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Cluster J and A repressor/ immunity repressor

| posted 14 Aug, 2017 22:43
In pham3247 (for example Kugel_77 there are calls for repressor and immunity repressor, but in the cluster J phages it appears to be called mostly as function unknown. It is pretty far on the right in the cluster J phages (Squint_188 ) that I called as a helix-turn-helix DNA binding domain. Without wet bench evidence in the cluster J's how should we be calling this? The best hit for the gene I am looking at right now is for an RNA polymerase sigma factor and then a number of HTH containg proteins. Ideas?

best, Dave
Edited 21 Feb, 2018 16:12
| posted 21 Feb, 2018 16:07
OK, these are not the same problem, so Allison, I am moving your post to a new thread. In general, unless you are looking at a phage in the exact same cluster, it is worth starting a new post —even if it seems like the same problem on the surface.

the issue with your phages is that you are looking at a Cluster J that appears to contain the immunity repressor of a Cluster A phage (Kugel is in Cluster A). The immunity repressor in cluster A is not adjacent to the integrase where it belongs, but way out in the right arm. So the immunity repressor in Squint is probably gene 90 (only found in Cluster J).
We have multiple instances of phages carrying around the Cluster A immunity repressor– in both Cluster C and Cluster J. So the correct name for Squint 188 is Cluster A immunity repressor.
This is such a weird thing that we didn't pick up on it right away when we started annotating all these, and so labeled it by the HTH DNA binding domain, which all immunity repressors have.
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