SEA-PHAGES | Cluster BI

Link to this post \| posted 11 May, 2019 17:36
scaruso	I am reviewing a BI1 and have a couple genes with functions assigned that are not on the official function list. Both were undoubtedly chosen because they were assigned historically. I just want to get a backstop of my plan. I'll post them as separate posts. One is endolysin, which I am changing to hydrolase. Eleven cluster BI phages have the function endolysin assigned to a gene in pham 3570 (https://phagesdb.org/phams/3570/) The protein does hits a bunch of previous endolysin and hydrolase calls (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DE1EXX8D015) and has a lysozyme domain when blasted. HHPred shows a strong lysozyme domain on the right side, and a weaker peptidase/hydrolase domain on the left (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_5a) and (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_5b) I see a general call of hydrolase as the safest choice. It has two domains, so I considered Lysin A, but I'm not confident in it. Thoughts? Steve Edited 11 May, 2019 20:19

Link to this post | posted 11 May, 2019 17:36

I am reviewing a BI1 and have a couple genes with functions assigned that are not on the official function list. Both were undoubtedly chosen because they were assigned historically. I just want to get a backstop of my plan. I'll post them as separate posts.

One is endolysin, which I am changing to hydrolase.

Eleven cluster BI phages have the function endolysin assigned to a gene in pham 3570 (https://phagesdb.org/phams/3570/)

The protein does hits a bunch of previous endolysin and hydrolase calls (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DE1EXX8D015) and has a lysozyme domain when blasted.

HHPred shows a strong lysozyme domain on the right side, and a weaker peptidase/hydrolase domain on the left (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_5a) and (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_5b)

I see a general call of hydrolase as the safest choice. It has two domains, so I considered Lysin A, but I'm not confident in it.

Thoughts?

Steve

Edited 11 May, 2019 20:19

Link to this post \| posted 13 May, 2019 16:28
welkin	is there another candidate for an endolysin/lysin A?

Link to this post \| posted 13 May, 2019 17:03
scaruso	These phages have a second gene identified as hydrolase immediately following two minor tail proteins and immediately before the holin, so it is hard to tell if it is another minor tail protein or a lysin by synteny, so the more generic call has been used in the past. That is - https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28a and https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28b Once this is resolved, it's ready, by the way. Steve Edited 13 May, 2019 17:03

Link to this post | posted 13 May, 2019 17:03

scaruso

These phages have a second gene identified as hydrolase immediately following two minor tail proteins and immediately before the holin, so it is hard to tell if it is another minor tail protein or a lysin by synteny, so the more generic call has been used in the past.

That is - https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28a and https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28b

Once this is resolved, it's ready, by the way.

Steve

Edited 13 May, 2019 17:03

Link to this post \| posted 16 May, 2019 18:56
scaruso	OK, so, after further consideration and looking at the second one, I think calling the first gene Lysin A is probably pretty safe. I don't know about calling the second one anything beyond hydrolase. Steve

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