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Integrase makes a 4bp overlap with immunity repressor?

| posted 23 Nov, 2022 14:20
Hi all,

We are annotating DY cluster phage Tarzan; there are only 5 members of this cluster, of which only 3 (Santhid, JoJo24, and Reyja) have been manually annotated. I am looking at the tyrosine integrase (gene 31 in Tarzan), and having trouble weighing the evidence for the best start. In short, I can call a favored 4bp overlap with the immunity repressor (gene 32) OR I can leave a gap and choose the start with the abysmal RBS (which is know is common for integrase genes). Are favorable overlaps also seen between integrase and immunity repressor if they're right next to each other? I seem to recall that integrase usually has an upstream gap…

Some details: Starterator is not very helpful. Though there are 45 members of the pham, there is no real consensus; the most annotated start is only called 9/42 times (and only present in 22% of genes), and none of the phages in this cluster have it anyway. Within the cluster - which do look similar, but not identical - they all call different starts. However, while none of them called it, all 3 (Santhid, JoJo24, and Reyja) could have called a start that would've given a favorable 4bp or 8bp overlap with the immunity repressor. I've attached a summary of start options for each of these 4 genes (including Tarzan).

Any insight would be appreciated. I'm leaning toward the 4bp overlap, but something tells me that's a "no no" for an integrase.
| posted 23 Nov, 2022 14:52
Hi Nikki,
I think the Starterator picture shows that the 25523 is a best call. You can see it line up across different clusters/subclusters. I would call 25523.
| posted 23 Nov, 2022 16:17
Thanks, Debbie! I really just needed someone else to confirm this for me (or to tell me favored overlaps are a thing with integrases sometimes).

Abysmal RBS it is (and yes, it is the best conserved of the options, even though it's not always the one called)!
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