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Missing Pathways in PTools compared to Microcyc

asked 2020-05-10 21:19:18 -0500

QuellT gravatar image

Hi I am trying to look at the pathways in a number of bacteria with in a genus. When I import the GenBank file and run the pathway procedure It seems to miss things such as the TCA cycle but appears when I look at the organism via MicroScope - MicroCyc site. The Pathway Tools Version for that site is 16 where as I am using 23.5 Am I doing something wrong when importing the GenBank file?

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answered 2020-05-11 12:10:43 -0500

Suzanne Paley gravatar image

It's hard to say -- it depends a lot on how good the annotation in the genbank file is, though in general I'd be surprised if the TCA cycle wouldn't be predicted in any reasonably well-annotated genome. I don't know the details of the MicroCyc pipeline, but version 16.0 is 7 years old and there have been many changes to the software and data since then. Of course, I would expect those changes to have improved predictions, but I can't say for sure what is going on without looking at the genbank file. Can you find the TCA cycle enzymes in your genbank file, and are they annotated in a way that the software should be able to identify them as such (i.e. EC numbers or descriptive enzyme names)? If you want someone to take a look at a particular example, you should try submitting a support request to

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Asked: 2020-05-10 21:19:18 -0500

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Last updated: May 11

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