SEA-PHAGES | WheeHeim Glycosyltransferase

Link to this post \| posted 19 Aug, 2018 22:27
scaruso	I am looking at WheeHeim_12322-12990, currently gp25 in PECAAN, and want to get a second opinion on a function call on it (an another gene in the previous post) As mentioned previously, 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. There are strong BlastP, HHPred, and CCD hits for lytic transglycoslyase and lytic murein transglycoslyase. That's certainly in line with an endolysin, and there are very. very poor hits to endolysin as well. The safest call would, of course be glycosyltransferase. But when I was searching in the HHPred results, one of the many lysozyme and other hits looked suggestive of lysin B. Could this be lysin B right after the Endolysin, LysM (lysin A) called two genes 5'? Any thoughts would be appreciated. 84Kb

Link to this post | posted 19 Aug, 2018 22:27

I am looking at WheeHeim_12322-12990, currently gp25 in PECAAN, and want to get a second opinion on a function call on it (an another gene in the previous post)

As mentioned previously, 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.

There are strong BlastP, HHPred, and CCD hits for lytic transglycoslyase and lytic murein transglycoslyase. That's certainly in line with an endolysin, and there are very. very poor hits to endolysin as well. The safest call would, of course be glycosyltransferase.

But when I was searching in the HHPred results, one of the many lysozyme and other hits looked suggestive of lysin B. Could this be lysin B right after the Endolysin, LysM (lysin A) called two genes 5'?

Any thoughts would be appreciated.

Link to this post \| posted 19 Aug, 2018 22:30
dbolliva	Steve, I have yet to look at the function aspect, but I would recommend you use the GenemarkS that you can run from phagesdb to look for coding potential. It has much more information to offer than what I see uploaded to PECAAN. Dave

Link to this post \| posted 19 Aug, 2018 22:44
dbolliva	Steve, Just my two cents. In looking at the catalytic activity of Lysin B, it appears to be an esterase, hydrolysing an ester bond. This domain seems to be a transglycosylase, which may lead to the cleavage of glycan strands but it is not a hydrolysis like the Lysin B. Thus I would suggest that the glycosyltransferase call is more appropriate. Dave

Link to this post \| posted 19 Aug, 2018 22:45
scaruso	David Bollivar Steve, I have yet to look at the function aspect, but I would recommend you use the GenemarkS that you can run from phagesdb to look for coding potential. It has much more information to offer than what I see uploaded to PECAAN. Dave I'll check it out. Thank you. Steve

Link to this post \| posted 19 Aug, 2018 22:47
scaruso	Thank you. And thank you for the tip about GenemarkS on PDB, that's very useful. Steve

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WheeHeim Glycosyltransferase