------------------------------------------------------------ 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 NUCLEASE_NON_SPEC 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 NUCLEASE_NON_SPEC.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: NUC1_YEAST 329 NUCA_ANASP 274 NUCE_STRPN 274 NUCG_BOVIN 299 NUC_SERMA 266 Pratt run started at Thu Feb 6 20:25:33 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.8503 5( 5) D-R-G-H-x(4)-A 2: 16.6802 5( 5) R-G-H-x(4)-A 3: 15.6802 5( 5) Y-x(3,4)-G-x(3)-G-x(2,3)-A 4: 15.1802 5( 5) L-x(1,3)-G-x(2,3)-A-x-T 5: 15.1802 7( 5) G-x(0,1)-L-x-G-x(1,3)-A 6: 15.1802 7( 5) G-L-x(0,1)-G-x(0,2)-A 7: 14.6802 6( 5) Y-x(1,3)-S-N-x(2,4)-P 8: 12.5102 5( 5) N-x(3)-Q-x(4)-N 9: 12.5102 5( 5) G-H-x(4)-A 10: 12.0102 5( 5) L-x(5)-V-x(0,1)-P 11: 12.0102 6( 5) G-L-x(3,4)-A 12: 12.0102 6( 5) E-x(3)-R-x(1,2)-L 13: 12.0102 5( 5) G-x(2,3)-A-x-T 14: 12.0102 5( 5) G-x(0,1)-L-x(5)-G 15: 12.0102 5( 5) V-x(4,5)-G-x-L 16: 12.0102 6( 5) L-x(4)-R-x(3,4)-R 17: 12.0102 6( 5) L-x(4,5)-R-x(4)-R 18: 12.0102 6( 5) L-x(2)-L-x(1,2)-V 19: 12.0102 6( 5) T-x(4)-N-x(3,4)-T 20: 12.0102 5( 5) V-x(2,3)-V-x(5)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 26.6472 5( 5) D-R-G-H-x-[AL]-[AGP]-x-A B 2: 22.4772 5( 5) R-G-H-x-[AL]-[AGP]-x-A C 3: 20.8758 5( 5) Y-x(3,4)-G-x(3)-G-x(2,3)-A-x-[AST]-x-[DNP] D 4: 19.6355 5( 5) N-x(2)-[IPV]-Q-x(4)-N-x-[ADGN]-x(2)-[AEGN] E 5: 18.6151 5( 5) V-x(2,3)-V-x(2)-[AGLP]-x(2)-L-[DNPS]-x(3)-[GPST] F 6: 18.3071 5( 5) G-H-x-[AL]-[AGP]-x-A G 7: 17.3226 6( 5) Y-x(1,3)-S-N-x(2,4)-P-[NQS] H 8: 16.5345 6( 5) L-x(4,5)-R-x(4)-R-x(3)-[ADGST]-x(3)-[DGT] I 9: 15.1981 5( 5) V-x(4,5)-G-[PS]-L J 10: 15.1802 5( 5) L-x(1,3)-G-x(2,3)-A-x-T K 11: 15.1802 7( 5) G-x(0,1)-L-x-G-x(1,3)-A L 12: 15.1802 7( 5) G-L-x(0,1)-G-x(0,2)-A M 13: 13.9362 6( 5) G-L-x(3,4)-A-[EGNQS] N 14: 13.8928 5( 5) L-x(4)-R-x(3,4)-R-[AGPTV] O 15: 12.0102 5( 5) L-x(5)-V-x(0,1)-P P 16: 12.0102 6( 5) E-x(3)-R-x(1,2)-L Q 17: 12.0102 5( 5) G-x(2,3)-A-x-T R 18: 12.0102 5( 5) G-x(0,1)-L-x(5)-G S 19: 12.0102 6( 5) L-x(4,5)-R-x(4)-R T 20: 12.0102 6( 5) L-x(2)-L-x(1,2)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 26.6472 5( 5) D-R-G-H-x-[AL]-[AGP]-x-A Occurences: 5(5) NUC1_YEAST : 135- 143: frsgy DRGHqAPaA dakfs NUCA_ANASP : 121- 129: sgsgy DRGHiAPsA drtkt NUCE_STRPN : 157- 165: ythav DRGHlLGyA liggl NUCG_BOVIN : 140- 148: rgsgf DRGHlAAaA nhrws NUC_SERMA : 107- 115: aalkv DRGHqAPlA slagv B 2: 22.4772 5( 5) R-G-H-x-[AL]-[AGP]-x-A Occurences: 5(5) NUC1_YEAST : 136- 143: rsgyd RGHqAPaA dakfs NUCA_ANASP : 122- 129: gsgyd RGHiAPsA drtkt NUCE_STRPN : 158- 165: thavd RGHlLGyA liggl NUCG_BOVIN : 141- 148: gsgfd RGHlAAaA nhrws NUC_SERMA : 108- 115: alkvd RGHqAPlA slagv C 3: 20.8758 5( 5) Y-x(3,4)-G-x(3)-G-x(2,3)-A-x-[AST]-x-[DNP] Occurences: 5(5) NUC1_YEAST : 129- 144: gklrd Yfrs-GydrGhq-ApAaD akfsq NUCA_ANASP : 115- 130: vtpsm Ysgs-GydrGhi-ApSaD rtktt NUCE_STRPN : 164- 179: ghllg Yali-GgldGfd-AsTsN pknia NUCG_BOVIN : 134- 149: atnad Yrgs-GfdrGhl-AaAaN hrwsq NUC_SERMA : 171- 188: vtgpl YerdmGklpGtqkAhTiP saywk D 4: 19.6355 5( 5) N-x(2)-[IPV]-Q-x(4)-N-x-[ADGN]-x(2)-[AEGN] Occurences: 5(5) NUC1_YEAST : 44- 58: ptqkp NsnIQshsfNvDpsG ffkyg NUCA_ANASP : 146- 160: tflmt NmmPQtpdnNrNtwG nledy NUCE_STRPN : 182- 196: tsnpk NiaVQtawaNqAqaE ystgq NUCG_BOVIN : 165- 179: tfyls NvaPQvphlNqNawN nleky NUC_SERMA : 131- 145: lnyls NitPQksdlNqGawA rledq E 5: 18.6151 5( 5) V-x(2,3)-V-x(2)-[AGLP]-x(2)-L-[DNPS]-x(3)-[GPST] Occurences: 5(5) NUC1_YEAST : 191- 205: kkyks Vri-VtgPlyLPkkdP idnkf NUCA_ANASP : 22- 37: vgcsp VqsqVppLteLSpsiS vhlll NUCE_STRPN : 254- 268: efnvl Vpn-VqkGlqLDyrtG evtvt NUCG_BOVIN : 42- 56: lsrlp Vlp-VaaAagLPavpG apagg NUC_SERMA : 42- 56: ggssn Vsi-VrhAytLNnnsT tkfan F 6: 18.3071 5( 5) G-H-x-[AL]-[AGP]-x-A Occurences: 5(5) NUC1_YEAST : 137- 143: sgydr GHqAPaA dakfs NUCA_ANASP : 123- 129: sgydr GHiAPsA drtkt NUCE_STRPN : 159- 165: havdr GHlLGyA liggl NUCG_BOVIN : 142- 148: sgfdr GHlAAaA nhrws NUC_SERMA : 109- 115: lkvdr GHqAPlA slagv G 7: 17.3226 6( 5) Y-x(1,3)-S-N-x(2,4)-P-[NQS] Occurences: 6(5) NUC1_YEAST : 157- 164: mddtf Yl--SNmc--PQ vgegf NUCA_ANASP : 254- 263: esltg YdflSNvs--PN iqtsi NUCE_STRPN : 225- 235: yrvtl Yya-SNedlvPS asqie NUCE_STRPN : 226- 235: rvtly Ya--SNedlvPS asqie NUCG_BOVIN : 162- 169: mddtf Yl--SNva--PQ vphln NUC_SERMA : 128- 135: wesln Yl--SNit--PQ ksdln H 8: 16.5345 6( 5) L-x(4,5)-R-x(4)-R-x(3)-[ADGST]-x(3)-[DGT] Occurences: 6(5) NUC1_YEAST : 126- 144: kfrgk Lrdyf-RsgydRghqApaaD akfsq NUCA_ANASP : 88- 106: lnssw Lgnae-RqdnfRpdkTlpaG wvrvt NUCE_STRPN : 116- 135: tvana LlskatRqyknRketGngsT swtpp NUCE_STRPN : 117- 135: vanal Lskat-RqyknRketGngsT swtpp NUCG_BOVIN : 101- 120: wvveq LrpeglRgdgnRsscDfheD dsvha NUC_SERMA : 147- 165: gawar Ledqe-RklidRadiSsvyT vtgpl I 9: 15.1981 5( 5) V-x(4,5)-G-[PS]-L Occurences: 5(5) NUC1_YEAST : 191- 198: kkyks Vrivt-GPL ylpkk NUCA_ANASP : 179- 186: kelyi Vagpn-GSL gkplk NUCE_STRPN : 62- 70: vltda VksqikGSL ewngs NUCG_BOVIN : 195- 202: rtyqn Vyvct-GPL flprt NUC_SERMA : 163- 170: adiss Vytvt-GPL yerdm J 10: 15.1802 5( 5) L-x(1,3)-G-x(2,3)-A-x-T Occurences: 5(5) NUC1_YEAST : 10- 17: illsg Lv--Glg-AgT gltyl NUCA_ANASP : 214- 221: spgsg Le--Git-AnT rviav NUCE_STRPN : 170- 177: aligg Ld--Gfd-AsT snpkn NUCG_BOVIN : 285- 295: fvpni LaraGslkAiT agsk NUC_SERMA : 178- 186: rdmgk Lp--GtqkAhT ipsay K 11: 15.1802 7( 5) G-x(0,1)-L-x-G-x(1,3)-A Occurences: 7(5) NUC1_YEAST : 9- 15: rills G-LvGlg-A gtglt NUCA_ANASP : 213- 219: dspgs G-LeGit-A ntrvi NUCE_STRPN : 159- 165: havdr GhLlGy--A liggl NUCE_STRPN : 168- 175: gyali GgLdGfd-A stsnp NUCE_STRPN : 169- 175: yalig G-LdGfd-A stsnp NUCG_BOVIN : 70- 75: elaky G-LpGv--A qlksr NUC_SERMA : 176- 184: yerdm GkLpGtqkA htips L 12: 15.1802 7( 5) G-L-x(0,1)-G-x(0,2)-A Occurences: 7(5) NUC1_YEAST : 9- 15: rills GLvGlgA gtglt NUC1_YEAST : 12- 15: lsglv GL-G--A gtglt NUCA_ANASP : 213- 219: dspgs GLeGitA ntrvi NUCE_STRPN : 169- 175: yalig GLdGfdA stsnp NUCG_BOVIN : 15- 18: lalga GL-G--A aaesw NUCG_BOVIN : 15- 19: lalga GL-Ga-A aesww NUCG_BOVIN : 15- 20: lalga GL-GaaA eswwr NUCG_BOVIN : 70- 75: elaky GLpGv-A qlksr NUC_SERMA : 9- 12: nnknv GL-G--A llfaa M 13: 13.9362 6( 5) G-L-x(3,4)-A-[EGNQS] Occurences: 6(5) NUC1_YEAST : 9- 16: rills GLvglgAG tglty NUCA_ANASP : 213- 220: dspgs GLegitAN trvia NUCE_STRPN : 169- 176: yalig GLdgfdAS tsnpk NUCG_BOVIN : 15- 21: lalga GLgaa-AE swwrq NUCG_BOVIN : 70- 76: elaky GLpgv-AQ lksra NUC_SERMA : 236- 242: iekrt GLiiw-AG lpddv N 14: 13.8928 5( 5) L-x(4)-R-x(3,4)-R-[AGPTV] Occurences: 5(5) NUC1_YEAST : 126- 137: kfrgk LrdyfRsgydRG hqapa NUCA_ANASP : 88- 99: lnssw LgnaeRqdnfRP dktlp NUCE_STRPN : 212- 222: kvrka LdqnkRvry-RV tlyya NUCG_BOVIN : 181- 191: nawnn LekysRslt-RT yqnvy NUC_SERMA : 147- 158: gawar LedqeRklidRA dissv O 15: 12.0102 5( 5) L-x(5)-V-x(0,1)-P Occurences: 5(5) NUC1_YEAST : 281- 288: erstg LellqkV-P pskkk NUC1_YEAST : 281- 289: erstg LellqkVpP skkka NUCA_ANASP : 190- 197: slgkp LkgkvtV-P kstwk NUCE_STRPN : 248- 255: ssdge LefnvlV-P nvqkg NUCG_BOVIN : 36- 44: ratpg LlsrlpVlP vaaaa NUC_SERMA : 251- 259: dvqas LkskpgVlP elmgc P 16: 12.0102 6( 5) E-x(3)-R-x(1,2)-L Occurences: 6(5) NUC1_YEAST : 178- 184: ywahl EyfcRg-L tkkyk NUCA_ANASP : 163- 169: twgnl EdycRe-L vsqgk NUCE_STRPN : 205- 212: gqnyy EskvRkaL dqnkr NUCG_BOVIN : 182- 188: awnnl EkysRs-L trtyq NUC_SERMA : 148- 154: awarl EdqeRk-L idrad NUC_SERMA : 230- 237: rvtvd EiekRtgL iiwag Q 17: 12.0102 5( 5) G-x(2,3)-A-x-T Occurences: 5(5) NUC1_YEAST : 12- 17: lsglv Glg-AgT gltyl NUCA_ANASP : 216- 221: gsgle Git-AnT rviav NUCE_STRPN : 172- 177: iggld Gfd-AsT snpkn NUCG_BOVIN : 289- 295: ilara GslkAiT agsk NUC_SERMA : 180- 186: mgklp GtqkAhT ipsay R 18: 12.0102 5( 5) G-x(0,1)-L-x(5)-G Occurences: 5(5) NUC1_YEAST : 9- 16: rills G-LvglgaG tglty NUCA_ANASP : 184- 192: vagpn GsLgkplkG kvtvp NUCE_STRPN : 68- 76: ksqik GsLewngsG afivn NUCG_BOVIN : 289- 297: ilara GsLkaitaG sk NUC_SERMA : 168- 176: vytvt GpLyerdmG klpgt S 19: 12.0102 6( 5) L-x(4,5)-R-x(4)-R Occurences: 6(5) NUC1_YEAST : 126- 136: kfrgk Lrdyf-RsgydR ghqap NUCA_ANASP : 88- 98: lnssw Lgnae-RqdnfR pdktl NUCE_STRPN : 116- 127: tvana LlskatRqyknR ketgn NUCE_STRPN : 117- 127: vanal Lskat-RqyknR ketgn NUCG_BOVIN : 101- 112: wvveq LrpeglRgdgnR sscdf NUC_SERMA : 147- 157: gawar Ledqe-RklidR adiss T 20: 12.0102 6( 5) L-x(2)-L-x(1,2)-V Occurences: 6(5) NUC1_YEAST : 281- 287: erstg LelLqkV ppskk NUCA_ANASP : 12- 17: lgvaa LvaLi-V gcspv NUCE_STRPN : 9- 14: ktrqt LigLl-V lllls NUCG_BOVIN : 37- 42: atpgl LsrLp-V lpvaa NUCG_BOVIN : 40- 45: gllsr LpvLp-V aaaag NUC_SERMA : 114- 120: ghqap LasLagV sdwes Number of patterns evaluated by Pratt:4076 Total running time: 2 seconds