Team:Carnegie Mellon/Week14

From 2013.igem.org

(Difference between revisions)
(Created page with "KillerRed DNA sequence (our plasmid):<br> ATGGGTTCAGAGGGCGGCCCCGCCCTGTTCCAGAGCGACATGACCTTCAAAATCTT CATCGACGGCGAGGTGAACGGCCAGAAGTTCACCATCGTGGCCGACGGCAGCAGCA AGTTCCCCCACGGCGACTTCAA...")
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  Strand=Plus/Plus
  Strand=Plus/Plus
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Query  1    ATGGGTAGTGAAGGCGGTCCTGCGTTATTTCAGAGCGACATGACTTTCAAAATTTTTATA  60<br>
 
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            ||||||  || ||||| || ||  | || |||||||||||||| |||||||| || || <br>
 
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Sbjct  1    ATGGGTTCAGAGGGCGGCCCCGCCCTGTTCCAGAGCGACATGACCTTCAAAATCTTCATC  60<br>
 
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<br>
 
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Query  61  GATGGTGAAGTGAACGGACAGAAGTTCACCATCGTAGCTGATGGGTCTAGCAAATTCCCC  120<br>
 
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            || || || |||||||| ||||||||||||||||| || || ||    ||||| ||||||<br>
 
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Sbjct  61  GACGGCGAGGTGAACGGCCAGAAGTTCACCATCGTGGCCGACGGCAGCAGCAAGTTCCCC  120<br>
 
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<br>
 
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Query  121  CATGGTGATTTCAACGTCCACGCGGTTTGTGAGACTGGTAAACTCCCGATGTCATGGAAA  180<br>
 
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            || || || |||||||| ||||| || || ||||| || || || || |||  ||||| <br>
 
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Sbjct  121  CACGGCGACTTCAACGTGCACGCCGTGTGCGAGACCGGCAAGCTGCCCATGAGCTGGAAG  180<br>
 
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<br>
 
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Query  181  CCAATCTGCCATCTGATACAGTATGGAGAGCCCTTTTTCGCCCGGTATCCTGATGGCATA  240<br>
 
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            || |||||||| ||||| ||||| || |||||||| |||||||| || || || ||||| <br>
 
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Sbjct  181  CCCATCTGCCACCTGATCCAGTACGGCGAGCCCTTCTTCGCCCGCTACCCCGACGGCATC  240<br>
 
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<br>
 
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Query  241  TCTCATTTTGCCCAAGAGTGTTTTCCTGAGGGTCTGAGTATCGATCGCACAGTGCGATTT  300<br>
 
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              ||||| ||||| ||||| || || ||||| ||||| ||||| ||||| ||||| || <br>
 
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Sbjct  241  AGCCATTTCGCCCAGGAGTGCTTCCCCGAGGGCCTGAGCATCGACCGCACCGTGCGCTTC  300<br>
 
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<br>
 
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Query  301  GAGAACGACGGTACCATGACTTCTCACCACACATATGAATTGGATGATACTTGCGTCGTC  360<br>
 
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            ||||||||||| ||||||||    |||||||| || ||  |||| || || ||||| || <br>
 
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Sbjct  301  GAGAACGACGGCACCATGACCAGCCACCACACCTACGAGCTGGACGACACCTGCGTGGTG  360<br>
 
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<br>
 
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Query  361  TCCCGAATCACCGTGAATTGTGATGGGTTTCAACCGGACGGGCCGATCATGCGGGATCAG  420<br>
 
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              ||| ||||||||||| || || || || || || ||||| || |||||||| || |||<br>
 
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Sbjct  361  AGCCGCATCACCGTGAACTGCGACGGCTTCCAGCCCGACGGCCCCATCATGCGCGACCAG  420<br>
 
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<br><br>
 
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Query  421  CTGGTTGATATCCTCCCAAACGAAACTCATATGTTTCCTCACGGGCCAAATGCTGTGAGA  480<br>
 
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            ||||| || ||||| || ||||| || || ||||| || ||||| || || || ||| | <br>
 
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Sbjct  421  CTGGTGGACATCCTGCCCAACGAGACCCACATGTTCCCCCACGGCCCCAACGCCGTGCGC  480<br>
 
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<br>
 
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Query  481  CAGCTGGCTTTCATCGGTTTTACGACCGCCGATGGCGGCCTCATGATGGGCCACTTTGAT  540<br>
 
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            |||||||| |||||||| || || |||||||| |||||||| |||||||||||||| || <br>
 
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Sbjct  481  CAGCTGGCCTTCATCGGCTTCACCACCGCCGACGGCGGCCTGATGATGGGCCACTTCGAC  540<br>
 
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<br>
 
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Query  541  AGCAAAATGACCTTTAATGGGAGTCGCGCAATAGAAATTCCAGGCCCGCATTTTGTTACA  600<br>
 
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            ||||| |||||||| || || || ||||| || || || || ||||| || || || || <br>
 
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Sbjct  541  AGCAAGATGACCTTCAACGGCAGCCGCGCCATCGAGATCCCCGGCCCACACTTCGTGACC  600<br>
 
-
<br>
 
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Query  601  ATTATCACCAAACAGATGCGTGACACGAGCGATAAGCGCGACCATGTTTGCCAGCGTGAG  660<br>
 
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            || |||||||| |||||| | ||||| ||||| ||||||||||| || |||||||| |||<br>
 
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Sbjct  601  ATCATCACCAAGCAGATGAGGGACACCAGCGACAAGCGCGACCACGTGTGCCAGCGCGAG  660<br>
 
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<br>
 
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Query  661  GTTGCGTATGCACATTCAGTGCCGCGAATCACAAGTGCAATCGGTTCAGACGAAGACTAA  720<br>
 
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            || || || || ||    ||||| || ||||| || || ||||||  ||||| || |||<br>
 
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Sbjct  661  GTGGCCTACGCCCACAGCGTGCCCCGCATCACCAGCGCCATCGGTAGCGACGAGGATTAA  720<br>
 
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<br>
 
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Query  721  TAA  723<br>
 
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            |||<br>
 
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Sbjct  721  TAA  723<br>
 
Problems with unoptimized KillerRed gene:
Problems with unoptimized KillerRed gene:

Revision as of 21:30, 26 September 2013

KillerRed DNA sequence (our plasmid):
ATGGGTTCAGAGGGCGGCCCCGCCCTGTTCCAGAGCGACATGACCTTCAAAATCTT CATCGACGGCGAGGTGAACGGCCAGAAGTTCACCATCGTGGCCGACGGCAGCAGCA AGTTCCCCCACGGCGACTTCAACGTGCACGCCGTGTGCGAGACCGGCAAGCTGCCC ATGAGCTGGAAGCCCATCTGCCACCTGATCCAGTACGGCGAGCCCTTCTTCGCCCG CTACCCCGACGGCATCAGCCATTTCGCCCAGGAGTGCTTCCCCGAGGGCCTGAGCA CGACCGCACCGTGCGCTTCGAGAACGACGGCACCATGACCAGCCACCACACCTACG AGCTGGACGACACCTGCGTGGTGAGCCGCATCACCGTGAACTGCGACGGCTTCCAG CCCGACGGCCCCATCATGCGCGACCAGCTGGTGGACATCCTGCCCAACGAGACCCA CATGTTCCCCCACGGCCCCAACGCCGTGCGCCAGCTGGCCTTCATCGGCTTCACCA CCGCCGACGGCGGCCTGATGATGGGCCACTTCGACAGCAAGATGACCTTCAACGGC AGCCGCGCCATCGAGATCCCCGGCCCACACTTCGTGACCATCATCACCAAGCAGAT GAGGGACACCAGCGACAAGCGCGACCACGTGTGCCAGCGCGAGGTGGCCTACGCCC ACAGCGTGCCCCGCATCACCAGCGCCATCGGTAGCGACGAGGATTAATAA

KillerRed Protein Sequence:
MGSEGGPALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLP MSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTY ELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFT TADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYA HSVPRITSAIGSDED

KillerRed Codon Optimized Sequence:
ATGGGTAGTGAAGGCGGTCCTGCGTTATTTCAGAGCGACATGACTTTCAAAATTTT TATAGATGGTGAAGTGAACGGACAGAAGTTCACCATCGTAGCTGATGGGTCTAGCA AATTCCCCCATGGTGATTTCAACGTCCACGCGGTTTGTGAGACTGGTAAACTCCCG ATGTCATGGAAACCAATCTGCCATCTGATACAGTATGGAGAGCCCTTTTTCGCCCG GTATCCTGATGGCATATCTCATTTTGCCCAAGAGTGTTTTCCTGAGGGTCTGAGTA TCGATCGCACAGTGCGATTTGAGAACGACGGTACCATGACTTCTCACCACACATAT GAATTGGATGATACTTGCGTCGTCTCCCGAATCACCGTGAATTGTGATGGGTTTCA ACCGGACGGGCCGATCATGCGGGATCAGCTGGTTGATATCCTCCCAAACGAAACTC ATATGTTTCCTCACGGGCCAAATGCTGTGAGACAGCTGGCTTTCATCGGTTTTACG ACCGCCGATGGCGGCCTCATGATGGGCCACTTTGATAGCAAAATGACCTTTAATGG GAGTCGCGCAATAGAAATTCCAGGCCCGCATTTTGTTACAATTATCACCAAACAGA TGCGTGACACGAGCGATAAGCGCGACCATGTTTGCCAGCGTGAGGTTGCGTATGCA CATTCAGTGCCGCGAATCACAAGTGCAATCGGTTCAGACGAAGACTAATAA


Alignment (Query=Optimized and Subject=Current plasmid)
Score = 583 bits (646), Expect = 9e-171

Identities = 563/723 (78%), Gaps = 0/723 (0%)

Strand=Plus/Plus


Problems with unoptimized KillerRed gene:

12x rare Proline codons in the unoptimized (CCC)
5x rare Lysine codons in the unoptimized (AAG)
11x rare Glutamic Acid codons in unoptimized (GAG)

Retrieved from "http://2013.igem.org/Team:Carnegie_Mellon/Week14"