SEA-PHAGES | RexAB systems

Link to this post \| posted 11 Apr, 2019 22:12
smolloy123	Hi All, I looking for guidance on how to call two genes in Sidious (cluster CZ7) that match the RexA and RexB abortive infections system proteins of E. coli. Graham let me peek at the CarolAnn and Sbash paper and gp41 and 43 in phamerator (gp40 and 41 in PECAAN as the forward gene between them was deleted) lookk like they fit the bill. gp41 has 4 transmembrane domains (rexB?) and gp43 has a 99.8% prob and 92% coverage hit to RexA Intracellular sensor of Lambda phage, Abi component. gp43 also has the DUF4747 domain that the CarolAnn RexA protein has. Do I leave these function calls as membrane protein and NKF for gp41 and 43 or do you want the RexAB system called? If the latter, what is the exact name you would like used? Thanks! Sally

Link to this post | posted 11 Apr, 2019 22:12

Hi All,
I looking for guidance on how to call two genes in Sidious (cluster CZ7) that match the RexA and RexB abortive infections system proteins of E. coli. Graham let me peek at the CarolAnn and Sbash paper and gp41 and 43 in phamerator (gp40 and 41 in PECAAN as the forward gene between them was deleted) lookk like they fit the bill. gp41 has 4 transmembrane domains (rexB?) and gp43 has a 99.8% prob and 92% coverage hit to RexA Intracellular sensor of Lambda phage, Abi component. gp43 also has the DUF4747 domain that the CarolAnn RexA protein has.

Do I leave these function calls as membrane protein and NKF for gp41 and 43 or do you want the RexAB system called? If the latter, what is the exact name you would like used?

Thanks!
Sally

Link to this post \| posted 13 Apr, 2019 18:58
debbie	Sally, I asked Graham, and he agrees we can call these RexA and RexB. I think that RexA and RexB are a sufficient name. I would not include toxin/antitoxin because it is a known abortive infection mechanism. Toxin/antitoxin is too broad and we know the specifics. For the official list, would you confirm that gene 41 is the RexA and gene 43 is the RexB? (or what genes they are when you re-number?) Cool! debbie

Link to this post | posted 13 Apr, 2019 18:58

debbie

Sally,
I asked Graham, and he agrees we can call these RexA and RexB.
I think that RexA and RexB are a sufficient name. I would not include toxin/antitoxin because it is a known abortive infection mechanism. Toxin/antitoxin is too broad and we know the specifics. For the official list, would you confirm that gene 41 is the RexA and gene 43 is the RexB? (or what genes they are when you re-number?) Cool!
debbie

Link to this post \| posted 13 Apr, 2019 21:19
smolloy123	Hi Deb, I am going to fix those two gene function calls and then Sidious will be ready for submitting to GenBank. Right now, gp40 is RexB and gp41 is RexA. But I will confirm one more time once I make the final flat file. That will have to wait until Monday when I am at my office computer due to a BLOB that is preventing me from using the "Submit to GenBank" function in DNA Master. I'll let you know how the immunity assays turn out too. Thanks for sending the Gordi panel for us to play with! Cheers Sally

Link to this post | posted 13 Apr, 2019 21:19

smolloy123

Hi Deb,
I am going to fix those two gene function calls and then Sidious will be ready for submitting to GenBank.
Right now, gp40 is RexB and gp41 is RexA. But I will confirm one more time once I make the final flat file. That will have to wait until Monday when I am at my office computer due to a BLOB that is preventing me from using the "Submit to GenBank" function smile

in DNA Master.

I'll let you know how the immunity assays turn out too. Thanks for sending the Gordi panel for us to play with!
Cheers
Sally

Link to this post \| posted 17 Apr, 2019 13:22
welkin	Hi Sally– Debbie and I spoke offline a bit, and we are going to amend the "RexA" only function. We try hard not to just use the protein names because students get stuck in the alphabet soup when there is no additional information (RecA and RexA are very different, no?) So I've added a bit to the designations: RexA family abortive infection protein RexB family abortive infection protein Thanks! Welkin

Link to this post | posted 17 Apr, 2019 13:22

welkin

Hi Sally– Debbie and I spoke offline a bit, and we are going to amend the "RexA" only function. We try hard not to just use the protein names because students get stuck in the alphabet soup when there is no additional information (RecA and RexA are very different, no?)

So I've added a bit to the designations:

RexA family abortive infection protein
RexB family abortive infection protein

Thanks!
Welkin

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RexAB systems