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No reactions for this EC number are present in MetaCyc database

asked 2019-11-26 07:36:30 -0600

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Hi,

I work with a genbank file of atelocyanobacteria thalassa aloha. I have built the PGDB. After the 'matching of Enzymes to Reactions' step by the software, a more detailed list of all matching and non-matching enzyme names is saved to a file called ptoolslocal/ pgdbs/user/ORGIDcyc/VERSION/reports/name-matching-report.txt One of the genes has been placed into one of the sections of the file: Ambiguous Match. In fact, when I looked closer : the gene name is phosphate acyltransferase plsX and the EC number is 2.3.1.274.

The problem is : No reactions for this EC number are present in MetaCyc database.

How can I do ?

Thanks ! :)

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answered 2019-11-27 12:53:29 -0600

Suzanne Paley gravatar image

I'm not sure why you say that. EC# 2.3.1.274 corresponds to RXN-9590 in MetaCyc. I'm not sure what other reaction this assignment was ambiguous with, but the report file should list the possible matching reactions. Also, if you use the manual refinement step Assign Probable Enzymes and click on this gene, it should show you the possibilities and allow you to select the correct one (which is likely RXN-9590, I'm guessing).

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Asked: 2019-11-26 07:36:30 -0600

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Last updated: Nov 27