Table 2.

Network properties for selected metabolic reconstructions

Organism	Reconstruction reference	Linksa (irr/rev)	Metsb	APL	D	〈k〉	SC	Network structure subsets
								GSC	S	P	IS
M. barkeri	This study	636/253	592	8.00	24	3.03	7	322	54	131	85
E. coli	Reed et al (2003)	1076/333	725	6.75	19	3.89	8	468	145	65	47
S. cerevisiae	Duarte et al (2004)	1073/536	972	8.00	31	3.36	11	629	98	125	120
E. coli	Ma and Zeng (2003)	NR	811	8.20	23	NR	29	274	93	161	283
S. cerevisiae	Ma and Zeng (2003)	NR	679	9.71	NR	NR	NR	206	54	164	255
NR, not reported; irr, irreversible; rev, reversible; Mets, metabolites; APL, average path length—average over the shortest paths between all metabolites; D, network diameter—shortest path length between the most distant metabolites in a network; 〈k〉, average degree—average number of links per metabolite; SC, strong components—fully connected subnetworks; GSC, giant strong component—the largest strong component; S, substrate subset—metabolites that can be converted to metabolites in the GSC; P, product subset—metabolites that can be produced from metabolites in the GSC; IS, isolated subset—metabolites that can not be converted to or produced from metabolites in the GSC.
The network properties for the metabolic reconstructions generated by Reed et al (2003), Duarte et al (2004), and those of the M. barkeri model were calculated in this study. These models were built specifically for use with constraint-based methods. The additional network properties were reported for reconstructions generated by Ma and Zeng (2003).

^aModel compartmentalization was conserved (Duarte et al, 2004).

^bCurrency metabolites were removed from each network.