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I have bacterium isolate after BLAST of its 16S the different between its and the similar seq. on NCBI was 4 nucleotides my question is, does it lead to difference between whole genome seq. or I will obtain the same seq. consequently. does this also leads to the same protein products from them.
The 16s ribosomal DNA does not code for any protein, it codes for the 16s ribosmal RNA, which is part of the (small subunit of the) ribosome.
The differences will most likely not affect the ribosome much, but to be sure you'd have to check the exact position of the mutations in a reference structure and see if they are at important positions (i.e. binding of the Shine-Dalgarno sequence)