Here is a sample of the data I collated for Actinobacillus_pleuropneumoniae_L20_(416269.5). This data is for the compound C00025, which is L-Glutamate.  Only the first 6 reactions are shown; there are about 150.

C00025:R00021:
Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis     Ferredoxin-dependent glutamate synthase (EC 1.4.7.1)            1.24
cAMP_signaling_in_bacteria      Ferredoxin-dependent glutamate synthase (EC 1.4.7.1)            0
Gamma-aminobutyrate_(GABA)_shunt        Ferredoxin-dependent glutamate synthase (EC 1.4.7.1)            0
Photorespiration_(oxidative_C2_cycle)   Ferredoxin-dependent glutamate synthase (EC 1.4.7.1)            -1
Ammonia_assimilation    Ferredoxin-dependent glutamate synthase (EC 1.4.7.1)            0
C00025:R00093:

C00025:R00114:
Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis     Glutamate synthase [NADPH] small chain (EC 1.4.1.13)            1.24
Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis     Glutamate synthase [NADPH] large chain (EC 1.4.1.13)            1.24
Iron-sulfur_experimental        Glutamate synthase [NADPH] small chain (EC 1.4.1.13)            0
Iron-sulfur_experimental        Glutamate synthase [NADPH] large chain (EC 1.4.1.13)            0
Ammonium_metabolism_H._pylori   Glutamate synthase [NADPH] large chain (EC 1.4.1.13)
YgfZ    Glutamate synthase [NADPH] small chain (EC 1.4.1.13)            0
Ammonia_assimilation    Glutamate synthase [NADPH] small chain (EC 1.4.1.13)            0
Ammonia_assimilation    Glutamate synthase [NADPH] large chain (EC 1.4.1.13)            0
CBSS-155864.1.peg.3753  Glutamate synthase [NADPH] small chain (EC 1.4.1.13)
C00025:R00239:
Proline_Synthesis       Glutamate 5-kinase (EC 2.7.2.11)        fig|416269.5.peg.849    1
Iojap   Glutamate 5-kinase (EC 2.7.2.11)        fig|416269.5.peg.849    0
Proline,_4-hydroxyproline_uptake_and_utilization        Glutamate 5-kinase (EC 2.7.2.11)        fig|416269.5.peg.849    1
CBSS-316058.9.peg.23    Glutamate 5-kinase (EC 2.7.2.11)
YggW    Glutamate 5-kinase (EC 2.7.2.11)        fig|416269.5.peg.849    0
PROSC   Glutamate 5-kinase (EC 2.7.2.11)        fig|416269.5.peg.849    0
C00025:R00240:

C00025:R00241:

…

In the data you can see examples of positive variant counts, negative variant counts, zero variant counts, and reactions that don’t exist in the genome.

The data eventually ‘simplifies down’ into:

C00025: 1.02    0.0001  2.03    2.01    0.0001  0.0001  …

Looking at the first reaction(1.02) the total gets +1 for the first subsystem ‘Glutamine,_Glutamate..’. It gets a +0.01 for the next subsystem ‘cAMP_signaling’.  Nothing is added for the next subsystem since it comes back as experimental.  Then nothing is added for ‘Phosorespiration’ since it is a negative variant count.  And a +0.01 is added for the last ammonium assimilation. Giving a 1.02, which is eventually simplified into a 1.

The second reaction returns a NULL and is empty, thus it gets a +0.0001.  Which ends up being 0.0001, which ends up as a 0.