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Immunity repressors in Cluster F

| posted 20 Feb, 2018 17:49
We have the same problem in our cluster F phage, QuickMath. Our gene (stop: 35,259) matches 100%, 1:1 alignment with Kimberlium_46 (function:helix-turn-helix DNA binding domain) and Bubbles123_42 (immunity repressor). E-values are also the same.

Any insight how to call this function?

Edited 20 Feb, 2018 18:00
| posted 21 Feb, 2018 16:12
Hi Allison,
Immunity repressors have HTH DNA binding domains, so this is why both terms show up in the pham. When we became more confident of the immunity repressor assignment, we switched the functional label in the newer annotations. This assignment is supported both by HHPred crystal structures, and by synteny– except for Cluster A, the majority of phage immunity repressors are found in this position in the genome relative to the integrase.

| posted 10 Jul, 2018 21:15
Hi. I'd like to ask for a bit of clarification here. I'm QCing MilleniumForce (another F1), and I've got 2 genes that both match to HTH DNA binding domains and immunity repressor when BLASTed. Both have pretty convincing HHPred data. Both are in the reverse direction. So my question is more about synteny. Which one is it? My options are (stop=34769) upstream and adjacent to Cro and antirepressor (both fwd), or further upstream than that by a few genes (stop=31573). I'm assuming it's the one directly adjacent to Cro?

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