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Recent Activity
All posts created by debbie
| 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 |
50Kb| 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. |
Posted in: Functional Annotation → Baseplate 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. |
Posted in: Cluster B Annotation Tips → Tail assembly chaperones?
| Link to this post | posted 19 Dec, 2022 21:18 | |
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Yep. |
| Link to this post | posted 13 Dec, 2022 02:04 | |
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2022 Genomics Workshop Participants, The genome we will annotate is Mycobacterium phage Ciao. Please add your annotation questions to this forum post. You will find Ciao in Phamerator and PECAAN. Be sure to identify the stop of the gene that you are interested in (it is the only unique identifier). Enjoy annotating! |
| Link to this post | posted 07 Dec, 2022 16:11 | |
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Working on Microbacterium phage Jefe at the 2022 Genomics Workshop! It is one of the members of this cluster where no slippery sequence can be identified. The upstream gene of the TAC pair has a Pfam hit to tail assembly chaperone, so call it. However, there is no data to support a tail assembly chaperone call for the second gene, NOR its there a slippery sequence present. that gene is a Hypothetical Protein. |
| Link to this post | posted 23 Nov, 2022 14:52 | |
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Hi Nikki, I think the Starterator picture shows that the 25523 is a best call. You can see it line up across different clusters/subclusters. I would call 25523. debbie |
| Link to this post | posted 18 Nov, 2022 02:45 | |
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Cluster GC genomes may have 2 capsid proteins. See the note at Cluster DC. https://seaphages.org/forums/topic/5430/?page=1#post-9831 |
Posted in: Cluster GC Annotation tips → 2 major capsid proteins
| Link to this post | posted 18 Nov, 2022 02:43 | |
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Cluster DE5 genomes may have 2 capsid proteins. See the note at Cluster DC. https://seaphages.org/forums/topic/5430/?page=1#post-9831 |
Posted in: Cluster DE Annotation Tips → 2 major capsid proteins