K and E are treated similar because they are both charged, according to the default matrix (EBLOSUM62), in which the score between K and E is positive 1. Maybe you could use parameter -matrix to set your specified score matrix.
On Thu, Oct 29, 2009 at 2:39 AM, Jean Mao <[email protected]> wrote: > Hi, > > A user of ours have a question regarding showaling. When running showalign > with the input file (attached), the consensus (and parental) residue is > Lysine (K) and one of her mutants residue is Glutamic acid (E). Lysine is > basic and Glutamic acid is basic, which are opposites and shouldn't be > similar. She was using all default setting which supposed to show (E) in the > alignment output. But instead, it shows (e) which indicate similarity > between Lysine and Glutamic acid. Can someone help? > > Thank you > > Jean Mao > > >>A1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSSQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>A2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>A4 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCEGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLRASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>A8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARVLWFRDWGKMDVWGKGTTVTVSVD >>A9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQTPGKGLEWMGIIYPDGSDTRYGPSFQGQVTISFDKSIDTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVS >>B2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B4 > ASQMTQSPSSLSASVGDRVAITCRVSQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYNFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>B5 > ASQMTQSPSSLSASVGDRVTITCRASQGIGNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGHSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>B6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGAIYPDDSDTRYSPSFQGQVTISFDKSTNTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSISTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVA >>C3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSA >>C4 > ASQMTQSPSSLPASVGDRVTITRRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDSTLTISSLQPEDFATYYCLQDYTYPRTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>C6 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>C8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTATYYCARALRFRDWGKMDVWGRGTTVTVSVD >>D2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D7 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>D8 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>D9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKGPGESLKISCRGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKVDVWGKGTTVTVSVD >>E4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTTVTVSVD >>E9 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>E11 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYAYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWLRDWGKMDVWGKGTTVTVSVD >>F1 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLRISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTAVTVSVD >>F2 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSAQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>F3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRTGARWTSGAKGPRSPSPS >>F4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSSTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G1 > ASQMAQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALRFRDWGKMDVWGKGTRSPSP >>G2 > QMTQSPSSLSASVGDRVTITCRASQGIRNNLGWYQQKPGEAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGEPLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVS >>G3 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDHTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFANYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLEASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G4 > ASQMTQSPSSLSASVGDRVTITCRASQGIRSDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQGYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGTIYPDDSDTRYGPSFRGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVPVD >>G5 > ASQMTQSPSSLSASVGDRVTITCRASQGIRNGLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAGVKKPGESLKISCKGSGYSFTDYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARALWFRDWGKMDVWGKGTTVTVSVD >>G6 > ASQMTQSPSSLSASVGGRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDSATYYCLQDYTYPWTFGQGTKLEIKRTGGGGSGGGGSGGGGSVQLLEQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMGIIYPDDSDTRYSPSFQGQVTISFDKSINTAYLQWSSLKASDTAIYYCARASWFRDWGKMDVWGKGTTVTVSVD > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
