Link to this post | posted 22 Oct, 2025 14:38

pchien

Hi Folks! We are busy annotated a few phage genomes and I've been following Krista Freeman's excellent powerpoint/information about using AF3 to model minor tail proteins. We are fairly confident we have found tail spike, Dit, and baseplate hub based on these models and Krista's guide. However, neither Dit nor baseplate hub seem to be listed on the official functions list. My major question is how we should proceed for calling them. I'd rather not just call them minor tail proteins when the structural prediction signature is super strong, but also appreciate that folks are working on a standardized approach. Thanks!

Link to this post | posted 22 Oct, 2025 14:51
debbie	Hi Peter, We are going to cautiously weigh in on what to name the various structures of siphoviruses. The data is coming to us fast and furious, and not all crystallographers are using the same nomenclature. I have added the features (as you have identified)to the Approved Function List that I think we can call with a modicum of confidence. Let me know if my list works! Thanks, debbie

Link to this post | posted 22 Oct, 2025 14:55
pchien	This is great! The updated list is excellent. Do we want to include oligomer requirements like Krista had on there, like Dit should model as a hexamer, hub as a trimer, spike as a trimer?

Link to this post | posted 22 Oct, 2025 15:00
debbie	Nope! But provide that here and I will add that to the function list, so others can pick the best model number. Would that work? Also provide me with the list of genes that you have called. I can add them as examples too. Thanks, debbie

Link to this post | posted 22 Oct, 2025 15:05
pchien	will do (as soon as I finish with class today!)

Link to this post | posted today, 18:05

pchien

Sorry about the "best intention, worst execution" of not getting back to this thread Our class is annotating three new EG genomes and with a combination of Krista's presentation, Alphafold server, and use of Foldseek, we were able to confidently assign some functions. Specifically, we propose that BaconCheese40 is the distal tip complex (dit), BaconCheese42 is the baseplate hub protein, and BaconCheese43 is the tail spike protein. I made a series of slides to show this interpretation along with the assignments for orthologs from Mila11 and Slysloth, the other EG genomes we annotated. For dit, we went the extra step of confirming the tail width using the EM images of the phage to show that it was consistent with the outer diameter of the predicted dit hexamer complex. Hope this helps others! Edited today, 18:08 2.71Mb

Link to this post | posted today, 18:09
pchien	would love to know what you think!