that makes sense, I was thinking it was something along those lines but I wasn't sure WHY they would use the notation ATP_base instead of Pi . I tried searching for v82 but that was the only part of the paper where v82 was mentioned. Thanks a lot for your help.
ATP = ADP + ATP_base? What is ATP_base?
I'm trying to manually convert a METATOOLS 5.0 model file into SBML format. I'm defining boundary species and the METATOOLS external species are marked simply as *_ext but in SBML format I must specify parameters for boundaryConditions which are explained here http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/Species.html
This makes sense to me, however, there is a reaction I can't decipher. Reaction from v82 Table 3.1, "ATP = ADP + ATP_base".
What is ATP_base? How can ATP produce both ADP and ATP? In the initial model file, there is ATP_main which I'm assuming is the main source of ATP generated by the cell. What is going on in this reaction?
I started reading Aaron Patrick Wlaschi's thesis but could not figure out what this reaction consists of and could not find his e-mail. If anyone is familiar with metabolism and knows the meaning of this reaction please help me out. Thank you
1 answer
Two pages after the stochiometry table (T 3.1) you are referencing in this question, there is a scheme of the model drawn out. If you look at this scheme (p. 46, F 3.1) you can see reaction R82, which corresponds to the stochiometry equation v82, which you are talking about. It's just the hydrolysis of ATP (ATP = ADP +Pi). ATP_base seems to mean inorganic phosphate here.
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