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Recent Activity
All posts created by debbie
| Link to this post | posted 18 Apr, 2019 13:27 | |
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Sara, This is a timely question. This summer Welkin learned that siphoviridae do not have to have 2 tail assembly chaperone genes. Some can have one. Our evidence for phage Laila is that it has one. When we originally called these genomes, we assumed 2. I think that little gene between the TAC and TMP, gene 14, is real, but not necessarily a tail assembly chaperone (and therefore a hypothetical protein). Make sense? thanks for the question! debbie |
Posted in: Cluster AN Annotation Tips → tail assembly chaperone
| Link to this post | posted 17 Apr, 2019 20:50 | |
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Thanks Claire! |
| Link to this post | posted 16 Apr, 2019 18:43 | |
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i haven't found it either. |
Posted in: Cluster C Annotation Tips → Model Cluster C genome
| Link to this post | posted 16 Apr, 2019 15:17 | |
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We can ask Claire about the glitch. Yes, you can still transfer data from PECAAN into DNA Master for your final file. debbie |
| Link to this post | posted 13 Apr, 2019 18:58 | |
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Sally, I asked Graham, and he agrees we can call these RexA and RexB. I think that RexA and RexB are a sufficient name. I would not include toxin/antitoxin because it is a known abortive infection mechanism. Toxin/antitoxin is too broad and we know the specifics. For the official list, would you confirm that gene 41 is the RexA and gene 43 is the RexB? (or what genes they are when you re-number?) Cool! debbie |
Posted in: Functional Annotation → RexAB systems
| Link to this post | posted 13 Apr, 2019 01:26 | |
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Jackie, It is annotated as a gene with 2 regions (just like a programmed frameshift). GenBank will squawk about it, phamerator won't like it, but that is how you will submit the file. Biologically, the phage doesn't care, it exists in the host as a circle. |
Posted in: Gene or not a Gene → Wrap around HNH endonuclease
| Link to this post | posted 11 Apr, 2019 18:43 | |
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Greg, Again I haven't looked, a 28% hit to terminase could be a DNA binding domain, an ATPase domain, or a nuclease domain hit. This may not even be related to a terminase. Let me know if you really need me to look. |
| Link to this post | posted 11 Apr, 2019 17:52 | |
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Greg, Without looking, could your terminase,large subunits be hitting different parts of terminase? so you have a modular configuration of as in Auxillium gp2 and gp3, with one gene matching ATPase domain and the other matching a nuclease domain? debbie |
| Link to this post | posted 11 Apr, 2019 17:42 | |
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Hi Deb, As I look at this more closely (I HHPred'd BeeBee8 and Velene), the hits are alignments to their N-terminals (the last 20-25 amino acids). The predominant hit is to zinc-finger domains. I think that is what our protein is hitting - a zinc finger domain. Without more information, we should label these as Hypothetical Proteins. FYI - the rationale to DNA binding domains is that I think the zinc fingers were a term coined to mean a structure that inevitably binds to DNA (or RNA) using zinc ions. I think Wikipedia does a nice job of describing the specific and general use of the term 'zinc finger' and why we have not adopted it (since it now holds such a generalized meaning). https://en.wikipedia.org/wiki/Zinc_finger |
| Link to this post | posted 08 Apr, 2019 17:05 | |
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Nice! |
Posted in: PECAAN → PECAAN Down?