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
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