Table 3.
Major features of the reconstructed gene set of LACA
| COG class | No. of arCOGs | Function | Implication for LACA |
| J | 152 | Translation | Complete translation system and essentially complete set of enzymes for tRNA and rRNA modification |
| including: | 61 | Ribosomal proteins | |
| 21 | aaRS and related enzymes | ||
| K | 55 | Transcription | Moderately sophisticated transcription control |
| including: | 22 | Transcription regulators | |
| 13 | RNA polymerase subunits | ||
| L | 61 | Replication, recombination and repair | Advanced DNA replication and repair system |
| including: | 6 | Topoisomerases | |
| 4 | DNA polymerase subunits | ||
| C | 84 | Energy production and conversion | Membrane-based redox bioenergetics; partial TCA cycle |
| including: | 13 | Pyruvate oxidation | |
| 9 | TCA cycle | ||
| 9 | NADH dehydrogenase or Na+/H+ antiporter | ||
| 8 | V-type ATPase-ATP synthase | ||
| G | 33 | Carbohydrate transport and metabolism | Moderately sophisticated sugar metabolism |
| including: | 8 | Glycolysis/Gluconeogenesis | |
| E | 108 | Amino acid transport and metabolism | Enzymes for the biosynthesis of all amino acids |
| including: | 72 | Amino acid biosynthesis | |
| F | 49 | Nucleotide transport and metabolism | Enzymes for the biosynthesis of all nucleotides |
| including: | 29 | Nucleotide biosynthesis | |
| 6 | Nucleotide salvage | ||
| H | 67 | Coenzyme transport and metabolism | Enzymes for the biosynthesis of all essential cofactors |
| including: | 60 | Cofactor biosynthesis | |
| I | 25 | Lipid transport and metabolism | Fully developed membrane |
| including: | 19 | Lipid biosynthesis | |
| M | 26 | Cell wall, membrane and envelope biogenesis | Fully developed cell wall |
| P | 48 | Inorganic ion transport and metabolism | Sophisticated ion uptake system |
| Q | 8 | Secondary metabolites biosynthesis, transport and catabolism | Limited or unknown |
| N | 5 | Cell motility | Limited motility and/or conjugation |
| O | 47 | Posttranslational modification, protein turnover, chaperones | Sophisticated system of protein fate control |
| including: | 2 | Proteasome | |
| D | 5 | Cell cycle control | Limited or unknown |
| T | 10 | Signal transduction mechanisms | Limited use of bacterial type signal transduction system; original signal transduction |
| including: | 3 | Serine/threonine kinase | |
| U | 10 | Intracellular trafficking and secretion | Fully developed secretion system |
| including: | 3 | Preprotein translocase | |
| V | 20 | Defense mechanisms | Viruses abundant at LACA times |
| including: | 6 | CASS proteins | |
| R, S | 183 | Poorly characterized or unknown |