Table 1.
Abundance of functional categories (FunCat level 1) in archaeal and bacterial effectomes
| Archaea | Bacteria | ||||||
|---|---|---|---|---|---|---|---|
| FunCat Category | Description | #Eff(Cat) | #All(Cat) | AbundEff | #Eff(Cat) | #All(Cat) | AbundEff |
| 1 | Metabolism | 594 | 15495 | -0.21 | 15948 | 461317 | -0.24 |
| 2 | Energy | 110 | 1508 | 0.07 | 5129 | 47263 | 0.25 |
| 10 | Cell cycle and DNA processing | 30 | 2557 | -0.73 | 1775 | 116118 | -0.60 |
| 11 | Transcription | 32 | 2746 | -0.73 | 2587 | 105731 | -0.39 |
| 12 | Protein synthesis | 1006 | 3576 | 0.65 | 29446 | 67653 | 0.86 |
| 14 | Protein fate (folding, modification, destination) | 91 | 2106 | -0.16 | 2502 | 71643 | -0.24 |
| 18 | Regulation of metabolism and protein function | 8 | 395 | -0.48 | 61 | 8494 | -0.95 |
| 20 | Cellular transport, transport facilitation and transport routes | 160 | 3798 | -0.17 | 5551 | 155592 | -0.23 |
| 30 | Cellular communication/signal transduction mechanism | 0 | 931 | -2.23 | 138 | 37418 | -1.22 |
| 32 | Cell rescue, defense and virulence | 27 | 590 | -0.13 | 1026 | 24273 | -0.16 |
| 34 | Interaction with the environment | 21 | 548 | -0.21 | 1059 | 26204 | -0.17 |
| 38 | Transposable elements, viral and plasmid proteins | 0 | 68 | - | 23 | 5107 | -1.13 |
| 40 | Cell fate | 0 | 9 | - | 76 | 6919 | -0.72 |
| 41 | Development (systemic) | 0 | 2 | - | 3 | 385 | -0.30 |
| 42 | Biogenesis of cellular components | 13 | 1235 | -0.77 | 1271 | 83665 | -0.60 |
| 70 | Subcellular localization | 191 | 3511 | -0.06 | 8601 | 175358 | -0.09 |
| Sum: | 2283 | 39075 | 75196 | 1393140 | |||
For archaeal and bacterial genomes, the number of gene products contributing to FunCat categories was determined. The column labeled #All(Cat) gives the number of genes deduced from the whole dataset. The column labeled #Eff(Cat) gives the number of genes belonging to the respective effectomes. The column AbundEff lists the ratio log(fEff (Cat)/fAll(Cat)) for the category, if #All(Cat) was at least 100. In all other cases a trend is given indicated by a "-" for underrepresentation. The line labeled Sum lists the number of genes being analyzed.