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 | Â |
| Â | 21 | aaRS and related enzymes | Â |
K | 55 | Transcription | Moderately sophisticated transcription control |
including: | 22 | Transcription regulators | Â |
| Â | 13 | RNA polymerase subunits | Â |
L | 61 | Replication, recombination and repair | Advanced DNA replication and repair system |
including: | 6 | Topoisomerases | Â |
| Â | 4 | DNA polymerase subunits | Â |
C | 84 | Energy production and conversion | Membrane-based redox bioenergetics; partial TCA cycle |
including: | 13 | Pyruvate oxidation | Â |
| Â | 9 | TCA cycle | Â |
| Â | 9 | NADH dehydrogenase or Na+/H+ antiporter | Â |
| Â | 8 | V-type ATPase-ATP synthase | Â |
G | 33 | Carbohydrate transport and metabolism | Moderately sophisticated sugar metabolism |
including: | 8 | Glycolysis/Gluconeogenesis | Â |
E | 108 | Amino acid transport and metabolism | Enzymes for the biosynthesis of all amino acids |
including: | 72 | Amino acid biosynthesis | Â |
F | 49 | Nucleotide transport and metabolism | Enzymes for the biosynthesis of all nucleotides |
including: | 29 | Nucleotide biosynthesis | Â |
| Â | 6 | Nucleotide salvage | Â |
H | 67 | Coenzyme transport and metabolism | Enzymes for the biosynthesis of all essential cofactors |
including: | 60 | Cofactor biosynthesis | Â |
I | 25 | Lipid transport and metabolism | Fully developed membrane |
including: | 19 | Lipid biosynthesis | Â |
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 | Â |
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 | Â |
U | 10 | Intracellular trafficking and secretion | Fully developed secretion system |
including: | 3 | Preprotein translocase | Â |
V | 20 | Defense mechanisms | Viruses abundant at LACA times |
including: | 6 | CASS proteins | Â |
R, S | 183 | Poorly characterized or unknown | Â |