Pairwise sequence comparison

Answers

1. How does the dot-plot of the sequence above look like and why?
   
   Parallell diagonals appear as the sequence contains internal repeats.
   
   
2. Obtain the Swissprot entries of the yeast hexokinase A
   and yeast hexokinase B proteins (see above) and create one fasta-file
   which contains both sequences.
   After having downloaded and compiled ReadSeq, the commandline to obtain the Fasta-File looks as follows:
   

   	readseq -f8 -p hxka_yeast hxkb_yeast > hxk_yeast.fasta
   

   
   And here is the content of the resulting file hxk_yeast.fasta:
   

   >HXKA_YEAST     STANDARD;      PRT;   485 AA., 485 bases, 8BF84D98 checksum.
   MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFID
   ELNKGLTKKGGNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLS
   GNHTFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDT
   LPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRE
   LPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKL
   EGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQA
   FEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARI
   EDDPFENLEDTDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGI
   AAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKDPI
   TIVPAEDGSGAGAAVIAALSEKRIAEGKSLGIIGA
   >HXKB_YEAST     STANDARD;      PRT;   486 AA., 486 bases, B05F4DF9 checksum.
   MVHLGPKKPQARKGSMADVPKELMQQIENFEKIFTVPTETLQAVTKHFIS
   ELEKGLSKKGGNIPMIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLG
   GDRTFDTTQSKYRLPDAMRTTQNPDELWEFIADSLKAFIDEQFPQGISEP
   IPLGFTFSFPASQNKINEGILQRWTKGFDIPNIENHDVVPMLQKQITKRN
   IPIEVVALINDTTGTLVASYYTDPETKMGVIFGTGVNGAYYDVCSDIEKL
   QGKLSDDIPPSAPMAINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQT
   FEKMSSGYYLGEILRLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARI
   EEDPFENLEDTDDLFQNEFGINTTVQERKLIRRLSELIGARAARLSVCGI
   AAICQKRGYKTGHIAADGSVYNRYPGFKEKAANALKDIYGWTQTSLDDYP
   IKIVPAEDGSGAGAAVIAALAQKRIAEGKSVGIIGA
   

   
   
   

3. Align the yeast hexokinase A and yeast hexokinase B protein.
   (hint: use LALIGN which is found at Swissprot -> Proteomics tools)
   here is the output of LAlign:
   

   
   
   ALIGN calculates a global alignment of two sequences
    version 2.0uPlease cite: Myers and Miller, CABIOS (1989) 4:11-17
   hxka_yeast                                          485 aa vs.
   hxkb_yeast                                          486 aa
   scoring matrix: BLOSUM50, gap penalties: -14/-4
   77.4% identity;         Global alignment score: 2596
   
                  10        20        30        40        50        60
   /tmp/w MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKG
          ::::::::::::::::::::::::..:...: .::: .:::. :.::::.::.:::.:::
   hxkb_y MVHLGPKKPQARKGSMADVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKG
                  10        20        30        40        50        60
   
                  70        80        90       100       110       120
   /tmp/w GNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKLPHDMRT
          :::::::::::.::::::::..:::::::::::::::::.:..:::::::::.::  :::
   hxkb_y GNIPMIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLGGDRTFDTTQSKYRLPDAMRT
                  70        80        90       100       110       120
   
                 130       140       150       160       170       180
   /tmp/w TKHQEELWSFIADSLKDFMVEQELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDI
          :.. .::: ::::::: :. ::   . .. .:::::::.:::::::::::::::::::::
   hxkb_y TQNPDELWEFIADSLKAFIDEQFPQGISEPIPLGFTFSFPASQNKINEGILQRWTKGFDI
                 130       140       150       160       170       180
   
                 190       200       210       220       230       240
   /tmp/w PNVEGHDVVPLLQNEISKRELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAF
          ::.:.:::::.::..:.::..:::.:::::::.:::.::::::::::::::::::::::.
   hxkb_y PNIENHDVVPMLQKQITKRNIPIEVVALINDTTGTLVASYYTDPETKMGVIFGTGVNGAY
                 190       200       210       220       230       240
   
                 250       260       270       280       290       300
   /tmp/w YDVVSDIEKLEGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQA
          ::: ::::::.:::.:::: ..:::::::::::::::.::::::::...::.:::::::.
   hxkb_y YDVCSDIEKLQGKLSDDIPPSAPMAINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQT
                 250       260       270       280       290       300
   
                 310       320       330       340       350       360
   /tmp/w FEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLED
          ::::.:::::::.:::.:... ..:...:.:::::. .:..::::::::::.::::::::
   hxkb_y FEKMSSGYYLGEILRLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARIEEDPFENLED
                 310       320       330       340       350       360
   
                 370       380       390       400       410       420
   /tmp/w TDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSV
          :::.::..::..::. :::::::: ::::.:::::.::::::::::::::::::::::::
   hxkb_y TDDLFQNEFGINTTVQERKLIRRLSELIGARAARLSVCGIAAICQKRGYKTGHIAADGSV
                 370       380       390       400       410       420
   
                 430       440        450       460       470         
   /tmp/w YNKYPGFKEAAAKGLRDIYGWTGDASKD-PITIVPAEDGSGAGAAVIAALSEKRIAEGKS
          ::.:::::: ::..:.::::::  .  : :: ::::::::::::::::::..::::::::
   hxkb_y YNRYPGFKEKAANALKDIYGWTQTSLDDYPIKIVPAEDGSGAGAAVIAALAQKRIAEGKS
                 430       440       450       460       470       480
   
        480     
   /tmp/w LGIIGA
          .:::::
   hxkb_y VGIIGA
                
   

   
   
   

   ---

   Comments are very welcome.
   luz@molgen.mpg.de