Jcvi code genitalium
Turns out, the code I was after was not in this genome!
- Disrupted WT gene: MG_408 , NP_073081.1 , pmsR
- methionine sulfoxide reductase A
- this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form a fusion protein of this enzyme with MsrB provides protection against oxidative stress in Neisseria gonorrhoeae this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form
- Inserted gene: ABY79711.1 , MGATCC33530_0530
- bifunctional AAC/APH (AAC(6'): 6'-aminoglycoside N-acetyltransferase and APH(2'): 2-aminoglycoside phosphotransferase
- Aminoglycoside antibiotic resistance is largely the result of the production of enzymes that covalently modify the drugs including kinases (Aph) with structural and functional similarity to protein and lipid kinases. One of the most important aminoglycoside resistance enzymes is Aac(6')-Aph(2), a bifunctional enzyme with both aminoglycoside acetyltransferase and kinase activities.
- Extract sequence: http://genomevolution.org/CoGe//SeqView.pl?featid=143193835_1&dsid=63956&chr=1&start=&upstream=-227770&downstream=228068&rc=0&dsgid=15768
- Perform 6-frame translation (using above link)
- search for anything that might match "com/cnm" "org/nrg" "net", "cvi" (jcvi)
- Nothing: could be wrong code