1. Go to the Entrez section.
2. Click on Proteins.
3. Enter the name of the protein you want in the text field and click Search. You can also limit your search by selecting a field to search, e.g. setting Search Field to Protein Name will restrict hits to sequences for your protein only, not returning results that have your protein named just incidentally.
4. Click on Retrieve Sequences at the next screen.
5. Browse the results to find your desired protein sequence. If you need more information about a sequence, click on GenPept Report.
6. Once you have chosen a sequence, you will need to save the FASTA format of the sequence. The FASTA format is the format accepted by most analysis programs. You can access this by clicking FASTA in the entry for your sequence in the list of hits.
1. Go to the ScanProsite submission page.
2. Copy and paste your protein sequence into the text box.
3. Check the "Exclude patterns with a high probability of occurence" box. This will reduce hits based on short amino acid patterns, which often are just random. You might want to uncheck the box if you are looking for a short pattern in your sequence.
4. Examine the results. Each hit has a link to more information about the pattern, so explore these links to learn more about any patterns found, and other proteins in which they are found as well. Note that the page describing a certain pattern or signature has a field marked Consensus Pattern. You can use this pattern for PHI-BLAST searches, described in the next section.
1. Go to the PHI-BLAST page.
2. Copy and paste your amino acid sequence into the box marked Enter here your amino acid sequence.
3. Paste the Consensus Pattern that you found in the ScanProsite search into the Pattern for use in PHI-BLAST box.
4. Click Submit Query and examine the list of hits you get. Note any groups of homologues that are not homologous to your protein -- these are good indications of a family related to your protein through your pattern.
1. Look at the three-dimensional structure of the protein using Rasmol (A how-to for this should be up shortly). Find functionally important parts -- this will need a good knowledge of the bioogy of the protein. Now use these sections of the protein sequence in BLAST and PSI-BLAST searches.
2. Use the program Divide-and-BLAST. More information about the program and its use can be found here.