Ferredoxin issues

[ReelGrrl1]

Hi all, I have tried a bunch of times to enter a half-reaction into the eQuilibrator query box without success.

The reaction I'm trying to enter is

Succinyl-CoA + 2 e- + CO2 = 2-oxoglutarate + CoA

I'm trying to get the free energy for this reaction using alternative ferredoxins with odd midpoint potentials and I think eQuilibrator has a feature for half-reactions where you can specify the midpoint potential of the electron donor (weird ferredoxins with weird midpoint potentials in my case).

I've tried every possible permutation, and also pasted some of the half-reactions written out on the eQuilibrator page ( ½ H₂ ⇌ H⁺ + e^-   as well as 

Pyruvate(aq) + CoA(aq) ⇌ Acetyl-CoA(aq) + CO2(aq) + 2e^-

and these don't work either.  Anyone had any success entering half-reactions so they can get to that cool interface where you can adjust the electron midpoint potentials?  

The FAQ includes the example above (for pyruvate oxidation), with a link that takes you directly to this sort of interface where you specify the redox potentials of the electrons, but I can't seem to get to this interface by entering reactions into the query box on the eQuilibrator webpage!

Anyone had luck entering half-reactions?!?

KT

[Elad Noor]

Hi KT,

I think the problem you encountered is a bug caused by the explicit use of "e-" as a reactant.

Could you try writing the half-reaction without the electrons:

Succinyl-CoA + CO2 = 2-oxoglutarate + CoA

Best,

Elad

[ReelGrrl1]

Totally fixed it!!!! Thank you!!!

[Elad Noor]

Hi KT,

Another quick update, I fixed the bug where using "e-" in the prompt caused the website to crash.

Now if you have electrons in the formula, they will be processed correctly, and a suggested link to move to the "half-reaction" interface would appear at the top of the page.

You can already test this now on the website, e.g. using this query:

Oxaloacetate + 2 e- = L-malate

If there are any remaining bugs or new ones, please use this gitlab "issue" to follow up on this. 

https://gitlab.com/equilibrator/equilibrator/-/issues/78

Cheers,

Elad