The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at

Two consecutive ATG start sites

| posted 02 Mar, 2017 19:15
(Also posted this on the external questions because I forgot my login).

In viral genes, when there is start configuration like this:
Is there some rule in bacteria/viruses that the second ATG is correct?

We have several ORFs where the annotated START in other genomes (thus in STARTerator) choose ATG #2; however, ATG #1 would allow for a 4bp overlap with the upstream ORF, and if the subject in question already has its STOP overlapped 4bp with the downstream ORF - this would be a beautiful operon, but in direct conflict with STARTerator.

start@ 51741 vs. 51738 (REV).
Pham 8105
| posted 03 Mar, 2017 16:54
Mass spec data of a few of these instances shows the protein starting at the amino acid next to the second start. Since it is common that the first methionine gets chopped of in post-translation processing, that NO methionine is present in the mass spec reads, it is likely that the second methionine initiated translation. So in this example, the 4 bp overlap gets 'trumped'. This decision is based on the simplest possible answer. and never forget, things do not have to be simple!
Login to post a reply.