Table 1. Representation of genomes in the COGs^a.

Species	Total no. of encoded proteins	No. of proteins assigned to COGs	Proteins in COGs (%)
Archaea
Archaeoglobus fulgidus	2420	1817	75
Methanococcus jannaschii	1786	1301	74
Methanobacterium thermoautotrophicum	1873	1365	73
P.abyssi	1767	1430	81
Pyrococcus horikoshiib	2080	1353	66
A.pernixb	2722	1157	43
Bacteria
Aquifex aeolicus	1560	1312	84
Bacillus subtilis	4118	2767	67
Borrelia burgdorferic	1637	693	43
Campylobacter jejuni	1634	1282	78
Chlamydia trachomatis	895	630	71
Chlamydia pneumoniae	1053	646	62
D.radiodurans	3194	2133	67
Escherichia coli	4285	3308	77
Haemophilus influenzae	1695	1497	88
Helicobacter pylori	1578	1070	68
Mycobacterium tuberculosis	3924	2456	63
Mycoplasma genitalium	471	374	79
Mycoplasma pneumoniae	680	419	62
Neisseria meningitidis	2081	1446	70
Pseudomonas aeruginosa	5567	4166	75
Rickettsia prowazekii	836	673	81
Synechocystis sp.	3168	2048	65
Thermotoga maritima	1858	1497	81
Treponema pallidum	1036	705	68
Vibrio cholerae	3828	2715	71
Ureaplasma urealyticum	613	398	64
Xylella fastidiosa	2766	1481	54
Eukaryotes
S.cerevisiae	5964	2158	36
Total	68571	45350	66

^aNewly added genomes are underlined.

^bThe low fraction of proteins assigned to COGs is probably due to over-prediction of protein-coding genes in the original genome annotation (see text and Table 2)

^cThe low fraction of proteins assigned to COGs is due to the fact that part of the genome consists of multiple plasmids that code for poorly conserved proteins