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Recent Activity
All posts created by debbie
Link to this post | posted 05 Jan, 2022 21:06 | |
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Hi Rick, We will wait for the cryoEM, but yes, the must surely be the major capsid subunit. Nice! debbie June 21, 2022 Rick Pollenz and Simon White have confirmed (experimentally) that Akoni_gp33 is the major capsid subunit! Please annotate! |
Posted in: Cluster EK Annotation Tips → major capsid protein
Link to this post | posted 30 Dec, 2021 14:08 | |
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There are lots of papers to read when annotating a Cluster F phage. 3 specific papers to consider are: Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site -specific integation vectors for mycobacteria T.T. Pham et al, Microbiology 2007. Mycobacteriophage Fruitloop gp52 inactivatesWag31 (DivIVA) to prevent heterotypic superinfection C. Ko and G.F. Hatfull, Mol Micro 2018. An NAD+ Phopsphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death D. M. Freire et al, Mol Cell 2019. |
Link to this post | posted 27 Dec, 2021 20:35 | |
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Ah, so you will have 2 different genes for the domains. Great! debbie |
Link to this post | posted 23 Dec, 2021 20:49 | |
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Chris, I added this, but I have a question. Are there 2 endolysin genes in this genome? Lysin genes are notorious for not having all domains match existing domains in the databases that we use. By that I mean, we can call a lysin A because ONE of the domains hit previously studied endolysins. so in the case of the gene you are interested in, is it possible that the 34% not covered is the missing protease domain? so the gene is a whole endolysin and not a gene broken into 2 pieces? I would recommend that we call the gene an endolysin if no protease domain is identified. Does that make sense? Would you also provide the genome/gene number to list it is an example int he function list. Thanks, debbie |
Link to this post | posted 17 Dec, 2021 17:45 | |
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Hi Ping, We have seen this before. I would call gene 2 "terminase, small subunit", gene 3 "terminase large subunit (ATPase domain)", and gene 4 "terminase large subunit (nuclease domain)". We have looked into this with the cluster AY phages and worked on a case study to show our investigation. It is still in draft form, but may be helpful. It is attached. |
Posted in: Cluster DT Annotation Tips → Terminase Genes
Link to this post | posted 13 Dec, 2021 18:06 | |
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Mary, Hi. Are you running as administrator? debbie |
Posted in: DNA Master → TbQueries
Link to this post | posted 13 Dec, 2021 17:44 | |
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Hi all, Did you go back through this forum post and unpack and repack your DNA Master file? That is the typical way to fix this. https://seaphagesbioinformatics.helpdocsonline.com/article-104 It is tedious, so be patient. Let me know if that corrects the problem. If not, please send me the file. Thanks, debbie |
Posted in: DNA Master → TbQueries
Link to this post | posted 12 Dec, 2021 00:22 | |
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Maybe the different pham gene is actually in a different frame. What do you think? debbie |
Posted in: Cluster F Annotation Tips → orpham BLAST data
Link to this post | posted 03 Dec, 2021 18:48 | |
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Unlike most of the Microbacterium phages we have found to date (12-2-21), Cluster EH phages are temperate and do have a serine integrase. We see 3 different phams of serine integrases in these genomes so far. There are 7 members in this cluster at this time - Floof, GardenState, Gretchen, Honk, IAmGroot, Percival and Zeta1847. Their starts are called correctly. Look for the serine residue ~ 8-20 bases of the start. Serine integrases are sometimes called large recombinases because of their size. A good read is found here: https://pubmed.ncbi.nlm.nih.gov/26350324/ |
Posted in: Cluster EH Annotation Tips → Serine Integrase
Link to this post | posted 03 Dec, 2021 15:32 | |
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Dear , It is a common morphology for some of our phages to do this. Six rounds of replating a well isolated plaque means you have purified well. Our Cluster A phages are notorious for doing this. I think that they are the same plaque morphology and it is the landscape differences that do this OR just as likely, it is a cell growth issue and not cells are in the same growth period when infection started so some plaques have a head start on the others. What is 'dangerous' is to 'over-purify' and find the clear plaque mutant that has lost /integration function. If there is a genotypic difference between the 2 populations, a good Illumina sequence run may show it. debbie |
Posted in: Phage Biology → Different Plaque Sizes for One Phage