SEA-PHAGES | R cluster Candle pham 4972 function

Link to this post \| posted 27 Feb, 2019 17:08
kaylafast	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 27 Feb, 2019 17:08

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
cdshaffer	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 17:20

cdshaffer

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
kaylafast	cdshaffer 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. Thanks very much!

Link to this post | posted 28 Feb, 2019 21:53

kaylafast

cdshaffer
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.

Thanks very much!

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R cluster Candle pham 4972 function