#40 EC:1.1.5.6

None
closed
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5
2013-10-24
2013-07-18
RFoulger
No

Hello,

Please could you create a RHEA reaction for EC:1.1.5.6/KEGG:R09494/MetaCyc:FORMATEDEHYDROG-RXN.

For mapping to my new GO term formate dehydrogenase (quinone) activity ; GO:0036397.

Let me know if you need any more information from me.
Thanks,
Becky

Discussion

  • Dear Becky,

    There is are several different reactions you can use.

    Rhea:29064 shows the reaction using 'a menaquinone'/'a menaquinol', and
    Rhea:29072 shows the reaction using 'a ubiquinone'/'a ubiquinol'.

    The MetaCyc:FORMATEDEHYDROG-RXN is cross referenced in Rhea:29072, while the KEGG reaction does not have any cross references in Rhea as it does not include the H+ transport in its reaction, so it is an oversimplification.

    It has until now not been possible to model 'a quinone'/'a quinol' in ChEBI which is the provider of chemical compounds for Rhea, as the quinones/quinols are simply too diverse.

    I hope you can use (one of) these two reactions for GO. If you need more help, please write back.

    Regards,

    Kristian

     
  • RFoulger
    RFoulger
    2013-10-24

    Thanks Kristian,

    I've created two new terms to map to the more specific Rhea reactions:
    formate dehydrogenase (ubiquinone) activity ; GO:0036444
    formate dehydrogenase (menaquinone) activity ; GO:0036445

    And moved the MetaCyc Xref FORMATEDEHYDROG-RXN to the new GO:0036445 term.

    We can create a union of Rhea mappings for the parent GO:0036397 term, so this SF item can be closed.
    Thanks,
    Becky

     
    • status: open --> closed
    • assigned_to: Kristian Axelsen
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