You can access the Protein BLAST (blastp) from NCBI's BLAST home page.
You can also launch a protein blast from the protein record in NCBI's protein database. There is a "BLAST" link in the right menu of every protein record in the protein database.
Here's a protein record you can use to practice on:
To BLAST from this record, just click the Run BLAST link on the right side of the page.
Similar to nucleotide BLAST, you can also enter a FASTA sequence in the sequence window or an accession number from the protein database. When you click the BLAST link from a protein record, the accession number is loaded in the sequence window.
You can also choose to query a subrange of the protein: you will need to know the amino acid numbers of the range you wish to query. You can get details of ranges of a protein by conserved domain type from the Details section of the NCBI protein record.
For protein BLASTS, you have fewer options for databases to search, but more algorithm and matrix choices. You can search:
You can choose to exclude environmental samples, models (proteins with reference numbers beginning with XP), or non-redundant RefSeq proteins.
Similar to nucleotide BLAST, you can also choose to limit to, or exclude, specific organisms, or query using an Entrez (NCBI) formatted search string.
(Hint: for the sample protein linked above, try limiting to viruses in the Organism section)
Remember to open the Algorithm Parameters using the link below the BLAST button. These are optional, but can greatly improve your results.
The general guidelines for algorithm selection described above for nucleotide BLAST apply also to protein BLAST, except you have slightly different gap costs and you now have the choice of scoring matrices.
PAM or BLOSUM?
PSI-BLAST and PHI-BLAST
PSI-BLAST is Position-Specific Iterated BLAST. It is especially useful if you suspect weak sequence similarity due to evolutionary change, but still suspect overall conservation (such as a specific protein fold or function). PSI-BLAST creates a positional matrix--a PSSM: Position Specific Scoring Matrix--after your first BLAST iteration. It finds regions in this matrix of highest correlation between your query and the database matches, then weights these regions more heavily on successive iterations of the BLAST.
PHI-BLAST (Pattern Hit Initiated BLAST) is a subset of protein BLAST in which you can input a specific pattern that you want to find in all protein matches. It is useful when you are looking for a region of functional importance in proteins (such as specific binding sites). The pattern syntax is from PROSITE.
An example: [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV] (taken from NCBI's PHI-BLAST training materials)
This translates to mean: any one of the amino acids LIVMF followed by G followed by E followed by any single character followed by any one of GAS followed by any one of LIVM followed by any 5 to 11 characters followed by R followed by one of STAQ followed by A followed by any single character followed by one of LIVMA followed by any single character followed by one of STACV.
For more information on PHI-BLAST syntax (along with the above example), see the NCBI PHI-BLAST rules page.
You can also choose Filters and Masking from the section on those options (see this guide's Nucleotide BLAST section).
After selecting your parameters (remember: it's helpful to click the checkbox "Show results in a new window":
Hit the BLAST button!