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 12 May, 2019 01:09

scaruso

I am reviewing a BI1 and have a another call that I am planning on deleting, thymidylate kinase. The call has been made based on a blast hit to several other phages, but I can't find any other evidence that it really is thymidylate kinase. If this were one of our phages, I would call it NKF for sure, but wanted to get a second opinion since it is the first one I am reviewing externally. Three members of pham 44619 (https://phagesdb.org/phams/44619/) have the call, the rest don't. The results for the gene are here https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_73a and https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_73b. No hint of a hit other than by blast - https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DEW588MA015. I think they are questionable hits. But the approved functions list uses Erdmann_94 as the example of the call, which is pham 46029 - https://phagesdb.org/phams/46029/, and has been changed to thymidylate synthase and is mostly filled with ThyX, etc. Upshot is, I think the kinase call wrong. Thoughts? Steve Edited 13 May, 2019 00:01

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 17:20

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