SEA-PHAGES | 5’nucleotidase v. phosphatase

Link to this post \| posted 18 Apr, 2023 12:26
EWisner	We’re having trouble deciding between two functions (5' nucleotidase v. phosphatase). The BLAST and HHPred results as well as the summary page on PhagesDB are split between “5’nucleotidase” and “phosphatase”. Are there any suggestions for how to differentiate between these two calls? Gene in question: Phage Culver, Gene stop 77577 Culver_136

Link to this post \| posted 18 Apr, 2023 14:08
lhughes	Can I add a wrinkle to your question (I also have a phage that we are currently annotating that has a member of this Phamily)? In the Official Functions list it gives ClubL144 as the example for the 5'nucleotidase function but when I look it up on PhagesDB that gene has a function of "phosphatase" showing on the Pham page. Lee

Link to this post \| posted 18 Apr, 2023 23:16
debbie	Lee, My guess is when we first called ClubL144, we called it a 5'nucleotidase and upon further review of pham functions, we reduced the function to phosphatase. However, we didn't go back to the example on the approved function list to make the change. I'll change it. Today, when deciding between “5’nucleotidase” and “phosphatase”, I'm going to recommend phosphatase. A phosphatase is a more general term (that likely includes 5’nucleotidase. I would need evidence that the ends has 5' specificity to be able to call that. By that I mean, what other genes would be needed for that function to occur. debbie Edited 18 Apr, 2023 23:25

Link to this post | posted 18 Apr, 2023 23:16

debbie

Lee,
My guess is when we first called ClubL144, we called it a 5'nucleotidase and upon further review of pham functions, we reduced the function to phosphatase. However, we didn't go back to the example on the approved function list to make the change.
I'll change it.

Today, when deciding between “5’nucleotidase” and “phosphatase”, I'm going to recommend phosphatase. A phosphatase is a more general term (that likely includes 5’nucleotidase. I would need evidence that the ends has 5' specificity to be able to call that. By that I mean, what other genes would be needed for that function to occur.
debbie

Edited 18 Apr, 2023 23:25

Link to this post \| posted 19 Apr, 2023 20:31
lhughes	Thanks, Debbie. I noticed all of our (UNT) more recent genomes that have a member of this Pham have used the "phosphatase" function so that makes the most sense given that we would need more evidence in order to call the more specific function. Lee

Link to this post \| posted 19 Apr, 2023 23:55
debbie	Lee, glad it makes sense. it is not that the 5'nucleotidase could be correct, we just don't know enough to be that specific…..yet. debbie

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5’nucleotidase v. phosphatase