Protein Design
Here I describe the design of the flagellin I am using for my DNA vaccine and double-check the sequence. Quoting from the 2008 Slovenian iGEM team's webpage
N terminus (from 1 to 176 AA) and C terminus (from 401 to 498 AA) from E. coli FliC and variable domain from H. pylori FlaA (from 178 to 418 AA) were amplified and joined with PCR ligation
1-176 (176 aas) from BAA85088.1 (http://www.ncbi.nlm.nih.gov/protein/BAA85088.1)
MAQVINTNSLSLITQNNINKNQSALSSSIERLSSGLRINSAKDDAAGQAIANRFTSNIKGLTQAARN ANDGISVAQTTEGALSEINNNLQRVRELTVQATTGTNSESDLSSIQDEIKSRLDEIDRVSGQTQFNG VNVLAKNGSMKIQVGANDNQTITIDLKQIDAKTLGLDGFSVK
178-418 (241 aas) from EJC28917 (http://www.ncbi.nlm.nih.gov/protein/EJC28917.1)
alitasgdisltfkqvdgvndvtlesvkvsssagtgigvlaevinknsnrtgvkayasvittsdvav qsgslsnltlngihlgniadikkndsdgrlvaainavtsetgveaytdqkgrlnlrsidgrgieikt dsvsngpsaltmvnggqdltkgstnygrlsltrldaksinvvsasdsqhlgftaigfgesqvaettv nlrdvtgnfnanvksasganynaviasgnqslgsgvttlr
401-498 (98 aas) from BAA85088.1 (http://www.ncbi.nlm.nih.gov/protein/BAA85088.1)
AVANGKTTDPLKALDDAIASVDKFRSSLGAVQNRLDSAVTNLNNTTTNLSEAQSRIQDADYATEVSN MSKAQIIQQAGNSVLAKANQVPQQVLSLLQG
Combined protein (516 aas)
MAQVINTNSLSLITQNNINKNQSALSSSIERLSSGLRINSAKDDAAGQAIANRFTSNIKGLTQAARN ANDGISVAQTTEGALSEINNNLQRVRELTVQATTGTNSESDLSSIQDEIKSRLDEIDRVSGQTQFNG VNVLAKNGSMKIQVGANDNQTITIDLKQIDAKTLGLDGFSVKalitasgdisltfkqvdgvndvtle svkvsssagtgigvlaevinknsnrtgvkayasvittsdvavqsgslsnltlngihlgniadikknd sdgrlvaainavtsetgveaytdqkgrlnlrsidgrgieiktdsvsngpsaltmvnggqdltkgstn ygrlsltrldaksinvvsasdsqhlgftaigfgesqvaettvnlrdvtgnfnanvksasganynavi asgnqslgsgvttlrAVANGKTTDPLKALDDAIASVDKFRSSLGAVQNRLDSAVTNLNNTTTNLSEA QSRIQDADYATEVSNMSKAQIIQQAGNSVLAKANQVPQQVLSLLQG
For reference, we can compare this sequence to the BioBrick from iGEM team (1583bp http://parts.igem.org/Part:BBa_K133038)
atggcacaagtcattaataccaacagcctctcgctgatcactcaaaataatatcaacaagaaccagt ctgcgctgtcgagttctatcgagcgtctgtcttctggcttgcgtattaacagcgcgaaggatgacgc agcgggtcaggcgattgctaaccgtttcacctctaacattaaaggcctgactcaggcggcccgtaac gccaacgacggtatctccgttgcgcagaccaccgaaggcgcgctgtccgaaatcaacaacaacttac agcgtgtgcgtgaactgacggtacaggccactaccggtactaactctgagtctgatctgtcttctat ccaggacgaaattaaatcccgtctggatgaaattgaccgcgtatctggtcagacccagttcaacggc gtgaacgtgctggcaaaaaatggctccatgaaaatccaggttggcgcaaatgataaccagactatca ctatcgatctgaagcagattgatgctaaaactcttggccttgatggttttagcgttaaagcgttaat cacggcttctggggatattagcttgacttttaaacaagtggatggcgtgaatgatgtaactttagag agcgtaaaagtttctagttcagcaggcacggggatcggtgtgttagcggaagtgattaacaaaaatt ctaaccgaacaggggttaaagcttatgcgagcgttatcaccacgagcgatgtggcggtccaatcagg aagtttgagtaatttaactttaaatgggatccatttgggtaatatcgcagatattaagaaaaatgac tcagacggaaggttagtcgcagcgatcaatgcggttacttcagaaaccggcgtggaagcttatacgg atcaaaaagggcgcttgaatttgcgcagtatagatggtcgtgggattgaaatcaaaaccgatagcgt cagtaatgggcctagtgctttaacgatggtcaatggcggtcaggatttaacaaaaggttctactaac tatgggaggctttctctcacacgcttagacgctaaaagcatcaatgtcgtttcggcttctgattcgc aacatttaggtttcacagcgattggttttggggaatctcaagtggcagaaaccacggtgaatttgcg cgatgttactgggaattttaacgctaatgtcaaatcagccagtggcgcgaactataacgccgtgatc gctagcggtaaccaaagcttgggatctggggttacaaccttaagagctgttgcaaatggtaaaacca cggatccgctgaaagcgctggacgatgctatcgcatctgtagacaaattccgttcttccctcggtgc ggtgcaaaaccgtctggattccgcggttaccaacctgaacaacaccactaccaacctgtctgaagcg cagtcccgtattcaggacgccgactatgcgaccgaagtgtccaatatgtcgaaagcgcagatcatcc agcaggccggtaactccgtgttggcaaaagctaaccaggtaccgcagcaggttctgtctctgttaca gggttactagagcgaggagaccaccaccaccaccaccactag
BBa_K133038 translated
MAQVINTNSLSLITQNNINKNQSALSSSIERLSSGLRINSAKDDAAGQAIANRFTSNIKGLTQAARN ANDGISVAQTTEGALSEINNNLQRVRELTVQATTGTNSESDLSSIQDEIKSRLDEIDRVSGQTQFNG VNVLAKNGSMKIQVGANDNQTITIDLKQIDAKTLGLDGFSVKALITASGDISLTFKQVDGVNDVTLE SVKVSSSAGTGIGVLAEVINKNSNRTGVKAYASVITTSDVAVQSGSLSNLTLNGIHLGNIADIKKND SDGRLVAAINAVTSETGVEAYTDQKGRLNLRSIDGRGIEIKTDSVSNGPSALTMVNGGQDLTKGSTN YGRLSLTRLDAKSINVVSASDSQHLGFTAIGFGESQVAETTVNLRDVTGNFNANVKSASGANYNAVI ASGNQSLGSGVTTLRAVANGKTTDPLKALDDAIASVDKFRSSLGAVQNRLDSAVTNLNNTTTNLSEA QSRIQDADYATEVSNMSKAQIIQQAGNSVLAKANQVPQQVLSLLQGY-SEETTTTTTT
Finally, I align translated BBa_K133038 to my protein, and the two are identical, apart from the final "Y-SEETTTTTTT" in BBa_K133038. I do not know why this is, but I don't believe it's important.