Team:Carnegie Mellon/Week14
From 2013.igem.org
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)