In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.)
The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full
indicates there could be GGGGG slippery sequence.

However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf.

Debbie added GeneMark output to illustrate. Agreed that something like what is described could be some sort of frameshift BUT an area of low coding potential that just happens to be higher CP in another frame is not unheard of. Only 1 ORF to call here. Bench data would be required here.
Edited 06 Jun, 2023 01:52
185Kb