Valine and Leucine Start Amino Acids

[Rob Bierman]

Hello,

I am using the JGI-IMG which uses Prodigal for protein prediction.

JGI reports predicted proteins that have a very high rate of starting with valines or leucines instead of methionines (see attached).

My question is does Prodigal produce predicted proteins with non-methionine starts, and if so why?

Thank you for your help,

-Rob

[dhyatt1]

Prodigal does not output proteins with non-methionine starts.  However, GTG and TTG are common alternative start codons

in bacteria/archaea, so it's possible they could be representing these codons as valine and leucine (even though they get

translated to methionine in the real world).  Hard to know without seeing the source of the histogram (or why it has so many

nonzero values for other amino acids... perhaps they're including incomplete genes?)

regards,

doug

[Rob Bierman]

Thanks for the quick reply Doug, that explains the V's and L's.

My guess would be the same as yours for why there is such a distribution of the other amino acids.