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Table 4 Genome wide analysis. Connected components' scores before and after resolving conflicts. For each component we list the names of the constituent pathways, the number of conflicts (shared assignments) and the component score. Note that not all conflicts are solvable. For example, the first connected component contains three pathways, and the best initial assignment results in 6 conflicts. Of these only two are solvable (i.e. there are multiple enzymes that can be assigned to these reactions). The final assignment resolves these conflicts while reducing the score of the connected component only slightly (9.31 compared to 10.22).

From: Automation of gene assignments to metabolic pathways using high-throughput expression data

Component Number Pathways Number of Conflicts (solvable conflicts) Component score
   Before After Before After
1 isoleucine biosynthesis I
valine biosynthesis
leucine biosynthesis
6(2) 4 10.22 9.31
2 aerobic glycerol degradation II
glycolysis
5(3) 2 7.58 7.22
3 asparagine biosynthesis I
glutamate – aspartate pathway
glutamate degradation VI
aspartate biosynthesis II
aspartate biosynthesis and degradation
4(0) 4 6.82 6.82
4 trehalose anabolism
galactose metabolism
UDP-glucose conversion
trehalose biosynthesis
4(1) 3 6.64 6.62
5 pentose phosphate pathway, Mycoplasma pneumoniae
ribose degradation
non-oxidative branch of the pentose phosphate pathway
5(2) 3 5.60 4.78
6 serine biosynthesis
cysteine biosynthesis II
3(0) 3 3.98 3.98
7 glycine biosynthesis I
glycine cleavage
folic acid biosynthesis
3(2) 1 3.41 3.41
8 arginine biosynthesis, Bacillus subtilis
de novo biosynthesis of pyrimidine ribonucleotides
0(0) 0 2.08 2.08
9 alanine degradation 3
alanine biosynthesis II
1(1) 0 0 0
10 phenylalanine biosynthesis I
tyrosine biosynthesis I
2(1) 1 -1.31 -1.33