EcoCyc cofactors

[Markus Krummenacker]

One of the things I promised was to send Jeremy a list of cofactors in
EcoCyc. Apparently, there are differences in meaning of the term. In
our usage, a cofactor is associated with the enzyme, and emerges
unmodified on the other side of a rxn, along with the enzyme.

In a detailed model, it makes sense to take cofactor requirements
into account, because in vivo, those rxns will only be traversed if the
enzyme has all its required cofactors.

Jeremy and I concluded that presumably the required cofactors
effectively end up in the "biomass" part of the cell.

Below is still a fairly raw list of those cofactors, from EcoCyc-9.0+
(we are close to a new release of data, within about a month).

Each of the following entries is a list that first lists the frame ID
of the cofactor, and then the rxn frame IDs that have some enzyme(s)
referring to the cofactor. Sometimes, the cofactor can actually be a
list, which means that any one of these will suffice.

Some cleanup is still needed. There are non-biological ions,
such as cadmium, which we probably should flag specially and not
include in a model.

In the first section of the list below, I would say these are "real"
cofactors. They are followed by a lot of references to what I would
think are really substrates in the rxn equation. In other words,
those "cofactors" do get converted to something else. I will ask our
EcoCyc curators to take a look at these.

There are some pretty weird strings that need to be analyzed, and
then there is also a long list of metal ions.

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Regards
Markus Krummenacker