Link to this post | posted 14 Mar, 2023 19:01

EWisner

Hey all, I am working on annotating the phage Culver (CQ1) and I am having a bit of difficulty confirming the putative function of the gene with the stop codon at 12727 bps. The BLASTp shows results that have a mix of functions between MuF-like minor capsid protein, head maturation protease, and hypothetical protein. For the MuF-like minor capsid protein, the official function list says that it should be called a hypothetical protein. HHpred only has one match that is viable which is labeled as “Gene 15 protein” further showing the gene in Culver is likely to have no known function. For the head maturation protease, none of the other programs used showed evidence of this function for the Culver gene. I am leaning towards calling the Culver gene a hypothetical protein but I wanted a second opinion if possible. Any help will be greatly appreciated!

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 18 May, 2023 16:37

dane.bowder

Hi all- I am running into the same problem with BearBQ gene 4 (stop coordinate is 4232). I am seeing the same mix of MuF-like minor capsid protein (I know to ignore this from the approved functions) and capsid maturation protease in other phages, but I am just not seeing the evidence for the latter. Our only HHPRED hits with E values worth anything are both MuF minor capsids. Seems like maybe this should be an NKF in spite of all of the other phages that have a function called?

Link to this post | posted 31 May, 2023 22:01
debbie	Hi Dane, Sorry for the delay in this response. I WOULD call this a capsid maturation protease because of the hit to the UniProt hit to gp 15 in D29. Probability and Evalue is great and these gene functions were assigned by Drs. Hatfull and Hendrix back in the day. It is also in the right place and is involved in capsid assembly. debbie. BTW, i hit no MuF proteins. debbie

Link to this post | posted 31 May, 2023 22:18
dane.bowder	Interesting Debbie- I see what I did wrong. We weren't running UniProt as part of our HHPRED runs, we were using SCOPE instead. I still don't see it in PECAAN. We ultimately did call it an NKF but noted it on our cover sheet. Thanks for the response!

Link to this post | posted 31 May, 2023 22:31
debbie	What you did was not wrong. It is good we do things different, though it may seem confusing. I look for the most basic structural genes in every phage and when I am missing what I expect to find, I just look elsewhere. debbie

Link to this post | posted 15 May, 2024 19:03

dane.bowder

Another year, another question about this function. We are finishing up HubbaBubba and are looking at Gene 25 (13776 is the stop site). This time I am seeing our hit to gp15 from D29 again, as well as the infamous MuF hits. However, with this particular gene, D29 gp15 is only hitting a small part of our gene (aa 288-395), but the E value (2.9e-16) and probability (99.75) are incredibly solid. Would you still call this a capsid maturation protease in this case? Based on this post from last year, I would, but want to make sure it isn't a situation where not enough of the gene is hitting. I also don't see another capsid maturation protease in other CR4 phages, but most of them call this MuF-like minor capsid protein. Let me know!

Link to this post | posted 15 May, 2024 23:13
debbie	Hi Dane, From the HHPred results, because of the limited nature of the hits, i would not call anything at this time. best, debbie

Link to this post | posted 16 May, 2024 19:50

fogartym1

Similar question here - PotPie: Gene 6 start 4858 , some evidence for minor capsid protein but unsure whether to call: The function list states ‘ "capsid morphogenesis protein" sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity. A significant hit to the CMP of D29 and L5 is sufficient evidence. We have a HHPred hit to D29 but not L5. https://toolkit.tuebingen.mpg.de/jobs/capsid 195/275 aligned P = 100 % Identities: 17%, Similarity: 0.223. Leaning towards NKF based on the low amino acid similarities/ Thanks Marie

Link to this post | posted 16 May, 2024 19:58
dane.bowder	debbie Hi Dane, From the HHPred results, because of the limited nature of the hits, i would not call anything at this time. best, debbie Awesome- thanks Debbie!