Table 2 |
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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) |
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|
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 |
|
|
|
|
|
Carbohydrates |
|
|
Glyoxylate synthesis |
|
|
|
|
|
Cell Division and Cell Cycle |
|
|
Cytoskeleton |
|
|
|
|
|
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 |
Carotenoids |
|
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 |
|
|
|
|
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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 |
|
|
Flagellum |
|
|
|
|
|
Nitrogen Metabolism |
|
|
Denitrification |
|
|
|
|
|
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 |
|
|
|
|
|
Respiration |
|
|
F0F1-type ATP synthase |
NiFe hydrogenase maturation |
|
Terminal cytochrome C oxidases |
|
|
Hydrogenases |
|
|
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 |
|
|
|
|
|
Virulence |
|
|
Resistance to fluoroquinolones |
|
|
|
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|
Edwards et al. BMC Genomics 2006 7:57 doi:10.1186/1471-2164-7-57 |
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