SEA-PHAGES | All posts created by welkin

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Link to this post \| posted 23 Mar, 2019 16:31
welkin	Hi Chris, It depends on the phage. We've had phages with all possible assortments.

Posted in: Cluster CY Annotation Tips → two integrases

Link to this post \| posted 22 Mar, 2019 21:49
welkin	Hi Deb, So I haven't looked at this one closely yet. In general, when I try to decide what/if any function a protein may have, I try to find out more about the possibilities. What do you know about RepA/RecA? Are they both the same size? Does one have a domain that the other doesn't? Are there key catalytic residues that need to be present for either one?

Posted in: Functional Annotation → Is pham 23434 a DNA recombinase or a helicase?

Link to this post \| posted 19 Mar, 2019 13:24
welkin	I think minor capsid protein is probably the best call for the Appa gene.

Posted in: Functional Annotation → capsid maturation protease

Link to this post \| posted 19 Mar, 2019 13:20
welkin	It sound to me like we can add ribonuclease toxin BrnT to the list. Thanks!

Posted in: Request a new function on the SEA-PHAGES official list → Ribonuclease toxin BrnT

Link to this post \| posted 17 Mar, 2019 14:09
welkin	Seems unlikely to me, but who knows. Just look really carefully through the HHPred data to make sure the relevant catalytic domains are present in the right places. MuF and the protease can certainly be separate.

Posted in: Functional Annotation → capsid maturation protease

Link to this post \| posted 14 Mar, 2019 13:57
welkin	Hi Hari, IT looks like you are correct to me. Best, Welkin

Posted in: Annotation → Annotations of Microbacterium foliorum

Link to this post \| posted 13 Mar, 2019 16:34
welkin	Hi Cristian, I've never seen the error that you are describing, but I can tell you that I've had difficulty performing simultaneous comparisons with 80 phages. I had to do it in smaller chunks (like 20 at a time) and then collect the answers in a spreadsheet. So it is possible you are maxing it out. Best, Welkin

Posted in: DNA Master → Genome Comparison

Link to this post \| posted 15 Feb, 2019 13:36
welkin	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 list → DNA delivery

Link to this post \| posted 14 Feb, 2019 12:54
welkin	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!

Link to this post | posted 14 Feb, 2019 12:54

welkin

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: PECAAN → New Features in PECAAN

Link to this post \| posted 04 Feb, 2019 14:12
welkin	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 Tips → Sigma factor vs DNA-directed RNA pol

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