------------------------------------------------------------ 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 9 sequences from file HIT PATTERN CONSERVATION: CM: min Nr of Seqs to Match 9 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 HIT.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HIT_YEAST 144 IPK1_BOVIN 125 YCFF_ECOLI 17 YCFF_HAEIN 116 YHIT_AZOBR 122 YHIT_MYCHR 111 YHIT_SYNP7 114 ZB14_BRAJU 113 ZB14_MAIZE 128 Pratt run started at Thu Feb 6 19:54:34 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 16.6802 9( 9) F-x(2)-I-x(3)-E-x-P 2: 12.5102 9( 9) I-x(3)-E-x-P 3: 12.0102 17( 9) I-x(2,3)-E-x-P 4: 8.3401 19( 9) I-P 5: 8.3401 12( 9) E-I 6: 8.3401 13( 9) K-x(4)-E 7: 8.3401 13( 9) T-x(4)-I 8: 8.3401 14( 9) E-x(5)-I 9: 8.3401 11( 9) A-E 10: 8.3401 12( 9) A-x-E 11: 8.3401 14( 9) A-x(3)-I 12: 7.8401 23( 9) I-x(2,3)-K 13: 7.8401 36( 9) I-x(1,2)-K 14: 7.8401 14( 9) E-x(0,1)-I 15: 7.3401 22( 9) I-x(0,2)-I 16: 7.3401 11( 9) I-x(0,2)-F 17: 7.3401 20( 9) E-x(2,4)-I 18: 7.3401 21( 9) E-x(0,2)-I Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 25.8973 9( 9) F-x-[KR]-I-[IL]-x(2)-E-x-P-[ACS] B 2: 18.4791 9( 9) I-[IL]-x(2)-E-x-P-[ACS] C 3: 17.7721 9( 9) I-x(1,2)-K-[AGILV]-[AGI]-x(2)-[DEG]-[FIM] D 4: 16.8977 9( 9) K-[ILV]-[AIL]-x(2)-E-x-[AP] E 5: 14.6924 17( 9) I-x(2,3)-E-x-P-[ACS] F 6: 12.7717 13( 9) I-x(0,2)-I-x-[KR]-x(3)-[AGSV] G 7: 11.0179 12( 9) T-x(4)-I-[AIP] H 8: 10.5986 13( 9) A-x(3)-I-x(3)-[AGIP] I 9: 10.2527 11( 9) A-x-E-x(3)-[ADEQS] J 10: 10.0793 12( 9) E-x(0,1)-I-x(4)-[AILV] K 11: 10.0019 15( 9) E-x(0,2)-I-x(4)-[ILV] L 12: 9.5966 16( 9) E-x(2,4)-I-[FILV] M 13: 8.3401 19( 9) I-P N 14: 8.3401 12( 9) E-I O 15: 8.3401 14( 9) E-x(5)-I P 16: 8.3401 11( 9) A-E Q 17: 7.8401 17( 9) I-x(2,3)-E R 18: 7.8401 23( 9) I-x(2,3)-K S 19: 7.3401 11( 9) I-x(0,2)-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 25.8973 9( 9) F-x-[KR]-I-[IL]-x(2)-E-x-P-[ACS] Occurences: 9(9) HIT_YEAST : 13- 23: daaci FcKIIksEiPS fklie IPK1_BOVIN : 18- 28: ggdti FgKIIrkEiPA kiiye YCFF_ECOLI : 7- 17: aeeti FsKIIrrEiPS YCFF_HAEIN : 7- 17: aeeti FsKIIrkEiPA nivyq YHIT_AZOBR : 11- 21: dpnnv FaRILrgEiPC kkvle YHIT_MYCHR : 9- 19: wqeel FlKIIkrEePA tilye YHIT_SYNP7 : 7- 17: sedti FgKIIrrEiPA divye ZB14_BRAJU : 4- 14: dti FgKIIskEiPS tvvye ZB14_MAIZE : 19- 29: dspti FdKIIkkEiPS tvvye B 2: 18.4791 9( 9) I-[IL]-x(2)-E-x-P-[ACS] Occurences: 9(9) HIT_YEAST : 16- 23: cifck IIksEiPS fklie IPK1_BOVIN : 21- 28: tifgk IIrkEiPA kiiye YCFF_ECOLI : 10- 17: tifsk IIrrEiPS YCFF_HAEIN : 10- 17: tifsk IIrkEiPA nivyq YHIT_AZOBR : 14- 21: nvfar ILrgEiPC kkvle YHIT_MYCHR : 12- 19: elflk IIkrEePA tilye YHIT_SYNP7 : 10- 17: tifgk IIrrEiPA divye ZB14_BRAJU : 7- 14: tifgk IIskEiPS tvvye ZB14_MAIZE : 22- 29: tifdk IIkkEiPS tvvye C 3: 17.7721 9( 9) I-x(1,2)-K-[AGILV]-[AGI]-x(2)-[DEG]-[FIM] Occurences: 9(9) HIT_YEAST : 12- 21: ldaac IfcKIIksEI psfkl IPK1_BOVIN : 17- 26: pggdt IfgKIIrkEI pakii YCFF_ECOLI : 6- 15: maeet IfsKIIrrEI ps YCFF_HAEIN : 6- 15: maeet IfsKIIrkEI paniv YHIT_AZOBR : 47- 55: thilv Ip-KGAyvDM ddfsa YHIT_MYCHR : 76- 84: falqe Ik-KLGatGF kllin YHIT_SYNP7 : 6- 15: msedt IfgKIIrrEI padiv ZB14_BRAJU : 3- 12: dt IfgKIIskEI pstvv ZB14_MAIZE : 18- 27: ddspt IfdKIIkkEI pstvv D 4: 16.8977 9( 9) K-[ILV]-[AIL]-x(2)-E-x-[AP] Occurences: 9(9) HIT_YEAST : 15- 22: acifc KIIksEiP sfkli IPK1_BOVIN : 20- 27: dtifg KIIrkEiP akiiy YCFF_ECOLI : 9- 16: etifs KIIrrEiP s YCFF_HAEIN : 9- 16: etifs KIIrkEiP anivy YHIT_AZOBR : 23- 30: eipck KVLetEhA lafhd YHIT_MYCHR : 11- 18: eelfl KIIkrEeP atily YHIT_SYNP7 : 9- 16: dtifg KIIrrEiP adivy ZB14_BRAJU : 6- 13: dtifg KIIskEiP stvvy ZB14_MAIZE : 21- 28: ptifd KIIkkEiP stvvy E 5: 14.6924 17( 9) I-x(2,3)-E-x-P-[ACS] Occurences: 17(9) HIT_YEAST : 16- 23: cifck IiksEiPS fklie HIT_YEAST : 17- 23: ifcki Iks-EiPS fklie IPK1_BOVIN : 21- 28: tifgk IirkEiPA kiiye IPK1_BOVIN : 22- 28: ifgki Irk-EiPA kiiye YCFF_ECOLI : 10- 17: tifsk IirrEiPS YCFF_ECOLI : 11- 17: ifski Irr-EiPS YCFF_HAEIN : 10- 17: tifsk IirkEiPA nivyq YCFF_HAEIN : 11- 17: ifski Irk-EiPA nivyq YHIT_AZOBR : 14- 21: nvfar IlrgEiPC kkvle YHIT_MYCHR : 12- 19: elflk IikrEePA tilye YHIT_MYCHR : 13- 19: lflki Ikr-EePA tilye YHIT_SYNP7 : 10- 17: tifgk IirrEiPA divye YHIT_SYNP7 : 11- 17: ifgki Irr-EiPA divye ZB14_BRAJU : 7- 14: tifgk IiskEiPS tvvye ZB14_BRAJU : 8- 14: ifgki Isk-EiPS tvvye ZB14_MAIZE : 22- 29: tifdk IikkEiPS tvvye ZB14_MAIZE : 23- 29: ifdki Ikk-EiPS tvvye F 6: 12.7717 13( 9) I-x(0,2)-I-x-[KR]-x(3)-[AGSV] Occurences: 13(9) HIT_YEAST : 48- 55: eghal I--IpKyhgA klhdi IPK1_BOVIN : 21- 28: tifgk I--IrKeipA kiiye YCFF_ECOLI : 10- 17: tifsk I--IrReipS YCFF_HAEIN : 10- 17: tifsk I--IrKeipA nivyq YHIT_AZOBR : 44- 53: qapth IlvIpKgayV dmddf YHIT_MYCHR : 12- 19: elflk I--IkReepA tilye YHIT_SYNP7 : 10- 17: tifgk I--IrReipA divye YHIT_SYNP7 : 40- 49: qapvh IlvIpKqpiA nllea ZB14_BRAJU : 7- 14: tifgk I--IsKeipS tvvye ZB14_BRAJU : 37- 46: qgpvh IllIpKvrdG ltglf ZB14_MAIZE : 22- 29: tifdk I--IkKeipS tvvye ZB14_MAIZE : 52- 61: qapth IliIpKvkdG ltgla ZB14_MAIZE : 54- 61: pthil I--IpKvkdG ltgla G 7: 11.0179 12( 9) T-x(4)-I-[AIP] Occurences: 12(9) HIT_YEAST : 66- 72: pdefl TdampIA krlak IPK1_BOVIN : 16- 22: rpggd TifgkII rkeip IPK1_BOVIN : 49- 55: spqap ThflvIP kkyis YCFF_ECOLI : 5- 11: maee TifskII rreip YCFF_HAEIN : 5- 11: maee TifskII rkeip YCFF_HAEIN : 38- 44: spqak ThiliIP nkvip YHIT_AZOBR : 42- 48: npqap ThilvIP kgayv YHIT_MYCHR : 101- 107: qsifh ThvhiIP yykk YHIT_SYNP7 : 5- 11: msed TifgkII rreip ZB14_BRAJU : 2- 8: d TifgkII skeip ZB14_MAIZE : 17- 23: lddsp TifdkII kkeip ZB14_MAIZE : 50- 56: npqap ThiliIP kvkdg H 8: 10.5986 13( 9) A-x(3)-I-x(3)-[AGIP] Occurences: 13(9) HIT_YEAST : 34- 42: tkysy AfldIqptA eghal IPK1_BOVIN : 39- 47: ddqcl AfhdIspqA pthfl YCFF_ECOLI : 2- 10: m AeetIfskI irrei YCFF_HAEIN : 2- 10: m AeetIfskI irkei YCFF_HAEIN : 28- 36: delvt AfrdIspqA kthil YCFF_HAEIN : 36- 44: dispq AkthIliiP nkvip YHIT_AZOBR : 32- 40: tehal AfhdInpqA pthil YHIT_AZOBR : 40- 48: dinpq ApthIlviP kgayv YHIT_MYCHR : 72- 80: karef AlqeIkklG atgfk YHIT_SYNP7 : 36- 44: dvapq ApvhIlviP kqpia ZB14_BRAJU : 25- 33: ddkvl AfrdItpqG pvhil ZB14_MAIZE : 40- 48: dekvl AfrdInpqA pthil ZB14_MAIZE : 48- 56: dinpq ApthIliiP kvkdg I 9: 10.2527 11( 9) A-x-E-x(3)-[ADEQS] Occurences: 11(9) HIT_YEAST : 121- 127: ivgwp AqEtdfD klgkl IPK1_BOVIN : 1- 7: AdEiakA qvarp IPK1_BOVIN : 64- 70: isqis AaEdddE sllgh YCFF_ECOLI : 2- 8: m AeEtifS kiirr YCFF_HAEIN : 2- 8: m AeEtifS kiirk YCFF_HAEIN : 73- 79: vaakl AkEegvA edgyr YHIT_AZOBR : 62- 68: dfsar AtEaeiA glfra YHIT_MYCHR : 68- 74: ylivk ArEfalQ eikkl YHIT_SYNP7 : 74- 80: vkaia AqEgltE gyrtv ZB14_BRAJU : 53- 59: tglfk AeErhiD ilgrl ZB14_MAIZE : 68- 74: tglak AeErhiE ilgyl J 10: 10.0793 12( 9) E-x(0,1)-I-x(4)-[AILV] Occurences: 12(9) HIT_YEAST : 20- 26: kiiks E-IpsfkL ietky IPK1_BOVIN : 3- 9: ad E-IakaqV arpgg IPK1_BOVIN : 25- 31: kiirk E-IpakiI yeddq YCFF_ECOLI : 4- 11: mae EtIfskiI rreip YCFF_HAEIN : 4- 11: mae EtIfskiI rkeip YCFF_HAEIN : 14- 20: kiirk E-IpaniV yqdel YHIT_AZOBR : 18- 24: rilrg E-IpckkV leteh YHIT_MYCHR : 75- 81: efalq E-IkklgA tgfkl YHIT_SYNP7 : 14- 20: kiirr E-IpadiV yeddl ZB14_BRAJU : 11- 17: kiisk E-IpstvV yeddk ZB14_MAIZE : 26- 32: kiikk E-IpstvV yedek ZB14_MAIZE : 74- 80: eerhi E-IlgylL yvakv K 11: 10.0019 15( 9) E-x(0,2)-I-x(4)-[ILV] Occurences: 15(9) HIT_YEAST : 20- 26: kiiks E--IpsfkL ietky IPK1_BOVIN : 3- 9: ad E--IakaqV arpgg IPK1_BOVIN : 25- 31: kiirk E--IpakiI yeddq YCFF_ECOLI : 3- 11: ma EetIfskiI rreip YCFF_ECOLI : 4- 11: mae Et-IfskiI rreip YCFF_HAEIN : 3- 11: ma EetIfskiI rkeip YCFF_HAEIN : 4- 11: mae Et-IfskiI rkeip YCFF_HAEIN : 14- 20: kiirk E--IpaniV yqdel YHIT_AZOBR : 18- 24: rilrg E--IpckkV leteh YHIT_MYCHR : 95- 103: nepda EqsIfhthV hiipy YHIT_SYNP7 : 3- 11: ms EdtIfgkiI rreip YHIT_SYNP7 : 14- 20: kiirr E--IpadiV yeddl ZB14_BRAJU : 11- 17: kiisk E--IpstvV yeddk ZB14_MAIZE : 26- 32: kiikk E--IpstvV yedek ZB14_MAIZE : 74- 80: eerhi E--IlgylL yvakv L 12: 9.5966 16( 9) E-x(2,4)-I-[FILV] Occurences: 16(9) HIT_YEAST : 43- 49: iqpta EghalII pkyhg HIT_YEAST : 111- 117: ipkrd EksglIV gwpaq IPK1_BOVIN : 25- 31: kiirk EipakII yeddq YCFF_ECOLI : 3- 7: ma Eet--IF skiir YCFF_HAEIN : 3- 7: ma Eet--IF skiir YCFF_HAEIN : 14- 20: kiirk EipanIV yqdel YHIT_AZOBR : 85- 91: gagaa EpgyrIL sncge YHIT_MYCHR : 7- 13: nnwqe ElflkII kreep YHIT_MYCHR : 16- 22: kiikr EepatIL yeddk YHIT_MYCHR : 17- 22: iikre Epat-IL yeddk YHIT_MYCHR : 95- 99: nepda Eqs--IF hthvh YHIT_SYNP7 : 3- 7: ms Edt--IF gkiir YHIT_SYNP7 : 14- 20: kiirr EipadIV yeddl ZB14_BRAJU : 55- 61: lfkae ErhidIL grlly ZB14_BRAJU : 79- 84: qegld Egfr-IV indgp ZB14_MAIZE : 70- 76: lakae ErhieIL gylly M 13: 8.3401 19( 9) I-P Occurences: 19(9) HIT_YEAST : 21- 22: iikse IP sfkli HIT_YEAST : 49- 50: ghali IP kyhga HIT_YEAST : 60- 61: aklhd IP deflt HIT_YEAST : 106- 107: vhfhl IP krdek IPK1_BOVIN : 26- 27: iirke IP akiiy IPK1_BOVIN : 54- 55: thflv IP kkyis YCFF_ECOLI : 15- 16: iirre IP s YCFF_HAEIN : 15- 16: iirke IP anivy YCFF_HAEIN : 43- 44: thili IP nkvip YCFF_HAEIN : 48- 49: ipnkv IP tvndv YHIT_AZOBR : 19- 20: ilrge IP ckkvl YHIT_AZOBR : 47- 48: thilv IP kgayv YHIT_MYCHR : 106- 107: thvhi IP yykk YHIT_SYNP7 : 15- 16: iirre IP adivy YHIT_SYNP7 : 43- 44: vhilv IP kqpia ZB14_BRAJU : 12- 13: iiske IP stvvy ZB14_BRAJU : 40- 41: vhill IP kvrdg ZB14_MAIZE : 27- 28: iikke IP stvvy ZB14_MAIZE : 55- 56: thili IP kvkdg N 14: 8.3401 12( 9) E-I Occurences: 12(9) HIT_YEAST : 20- 21: kiiks EI psfkl IPK1_BOVIN : 3- 4: ad EI akaqv IPK1_BOVIN : 25- 26: kiirk EI pakii YCFF_ECOLI : 14- 15: kiirr EI ps YCFF_HAEIN : 14- 15: kiirk EI paniv YHIT_AZOBR : 18- 19: rilrg EI pckkv YHIT_AZOBR : 66- 67: ratea EI aglfr YHIT_MYCHR : 75- 76: efalq EI kklga YHIT_SYNP7 : 14- 15: kiirr EI padiv ZB14_BRAJU : 11- 12: kiisk EI pstvv ZB14_MAIZE : 26- 27: kiikk EI pstvv ZB14_MAIZE : 74- 75: eerhi EI lgyll O 15: 8.3401 14( 9) E-x(5)-I Occurences: 14(9) HIT_YEAST : 43- 49: iqpta EghaliI pkyhg IPK1_BOVIN : 25- 31: kiirk EipakiI yeddq YCFF_ECOLI : 4- 10: mae EtifskI irrei YCFF_HAEIN : 4- 10: mae EtifskI irkei YCFF_HAEIN : 80- 86: eegva EdgyrlI vncnk YHIT_AZOBR : 101- 107: edanq EvphlhI hvfag YHIT_MYCHR : 6- 12: mnnwq EelflkI ikree YHIT_MYCHR : 7- 13: nnwqe ElflkiI kreep YHIT_MYCHR : 59- 65: fsisd EdlsylI vkare YHIT_MYCHR : 70- 76: ivkar EfalqeI kklga YHIT_SYNP7 : 80- 86: qeglt EgyrtvI ntgpa ZB14_BRAJU : 54- 60: glfka EerhidI lgrll ZB14_BRAJU : 79- 85: qegld EgfrivI ndgpq ZB14_MAIZE : 69- 75: glaka EerhieI lgyll P 16: 8.3401 11( 9) A-E Occurences: 11(9) HIT_YEAST : 42- 43: diqpt AE ghali IPK1_BOVIN : 65- 66: sqisa AE dddes YCFF_ECOLI : 2- 3: m AE etifs YCFF_HAEIN : 2- 3: m AE etifs YCFF_HAEIN : 79- 80: keegv AE dgyrl YHIT_AZOBR : 65- 66: arate AE iaglf YHIT_AZOBR : 84- 85: rgaga AE pgyri YHIT_MYCHR : 94- 95: nnepd AE qsifh YHIT_SYNP7 : 56- 57: lleat AE hqall ZB14_BRAJU : 53- 54: tglfk AE erhid ZB14_MAIZE : 68- 69: tglak AE erhie Q 17: 7.8401 17( 9) I-x(2,3)-E Occurences: 17(9) HIT_YEAST : 16- 20: cifck IiksE ipsfk HIT_YEAST : 17- 20: ifcki Iks-E ipsfk IPK1_BOVIN : 21- 25: tifgk IirkE ipaki IPK1_BOVIN : 22- 25: ifgki Irk-E ipaki YCFF_ECOLI : 10- 14: tifsk IirrE ips YCFF_ECOLI : 11- 14: ifski Irr-E ips YCFF_HAEIN : 10- 14: tifsk IirkE ipani YCFF_HAEIN : 11- 14: ifski Irk-E ipani YHIT_AZOBR : 14- 18: nvfar IlrgE ipckk YHIT_MYCHR : 12- 16: elflk IikrE epati YHIT_MYCHR : 13- 16: lflki Ikr-E epati YHIT_SYNP7 : 10- 14: tifgk IirrE ipadi YHIT_SYNP7 : 11- 14: ifgki Irr-E ipadi ZB14_BRAJU : 7- 11: tifgk IiskE ipstv ZB14_BRAJU : 8- 11: ifgki Isk-E ipstv ZB14_MAIZE : 22- 26: tifdk IikkE ipstv ZB14_MAIZE : 23- 26: ifdki Ikk-E ipstv R 18: 7.8401 23( 9) I-x(2,3)-K Occurences: 23(9) HIT_YEAST : 12- 15: ldaac Ifc-K iikse HIT_YEAST : 21- 25: iikse IpsfK lietk HIT_YEAST : 27- 30: psfkl Iet-K ysyaf HIT_YEAST : 48- 51: eghal Iip-K yhgak IPK1_BOVIN : 17- 20: pggdt Ifg-K iirke IPK1_BOVIN : 21- 24: tifgk Iir-K eipak IPK1_BOVIN : 26- 29: iirke Ipa-K iiyed IPK1_BOVIN : 54- 57: thflv Ipk-K yisqi IPK1_BOVIN : 78- 81: lghlm Ivg-K kcaad IPK1_BOVIN : 78- 82: lghlm IvgkK caadl YCFF_ECOLI : 6- 9: maeet Ifs-K iirre YCFF_HAEIN : 6- 9: maeet Ifs-K iirke YCFF_HAEIN : 10- 13: tifsk Iir-K eipan YCFF_HAEIN : 42- 46: kthil IipnK viptv YCFF_HAEIN : 43- 46: thili Ipn-K viptv YHIT_AZOBR : 19- 22: ilrge Ipc-K kvlet YHIT_AZOBR : 19- 23: ilrge IpckK vlete YHIT_MYCHR : 106- 110: thvhi IpyyK k YHIT_SYNP7 : 6- 9: msedt Ifg-K iirre ZB14_BRAJU : 3- 6: dt Ifg-K iiske ZB14_BRAJU : 7- 10: tifgk Iis-K eipst ZB14_MAIZE : 18- 21: ddspt Ifd-K iikke ZB14_MAIZE : 22- 25: tifdk Iik-K eipst ZB14_MAIZE : 54- 57: pthil Iip-K vkdgl ZB14_MAIZE : 55- 59: thili IpkvK dgltg S 19: 7.3401 11( 9) I-x(0,2)-F Occurences: 11(9) HIT_YEAST : 12- 13: ldaac I--F ckiik HIT_YEAST : 21- 24: iikse IpsF kliet IPK1_BOVIN : 17- 18: pggdt I--F gkiir YCFF_ECOLI : 6- 7: maeet I--F skiir YCFF_HAEIN : 6- 7: maeet I--F skiir YHIT_AZOBR : 107- 110: vphlh IhvF agrrl YHIT_MYCHR : 29- 31: eddkv Ia-F ldkya YHIT_MYCHR : 98- 99: daeqs I--F hthvh YHIT_SYNP7 : 6- 7: msedt I--F gkiir ZB14_BRAJU : 3- 4: dt I--F gkiis ZB14_MAIZE : 18- 19: ddspt I--F dkiik Number of patterns evaluated by Pratt:47 Total running time: 0 seconds