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Upper and lower collar proteins

| posted 03 Nov, 2021 19:04
Hi folks,

We're annotating a singleton Microbacteriophage PineapplePizza, and have found 2 genes (gp 10 and 11) that have good BLAST and HHPred hits to upper collar and lower collar proteins. The BLAST hits are from Arthrobacter phages Mendel and Anjali, which have these functions listed in Genbank, however the upper collar and lower collar proteins are not on the official function list. Should they be?

Thanks so much,
| posted 03 Nov, 2021 22:49
Hi Jess,
Cool genome. I can't answer your question out of context of the entire genome. Tell me if yo agree with my interpretations.
Here is what I see so far, you have a small genome phage that is likely a podoviridae. You have only provided one virion particle. do you have more. If not can you get more particles photographed. Also, I note that you have a thumbnail uploaded - which is great!!!, but not a 'raw' data file uploaded. That file can be very helpful, so please upload it.

Because it is a podo, we haven't thought very much about the structures at the portal. Could the upper collar be the portal?

Your phage is like phi29, S. aureus phage P68 and maybe Streptococcus phage C1. Here is a lovely paper about the structure of the Staph aureus phage.

I don't think there is anything difficult about this phage, but we don't have a good handle on what to call the structural pieces that are identified. If you could find the papers about phi29 and maybe even C1, we could put the pieces together and identify the best names for the proteins.

Maybe we could set up a time to talk.
Cool beans!
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