Link to this post | posted 21 Nov, 2018 12:15

debbie

Steve, I am usually reluctant to call that hit to the Pfam data. There is no primary evidence provided. I see that no transmembrane domains are found by TmHmm; Sosui calls 1 transmembrane helix. Can you explain that HHPred (at HHPred) reports a probability of 89.9% but is 34.6% in PECAAN? It is in a believable position in the genome (next to the lysins). Are there any other membrane proteins in the genome?

Link to this post | posted 13 Nov, 2018 17:50
debbie	Done!

Link to this post | posted 31 Oct, 2018 21:11
debbie	Kayla, I have been looking closely at the Cluster B1 phages. I concur with the genes being polynucleotide kinase and terminase. There is no evidence that a small terminase is present in the genome……yet. debbie

Link to this post | posted 31 Oct, 2018 14:17
debbie	Jordan, Hi. I would recommend that you not cite it independently, but rather consider it included in a citation for using the SEA-PHAGES Bioinformatics Guide and procedures. debbie

Link to this post | posted 28 Oct, 2018 14:40

debbie

Rick, Hi. You can find out which clusters of actinobacteriophages are predicted to be temperate by checking the cluster list. http://phagesdb.org/clusters/ There can always be exceptions, but the clues will be present in the genomes. My student researchers have been looking for lysogens by microbacterium phages for a while now. To date, we have one. It appears Zeta1847 forms lysogens. It is a M. paraoxydans phage. debbie Edited 28 Oct, 2018 14:41

Link to this post | posted 24 Oct, 2018 19:10

debbie

Hi all! Sometimes you may be looking for a reference genome and this might help. As of Sept., 2018 I am trying to clear the backlog of genomes and am attacking them cluster by cluster. Cluster B1s are on my list. As of today, October 24, 2018, I have QC'd 9 Cluster B1 phages to the best of my ability. I have cross-checked starts, respected Start-Associated-Sequences and addressed functions as well as I could. I will continue to bust through the list of whatever else is out there, but please use the following genomes as well scrutinized guides for your current/future Cluster B1 annotations: Altwerkus, Cannibal, Dione, Jillium, Keitherie, LuckyMarjie, Riggan, Spartan300, and Zelda. As I do more, I will add them to the list.

Link to this post | posted 21 Oct, 2018 13:18
debbie	Hi. Yes. Clustering is the same across the phylum. What strain are you using? I won't tell. debbie

Link to this post | posted 19 Oct, 2018 19:05
debbie	Claire, Good find! I would label it as Hypothetical Protein. Then I would write this note in the notes section of the DNA Master file and in the "Discovery Notes" of the phage page. We don't have an annotation field on the page page, so that is why I would put it there. debbie

Link to this post | posted 28 Sep, 2018 16:07
debbie	Terrific!

Link to this post | posted 18 Sep, 2018 20:58
debbie	The gene that has historically been called an RNAseE (gene 69 in Altwerkus) is a helix-turn-helix DNA binding protein.