. 2015 Apr 14;6(2):e00389-15. doi: 10.1128/mBio.00389-15

TABLE 2 .

Most significantly enriched biochemical pathways when comparing clade B- to clade E-containing gammaproteobacteria

Pathways enriched in clade B-containing gammaproteobacteria, P < 0.05	Pathways enriched in clade E-containing gammaproteobacteria, P < 0.05
Cytochrome bc₁ complex respiratory unit	Fumarate reductase, prokaryotes
Cytochrome bc₁ complex	Dissimilatory nitrate reduction, nitrate → ammonia
Cytochrome c oxidase	Malonate semialdehyde pathway, propionyl-CoA → acetyl-CoA
Cytochrome c oxidase, prokaryotes	Valine/isoleucine biosynthesis, pyruvate → valine/2-oxobutanoate → isoleucine
RaxAB-RaxC type I secretion system	Isoleucine biosynthesis, threonine → 2-oxobutanoate → isoleucine
Type IV secretion system	Ascorbate degradation, ascorbate → d-xylulose-5P
Helicobacter pylori pathogenicity signature, cagA pathogenicity island	Catechol ortho-cleavage, catechol → 3-oxoadipate
HydH-HydG (metal tolerance) two-component regulatory system	Type III secretion system
CheA-CheYBV (chemotaxis) two-component regulatory system	Enterohemorrhagic/enteropathogenic E. coli pathogenicity signature, T3SS and effectors
Cph1-Rcp1 (light response) two-component regulatory system	RstB-RstA two-component regulatory system
PleC-PleD (cell fate control) two-component regulatory system	Sulfate transport system
Cysteine biosynthesis, homocysteine and serine → cysteine	Iron(III) transport system
Putative ABC transport system	Thiamine transport system
ABC-2-type transport system	Putative spermidine/putrescine transport system
Fatty acid biosynthesis, elongation	Glycine betaine/proline transport system
Ribosome, bacteria	l-Arabinose transport system
NADH:quinone oxidoreductase, prokaryotes^a	Lysine/arginine/ornithine transport system
	Histidine transport system
	Glutamate/aspartate transport system
	General l-amino acid transport system
	Cystine transport system
	Branched-chain amino acid transport system
	Peptides/nickel transport system
	Iron complex transport system
	PTS system, glucose-specific II component
	PTS system, cellobiose-specific II component
	PTS system, ascorbate-specific II component
	Dipeptide transport system
	Microcin C transport system
	Taurine transport system
	Sulfonate transport system
	Oligopeptide transport system

^{^a}

Only 2 of the 14 genes encoding complex I (nuoC and nuoD) were enriched in clade B-containing gammaproteobacteria. This is because these genes are separate in clade B operons (counted as 2 genes) and fused in clade E operons (counted as 0 genes). Thus, clade B-containing gammaproteobacteria appear to be enriched for complex I (NADH:quinone oxidoreductase, prokaryotes).