TABLE 4.

Genes activated in NO₃⁻-containing PseudoCyc metabolic pathways^a

Functional category or metabolic pathway	Genes activated in NO3−-containing medium		Genes in P. aeruginosa genome		P valueb
	No. of genes identified	% of genes identified	No. of genes	% of genes
COG functional categories
Unclassified	20	37.74	1,054	16.99	0.001739*
Energy production and conversion	8	15.09	320	5.16	0.03622*
General function prediction only	8	15.09	604	9.74	0.3502
Function unknown	6	11.32	498	8.03	0.5835
Inorganic ion transport and metabolism	4	7.55	303	4.88	0.5679
Transcription	3	5.66	482	7.77	0.7828
Coenzyme metabolism	1	1.89	204	3.29	1
DNA replication, recombination, and repair	1	1.89	132	2.13	1
Nucleotide transport and metabolism	1	1.89	108	1.74	1
Posttranslational modification, protein turnover, chaperones	1	1.89	191	3.08	1
Amino acid transport and metabolism	0	0	486	7.83	0.006755*
Signal transduction mechanisms	0	0	337	5.43	0.05938
PseudoCyc metabolic pathways
Unclassified	41	71.93	4,701	77.64	0.4433
Denitrification	7	12.28	17	0.28	0.001346*
Biosynthesis of heme d1	4	7.02	9	0.15	0.01402*
Nitrogen metabolism	4	7.02	35	0.58	0.06486
Molybdopterin biosynthesis	1	1.75	11	0.18	0.4975

^aA significantly greater proportion of genes were involved in denitrification than that for the whole genome (P = 0.0013); 7 of 17 genes in the genome were identified in this study. Also, a significantly greater proportion of genes were involved in biosynthesis of heme d₁ than that for the genome (P = 0.014); four of nine genes in the genome were identified in this study. A significantly greater proportion of genes were classified as being involved in energy production and conversion than that for the genome (P = 0.036).

^bPearson's chi-square test with Yates's continuity correction. For those categories with small values (<5), Fisher's exact test was performed instead. Asterisks indicate statistical significance (P < 0.05).