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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
minor fix for approved terms
Link to this post | posted 23 Dec, 2021 20:41 | |
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We have a streptomyces phage which does not have the typical Lysin A/B pair, we have found one protein that hits quite well by HHPRED to an N-acetylmuramoyl-L-alanine amidase (crystal 6SSC with 99.5% probability, and 100% coverage of the crystal and ~66% coverage of the phage protein). Looking at the approved list in the notes column for lysin A, N-acetylmuramoyl-L-alanine amidase domain it says:
However the term "endolysin, N-acetylmuramoyl-L-alanine amidase domain" is not officially an approved term (i.e. not listed in column A). I mention this only to request "endolysin, N-acetylmuramoyl-L-alanine amidase domain" be added to the list so it gets updated on pecaan. |
Link to this post | posted 23 Dec, 2021 20:49 | |
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Chris, I added this, but I have a question. Are there 2 endolysin genes in this genome? Lysin genes are notorious for not having all domains match existing domains in the databases that we use. By that I mean, we can call a lysin A because ONE of the domains hit previously studied endolysins. so in the case of the gene you are interested in, is it possible that the 34% not covered is the missing protease domain? so the gene is a whole endolysin and not a gene broken into 2 pieces? I would recommend that we call the gene an endolysin if no protease domain is identified. Does that make sense? Would you also provide the genome/gene number to list it is an example int he function list. Thanks, debbie |
Link to this post | posted 26 Dec, 2021 19:42 | |
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All good questions. We have not finished the analysis on these proteins yet, so I am not sure what the final annotation on these proteins should be. I just noted the implied missing term from the note and so posted the above request. I will get back with more details once I work with the student. This phage is not yet in phagesdb. In case you want to take a look, see PECAAN phage stanimal, gene that end at 22299 is the one discussed above and has the really good hit to the amidase domain; while the other gene which might also be annotated "endolysin" (based on membership in pham 93752) ends at 16907. |
Link to this post | posted 27 Dec, 2021 20:35 | |
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Ah, so you will have 2 different genes for the domains. Great! debbie |