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JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
R cluster Candle pham 4972 function
Link to this post | posted 27 Feb, 2019 17:08 | |
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We are trying to decide which of 3 functional assignments is most appropriate for an R cluster phage [Candle gp68 (stop 5381/pham 4972)]. I see support for all three, though the last is not an approved function. Our evidence for each functional assignment is below. AAA-ATPase AAA-ATPase, Nilo gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164 AAA domain, HHPred, PF13479.6, % probability = 99.81% , % alignment = 79%, e = 3.6e-21 RecA-like DNA recombinase RecA-like DNA recombinase, Riparian gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164 Protein RecA, HHPred, 4PPF_A, Mycobacterium tuberculosis, % probability = 98.87%, % alignment = 86.3%, e = 3.9E-10 nucleotide binding protein (not on official function list) nucleotide binding protein, Zenon gp72 and 6 others, phagesDB, 1:1, 100% alignment, e = e-164 ATP-binding,HHPred, 2ZTS_C, Pyrococcus horikoshii, % probability = 98.87%, % alignment = 90.3%, e = 8.7e-10 Other HHPred hits RecA protein Recombination, Radioresistance, DNA-repair, ATPase, DNA-binding; 1XP8_A; Deinococcus radiodurans; % probability = 98.85%; % alignment = 85.9%; e = 3.9e-10 Protein RecA, DNA-binding protein, ATP-dependent DNA protein; 5JRJ_A; Herbaspirillum seropedicae; % probability = 98.83%, % alignment = 86.3%; e = 4.3e-10 |
Link to this post | posted 28 Feb, 2019 17:20 | |
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These are not mutually exclusive results. Looking at the internal structure for RecA, {I used this link: [Rec A page at UniProt]} I can see that RecA includes a AAA-ATPase like domain. So both term apply, it's just a question of specificity. To me RecA is a much better description of a function than a general ATPase fold seen in diverse cellular activities {see this}. So if you have a good match to RecA across most of RecA I would say use RecA. If, on the other hand, the match is simply to the AAA ATPase as found in RecA I would go with the less specific AAA-ATPase. A detailed look at which parts of RecA is aligning to your protein by looking at the actual HHPred alignment should answer that question. |
Link to this post | posted 28 Feb, 2019 21:53 | |
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cdshafferThanks very much! |