Genomes …

Genomes are grouped by domain in the pop-up menus. First the Bacteria are listed, then the Archaea and then Eukaryota.

Within each domain genomes are listed in alphabetical order.

Genome query for

List best matches

This query simply lists each ORF's best BLASTP matches, from the selected genome.
more information...

Choose a BLASTP cutoff e-value (1.0e-300 to 1.0e-3): 1.0e-
(You may select a range of BLASTP cutoff e-values for this analysis by entering first.last.step (e.g., 10.100.5 would result in 19 separate analyses, at 10, 15, 20, 25, ..., 95, 100. If you omit the final number (e.g. 10.100) the step size defaults to 10. If you enter only a single number (e.g. 10) the query runs a single analysis. Note that "Results from my last query" is not updated if you select a range of BLASTP e-values.))

Choose a genome:

Maximum number of hits displayed per ORF:

Include any match.
Exclude self-match.
Exclude matches to self genome.

Display ORFs with no matches.
Display ORFs with at least one match.