Domain families sequence motifs

In the absence of activating cofactors, the catalytic domain is subject to autoinhibition by the regulatory domain. A sequence motif is found in the regulatory domain, which serves as a pseudosubstrate. It resembles the consensus sequence for phosphorylation sites of protein kinase C, but does not have a Ser or Thr residue for phosphorylation. This sequence motif is found in all protein kinase C family members. It is assumed that the active center is inhibited by occupation by the pseudosubstrate. 

The GEFs for the Rho-family of small GTPases contain a characteristic sequence motif, the Dbl homology domain, which encodes the nucleotide exchange activity... 

Motif detection involves searching for one sequence within another and is based on the assumption that one sequence is a part of another. Protein motifs are generally short sequences that represent conserved domains (CDs) or characterize protein families. Nucleotide motifs can range in size from full genes within the genome to short enhancer elements. 

Members from the KorB domain family are characterized by the DNA-binding helix-turn-helix motif (a-3 and a-4). Examples of this protein domain family include the well-studied DNA-binding KorB domain protein, the three-dimensional structure of which has been solved with its operator (PDB accession code lr71, DNA/RNA-binding 3-helical bundle fold Fig. 2a). Amino acid residues outside the HTH motif (Thr-211 and Arg-240) determine the sequence-specific DNA binding (35) (Fig. 2a). 

To discover protein functional or structural sequence motifs, you could select proteins belonging to a given protein family based on sequence similarity, structure, annotation, or other means (23,37,38). You might further refine the selection to only include proteins from organisms with a particular feature, such as the ability to live in extreme environments (39). Another protein motif discovery application uses information from protein-protein interaction experiments. You can assemble a set of proteins that bind to a common host protein, to discover sequence motifs for the interacting domains. 

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