TABLE 2 

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

Pathways enriched in clade B-containing gammaproteobacteria, P  < 0.05Pathways enriched in clade E-containing gammaproteobacteria, P < 0.05
Cytochrome bc1 complex respiratory unitFumarate reductase, prokaryotes
Cytochrome bc1 complexDissimilatory nitrate reduction, nitrate → ammonia
Cytochrome c oxidaseMalonate semialdehyde pathway, propionyl-CoA → acetyl-CoA
Cytochrome c oxidase, prokaryotesValine/isoleucine biosynthesis, pyruvate → valine/2-oxobutanoate → isoleucine
RaxAB-RaxC type I secretion systemIsoleucine biosynthesis, threonine → 2-oxobutanoate → isoleucine
Type IV secretion systemAscorbate degradation, ascorbate → d-xylulose-5P
Helicobacter pylori pathogenicity signature, cagA pathogenicity islandCatechol ortho-cleavage, catechol → 3-oxoadipate
HydH-HydG (metal tolerance) two-component regulatory systemType III secretion system
CheA-CheYBV (chemotaxis) two-component regulatory systemEnterohemorrhagic/enteropathogenic E. coli pathogenicity signature, T3SS and effectors
Cph1-Rcp1 (light response) two-component regulatory systemRstB-RstA two-component regulatory system
PleC-PleD (cell fate control) two-component regulatory systemSulfate transport system
Cysteine biosynthesis, homocysteine and serine → cysteineIron(III) transport system
Putative ABC transport systemThiamine transport system
ABC-2-type transport systemPutative spermidine/putrescine transport system
Fatty acid biosynthesis, elongationGlycine betaine/proline transport system
Ribosome, bacterial-Arabinose transport system
NADH:quinone oxidoreductase, prokaryotesaLysine/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).