Question

You have the gene sequence of a protein which has a proteolytic activity. How will you establish through tools of bioinformatics that this protein: (a) Has homologues in other organisms (b) Belongs to the chymotrypsin family (c) Has a database that can we used to trace the evolutionary history of this proteolytic protein

Answer 1

To establish the given information through tools of bioinformatics, the following steps can be taken:

(a) To find homologues in other organisms, the protein sequence can be used to perform a BLAST search against various protein databases such as UniProt, NCBI, and PDB. This will help in identifying similar proteins in other organisms and establishing their evolutionary relationship.

(b) To determine whether the protein belongs to the chymotrypsin family, the protein sequence can be compared to other known members of the family using tools such as CLUSTAL Omega or MUSCLE for multiple sequence alignment. The conserved residues and motifs of the chymotrypsin family can also be identified using PROSITE or Pfam databases.

(c) To trace the evolutionary history of the proteolytic protein, the protein sequence can be used to construct a phylogenetic tree using tools such as MEGA or Phylogeny.fr. The tree will show the evolutionary relationship of the protein with other related proteins and their divergence over time.

Overall, bioinformatics tools such as BLAST, multiple sequence alignment, and phylogenetic analysis can be used to establish the homology, family membership, and evolutionary history of a proteolytic protein.