Team:Carnegie Mellon/Week14

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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

Query 1 ATGGGTAGTGAAGGCGGTCCTGCGTTATTTCAGAGCGACATGACTTTCAAAATTTTTATA 60

           ||||||   || ||||| || ||  | || |||||||||||||| |||||||| || ||

Sbjct 1 ATGGGTTCAGAGGGCGGCCCCGCCCTGTTCCAGAGCGACATGACCTTCAAAATCTTCATC 60

Query 61 GATGGTGAAGTGAACGGACAGAAGTTCACCATCGTAGCTGATGGGTCTAGCAAATTCCCC 120

           || || || |||||||| ||||||||||||||||| || || ||    ||||| ||||||

Sbjct 61 GACGGCGAGGTGAACGGCCAGAAGTTCACCATCGTGGCCGACGGCAGCAGCAAGTTCCCC 120

Query 121 CATGGTGATTTCAACGTCCACGCGGTTTGTGAGACTGGTAAACTCCCGATGTCATGGAAA 180

           || || || |||||||| ||||| || || ||||| || || || || |||   |||||

Sbjct 121 CACGGCGACTTCAACGTGCACGCCGTGTGCGAGACCGGCAAGCTGCCCATGAGCTGGAAG 180

Query 181 CCAATCTGCCATCTGATACAGTATGGAGAGCCCTTTTTCGCCCGGTATCCTGATGGCATA 240

           || |||||||| ||||| ||||| || |||||||| |||||||| || || || |||||

Sbjct 181 CCCATCTGCCACCTGATCCAGTACGGCGAGCCCTTCTTCGCCCGCTACCCCGACGGCATC 240

Query 241 TCTCATTTTGCCCAAGAGTGTTTTCCTGAGGGTCTGAGTATCGATCGCACAGTGCGATTT 300

              ||||| ||||| ||||| || || ||||| ||||| ||||| ||||| ||||| ||

Sbjct 241 AGCCATTTCGCCCAGGAGTGCTTCCCCGAGGGCCTGAGCATCGACCGCACCGTGCGCTTC 300

Query 301 GAGAACGACGGTACCATGACTTCTCACCACACATATGAATTGGATGATACTTGCGTCGTC 360

           ||||||||||| ||||||||    |||||||| || ||  |||| || || ||||| ||

Sbjct 301 GAGAACGACGGCACCATGACCAGCCACCACACCTACGAGCTGGACGACACCTGCGTGGTG 360

Query 361 TCCCGAATCACCGTGAATTGTGATGGGTTTCAACCGGACGGGCCGATCATGCGGGATCAG 420

             ||| ||||||||||| || || || || || || ||||| || |||||||| || |||

Sbjct 361 AGCCGCATCACCGTGAACTGCGACGGCTTCCAGCCCGACGGCCCCATCATGCGCGACCAG 420

Query 421 CTGGTTGATATCCTCCCAAACGAAACTCATATGTTTCCTCACGGGCCAAATGCTGTGAGA 480

           ||||| || ||||| || ||||| || || ||||| || ||||| || || || ||| |

Sbjct 421 CTGGTGGACATCCTGCCCAACGAGACCCACATGTTCCCCCACGGCCCCAACGCCGTGCGC 480

Query 481 CAGCTGGCTTTCATCGGTTTTACGACCGCCGATGGCGGCCTCATGATGGGCCACTTTGAT 540

           |||||||| |||||||| || || |||||||| |||||||| |||||||||||||| ||

Sbjct 481 CAGCTGGCCTTCATCGGCTTCACCACCGCCGACGGCGGCCTGATGATGGGCCACTTCGAC 540

Query 541 AGCAAAATGACCTTTAATGGGAGTCGCGCAATAGAAATTCCAGGCCCGCATTTTGTTACA 600

           ||||| |||||||| || || || ||||| || || || || ||||| || || || ||

Sbjct 541 AGCAAGATGACCTTCAACGGCAGCCGCGCCATCGAGATCCCCGGCCCACACTTCGTGACC 600

Query 601 ATTATCACCAAACAGATGCGTGACACGAGCGATAAGCGCGACCATGTTTGCCAGCGTGAG 660

           || |||||||| |||||| | ||||| ||||| ||||||||||| || |||||||| |||

Sbjct 601 ATCATCACCAAGCAGATGAGGGACACCAGCGACAAGCGCGACCACGTGTGCCAGCGCGAG 660

Query 661 GTTGCGTATGCACATTCAGTGCCGCGAATCACAAGTGCAATCGGTTCAGACGAAGACTAA 720

           || || || || ||    ||||| || ||||| || || ||||||   ||||| || |||

Sbjct 661 GTGGCCTACGCCCACAGCGTGCCCCGCATCACCAGCGCCATCGGTAGCGACGAGGATTAA 720

Query 721 TAA 723

|||

Sbjct 721 TAA 723

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)