TABLE 2.

Specific functional categories where K. pneumoniae 342 genes are mostly of high identity (group A), mostly of intermediate identity (group B), or have little or no identity (group C) with genes from E. coli K-12^a

Group	Specific function category	No. of genes at level of DNA identity						% Total >75%	Wt (%)
		>75%	55–75%	<55%	Uncertain	Absent	Total
A	Specific functions with high identity
	Pyruvate dehydrogenase	5	0	0	0	0	5	100	100
	Entner-Douderoff	3	0	0	0	0	3	100	100
	Miscellaneous glucose metabolism	3	0	0	0	0	3	100	100
	ATP–proton-motive-force interconversion	9	0	0	0	0	9	100	100
	Plasmid-related functions	1	0	0	0	0	1	100	100
	Pyrimidine ribonucleotide biosynthesis	9	1	0	0	0	10	90	97
	2′-Deoxyribonucleotide metabolism	8	1	0	0	0	9	89	97
	Glycolysis	15	2	0	0	0	17	88	97
	Ribosomal protein synthesis and modification	53	1	0	1	1	56	95	96
	Colicin-related functions	4	1	0	0	0	5	80	95
	Fatty acid and phosphatidic acid biosynthesis	18	5	0	0	0	23	78	94
	Amino acid biosynthesis	93	11	1	1	3	109	85	93
	Transport of amino acids and amines	46	7	3	0	0	56	82	91
	Degradation of amines	8	0	1	0	0	9	89	89
	Osmotic adaptation	8	6	0	0	0	14	57	89
	Phospholipid synthesis	9	1	0	0	1	11	82	88
	Fermentation	14	5	0	0	1	20	70	88
	Proteins: translation and modification	29	1	2	1	1	34	85	87
	Sulfur metabolism	8	1	1	0	0	10	80	87
	Amino acyl tRNA synthesis; tRNA modification	31	5	0	1	3	40	78	87
	Tricarboxylic acid cycle	14	1	0	0	2	17	82	87
	Phosphorus compounds	11	5	0	0	1	17	65	86
	Detoxification	8	2	0	1	0	11	73	86
	RNA synthesis modification and DNA transcription	15	5	0	0	2	22	68	85
	Salvage of nucleosides and nucleotides	13	3	1	1	0	18	72	84
	Biosynthesis of cofactors, carriers	74	29	5	3	2	113	65	84
	Polyamine biosynthesis	6	1	0	0	1	8	75	84
	DNA replication, repair, restriction/modification	56	18	6	1	2	83	67	83
	Transport of nucleosides, purines, and pyrimidines	5	0	1	0	0	6	83	83
	Aerobic respiration	25	2	5	0	0	32	78	83
	Global regulatory functions	33	12	3	1	2	51	65	82
	Chaperone folding and ushering	5	1	0	0	1	7	71	82
	Transport of anions	12	8	2	0	0	22	55	81
	Purine ribonucleotide biosynthesis	17	1	1	0	3	22	77	81
	Transport of cations	30	15	5	1	0	51	59	80
	Glyoxylate bypass	4	0	1	0	0	5	80	80
	Degradation of proteins, peptides, and glycogen	21	3	3	0	2	29	72	80
	Murein sacculus and peptidoglycan	22	6	2	0	3	33	67	80
	Adaptations, atypical conditions	9	5	2	0	0	16	56	79
	Polysaccharides (cytoplasmic)	4	1	1	0	0	6	67	79
	Transport of protein or peptide secretion	16	4	4	0	0	24	67	79
	Basic proteins: synthesis and modification	4	2	0	1	0	7	57	78
	Nucleotide interconversions	7	3	2	0	0	12	58	77
	Transport of other	7	3	0	0	2	12	58	77
	Nonoxidative branch, pentose pathway	6	0	1	0	1	8	75	75
	Gluconeogenesis	3	0	0	0	1	4	75	75
	Transport of carbohydrates, organic acids, and alcohols	53	13	16	0	2	84	63	75
	Cell division	20	5	4	1	2	32	63	75
	Subtotals for each category	874	196	73	14	39	1,196	73	75
B	Specific functions with intermediate identity
	Undefined in central intermediary metabolism	1	2	0	0	0	3	33	82
	Lipoprotein	4	5	0	1	0	10	40	77
	Nucleotide hydrolysis	0	2	0	0	0	2	0	73
	Anaerobic respiration	44	19	15	1	1	80	55	72
	Sugar-nucleotide biosynthesis or conversions	7	8	2	0	1	18	39	71
	Degradation of amino acids	9	5	3	0	1	18	50	70
	Degradation of carbon compounds	53	35	25	0	0	113	47	70
	Drug or analog sensitivity	19	11	5	0	5	40	48	68
	Degradation of DNA	13	5	6	0	1	25	52	67
	Degradation of RNA	5	2	0	1	2	10	50	65
	Pool, multipurpose conversions of intermediate metabolism	30	12	17	0	4	63	48	62
	Subtotal for each category	185	106	73	3	15	382	48	69
C	Specific functions with little identity
	Degradation of polysaccharides	1	1	0	0	1	3	33	58
	Cell killing	1	1	0	1	0	3	33	58
	Amino sugars	5	1	3	0	1	10	50	57
	Outer membrane constituents	4	7	5	0	0	16	25	57
	Unknown function	445	450	382	23	63	1,363	33	57
	Ribosomes: maturation and modification	2	1	1	0	1	5	40	55
	Electron transport	7	9	9	0	0	25	28	54
	Not classified	345	301	352	21	62	1,081	32	52
	Surface polysaccharides and antigens	8	4	5	0	4	21	38	52
	Oxidative branch, pentose pathway	1	0	0	0	1	2	50	50
	Lipopolysaccharide	3	3	7	0	0	13	23	40
	Degradation of fatty acids	3	1	5	0	1	10	30	37
	Inner membrane	0	2	1	0	1	4	0	37
	Phage-related functions and prophages	5	7	11	6	0	29	17	35
	Surface structures	3	10	44	0	0	57	5	18
	Chemotaxis and mobility	0	2	10	0	0	12	0	12
	Transposon-related functions	2	4	49	0	3	58	3	9
	Subtotals for each category	835	804	884	51	138	2,712	31	53
	Total across all functions	1,894	1,106	1,030	68	192	4,290

^aThe “uncertain” category refers to genes for which the fluorescence signal from the positive control E. coli DNA was too low to obtain a reasonable fluorescence ratio. The “absent” category refers to E. coli genes that were not on the microarray. In the far right column, note that all data are sorted by a weight factor that takes into account the number of genes of intermediate as well as high identity, calculated as follows: weight = (% genes with >75% identity) + [(% genes with 55 to 75% identity) × (0.55/0.75)].