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All posts created by welkin

| posted 21 Jul, 2017 15:21
The main server is currently disconnected due to construction here at Pitt. We are working on an alternate plan.
Posted in: DNA MasterDNA Master Issue
| posted 19 Jul, 2017 16:16
So I think this comes from the idea that there must be tail assembly chaperones in the Bs, and the most likely candidates are the genes between the major tail and tape measure proteins. We need two adjacent ORFs that are not in the same frame that have an overlap. Then, there are only two choices, the equivalent of FriarPreacher genes 22/23 or 25/26. 25 belongs to pham 10859, and has the hhpred hit to a tail protein (although it is the capping protein and not the assembly chaperone.) 22 also hits to some phage structural proteins that are not the assembly chaperones. Perhaps the best thing to do is to scrap all the TAC assignmnets in the Bs and set them all back to NKF.
Posted in: Functional AnnotationTail assembly chaperones in B phages
| posted 19 Jul, 2017 15:06
hi Steve— send data! DNA Master file, screenshots?

I also like to get a sense of exactly what the putative functional match is before I use something specific: here is a nice description on Ocr and its characteristics that are essential for functionality.

Edited 19 Jul, 2017 15:14
Posted in: Functional AnnotationGene with homology to T7 Ocr gene
| posted 07 Jul, 2017 19:17
Dan, is it worth doing a Sanger run across the area to resolve?
Posted in: Gene or not a GeneGene split in 2
| posted 07 Jul, 2017 19:16
Yep, we can add officially. give me a phage name and gene number.
Posted in: Functional AnnotationFunctions not on the approved list
| posted 08 Jun, 2017 15:27
I agree! Stick to NKF.
Posted in: Functional Annotation Ead/Ea22-like protein
| posted 06 Jun, 2017 13:00
Sounds fine.
Posted in: Functional AnnotationPhosphoesterase with intein domain
| posted 06 Jun, 2017 12:59
I don't know what an Ead/Ead22 -like protein is. Can you elaborate? Does it make sense in the context of phage biology?
Posted in: Functional Annotation Ead/Ea22-like protein
| posted 06 Jun, 2017 12:58
do both parts have good coding potential?
Posted in: Gene or not a GeneGene split in 2
| posted 19 May, 2017 16:36
Found a ParB in a Cluster B phage? As far as we know, the ParB domain containing gene in the Cluster B phages is not a true ParB protein. We have been unable to make lysogens from Cluster B phages, and so we do not think this is a Partitioning Protein like the ParAB system found in some Cluster A phages. As a general rule of thumb, we never assign "ParB" as a function to a gene in which we can not also identify a ParA.
If your "ParB" has really good evidence, you may assign it the function of "ParB-like nuclease domain".
Edited 01 Mar, 2018 15:41
Posted in: Cluster B Annotation TipsParB