Link to this post | posted 26 Mar, 2019 13:42

jawsWPI

What current official function should be assigned to this pham in Rachaly and other drafts? Lokk has called it a “DNA binding domain protein”, CRB1 calls it a putative Rep protein. The research I have done suggests a best fit to “helix-turn-helix DNA binding domain". I know that Debbie (et.al.?) were going to start investigating this gene and the Par system genes in Lokk and Rachaly back in 2017. Do you have any results that would give us the answer to this question?

Link to this post | posted 26 Mar, 2019 14:03
welkin	Hi JoAnn– what is the gene number and/or coordinates in the current Phamerator draft? Pham numbers can change when we update the database and I just want to make sure I am looking at the right gene.

Link to this post | posted 26 Mar, 2019 15:15
jawsWPI	Lokk gene 36 (26423 - 27289 ) | pham 23651 Rachaly_Draft gene 36 (26457 - 27356 ) | pham 23651 Both are reverse genes. Right now there are only 5 members in the pham; two subclusters (A2 and A14); Lokk and CRB1 are the only non-draft genomes. Edited 26 Mar, 2019 15:24

Link to this post | posted 26 Mar, 2019 18:43
welkin	Hi JoAnn, So this protein is being investigated at the bench by one of the Hatfull Lab postdocs, Katie Wetzel. It is a "RepA-like replication initiator" and I will add that to the official list. Thanks for asking!

Link to this post | posted 26 Mar, 2019 19:01
debbie	Cool!

Link to this post | posted 11 Jun, 2020 21:25
cdshaffer	as the pham number is likely to change, here is the link to the Lokk gene 39 to check the current pham number: Lokk_CDS_35 P.S remember gene numbers can change by annotation and whether you are counting tRNA genes as well as protein genes. so confirming genes by coordinates is always recommended.