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All posts created by welkin

| posted 15 Feb, 2019 13:36
Hi Steve,
Let's go with "phage membrane DNA delivery"; and i am going to make a note that it is restricted to the tectiviridae for now.
Posted in: Request a new function on the SEA-PHAGES official listDNA delivery
| posted 14 Feb, 2019 12:54
Claire Rinehart
First let me point out that we have added two new fields to the Phagesdb BLAST table, Cluster and Pham. We added these two fields because when considering the functions in Phagesdb BLAST we often found ourselves asking, is this phage from the same sub cluster or is this a gene function that has been acquired from another group of phages? Once we added these fields we found it much easier to sort based on cluster and pham. While clicking on the headers to sort and using the search tool is a wonderful way to explore the Phageseb BLAST information, we found ourselves thinking, wouldn't it be nice if we just had a summary count of the functions along with the cluster and pham information. That is why the summary table was created. The count just shows the number of hits for each function/cluster/pham while the frequency shows the fraction of the total number of phages with an assigned function.
When checking genes with no assigned function, NKF, I find it very useful to be able to check the Phagesdb Summary and if there are no function/cluster/pham lines then I know it is not really useful to sort and search the Phagesdb BLAST table.
Another interesting feature of this summary table is that it shows the variety of names for the same function. This may be useful to point out to students as a reason for using the "approved function list" represented in the drop down window that appears as functions are typed in.
Finally, the Phagesdb Summary is useful to see which clusters may have exchanged this gene and you can use the Pham to make sure that they are fairly close relatives.
Hope that this helps and that the new features are useful to you and your students.
Thanks,
Claire

Hi Claire,
I think these fields are tremendously helpful! Thank you so much!

One additional column that might help in the table would be to include the date a phage was annotated. As we start revising functional assignments, the latest, most accurate assignment may appear on the table only once–and that's the one we would like everyone to switch to.

Great new feature!
Posted in: PECAANNew Features in PECAAN
| posted 04 Feb, 2019 14:12
Some cluster A phages contain a sigma factor that is mislabeled as "DNA directed RNA polymerase". This is due to a misinterpretation of a PDB crystal structure comprised of a complex of proteins. The gene in question aligns to the sigma factor in the complex, not the RNA pol.
At this time, no cluster A phages contain a verifiable RNA polymerase.
Posted in: Cluster A Annotation TipsSigma factor vs DNA-directed RNA pol
| posted 20 Jan, 2019 00:31
Hi Nikki,
So this is a very specific enzymatic activity. Can you differentiate between this, and say, just a generic amidase? HHPred can't always discern that level of specificity.

IF you have good evidence for the specific activity, then sure. Otherwise, go with more generic.
Posted in: Functional Annotationlysin A domains in Arthrobacter AN phages
| posted 19 Jan, 2019 13:55
No. Band-7 proteins are their own class.

Thanks for asking!
Posted in: Functional AnnotationMembrane protein
| posted 14 Jan, 2019 20:08
I agree with Dan—
It still looks like admin issues.

I *think* you can move the entire already installed DNA Master folder from /Program Files to another location without reinstalling.

Otherwise, make sure you set up the Desktop shortcut such that the program always launches with admin rights.

Best,
Welkin
Posted in: DNA MasterProblem installing DNA Master on Windows 10
| posted 14 Jan, 2019 18:54
Hi Jackie,
I think this still counts at MPME1.

Best,
Welkin
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 14 Jan, 2019 18:53
Hi Manuel,
that is definitely an out of date version. Current version on my computer is dated Nov 2019, and I just ran the updater and there is even a more recent one than that.

Usually when the program refuses to update it is not being launched with admin rights.

Best,
Welkin
Posted in: DNA MasterProblem installing DNA Master on Windows 10
| posted 14 Jan, 2019 16:48
One step growth curves in Mycobacteria are really hard. I've tried a number of times, but never really been satisfied with the data; it just doesn't look as nice as ones with E. coli or Salmonella phages.

In general, we try for exponential cells with an OD of 0.4, and MOI of at least ten. We do the infection in a small volume (so you pellet your cells, resuspend in 1/10 or even smaller a volume); add phage; wait 15 min; and then bring back up to the initial volume. Shake at 37 for 3 hours or so while you sample.

Latent periods seem to run around 3 hours-ish.

Posted in: MycobacteriumOne Step Growth Curve
| posted 10 Jan, 2019 13:14
yes, i agree— it stays a tail protein.
Posted in: Functional Annotationminor tail proteins in Arthrobacter AN cluster