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All posts created by welkin

| posted 18 Apr, 2019 13:09
Hi Sally,
I thought M23 was on the list already– go head and use it. and I don't think we can be more specific and use M23B without better data.

Best,
Welkin
Posted in: Functional AnnotationLysin A in Rhodococcus phage
| posted 17 Apr, 2019 17:17
As of April 2019, we have been unable to identify the major capsid protein, and so you do not need to include it in your annotation.
Posted in: Cluster EK Annotation Tipsmajor capsid protein
| posted 17 Apr, 2019 13:22
Hi Sally– Debbie and I spoke offline a bit, and we are going to amend the "RexA" only function. We try hard not to just use the protein names because students get stuck in the alphabet soup when there is no additional information (RecA and RexA are very different, no?)

So I've added a bit to the designations:

RexA family abortive infection protein
RexB family abortive infection protein

Thanks!
Welkin
Posted in: Functional AnnotationRexAB systems
| posted 11 Apr, 2019 15:39
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
Posted in: Functional AnnotationFUNCTION: Tail Terminator - Current Official Function List Confirmatory Question
| posted 05 Apr, 2019 16:10
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!
Posted in: Phage BiologyMass Spec and Post Translational Modifications
| posted 02 Apr, 2019 15:40
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.
Posted in: Cluster EA Annotation Tipsframe shift
| posted 27 Mar, 2019 18:22
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!
Posted in: Frameshifts and Intronstail assembly chaperones in Microbacterium foliorum EA1 phages
| posted 27 Mar, 2019 13:03
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.
Posted in: DNA MasterDNAM failing to use proper translation code
| posted 26 Mar, 2019 18:43
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!
Posted in: Cluster A Annotation TipsPham 23651 function assignment
| posted 26 Mar, 2019 14:03
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.
Posted in: Cluster A Annotation TipsPham 23651 function assignment