Link to this post | posted 14 May, 2022 16:54

kcornely

Greetings, all! We are finishing up Langerak and checking our functions. gp4 has hits to the capsid maturation protease as well as ClpP-like proteases. On the SEA PHAGES official function list, we are told that sometimes the capsid maturation proteases has hits to ClpP-like proteases and in the notes, we are told "sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity". gp4 in Langerak does have hits to serine-type endopeptidase activity. To me, the directions aren't clear: If there are hits to endopeptidase activity does that mean that it is a ClpP-like protease? Or is it not a ClpP-like protease and we should assign "capsid maturation protease" instead? Thanks for help! Kathleen

Link to this post | posted 28 Mar, 2022 21:31

kcornely

Greetings, all! If you have a choice of a start that provides a single initial Met, or a start three bases earlier that would result in the translation of a protein with two methionines at the N-terminus, is there a rule regarding which start site is the correct one? Looking at the BLAST data for this particular gene, some annotators went with one Met and others went with two. Thanks in advance for the help! Kathleen

Link to this post | posted 25 Mar, 2022 22:51

kcornely

Thank you, Steve and Debbie! We saw the pfam hit and it was one of the lines of evidence that convinced us that we should assign the function as a holin, but we didn't have convincing data that gp28 is a transmembrane protein. SOSUI classifies it as soluble, and TmmHm shows 0 predicted TMH. So thank you for letting us know that we should also be checking TOPCONS, which convincingly shows two transmembrane domains. In the future, we will check all three programs when we suspect a membrane protein. Thanks again!

Link to this post | posted 24 Mar, 2022 22:44

kcornely

Our team has a question on gp28 (pham 101034) of Langerak. We have a lot of evidence to assign its function as holin (synteny–follows lysins A and B, BLAST hits and HHPred hits), but according to the SEA PHAGES official function list, holins must have multiple transmembrane domains (which totally makes sense). But according to TmHmm and SOSUI, gp28 is soluble. Do we assign it as a holin? If we don't, is it all right to have lysin A and lysin B but not holin? We did notice that this protein is not assigned a function in closely related P1 cluster phages Donovan, Techage, Jebeks and HUHilltop. Thanks in advance for the help!

Link to this post | posted 17 Sep, 2021 19:39
kcornely	Hello all, I checked all of my preferences and they were exactly as Debbie's attachments showed, with the exception that I had checked "use active FTP protocol". When I unchecked the box, and then ran the auto-annotation after Debbie reported that GeneMark was back on line, it worked like a charm. Thanks for all of the help! Kathleen Edited 17 Sep, 2021 19:40

Link to this post | posted 15 Sep, 2021 23:52
kcornely	Thanks, Debbie! Unfortunately, I tried the auto-annotation again and it's still not working. I feel that maybe my Preferences aren't set correctly but I'm not sure what I'm doing wrong. Thanks for the offer of help; much appreciated! Kathleen

Link to this post | posted 15 Sep, 2021 19:29

kcornely

Greetings, all! I have a research student who is in the process of annotating a phage she discovered this past summer. When we did the auto-annotation, we got the genes called by Glimmer, but none called by GeneMark. We can get the GeneMark data from PECAAN, but it would be nice to have the GeneMark calls in DNA Master. We are running the most current version of DNA Master (5.23.6) and we set our Preferences to use the PBI server and we unchecked the boxes to the Glimmer and GeneMark servers. I am using a PC with Windows 10. I did have one question on the "Unlock Code" and "Password". The Word document shows an entry for the "Unlock Code" but "Password" is left blank. I tried it two ways (1) I entered the case-sensitive Unlock Code and left the Password blank and (2) I entered the same case-sensitive word in both the Unlock Code and Password. I got the same results both times–no GeneMark calls. As always, any help that anyone could provide would be much appreciated. Thanks, Kathleen

Link to this post | posted 21 Jun, 2021 22:33
kcornely	Chris, I hope that you had a nice visit with your sister. Thanks for the "whole page" Starterator report–I just downloaded it! I also had my student watch Kristin's video. Best wishes to you both, Kathleen

Link to this post | posted 21 Jun, 2021 17:21
kcornely	Kristin, we are accessing the reports through phagesdb, but I'd love to see your video! If we can't get the reports on phagesdb, we can go to PECAAN. I'm trying to wait as long as possible to introduce PECAAN because I want the new students to engage as much as possible with all of the other programs used in the annotation. Thanks!

Link to this post | posted 21 Jun, 2021 14:55

kcornely

Greetings, all, I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports? Thanks very much! Kathleen