Link to this post | posted 11 Apr, 2019 15:39
welkin	Hi Greg, Thanks for your question. yes, this is the tail terminator. The Lambda U crystal structure 3FZ2 is of a homohexamer complex— all six chains are from the same polypeptide. so 3FZ2_B is valid, as are chains _A through _F. I will update the official function notes. Best, Welkin

Link to this post | posted 05 Apr, 2019 16:10

welkin

Hi Steve, Those are good places to start. I've spent a lot of time trying lots of different combinations of PTMs with our data and haven't felt like I've really improved my protein IDs by any statistically significant amount. It seems like you can always match a few peptides in which the PTMs have come off during the collisions; so as long as you are doing ID and not quantitation, it doesn't seem like it makes much of a difference to me. If you do try to add some PTMs to the search, I wouldn't try to do more than 2-3 at a time; eventually if you add enough possibilities in there you'll find anything! Good luck!

Link to this post | posted 02 Apr, 2019 15:40
welkin	As of April 2019, we do not know where the frameshift is in the tail assembly chaperones in the EA1 phages, and so therefore the tail assembly chaperones should be kept as two separate un-shifted genes.

Link to this post | posted 27 Mar, 2019 18:22

welkin

Hi Nikki, There are a number of clusters in which we can not find the correct slippery sequence (+1 sequences in particular can be tricky). I feel pretty good about these two because they are the only two open reading frames between the major tail subunit and the tapemeasure, and because the coding potential in the GeneMArkS output drops in the upstream gene before it reaches the stop codon, and it picks up in the downstream gene right about where it drops in the upstream one. so tail assembly chaperone it is!

Link to this post | posted 27 Mar, 2019 13:03
welkin	Hi Joe– No, it won't cause any problems. As long as those alternate start codons are selected in the preferences you don't need to worry about the standard vs bacteria codes here. We reset the entire annotation to the bacterial code enmass when we submit to GenBank.

Link to this post | posted 26 Mar, 2019 18:43
welkin	Hi JoAnn, So this protein is being investigated at the bench by one of the Hatfull Lab postdocs, Katie Wetzel. It is a "RepA-like replication initiator" and I will add that to the official list. Thanks for asking!

Link to this post | posted 26 Mar, 2019 14:03
welkin	Hi JoAnn– what is the gene number and/or coordinates in the current Phamerator draft? Pham numbers can change when we update the database and I just want to make sure I am looking at the right gene.

Link to this post | posted 25 Mar, 2019 16:59

welkin

Hi Steve, At this point we are not differentiating in our function names for other capsid-scaffolding fusions; as this is not uncommon in phages. In the case of HK97, the scaffolding is called the "delta domain" of the major capsid protein, and the literature refers to the procapsid or uncleaved form vs the mature form. So to be consistent, we have not labeled our capsids with delta domains anything other than "major capsid protein"–and so therefore, don't mention specifically it here either.

Link to this post | posted 25 Mar, 2019 16:43
welkin	Hi Greg, We are aware of the new suggestion, but do not plan to change our nomenclature at this time. We will keep you posted should anything change on that front.

Link to this post | posted 25 Mar, 2019 16:03
welkin	there is a tRNA with a low-ish infernal score— we think that it should be included in the annotations.