IGEM:UNAM-Genomics Mexico/2009/Notebook/H2/2011/04/04

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  • We are continuing our FBA analysis. We ran into some issues trying to understand the matrix we had (for R.etli), as the stochiometry was odd. The rate in the literature, as per EC, code is: 8 reduced ferredoxin + 8 H+ + N2 + 16 ATP + 16 H2O = 8 oxidized ferredoxin + H2 + 2 NH3 + 16 ADP + 16 phosphate. However, the rate we've found on the matrix is: (16) atp + (6) fdred + (16) h2o + n2 --> (16) adp + (6) fdox + (8) h + (2) nh4 + (16) pi. What troubles us is the fact that the stochiometry for the redox potential is odd. We sent a mail to the researcher who did the reconstruction (O.Resendis) and are awaiting reply.
  • In the mean time, we've decided to model our system in a Franken-critter fashion: we'll add the N2 pathway to the existing E.coli network, then add the H2 pathway and limit O2 uptake. Perhaps something interesting will happen, though this model is just to practice editing matrices within the COBRA toolbox.
    • We still don't know how to add a metabolite...
    • If O.Resendis doesn't have a MatLab compatible version of the stochiometry matrix, we might use the function parseRxnFormula.
      • Should the model prove extremely easy and our desires for glory extremely ambitious, we could use this [1].