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JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
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?) |
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 |
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. |
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! |
Link to this post | posted 11 Jan, 2023 00:12 | |
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Amy, This is good stuff. It will make you more prepared for what your students will do. It is all good! debbie |
Link to this post | posted 03 Jan, 2023 03:47 | |
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Hi Megan, I agree that Ciao sequence in the first 4-8 amino acids is unlike others in the pham. However, the gene does stop at 42523. So the only start to call is 42699. I think that starterator shows the data well. in addition, check the GeneMark using smeg and tb as the target. You will see that the best coding potential is in the frame identified. Make sense? debbie |
Link to this post | posted 21 Dec, 2022 11:30 | |
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I would keep this simple and call this a minor tail protein. |
Link to this post | posted 19 Dec, 2022 22:29 | |
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I agree. While this has to be a structural protein, i agree it likely not a TAC. Interestingly, Usavi_26 does have a Pfam hit of 94%, e-value of .95 (which is not great) to TAC. (That is not typical at all.) This article might shed some light. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL. J. Mol. Biol. 425, 2436-49, (2013). View articlePMID: 23542344 Let me know what you find, debbie PS, change what databases you are checking to see what else you can find. |
Link to this post | posted 19 Dec, 2022 21:18 | |
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Yep. |