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Make reaction assignments to polypeptides classified in the "No match" category

asked 2019-10-02 04:50:04 -0500

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Hello,

I am working in the curation of a PGDB. I have found experimental evidence to assign a polypeptide to a certain reaction, which pathway tools has been classified in the "No match" category after running name_matching analysis.

The only way I have found is by using the gene Editor, assigning a new Reaction Frame to the gene. Is that correct?

Thank you so much

Beatriz

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Dear Suzanne, Finally, I have found how to do the manually assignment of proteins to a reaction, as you explained. At the begining I didn't know where to right-click. Thank you so much Beatriz

bcamara gravatar imagebcamara ( 2019-10-03 08:56:32 -0500 )edit

I'm assuming you figured out that you need to right-click on the protein name, not the gene name...

Suzanne Paley gravatar imageSuzanne Paley ( 2019-10-03 12:36:27 -0500 )edit

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answered 2019-10-03 03:45:30 -0500

bcamara gravatar image

Dear Suzanne,

Thank you so much for your promtp answer.

Following your instructions, I have tried the 2 ways you have proposed me:

  1. When I right-click on the reaction, I see two options: Edit and Show Edit only shows : - propagate reaction to DB - add object to smart table - copy frame name to frame editor - add object to file

I can not see the "Create/add enzyme" option

  1. When I look for the protein by string or id, pathway tools shows me the associated gene. When I right-click in the gene, I cannot see the options you indicate. These are the options that I can see:
  • Edit: - gene editor -isoform/coding-segment editor -add gene knockout growth information - frame editor -synonym editor - relationships editor -ontology editor - merge genes -export gene to db - add object to smartable -copy frame name to frame editor history - add object to file export list - create frame - delete Frame - Edit nucleotide sequence near gene

I was wrong when I told you about the gene editor. The way I have found to assign a new reaction to a gene is by right-click to gene, Edit/Create Frame/Reactions.

But I couldn't find neither of the options you have proposed me. Maybe, Am I missing something? Thank you so much

Beatriz

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When you are right-clicking on the reaction, I assume that is the reaction in MetaCyc. Other options won't appear in the Edit menu, because you cannot edit MetaCyc. You should first propagate the reaction to your PGDB. If you right-click on the reaction in your PGDB, you should be able to add your enzyme to it.

Suzanne Paley gravatar imageSuzanne Paley ( 2019-10-03 12:35:14 -0500 )edit
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answered 2019-10-02 12:38:06 -0500

Suzanne Paley gravatar image

Hi Beatriz,

There are 2 possible ways to manually assign a protein to a reaction. You can right-click on the reaction and select Edit -> Create/Add Enzyme, or you can right-click on the protein and select Edit -> Add Reaction(s) (additionally, if the protein is already assigned to a different reaction, you can add a reaction from the Enzymatic-Reaction tab of the Protein Editor, but that tab isn't present if the protein is not yet assigned to any reaction).

I'm not sure what you're referring to with respect to the Gene Editor -- I don't see a way to assign a reaction directly from there.

Suzanne

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Asked: 2019-10-02 04:50:04 -0500

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Last updated: Oct 03