Link to this post | posted 11 May, 2019 17:20

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 chitosinase, which I am changing to glycoside hydrogenase. Eight cluster BI phages have the function chitosinase assigned to a gene in pham 16099 (https://phagesdb.org/phams/16099/). The protein does hit chitosinase in Strep and other bacterial spp. by both blastp (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DE09SEP6015) and HHPred (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_22a) and (https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_22b). The closest approved function is a glycoside hydrogenase, of which chitosinase is a type. The other option is to put in a petition to have it added to the list. Thoughts? Steve Edited 11 May, 2019 17:40

Link to this post | posted 05 Apr, 2019 13:12

scaruso

Good morning, We have some mass spec data to look at and are being told that it likely is suffering from all sorts of post translational modifications, which make it harder for their system to match up the results to the provided data, it seems. Unless, of course, we tell them which to look for. Oh and each one included adds to the computing time. So best to chose judiciously. OK, so, with that in mind, we have come up with only a couple common one identified in the host bacteria. Strep apparently does a lot of acetylation, adenylylation, and modification with prokaryotic ubiquitin-like protein (Pup). But anyone have some suggestions of the best choices to include for Actinobacteriophages in general? Thanks, Steve

Link to this post | posted 25 Mar, 2019 16:45
scaruso	We used the function "major capsid and protease fusion protein," the current version of "capsid & capsid maturation protease" of the cluster AM phages (see Pham 17557). Should another function be created, perhaps that recognizes all three domains? Steve

Link to this post | posted 14 Mar, 2019 18:44

scaruso

If you look at the tape measure protein in coliphage HK97: https://www.ncbi.nlm.nih.gov/protein/NP_037710.1. It's a big protein, 1089 amino acids long. I think what HHPred is seeing is your protein looks like a small chunk of it, but clearly you have a much better candidate in gp17 for tape measure. Since it is far past tape measure, and not one of the large genes immediately following it, it's hard to justify using synteny to call it a minor tail protein. Your best HHPred hit is to a DUF, as is your second good match, then human signaling proteins. It would be hard for me to make a call on this one other than NKF. Steve Edited 14 Mar, 2019 18:45

Link to this post | posted 13 Mar, 2019 16:24
scaruso	I don't know. I wouldn't be surprised it that wasn't an error code or below the measurable threshold code, but I don't know offhand, I'm afraid.

Link to this post | posted 11 Mar, 2019 22:40
scaruso	I know you can run OrthoANI as a stand alone program and do so. I let Ivan do that, though, since it's command line. The GUI based one has a limit of 10 genomes. It didn't seem to be particularly challenging for him. Might give him a shout if you run into any trouble. Steve

Link to this post | posted 11 Mar, 2019 19:22
scaruso	Christian, We use that one as well, and also OrthoANI, here: https://www.ezbiocloud.net/tools https://www.ezbiocloud.net/tools/ani Steve

Link to this post | posted 11 Mar, 2019 19:03
scaruso	Claire, Thank you very much for the response, that was very helpful. And I can delete Anthony now, we are done with it. Though the answer will, no doubt, be useful for other duplicates in the future. Steve

Link to this post | posted 09 Mar, 2019 22:07

scaruso

Claire, Can you tell me what the Phagesdb Function Frequency is based on? I see a list of various function assignments for a variety of PHAMS, but what brings them up? I don't see the same hits on Blastp or HHPred, always, and the PHAMS are different than the gp being examined, so I'm not clear. By the way, I posted another question about HHPred results in PECAAN and external, any thoughts about that? Thanks! Steve

Link to this post | posted 05 Mar, 2019 19:12
scaruso	Excellent. That's very helpful. Thank you! Steve