SEA-PHAGES | tail assembly chaperones in Microbacterium foliorum EA1 phages

tail assembly chaperones in Microbacterium foliorum EA1 phages

Link to this post \| posted 27 Mar, 2019 16:32
c.sunnen	Hi! So tail assembly chaperone has been called a lot for the two genes immediately upstream of tapemeasure in the EA1 phages that we are comparing to, but I am finding no evidence for this, other than synteny, in our EA1 phage, Shee. I can't find a slippery sequence (none of these phages seem to have annotated one, either), and it seems that these phams are only found in EA cluster (and sub-cluster) phages. Is there some compelling evidence I'm missing, or is this one of those cases of perpetuating a mistake? I know that usually, we try NOT to call tail assembly chaperone unless we can annotate the frameshift. Should these actually be NKF? Thanks! Nikki

Link to this post | posted 27 Mar, 2019 16:32

Hi!

So tail assembly chaperone has been called a lot for the two genes immediately upstream of tapemeasure in the EA1 phages that we are comparing to, but I am finding no evidence for this, other than synteny, in our EA1 phage, Shee. I can't find a slippery sequence (none of these phages seem to have annotated one, either), and it seems that these phams are only found in EA cluster (and sub-cluster) phages. Is there some compelling evidence I'm missing, or is this one of those cases of perpetuating a mistake? I know that usually, we try NOT to call tail assembly chaperone unless we can annotate the frameshift. Should these actually be NKF?

Thanks!
Nikki

Link to this post \| posted 27 Mar, 2019 18:22
welkin	Hi Nikki, There are a number of clusters in which we can not find the correct slippery sequence (+1 sequences in particular can be tricky). I feel pretty good about these two because they are the only two open reading frames between the major tail subunit and the tapemeasure, and because the coding potential in the GeneMArkS output drops in the upstream gene before it reaches the stop codon, and it picks up in the downstream gene right about where it drops in the upstream one. so tail assembly chaperone it is!

Link to this post | posted 27 Mar, 2019 18:22

welkin

Hi Nikki,
There are a number of clusters in which we can not find the correct slippery sequence (+1 sequences in particular can be tricky). I feel pretty good about these two because they are the only two open reading frames between the major tail subunit and the tapemeasure, and because the coding potential in the GeneMArkS output drops in the upstream gene before it reaches the stop codon, and it picks up in the downstream gene right about where it drops in the upstream one.
so tail assembly chaperone it is!

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tail assembly chaperones in Microbacterium foliorum EA1 phages