SEA-PHAGES | RecA-like recombinase or UvsX-like recombinase for KentuckyRacer 62351-62378

Link to this post \| posted 15 Feb, 2024 20:46
powelleann	The start of KentuckyRacer Gene 84 was changed from 62351 to 62378 due to having more 1:1 alignment with similar phage in BLAST on PhagesDB and BLAST on NCBI. Starterator also called this start with 52 MAs. After running BLAST on both NCBI and PhagesDB, two different functions were identified. On PhagesDB all hits called for RecA-like DNA recombinase with 1:1 alignment with more than 10 Streptomyces phage. However, on NCBI BLAST top hits called for UvsX-like recombinase with more than 10 Streptomyces phage. One of the top hits was with Streptomyces StarPlatinum with 99.40% identity, 99% query coverage, e-value of 0.0, and 1:1 alignment. However, the Official SEAPHAGES function list does not make UvsX-like recombinase an approved function. After running the protein sequence through HHPred, top hits also called for RecA. One hit from Mycobacterium tuberculosis for RecA had a 100% probability, e-value of 3.5e-36, and 98.8% coverage. Our question is which function should we go with because NCBI and Phage DB have different functions? Lanae Canen and Gabby Carter

Link to this post | posted 15 Feb, 2024 20:46

The start of KentuckyRacer Gene 84 was changed from 62351 to 62378 due to having more 1:1 alignment with similar phage in BLAST on PhagesDB and BLAST on NCBI. Starterator also called this start with 52 MAs.
After running BLAST on both NCBI and PhagesDB, two different functions were identified. On PhagesDB all hits called for RecA-like DNA recombinase with 1:1 alignment with more than 10 Streptomyces phage. However, on NCBI BLAST top hits called for UvsX-like recombinase with more than 10 Streptomyces phage. One of the top hits was with Streptomyces StarPlatinum with 99.40% identity, 99% query coverage, e-value of 0.0, and 1:1 alignment. However, the Official SEAPHAGES function list does not make UvsX-like recombinase an approved function.
After running the protein sequence through HHPred, top hits also called for RecA. One hit from Mycobacterium tuberculosis for RecA had a 100% probability, e-value of 3.5e-36, and 98.8% coverage.
Our question is which function should we go with because NCBI and Phage DB have different functions?

Lanae Canen and Gabby Carter

Link to this post \| posted 16 Feb, 2024 18:33
cdshaffer	Very short answer: use the official function list. Long answer: Many times when you do a deep dive into issues like this (where the evidence is strong enough to call two different terms), you find one of two things going on. Usually it turns out the two terms are mostly synonymous. Like one term traces back to an E coli protein and the other term comes from studies in B subtilis. Both proteins probably fulfill the same biological role so they are pretty much the "same protein", they just have different names. The other likely result is that one term is a more specific term that the other. Like is it a "Car" or a "Ford" or a "Mustang". All these terms might apply. In this case, and I am guessing here, but I would not be surprised if Rec A and UvsX are very similar to each other and we really just have two synonyms. This is easy to check, do an HHPred search with Rec A or UvsX and see how well they align to each other. If they are basically the same protein then you know you are in the first situation above. I am going to assume that the two proteins are mostly the same and not levels of specificity, then the way to proceed is to use the Official function list. If one term is on the list and the other is not, you have two choices: 1. use the term on the list OR 2. Decide that even thought they are "mostly" the same they are in fact different enough that both terms should be on the list. If you think that is the case, post your proposal to add the term to the approved list on the proper forum; once you get it approved then everyone can use it and everyone's annotations are all the better for your contribution. This is why I always tell my students that while this second option can be a lot of work it is also a real accomplishment. Finding a new, novel, and fundamentally different function that is not on the list and convincing the list keepers of this, is very impressive indeed! But it takes time and effort, reading papers and developing the evidence to get to a convincing argument that the two terms are distinct enough to justify both on the list. Edited 16 Feb, 2024 18:37

Link to this post | posted 16 Feb, 2024 18:33

cdshaffer

Very short answer: use the official function list.

Long answer:
Many times when you do a deep dive into issues like this (where the evidence is strong enough to call two different terms), you find one of two things going on. Usually it turns out the two terms are mostly synonymous. Like one term traces back to an E coli protein and the other term comes from studies in B subtilis. Both proteins probably fulfill the same biological role so they are pretty much the "same protein", they just have different names. The other likely result is that one term is a more specific term that the other. Like is it a "Car" or a "Ford" or a "Mustang". All these terms might apply.

In this case, and I am guessing here, but I would not be surprised if Rec A and UvsX are very similar to each other and we really just have two synonyms. This is easy to check, do an HHPred search with Rec A or UvsX and see how well they align to each other. If they are basically the same protein then you know you are in the first situation above.

I am going to assume that the two proteins are mostly the same and not levels of specificity, then the way to proceed is to use the Official function list. If one term is on the list and the other is not, you have two choices: 1. use the term on the list OR 2. Decide that even thought they are "mostly" the same they are in fact different enough that both terms should be on the list. If you think that is the case, post your proposal to add the term to the approved list on the proper forum; once you get it approved then everyone can use it and everyone's annotations are all the better for your contribution.

This is why I always tell my students that while this second option can be a lot of work it is also a real accomplishment. Finding a new, novel, and fundamentally different function that is not on the list and convincing the list keepers of this, is very impressive indeed! But it takes time and effort, reading papers and developing the evidence to get to a convincing argument that the two terms are distinct enough to justify both on the list.

Edited 16 Feb, 2024 18:37

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RecA-like recombinase or UvsX-like recombinase for KentuckyRacer 62351-62378