Link to this post | posted 14 Jan, 2023 01:18
debbie	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
debbie	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

debbie

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
debbie	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
debbie	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
debbie	I would keep this simple and call this a minor tail protein.

Link to this post | posted 19 Dec, 2022 22:29

debbie

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
debbie	Yep.

Link to this post | posted 13 Dec, 2022 02:04
debbie	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

debbie

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.