Distantly similar sequences

Now that we know the amino acid sequences of many thousands of proteins from many himdreds of different biological species, it is obvious that different proteins fall into families more or less distantly related to one another. Proteins with different but similar functions tend to have very obviously similar amino acid sequences, indicating a common ancestry. Accordingly, we can argue the other way round, and, if we find a protein (or gene) of unknown function but with a similar sequence to one whose function is known, we can infer that the function of the new protein is likely to be similar to that of its cousin protein. 

Normal hemoglobin molecules are complex, three-dimensional structures consisting of four chains of amino acids known as polypeptide chains. Two of these chains are known as alpha subunits with 141 amino acid residues each, and the remaining polypeptide chains are the beta subunits with 146 amino acid residues each. The sequences of amino acids in the alpha and beta subunits are different, but fold up via noncovalent interactions to form similar three-dimensional structures. When a polypeptide chain arranges itself in space, i.e., when it folds, amino acids that were far apart in the chain are brought closer in proximity. The final overall shape of the protein molecule is influenced by (1) the amino acids in the chain, and (2) the interactions that are possible between distant amino acids. 

Finally, it should be mentioned that there are a number of protein domains that have some structural resemblance to ubiquitin, although a sequence similarity cannot be established - not even by the most sophisticated methods available today. It cannot be excluded that there are true instances of convergent evolution among these cases. However, it appears more likely that these proteins and domains represent distant members of the ubiquitin superfamily, which have undergone a fundamental change of function and no longer need to conserve sequence positions that are considered hallmarks of ubiquitin-like molecules. In particular three domain classes should be mentioned in this context. The PERM domain (4.1, ezrin,... 

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