Table 2

Structural and functional predictions for uncharacterized proteins in COGs.

Phylogenetic pattern and COG ID*Proteins in COGActivity and function Homolog in PDB ·BeTs detected (no.) ·Lowest P with a COG member Comment
e_gpcmy COG0595RPhnP, ElaC-2g-2p-5c-8m-YLR277c, YMR137c, YKR079cPredicted Zn-dependent hydrolases Beta-lactamase (1BMC) ·2 ·0.039Activity is not known for any protein in this ubiquitous COG. Biochemical and genetic data indicate that YLR277c is involved in messenger RNA 3′-end processing (31), whereas YMR137c is DNA cross-link repair protein SNM1 (39). A motif including the Zn-coordinating histidines of beta-lactamase is conserved.
eh__cmy COG0607R SseA, PspE, GlpE, YibN, YbbB, YnjE, YgaP-2h-5c-MJ0052-4y Predicted sulfur-transferases Rhodanese (1RHD, 2ORA, 1ORB) ·2 ·10−41 The sulfurtransferase activity of SseA has been demonstrated (40), but the rest of the proteins in this COG have no known activity. PspE (phage shock protein), GlpE (uncharacterized protein involved in glycerol metabolism), and other small proteins correspond to one of the two rhodanese domains.
ehgpc_y COG0596R PldB, MhpC, YcdJ, YnbC-HIN0065- MG020-MP132–6c-YNR064c, YKL094w Predicted hydrolases and acyltransferases Lipases (2LIP, 1TAH|B, 1CVL) ·3 ·8 × 10−5 PldB is known to possess triglyceride lipase activity (41). All other proteins in the COG have not been characterized but now can be predicted to possess the α- or β-hydrolase fold.
e___cm_ COG0068CHypF-sll0322-MJ0713 Hydrogenase maturation factorAcylphosphatase (1APS) ·2 ·2 × 10−5 HypF is required for hydrogenase biosynthesis (42), but no biochemical activity is known. The ∼100 amino acid, NH2-terminal domain aligns with acylphosphatase, with the catalytic residues conserved, suggesting that HypF orthologs indeed possess acylphosphatase activity. A PSI-BLAST search with this domain as the query detected five additional likely acylphosphatases, namelyE. coli YccX and M. jannaschii MJ0809, MJ0553, MJ1331, and MJ1405 (43).
e___cm_ COG0663R CaiE, YrdA, YdbZ-sll1636, sll1031-MJ0304 Predicted carbonic anhydrasesCarbonic anhydrase from Methanosarcina thermophila (1THJ) ·3 ·10−29 The biochemical activity of the proteins in this COG is not known. They show not only conservation of histidine residue comprising the active center of this unusual carbonic anhydrase (44) but also significant similarity to acetyltransferases of the isoleucine patch superfamily (45), suggesting an unexpected connection between the two types of enzymes.
  • * The designations are as in Table 1 and Fig. 3.

  • 2g indicates two proteins from M. genitalium, 2p indicates two proteins from M. pneumoniae, and so forth.

  • The PDB accession is indicated in parentheses.