Link to this post | posted 12 Aug, 2022 15:33
debbie	Hi Amanda, I see no clear evidence for calling this one anything but a Hypothetical Protein. (My best explanation for why some members of the pham are called terminase, small subunit is there was a moment in time when we thought we could call by synteny. But I would not recommend that today.) Best, debbie

Link to this post | posted 09 Aug, 2022 14:47
debbie	I guess I am going to weigh in as grateful for this post. We have a record and that will help as we go forward. For now, I am going to suggest that we do not add DPS family protein into the approved list. I would recommend that this protein be called a Hypothetical Protein for now. debbie

Link to this post | posted 05 Aug, 2022 15:45

debbie

Kathleen, I am going to answer that question. It is because once a function is identified, it gets propagated. Doesn't matter who said it, or what the supporting evidence is. For SMART, our focus this year has really been to work through these mis-identifications. So questions like yours will help us all get there. The best way to identify where the calls are difficult is to look at phams with multiple functional calls. We all need to work through the data and learn a little bit of structural biology/chemistry and biochemistry to make better decisions. Not always clear and we all bring a different understanding. And the answer to your question about phams is no, not all members in a pham will have the same function. Simplistically, I can see why we think that they should. But if we understand how a pham is built, then we would know that all things in the pham are not the same. A simple explanation is the one member may not have a 'domain' that another one has, so part of the gene is homologues, but missing a particular functional domain would imply that it has a different function. Maybe! An important component is that context is important. debbie

Link to this post | posted 02 Aug, 2022 01:07
debbie	Veronique, I just blasted one gene with no issues. there have been no changes in DNA Master for a while now. debbie

Link to this post | posted 02 Aug, 2022 01:04
debbie	Yep. You got it! debbie

Link to this post | posted 01 Aug, 2022 16:43

debbie

Hi Nick, Membrane proteins, especially those containing 1 transmembrane proteins, are tricky. Very much is dependent on how good the program used to call it is. We are formulating a plan to improve how this work is done, but it is still in process. In the meantime, here is the status of reporting transmembrane proteins. As it turns out, as Travis revamped the database that informs phamerator, he removed certain products because they were problematic. These include hypothetical, gp, orf, putative, and many more. Membrane protein was included on the list because of the 'iffy' nature of how membrane proteins are called. So what you describe is exactly correct. and unfortunately, a bit confusing. (Today we would make a different decision about this, but that is what we have for now.) Call membrane proteins to the best of your ability. Hopefully more news to follow soon. Best, debbie

Link to this post | posted 29 Jul, 2022 15:32
debbie	Hi Kristen, As of July 29, 2022, 11:30 am, auto-annotation is back up. debbie

Link to this post | posted 18 Jul, 2022 23:43
debbie	Fernando, Yes, the immunity repressor is called correctly in those genomes. And yes, that area is omitted in Caviar, so you most likely have a lytic phage. Likely a derivative a temperant one. debbie

Link to this post | posted 14 Jul, 2022 19:22
debbie	Hi Amanda, Here is thought, that may help. You can BLAST a subset of genes at a time in DNA Master. Here is the Bioinformatics Guide entry that explains: https://seaphagesbioinformatics.helpdocsonline.com/article-70

Link to this post | posted 07 Jul, 2022 23:46

debbie

Have you wondered what the settings for HHPred, NCBI-blastp, and CDD are used by PECAAN? The parameters that we run for HHPred are as follows: Hhsuitedb: "mmcif70/pdb70 NCBI_CD/NCBI_CD scope70/scope70 pfama/pfama", Proteomes: "", MsaGenMethod: "UniRef30", MsaGenMaxIter: "3", HhpredInclEval: "1e-3", MinSeqidQuery: "0", MinCov: "20", SSScoring: "2", AlignMacMode: "loc", MacThreshold: "0.3", Desc: "250", Pmin: "20", and Blastp from ncbi blast 2.13.0+ is ran remotely with -db nr -gapopen 11 -gapextend 1 -word_size 6 -threshold 21 -window_size 40 -evalue 0.05 -max_target_seqs 100 -outfmt 5 -remote and The CDD database is searched by rpsblast from ncbi blast 2.13.0+ with the following arguments -num_alignments=50 -evalue 0.01 7/7/2022 Edited 07 Jul, 2022 23:48