SEA-PHAGES | WheeHeim LysM

Link to this post \| posted 19 Aug, 2018 22:18
scaruso	I am looking at WheeHeim_11390-12103, currently gp23 in PECAAN, and want to get a second opinion on a function call on it (an another gene in the next post) WheeHeim is a singleton, and so is pretty weird looking. It has virtually no useful GM_Web coding potential, for example. Only three genes are in occupied phams, the rest are orphams. The BlastP and HHPred alignments for this gene are poor hits for 'endolysin, LysM-like,' but the CDD result is much stronger, something I rarely get to use. I think that makes the poor BlastP and HHPred hits more interesting and supportive. Any thoughts would be appreciated. Edited 19 Aug, 2018 22:50 88Kb

Link to this post | posted 19 Aug, 2018 22:18

I am looking at WheeHeim_11390-12103, currently gp23 in PECAAN, and want to get a second opinion on a function call on it (an another gene in the next post)

WheeHeim is a singleton, and so is pretty weird looking. It has virtually no useful GM_Web coding potential, for example. Only three genes are in occupied phams, the rest are orphams.

The BlastP and HHPred alignments for this gene are poor hits for 'endolysin, LysM-like,' but the CDD result is much stronger, something I rarely get to use. I think that makes the poor BlastP and HHPred hits more interesting and supportive.

Any thoughts would be appreciated.

Edited 19 Aug, 2018 22:50

Link to this post \| posted 19 Aug, 2018 23:00
dbolliva	This is a tougher one. Again, just my two cents. The evidence points to this having a LysM domain, but that can be a little misleading because the LysM domain essentially is a peptidoglycan binding domain. Your CDD hit is just to that part of the predicted protein. Unfortunately, there is not an approved function with just the LysM domain, so the question is do you have enough evidence for the endolysin part. There are suggestions (the LD transpeptidase hit for example) but I would suggest it is not strong enough to make this call. I personally would leave this NKF.

Link to this post | posted 19 Aug, 2018 23:00

dbolliva

This is a tougher one. Again, just my two cents. The evidence points to this having a LysM domain, but that can be a little misleading because the LysM domain essentially is a peptidoglycan binding domain. Your CDD hit is just to that part of the predicted protein. Unfortunately, there is not an approved function with just the LysM domain, so the question is do you have enough evidence for the endolysin part. There are suggestions (the LD transpeptidase hit for example) but I would suggest it is not strong enough to make this call. I personally would leave this NKF.

Link to this post \| posted 20 Aug, 2018 17:22
scaruso	David Bollivar This is a tougher one. Again, just my two cents. The evidence points to this having a LysM domain, but that can be a little misleading because the LysM domain essentially is a peptidoglycan binding domain. Your CDD hit is just to that part of the predicted protein. Unfortunately, there is not an approved function with just the LysM domain, so the question is do you have enough evidence for the endolysin part. There are suggestions (the LD transpeptidase hit for example) but I would suggest it is not strong enough to make this call. I personally would leave this NKF. I can buy that. Thank you for your second look. Steve

Link to this post | posted 20 Aug, 2018 17:22

scaruso

David Bollivar
This is a tougher one. Again, just my two cents. The evidence points to this having a LysM domain, but that can be a little misleading because the LysM domain essentially is a peptidoglycan binding domain. Your CDD hit is just to that part of the predicted protein. Unfortunately, there is not an approved function with just the LysM domain, so the question is do you have enough evidence for the endolysin part. There are suggestions (the LD transpeptidase hit for example) but I would suggest it is not strong enough to make this call. I personally would leave this NKF.

I can buy that. Thank you for your second look.
Steve

Recent Activity

WheeHeim LysM