SEA-PHAGES | Cluster DC - tail assembly chaperones

Link to this post \| posted 05 May, 2020 15:22
EWisner	My class is annotating Portcullis, a DC1 phage. We called Portcullis_Draft gene 27 (18088 - 18696 ) a tail assembly chaperone, but were uncertain whether or not to call Portcullis_Draft gene 28 (18693 - 19379) also a tail assembly chaperone. The reason we were considering it is because of other phages in our cluster, specifically RogerDodger. I noticed in PECAAN that RogerDodger has two genes in a row called tail assembly chaperones (#30 & 31). Our phages (Portcullis) seems to have very similar genes 27 & 28 in PECAAN. For gene 27, based on the BLAST result I agreed with my students that we should call it a tail assembly chaperone. For 28, I am less sure because there are far fewer BLAST matches. However, gene 28 is in the same Pham as RogerDodger's gene 31. I reached out to Sally Molloy about this, as she has been helping with my annotation questions, and her group annotated RogerDodger. I will post her response below, she suggested I post here to get more feedback from you all. Thanks! Ellen From Sally: This is a very good question! There is really no evidence at all that points to RogerDoger_31 being a tail assembly chaperone other than it is between the other chaperone and tape measure. Upstream of gp 30, others have called gp29 the other chaperone and at least it has hits to HK97 tail component gp10. I am wondering if gp29 should be called the tail assembly chaperone or if to be on the safe side we should only call one tail assembly chaperone. I am leaning on the latter decision.

Link to this post | posted 05 May, 2020 15:22

My class is annotating Portcullis, a DC1 phage. We called Portcullis_Draft gene 27 (18088 - 18696 ) a tail assembly chaperone, but were uncertain whether or not to call Portcullis_Draft gene 28 (18693 - 19379) also a tail assembly chaperone. The reason we were considering it is because of other phages in our cluster, specifically RogerDodger. I noticed in PECAAN that RogerDodger has two genes in a row called tail assembly chaperones (#30 & 31). Our phages (Portcullis) seems to have very similar genes 27 & 28 in PECAAN. For gene 27, based on the BLAST result I agreed with my students that we should call it a tail assembly chaperone. For 28, I am less sure because there are far fewer BLAST matches. However, gene 28 is in the same Pham as RogerDodger's gene 31.

I reached out to Sally Molloy about this, as she has been helping with my annotation questions, and her group annotated RogerDodger. I will post her response below, she suggested I post here to get more feedback from you all.

Thanks!
Ellen

From Sally:
This is a very good question! There is really no evidence at all that points to RogerDoger_31 being a tail assembly chaperone other than it is between the other chaperone and tape measure. Upstream of gp 30, others have called gp29 the other chaperone and at least it has hits to HK97 tail component gp10.

I am wondering if gp29 should be called the tail assembly chaperone or if to be on the safe side we should only call one tail assembly chaperone. I am leaning on the latter decision.

Link to this post \| posted 10 May, 2020 21:17
debbie	Here is my rule of thumb on this. We used to always call the two genes upstream of TMP "tail assembly chaperones". Because we thought that all Siphoviridae had to have the programmed frameshift. That is no longer the case, so now we look for evidence that we are matching tail assembly chaperones (G and G/T). Protein "G" has a long history of being well conserved, so it can be somewhat easy to find hits. "T" does not. So I don't necessarily need to have a match to the second gene. HOWEVER, I would need to see a slippery sequence, connecting the "T" to the "G" to be able to call it. Therefore if the "G" protein has hits I will call it. If the "T" has no hits and I can't find a canonical 'slippery' sequence, I call the second gene a "Hypothetical Protein". Bottom line, I agree with Sally! I hope that helps, debbie

Link to this post | posted 10 May, 2020 21:17

debbie

Here is my rule of thumb on this. We used to always call the two genes upstream of TMP "tail assembly chaperones". Because we thought that all Siphoviridae had to have the programmed frameshift. That is no longer the case, so now we look for evidence that we are matching tail assembly chaperones (G and G/T). Protein "G" has a long history of being well conserved, so it can be somewhat easy to find hits. "T" does not. So I don't necessarily need to have a match to the second gene. HOWEVER, I would need to see a slippery sequence, connecting the "T" to the "G" to be able to call it.
Therefore if the "G" protein has hits I will call it. If the "T" has no hits and I can't find a canonical 'slippery' sequence, I call the second gene a "Hypothetical Protein".

Bottom line, I agree with Sally!

I hope that helps,
debbie

Link to this post \| posted 11 May, 2020 11:06
smolloy123	Thanks Debbie! I am actually QCing another DC phage so Ellen's question and your answer helped me as well!

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Cluster DC - tail assembly chaperones