Reference set of Captain YR Recombinases

[Adamtaranto]

Hi Emile,

I'm looking for a minimal curated set of Captain AA sequences that represent the diversity of YR recombinases across all 11 Starship families.

Looking at YRsuperfamRefs.faa there are 1222 AA sequences with a wide size distribution from ~200 to ~3000 AA.

Is this the dataset that you used for the Captain phylogeny in the Starfish paper? or does it contain other non-Captain recombinases?

If these are all Captains from predicted Starships, were they annotated with MetaEuk? Could the variation in length be due to some of the CDSs being truncated but still including the DUF3435 domain?

[egluckthaler]

Hi Adam, sorry for the delay. Great questions. The 1222 YR sequence dataset was indeed used for the captain phylogeny in the starfish paper. Due to a lack of available "captain" sequences at the time, it mostly consists of metaeuk predicted sequences. Variation in length is almost certainly due to truncated CDSs that still contain the relevant DUF3435 domain.

I've extracted here the 3 outgroup Crypton sequences and the 25 validated captain sequences that were included in the captain phylogeny in case they are helpful for you. I also included a set of sequences with 1 captain representative from each family that we have been using for some projects. We do really need to eventually make a minimally curated set with multiple verified captains from all 11 families.

family_reference_captains_YR.faa.txt

cryp3_cap25.faa.txt