SEA-PHAGES | All posts created by EWisner

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.

Posted in: Functional Annotation → Cluster DC - tail assembly chaperones

Link to this post \| posted 29 Apr, 2020 20:34
EWisner	This question actually relates to all SIF documentation, not just HHPred. Let's say you have good evidence that something is a capsid maturation protease, but you don't get a good HHPred hit. And based on all of the evidence you have, you call it a "capsid maturation protease", how do you then document the SIF-HHPred information? Would it be: SIF-HHPred: NKF - No matches with other 90% probability SIF-HHPred: No matches with other 90% probability SIF-HHPred: capsid maturation protease - No matches with other 90% probability I guess my more general question is with SIF, even if the piece of information doesn't support your call, how to you list it. Thanks! Ellen

Link to this post | posted 29 Apr, 2020 20:34

EWisner

This question actually relates to all SIF documentation, not just HHPred. Let's say you have good evidence that something is a capsid maturation protease, but you don't get a good HHPred hit. And based on all of the evidence you have, you call it a "capsid maturation protease", how do you then document the SIF-HHPred information?

Would it be:
SIF-HHPred: NKF - No matches with other 90% probability
SIF-HHPred: No matches with other 90% probability
SIF-HHPred: capsid maturation protease - No matches with other 90% probability

I guess my more general question is with SIF, even if the piece of information doesn't support your call, how to you list it.

Thanks!
Ellen

Posted in: Notes and Final Files → SIF HHPred Notation

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