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Recent Activity
All posts created by debbie
| 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?
| Link to this post | posted 05 Apr, 2019 17:58 | |
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Friday at 2pm. Seems to be working fine. Were you adding a phage? I did not try that, but I could review phages. |
Posted in: PECAAN → PECAAN Down?
| Link to this post | posted 03 Apr, 2019 02:23 | |
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Hi! Wow! More details are needed. Would you provide who you are, Where you are from, What host you are using? Once I get some basics, I may have more questions. |
| Link to this post | posted 28 Mar, 2019 23:51 | |
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Joann, I do't believe a sequence has to be very long to contain a transmembrane domain. for me the 2 sides of the coin are: 1. is one membrane real? (so we ask that you can find it with 2 different finder programs) 2. It appears that defense systems (toxins, for example) can be 'attached' to the cell membrane, so that membrane protein might be a good place to look into that if you have a phenotype that suggests that phage has provided a defense. i.e. it would just be good to know. It will also be found out once you have a phenotype to investigate, so there is no harm by not calling it. Not helpful, right? So, I think my take on this is if you take the time look and confirm, report it. If this is all you miss in the genome, it is small potatoes. |
Posted in: Functional Annotation → Membrane protein
| Link to this post | posted 26 Mar, 2019 19:01 | |
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Cool! |
Posted in: Cluster A Annotation Tips → Pham 23651 function assignment
| Link to this post | posted 26 Mar, 2019 19:00 | |
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Joe, I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them. You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes? What is changing on you? debbie |
Posted in: DNA Master → DNAM failing to use proper translation code
| Link to this post | posted 26 Mar, 2019 18:52 | |
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I still like my little gene call. This area is definitely tricky. |
Posted in: Gene or not a Gene → Forward or reverse gene?