SEA-PHAGES | AAA ATPase or RecA recombinase?

Link to this post \| posted 06 Feb, 2025 17:39
hnance@ccga.edu	Gene 35 (stop 23126) in LilTerminator is called AAA ATPase in most phage in the PhagesDB database. However, the Function List says not to call this anymore. Based on Sally Malloy's ppt on when to call it RecA-like recombinase and when to call it ASCE ATPase, I don't think LilTerminator 35 has all features to call it RecA. But cluster EA is not listed under those clusters that don't have RecA recombinase, but do align to a core ATPase. Any advice on what to call this gene? Thank you!

Link to this post | posted 06 Feb, 2025 17:39

Gene 35 (stop 23126) in LilTerminator is called AAA ATPase in most phage in the PhagesDB database. However, the Function List says not to call this anymore. Based on Sally Malloy's ppt on when to call it RecA-like recombinase and when to call it ASCE ATPase, I don't think LilTerminator 35 has all features to call it RecA. But cluster EA is not listed under those clusters that don't have RecA recombinase, but do align to a core ATPase. Any advice on what to call this gene? Thank you!

Link to this post \| posted 06 Feb, 2025 18:04
debbie	Hi Holly, I recommend that you follow Sally's advice and call it an "ASCE ATPase". Thanks! debbie

Link to this post \| posted 06 Feb, 2025 18:06
hnance@ccga.edu	debbie Hi Holly, I recommend that you follow Sally's advice and call it an "ASCE ATPase". Thanks! debbie Got it - thank you! Holly

Link to this post \| posted 07 Feb, 2025 18:25
cdshaffer	Just adding a note here in case anyone searches and finds this thread later. The powerpoint and video on the topic of RecA & ATPases are discussed here in this thread.

Link to this post \| posted 03 Apr, 2025 14:35
engstrom	Hi Folks, Monmouth College is annotating an EA1 phage genome, Symere, and we would like a check on a couple of Phams for which we have ascribed "Hypothetical Function". First is Stop-29,411. Lots of high probability HHPred hits, and everyone seems to favor a helicase or DNA helicase function, but we are not sure. You can view our detailed notes on Pecaan, but in brief the common functions seem to be nucleotide binding and a likely ATPase function. Not a RecA or ASCE ATPase as we can not identify WalkerA or WalkerB sequence motifs (and we have looked). Likewise with Stop-24,923, we can't find WalkerA (almost but just misses) or WalkerB motifs, so we cannot call either RecA of ASCE, yet this protein clearly has structural homology to these ATPases. We are happy to leave them as hypothetical proteins but this is going against the consensus so we thought to check. Many thanks for your thoughts!

Link to this post | posted 03 Apr, 2025 14:35

engstrom

Hi Folks,

Monmouth College is annotating an EA1 phage genome, Symere, and we would like a check on a couple of Phams for which we have ascribed "Hypothetical Function". First is Stop-29,411. Lots of high probability HHPred hits, and everyone seems to favor a helicase or DNA helicase function, but we are not sure. You can view our detailed notes on Pecaan, but in brief the common functions seem to be nucleotide binding and a likely ATPase function. Not a RecA or ASCE ATPase as we can not identify WalkerA or WalkerB sequence motifs (and we have looked). Likewise with Stop-24,923, we can't find WalkerA (almost but just misses) or WalkerB motifs, so we cannot call either RecA of ASCE, yet this protein clearly has structural homology to these ATPases. We are happy to leave them as hypothetical proteins but this is going against the consensus so we thought to check. Many thanks for your thoughts!

Link to this post \| posted 04 Apr, 2025 17:03
debbie	I think the best call is "ASCE ATPase", that is the term when you can't call it a RecA or provide more specificity. But you know you have an ATP-ase domain, yes? Seems to be missing the C terminus domain of a RecA. Is that what you are asking? debbie

Link to this post \| posted 04 Apr, 2025 18:51
engstrom	debbie I think the best call is "ASCE ATPase", that is the term when you can't call it a RecA or provide more specificity. But you know you have an ATP-ase domain, yes? Seems to be missing the C terminus domain of a RecA. Is that what you are asking? debbie Hi Debbie, Thanks for your reply. We are pretty sure that we have structural homology to an ATPase domain, as it is the ATPase domain that HHPred finds. However, if we look at the slides for "How to call a RecA recombinase" we do see that to call an ASCE ATPase, our Pham must "Ha(ve) complete ATPase with Walker A, Walker B, and hydrolytic motif" That is the rub. We do not find the Walker A (almost there but missing the A/G) or the Walker B sequence motifs. We are also following Iyer et al 2004 Nucleic Acids Res Vol 32 p5260 which likewise indicates that any ASCE ATPase must have the Walker A and Walker B motifs. We are working up a poster on this problem, so maybe that will clear things up. Eric

Link to this post | posted 04 Apr, 2025 18:51

engstrom

debbie
I think the best call is "ASCE ATPase", that is the term when you can't call it a RecA or provide more specificity. But you know you have an ATP-ase domain, yes? Seems to be missing the C terminus domain of a RecA.
Is that what you are asking?
debbie

Hi Debbie,

Thanks for your reply. We are pretty sure that we have structural homology to an ATPase domain, as it is the ATPase domain that HHPred finds. However, if we look at the slides for "How to call a RecA recombinase" we do see that to call an ASCE ATPase, our Pham must "Ha(ve) complete ATPase with Walker A, Walker B, and hydrolytic motif" That is the rub. We do not find the Walker A (almost there but missing the A/G) or the Walker B sequence motifs. We are also following Iyer et al 2004 Nucleic Acids Res Vol 32 p5260 which likewise indicates that any ASCE ATPase must have the Walker A and Walker B motifs. We are working up a poster on this problem, so maybe that will clear things up.

Eric

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AAA ATPase or RecA recombinase?