SEA-PHAGES | Alphafold models of minor tail proteins

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 14:38

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!)

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Alphafold models of minor tail proteins