1. Determine a sequence alignment for your protein

    1.1 BLAST
    1.2 CLUSTAL W
    1.3 MSF - GCG


    1.1 BLAST - Click here to open a BLAST window - 

Use BLAST to generate a sequence alignement for your protein of interest :
Paste your protein sequence in one-letter code in the Enter Query Sequence field, choose your database and other relevant options, then press the BLAST! button.
After the result page is displayed, open the Formatting options section and select "Alignment as Plain Text" in the Show field
and "Flat query anchored with letters for identities" in the Alignment view field, then press the Reformat button.

CD-Search :
If you selected the "Do CD-Search" option and a putative conserved domain was detected, you can click on the image and then on one of the boxes, and you will be taken to the Conserved Domain Database of NCBI.
From there, select "Format: Plain Text" instead of "Format: Hypertext" in the "Sequence Alignment" section, then click on "Reformat".

Save your alignment :
Use the "Save as..." function of your browser to save this alignement to a file (Save as text). Be sure to remember in which directory you save this file as you will use it in step 2.

    1.2 CLUSTAL W - Click here to open a CLUSTAL W window - 

Use CLUSTAL W to generate a multiple sequence alignement for your protein of interest :
Paste several protein sequences in Pearson/Fasta format. The first sequence will be your "query" sequence and should be identical to the sequence used in your structure file (PDB).

Select "Clustalw" in the Output format field, and "aligned" in the Output order field, chose any relevant parameters and press the SUBMIT button.

Scroll the next page down to "Result files (text)" and click on the CLUSTALW hypertext link.
Use the "Save as..." function of your browser to save this alignement to a file (Save as text). Be sure to remember in which directory you save this file as you will use it in step 2.

    1.3 MSF - GCG

MSF is the multiple sequence alignment format of the GCG sequence analysis package.
If you have access to the GCG package, you can use an alignment file in NSF format with ProtSkin (go to step 2)