SEA-PHAGES | minor fix for approved terms

Link to this post \| posted 23 Dec, 2021 20:41
cdshaffer	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: `if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, N-acetylmuramoyl-L-alanine amidase domain` 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. Edited 23 Dec, 2021 20:43

Link to this post | posted 23 Dec, 2021 20:41

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:

if not a Mycobacteriophage, must have a lysin B, otherwise
it is endolysin, N-acetylmuramoyl-L-alanine amidase domain

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.

Edited 23 Dec, 2021 20:43

Link to this post \| posted 23 Dec, 2021 20:49
debbie	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 Edited 23 Dec, 2021 20:50

Link to this post | posted 23 Dec, 2021 20:49

debbie

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

Edited 23 Dec, 2021 20:50

Link to this post \| posted 26 Dec, 2021 19:42
cdshaffer	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 26 Dec, 2021 19:42

cdshaffer

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
debbie	Ah, so you will have 2 different genes for the domains. Great! debbie

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minor fix for approved terms