Link to this post | posted 31 Jan, 2024 10:54
hnance@ccga.edu	Thanks for clarifying this. So we only need one domain identified by TMHMM to call a membrane protein? Thanks again! Holly

Link to this post | posted 30 Jan, 2024 16:57
hnance@ccga.edu	I'm having trouble finding another program besides TMHMM to run online to predict membrane proteins. I've got evidence of one domain with TMHMM, but it sounds like I need another prediction program to call this a membrane protein. I can't find how to access SOSUI online. Thanks! Holly

Link to this post | posted 29 Jan, 2024 10:42
hnance@ccga.edu	Thanks for looking into this! I will share the attached paper with my students as a great reminder for why we annotate. Thanks again! Holly

Link to this post | posted 26 Jan, 2024 20:41
hnance@ccga.edu	Hi Debbie, Thanks for the prompt reply. I understand that numbers won't match, and the stop is how they ought to be identified. But I'd never seen a gene number skipped in Phamerator. However, it sounds like it's not a big deal, so I will move ahead! Thanks again for your help!! Holly

Link to this post | posted 26 Jan, 2024 19:38

hnance@ccga.edu

Hi, It looks like Poultress is missing Gene 33 in the PhagesDB database. The draft genome in PhagesDB counts Gene 32 and the next is 34. Gene 34 in PhagesDB corresponds to the coordinates I have for Gene 33 (start 22659, stop 22994) in my autoannotation file. Is there a reason the database would skip a gene number? This skipped gene number (Gene 33) is missing in Phamerator, too. Thoughts? Thanks!!

Link to this post | posted 20 Jan, 2023 11:52

hnance@ccga.edu

Hi Debbie, Thanks for your prompt reply! Mopey_14 doesn't hit D29_16 in HHPred or BLAST, but it hits the same protein that D29_16 hits if you run D29_16 in HHPred (both Mopey_14 and D29_16 hit 6BOXG, which is a scaffolding protein). After asking my question yesterday, I had convinced myself that it was a silly question because Mopey_14 and D29_16 are not in the same phamilies. But it sounds like despite that, the structural homology warrants both being scaffolding proteins. So far, Mopey has several genes for which the function call is tricky as there is not consensus in the cluster. The timing of your meeting last Friday was great! Thanks again so much for your help - Holly

Link to this post | posted 19 Jan, 2023 16:37

hnance@ccga.edu

Hi, This function is on the Official List and the example to check is D29_16. This gene has no functional domains and the HHPred match is to 6BOXG (a scaffolding protein), probability 97.98%. In the phage we're annotating, Mopey, gene 14 has BLAST hits to scaffolding protein and the same HHPred hit to 6BOXG, probability 96.2%. In phage most similar to Mopey in cluster D1, this gene is most often called NKF. HHPred results for both Mopey_14 and D29_16 seem similar in their alignment to 6BOXG, and it seems the only compelling reason to not call Mopey_14 a scaffold protein is because most other D1 phage call this gene NKF. I guess I'm really considering the Bioinformatics meeting last Friday (1/13) and trying to not just call a function a certain way because that's what everyone else did. Is there a compelling reason to not call Mopey_14 a scaffolding protein? Thanks!!!

Link to this post | posted 17 Feb, 2022 00:15
hnance@ccga.edu	Can you suggest a format for students to use when referencing or citing their annotation in a CV or resume? Thanks!

Link to this post | posted 25 Nov, 2020 00:51
hnance@ccga.edu	Thanks so much for your insight here! I appreciate the help - Holly

Link to this post | posted 24 Nov, 2020 17:10

hnance@ccga.edu

Has anyone determined they had evidence to call a function as metallopeptidase, rather than metalloprotease? I asked Debbie and she gave this very helpful response: First, does your protein have the sequence to be able to call it a metallo-(whatever)? That sequence is HELGH The answer: Yes! it does: MGVRVRTAVTPNGWWGAYDHRRRLITLRPGLGPIQLKCTLMHELGHAHYGHTGVTGKQEALANRWAAYRLINFEDVLALASVEQSSSGVAAALEVMPDVLETYLQLLTRAQLGALRTAALSRVA From my quick reading, a peptidase is a particular kind of protease, specifically cleaving peptide bonds at the N or C terminus of a protein. Because we don’t know where it cleaves (and this is the part that I don’t know enough), I would stick with metalloprotease (because it includes the peptidases). I would be inclined to keep it a broader term, but if you can provide evidence that it contains a specific activity, metallopeptidase is not off the table. We thought this may be a good question to ask the forum - any additional insight would be appreciated! Thanks!