Difference between revisions of "Part:BBa K5492200:Design"
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===Design Notes=== | ===Design Notes=== | ||
| − | Codon | + | Codon optimised in the following positions in the sequence: |
| − | + | agg at position 1 was changed to cgt | |
| − | + | ata at position 15 was changed to atc | |
| + | cta at position 18 was changed to ctg | ||
| + | agg at position 28 was changed to cgt | ||
| + | agg at position 35 was changed to cgt | ||
| + | ccc at position 42 was changed to ccg | ||
| + | ata at position 45 was changed to atc | ||
| + | agg at position 55 was changed to cgt | ||
| + | cta at position 79 was changed to ctg | ||
| + | ccc at position 81 was changed to ccg | ||
| + | gga at position 93 was changed to ggc | ||
| + | aga at position 94 was changed to cgt | ||
| + | cgg at position 99 was changed to gct | ||
| + | agg at position 102 was changed to cgt | ||
| + | ccc at position 113 was changed to ccg | ||
| + | ccc at position 122 was changed to ccg | ||
| + | cgg at position 125 was changed to gct | ||
| + | cta at position 132 was changed to ctg | ||
| + | ccc at position 134 was changed to ccg | ||
| + | agg at position 135 was changed to cgt | ||
| + | agg at position 145 was changed to cgt | ||
| + | ccc at position 146 was changed to ccg | ||
| + | aga at position 161 was changed to cgt | ||
| + | cta at position 179 was changed to ctg | ||
| + | aga at position 202 was changed to cgt | ||
| + | cta at position 224 was changed to ctg | ||
| + | aga at position 236 was changed to cgt | ||
| + | cgg at position 255 was changed to gct | ||
| + | gga at position 260 was changed to ggc | ||
| + | ccc at position 272 was changed to ccg | ||
| + | ccc at position 278 was changed to ccg | ||
| + | ccc at position 286 was changed to ccg | ||
| + | cgg at position 287 was changed to gct | ||
| + | ccc at position 299 was changed to ccg | ||
| + | ccc at position 304 was changed to ccg | ||
| + | ccc at position 307 was changed to ccg | ||
| + | cta at position 311 was changed to ctg | ||
| + | gga at position 319 was changed to ggc | ||
| + | cgg at position 326 was changed to gct | ||
| + | cta at position 327 was changed to ctg | ||
| + | aga at position 328 was changed to cgt | ||
| + | gga at position 341 was changed to ggc | ||
| + | cta at position 357 was changed to ctg | ||
| + | gga at position 359 was changed to ggc | ||
| + | gga at position 360 was changed to ggc | ||
| + | ccc at position 421 was changed to ccg | ||
| + | ccc at position 425 was changed to ccg | ||
| + | agg at position 427 was changed to cgt | ||
| + | gga at position 446 was changed to ggc | ||
| + | cta at position 451 was changed to ctg | ||
| + | cgg at position 452 was changed to gct | ||
| + | gga at position 493 was changed to ggc | ||
| + | ccc at position 541 was changed to ccg | ||
| + | ccc at position 551 was changed to ccg | ||
| + | gga at position 569 was changed to ggc | ||
| + | ccc at position 573 was changed to ccg | ||
| + | ccc at position 581 was changed to ccg | ||
| + | agg at position 589 was changed to cgt | ||
| + | cgg at position 612 was changed to gct | ||
| + | agg at position 618 was changed to cgt | ||
| + | cgg at position 627 was changed to gct | ||
| + | ccc at position 642 was changed to ccg | ||
| + | ccc at position 645 was changed to ccg | ||
| + | ccc at position 646 was changed to ccg | ||
| + | cgg at position 654 was changed to gct | ||
| + | ccc at position 682 was changed to ccg | ||
| + | gga at position 688 was changed to ggc | ||
| + | cgg at position 696 was changed to gct | ||
| + | ccc at position 697 was changed to ccg | ||
| + | aga at position 710 was changed to cgt | ||
| + | ata at position 714 was changed to atc | ||
| + | ccc at position 717 was changed to ccg | ||
| + | agg at position 733 was changed to cgt | ||
| + | ccc at position 739 was changed to ccg | ||
===Source=== | ===Source=== | ||
| − | The source of the part is its amino acid sequence which was retrieved from Uniprot (https://www.uniprot.org/uniprotkb/Q498N2/entry#sequences), and the work of iGEM20_SEHS-China | + | The source of the part is its amino acid sequence which was retrieved from Uniprot (https://www.uniprot.org/uniprotkb/Q498N2/entry#sequences), and the work of iGEM20_SEHS-China [https://parts.igem.org/Part:BBa_K3684002 BBa_K3684002] which provided the dna sequence we improved on. |
| + | https://www.twistbioscience.com/faq/gene-synthesis/what-are-adapter-sequences-used-adapter-gene-fragments | ||
===References=== | ===References=== | ||
| + | |||
| + | Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996 Aug 2;260(5):649-63. doi: 10.1006/jmbi.1996.0428. PMID: 8709146. | ||
| + | |||
| + | Lipinszki Z, Vernyik V, Farago N, Sari T, Puskas LG, Blattner FR, Posfai G, Gyorfy Z. Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias. ACS Synth Biol. 2018 Nov 16;7(11):2656-2664. doi: 10.1021/acssynbio.8b00332. Epub 2018 Nov 2. PMID: 30351909. | ||
Latest revision as of 07:03, 2 October 2024
Diamine oxidase - DAO
Assembly Compatibility:
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 55
- 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 55
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 1932
Illegal BamHI site found at 2186
Illegal XhoI site found at 802 - 23INCOMPATIBLE WITH RFC[23]Illegal PstI site found at 55
- 25INCOMPATIBLE WITH RFC[25]Illegal PstI site found at 55
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
Codon optimised in the following positions in the sequence:
agg at position 1 was changed to cgt ata at position 15 was changed to atc cta at position 18 was changed to ctg agg at position 28 was changed to cgt agg at position 35 was changed to cgt ccc at position 42 was changed to ccg ata at position 45 was changed to atc agg at position 55 was changed to cgt cta at position 79 was changed to ctg ccc at position 81 was changed to ccg gga at position 93 was changed to ggc aga at position 94 was changed to cgt cgg at position 99 was changed to gct agg at position 102 was changed to cgt ccc at position 113 was changed to ccg ccc at position 122 was changed to ccg cgg at position 125 was changed to gct cta at position 132 was changed to ctg ccc at position 134 was changed to ccg agg at position 135 was changed to cgt agg at position 145 was changed to cgt ccc at position 146 was changed to ccg aga at position 161 was changed to cgt cta at position 179 was changed to ctg aga at position 202 was changed to cgt cta at position 224 was changed to ctg aga at position 236 was changed to cgt cgg at position 255 was changed to gct gga at position 260 was changed to ggc ccc at position 272 was changed to ccg ccc at position 278 was changed to ccg ccc at position 286 was changed to ccg cgg at position 287 was changed to gct ccc at position 299 was changed to ccg ccc at position 304 was changed to ccg ccc at position 307 was changed to ccg cta at position 311 was changed to ctg gga at position 319 was changed to ggc cgg at position 326 was changed to gct cta at position 327 was changed to ctg aga at position 328 was changed to cgt gga at position 341 was changed to ggc cta at position 357 was changed to ctg gga at position 359 was changed to ggc gga at position 360 was changed to ggc ccc at position 421 was changed to ccg ccc at position 425 was changed to ccg agg at position 427 was changed to cgt gga at position 446 was changed to ggc cta at position 451 was changed to ctg cgg at position 452 was changed to gct gga at position 493 was changed to ggc ccc at position 541 was changed to ccg ccc at position 551 was changed to ccg gga at position 569 was changed to ggc ccc at position 573 was changed to ccg ccc at position 581 was changed to ccg agg at position 589 was changed to cgt cgg at position 612 was changed to gct agg at position 618 was changed to cgt cgg at position 627 was changed to gct ccc at position 642 was changed to ccg ccc at position 645 was changed to ccg ccc at position 646 was changed to ccg cgg at position 654 was changed to gct ccc at position 682 was changed to ccg gga at position 688 was changed to ggc cgg at position 696 was changed to gct ccc at position 697 was changed to ccg aga at position 710 was changed to cgt ata at position 714 was changed to atc ccc at position 717 was changed to ccg agg at position 733 was changed to cgt ccc at position 739 was changed to ccg
Source
The source of the part is its amino acid sequence which was retrieved from Uniprot (https://www.uniprot.org/uniprotkb/Q498N2/entry#sequences), and the work of iGEM20_SEHS-China BBa_K3684002 which provided the dna sequence we improved on. https://www.twistbioscience.com/faq/gene-synthesis/what-are-adapter-sequences-used-adapter-gene-fragments
References
Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996 Aug 2;260(5):649-63. doi: 10.1006/jmbi.1996.0428. PMID: 8709146.
Lipinszki Z, Vernyik V, Farago N, Sari T, Puskas LG, Blattner FR, Posfai G, Gyorfy Z. Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias. ACS Synth Biol. 2018 Nov 16;7(11):2656-2664. doi: 10.1021/acssynbio.8b00332. Epub 2018 Nov 2. PMID: 30351909.