Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
Ruth Plymale posted in Tenure track Microbiology faculty position at Ouachita Baptist University in Arkansas
bburnes posted in Calling start in FC phage Phrampa
cdshaffer posted in Calling start in FC phage Phrampa
bburnes posted in Calling start in FC phage Phrampa
Debbie Jacobs-Sera posted in Calling start in FC phage Phrampa
two holins in AR?
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 | |
---|---|
|
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 |