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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 2020-07-08 02:50:54 -0500

mdubois gravatar image

updated 2020-07-08 02:58:04 -0500

As Suzanne said, MicroScope currently uses an old version of pathway-tools (16.0). We are currently working on updating it and we also noticed that current versions (23.5) find less pathways. However, we think that the prediction of new versions is rather good so maybe version 16.0 finds too much pathways.

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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: Jul 08 '20

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