Team:Carnegie Mellon/Week14

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)