------------------------------------------------------------ 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 14 sequences from file HIPIP PATTERN CONSERVATION: CM: min Nr of Seqs to Match 14 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 HIPIP.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HPI1_ECTHA 71 HPI1_ECTVA 72 HPI2_ECTHA 76 HPI2_ECTVA 71 HPIS_CHRGR 83 HPIS_CHRTE 83 HPIS_CHRVI 85 HPIS_PARSP 71 HPIS_RHOGE 74 HPIS_RHOGL 57 HPIS_RHOTE 63 HPIS_THIPF 81 HPIS_THIRO 85 HPIT_RHOTE 62 Pratt run started at Thu Feb 6 19:54:07 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 22( 14) G-x-C 2: 8.3401 14( 14) C-x(2)-C 3: 7.8401 57( 14) A-x(0,1)-A 4: 7.8401 24( 14) S-x(3,4)-A 5: 7.8401 21( 14) C-x(1,2)-F 6: 7.8401 32( 14) G-x(1,2)-C 7: 7.3401 23( 14) G-x(1,3)-S 8: 7.3401 23( 14) N-x(2,4)-A 9: 7.3401 24( 14) V-x(1,3)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 17.0349 14( 14) G-[WY]-C-x-[ASV]-[FWY] B 2: 12.8131 17( 14) G-x(1,2)-C-x-[ANSV]-[FWY] C 3: 10.9976 14( 14) C-x-[GNT]-C D 4: 9.0101 16( 14) G-x(1,3)-S-x(4)-[ACGNST] E 5: 8.7597 20( 14) V-x(1,3)-A-[ADGNPST] F 6: 7.8401 57( 14) A-x(0,1)-A G 7: 7.8401 24( 14) S-x(3,4)-A H 8: 7.8401 21( 14) C-x(1,2)-F I 9: 7.3401 23( 14) N-x(2,4)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 17.0349 14( 14) G-[WY]-C-x-[ASV]-[FWY] Occurences: 14(14) HPI1_ECTHA : 62- 67: lvkae GWCsVY apas HPI1_ECTVA : 63- 68: lvnan GWCtAY varg HPI2_ECTHA : 68- 73: lvrge GWCsVY apa HPI2_ECTVA : 63- 68: lvsan GWCtAW var HPIS_CHRGR : 73- 78: linld GWCaSW tlrag HPIS_CHRTE : 73- 78: linvn GWCaSW tlkag HPIS_CHRVI : 75- 80: linvd GWCaSW tlkag HPIS_PARSP : 62- 67: svepa GWCqSW taqn HPIS_RHOGE : 65- 70: qvank GWCsAW akka HPIS_RHOGL : 44- 49: kispn GWCiAY apmed HPIS_RHOTE : 54- 59: qiqpt GYCdAY ivkk HPIS_THIPF : 71- 76: tvsed GWClSW ahkta HPIS_THIRO : 75- 80: linvd GWCaSW tlkag HPIT_RHOTE : 53- 58: qiapg GYCdAF ivkk B 2: 12.8131 17( 14) G-x(1,2)-C-x-[ANSV]-[FWY] Occurences: 17(14) HPI1_ECTHA : 62- 67: lvkae Gw-CsVY apas HPI1_ECTVA : 49- 54: satew Gg-CaVF pnklv HPI1_ECTVA : 63- 68: lvnan Gw-CtAY varg HPI2_ECTHA : 68- 73: lvrge Gw-CsVY apa HPI2_ECTVA : 49- 54: saqdw Gp-CsVF pgklv HPI2_ECTVA : 63- 68: lvsan Gw-CtAW var HPIS_CHRGR : 73- 78: linld Gw-CaSW tlrag HPIS_CHRTE : 73- 78: linvn Gw-CaSW tlkag HPIS_CHRVI : 75- 80: linvd Gw-CaSW tlkag HPIS_PARSP : 62- 67: svepa Gw-CqSW taqn HPIS_RHOGE : 65- 70: qvank Gw-CsAW akka HPIS_RHOGL : 44- 49: kispn Gw-CiAY apmed HPIS_RHOTE : 54- 59: qiqpt Gy-CdAY ivkk HPIS_THIPF : 71- 76: tvsed Gw-ClSW ahkta HPIS_THIRO : 75- 80: linvd Gw-CaSW tlkag HPIT_RHOTE : 52- 58: nqiap GgyCdAF ivkk HPIT_RHOTE : 53- 58: qiapg Gy-CdAF ivkk C 3: 10.9976 14( 14) C-x-[GNT]-C Occurences: 14(14) HPI1_ECTHA : 31- 34: qegql CeNC afwge HPI1_ECTVA : 34- 37: aagqk CiNC llytd HPI2_ECTHA : 38- 41: qegql CeNC qfwvd HPI2_ECTVA : 34- 37: eegqt ClNC llytd HPIS_CHRGR : 43- 46: peeqh CeNC qfmlp HPIS_CHRTE : 43- 46: peeqh CaNC qfmqa HPIS_CHRVI : 43- 46: peeqh CaNC qfmqa HPIS_PARSP : 37- 40: qegeq CdNC mffqa HPIS_RHOGE : 36- 39: vagsh CgNC alfqg HPIS_RHOGL : 21- 24: kdgnk CsTC vnfea HPIS_RHOTE : 23- 26: tagkn CaNC aqfip HPIS_THIPF : 43- 46: gseqf ChNC sfiqa HPIS_THIRO : 43- 46: paeqh CaNC qfhld HPIT_RHOTE : 22- 25: kngkk CsGC aqfvp D 4: 9.0101 16( 14) G-x(1,3)-S-x(4)-[ACGNST] Occurences: 16(14) HPI1_ECTHA : 62- 70: lvkae Gwc-SvyapA s HPI1_ECTVA : 20- 27: nykhd Ga--SvdhpS haagq HPI2_ECTHA : 68- 76: lvrge Gwc-SvyapA HPI2_ECTVA : 56- 65: csvfp GklvSangwC tawva HPIS_CHRGR : 73- 82: linld GwcaSwtlrA g HPIS_CHRTE : 73- 82: linvn GwcaSwtlkA g HPIS_CHRVI : 75- 84: linvd GwcaSwtlkA g HPIS_PARSP : 62- 71: svepa GwcqSwtaqN HPIS_RHOGE : 14- 22: qaval Gyv-SdaakA dkaky HPIS_RHOGL : 38- 46: ckiva Gki-SpngwC iayap HPIS_RHOTE : 32- 39: aqfip Ga--SasaaG ackvi HPIS_RHOTE : 32- 41: aqfip GasaSaagaC kvipg HPIS_RHOTE : 46- 53: ckvip Gd--SqiqpT gycda HPIS_THIPF : 64- 73: ctlyp GytvSedgwC lswah HPIS_THIPF : 71- 80: tvsed GwclSwahkT a HPIS_THIRO : 75- 84: linvd GwcaSwtlkA g HPIT_RHOTE : 31- 38: aqfvp Ga--SptaaG gckvi E 5: 8.7597 20( 14) V-x(1,3)-A-[ADGNPST] Occurences: 20(14) HPI1_ECTHA : 13- 17: hahdy Vne-AA dasgh HPI1_ECTHA : 13- 18: hahdy VneaAD asghp HPI1_ECTHA : 66- 69: egwcs Vy--AP as HPI1_ECTHA : 66- 71: egwcs VyapAS HPI1_ECTVA : 59- 62: fpnkl Vn--AN gwcta HPI2_ECTHA : 21- 25: hahdy Vnd-AA dtdha HPI2_ECTHA : 21- 26: hahdy VndaAD tdhar HPI2_ECTHA : 72- 75: egwcs Vy--AP a HPI2_ECTVA : 59- 62: fpgkl Vs--AN gwcta HPIS_CHRGR : 2- 5: e Vp--AN avtes HPIS_CHRGR : 29- 32: easer Va--AA rpglp HPIS_CHRTE : 7- 10: apana Vt--AD dptai HPIS_CHRTE : 29- 32: tkser Va--AA rpglp HPIS_CHRVI : 7- 10: apana Va--AD datai HPIS_CHRVI : 29- 32: tkser Va--AA rpglp HPIS_PARSP : 58- 62: fpqns Vep-AG wcqsw HPIS_RHOGE : 16- 20: valgy Vsd-AA kadka HPIS_RHOGL : 25- 30: kcstc VnfeAP sscki HPIS_RHOTE : 15- 20: fnyqe VsktAG kncan HPIS_THIPF : 6- 9: edlph Vd--AA tnpia HPIS_THIPF : 6- 10: edlph Vda-AT npiaq HPIS_THIRO : 7- 10: apana Va--AN dptav HPIS_THIRO : 53- 57: fhldd Vag-AT eewhg HPIT_RHOTE : 29- 33: gcaqf Vpg-AS ptaag F 6: 7.8401 57( 14) A-x(0,1)-A Occurences: 57(14) HPI1_ECTHA : 16- 17: dyvne A-A dasgh HPI1_ECTHA : 17- 19: yvnea AdA sghpr HPI1_ECTHA : 68- 70: wcsvy ApA s HPI1_ECTVA : 11- 13: enspe AlA lnykh HPI1_ECTVA : 29- 30: dhpsh A-A gqkci HPI2_ECTHA : 24- 25: dyvnd A-A dtdha HPI2_ECTHA : 74- 76: wcsvy ApA HPI2_ECTVA : 10- 11: seddp A-A qaley HPI2_ECTVA : 11- 13: eddpa AqA leyrh HPI2_ECTVA : 43- 45: llytd AsA qdwgp HPIS_CHRGR : 4- 6: evp AnA vtesd HPIS_CHRGR : 14- 16: esdpt AvA lkyhr HPIS_CHRGR : 23- 25: kyhrn AeA serva HPIS_CHRGR : 30- 31: aserv A-A arpgl HPIS_CHRGR : 30- 32: aserv AaA rpglp HPIS_CHRGR : 31- 32: serva A-A rpglp HPIS_CHRTE : 1- 2: A-A panav HPIS_CHRTE : 2- 4: a ApA navta HPIS_CHRTE : 4- 6: aap AnA vtadd HPIS_CHRTE : 14- 16: addpt AiA lkynq HPIS_CHRTE : 30- 31: kserv A-A arpgl HPIS_CHRTE : 30- 32: kserv AaA rpglp HPIS_CHRTE : 31- 32: serva A-A rpglp HPIS_CHRVI : 2- 4: s ApA navaa HPIS_CHRVI : 4- 6: sap AnA vaadd HPIS_CHRVI : 6- 8: sapan AvA addat HPIS_CHRVI : 8- 9: panav A-A ddata HPIS_CHRVI : 12- 14: vaadd AtA ialky HPIS_CHRVI : 14- 16: addat AiA lkynq HPIS_CHRVI : 30- 31: kserv A-A arpgl HPIS_CHRVI : 30- 32: kserv AaA rpglp HPIS_CHRVI : 31- 32: serva A-A rpglp HPIS_CHRVI : 51- 53: cqfmq AdA agatd HPIS_CHRVI : 53- 54: fmqad A-A gatde HPIS_CHRVI : 54- 56: mqada AgA tdewk HPIS_PARSP : 13- 15: psaeq AqA lnyvk HPIS_PARSP : 23- 25: yvkdt AeA adhpa HPIS_PARSP : 25- 26: kdtae A-A dhpah HPIS_RHOGE : 10- 12: eknpq AvA lgyvs HPIS_RHOGE : 19- 20: gyvsd A-A kadka HPIS_RHOGE : 20- 22: yvsda AkA dkaky HPIS_RHOGE : 69- 71: kgwcs AwA kka HPIS_RHOGL : 48- 50: ngwci AyA pmedk HPIS_RHOTE : 33- 35: qfipg AsA saaga HPIS_RHOTE : 35- 37: ipgas AsA agack HPIS_RHOTE : 37- 38: gasas A-A gackv HPIS_RHOTE : 38- 40: asasa AgA ckvip HPIS_THIPF : 8- 9: lphvd A-A tnpia HPIS_THIPF : 23- 25: hyied AnA sernp HPIS_THIRO : 2- 4: e ApA navaa HPIS_THIRO : 4- 6: eap AnA vaand HPIS_THIRO : 6- 8: eapan AvA andpt HPIS_THIRO : 8- 9: panav A-A ndpta HPIS_THIRO : 14- 16: andpt AvA lkyna HPIS_THIRO : 21- 23: alkyn AdA tksdr HPIS_THIRO : 30- 31: ksdrl A-A arpgl HPIS_THIRO : 30- 32: ksdrl AaA rpglp HPIS_THIRO : 31- 32: sdrla A-A rpglp HPIS_THIRO : 54- 56: hlddv AgA teewh HPIT_RHOTE : 4- 5: gtn A-A mrkaf HPIT_RHOTE : 36- 37: gaspt A-A ggckv G 7: 7.8401 24( 14) S-x(3,4)-A Occurences: 24(14) HPI1_ECTHA : 65- 70: aegwc SvyapA s HPI1_ECTVA : 8- 13: rlden SpealA lnykh HPI2_ECTHA : 71- 76: gegwc SvyapA HPI2_ECTVA : 5- 10: merl SeddpA aqale HPI2_ECTVA : 22- 27: rhdas SvqhpA yeegq HPIS_CHRGR : 10- 14: navte Sdpt-A valky HPIS_CHRGR : 26- 30: rnaea Serv-A aarpg HPIS_CHRGR : 26- 31: rnaea ServaA arpgl HPIS_CHRGR : 77- 82: dgwca SwtlrA g HPIS_CHRTE : 26- 30: qdatk Serv-A aarpg HPIS_CHRTE : 26- 31: qdatk ServaA arpgl HPIS_CHRTE : 77- 82: ngwca SwtlkA g HPIS_CHRVI : 1- 6: SapanA vaadd HPIS_CHRVI : 26- 30: qdatk Serv-A aarpg HPIS_CHRVI : 26- 31: qdatk ServaA arpgl HPIS_CHRVI : 79- 84: dgwca SwtlkA g HPIS_PARSP : 9- 13: ppldp Saeq-A qalny HPIS_PARSP : 57- 61: lfpqn Svep-A gwcqs HPIS_RHOGE : 17- 22: algyv SdaakA dkaky HPIS_RHOGL : 32- 37: feaps SckivA gkisp HPIS_RHOTE : 5- 9: gtna Smrk-A fnyqe HPIS_RHOTE : 34- 38: fipga Sasa-A gackv HPIS_RHOTE : 36- 40: pgasa Saag-A ckvip HPIS_THIPF : 47- 51: fchnc Sfiq-A dsgaw HPIS_THIRO : 26- 30: adatk Sdrl-A aarpg HPIS_THIRO : 26- 31: adatk SdrlaA arpgl HPIS_THIRO : 79- 84: dgwca SwtlkA g HPIT_RHOTE : 33- 37: fvpga Spta-A ggckv H 8: 7.8401 21( 14) C-x(1,2)-F Occurences: 21(14) HPI1_ECTHA : 34- 36: qlcen Ca-F wgeav HPI1_ECTVA : 51- 54: tewgg CavF pnklv HPI2_ECTHA : 41- 43: qlcen Cq-F wvdyv HPI2_ECTVA : 51- 54: qdwgp CsvF pgklv HPIS_CHRGR : 46- 48: qhcen Cq-F mlpdq HPIS_CHRGR : 61- 64: dewrg CslF pgkli HPIS_CHRTE : 46- 48: qhcan Cq-F mqanv HPIS_CHRTE : 61- 64: gdwkg CqlF pgkli HPIS_CHRVI : 46- 48: qhcan Cq-F mqada HPIS_CHRVI : 63- 66: dewkg CqlF pgkli HPIS_PARSP : 40- 42: eqcdn Cm-F fqads HPIS_PARSP : 40- 43: eqcdn CmfF qadsq HPIS_PARSP : 50- 53: adsqg CqlF pqnsv HPIS_RHOGE : 39- 42: shcgn CalF qgkat HPIS_RHOGE : 53- 56: davgg CplF agkqv HPIS_RHOGL : 24- 27: nkcst CvnF eapss HPIS_RHOTE : 26- 29: kncan CaqF ipgas HPIS_THIPF : 46- 48: qfchn Cs-F iqads HPIS_THIRO : 46- 48: qhcan Cq-F hlddv HPIS_THIRO : 63- 66: eewhg CslF pgkli HPIT_RHOTE : 25- 28: kkcsg CaqF vpgas HPIT_RHOTE : 55- 58: apggy CdaF ivkk I 9: 7.3401 23( 14) N-x(2,4)-A Occurences: 23(14) HPI1_ECTHA : 14- 17: ahdyv Nea--A dasgh HPI1_ECTHA : 14- 19: ahdyv NeaadA sghpr HPI1_ECTVA : 7- 11: erlde Nspe-A lalny HPI1_ECTVA : 56- 61: cavfp NklvnA ngwct HPI1_ECTVA : 62- 67: klvna NgwctA yvarg HPI2_ECTHA : 22- 25: ahdyv Nda--A dtdha HPI2_ECTVA : 62- 67: klvsa NgwctA wvar HPIS_CHRGR : 22- 25: lkyhr Nae--A serva HPIS_CHRTE : 5- 9: aapa Navt-A ddpta HPIS_CHRTE : 20- 23: ialky Nqd--A tkser HPIS_CHRTE : 72- 76: klinv Ngwc-A swtlk HPIS_CHRVI : 5- 8: sapa Nav--A addat HPIS_CHRVI : 5- 9: sapa Nava-A ddata HPIS_CHRVI : 20- 23: ialky Nqd--A tkser HPIS_PARSP : 56- 61: qlfpq NsvepA gwcqs HPIS_RHOGE : 7- 10: pvdek Npq--A valgy HPIS_RHOGE : 7- 12: pvdek NpqavA lgyvs HPIS_RHOGL : 26- 29: cstcv Nfe--A pssck HPIS_RHOGL : 43- 48: gkisp NgwciA yapme HPIS_RHOTE : 22- 27: ktagk NcancA qfipg HPIS_THIPF : 11- 14: vdaat Npi--A qslhy HPIS_THIRO : 5- 8: eapa Nav--A andpt HPIS_THIRO : 5- 9: eapa Nava-A ndpta HPIS_THIRO : 10- 14: navaa Ndpt-A valky HPIS_THIRO : 20- 23: valky Nad--A tksdr HPIT_RHOTE : 11- 16: mrkaf NyqdtA kngkk HPIT_RHOTE : 47- 50: vipgd Nqi--A pggyc Number of patterns evaluated by Pratt:14 Total running time: 0 seconds