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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Distant homologs seen in some bacteria (L.A., K.S. Makarova and E.V.K., unpublished.observations)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

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