SEA-PHAGES | B1 Portal proteins vs Capsid Morphogenesis Protein

Link to this post \| posted 27 Apr, 2018 16:35
smg366	I confused about the functional assignment for gp8 and gp9 in the B1 cluster. My phage genome is identical to phages JacAttac and Newman at this region of the genome. But different phages have assigned different functions to the same genes. In phage Newman gp8 has been assigned the function Portal protein, however in phage JacAttac gene 8 has NKF, and in Newman gp9 has been assigned Portal protein (similar to phages Chah, Badfish and many other B1 cluters). For my phage (Vaticameos) the Portal function for gp8 is supported by PhagedDB BLAST, HHPRED, but NCBIBLAST and Phamerator say NKF. For gp9 in Vaticameos, PhagesDB BLAST says Capsid Morphogenesis Protein, where as NCBIBLAST and Phamerator say Portal protein. In terms of analyzing the evidence, how should I prioritize the functional results for gp8 and gp9?

Link to this post | posted 27 Apr, 2018 16:35

I confused about the functional assignment for gp8 and gp9 in the B1 cluster. My phage genome is identical to phages JacAttac and Newman at this region of the genome. But different phages have assigned different functions to the same genes. In phage Newman gp8 has been assigned the function Portal protein, however in phage JacAttac gene 8 has NKF, and in Newman gp9 has been assigned Portal protein (similar to phages Chah, Badfish and many other B1 cluters).

For my phage (Vaticameos) the Portal function for gp8 is supported by PhagedDB BLAST, HHPRED, but NCBIBLAST and Phamerator say NKF.

For gp9 in Vaticameos, PhagesDB BLAST says Capsid Morphogenesis Protein, where as NCBIBLAST and Phamerator say Portal protein.

In terms of analyzing the evidence, how should I prioritize the functional results for gp8 and gp9?

Link to this post \| posted 01 May, 2018 15:34
welkin	Hi Susan, I am delighted that you asked this. you've identified that you have lines of evidence for two "portal" proteins in your genome, and you've realized that this is unlikely, as far as phage biology goes. This is a perfect example of why we have requested three lines of functional evidence for every gene this year. The root of this issue stems from some old mislabeled maps of the B phages– the portal function was written above the wrong gene. thus, in a number of older genome annotations, the portal is misassigned, and needs to be corrected. We just haven't gotten to it yet. So when you use BLAST and Phamerator, you will find that your gene aligns to a "portal" that is not, in fact, a portal. HHPred data will save you here, the gene with the amino acid sequence that aligns to the portal crystal structure is the correct portal. The other gene encodes the capsid morphogenesis protein.

Link to this post | posted 01 May, 2018 15:34

welkin

Hi Susan,
I am delighted that you asked this. you've identified that you have lines of evidence for two "portal" proteins in your genome, and you've realized that this is unlikely, as far as phage biology goes. This is a perfect example of why we have requested three lines of functional evidence for every gene this year.

The root of this issue stems from some old mislabeled maps of the B phages– the portal function was written above the wrong gene. thus, in a number of older genome annotations, the portal is misassigned, and needs to be corrected. We just haven't gotten to it yet.

So when you use BLAST and Phamerator, you will find that your gene aligns to a "portal" that is not, in fact, a portal.

HHPred data will save you here, the gene with the amino acid sequence that aligns to the portal crystal structure is the correct portal. The other gene encodes the capsid morphogenesis protein.

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B1 Portal proteins vs Capsid Morphogenesis Protein