SEA-PHAGES | All posts created by hnance@ccga.edu

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 19 Jan, 2023 16:37

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!!!

Posted in: Functional Annotation → Scaffolding protein

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!

Posted in: Annotation → In Genbank

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

Posted in: Functional Annotation → Metalloprotease or metallopeptidase

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!

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!

Posted in: Functional Annotation → Metalloprotease or metallopeptidase

Link to this post \| posted 07 Feb, 2020 18:38
hnance@ccga.edu	Was Starterator just updated? I cannot find any Starterator data for genes that are not orphams. Should I just wait a day to have it updated? All was fine until about 30 minutes ago. I'm not sure how to check my gene list to see if it is up to date as suggested in these other posts. Thanks!

Posted in: Starterator → Pham not found in Starterator

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