SEA-PHAGES | LO or insert gene in J cluster Beem

Link to this post \| posted 10 Nov, 2020 16:55
c.sunnen	Hi! While annotating cluster J phage Beem, I came across a spot where I could either insert a gene or pick a further upstream start site (it is reverse) to minimize the gap. This is gene 71 in Phamerator. The evidence supporting picking a further upstream start site is the fact that it has a lot of 1:1 hits when blasted, and it includes all the coding potential. However, inserting a gene between 71 and 72 is supported by the fact that it would allow for a 4 bp overlap (the gene is surrounded by genes with 4 bp overlaps). Also, it has multiple 1:1 hits, especially with phages (such as NihilNomen) that have been very similar to Beem, as noted throughout the annotation process. But, inserting the gene would cut off about 75 bp of coding potential for gene 71. Which piece of evidence should be weighted more heavily (coding potential or 4 bp overlap)? Thank you! (posted on behalf of) Christina Scanlon, a freshman at the University of the Sciences

Link to this post | posted 10 Nov, 2020 16:55

Hi! While annotating cluster J phage Beem, I came across a spot where I could either insert a gene or pick a further upstream start site (it is reverse) to minimize the gap. This is gene 71 in Phamerator. The evidence supporting picking a further upstream start site is the fact that it has a lot of 1:1 hits when blasted, and it includes all the coding potential. However, inserting a gene between 71 and 72 is supported by the fact that it would allow for a 4 bp overlap (the gene is surrounded by genes with 4 bp overlaps). Also, it has multiple 1:1 hits, especially with phages (such as NihilNomen) that have been very similar to Beem, as noted throughout the annotation process. But, inserting the gene would cut off about 75 bp of coding potential for gene 71. Which piece of evidence should be weighted more heavily (coding potential or 4 bp overlap)?

Thank you!

(posted on behalf of)
Christina Scanlon, a freshman at the University of the Sciences

Link to this post \| posted 11 Nov, 2020 20:57
debbie	Hi Christina and Nikki, I think I would first rely on the coding potential and call the longer version of 71. While I would likely fill in this space with genes of the 4 bp overlap variety when I didn't have compelling coding potential choices, i like the coding potential better here. While this may not help (but I haven't looked lately), there is a paper with mass spec for the genes of some of the Cluster J phages. I am sure if we had evidence of the 2 genes for the phages in that paper, we would have called them. From my quick glance, we did not. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273 debbie

Link to this post | posted 11 Nov, 2020 20:57

debbie

Hi Christina and Nikki,
I think I would first rely on the coding potential and call the longer version of 71. While I would likely fill in this space with genes of the 4 bp overlap variety when I didn't have compelling coding potential choices, i like the coding potential better here.

While this may not help (but I haven't looked lately), there is a paper with mass spec for the genes of some of the Cluster J phages. I am sure if we had evidence of the 2 genes for the phages in that paper, we would have called them. From my quick glance, we did not.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273

debbie

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LO or insert gene in J cluster Beem