------------------------------------------------------------ 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 11 sequences from file ARTHROPOD_DEFENSINS PATTERN CONSERVATION: CM: min Nr of Seqs to Match 11 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 ARTHROPOD_DEFENSINS.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: DEF4_LEIQH 38 DEFA_ZOPAT 43 DEFI_AESCY 38 DEFI_APIME 51 DEFI_DROME 92 DEFI_PALPR 43 DEFI_PROTE 94 DEFI_PYRAP 43 SAPB_SARPE 34 SAPC_SARPE 40 SAPE_SARPE 94 Pratt run started at Thu Feb 6 18:53:52 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.0102 11( 11) C-x(3,4)-G-x(5)-C 2: 11.0102 12( 11) C-x(1,3)-C-x(0,1)-R 3: 8.3401 11( 11) C-x-C 4: 8.3401 19( 11) G-x(5)-C 5: 8.3401 12( 11) H-C 6: 8.3401 12( 11) C-x(3)-C 7: 8.3401 13( 11) T-C 8: 7.8401 15( 11) C-x(0,1)-R 9: 7.8401 17( 11) K-x(3,4)-C 10: 7.8401 18( 11) C-x(0,1)-L 11: 7.8401 15( 11) C-x(2,3)-R 12: 7.3401 16( 11) K-x(1,3)-C 13: 7.3401 15( 11) C-x(2,4)-K Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 12.0102 11( 11) C-x(3,4)-G-x(5)-C B 2: 11.0102 12( 11) C-x(1,3)-C-x(0,1)-R C 3: 10.9318 11( 11) T-C-[DET] D 4: 10.5166 11( 11) K-x(1,3)-C-x-[CN] E 5: 10.0255 12( 11) C-x(2,4)-K-x(4)-[CGV] F 6: 8.3401 11( 11) C-x-C G 7: 8.3401 19( 11) G-x(5)-C H 8: 8.3401 12( 11) H-C I 9: 8.3401 12( 11) C-x(3)-C J 10: 7.8401 15( 11) C-x(0,1)-R K 11: 7.8401 17( 11) K-x(3,4)-C L 12: 7.8401 18( 11) C-x(0,1)-L M 13: 7.8401 15( 11) C-x(2,3)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 12.0102 11( 11) C-x(3,4)-G-x(5)-C Occurences: 11(11) DEF4_LEIQH : 4- 15: gfg CplnqGachrhC rsirr DEFA_ZOPAT : 24- 34: acgah Clal-GrrggyC nsksv DEFI_AESCY : 15- 26: qchrh CqtitGrsggyC sgplk DEFI_APIME : 21- 31: acaan Clsl-GkagghC ekgvc DEFI_DROME : 72- 82: acagh Ciak-GfkggyC ndkav DEFI_PALPR : 24- 34: acaih Cltk-GykggrC vntic DEFI_PROTE : 74- 84: acaah Cllr-GnrggyC ngkgv DEFI_PYRAP : 24- 34: gcalh Cvik-GykggqC kitvc SAPB_SARPE : 14- 24: lcllh Crlk-GylrayC sqqkv SAPC_SARPE : 20- 30: acalh Cvfr-GnrggyC tgkgi SAPE_SARPE : 74- 84: acaah Cllr-GnrggyC ngkav B 2: 11.0102 12( 11) C-x(1,3)-C-x(0,1)-R Occurences: 12(11) DEF4_LEIQH : 11- 16: lnqga ChrhC-R sirrr DEF4_LEIQH : 33- 37: ffkqt Ct--CyR n DEFA_ZOPAT : 40- 43: nsksv Cv--C-R DEFI_AESCY : 34- 38: plklt Ct--CyR DEFI_APIME : 36- 39: cekgv Ci--C-R ktsfk DEFI_DROME : 88- 91: ndkav Cv--C-R n DEFI_PALPR : 39- 42: cvnti Cn--C-R n DEFI_PROTE : 90- 93: ngkgv Cv--C-R n DEFI_PYRAP : 39- 42: ckitv Ch--C-R r DEFI_PYRAP : 39- 43: ckitv Ch--CrR SAPB_SARPE : 10- 15: idrsl CllhC-R lkgyl SAPC_SARPE : 36- 39: tgkgi Cv--C-R n SAPE_SARPE : 90- 93: ngkav Cv--C-R n C 3: 10.9318 11( 11) T-C-[DET] Occurences: 11(11) DEF4_LEIQH : 32- 34: gffkq TCT cyrn DEFA_ZOPAT : 2- 4: f TCD vlgfe DEFI_AESCY : 33- 35: gplkl TCT cyr DEFI_APIME : 2- 4: v TCD llsfk DEFI_DROME : 54- 56: rqkra TCD llskw DEFI_PALPR : 2- 4: a TCD alsfs DEFI_PROTE : 56- 58: rykra TCD llsgt DEFI_PYRAP : 2- 4: a TCD ilsfq SAPB_SARPE : 2- 4: l TCE idrsl SAPC_SARPE : 2- 4: a TCD llsgi SAPE_SARPE : 56- 58: rykra TCD llsgt D 4: 10.5166 11( 11) K-x(1,3)-C-x-[CN] Occurences: 11(11) DEF4_LEIQH : 30- 35: cagff Kqt-CtC yrn DEFA_ZOPAT : 37- 42: gycns Ksv-CvC r DEFI_AESCY : 31- 36: csgpl Klt-CtC yr DEFI_APIME : 33- 38: gghce Kgv-CiC rktsf DEFI_DROME : 85- 90: gycnd Kav-CvC rn DEFI_PALPR : 30- 36: ltkgy KggrCvN ticnc DEFI_PROTE : 87- 92: gycng Kgv-CvC rn DEFI_PYRAP : 35- 41: kggqc KitvChC rr SAPB_SARPE : 28- 32: ycsqq Kv--CrC vq SAPC_SARPE : 33- 38: gyctg Kgi-CvC rn SAPE_SARPE : 87- 92: gycng Kav-CvC rn E 5: 10.0255 12( 11) C-x(2,4)-K-x(4)-[CGV] Occurences: 12(11) DEF4_LEIQH : 25- 35: rrggy CagffKqtctC yrn DEFA_ZOPAT : 34- 42: rrggy Cns--KsvcvC r DEFI_AESCY : 26- 36: rsggy CsgplKltctC yr DEFI_APIME : 21- 31: acaan ClslgKagghC ekgvc DEFI_DROME : 72- 80: acagh Cia--KgfkgG ycndk DEFI_DROME : 82- 90: fkggy Cnd--KavcvC rn DEFI_PALPR : 24- 32: acaih Clt--KgykgG rcvnt DEFI_PROTE : 84- 92: nrggy Cng--KgvcvC rn DEFI_PYRAP : 24- 32: gcalh Cvi--KgykgG qckit SAPB_SARPE : 24- 33: ylray Csqq-KvcrcV q SAPC_SARPE : 30- 38: nrggy Ctg--KgicvC rn SAPE_SARPE : 84- 92: nrggy Cng--KavcvC rn F 6: 8.3401 11( 11) C-x-C Occurences: 11(11) DEF4_LEIQH : 33- 35: ffkqt CtC yrn DEFA_ZOPAT : 40- 42: nsksv CvC r DEFI_AESCY : 34- 36: plklt CtC yr DEFI_APIME : 36- 38: cekgv CiC rktsf DEFI_DROME : 88- 90: ndkav CvC rn DEFI_PALPR : 39- 41: cvnti CnC rn DEFI_PROTE : 90- 92: ngkgv CvC rn DEFI_PYRAP : 39- 41: ckitv ChC rr SAPB_SARPE : 30- 32: sqqkv CrC vq SAPC_SARPE : 36- 38: tgkgi CvC rn SAPE_SARPE : 90- 92: ngkav CvC rn G 7: 8.3401 19( 11) G-x(5)-C Occurences: 19(11) DEF4_LEIQH : 9- 15: cplnq GachrhC rsirr DEF4_LEIQH : 27- 33: ggyca GffkqtC tcyrn DEFA_ZOPAT : 28- 34: hclal GrrggyC nsksv DEFI_AESCY : 20- 26: cqtit GrsggyC sgplk DEFI_AESCY : 28- 34: ggycs GplkltC tcyr DEFI_APIME : 25- 31: nclsl GkagghC ekgvc DEFI_DROME : 76- 82: hciak GfkggyC ndkav DEFI_PALPR : 28- 34: hcltk GykggrC vntic DEFI_PROTE : 64- 70: llsgt GinhsaC aahcl DEFI_PROTE : 78- 84: hcllr GnrggyC ngkgv DEFI_PROTE : 86- 92: ggycn GkgvcvC rn DEFI_PYRAP : 28- 34: hcvik GykggqC kitvc SAPB_SARPE : 18- 24: hcrlk GylrayC sqqkv SAPC_SARPE : 10- 16: llsgi GvqhsaC alhcv SAPC_SARPE : 24- 30: hcvfr GnrggyC tgkgi SAPC_SARPE : 32- 38: ggyct GkgicvC rn SAPE_SARPE : 64- 70: llsgt GinhsaC aahcl SAPE_SARPE : 78- 84: hcllr GnrggyC ngkav SAPE_SARPE : 86- 92: ggycn GkavcvC rn H 8: 8.3401 12( 11) H-C Occurences: 12(11) DEF4_LEIQH : 14- 15: gachr HC rsirr DEFA_ZOPAT : 23- 24: aacga HC lalgr DEFI_AESCY : 14- 15: mqchr HC qtitg DEFI_APIME : 30- 31: gkagg HC ekgvc DEFI_DROME : 71- 72: tacag HC iakgf DEFI_PALPR : 23- 24: sacai HC ltkgy DEFI_PROTE : 73- 74: sacaa HC llrgn DEFI_PYRAP : 23- 24: agcal HC vikgy DEFI_PYRAP : 40- 41: kitvc HC rr SAPB_SARPE : 13- 14: slcll HC rlkgy SAPC_SARPE : 19- 20: sacal HC vfrgn SAPE_SARPE : 73- 74: sacaa HC llrgn I 9: 8.3401 12( 11) C-x(3)-C Occurences: 12(11) DEF4_LEIQH : 11- 15: lnqga ChrhC rsirr DEFA_ZOPAT : 20- 24: lnsaa CgahC lalgr DEFI_AESCY : 11- 15: ldqmq ChrhC qtitg DEFI_APIME : 17- 21: vndsa CaanC lslgk DEFI_DROME : 68- 72: wnhta CaghC iakgf DEFI_PALPR : 20- 24: vnhsa CaihC ltkgy DEFI_PROTE : 12- 16: fvvtf ClavC fvsqs DEFI_PROTE : 70- 74: inhsa CaahC llrgn DEFI_PYRAP : 20- 24: pnhag CalhC vikgy SAPB_SARPE : 10- 14: idrsl CllhC rlkgy SAPC_SARPE : 16- 20: vqhsa CalhC vfrgn SAPE_SARPE : 70- 74: inhsa CaahC llrgn J 10: 7.8401 15( 11) C-x(0,1)-R Occurences: 15(11) DEF4_LEIQH : 11- 13: lnqga ChR hcrsi DEF4_LEIQH : 15- 16: achrh C-R sirrr DEF4_LEIQH : 35- 37: kqtct CyR n DEFA_ZOPAT : 42- 43: ksvcv C-R DEFI_AESCY : 11- 13: ldqmq ChR hcqti DEFI_AESCY : 36- 38: kltct CyR DEFI_APIME : 38- 39: kgvci C-R ktsfk DEFI_DROME : 90- 91: kavcv C-R n DEFI_PALPR : 41- 42: nticn C-R n DEFI_PROTE : 92- 93: kgvcv C-R n DEFI_PYRAP : 41- 42: itvch C-R r DEFI_PYRAP : 41- 43: itvch CrR SAPB_SARPE : 14- 15: lcllh C-R lkgyl SAPB_SARPE : 30- 31: sqqkv C-R cvq SAPC_SARPE : 38- 39: kgicv C-R n SAPE_SARPE : 92- 93: kavcv C-R n K 11: 7.8401 17( 11) K-x(3,4)-C Occurences: 17(11) DEF4_LEIQH : 30- 35: cagff KqtctC yrn DEFA_ZOPAT : 37- 42: gycns KsvcvC r DEFI_AESCY : 31- 36: csgpl KltctC yr DEFI_APIME : 26- 31: clslg KagghC ekgvc DEFI_APIME : 33- 38: gghce KgvciC rktsf DEFI_DROME : 51- 55: qhsrq Krat-C dllsk DEFI_DROME : 78- 82: iakgf Kggy-C ndkav DEFI_DROME : 85- 90: gycnd KavcvC rn DEFI_PALPR : 30- 34: ltkgy Kggr-C vntic DEFI_PROTE : 53- 57: lhgry Krat-C dllsg DEFI_PROTE : 87- 92: gycng KgvcvC rn DEFI_PYRAP : 30- 34: vikgy Kggq-C kitvc DEFI_PYRAP : 35- 39: kggqc Kitv-C hcrr SAPB_SARPE : 28- 32: ycsqq Kvcr-C vq SAPC_SARPE : 33- 38: gyctg KgicvC rn SAPE_SARPE : 53- 57: lhgry Krat-C dllsg SAPE_SARPE : 87- 92: gycng KavcvC rn L 12: 7.8401 18( 11) C-x(0,1)-L Occurences: 18(11) DEF4_LEIQH : 4- 6: gfg CpL nqgac DEFA_ZOPAT : 24- 25: acgah C-L algrr DEFI_AESCY : 4- 6: gfg CpL dqmqc DEFI_APIME : 3- 5: vt CdL lsfkg DEFI_APIME : 21- 22: acaan C-L slgka DEFI_DROME : 55- 57: qkrat CdL lskwn DEFI_PALPR : 24- 25: acaih C-L tkgyk DEFI_PROTE : 12- 13: fvvtf C-L avcfv DEFI_PROTE : 57- 59: ykrat CdL lsgtg DEFI_PROTE : 74- 75: acaah C-L lrgnr DEFI_PROTE : 74- 76: acaah ClL rgnrg DEFI_PYRAP : 20- 22: pnhag CaL hcvik SAPB_SARPE : 10- 11: idrsl C-L lhcrl SAPB_SARPE : 10- 12: idrsl ClL hcrlk SAPB_SARPE : 14- 16: lcllh CrL kgylr SAPC_SARPE : 3- 5: at CdL lsgig SAPC_SARPE : 16- 18: vqhsa CaL hcvfr SAPE_SARPE : 12- 13: lavtl C-L aaffm SAPE_SARPE : 57- 59: ykrat CdL lsgtg SAPE_SARPE : 74- 75: acaah C-L lrgnr SAPE_SARPE : 74- 76: acaah ClL rgnrg M 13: 7.8401 15( 11) C-x(2,3)-R Occurences: 15(11) DEF4_LEIQH : 15- 19: achrh CrsiR rrggy DEF4_LEIQH : 33- 37: ffkqt CtcyR n DEFA_ZOPAT : 40- 43: nsksv Cvc-R DEFI_AESCY : 34- 38: plklt CtcyR DEFI_APIME : 36- 39: cekgv Cic-R ktsfk DEFI_DROME : 88- 91: ndkav Cvc-R n DEFI_PALPR : 39- 42: cvnti Cnc-R n DEFI_PROTE : 74- 77: acaah Cll-R gnrgg DEFI_PROTE : 90- 93: ngkgv Cvc-R n DEFI_PYRAP : 39- 42: ckitv Chc-R r DEFI_PYRAP : 39- 43: ckitv ChcrR SAPB_SARPE : 3- 7: lt CeidR slcll SAPC_SARPE : 20- 23: acalh Cvf-R gnrgg SAPC_SARPE : 36- 39: tgkgi Cvc-R n SAPE_SARPE : 74- 77: acaah Cll-R gnrgg SAPE_SARPE : 90- 93: ngkav Cvc-R n Number of patterns evaluated by Pratt:26 Total running time: 0 seconds