path :: protein back-translation and alignment

Examples

Human and Rat platelet-derived growth factor
Platelet-derived growth factor is a potent mitogen for cells of mesenchymal origin. Binding of this growth factor to its affinity receptor elicits a variety of cellular responses. It is released by platelets upon wounding and plays an important role in stimulating adjacent cells to grow and thereby heals the wound.
The two proteins share high similarity at the amino acid level on the subsequences 1 – 83 and 112 – 194. The amino acids 84 – 111 can be easily aligned with a frameshift, while classic protein alignment reveals little similarity in these areas.
Serpant venon neurotoxins
Two presynaptic neurotoxins from two higher snakes of the Elapidae family (Bungarus candidus and Naja mossambica), aligned using a translation-dependent matrix of evolutionary distance 0.5. Most of the sites are conserved: the primary metal binding site and the putative hidrophobic channel are before the frameshift, only the last fourth part of the catalitic network seems affected.
ABO antigens
The ABO locus is located on chromosome 9. It contains 7 exons that span more than 18 kb of genomic DNA. Exon 7 is the largest and contains most of the coding sequence. The ABO locus has three main alleleic forms: A, B, and O. The A allele encodes a glycosyltransferase that bonds α-N-Acetylgalactosamine to D-galactose end of H antigen, producing the A antigen. The B allele encodes a glycosyltransferase that joins α-D-galactose bonded to D-galactose end of H antigen, creating the B antigen.
In case of O allele the exon 6 contains a deletion that results in a loss of enzymatic activity. The O allele differs slightly from the A allele by deletion of a single nucleotide – Guanine at position 261. The deletion causes a frameshift and results in translation of an almost entirely different protein that lacks enzymatic activity. This results in H antigen remaining unchanged in case of O groups.