Link to this post | posted 19 Jul, 2017 16:16

welkin

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.

Link to this post | posted 19 Jul, 2017 15:06
welkin	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. https://academic.oup.com/nar/article/40/16/8129/1031862/Exploring-the-DNA-mimicry-of-the-Ocr-protein-of Edited 19 Jul, 2017 15:14

Link to this post | posted 07 Jul, 2017 19:17
welkin	Dan, is it worth doing a Sanger run across the area to resolve?

Link to this post | posted 07 Jul, 2017 19:16
welkin	Yep, we can add officially. give me a phage name and gene number.

Link to this post | posted 08 Jun, 2017 15:27
welkin	I agree! Stick to NKF.

Link to this post | posted 06 Jun, 2017 13:00
welkin	Sounds fine.

Link to this post | posted 06 Jun, 2017 12:59
welkin	I don't know what an Ead/Ead22 -like protein is. Can you elaborate? Does it make sense in the context of phage biology?

Link to this post | posted 06 Jun, 2017 12:58
welkin	do both parts have good coding potential?

Link to this post | posted 19 May, 2017 16:36

welkin

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

Link to this post | posted 19 May, 2017 16:32
welkin	Can't find lysin B? No worries! Cluster B2 phages do not have a lysin B! Edited 20 Aug, 2018 15:56