T-x(0,1)-V-x(2,4)-G-[DHK]-x(4)-T T 20: 15.1802 7( 5) T-x(0,1)-V-x(2,4)-G-x(5)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 45.5654 5( 5) Y-x(3)-T-x(2)-[CG]-[NQ]-S-x-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 5(5) ETA_STAAU : 224- 250: srglr YygfTvpGNSgSGIFNsnGElvGihsS kvshl ETB_STAAU : 208- 234: fndsq YfgyTevGNSgSGIFNlkGEliGihsG kggqh GSEP_BACLI : 252- 278: tyklq YamdTygGQSgSPVFEqsSSrtNcsgP cslav MPR_BACSU : 258- 284: tyklt YttdTygCQSgSPVYRnySDtgQtaiA ihtng STSP_STAAU : 228- 254: geamq YdlsTtgGNSgSPVFNekNEviGihwG gvpne B 2: 42.2422 5( 5) T-x(2,3)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 5(5) ETA_STAAU : 228- 250: ryygf Tvp-Gn-SGSGIFNsnGElvGihsS kvshl ETB_STAAU : 212- 234: qyfgy Tev-Gn-SGSGIFNlkGEliGihsG kggqh GSEP_BACLI : 256- 278: qyamd Tyg-Gq-SGSPVFEqsSSrtNcsgP cslav MPR_BACSU : 260- 284: kltyt TdtyGcqSGSPVYRnySDtgQtaiA ihtng STSP_STAAU : 232- 254: qydls Ttg-Gn-SGSPVFNekNEviGihwG gvpne C 3: 42.2422 6( 5) T-x(1,2)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 6(5) ETA_STAAU : 228- 250: ryygf TvpGn-SGSGIFNsnGElvGihsS kvshl ETB_STAAU : 212- 234: qyfgy TevGn-SGSGIFNlkGEliGihsG kggqh GSEP_BACLI : 256- 278: qyamd TygGq-SGSPVFEqsSSrtNcsgP cslav GSEP_BACLI : 256- 278: qyamd Ty-GgqSGSPVFEqsSSrtNcsgP cslav MPR_BACSU : 262- 284: tyttd Ty-GcqSGSPVYRnySDtgQtaiA ihtng STSP_STAAU : 232- 254: qydls TtgGn-SGSPVFNekNEviGihwG gvpne STSP_STAAU : 232- 254: qydls Tt-GgnSGSPVFNekNEviGihwG gvpne STSP_STAAU : 233- 254: ydlst Tg-Gn-SGSPVFNekNEviGihwG gvpne D 4: 41.7422 5( 5) Y-x(3,5)-G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 5(5) ETA_STAAU : 225- 250: rglry YgftvpGn-SGSGIFNsnGElvGihsS kvshl ETB_STAAU : 211- 234: sqyfg Ytev--Gn-SGSGIFNlkGEliGihsG kggqh GSEP_BACLI : 252- 278: tyklq YamdtyGgqSGSPVFEqsSSrtNcsgP cslav MPR_BACSU : 258- 284: tyklt YttdtyGcqSGSPVYRnySDtgQtaiA ihtng STSP_STAAU : 228- 254: geamq YdlsttGgnSGSPVFNekNEviGihwG gvpne E 5: 38.5722 7( 5) G-x(1,2)-S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 7(5) ETA_STAAU : 231- 250: gftvp Gn-SGSGIFNsnGElvGihsS kvshl ETB_STAAU : 215- 234: gytev Gn-SGSGIFNlkGEliGihsG kggqh GSEP_BACLI : 258- 278: amdty GgqSGSPVFEqsSSrtNcsgP cslav GSEP_BACLI : 259- 278: mdtyg Gq-SGSPVFEqsSSrtNcsgP cslav MPR_BACSU : 264- 284: ttdty GcqSGSPVYRnySDtgQtaiA ihtng STSP_STAAU : 234- 254: dlstt GgnSGSPVFNekNEviGihwG gvpne STSP_STAAU : 235- 254: lsttg Gn-SGSPVFNekNEviGihwG gvpne F 6: 34.9021 5( 5) S-G-S-[GP]-[IV]-[FY]-[ENR]-x(2)-[GNS]-[DES]-x(2)-[GNQ]-x(3)-[AGPS] Occurences: 5(5) ETA_STAAU : 233- 250: tvpgn SGSGIFNsnGElvGihsS kvshl ETB_STAAU : 217- 234: tevgn SGSGIFNlkGEliGihsG kggqh GSEP_BACLI : 261- 278: tyggq SGSPVFEqsSSrtNcsgP cslav MPR_BACSU : 267- 284: tygcq SGSPVYRnySDtgQtaiA ihtng STSP_STAAU : 237- 254: ttggn SGSPVFNekNEviGihwG gvpne G 7: 33.1702 5( 5) T-x(2,3)-G-x(0,1)-N-[GS]-[GST]-S-x-[IPV]-[FY]-[GN]-x(3)-[EGS] Occurences: 5(5) ETA_STAAU : 228- 243: ryygf Tvp-G-NSGSgIFNsngE lvgih ETB_STAAU : 212- 227: qyfgy Tev-G-NSGSgIFNlkgE ligih GSEP_BACLI : 156- 173: fagta TvspGrNGTSyPYGsvkS tryfi MPR_BACSU : 160- 177: wasti TaapGrNGSSyPYGtysG tmfys STSP_STAAU : 232- 247: qydls Ttg-G-NSGSpVFNeknE vigih H 8: 29.4271 5( 5) G-x-S-[GS]-S-x(2,3)-F-[ENP]-x(3)-[EST]-x(2)-[GNT]-x(3)-[DGPS] Occurences: 5(5) ETA_STAAU : 231- 250: gftvp GnSGSgi-FNsngElvGihsS kvshl ETB_STAAU : 215- 234: gytev GnSGSgi-FNlkgEliGihsG kggqh GSEP_BACLI : 259- 278: mdtyg GqSGSpv-FEqssSrtNcsgP cslav MPR_BACSU : 224- 244: ssspv GlSSSvtgFPcdkTfgTmwsD tkpir STSP_STAAU : 235- 254: lsttg GnSGSpv-FNeknEviGihwG gvpne I 9: 26.8220 5( 5) G-x-[LPV]-x-[DG]-K-x(0,1)-T-x-[GLV]-T-x(4)-[ASTV] Occurences: 5(5) ETA_STAAU : 97- 112: qtsat GvLiGKnTvLTnrhiA kfang ETB_STAAU : 83- 98: stlat GvLiGKnTiVTnyhvA reaak GSEP_BACLI : 225- 239: tvtis GyPgDK-TaGTqwqhS gpiai MPR_BACSU : 231- 245: sssvt GfPcDK-TfGTmwsdT kpirs STSP_STAAU : 106- 121: tfias GvVvGKdTlLTnkhvV dathg J 10: 24.3774 5( 5) G-x-[DENR]-[AST]-x(2)-T-x(0,1)-N-x(3,5)-A-x(2)-[AGLV]-[ADNS] Occurences: 5(5) ETA_STAAU : 101- 116: tgvli GkNTvlT-Nrhi--AkfAN gdpsk ETB_STAAU : 87- 102: tgvli GkNTivT-Nyhv--AreAA knpsn GSEP_BACLI : 181- 197: yfips GwRSgnT-Nydyg-AieLS epign MPR_BACSU : 46- 63: svsnt GkEAdaTkNqtsk-AdqVS apyeg STSP_STAAU : 110- 127: sgvvv GkDTllT-NkhvvdAthGD phalk K 11: 22.2312 5( 5) G-x(0,2)-T-x-[AILV]-T-x(1,3)-V-[FLV]-x-[AGN] Occurences: 5(5) ETA_STAAU : 91- 101: nvfvk Gq-TsATg--VLiG kntvl ETB_STAAU : 77- 87: tvfvk Gs-TlATg--VLiG kntiv GSEP_BACLI : 297- 307: ssynr G--TrITke-VFdN ltnwk MPR_BACSU : 296- 306: ssynl G--TrVTnd-VFnN iqywa STSP_STAAU : 110- 123: sgvvv GkdTlLTnkhVVdA thgdp L 12: 22.1764 9( 5) G-x(0,2)-S-G-x(1,3)-F-x(4)-[EGS]-x(2)-[EGN]-x(3)-[GPST] Occurences: 9(5) ETA_STAAU : 231- 250: gftvp Gn-SGsgiFnsngElvGihsS kvshl ETA_STAAU : 234- 250: vpgns G--SGi--FnsngElvGihsS kvshl ETB_STAAU : 215- 234: gytev Gn-SGsgiFnlkgEliGihsG kggqh ETB_STAAU : 218- 234: evgns G--SGi--FnlkgEliGihsG kggqh GSEP_BACLI : 258- 278: amdty GgqSGspvFeqssSrtNcsgP cslav GSEP_BACLI : 259- 278: mdtyg Gq-SGspvFeqssSrtNcsgP cslav MPR_BACSU : 173- 192: ssypy GtySGtm-FysvkGwtEskdT nydyg STSP_STAAU : 234- 254: dlstt GgnSGspvFneknEviGihwG gvpne STSP_STAAU : 235- 254: lsttg Gn-SGspvFneknEviGihwG gvpne M 13: 20.6885 5( 5) G-x(2,3)-G-x(2)-T-x(0,2)-T-[AN]-x(3)-[AIPV] Occurences: 5(5) ETA_STAAU : 97- 112: qtsat GvliGknTvlTNrhiA kfang ETB_STAAU : 83- 98: stlat GvliGknTivTNyhvA reaak GSEP_BACLI : 128- 143: igsct GwmiGpkTvaTAghcI ydtss MPR_BACSU : 210- 222: pgntv Gwy-GyrT--TNsssP vglss STSP_STAAU : 106- 121: tfias GvvvGkdTllTNkhvV dathg N 14: 20.4139 5( 5) Y-x(3,4)-T-x-G-x(3,5)-G-[NQS]-[DPT] Occurences: 5(5) ETA_STAAU : 79- 93: kdrqk Ypyn-TiGnvfvkGQT satgv ETB_STAAU : 255- 268: kissl YsvdnTfGdtl--GND lkkra GSEP_BACLI : 252- 264: tyklq Yamd-TyGgqs--GSP vfeqs MPR_BACSU : 258- 270: tyklt Yttd-TyGcqs--GSP vyrny STSP_STAAU : 228- 240: geamq Ydls-TtGgns--GSP vfnek O 15: 19.4933 5( 5) A-x(1,3)-G-x(1,3)-G-K-[DNTV]-[NST] Occurences: 5(5) ETA_STAAU : 95- 104: kgqts At--GvliGKNT vltnr ETB_STAAU : 81- 90: kgstl At--GvliGKNT ivtny GSEP_BACLI : 67- 75: glysk Aft-Gt--GKVN etkek MPR_BACSU : 64- 73: adqvs ApyeGt--GKTS kslyg STSP_STAAU : 104- 113: tgtfi As--GvvvGKDT lltnk P 16: 18.3343 5( 5) T-x(0,1)-V-x(0,1)-G-x(2)-G-x(4)-[ANT] Occurences: 5(5) ETA_STAAU : 228- 239: ryygf T-VpGnsGsgifN sngel ETB_STAAU : 212- 223: qyfgy TeV-GnsGsgifN lkgel GSEP_BACLI : 203- 213: epign T-V-GyfGysytT sslvg MPR_BACSU : 208- 218: gspgn T-V-GwyGyrttN ssspv STSP_STAAU : 198- 209: vnqni T-VtGypGdkpvA tmwes Q 17: 18.3031 6( 5) Y-x(2,3)-T-x(2)-G-x(3,4)-S-[GPV] Occurences: 6(5) ETA_STAAU : 224- 236: srglr YygfTvpGnsg-SG ifnsn ETA_STAAU : 225- 236: rglry Ygf-TvpGnsg-SG ifnsn ETB_STAAU : 208- 220: fndsq YfgyTevGnsg-SG ifnlk GSEP_BACLI : 252- 264: tyklq YamdTygGqsg-SP vfeqs MPR_BACSU : 170- 183: rngss YpygTysGtmfySV kgwte STSP_STAAU : 228- 240: geamq YdlsTtgGnsg-SP vfnek R 18: 17.8674 5( 5) G-x-[LPV]-x-[DG]-K-x(0,1)-T Occurences: 5(5) ETA_STAAU : 97- 104: qtsat GvLiGKnT vltnr ETB_STAAU : 83- 90: stlat GvLiGKnT ivtny GSEP_BACLI : 225- 231: tvtis GyPgDK-T agtqw MPR_BACSU : 231- 237: sssvt GfPcDK-T fgtmw STSP_STAAU : 106- 113: tfias GvVvGKdT lltnk S 19: 17.8600 5( 5) T-x(0,1)-V-x(2,4)-G-[DHK]-x(4)-T Occurences: 5(5) ETA_STAAU : 96- 107: gqtsa TgVli--GKntvlT nrhia ETB_STAAU : 82- 93: gstla TgVli--GKntivT nyhva GSEP_BACLI : 135- 146: migpk T-Vata-GHciydT ssgsf MPR_BACSU : 40- 52: aenpq TsVsnt-GKeadaT knqts STSP_STAAU : 198- 210: vnqni T-VtgypGDkpvaT mwesk T 20: 15.1802 7( 5) T-x(0,1)-V-x(2,4)-G-x(5)-T Occurences: 7(5) ETA_STAAU : 96- 107: gqtsa TgVli--GkntvlT nrhia ETB_STAAU : 82- 93: gstla TgVli--GkntivT nyhva GSEP_BACLI : 135- 146: migpk T-Vata-GhciydT ssgsf GSEP_BACLI : 219- 231: sslvg TtVtis-GypgdkT agtqw GSEP_BACLI : 220- 231: slvgt T-Vtis-GypgdkT agtqw MPR_BACSU : 40- 52: aenpq TsVsnt-GkeadaT knqts STSP_STAAU : 198- 210: vnqni T-VtgypGdkpvaT mwesk Number of patterns evaluated by Pratt:4766 Total running time: 3 seconds