Can Letter U appear in one amino acids sequence?

Question

Cai 2014-6-17

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https://ww2.mathworks.cn/matlabcentral/answers/134818-can-letter-u-appear-in-one-amino-acids-sequence

回答： Cai 2014-6-17

I used swalign function to align two amino acids sequences. The first sequence includes letter U in the last row, but the second one does not have. When run this function, I get the following error: ??? Error using ==> swalign at 95 Both sequences must be amino acids, use ALPHABET = 'NT' for aligning nucleotides. First sequence:

>sp|Q16881|TRXR1_HUMAN Thioredoxin reductase 1, cytoplasmic OS=Homo sapiens GN=TXNRD1 PE=1 SV=3
MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQ
AYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDL
PVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKE
AAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKV
EETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEK
IYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLA
GIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVV
AQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIY
AIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKA
VEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQ
GFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG

Second sequence:

>sp|P31645|SC6A4_HUMAN Sodium-dependent serotonin transporter OS=Homo sapiens GN=SLC6A4 PE=1 SV=1
METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTR
HSIPATTTTLVAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLP
YTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIM
AWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIH
RSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGA
TLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQD
ALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPAS
TFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVT
LTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRIC
WVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIIT
PGTFKERIIKSITPETPTEIPCGDIRLNAV

I used other align tool, such as the tool in UniProt website, but these two sequences could be aligned successfully.My Matlab version is R2010a, How to solve this problem?

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David Sanchez 2014-6-17

Could you please paste the code you use, specially the part that yields the error?

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Answer 1

David Sanchez 2014-6-17

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/134818-can-letter-u-appear-in-one-amino-acids-sequence#answer_141326

在 MATLAB Online 中打开

As you can see, for example in this link:

http://www.hgvs.org/mutnomen/codon.html

U can not be in the sequence

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Answer 2

David Sanchez 2014-6-17

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https://ww2.mathworks.cn/matlabcentral/answers/134818-can-letter-u-appear-in-one-amino-acids-sequence#answer_141311

在 MATLAB Online 中打开

Your sequences are not of the same length, when A is restricted to same size than B, you do not get the error:

A = 'MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG';
B='METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTRHSIPATTTTLVAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETPTEIPCGDIRLNAV';
    LA = length(A)
    LB = length(B)
    [Score,Alignment]= swalign(A(1:630),B(1:630))
    LA =
       649
    LB =
       630
    Score =
        24
    Alignment =
    AAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIG-SLNWGYRVALREKKVVYENAYGQFIGPHRIKA
    :| | ::  ::  ||: |:||| | :   |    : : :|:    : :  :     :   : ::::  :: | : :: : : || ::: |  |  |   : |:|: | |: |: | |
    SACEDGEDCQENGVLQKVVPTP-GDKVESGQISNGYSAVPSPGAGDDTRHSIPATTTTLVA-ELHQGERETWGKKVDFLLSVIGYAVDLG-NV-WRFPYICYQNGGGAFLLPYTIMA

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Answer 3

Cai 2014-6-17

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/134818-can-letter-u-appear-in-one-amino-acids-sequence#answer_141313

Mr David Sanchez,

Thanks for your reply. But the reason of this problem did not be caused by their length. If I delete the letter U where located in the last row of the A sequence, the alignment operation can be successfully. So I doubt whether U can't appear in the amino acids sequence.