I am having some trouble in understanding the nomenclature for mutations in the gyrB cds of M. tuberculosis. The gyrB gene of strain H37rv is 2028 bp long corresponding to a 675 aa protein (http://www.ncbi.nlm.nih.gov/gene/887081). The first reported sequence for gyrB in M. tuberculosis is somewhat longer (http://aac.asm.org/content/38/4/773.full.pdf+html). Neither of the sequences seems to correspond to the most used nomenclature in papers reporting gyrB mutations (e.g. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120470#sec011, or http://aac.asm.org/content/55/10/4524.full.pdf+html). I also found some sequences (http://www.ncbi.nlm.nih.gov/nuccore/378408791?from=1&to=2145&sat=4&sat_key=67263822&report=gbwithparts) reporting a longer gyrB sequence, but I don't understand how the same gene, which is also highly conserved, can have different lenghts within the same species.
Thanks for your help.
http://www.biomedcentral.com/content/pdf/1756-0500-6-274.pdf
Karkare et al. BMC Research Notes 2013, 6:274
This article explains the differences in amino acid content of two different GyrB numbering. There is the extra 40 amino acids in the longer GyrB. The additional amino acids do not have any impact on Gyrase activity.
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