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Potential minor capsid protein

| posted 22 Jul, 2021 22:34
I'm going over the annotation for phage SBlackberry (cluster EJ) and I'm trying to determine the right call for gene 14. Gene 14 is part of Pham 53136 and in cluster CZ it has been annotated as a minor capsid protein whereas in cluster EJ it has been annotated as NKF. According to HHPRED there's a match to a minor capsid protein (99.4% probability, 83% coverage, 3.1e-12 e-value). Based on this info I'm leaning towards calling it a minor capsid protein but any advice is appreciated.
| posted 28 Jul, 2021 01:22
Hi Arturo,
Sorry for the delay on this one. One of the hits is with HK97_gp10. This phage was well studied in the Hendrix lab here at Pitt, and they are have studied capsid proteins in depth. They could not determine what its function was, so I would not call it a minor capsid protein, and stick with Hypothetical Protein for now.
| posted 17 Nov, 2021 00:04
Thank you for the question Arturo and the answer Debbie - we had the same question for our Cluster DE phage ObLaDi. Much appreciated!
| posted 03 Feb, 2023 19:13
I have a similar question about Polkaroo, a P1 cluster phage. Polkaroo_12 (7912-8325) (current pham# 68611) is annotated as NKF for virtually every pham member, but has high HHpred hits to a putative tail component and a minor capsid protein. Similar hits to HK97_10, but also other proteins. See:

Why are so many of the hits calling it a minor capsid protein?
| posted 03 Feb, 2023 20:19
From HHPred, this gene hits HK97_gp10, a minor capsid protein and a tail protein. So one must ask which is it? HK97 is the prototype phage for understanding how the capsid is formed. The lab that studied it was the lab of Roger Hendrix, from the University of Pittsburgh. As we hit gp10 of HK97, I asked if they knew the function of that gene and they could not identify it in their studies. As per the Approved Function List, when you hit HK97_gp10, stick with Hypothetical Protein until someone finds more data to support a call.
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