Hi,

To check for conserved sequences in your protein sequences, you please try your hand at protein BLAST/ SMART BLAST respectively.

This step will help you to retrieve a long list of proteins which are similar to your query protein.

Once that is done, the second step that you must follow is of - MULTIPLE SEQUENCE ALIGNMENT (MSA) using COBALT (NCBI based tool that you can use directly after your BLAST) or Clustal W or Clustal Omega.

Suppose, you used Clustal Omega, okay, so, in the query box, you will attach the BLAST result (query protein + similar proteins in FASTA format).

Simply submit these and run MSA.

You will get your output where you will be able to see the completely matching, mismatching or gaps.

To find out CONSERVED sequences, you will notice that the domains and motifs in all the sequences will be somewhat same, with only 1-2 changed amino acid residues. The rest will be the same. Those patches of sequences will be your highly conserved sequences.

I hope my answer was helpful.

Best regards,

SQ

Dear Sahar,

Thank you for the explicit answer. Would begin the BLAST journey

All the best!