Table 5.
COGs represented in all archaea but not in other species: probable archaeal synapomorphies
| COG number | (Predicted) function | Comments |
| 2511 | Glu-tRNAGln amidotransferase B subunit | This protein is homologous to bacterial B subunits and an archaeal paralog but contains a synapomorphic insert, the so-called GAD domain, shared with bacterial aspartyl-tRNA synthetases [49] |
| 2016 | Predicted RNA-binding protein, contains PUA domain | PUA domain is most common in archaea and is found also in pseudouridine synthases, archaeosine synthases and glutamate kinases [50] |
| 1370 | Predicted RNA-binding protein, contains PUA domain | This form of the PUA domain is present as a stand-alone protein in A. pernix and A. fulgidus but is fused with the archaeosine synthase in the other euryarchaea [50] |
| 1746 | tRNA nucleotidyltransferase (CCA-adding enzyme) | Archaeal CCA-adding enzyme is only very distantly related to other members of the Polβ superfamily of nucleotidyltransferases [51] |
| 1395 | Predicted transcription regulators | The proteins of this family do not share similarity with other proteins beyond the DNA-binding helix-turn-helix domain [32] |
| 1389 | DNA topoisomerase VI, subunit B | These proteins contain an ATPase domain of the TopoII/MutL/HSP90/histidine kinase fold, but do not show a specific relationships to any other proteins of this class |
| 1591 | Holliday junction resolvase, archaeal-type | Distant homologs seen in some bacteria (L.A., K.S. Makarova and E.V.K., unpublished.observations) |
| 1571 | Predicted DNA-binding proteins, possibly nucleotidyl transferase or nuclease | These proteins consist of two distinct, predicted DNA-binding domains (OB-fold and Zn-ribbon) and an uncharacterized, probably enzymatic domain that is unique for archaea (see text) |
| 1491 | Predicted DNA-binding protein | These proteins contain the helix-hairpin-helix module, but otherwise, do not show significant similarity to any other proteins |
| 1938 | Predicted ATP-grasp-domain-containing enzymes | Only distantly related to other ATP-grasp proteins; predicted to possess ATP-dependent carboligase or similar activity [19] |
| 1407 | Predicted calcineurin-type phosphoesterase | Only distantly related to other phosphohydrolases of the calcineurin fold [37] |
| 1782 | Predicted metal-dependent RNase of the metallo-β-lactamase fold | In spite of significant similarity to other families of metallo-β-lactamases, this family shows a clear synapomorphy, the presence of the RNA-binding KH domain [52] |
| 1608 | Predicted kinase related to acetylglutamate kinase | Only distantly related to other kinases of the same fold |
| 1829 | Predicted kinase of the actin/HSP70/sugar kinase fold | Only distantly related to other kinases of the same fold |
| 1907 | Predicted kinase of the actin/HSP70/sugar kinase fold | Only distantly related to other kinases of the same fold |
| 1831 | Predicted metal-dependent hydrolase of the urease superfamily | Only distantly related to other hydrolases of the same superfamily [53] |
| 1571 | Predicted DNA-binding protein containing the Zn-ribbon module | |
| 2034 | Conserved membrane protein | |
| 2064 | Conserved membrane protein | |
| 1339, 2090, 1581, | Uncharacterized proteins unique to archaea | |
| 1460, 1786, 1701, 1931, 1909, 1888, 1382, 1849, 1630, 1303, 1325, 1679 |