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Table 5 COGs represented in all archaea but not in other species: probable archaeal synapomorphies

From: Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

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 Polß 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1591 Holliday junction resolvase, archaeal-type Distant homologs seen in some bacteria (L.A., K.S. Makarova and E.V.K., unpublished.observations)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-ß-lactamase fold In spite of significant similarity to other families of metallo-ß-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