Geneious automatically determines the sequence type (nucleotide or protein) and shows the appropriate settings for that type. The default database selected is Nucleotide Collection (nr/nt), which contains protein (nr) and nucleotide (nt) accessions. As P00656 is a protein sequence, you can either use tblastn to query the amino acid sequence against the translated nucleotide database, or use blastp to query the protein database. See Section 4 for more information on the different BLAST algorithms available.
Select blastp for the Program, and ensure Results is set to Hit Table, and Retrieve is set to Matching Region. This setting will return a list of the top hits and an alignment for each one, plus a query-centric alignment.
Leave the other settings as they are, then click the Search button. Geneious will then send your query to the NCBI and create a new search folder. This will appear as a subfolder of the folder that contains your query sequence.
The folder name shows the sequence used for the query, the database searched, the program used to perform the search, and the number of results returned in brackets.
Section 2: Viewing the results
Section 3: Batch searching
Section 4: Search options