Reactions not found in MetaCyc

asked 2019-11-18 03:47:48 -0600

This post is a wiki. Anyone with karma >75 is welcome to improve it.

Hello!

I am starting working on MetaFlux with my PGDB. After running MetaFLux in Development Mode, I have looked through the file.log and I have seen that there are many reactions that are blocked because of a nutrient (Co2+). I have seen that there are no transporters assigned to this nutrient. But one of the transporters that is probably present in my PGDB is not present in MetaCyc. What can I do? Is it possible to add this transporter and corresponding reaction to MetaCyc?

Thank you very much

Beatriz

answered 2019-11-18 13:04:32 -0600

waikit
1

updated 2019-11-18 13:22:18 -0600

Suzanne Paley
329 ●2 ●6

Hi Beatriz,

Reactions shouldn't be blocked by adding nutrients. Is Co2+ a biomass metabolite in your .fba file? Did you use the "transport-all" keyword under the "reactions:" section to also include all transport reactions from your PGDB in the MetaFlux model? Check your .log file to see if you can find your transport reaction for Co2+. If it is not there, you have not included it. If it is there, there may be additional information telling you whether that reaction is problematic (e.g., unbalanced). The transport reaction does not have to be present in MetaCyc for MetaFlux to work.

If none of these helped, please send the .sol and .log files to ptools-support@ai.sri.com and we can have a closer look.

Regards, Wai Kit

edit flag offensive delete link

add a comment

Your Answer

Please start posting anonymously - your entry will be published after you log in or create a new account.

Add Answer

Pathway Tools Question & Answer forum for SRI's Pathway Tools

Reactions not found in MetaCyc

1 Answer

Your Answer

Question Tools

Stats

Related questions

Pathway Tools Question & Answer forum for SRI's Pathway Tools

Reactions not found in MetaCyc edit

1 Answer

Your Answer

Question Tools

Stats

Related questions

Reactions not found in MetaCyc