Link to this post | posted 14 Nov, 2017 00:12

cdshaffer

This is a proposed funtion based on Pham 28735 (example member Mildred21 gp255) The HHPred has a 100.0%/e=9E-39 93% length alignment to an NMR structure to e coli YibA in PDB and to COG3236 see screen capture of hhpred alignment here. The phyre2 3d prediction is a 100% confidence with 91% coverage to the same pdb structure. This link should work for about a week. here is the screen capture which should work for the foreseeable future. YibA is a founding member of COG3263, the function for COG3263 is based mostly on this paper: A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis. Biochem. J. 2015 Feb 15; 466(1):137-145 This paper clearly shows that this e coli protein (and a couple of others like it) can enzymatically function to cleave N-glycosidic bonds in vitro as part of a large complex that carries out the first few steps of riboflavin biosynthesis. So there is really good evidence for enzymes of this type to be able to hydrolyse N-glycosidic bonds. I am certainly not proposing that this enzyme in phage is involved in riboflavin biosynthesis, but the wet bench is pretty good that the e coli YibA does have a glycosylase activity and there are many different glycosylases. The issue as to naming is one of specificity, should we use the more specific N-glycosylase or the more generic glycosylase? There are also S, O and C- type glycosylases. I feel that without biochemical evidence or a published analysis of the amino acids present at the active site and how they interact with a particular glycosidic bonds (i.e. how does the active site change with N, S, C and O type glycosidic bonds) that specifically adding the term N-glycoslyase may be too specific given the evidence above is simply bioinformatic alignments. Following this logic, I would say the more general glycosylase term is preferable. On the other hand, of all the glycosylases, one might argue that the most likely activity for a phage enzyme is as a DNA glycosylase. All of the DNA glycosylases are of course N-glycosylases (i.e. all 4 bases connect to the ribose through a nitrogen). I think the evidence for this phage protein family to be an enzyme is about as good as you can get with just bioinformatic alignment so adding something is probably appropriate, the question is how specific do we want to go, the generalized glycosylase or the more specific N-glycosylase.

Link to this post | posted 09 Nov, 2017 20:42
cdshaffer	What is the recommended protocol for suggesting updates to the newly posted list? For now I will just suggest here that we add "dNMP kinase" to the "do NOT Use" column for the written out entry "deoxynucleoside monophosphate kinase".

Link to this post | posted 31 Oct, 2017 14:51
cdshaffer	Wait, there is a new list posted? I looked at seaphages.org under faculty info and phagesdb.org under workflow/annotations. Both those are the Nov 2015 version. Link please. Edited 31 Oct, 2017 14:53

Link to this post | posted 30 Oct, 2017 15:23

cdshaffer

I am not sure if this is the same issue since I did not see the exact error message but I had a student with a failed install. It turned out he had a high end "gaming" laptop which had two hard drives. A small fast SSD drive which was the "C:" drive, and a slower much larger "D:" drive. He chose to install on the D: drive and was never able to get DNA Master to work properly. It did work when he removed DNA Master and then ran an install on the C: drive. You might want to check with the student and see if he also had two hard drives and if so be sure to install on the C: drive.

Link to this post | posted 19 Oct, 2017 16:13
cdshaffer	If you are getting the "Database setup required" window that looks like this. you just need to enter the root database password "phage" (without the quotes) to authorize updating the system. If you are getting a different kind of password error box can you send the exact wording or a pic. Edited 19 Oct, 2017 16:18

Link to this post | posted 03 Oct, 2017 21:12

cdshaffer

As a follow up. I just tried running auto-annotation on DNA Master and got yet a different set of genes from what is on phagesdb. So my suggestion above will not actually help. I don't know where the discrepancies are coming from, but again likely from using different installations of glimmer/genemark to get the auto-annotation gene lists. The only way for you to get your DNA Master file in sync with the starterator/phagesdb would be to edit the DNA Master file by adding and deleting genes until the list matches up. We will have to wait and hear from Dan on why the phagesdb gene list does mot match the DNA Master auto-annotation.

Link to this post | posted 03 Oct, 2017 20:53

cdshaffer

I can confirm your results, when I run yeezus through the pecaan auto-annotation I get 86 gene prediction. Looking at the gene list on phagesdb I see 93 gene calls. Looking at it I can see for example that yeezus gene 7 called in phagesdb is missing from the pecaan auto-annotation. This difference in number of gene calls is likely due to minor differences in the settings used when running glimmer and genemark at the two different sites. When I run glimmer and genemark on my local machine I often get different results than what DNA Master got from the NCBI glimmer and genemark servers. Since the starterator results are based on the gene calls done by phagesdb, gene numbers will quite likely get out of sync with your DNAMaster file. Your best bet is to switch over to the new auto-annotation server inside DNA Master. There was an email with the instructions a couple of weeks back but here is a link to the pdf with instructions on how to get auto-annotation working in DNA Master. I believe once you set it up, you can just re-run auto-annotation in DNA Master and you should get the same 93 genes that are in phagesdb and starterator.

Link to this post | posted 27 Sep, 2017 18:44

cdshaffer

You can't really "merge" the two databases since mysql will just use pham numbers to decide whether to put proteins in the same pham. You want all similar proteins from both phage collections to be put in the same pham when they are similar to each other. The only way to do that is to rerun all the protein comparisons with all the proteins in the database. There is a thread on how to make databases using a web based program called phamDB. See this thread. The program is old enough now that the installation instructions are likely out of date and it will take some tweaking to install but the basic code is still sound. Alternatively, you could use K_phamerate scripts to create your database, you need to check out and use the code at the sea-phages github repository. That repository holds the code currently being used to create the phamerator databases and is being actively maintained by Travis Mavrich. Unfortunately you will have to install and run using command line.

Link to this post | posted 22 Sep, 2017 16:27

cdshaffer

Too bad none of the easy work arounds helped. I am going to assume that there are no important files inside the SEA VM, do NOT do the following if there are important files you need to recover from inside the VM. If you have files to recover you are going to need local expert who can work with your computer to get Ubuntu to boot so the files can be recovered, could be a long and arduous trial and error process of fixing Ubuntu. So assuming there are no files to recover, I would try to fix it by simply deleting and replacing the SEA VM. Sorry I don't use Virtualbox in Windows so some of this might be a little off but should suffice: 1. Open virtualBox program so you get something like this window (i think the pic is from mac, the windows version should look similar): 2. click on the "2017 SEA VM" in the left column and select "Remove…" from the machine menu 3. You should see a message about how you are "about to remove a machine from the machine list" and three buttons. Select "Delete all files" to completely remove and delete the SEA VM and all associated files 4. Go back to https://seaphages.org/software/virtualmachine/ and start with step two to reinstall the SEA VM, booting into Ubuntu and installing the guest additions.

Link to this post | posted 21 Sep, 2017 16:14
cdshaffer	Few things to try and report back: 1. Can you ignore the box, and just start phamerator? 2. What happens if you just click the red close button at the very top left? Does it still kick you back to the login screen? 3. Does this happen on both the student and faculty accounts? Edited 21 Sep, 2017 16:15