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

ORFs found in a set of genomes

Construct a set of genomes by adding or removing genomes from one of the following preselects:

A blank list.
All genomes preselected.
All archaeal genomes preselected.
All bacterial genomes preselected.

After you have defined this set, this query then returns all ORFs from a selected genome that match, or that do not match, subsets of the chosen set.
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:

List genomes that match an ORF.
List genomes that do not match an ORF.

Use simple matches.
Use reciprocal best matches (with allowance for near ties, at 95% tolerance).