Link to this post | posted 17 Mar, 2023 14:51

debbie

Nikki, That is not entirely correct. Some folks capture all of the slip in one region, where it is to be slipped between the 2 (meaning the annotation of the shared nucleotide occurs in the middle). Because the slippage happens around a lot of glycines, the sequence can look right but be actually annotated incorrectly. In this particular case, there are 2 predicted overlapping slippery sequences. The run of Gs and the canonical XXXYYYZ. In this particular case, I can't tell which one is used without some bench work. debbie Edited 17 Mar, 2023 16:07

Link to this post | posted 17 Mar, 2023 01:00
debbie	Nikki, Hi. Both choices produce the same protein sequence and unless the experiment is done to label the amino acids in the sequence, I don't think one is better than the other. There is no GN or GK decision, it is whether the second G in the final sequence of AGGK is in the first frame or the second. Does that make sense? debbie

Link to this post | posted 16 Mar, 2023 23:42

debbie

Ellen, Hi. There is no data that supports "secreted protein". I am not sure where that came from, but is no longer in use. when you run this protein through DeepTMHMM, it does have a single transmembrane domain, so "membrane protein" can be assigned to this protein. Note that when you look at pham data on phagesDB, you don't find "secreted protein" as a function call across the pham but the NCBI blast hits that do call it are from RefSeqs. So it appears that the RefSeq's at NCBI are not as current. Supporting data to a call will be present outside of blast if it is a true call (most of the time)> debbie

Link to this post | posted 14 Mar, 2023 19:33

debbie

Hi Ellen, I have attached a screen shot of my HHPRed. The significant hits are 1. e-27/ probability score of 99.9 to gp15 of D29 (sometimes there are hits to gp# that do not connect to a phage, but in this case, hitting the prototypic phage D29, I would recommend paying attention to it). gp15 of D29 is its capsid maturation protease (CMP). Additionally, i can be skeptical of any minor capsid hits, because many times it is hitting some component that i know is structural but can't tell if it is heads or tails. BUT, having said that, hitting minor capsid doesn't negate it being the CMP. Any hits to MuF are problematic. It does not appear to be structural (can't be found in come cryo EM that Simon White has done) and appears to always be part of something else. But never really hits the something else. But maybe MuF is Mu's version of the capsid assembly protein? Is there an instance of both MuF and CMP are present? I would easily call this gene capsid maturation protease. debbie

Link to this post | posted 13 Mar, 2023 18:34
debbie	I looked at this too and I agree with Nikki. there is not strong evidence that there is a gene here at all, but I'm inclined to call the gene with the 4 bp overlap. Interesting that in some genomes the sequence, though not identical, does have coding potential in that frame. It is a clear demonstration of how the math of coding potential prediction breaks down with small genes. debbie

Link to this post | posted 07 Mar, 2023 16:15

debbie

Hi Mitch and students, I would refer to the structures of phi29 and P68, both of which are prototypes for podoviruses. https://pubmed.ncbi.nlm.nih.gov/31147544/ https://pubmed.ncbi.nlm.nih.gov/31663016/ Last year, I took a close look at the podovirus PineapplePizza and thought I could apply the terminology of those papers to the gene hits. I quickly looked at the whole lot of genes in the vicinity and the only one that has a significant hit is 45. BUT, I couldn't quickly discern if it is a tail needle, tail knob, or collar protein. So i would want to think about this. Looking forward to what you come up with! Rick Pollenz (U of South Florida) and Simon White (U Conn) have worked out some of the structural proteins, finding the major capsid. Check with them to see if they have further identified any other genes. debbie

Link to this post | posted 06 Mar, 2023 23:43
debbie	Tiara, I can't tell what is gong on. Can they do everything else in DNA Master? Please provide a screen shot of the error. thanks, debbie

Link to this post | posted 06 Mar, 2023 18:56

debbie

Hi! there is some confusing that can be easily remedied. Syntenically, this gene is positioned to be the capsid maturation protease (CMP). "The herpesviruses and many phages utilize a maturation protease that acts in this transition from prohead to head, and the main function of the capsid protease is to degrade the parts of the prohead that are required for prohead assembly, but must be removed to complete maturation." So if we can find it, we want this gene's protein to have some protease function. The HHPred results hit minor head protein of SPP1, putative capsid assembly protein (likely another way of saying CMP), Phage Mu protein F like - which as per our approved function list is not anything we will call), and gp15 of D29 - which is D29's capsid maturation protease. Note that all of these are based on inferred calls. I am going to agree with the work of Hatfull and Hendrix, that they were satisfied to call this gene of D29 and L5 a capsid maturation protease some 30 years ago. I would assign this gene protein the function - capsid maturation protease. Best, debbie

Link to this post | posted 02 Mar, 2023 17:42
debbie	Thanks Chris.

Link to this post | posted 27 Feb, 2023 19:20
debbie	Hi Amy, We took Muf-like calls off of the official function list because it appears to not be a structural call and while is appears everywhere, we don't see a good indication of what it is doing. Please do not call it. Best, debbie