Evolutionary classification of homeodomains.
OBJECTIVE
We performed multiple comparisons between available amino acid (aa) sequences of homeodomain(HOM)-containing proteins from a wide spectrum of animals to create an evolutionary classification of the proteins.


RESULTS
Based on results of statistical and special computational analyses of over 500 homeodomain aa sequences (HOMs) a novel system of concepts describing complex structural correlations between homologous proteins is proposed. This system includes such notions as differentiated isofunctionality of aa, chemotype, stereotype, local functional motifs, gradual conservativeness of aa positions, and group-specific domain patterns, as well as major categories of the evolutionary classification of HOMs (Division, Type, Branch, Class, Family, Series, Variety, Sort). Using this approach, a complete structural systematics of HOMs belonging to proteomes of eukaryotic animals is proposed.


CONCLUSIONS
The proposed structural classification of HOMs is in full agreement with the bulk of experimental data revealing complex functional similarities and differences among HOMs in terms of their expression patterns in developing embryos. It turn, this classification can provide answers regarding homology among homeodomains when experimental data are conflicting.
Gindilis
V
V
Reproductive Genetics Institute, Chicago, Illinois 60657, USA.
Goltsman
E
E
Verlinsky
Y
Y
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary
D018398:Homeodomain Proteins