------------------------------------------------------------ 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 YBR177C 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 YBR177C.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HPS1_HUMAN 425 YB27_YEAST 451 YHET_ECOLI 340 Pratt run started at Thu Feb 6 21:36:01 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 23.0203 3( 3) L-V-V-x(1,3)-G-x(0,2)-L-x-G 2: 19.8503 3( 3) V-x(4)-G-x-L-x(0,2)-P-x(3)-L 3: 19.8503 3( 3) G-x(2)-G-x(3)-G-x(1,2)-L-x(2,3)-P 4: 19.8503 3( 3) V-x(3)-L-x(2,4)-H-G-x(3)-G 5: 19.8503 3( 3) E-x(2,3)-P-x(3,4)-Y-x(2)-T-x(3)-G 6: 19.8503 3( 3) I-x(2)-P-x(1,2)-L-x(5)-D-x(0,1)-P 7: 19.8503 3( 3) L-x-A-x(0,1)-A-A-x(1,2)-L 8: 19.8503 3( 3) F-x(4,5)-Q-x(0,1)-R-x(5)-L-x-A 9: 19.8503 3( 3) G-x(2)-G-x-V-x(1,3)-H-x(2)-G 10: 19.3503 3( 3) L-x(2,3)-P-x(3)-L-x-S-x(0,2)-R 11: 19.3503 3( 3) V-x(2,3)-L-x(2,4)-H-G-x(3)-G 12: 19.3503 4( 3) V-x(2,3)-L-x(0,2)-H-G-x(3)-G 13: 19.3503 3( 3) P-x(4)-Y-x(2)-T-x(3,5)-G-x(4,5)-I 14: 19.3503 3( 3) L-K-x(2,3)-A-x(3)-L-x(0,2)-Y 15: 19.3503 3( 3) N-x-L-x(2)-L-x(1,3)-E-x(3,4)-P 16: 19.3503 3( 3) T-x(2)-V-x(0,2)-G-x(1,2)-L-G 17: 19.3503 3( 3) H-x(4,5)-S-x-E-x(4)-S-x(0,2)-L 18: 19.3503 3( 3) G-x(2)-G-x(0,1)-V-x(1,3)-H-x(2)-G 19: 18.8503 4( 3) L-x(1,3)-P-x(3)-L-x-S-x(0,2)-R 20: 18.8503 4( 3) L-x(0,2)-P-x(3)-L-x-S-x(0,2)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 52.5075 3( 3) I-x(2)-P-x(1,2)-L-[IV]-x(2)-[AS]-[DKR]-D-x(0,1)-P-[FLV]-[MV]-x(2)-[DQS]-x-[ILP]-x(2)-[IP]-x-[ES]-x-[NPS]-[EP] B 2: 47.6037 3( 3) L-K-x(2,3)-A-x(2)-[DK]-L-x(0,2)-Y-x(2)-[DT]-x-[GIP]-[IL]-[NQS]-x(3)-L-x-[AS]-[ACV]-x(4)-[EK] C 3: 45.3185 3( 3) G-[EH]-[LV]-G-[FV]-x-[EGN]-G-x(1,2)-L-x(2,3)-P-x(4)-[DEN]-x(2)-[FIV]-x(2)-[FWY]-x-[NPT]-[AET] D 4: 42.7645 3( 3) F-x(4,5)-Q-x(0,1)-R-x(3)-[NR]-x-L-x-A-[DNV]-[AGN]-x(3)-[GIL]-[AI]-x(4)-[NQT]-x-[LP]-x-[EGN] E 5: 40.6251 3( 3) V-x(3)-L-x(2,4)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] F 6: 40.1251 3( 3) V-x(2,3)-L-x(2,4)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] G 7: 40.1251 4( 3) V-x(2,3)-L-x(0,2)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] H 8: 36.8402 3( 3) H-x(4,5)-S-x-E-[DPT]-x(3)-S-x(0,2)-L-x(4)-[RS]-x(2)-[GQ]-x(2)-[DPQ]-[NTV]-[AV] I 9: 31.4352 3( 3) V-x(4)-G-[AET]-L-x(0,2)-P-[NQ]-x(2)-L-[EPT]-[DS] J 10: 30.9977 3( 3) T-x(2)-V-x(0,2)-G-x(1,2)-L-G-[GV]-[NP]-x-[GLV]-[ACS] K 11: 28.4395 3( 3) L-x(2,3)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] L 12: 28.3033 3( 3) L-V-V-x(1,3)-G-x(0,2)-L-[AEG]-G-[GNS] M 13: 27.9395 4( 3) L-x(1,3)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] N 14: 27.9395 4( 3) L-x(0,2)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] O 15: 26.6711 3( 3) L-x-A-x(0,1)-A-A-x(1,2)-L-x-[ANV]-x(4)-L P 16: 25.6738 3( 3) G-x(2)-G-x-V-x(1,3)-H-x(2)-G-x-[NRS]-x(2)-[IP] Q 17: 25.2865 3( 3) E-x(2,3)-P-x(3,4)-Y-x(2)-T-x(3)-G-x-[LMV]-[AGV] R 18: 25.1738 3( 3) G-x(2)-G-x(0,1)-V-x(1,3)-H-x(2)-G-x-[NRS]-x(2)-[IP] S 19: 24.6832 3( 3) P-x(3)-[EGT]-Y-[GNQ]-x-T-x(3,5)-G-x(4,5)-I T 20: 21.9803 3( 3) N-x-L-[AEG]-x-L-x(1,3)-E-x(3,4)-P Best patterns with alignements: fitness hits(seqs) Pattern A 1: 52.5075 3( 3) I-x(2)-P-x(1,2)-L-[IV]-x(2)-[AS]-[DKR]-D-x(0,1)-P-[FLV]-[MV]-x(2)-[DQS]-x-[ILP]-x(2)-[IP]-x-[ES]-x-[NPS]-[EP] Occurences: 3(3) HPS1_HUMAN : 333- 361: rylhr IyvPlmLVnaADD-PLVheSlLtiPkSlSE krenv YB27_YEAST : 383- 411: nrvdt IrvPt-LVinSRDdPVVgpDqPysIvEkNP rilyc YHET_ECOLI : 268- 296: pmlnr IakPt-LIihAKDdPFMdhQvIpkPeSlPP qveyq B 2: 47.6037 3( 3) L-K-x(2,3)-A-x(2)-[DK]-L-x(0,2)-Y-x(2)-[DT]-x-[GIP]-[IL]-[NQS]-x(3)-L-x-[AS]-[ACV]-x(4)-[EK] Occurences: 3(3) HPS1_HUMAN : 35- 64: vrcln LKsptAppDL--YfqDsGLSrflLkSCplltK eyipp YB27_YEAST : 55- 85: kyvpt LKng-AqfKLspYlfTgILQtlyLgAAdfskK fpvfy YHET_ECOLI : 207- 237: yllnl LKan-AarKLaaYpgTlPINlaqLkSVrrirE fddli C 3: 45.3185 3( 3) G-[EH]-[LV]-G-[FV]-x-[EGN]-G-x(1,2)-L-x(2,3)-P-x(4)-[DEN]-x(2)-[FIV]-x(2)-[FWY]-x-[NPT]-[AET] Occurences: 3(3) HPS1_HUMAN : 375- 403: lplhg GHLGFfEGsvLfpePltwmDklVveYaNA icqwe YB27_YEAST : 312- 339: vqvnm GELGVpNGs-LpdhPptvkNpsFymFtPE nlika YHET_ECOLI : 307- 333: ltehg GHVGFiGGt-Llh-PqmwlEsrIpdWlTT yleak D 4: 42.7645 3( 3) F-x(4,5)-Q-x(0,1)-R-x(3)-[NR]-x-L-x-A-[DNV]-[AGN]-x(3)-[GIL]-[AI]-x(4)-[NQT]-x-[LP]-x-[EGN] Occurences: 3(3) HPS1_HUMAN : 246- 277: raqet Fmqwd-QcRrfyNfLmADNmkkIIlshrQaLfG dhvkk YB27_YEAST : 228- 259: mdire FlqrekQ-RhpdRkLyAVGcsfGAtmlaNyLgE egdks YHET_ECOLI : 195- 225: hmekg Fsrvy-Q-RyllNlLkANAarkLAaypgTlPiN laqlk E 5: 40.6251 3( 3) V-x(3)-L-x(2,4)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] Occurences: 3(3) HPS1_HUMAN : 366- 388: ekren VmfvLpl--HGGhLGffEGsVlfPE pltwm YB27_YEAST : 163- 187: eelre VdlpLvvilHGLaGGshEPiIrsLA enlsr YHET_ECOLI : 298- 320: slppq VeyqLte--HGGhVGfiGGtLlhPQ mwles F 6: 40.1251 3( 3) V-x(2,3)-L-x(2,4)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] Occurences: 3(3) HPS1_HUMAN : 366- 388: ekren VmfvLpl--HGGhLGffEGsVlfPE pltwm YB27_YEAST : 163- 187: eelre VdlpLvvilHGLaGGshEPiIrsLA enlsr YHET_ECOLI : 298- 320: slppq VeyqLte--HGGhVGfiGGtLlhPQ mwles G 7: 40.1251 4( 3) V-x(2,3)-L-x(0,2)-H-G-[GL]-x-[GLV]-G-x(2)-[EG]-[GP]-x-[ILV]-x(2)-[LP]-[AEQ] Occurences: 4(3) HPS1_HUMAN : 366- 388: ekren VmfvLplHGGhLGffEGsVlfPE pltwm HPS1_HUMAN : 369- 388: envmf Vlp-L--HGGhLGffEGsVlfPE pltwm YB27_YEAST : 168- 187: vdlpl Vvi-L--HGLaGGshEPiIrsLA enlsr YHET_ECOLI : 298- 320: slppq VeyqLteHGGhVGfiGGtLlhPQ mwles H 8: 36.8402 3( 3) H-x(4,5)-S-x-E-[DPT]-x(3)-S-x(0,2)-L-x(4)-[RS]-x(2)-[GQ]-x(2)-[DPQ]-[NTV]-[AV] Occurences: 3(3) HPS1_HUMAN : 279- 307: alfgd HvkkpqSlEDtdlSr-LytatSlmQidDNV mrkfh YB27_YEAST : 172- 199: lvvil HglaggShEPiirS--LaenlSrsGrfQVV vlntr YHET_ECOLI : 120- 148: epnrm Hriyh-SgETedaSwfLrwlqRefGhaPTA avgys I 9: 31.4352 3( 3) V-x(4)-G-[AET]-L-x(0,2)-P-[NQ]-x(2)-L-[EPT]-[DS] Occurences: 3(3) HPS1_HUMAN : 159- 173: gyrca VlnhlGAL--PNieLTS prmft YB27_YEAST : 307- 323: fltrt VqvnmGELgvPNgsLPD hpptv YHET_ECOLI : 309- 325: ehggh VgfigGTLlhPQmwLES ripdw J 10: 30.9977 3( 3) T-x(2)-V-x(0,2)-G-x(1,2)-L-G-[GV]-[NP]-x-[GLV]-[ACS] Occurences: 3(3) HPS1_HUMAN : 199- 214: ktypl TqlVvvGfsLGGNiVC kylge YB27_YEAST : 306- 320: qfltr TvqVnmGe-LGVPnGS lpdhp YHET_ECOLI : 147- 160: fghap TaaV--GysLGGNmLA cllak K 11: 28.4395 3( 3) L-x(2,3)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] Occurences: 3(3) HPS1_HUMAN : 163- 182: avlnh LgalPnieLtSp-RMfTygcT wefga YB27_YEAST : 272- 291: saaat Lcn-PwdlLlSaiRMsQdwwS rtlfs YHET_ECOLI : 316- 333: figgt Llh-PqmwLeS--RIpDwltT yleak L 12: 28.3033 3( 3) L-V-V-x(1,3)-G-x(0,2)-L-[AEG]-G-[GNS] Occurences: 3(3) HPS1_HUMAN : 201- 211: ypltq LVVv--GfsLGGN ivcky YB27_YEAST : 167- 177: evdlp LVVilhG--LAGG shepi YHET_ECOLI : 75- 84: qhkpr LVVfh-G--LEGS lnspy M 13: 27.9395 4( 3) L-x(1,3)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] Occurences: 4(3) HPS1_HUMAN : 163- 182: avlnh LgalPnieLtSp-RMfTygcT wefga YB27_YEAST : 272- 291: saaat Lcn-PwdlLlSaiRMsQdwwS rtlfs YHET_ECOLI : 316- 333: figgt Llh-PqmwLeS--RIpDwltT yleak YHET_ECOLI : 317- 333: iggtl Lh--PqmwLeS--RIpDwltT yleak N 14: 27.9395 4( 3) L-x(0,2)-P-x(3)-L-x-S-x(0,2)-R-[IM]-x-[DQT]-x(3)-[ST] Occurences: 4(3) HPS1_HUMAN : 166- 182: nhlga L--PnieLtSp-RMfTygcT wefga YB27_YEAST : 272- 291: saaat LcnPwdlLlSaiRMsQdwwS rtlfs YHET_ECOLI : 316- 333: figgt LlhPqmwLeS--RIpDwltT yleak YHET_ECOLI : 317- 333: iggtl Lh-PqmwLeS--RIpDwltT yleak O 15: 26.6711 3( 3) L-x-A-x(0,1)-A-A-x(1,2)-L-x-[ANV]-x(4)-L Occurences: 3(3) HPS1_HUMAN : 19- 33: fdgvk LaAvAAv-LyVivrcL nlksp YB27_YEAST : 266- 279: gdksp LsA-AAt-LcNpwdlL lsair YHET_ECOLI : 207- 222: yllnl LkAnAArkLaAypgtL pinla P 16: 25.6738 3( 3) G-x(2)-G-x-V-x(1,3)-H-x(2)-G-x-[NRS]-x(2)-[IP] Occurences: 3(3) HPS1_HUMAN : 84- 101: qtaly GkmGrVrspHpyGhRkfI tmsdg YB27_YEAST : 16- 31: npfhw GynGtVs--HivGeNgsI klhlk YHET_ECOLI : 101- 116: aaqkr GwlGvVm--HfrGcSgeP nrmhr Q 17: 25.2865 3( 3) E-x(2,3)-P-x(3,4)-Y-x(2)-T-x(3)-G-x-[LMV]-[AGV] Occurences: 3(3) HPS1_HUMAN : 170- 189: alpni EltsPrmftYgcTwefGaMV nyikk YB27_YEAST : 408- 425: pysiv Ekn-Pril-YcrTdlgGhLA yldkd YHET_ECOLI : 292- 310: vipkp EslpPqve-YqlTehgGhVG figgt YHET_ECOLI : 292- 310: vipkp Esl-PpqveYqlTehgGhVG figgt R 18: 25.1738 3( 3) G-x(2)-G-x(0,1)-V-x(1,3)-H-x(2)-G-x-[NRS]-x(2)-[IP] Occurences: 3(3) HPS1_HUMAN : 84- 101: qtaly GkmGrVrspHpyGhRkfI tmsdg YB27_YEAST : 16- 31: npfhw GynGtVs--HivGeNgsI klhlk YHET_ECOLI : 101- 116: aaqkr GwlGvVm--HfrGcSgeP nrmhr YHET_ECOLI : 101- 116: aaqkr GwlG-Vvm-HfrGcSgeP nrmhr S 19: 24.6832 3( 3) P-x(3)-[EGT]-Y-[GNQ]-x-T-x(3,5)-G-x(4,5)-I Occurences: 3(3) HPS1_HUMAN : 174- 192: ielts PrmfTYGcTwef--GamvnyI kktyp YB27_YEAST : 12- 31: wpain PfhwGYNgTvshivGengs-I klhlk YHET_ECOLI : 295- 312: kpesl PpqvEYQlTehg--Ghvgf-I ggtll T 20: 21.9803 3( 3) N-x-L-[AEG]-x-L-x(1,3)-E-x(3,4)-P Occurences: 3(3) HPS1_HUMAN : 161- 174: rcavl NhLGaLpniElts-P rmfty YB27_YEAST : 155- 166: rylkd NeLEeLr--Evdl-P lvvil YHET_ECOLI : 157- 171: yslgg NmLAcLlakEgndlP vdaav Number of patterns evaluated by Pratt:13911 Total running time: 4 seconds