Table 2.
Functional categories (FunCat level 2) and their abundance in archaeal and bacterial effectomes
| FunCat Category | Description | Archaea | Bacteria | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HT | MS | AQU | ANE | AB | TH | MS | PS | AQU | TER | HOA | AER | ANE | NHAL | MHAL | HITR | ||
| 2.01 | Glycolysis and gluconeogenesis | + | -0.32 | -0.01 | -0.17 | 0.49 | 0.34 | 0.52 | 0.42 | 0.44 | 0.51 | 0.46 | 0.35 | 0.55 | 0.56 | 0.36 | 0.60 |
| 2.04 | Glyoxylate cycle | x | x | x | x | 0.20 | + | 0.20 | + | 0.20 | 0.45 | -0.12 | 0.30 | + | 0.34 | + | -0.78 |
| 2.07 | Pentose-phosphate pathway | - | - | - | - | 0.00 | -0.32 | 0.00 | 0.03 | -0.03 | 0.12 | -0.12 | -0.26 | 0.09 | 0.04 | 0.23 | |
| 2.08 | Pyruvate dehydrogenase complex | x | x | x | x | 0.35 | - | 0.40 | + | + | + | 0.40 | 0.08 | x | 0.60 | + | 0.73 |
| 2.09 | Anaplerotic reactions | x | x | x | x | 0.48 | + | 0.48 | + | + | + | + | 0.60 | + | + | + | 0.00 |
| 2.10 | Tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle) | x | + | + | x | 0.49 | + | 0.50 | 0.40 | 0.51 | 0.58 | 0.37 | 0.58 | 0.43 | 0.49 | 0.46 | 0.39 |
| 2.11 | Electron transport and membrane-associated energy conservation | 0.10 | 0.30 | 0.10 | 0.25 | 0.28 | 0.18 | 0.28 | 0.21 | 0.32 | 0.37 | 0.22 | 0.31 | 0.21 | 0.26 | 0.28 | 0.25 |
| 2.30 | Photosynthesis | x | x | x | x | -0.12 | - | -0.12 | x | -0.12 | 0.33 | -0.48 | -0.60 | + | -0.48 | x | -0.30 |
| 2.45 | Energy conversion and regeneration | + | 0.29 | + | + | 0.32 | 0.19 | 0.31 | 0.30 | 0.39 | 0.44 | 0.23 | 0.39 | 0.17 | 0.29 | 0.27 | 0.33 |
| 12.01 | Ribosome biogenesis | 0.79 | 0.85 | 0.79 | 0.82 | 1.03 | 0.92 | 1.04 | 1.00 | 1.07 | 1.06 | 0.94 | 1.05 | 1.00 | 1.07 | 1.08 | 1.10 |
| 12.04 | Translation | 0.63 | 0.66 | 0.62 | 0.65 | 0.84 | 0.73 | 0.85 | 0.82 | 0.88 | 0.87 | 0.75 | 0.86 | 0.81 | 0.87 | 0.90 | 0.91 |
| 12.07 | Translational control | + | + | + | + | 0.68 | + | 0.68 | + | 0.64 | + | 0.65 | 0.75 | + | 0.74 | + | 0.75 |
| 12.10 | Aminoacyl-tRNA synthetases | - | - | - | - | -0.32 | - | -0.32 | - | - | - | - | - | - | - | - | 0.21 |
| 14.01 | Protein folding and stabilization | + | 0.46 | + | + | 0.45 | 0.53 | 0.47 | 0.35 | 0.46 | 0.55 | 0.36 | 0.48 | 0.46 | 0.46 | 0.50 | 0.52 |
| 32.07 | Detoxification | + | - | + | + | 0.09 | 0.20 | 0.09 | 0.10 | 0.11 | 0.20 | -0.01 | 0.09 | 0.00 | 0.12 | 0.15 | 0.26 |
| 34.01 | Homeostasis | + | - | + | + | 0.09 | -0.02 | 0.11 | 0.02 | 0.13 | 0.12 | 0.03 | 0.07 | 0.10 | 0.07 | 0.02 | 0.22 |
| 34.05 | Cell motility | - | + | 0.08 | 0.01 | -0.04 | -0.08 | -0.02 | -0.22 | -0.25 | 0.16 | 0.17 | 0.12 | 0.06 | -0.09 | -0.38 | -0.50 |
| 42.33 | Pilus/fimbria | x | x | x | x | 0.00 | 0 | 0.00 | + | + | 0 | -0.40 | 0.18 | - | 0.00 | + | 0.00 |
| 70.03 | Cytoplasm | x | x | x | x | 0.02 | -0.07 | 0.03 | 0.03 | 0.04 | 0.08 | -0.02 | 0.05 | -0.01 | 0.04 | 0.05 | 0.10 |
| 70.27 | Extracellular/secretion proteins | + | - | + | + | 0.34 | + | 0.36 | + | 0.18 | 0.22 | 0.39 | 0.28 | 0.40 | 0.44 | + | 0.26 |
| 70.34 | Prokaryotic cell envelope component | x | x | x | x | 0.05 | x | 0.07 | 0.02 | 0.01 | 0.04 | 0.09 | -0.04 | -0.14 | 0.17 | 0.07 | 0.12 |
For archaeal and bacterial genomes, the number of gene products contributing to FunCat categories of level 2 was determined (see Methods). The columns lists the ratio log(fEff (Cat)/fAll (Cat)) for the categories, if #All(Cat) was at least 100 (compare Table 1). In all other cases a trend is given indicated by a "+" for overrepresentation, a "-" for underrepresentation and a 0 for a score value of 0.0. An "x" indicates categories not occurring in the respective dataset. Abbreviations of subsets: AB all Bacteria, HT hyperthermophilic, TH thermophilic, MS mesophilic, PS psychrophilic, AQU aquatic, TER terrestrial, HOA host-associated, AER aerobic, ANE anaerobic, NHAL non halophilic, MHAL moderately halophilic species, and HITR the subset of bacterial species possessing an extreme number of tRNA genes, i.e. MG_CUB(Bacteria_HITR).