Link to this post | posted 07 Aug, 2017 16:26
welkin	Aug 2017. Full time position at a phage therapy company for a BS/MS with phage experience. Located in Gaithersburg, Maryland. Edited 07 Aug, 2017 22:09 87Kb

Link to this post | posted 03 Aug, 2017 15:18
welkin	Sure. I wonder if there is a way to shorten the name and remain clear.

Link to this post | posted 31 Jul, 2017 15:12
welkin	Hi Claire, I think we can add it back. We will just have to make a note that it should only be used if a more specific assignment can't be justified.

Link to this post | posted 31 Jul, 2017 15:11
welkin	Hi Jackie, I am not familiar enough with transposase classifications to know if LouisV14 meets all the criteria for the specific assignments you propose. Are there specific catalytic residues we have to look for? Or is the classification based solely on the architecture of the transposon?

Link to this post | posted 31 Jul, 2017 15:07

welkin

Hi Karen, I think we annotated the Cluster J phages in the paper before we started using HHPred regularly. It sounds like from your comments that you are suggesting that all of pham 1260 should be reassigned to ATPase domain, is that correct? The additional data of the other pham with the DnaB helicase assignment is interesting. Is there another DnaB helicase in any of the genomes? If that annotation is better supported, then perhaps 1260 should all be DnaB helicase, nad 1260 is a sequence variant that we haven't seen before.

Link to this post | posted 31 Jul, 2017 15:03
welkin	Sounds like it is not AlpA, and it is not likely to be excise either. I have tried to steer clear of names with just protein structures without any idea about what they do (so we don't say "alpha-helix protein", but "helix-turn-helix DNA binding protein" is OK). Do winged helix proteins all have similar functions? Or is this a structural motif found in a variety of proteins ?

Link to this post | posted 31 Jul, 2017 14:57
welkin	Thanks Dave– this is a really helpful analysis of a tricky protein. It sounds like the phage is using a multifunction replication protein like pRN1. I am going to check in with Graham and get an official answer.

Link to this post | posted 31 Jul, 2017 14:30
welkin	Nope. Post away!

Link to this post | posted 31 Jul, 2017 14:30
welkin	Hi JAckie, sounds pretty solid. Do you have any thoughts on what the official name be? I don't really like either just the alphabet soup or the full length Activating Signal Cointegrator - 1 transcriptional coactivation protein. ASC-1 transcription coactivator? IS that too long? Welkin

Link to this post | posted 21 Jul, 2017 15:30

welkin

Thanks for posting the data! Based on your HHPred results and the db entries, ocr is 119 residues long, your protein is more than twice that at 295. you also have an equally good alignment to part of a restriction enzyme in the same area at the ocr alignment. So my questions is, what do the restriction enzyme and ocr have in common? And yes, key residues in the right spot always help, but I don't think we are there yet.