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Recent Activity
dane.bowder posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
Marie Fogarty posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
Debbie Jacobs-Sera posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
dane.bowder posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
All posts created by welkin
| Link to this post | posted 21 Jul, 2017 15:21 | |
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The main server is currently disconnected due to construction here at Pitt. We are working on an alternate plan. |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 19 Jul, 2017 16:16 | |
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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 | |
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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 |
Posted in: Functional Annotation → Gene with homology to T7 Ocr gene
| Link to this post | posted 07 Jul, 2017 19:17 | |
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Dan, is it worth doing a Sanger run across the area to resolve? |
Posted in: Gene or not a Gene → Gene split in 2
| Link to this post | posted 07 Jul, 2017 19:16 | |
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Yep, we can add officially. give me a phage name and gene number. |
Posted in: Functional Annotation → Functions not on the approved list
| Link to this post | posted 08 Jun, 2017 15:27 | |
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I agree! Stick to NKF. |
Posted in: Functional Annotation → Ead/Ea22-like protein
| Link to this post | posted 06 Jun, 2017 13:00 | |
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Sounds fine. |
Posted in: Functional Annotation → Phosphoesterase with intein domain
| Link to this post | posted 06 Jun, 2017 12:59 | |
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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
| Link to this post | posted 06 Jun, 2017 12:58 | |
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do both parts have good coding potential? |
Posted in: Gene or not a Gene → Gene split in 2
| Link to this post | posted 19 May, 2017 16:36 | |
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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". |
Posted in: Cluster B Annotation Tips → ParB