TABLE 1.

KEGG pathway analysis of proteome changes

Description	Observed gene count	Background gene count	False-discovery rate
Enriched pathways
Metabolic pathways	179	708	1E−18
Biosynthesis of secondary metabolites	107	301	1E−18
Biosynthesis of antibiotics	82	209	4E−16
Biosynthesis of amino acids	60	116	7E−16
Microbial metabolism in diverse environments	75	278	4E−08
Carbon metabolism	40	108	3E−07
Phenylalanine, tyrosine, and tryptophan biosynthesis	13	21	4E−04
Glycine, serine, and threonine metabolism	17	37	4E−04
2-Oxocarboxylic acid metabolism	14	26	4E−04
Cysteine and methionine metabolism	15	32	7E−04
Citrate cycle (TCA cycle)a	13	27	2E−03
Glutathione metabolism	11	20	2E−03
Histidine metabolism	7	8	4E−03
Bacterial chemotaxis	10	20	6E−03
Oxidative phosphorylation	15	43	6E−03
Methane metabolism	10	26	2E−02
Glyoxylate and dicarboxylate metabolism	13	41	2E−02
Pyruvate metabolism	15	52	2E−02
Vitamin B6 metabolism	6	10	2E−02
Sulfur metabolism	11	32	2E−02
Novobiocin biosynthesis	4	4	3E−02
Monobactam biosynthesis	5	8	4E−02
Valine, leucine, and isoleucine biosynthesis	7	16	4E−02
Lysine biosynthesis	6	13	5E−02
Depleted pathways
Metabolic pathways	103	708	1E−07
Flagellar assembly	17	37	6E−06
Aminoacyl-tRNA biosynthesis	12	25	2E−04
Amino sugar and nucleotide sugar metabolism	15	46	5E−04
Biosynthesis of antibiotics	33	209	6E−03
Glycolysis/gluconeogenesis	12	43	8E−03
Pyruvate metabolism	13	52	9E−03
Fatty acid biosynthesis	6	13	2E−02
Pyrimidine metabolism	14	66	2E−02
Carbon metabolism	19	108	2E−02
Fatty acid metabolism	7	21	3E−02
Oxidative phosphorylation	10	43	3E−02
Purine metabolism	16	91	3E−02
Glycine, serine, and threonine metabolism	9	37	4E−02
Lipopolysaccharide biosynthesis	8	31	4E−02
Alanine, aspartate, and glutamate metabolism	8	32	4E−02
Ribosome	11	56	5E−02

^aTCA, tricarboxylic acid.