Link to this post | posted 10 May, 2020 21:17

debbie

Here is my rule of thumb on this. We used to always call the two genes upstream of TMP "tail assembly chaperones". Because we thought that all Siphoviridae had to have the programmed frameshift. That is no longer the case, so now we look for evidence that we are matching tail assembly chaperones (G and G/T). Protein "G" has a long history of being well conserved, so it can be somewhat easy to find hits. "T" does not. So I don't necessarily need to have a match to the second gene. HOWEVER, I would need to see a slippery sequence, connecting the "T" to the "G" to be able to call it. Therefore if the "G" protein has hits I will call it. If the "T" has no hits and I can't find a canonical 'slippery' sequence, I call the second gene a "Hypothetical Protein". Bottom line, I agree with Sally! I hope that helps, debbie

Link to this post | posted 10 May, 2020 18:51
debbie	Fred, Just make a note in your cover sheet when you submit. No worries. debbie

Link to this post | posted 08 May, 2020 03:00
debbie	Fred, That function that I would assign Hypothetical Protein to this gene. The evidence is not strong enough for me to assign any of the choices you have pointed out. debbie

Link to this post | posted 08 May, 2020 02:51
debbie	Ellen, I would call this gene. There is enough coding potential for me to think it is real. It is good that you ruled out the gene in the reverse frame. debbie

Link to this post | posted 05 May, 2020 03:20
debbie	Fred, I would not delete the circled gene on your attached doc. It is an orpham. That is great! debbie

Link to this post | posted 04 May, 2020 21:20

debbie

Fred, It may not have been called. truly. the auto-annotaion is done 'on the fly' by taking a sample of the sequence provided and using that to determine the nucleotide patterns. So that 'key' it creates to identify the orfs with coding potential is done each time GeneMark (or glimmer) is run. So there will be differences. when I ran the auot-annotation today, my output did not include it. I would look for it as I investigate the gap and call it because other auto-annotations see a wee glimmer of coding potential AND it has a 4 bp overlap with the next gene. make sense? debbie

Link to this post | posted 04 May, 2020 20:10

debbie

Jamie, Hi. The difference between blast hits and HHpred is based on blast and psi-blast results. So HHpred will always be a 'further stretch' to the function you want to call than a blast hit. The problem with Blast hits is, that the blast hit shows homology, but doesn't show credibility to what is said to be the function. So if someone mislabeled a gene function, it can easily be perpetuated. By all of that, I am not unhappy that blast confidence and HHPred do not match. I would call this gene a Hypothetical Protein because I don't know enough about DNA polymerases to know how necessary a sigma factor would be. Do you? I think the hits are to an RNA sigma factor? Does that fit? What does your expertise tell you about the collection of genes in the vicinity? Your insight would be appreciated! Thanks, debbie

Link to this post | posted 04 May, 2020 19:59

debbie

Fred, Not that weird. First of all, it was called in the auto-annotation, just not when you did it. (or how else did it get into phamerator?) So can auto-annotations differ? Can you explain how they can differ (if they can.) Second, it has weak coding potential. Weak is different than none. It also has homology of varying degrees across the genes that it matches. That could mean a couple of different things, - like it could withstand lots of changes and still function (and has been around for a long time), or it is really just falling apart. Regardless, I would call it. and assign Hypothetical Protein as its function. Again, this is an example of why we hand curate the genomes.

Link to this post | posted 04 May, 2020 11:17
debbie	Fred, Good choice! debbie

Link to this post | posted 01 May, 2020 20:16

debbie

Ellen, Historically, we called the capsid maturation protease based on synteny. We would like to have more evidence than that when calling it now. So it depends on which gene and phage genome you are talking about. However, to answer you question generally, if you have the evidence you describe above, you would record exactly what you said for the SIFs, and the function call would be Hypothetical Protein. If you let me know what gene/genome, i could be of greater help. debbie