SEA-PHAGES | two holins in AR?

Link to this post \| posted 02 Nov, 2019 23:28
jparker	I am QCing the annotation of DrYang and it looks like it might have two holins. There is a 4 TMD protein (gp_30), then Lysin A, then the officially called holin (3 TMD - gp_32). Some AO phages have the same gp30 pham and name it holin. DrYang_gp30 (membrane protein) >MKREIATGVGVMLLASLTFLTTEHASVTVALLVILASSFAVLTVYYMHRARWRQYPSGRTFLYLLWAFDALVGFLLISRLVEPRELRLTIYNVLIAGLVAAVWLITATFWKAQKEARAERLRKRAALKEKEENQP DrYang_gp32 (holin) >MIVFDVPQWQFLVQVFGGTVMTLLVGLVTTRVTSSQVRAILLAALSVLSSIVTELVAALQTNTPYNLGTALTFGLLTFLVAVGTHYGILKHTNLETAAQNTLVTASAAEVRAHEQAKALELLAKAGVKTQETSPDGATPAIKYVPRHSTRE

Link to this post | posted 02 Nov, 2019 23:28

I am QCing the annotation of DrYang and it looks like it might have two holins. There is a 4 TMD protein (gp_30), then Lysin A, then the officially called holin (3 TMD - gp_32). Some AO phages have the same gp30 pham and name it holin.

DrYang_gp30 (membrane protein)
>MKREIATGVGVMLLASLTFLTTEHASVTVALLVILASSFAVLTVYYMHRARWRQYPSGRTFLYLLWAFDALVGFLLISRLVEPRELRLTIYNVLIAGLVAAVWLITATFWKAQKEARAERLRKRAALKEKEENQP

DrYang_gp32 (holin)
>MIVFDVPQWQFLVQVFGGTVMTLLVGLVTTRVTSSQVRAILLAALSVLSSIVTELVAALQTNTPYNLGTALTFGLLTFLVAVGTHYGILKHTNLETAAQNTLVTASAAEVRAHEQAKALELLAKAGVKTQETSPDGATPAIKYVPRHSTRE

Link to this post \| posted 05 Nov, 2019 15:55
debbie	Hi Jordan, If I were calling this genome, I would label both of these proteins as membrane proteins. Neither are great matches to known holins, phages can have more than one holin, and while I may not know which one is a holin, I am confident that they are both membrane proteins. If you are compelled to call a holin, 32 is in a 'more canonical' place. Historically, we called the small protein after lysin A the holin. Now that we are moving away from relying on the location as the sole reason for calling a holin, I am most willing to call these proteins 'membrane proteins'. (Because I can't tell which is the holin, although they both may be holins.) The best writing about holins is from Ry Young, Texas A&M. I don't know if there is a definitive article that he has written that helps, becuase he has written a lot. I kinda liked his J Mol Microbiol, Biotechnol (2002) paper, "Bacteriophage Holins: Deadly Diversity". debbie

Link to this post | posted 05 Nov, 2019 15:55

debbie

Hi Jordan,
If I were calling this genome, I would label both of these proteins as membrane proteins. Neither are great matches to known holins, phages can have more than one holin, and while I may not know which one is a holin, I am confident that they are both membrane proteins. If you are compelled to call a holin, 32 is in a 'more canonical' place.

Historically, we called the small protein after lysin A the holin. Now that we are moving away from relying on the location as the sole reason for calling a holin, I am most willing to call these proteins 'membrane proteins'. (Because I can't tell which is the holin, although they both may be holins.)

The best writing about holins is from Ry Young, Texas A&M. I don't know if there is a definitive article that he has written that helps, becuase he has written a lot. I kinda liked his J Mol Microbiol, Biotechnol (2002) paper, "Bacteriophage Holins: Deadly Diversity".

debbie

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two holins in AR?