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Lysin A and Holin in BI1 cluster Streptomyces phage

| posted 28 Feb, 2019 19:34
In our annotation of Streptomyces phage Esketit (cluster BI1), we have been unable to locate a Lysin A gene, but we have found a gene coding for LysM-Like endolysin. We also noted that similar phage (OylmpicHelado and Spectropatronm) are also missing this gene. Please advise us on how to proceed before we submit the genome.

In addition, our holin is much longer than the typical holin length. Ours is about 360 aa whereas the length is usually about 110 aa. Only the first part of our product actally matches (HHpred) with holin function. We have found no other holin in the genome. We were wondering if it is possible to have a longer holin or a holin that is continuous with another protein sequence added on to the terminal portion of the functional holin?.


| posted 01 Mar, 2019 17:55
Have you also looked at some of the other BI1 phages on Phamerator. Several were just added to GenBank and might not have come up during your initial review. These would include IceWarrior, Popy, and Namo. Those all have a holin identified that was not labeled in older genomes like OlympicHelado and Spectropatronm.

There is an endolysin gene identified in all the BI1 genomes mentioned above. That is gp5 in all of those.

| posted 01 Mar, 2019 19:53
I think you have a clear holin already as well, Esketit_Draft gene 30 (25259 - 25618 ), and it's the same length as the other BI1s (119 aa) and similar to the BI2 Scap1 that has it as well (129 aa). I don't know if we have confirmed cases of two holins (Lee?). I would be hesitant to call a second one, I think.

Edited 01 Mar, 2019 19:57
| posted 01 Mar, 2019 19:59
Thank you for the suggestions!
| posted 01 Mar, 2019 22:15
I think Ry Young (from Texas A&M) has papers written about multiple holins in the phages that he studies. It is just hard to know if a membrane protein is a holin. and if a pfam hit to holin is believable.
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