Link to this post | posted 28 Jul, 2021 01:22
debbie	Hi Arturo, Sorry for the delay on this one. One of the hits is with HK97_gp10. This phage was well studied in the Hendrix lab here at Pitt, and they are have studied capsid proteins in depth. They could not determine what its function was, so I would not call it a minor capsid protein, and stick with Hypothetical Protein for now. debbie

Link to this post | posted 25 Jul, 2021 16:39
debbie	Hi Susan, You will likely have to delete the project and start again. Does DNA master let you do that? debbie

Link to this post | posted 21 Jul, 2021 22:38
debbie	Fred, I am just learning about the Uni-Prot-Swiss Protein database, and all data there is not the same. I don't think i have had any significant data reported from Scope, which is why i started using Uni-Prot. I feel like i am beta testing it for now. Try it out and see what you find! debbie

Link to this post | posted 20 Jul, 2021 14:44

debbie

Hi Fred, I HHPred'd Mach genes 5,6,7 (as found on phamerator). I would call all 3 as minor tail proteins. I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral. I did not use Scope. Because you are calling structural genes in cluster A, A2 in particular, I would want to be sure to not overwrite any historical data (that would include some bench work) that has been derived about well studied phages such as D29. When you include the HHPred results from the Uni-Prot database, you have significant hits to minor tail proteins. In addition, when you phamerator MaCh and Duplo together, gene 7 of MaCh hits gene 34 of Duplo, a much more canonical orientation for a minor tail protein. See what you think! debbie

Link to this post | posted 20 Jul, 2021 14:07
debbie	Hi. I think that this forum post will help. https://seaphages.org/forums/post/8693/ Let me know, debbie

Link to this post | posted 23 Jun, 2021 20:20

debbie

D29 was recently (2017) resequenced and found to have some discrepancies with the original published sequence. This sequencing project yielded 7 differences: D29 “wt" vs (D29 new!!!) 12442 (12433) 100% C to A 23910 (23901) 100% G to A 31726 (31717) 100% T to C 36667 (36658 ) 100% C to A 43657 (43648 ) 100% A to T 47438 (47429) 95% T to C 47936-47937 (47927-47928 ) 100% G addition The original sequence has the 3' overhang on both ends, so the overlap on the left end has been removed from the original sequence. It is going into GenBank with a length of 49,127. Numbering of genes and some gene calls have been made to coincide with published data. The numbering was an original attempt to keep genes numbered as they were in phage L5. There are instances where one might call additional small genes (<40 amino acids). We are choosing to stay consistent with the published literature. The papers to review for this cluster are numerous. Two stand out as relevant: Genome Structure of Mycobacteriophage D29: Implications for Phage Evolution (1998 ) and Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives (2017). Edited 23 Jun, 2021 20:22 2.04Mb 2.26Mb

Link to this post | posted 16 Jun, 2021 21:26

debbie

Simon White’s cryo EMs of mycobacteriophage Rosebush show that the MuF-like minor capsid is NOT part of the capsid. (SO do not call it.) He did find 2 different capsid proteins in RoseBush, one that makes the hexamer (gp 15) and one that makes the pentamer (gp16). These two capsid proteins are in all of the Cluster B genomes. See the SEA-PHAGES Functional Assignment Sheet for correct naming. Edited 06 Apr, 2022 17:42

Link to this post | posted 09 Jun, 2021 15:49
debbie	Steve, I think that Pitt servers were down for a bit this am. Here is the install download. https://www.dropbox.com/sh/ygbayg8zqy32wiq/AADM8F9-RXkkSYXVFA-hhhPza?dl=0

Link to this post | posted 03 Jun, 2021 23:49

debbie

I am adding a response from Chris Shaffer: I did a bit on this. Mostly on the question of nomenclature, not on the validity of the specific gene call. Because of this investigation, I am removing the DnaC-like helicase loader from the approved list. I also ran across this site in poking around the web which is kinda interesting site: https://proteopedia.org/wiki/index.php/DnaC_helicase_loader It says there are two types of helicase loaders: DnaC helicase loader (DnaC) transfers helicase to replication origins. The helicase loaders belong to two classes. The ‘ring breakers’ break the hexameric helicase to allow the DNA to pass through. The ‘ring makers’ assemble the helicase monomers to hexamers around the DNA. Here is a good paper that summarizes these two methods: https://pubmed.ncbi.nlm.nih.gov/12906810/ Unfortunately, there is a complication in that the E coli DnaC is a breaker type and the B subtilis DnaC is a maker type so we have a name crash. This is the kind of thing that makes it really easy to make mis-assignments and/or cause a lot of confusion. If we say "DnaC-like" do we mean the E coli or B sublitis version. So I would argue for this situation, the best solution is to update the terms list to just "helicase loader" and avoid the "DnaC like". I will note in my BLAST searches I found two Bacillus phage proteins that Veronique has published using the term "helicase loader" so she agrees with me.

Link to this post | posted 03 Jun, 2021 23:14
debbie	You are welcome!