SEA-PHAGES | All posts created by pchien

Link to this post \| posted yesterday, 19:49
pchien	Thanks for the feedback Chris. I totally agree there is more to dig in, especially with putative tail cage bits. The correlation of tube width by EM and Alphafold model was very satisfying - hope its generalizable to others as well as it's something that I think is within scope for what we already have students do! I have some slides on how to do those measurements on Alphafoldserver if that would be helpful to anyone.

Link to this post | posted yesterday, 19:49

Thanks for the feedback Chris. I totally agree there is more to dig in, especially with putative tail cage bits. The correlation of tube width by EM and Alphafold model was very satisfying - hope its generalizable to others as well as it's something that I think is within scope for what we already have students do! I have some slides on how to do those measurements on Alphafoldserver if that would be helpful to anyone.

Posted in: Functional Annotation → Alphafold models of minor tail proteins

Link to this post \| posted 05 Dec, 2025 18:09
pchien	would love to know what you think!

Posted in: Functional Annotation → Alphafold models of minor tail proteins

Link to this post \| posted 05 Dec, 2025 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 05 Dec, 2025 18:08 2.71Mb

Link to this post | posted 05 Dec, 2025 18:05

pchien

Sorry about the "best intention, worst execution" of not getting back to this thread smile

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 05 Dec, 2025 18:08

Posted in: Functional Annotation → Alphafold models of minor tail proteins

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

Posted in: Functional Annotation → Alphafold models of minor tail proteins

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?

Posted in: Functional Annotation → 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

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!

Posted in: Functional Annotation → Alphafold models of minor tail proteins

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