Link to this post | posted 23 Feb, 2023 01:14

debbie

Hi Allison, Minor tail proteins are the most common functional assignments that are acceptable to call with no CDD or HHPred supporting data. The genes that are "eligible" are the 4-6 large genes downstream of tape measure. I would not make the assignment if the gene is not a relatively big gene. In the case of Kyle's question, there is discrepant data that contradicts a minor tail protein call - synteny and HHPred hits. Best, debbie

Link to this post | posted 17 Feb, 2023 20:24

debbie

Hi Kyle, Well, this is quite messed up, isn't it. I will investigate further. in the meantime, I would like to provide what I think of BLASTp functions calls at NCBI, i don't value them very much - not without supporting evidence. So if you continue to investigate, there is no supporting data for a minor tail protein except NCBI said so. there is no way that a functional call can be made from the blast data that HHPred data sources does not support. (HHPred does a Psi blast, so it is finding more distant relationships to a protein than a single blast could.) Looks like this is a terminase, small subunit to me. debbie

Link to this post | posted 13 Feb, 2023 13:45

debbie

Amanda, This answer is all about context. I don't know the answer with the information provided. Look at the whole genome. What makes sense? Now that we know that N terminal hits can be signal proteins, i think where in the gene the membrane protein is found impacts my thinking. Just because we moved to Deep THHMM doesn't mean you can't use other tools to continue your evaluation. In general, keep it simple. Membrane proteins are not functions. And when Phamerator gets this in place, the data is not lost. debbie

Link to this post | posted 12 Feb, 2023 23:19
debbie	Rick, For now, I would call the big overlap, which I assume is the way that Survivors was called. Let's continue to consider the Guiding Principles as guidelines. debbie

Link to this post | posted 08 Feb, 2023 03:15
debbie	Amanda, I vote for not calling any TACs. debbie

Link to this post | posted 03 Feb, 2023 20:19

debbie

From HHPred, this gene hits HK97_gp10, a minor capsid protein and a tail protein. So one must ask which is it? HK97 is the prototype phage for understanding how the capsid is formed. The lab that studied it was the lab of Roger Hendrix, from the University of Pittsburgh. As we hit gp10 of HK97, I asked if they knew the function of that gene and they could not identify it in their studies. As per the Approved Function List, when you hit HK97_gp10, stick with Hypothetical Protein until someone finds more data to support a call.

Link to this post | posted 02 Feb, 2023 00:09
debbie	My advice is to ask the IT administrator to set the preferences. Whatever they do, should stick. debbie

Link to this post | posted 29 Jan, 2023 21:50
debbie	Hi Robert, Please check you DNA master preferences and make sure you follow #2 and #6 correctly. https://seaphagesbioinformatics.helpdocsonline.com/article-66

Link to this post | posted 26 Jan, 2023 23:45
debbie	Nope, not yet. all help is welcome! debbie

Link to this post | posted 20 Jan, 2023 15:37
debbie	Holly, Exactly! You've got it! debbie