Link to this post | posted 21 Jun, 2023 19:03
debbie	Sally Molloy (University of Maine, Honors College) has shown an in-depth investigation of what is needed to call a protein RecA. Attached is a doc with links to her Power Point presentation and her video describing her presentation. Edited 23 Aug, 2023 16:20 12Kb

Link to this post | posted 21 Jun, 2023 18:36
debbie	Maria, Thanks for sharing this. i hope others find it helpful. best, debbie

Link to this post | posted 16 Jun, 2023 14:30
debbie	If you are unsure of how to call the sigma factor, we recommend not calling it as such, instead use DNA binding protein.

Link to this post | posted 16 Jun, 2023 12:41

debbie

Cluster A phages can have tyrosine, serine integrases, or partitioning genes. For the serine integrates, see the note about Bxb1 starts. Serine recombinases are called jumbo integrases because their size hovers around 500 amino acids (can go up over 700 amino acids). Look for serine residues in the N-terminus. Historically we didn't differentiate serine integrases from tyrosine integrases. Ask for help if you can't tell which one is in your genome. Some Cluster A phages, (I believe the first one identified is RedRock) don't have an integrase, but exist as an extra-chromosomal inhabitant of a bacterial cell. In order to be propagated, a partitioning system is utilized. See this paper for details: Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol Microbiol. 2016 Aug;101(4):625-44. doi: 10.1111/mmi.13414. Epub 2016 Jun 10. PMID: 27146086; PMCID: PMC4998052.

Link to this post | posted 15 Jun, 2023 02:50

debbie

The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in? This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips. Hi all, This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments! debbie

Link to this post | posted 15 Jun, 2023 02:10
debbie	Kirk, This pham is quite messy. I would call the longest ORF and call the r-h-h for this one even though other members of this pham cannot call it. debbie

Link to this post | posted 15 Jun, 2023 00:33
debbie	I would call this a phosphoesterase too. debbie

Link to this post | posted 14 Jun, 2023 18:16
debbie	Please Read! https://pubmed.ncbi.nlm.nih.gov/24335314/

Link to this post | posted 07 Jun, 2023 23:30
debbie	Rick, I think that this version of TAC matches L5's -1 frameshift. https://seaphagesbioinformatics.helpdocsonline.com/article-54 G_GG.G_GA. Wanna check? debbie

Link to this post | posted 07 Jun, 2023 20:23

debbie

Lee, The confusing part of Kathleen's post is the sentence that states "But we don't understand why Starterator didn't call the most annotated start." But she is here today so we are able to discuss. The reason that Starterator doesn't make the right call is becuase it only reports what is in in the files submitted to phamerator. –Meaning in this particular case, Frankenweenie's auto-annotated is not what others ID'd as the best start to call. In fact, Kathleen and her students went to Starterator to justify making a change. That sentence in Starterator is to be coupled with the yellow line in the Frankenweenie graph and recogonized as in DRAFT form. What Kathleen and her students wanted was for Starterator to make the right call. Technically, it makes NO calls and just reports what was called (making human calls green and auto calls yellow).