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Recent Activity
All posts created by debbie
| Link to this post | posted 03 Feb, 2023 20:19 | |
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From HHPred, this gene hits HK97_gp10, a minor capsid protein and a tail protein. So one must ask which is it? HK97 is the prototype phage for understanding how the capsid is formed. The lab that studied it was the lab of Roger Hendrix, from the University of Pittsburgh. As we hit gp10 of HK97, I asked if they knew the function of that gene and they could not identify it in their studies. As per the Approved Function List, when you hit HK97_gp10, stick with Hypothetical Protein until someone finds more data to support a call. |
Posted in: Cluster EJ Annotation Tips → Potential minor capsid protein
| Link to this post | posted 02 Feb, 2023 00:09 | |
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My advice is to ask the IT administrator to set the preferences. Whatever they do, should stick. debbie |
Posted in: DNA Master → DNA Master errors
| Link to this post | posted 29 Jan, 2023 21:50 | |
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Hi Robert, Please check you DNA master preferences and make sure you follow #2 and #6 correctly. https://seaphagesbioinformatics.helpdocsonline.com/article-66 |
Posted in: DNA Master → Glimmer failure during autoannotation
| Link to this post | posted 26 Jan, 2023 23:45 | |
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Nope, not yet. all help is welcome! debbie |
| Link to this post | posted 20 Jan, 2023 15:37 | |
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Holly, Exactly! You've got it! debbie |
Posted in: Functional Annotation → Scaffolding protein
| Link to this post | posted 20 Jan, 2023 03:24 | |
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Hi Holly, hmmm. I think that Mopey_14 (stop codon 10436), can be called the scaffolding protein because of the InterPro hit at HHPred (Q38580). It is a 99.5% probability (evalue is e-12) and has protein homology to the scaffolding protein of SPP1 (evidence is from UniProt database. Granted that the example used by the approved function list is D29, but your protein doesn't have to hit the example (and it doesn't, does it?) |
Posted in: Functional Annotation → Scaffolding protein
| Link to this post | posted 17 Jan, 2023 14:11 | |
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Hi Amy, There are lots of reasons why Glimmer and GeneMark don't call the same things exactly the same. Mostly their algorithms are different. and the math breaks down with small proteins. It is why we use both. And they can both miss a call and predict something that we throw away. If automation made the best calls, we would not be doing this one gene at a time. debbie |
| Link to this post | posted 14 Jan, 2023 01:18 | |
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Nancy, It just takes a long time. In the meantime, it will look like it is not responding! Wait for the log that pops up long after you see 100% done. Good luck! debbie |
Posted in: Using WINE to run DNA Master on a Mac → Help with WINE
| Link to this post | posted 13 Jan, 2023 04:15 | |
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In our investigations, we determined that a MerR-like HTH will have 3 helix-coil motifs followed by a "wing' of a coil-coil. As I review your seqeunce int he link above, I do not see the 'wing' with a coil-coil at the end. so i would call this a helix-turn-helix DNA binding protein. |
Posted in: Annotation → helix-turn-helix binding domain or protein?
| Link to this post | posted 12 Jan, 2023 16:12 | |
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Hi Joe, It is common that minor tail genes contain enzymes that help get the phage attached to the cell wall. So it is common to find them containing collagen, beta-lactamse, peptidoglucan domain (to name a few) hits. The big genes (maybe 4-6 of them) following the tape measure protein are really the only genes we can call by synteny alone as "minor tail protein". If the genes following the tape measure are not big, we look for additional evidence and sometmes find it. this gene is 493 aa, so I think we are good! |