Note onThe COG databaseS. Saengamnatdej August 15, 2009COG standing for Clusters of Orthologous Groupsof proteins is a database that classifies predicted proteins from orthologues, homologous genes which arederived by vertical descent from a single ancestralgene in the last common ancestor of the compared species and typically have the same function and domain architecture, and can be used to annotate proteins in a new genome. VERSIONSCurrent version (Figure 1)Initial version (enter through the link on thecurrent version page, Figure 2.)Figure 1 Current version of the COG database1

FEATURES1. 4873 COGs as reported

[1]

(begun with 720 then860, to 2091

[2]

, currently 3307 COGs

[3]

includinggroups with known function(s) such as chemotaxis proteins, predicted functions (e.g. predicted extracellular nucleases), and uncharacterized functions.)2. 138,458 proteins

[1]

(75% of the 185,505 predicted proteins) currently, 192,987 proteins

[3]

3. 66 genomes of prokaryotes (started from 5then 6 to 43 and, now, 63 genomes) and unicellulareukaryotes (the only S. cerevisiae at the beginningto, now, 3). COG coverage of most genomes isapproaching saturation (~80% of the genes of mostfree-living prokaryotes belong to COGs).4. 1% conserved phyletic patterns5. Many new microbial genomes are being added (See Figure 3).Figure 2 Initial version of the COG database2

5. KOGs (eukaryotic orthologous groups)5.1) predicted orthologs for seven complex multicellular eukaryotic genomes including 3 animals(nematode, Caenorhabditis elegans ; fruit fly,Drosophila melanogaster ; and human, Homo sapiens), 1 plant (thale cress, Arabidopsis thaliana), 2 fungi(Saccharomyces cerevisiae ; Schizosaccharomyces pombe) , and 1 parasite (Encephalitozoon cuniculi).5.2) 4852 clusters5.3) 59,838 proteins (54%of 110,655 gene products)5.4) 20% conserved phyletic patterns (probablydue to the small numbers of included eukaryoticgenomes)5.5) KOG coverages are still far from saturation.5.6) The upcoming eukaryote genomes are Oryzasativa (rice), Anopheles gambiae (mosquito), Pantroglodytes (chimpanzee), Canis familiaris (dog), Mus musculus (mouse), Rattus norvegicus (rat), and Ascomycota genomes including Magnaporthe grisea & Neurospora crassa.Figure 3 The upcoming mycobial genomes.3