Table 2.

List of target organisms used in the experiments.

short name	full name	#gen.	#w/fn.	#enz.	#samp.	%pos	weight
ECK12	Escherichia coli K-12 substr. MG1655	4496	3185	1000	495510	0.621	1.000
EC157	Escherichia coli O157:H7 EDL933	5475	1032	706	248865	1.327	0.884
ECCFT	Escherichia coli CFT073	5379	721	577	166176	0.968	0.856
SHIG	Shigella flexneri 2a str. 2457T	4207	886	597	177310	1.020	0.795
VCHO	Vibrio cholerae O1 biovar El Tor str. N16961	3949	863	583	169653	1.244	0.528
CAULO	Caulobacter crescentus CB15	3818	919	615	188805	0.964	0.362
MTBC	Mycobacterium tuberculosis CDC1551	4235	760	569	161596	1.157	0.238
MTBR	Mycobacterium tuberculosis H37Rv	3968	811	578	166753	1.409	0.238
FRANT	Francisella tularensis tularensis SCHU S4	1671	491	317	50086	1.512	0.230
HPY	Helicobacter pylori 26695	1609	415	228	25878	1.946	0.155

The columns correspond to the short and full names for the organism, the total number of genes in the genome, the number of genes with some functional annotation, the number of genes that encode enzymes that catalyze small-molecule reactions, the total number of pairs of such genes (which corresponds to the number of samples used to report results, except in Sections 4.7 and for some results in Section 4.8 where all known-function genes are paired to create samples instead of just small-molecule enzymes), the proportion of positive samples among these samples, and the fraction of genes in the genome that have homologous sequences in ECK12. Organisms are sorted by this last column.