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

Link to this post | posted 05 Jul, 2022 18:26
debbie	June 21, 2022 Rick Pollenz and Simon White have confirmed (experimentally) that Akoni_gp33 (Cluster EK) is the major capsid subunit! Please annotate! The homolog in Cluster EM is Burro_gp29.

Link to this post | posted 17 Jun, 2022 13:31

debbie

Hi all, As of today, June 17, 2022, there are 88 Cluster EE genomes in our records. They are closely related genomes that contain only ~28 genes. In an effort to make the records congruent, my students and I have reviewed ~75 of them and revised 71 of the records. The template we used is attached here, along with a list of 71 records that we touched. We spent an abundant amount of time on the helix-turn-helix DNA binding proteins at the right end of the genome. We investigated 'types' of helix-turn-helix choices and decided the best path is to call them helix-turn-helix DNA binding proteins. August 23, 2022 - I just received word that the genomes that we sent to GenBank have been processed. This cluster just might have congruent calls! Edited 23 Aug, 2022 16:13 74Kb 12Kb

Link to this post | posted 16 Jun, 2022 18:05
debbie	Kathleen and Chris, After reading Chris' entry, he is right -the slippage called in Satis, though it looks very slippery, is not canonical, i.e. not found in the literature. To that end, if we indeed are not calling any of the slippages, I would be inclined to NOT assign the function of a tail assembly chaperone (because there is no HHPred evidence of a TAC) unless I overlooked something.

Link to this post | posted 16 Jun, 2022 17:52

debbie

I just looked at the tail assembly chaperones of Cluster BM. Here is my take: currently there are six members: Satis Kradla EhyElimyoE JustBecause Kela Frankenweenie To the best of my knowledge none of the protein sequences in question here show an HHPred hit to a tail assembly chaperone (TAC). In order to call them TACs, if they possessed a canonical slippage, they could be called TACs and the slippage would be annotated. The ribosomal slippage found in Satis looks great, AND is identical to what is in Kradal and EhyElimyoE (though they are not called….. yet). Neither JustBecause or Kela have that same slippage. And Frankenweenie doesn't look at bit like the others in the c-terminus. (do a blastp - sequence alignment with Satis_58 and you will see how the alignment falls apart. However, the sequence homology with Satis is compelling. i would be inclined to call both genes TACs, but do not slip them together. I think that is what I would do. Good luck! debbie

Link to this post | posted 16 Jun, 2022 16:37
debbie	Welcome!