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Refining the call for Cas4 family exonuclease vs. RecE-like exonuclease

| posted 07 May, 2021 15:56
I'd like some community input on how everyone is thinking about the call of Cas4 family exonuclease vs. RecE-like exonuclease. According to the approved functions list, we call RecB-like exonuclease/helicase if we can confidently identify both a helicase and an exonuclease domain present in the protein. Cas4 family exonuclease is called if we see alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others) according to the functions list. It's a little more unclear on calling the RecE-like exonuclease. Presumably we should be looking for alignments to RecE crystal structures. I've been using this as a guide for my own annotations.

Using Che9c_60 as a model for RecE-like exonuclease (from approved list), HHPred reveals matches to 3H4R_A and PF12705.7. Che9c_61 is called as a RecT-like ssDNA binding protein. There are no alignments to anything labeled as RecE.

My question is: should we be calling RecE-like exonuclease for a gene that has the exonuclease only domains and is immediately upstream of a RecT-like ssDNA binding protein (regardless of hits to 3H4E_A and PD-(D/E)XK nuclease superfamilies), and reserve Cas4 family exonuclease for genes that are not immediately upstream or very close to a RecT-like ssDNA binding protein? My immediate thoughts are to use the presence of RecT as a guide to call RecE-like exonuclease, but I want to hear what you all think.
| posted 07 May, 2021 19:23
Hi Kristen and all,
This is one of those genes that needs a dig deep. Here are some of what i have been thinking.
I am reluctant to call a RecE without a RecT.
I don't know how to differentiate between a RecE, a generic exonuclease or the Cas4 family exonuclease. I am looking forward to what we can figure out about these.
Good question, sorry to not be of much help.
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