------------------------------------------------------------ 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 17 sequences from file PENTAXIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 17 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 PENTAXIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CRP1_LIMPO 242 CRP3_LIMPO 242 CRP4_LIMPO 242 CRP_HUMAN 224 CRP_MOUSE 225 CRP_MUSCA 20 CRP_PLEPL 32 CRP_RABIT 225 CRP_XENLA 238 FP_CRIMI 231 LIMU_LIMPO 84 PTX3_HUMAN 381 SAMP_HUMAN 223 SAMP_MESAU 234 SAMP_MOUSE 224 SAMP_MUSCA 9 SAMP_RAT 228 Pratt run started at Thu Feb 6 20:31:08 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 10.5102 23( 17) K-x(1,3)-L-x(0,2)-F 2: 7.8401 48( 17) L-x(1,2)-F 3: 7.8401 55( 17) K-x(1,2)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 10.5102 23( 17) K-x(1,3)-L-x(0,2)-F B 2: 7.8401 48( 17) L-x(1,2)-F C 3: 7.8401 55( 17) K-x(1,2)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 10.5102 23( 17) K-x(1,3)-L-x(0,2)-F Occurences: 23(17) CRP1_LIMPO : 71- 77: kvnrl Kgt-LhmF syata CRP3_LIMPO : 71- 77: kvncl Kgt-LhmF syata CRP4_LIMPO : 71- 77: kvnhl Kst-LtiF synta CRP_HUMAN : 3- 7: me Kl--Lc-F lvlts CRP_HUMAN : 46- 51: kaplt Kp--LkaF tvclh CRP_MOUSE : 46- 52: leaes Kkp-LntF tvclh CRP_MOUSE : 47- 52: eaesk Kp--LntF tvclh CRP_MUSCA : 16- 20: aglag Ka--Ld-F CRP_PLEPL : 4- 8: vvi Kt--Lv-F qsesn CRP_PLEPL : 23- 30: elipm KplnLraF xl CRP_RABIT : 3- 8: me Kl--LwcF ltlvs CRP_RABIT : 46- 52: lnaql Kkp-LkaF tvcly CRP_RABIT : 47- 52: naqlk Kp--LkaF tvcly CRP_XENLA : 189- 192: pdhiq Kv--L--F anmdf FP_CRIMI : 47- 52: iprle Kp--LenF tlcfr LIMU_LIMPO : 66- 73: yatak KdneLltF ldeqg PTX3_HUMAN : 221- 225: tdvln Kti-L--F sygtk SAMP_HUMAN : 47- 52: itple Kp--LqnF tlcfr SAMP_MESAU : 50- 55: iprld Kp--LqnF tvcfr SAMP_MOUSE : 3- 9: md Kll-LwmF vftsl SAMP_MOUSE : 48- 53: iphle Kp--LqnF tlcfr SAMP_MUSCA : 5- 9: gfpg Ks--Li-F SAMP_RAT : 48- 53: ipwle Kp--LqnF tlcfr B 2: 7.8401 48( 17) L-x(1,2)-F Occurences: 48(17) CRP1_LIMPO : 17- 20: avslc LllF ltsal CRP1_LIMPO : 18- 20: vslcl Ll-F ltsal CRP1_LIMPO : 74- 77: rlkgt LhmF syata CRP3_LIMPO : 17- 20: avslc LllF ltsal CRP3_LIMPO : 18- 20: vslcl Ll-F ltsal CRP3_LIMPO : 74- 77: clkgt LhmF syata CRP4_LIMPO : 17- 20: avfly LllF lpsal CRP4_LIMPO : 18- 20: vflyl Ll-F lpsal CRP4_LIMPO : 74- 77: hlkst LtiF synta CRP_HUMAN : 4- 7: mek LlcF lvlts CRP_HUMAN : 5- 7: mekl Lc-F lvlts CRP_HUMAN : 48- 51: pltkp LkaF tvclh CRP_HUMAN : 55- 57: aftvc Lh-F ytels CRP_HUMAN : 82- 84: qdnei Li-F wskdi CRP_MOUSE : 49- 52: eskkp LntF tvclh CRP_MOUSE : 56- 58: tftvc Lh-F ytals CRP_MOUSE : 83- 85: nsndi Li-F wnkdk CRP_MUSCA : 18- 20: lagka Ld-F CRP_PLEPL : 6- 8: vvikt Lv-F qsesn CRP_PLEPL : 27- 30: mkpln LraF xl CRP_RABIT : 5- 8: mekl LwcF ltlvs CRP_RABIT : 11- 14: wcflt LvsF snmsd CRP_RABIT : 49- 52: qlkkp LkaF tvcly CRP_RABIT : 56- 58: aftvc Ly-F ytdls CRP_RABIT : 83- 85: qfnei Ll-F wskdi CRP_XENLA : 6- 8: merfa Lw-F iflag CRP_XENLA : 59- 62: rsytt LtrF hslls CRP_XENLA : 80- 82: qdnaf Ll-F skppn FP_CRIMI : 49- 52: rlekp LenF tlcfr FP_CRIMI : 54- 56: lenft Lc-F rtytd LIMU_LIMPO : 56- 59: ghsrv LbmF syata LIMU_LIMPO : 70- 73: kkdne LltF ldeqg LIMU_LIMPO : 71- 73: kdnel Lt-F ldeqg PTX3_HUMAN : 204- 207: vrpmr LesF saciw PTX3_HUMAN : 327- 329: gfdet La-F sgrlt PTX3_HUMAN : 333- 336: afsgr LtgF niwds SAMP_HUMAN : 15- 18: vltsl LeaF ahtdl SAMP_HUMAN : 49- 52: plekp LqnF tlcfr SAMP_HUMAN : 54- 56: lqnft Lc-F raysd SAMP_MESAU : 18- 21: lagll LeaF aqtdl SAMP_MESAU : 52- 55: rldkp LqnF tvcfr SAMP_MOUSE : 6- 9: mdkll LwmF vftsl SAMP_MOUSE : 50- 53: hlekp LqnF tlcfr SAMP_MOUSE : 55- 57: lqnft Lc-F rtysd SAMP_MUSCA : 7- 9: fpgks Li-F SAMP_RAT : 50- 53: wlekp LqnF tlcfr SAMP_RAT : 55- 57: lqnft Lc-F raysd SAMP_RAT : 105- 108: vtvrg LeeF pspih C 3: 7.8401 55( 17) K-x(1,2)-L Occurences: 55(17) CRP1_LIMPO : 71- 74: kvnrl KgtL hmfsy CRP1_LIMPO : 202- 204: nheqi Ky-L skcah CRP3_LIMPO : 71- 74: kvncl KgtL hmfsy CRP3_LIMPO : 202- 204: nheqi Ky-L skcah CRP4_LIMPO : 71- 74: kvnhl KstL tifsy CRP4_LIMPO : 202- 204: nheqi Kh-L skcah CRP_HUMAN : 3- 5: me Kl-L cflvl CRP_HUMAN : 41- 44: syvsl KapL tkplk CRP_HUMAN : 46- 48: kaplt Kp-L kaftv CRP_HUMAN : 137- 139: kprvr Ks-L kkgyt CRP_HUMAN : 219- 222: gevft KpqL wp CRP_MOUSE : 3- 5: me Kl-L wclli CRP_MOUSE : 46- 49: leaes KkpL ntftv CRP_MOUSE : 47- 49: eaesk Kp-L ntftv CRP_MOUSE : 138- 140: kakvr Ks-L hkgyt CRP_MOUSE : 168- 171: gdfda KqsL vgdig CRP_MOUSE : 220- 223: gdvfi KpqL ws CRP_MUSCA : 16- 18: aglag Ka-L df CRP_PLEPL : 4- 6: vvi Kt-L vfqse CRP_PLEPL : 23- 25: elipm Kp-L nlraf CRP_RABIT : 3- 5: me Kl-L wcflt CRP_RABIT : 46- 49: lnaql KkpL kaftv CRP_RABIT : 47- 49: naqlk Kp-L kaftv CRP_RABIT : 138- 140: kpmvr Ks-L kkgyi CRP_RABIT : 220- 223: gevhv KpqL wp CRP_XENLA : 44- 46: kpeve Kp-L knltv CRP_XENLA : 47- 49: vekpl Kn-L tvclr CRP_XENLA : 189- 191: pdhiq Kv-L fanmd CRP_XENLA : 224- 226: pkrqc Kt-L ehhyg FP_CRIMI : 3- 5: md Km-L lllgv FP_CRIMI : 3- 6: md KmlL llgvs FP_CRIMI : 47- 49: iprle Kp-L enftl FP_CRIMI : 135- 138: gipwv KkgL kkgyt FP_CRIMI : 136- 138: ipwvk Kg-L kkgyt LIMU_LIMPO : 47- 50: kvnql KgtL ghsrv PTX3_HUMAN : 221- 224: tdvln KtiL fsygt SAMP_HUMAN : 3- 5: mn Kp-L lwisv SAMP_HUMAN : 3- 6: mn KplL wisvl SAMP_HUMAN : 47- 49: itple Kp-L qnftl SAMP_HUMAN : 135- 138: gtplv KkgL rqgyf SAMP_HUMAN : 136- 138: tplvk Kg-L rqgyf SAMP_HUMAN : 149- 152: veaqp KivL gqeqd SAMP_HUMAN : 218- 220: gyvii Kp-L vwv SAMP_MESAU : 3- 5: md Kl-L sllgv SAMP_MESAU : 50- 52: iprld Kp-L qnftv SAMP_MESAU : 138- 141: gkpwv KkgL qkgyt SAMP_MESAU : 139- 141: kpwvk Kg-L qkgyt SAMP_MOUSE : 3- 5: md Kl-L lwmfv SAMP_MOUSE : 3- 6: md KllL wmfvf SAMP_MOUSE : 48- 50: iphle Kp-L qnftl SAMP_MOUSE : 136- 139: gkpwv KksL qreyt SAMP_MOUSE : 137- 139: kpwvk Ks-L qreyt SAMP_MUSCA : 5- 7: gfpg Ks-L if SAMP_RAT : 3- 5: md Kl-L lwmsv SAMP_RAT : 3- 6: md KllL wmsvf SAMP_RAT : 48- 50: ipwle Kp-L qnftl SAMP_RAT : 85- 88: elliy KakL eqysl SAMP_RAT : 136- 139: gkpwv KkgL qkgyt SAMP_RAT : 137- 139: kpwvk Kg-L qkgyt Number of patterns evaluated by Pratt:4 Total running time: 0 seconds