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lysin A

| posted 24 Apr, 2018 14:26
BD phages have a single endolysin, it should be labeled "lysin A".
| posted 09 Mar, 2020 00:38
Based on this posting from Feb 2020:

Which I will repost here:
Just looked at 2 cluster AO2 phages, JKerns and StevieBAY. StevieBAY's
gene 28 is an endolysin. It possesses all of domains we expect to see in an
endolysin. Gene 64 codes for the CHAP endopeptidase domain of LysK (a
Staphylococcus phage lysin gene). It is reported out as an endolysin also.
We won't call either of them lysin A (Reserved only for mycobacteriophages
for now, unless the phage genomes contains a lysin A and a lysin B. 

And this in the approved terms (as of Feb 2020):
some arthrobacter and streptomyces phages have a single endolysin
with domains not found in the Mycobacteriophages (like the CHAP domain).
use "endolysin" rather than lysin A if the phage does not infect
Mycobacterium and no lysin b can be identified.

The BD6 phage appear to have a lysin which is a very high quality HHpred hit (99.8 Prob, 97.2 coverage) to the N-ACETYLMURAMOYL-L-ALANINE AMIDASE crystal (2WKX_A)

should annotation be the approved term "endolysin" or "lysin A, N-acetylmuramoyl-L-alanine amidase domain"
Edited 09 Mar, 2020 00:50
| posted 09 Mar, 2020 12:33
Thanks Chris.
This should be "endolysin". According to my most recent conversation with Graham about this, the Lysin A and B designations arose because there are two in the Mycobacteriophages. Other phages, which just have one, have historically just used the term "endolysin". So we will be changing all of the non-Mycobacteriophage lysins to "endolysin" except in cases in which we can identify a clear lysin B (I think this only applies to some of the Gordonia phages).

I haven't gotten to updating the Streptomyces yet.
| posted 09 Mar, 2020 13:00
I appreciate this conversation, by the way, and the new notes on the approved functions list. There was a lot written on lysin A structure (in Mycos) but not the limit on using the designation. So it's good to get the clarification.

| posted 09 Mar, 2020 16:28
OK the rule that "you must have a B, in order to have an A" makes sense to me. Thanks for the clarification.
| posted 09 Mar, 2020 18:52
I *think* we've been trying to use "endolysin" unless it was specifically the Lysin A and B situation, so hopefully most of our more recent ones are already correct. Good to have the clarification.
| posted 17 Mar, 2020 00:42
Do you have any Streptomyces phage genomes with a lysin B?
| posted 17 Mar, 2020 18:37
I just searched the phamerator database. There are no genes from amy phage with host streptomyces that have lysin B as an annotation.
| posted 17 Mar, 2020 19:14
Thanks! Someday I will learn how to do the queries.
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