Link to this post | posted 01 Mar, 2018 17:03
welkin	Lucky annotators of Cluster B phages are off the hook for adding frameshifts to their annotations, as we have not yet been able to identify which genes are the tail assembly chaperones in Cluster B.

Link to this post | posted 01 Mar, 2018 22:31
scaruso	We have looked very closely on all our Strep. phages (BG, BH, BI, etc.), and couldn't find them. I'm glad it's not just us. But we'll keep looking!

Link to this post | posted 02 Mar, 2018 15:17

lhughes

Steven Caruso We have looked very closely on all our Strep. phages (BG, BH, BI, etc.), and couldn't find them. I'm glad it's not just us. But we'll keep looking! Steve - Be careful not to confuse "B" cluster with the double letter "BB,BG" etc. clusters. Welkin is talking about just the Cluster B phages in this topic. Several of the Streptomyces-associated clusters have the Tail assembly chaperone frameshift (including Clusters BC, BD, and BL). Lee

Link to this post | posted 02 Mar, 2018 16:08
welkin	Yep– this thread is just about Cluster B, which currently only has Mycobacterium phage members.

Link to this post | posted 02 Mar, 2018 16:50
scaruso	Well, I inadvertently expanded it to other clusters that are missing them, I apologize. But it is an interesting problem we have run into. We didn't see them in our BG phage, and haven't found them in any of our BI(2 or 4) phages. Steve Edited 02 Mar, 2018 16:58

Link to this post | posted 16 Apr, 2018 17:13
ClaireRinehart	Welkin, So, you are implying that we should not call any gene as a Tail Assembly Chaperone at this point in the B1 Cluster? If we can call genes that match tail assembly chaperones in other B cluster phages, how many can we call, I see some with one, some with two, and some with none? Edited 16 Apr, 2018 17:15

Link to this post | posted 18 Apr, 2018 15:58
welkin	I think we should be conservative here and not call anything. I have seen some BLAST results between Bs and other clusters, but the gene organization is not conserved: that is, the genes in Bs with BLAST hits don't have a downstream ORF with a substantial overlap in a different frame. There is something else going on in these phages.

Link to this post | posted 19 Dec, 2022 21:36
afreise	As of Dec 2022 I see many calls for a (single) tail assembly chaperone gene in B1 phages, so I assume sufficient supporting evidence has been found to make this call - but I'm not sure what it is? I have attached a screenshot of the HHpred results for Usavi_25. https://phagesdb.org/genes/Usavi_CDS_25/ Edited 19 Dec, 2022 21:39 140Kb

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 24 Jan, 2023 00:21

afreise

Hi Debbie, I looked further into Usavi_26 using the paper you sent. I summarized my results in the attached PDF. Basically, I think Usavi_25 should be NKF for now, and I'm still torn about Usavi_26. The Pfam hit wasn't very good e-value-wise, but I think I'm seeing some potential alignment in secondary structures? I'm not very confident in calling it a TAC at this time given the weakness of this hit, but it IS also two genes upstream of the TMP… Thanks, Amanda 338Kb