Table 2.

Summary of BLAST similarity searches, showing the distribution of best hits across the three domains of life (and viruses/phages). (Only open reading frames of at least 300 bp were considered. Database searched: UniREF (08/2004). ORFs generating no hits or hits below 80 bits were counted under ‘no homology’. Assembly depth correction: ORFs from highly covered parts of the assembly were given proportionally more weight, because they represent more abundant species in the environment. The analysis was repeated with other parameters, and for longer, more reliable ORFs (greater than or equal to 450 nt), similar results were obtained. When lowering the threshold for accepting homologies from 80 to 60 bits in the BLAST scoring scheme, ca 20% more assignments were possible, but they are likely to include a considerable number of false positives.)

	best hit prokaryotic (%)	best hit archaeal (%)	best hit eukaryotic (%)	best hit phage/virus (%)	no homology (%)
farm soil	48.7	2.3	1.1	0.2	47.7
Sargasso sea	69.5	2.0	2.4	0.3	25.8
whale falls	61.4	1.3	1.2	0.2	35.9
acid mine drainage	26.6	42.5	0.5	0.1	30.3