Table 2.

Reaction file

Reaction	Input species		Output species		Rate constant
1	− 1	0	3	0	0.1930
2	3	0	2	0	0.0007
3	3	4	5	0	0.0148
4	5	0	3	4	1.6733
5	5	6	7	0	0.2681
6	7	0	5	6	0.0809
7	− 23	0	8	0	0.0400
8	8	0	9	0	= k7
9	9	0	10	0	= k7
10	10	0	11	0	= k7
11	11	0	2	0	0.0400
12	3	12	13	0	1.5478
13	13	0	3	12	0.0416
14	13	− 20	12	14	0.0226
15	5	12	15	0	= k12
16	15	0	5	12	= k13
17	15	− 20	12	16	= k14
18	14	17	18	0	0.4738
19	18	0	14	17	0.1392
20	18	0	17	0	0.2144
21	4	14	16	0	= k3
22	16	0	4	14	= k4
29	6	16	22	0	= k5
30	22	0	6	16	= k6
31	− 7	− 22	0	23	c23=c7+c22
32	− 11	0	12	0	0.0400

These files (Tables 1 and 2) were used as input for the simulations shown in Figure 7B. The numbers under the columns headed input species and output species correspond to the reaction identifiers (underlined numbers in Figure 2A). The number preceded by “c” refers to the concentration of that species. A minus sign before a species identifier number flags the program not to decrement that species during the reaction. It is used when a species concentration, such as oxygen, is to be held constant. An equal sign in the right-most column signals the indicated linkage of rate constants. The rate constants shown here are similar to k-set3 in Table 3, with k7-11 and k32 all set equal to 0.04 (see Figure 2A).