Link to this post | posted 31 Aug, 2021 02:11
debbie	Hi all. Kristen is correct. We are aware of this issue and are working on it. debbie

Link to this post | posted 20 Aug, 2021 15:44
debbie	Yes. I think so.

Link to this post | posted 20 Aug, 2021 14:56
debbie	Hi! I think that this is the issue: If the 'Use PBI server…" is not on your screen, you still need to update DNA Master to continue. Be sure to update as an administer. debbie

Link to this post | posted 04 Aug, 2021 19:04
debbie	In addition to the terminase, large subunit in cluster J phages, they contain another gene (gp3 in Omega) that hits the N-terminus of terminase. Please refer to the Cluster J paper for further explanation of this gene call. https://pubmed.ncbi.nlm.nih.gov/23874930/

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