Table 2

Subsystems statistically more likely to be present in either the Red or Black samples. These subsystems are more frequently found among sequences from either the Red or Black samples with a sample size of 5,000 proteins, 20,000 repeated samples, and P < 0.05.

Red Sample (Oxidized, pH4.37, Eh-8)

Black Sample (Reduced, pH 6.70, Eh-142)

Amino Acids and Derivatives

Arginine biosynthesis

Urea decomposition

Tryptophan synthesis

Chorismate synthesis

Asp-Glu-tRNA(Asn-Gln) transamidation

Branched-chain amino acid biosynthesis

Histidine biosynthesis

Isoleucine degradation

Leucine biosynthesis

Leucine degradation and HMG-CoA metabolism

Valine degradation

Methionine salvage


Glyoxylate synthesis

Cell Division and Cell Cycle


Cell Wall and Capsule

N-linked glycosylation in Bacteria

Teichoic acid biosynthesis

Cofactors, Vitamins, Prosthetic Groups, Pigments

Folate biosynthesis

Coenzyme A biosynthesis in pathogens

Methylglyoxal metabolism

Molybdopterin biosynthesis

Pyruvate metabolism I: anaplerotic rx, PEP


Ubiquinone biosynthesis

Polyisoprenoid biosynthesis

Ubiquinone menaquinone-cytochrome c reductase

NAD and NADP cofactor biosynthesis global

Riboflavin metabolism

Coenzyme PQQ synthesis

Pyrroloquinoline quinone biosynthesis

Siderophore enterobactin biosynthesis

Siderophore enterobactin biosynthesis and ferric enterobactin transport

Thiamin biosynthesis

DNA metabolism

DNA repair, bacterial

Fatty Acids and Lipids

Fatty acid metabolism

Glycerolipid and glycerphospholipid metabolism

Fatty acid oxidation pathway

Membrane Transport

ABC transporter maltose

ABC transporter ferrichrome

ABC transporter heme

CbiQO-type ABC transporter systems

Sodium hydrogen antiporter

Metabolism of aromatic compounds

Phenylacetate pathway of aromatic compound degradation

Homogentisate pathway of aromatic compound degradation

Motility and Chemotaxis

Bacterial chemotaxis


Nitrogen Metabolism


Nucleosides and Nucleotides

De novo purine biosynthesis

Ribonucleotide reduction

Protein Metabolism

Ribosome LSU bacterial

Phenylpropionate degradation

Ribosome SSU bacterial

Translation factors bacterial

Universal GTPases

Protein degradation


F0F1-type ATP synthase

NiFe hydrogenase maturation

Terminal cytochrome C oxidases


Membrane-bound Ni, Fe-hydrogenase

Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes

Respiratory complex I

Respiratory dehydrogenases 1

RNA metabolism

Polyadenylation bacterial

RNA polymerase bacterial

tRNA aminoacylation

Stress response

Glutathione redox metabolism

ppGpp biosynthesis

Sulfur Metabolism

Sulfate assimilation


Resistance to fluoroquinolones

Edwards et al. BMC Genomics 2006 7:57   doi:10.1186/1471-2164-7-57

Open Data