A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?
The question of protein homology versus analogy arises when proteins share a common function or a common structural fold without any statistically significant amino acid sequence similarity. Even though two or more proteins do not have similar sequences but share a common fold and the same or closely related function, they are assumed to be homologs, descendant from a common ancestor. The problem of homolog identification is compounded in the case of proteins of 100 or less amino acids. This is due to a limited number of basic single domain folds and to a likelihood of identifying by chance sequence similarity. The latter arises from two conditions: first, any search of the currently very large protein database is likely to identify short regions of chance match; secondly, a direct sequence comparison among a small set of short proteins sharing a similar fold can detect many similar patterns of hydrophobicity even if proteins do not descend from a common ancestor. In an effort to identify distant homologs of the many ubiquitin proteins, we have developed a combined structure and sequence similarity approach that attempts to overcome the above limitations of homolog identification. This approach results in the identification of 90 probable ubiquitin-related proteins, including examples from the two prokaryotic domains of life, Archaea and Bacteria.
Bienkowska
Jadwiga R
JR
Serono Reproductive Biology Institute, One Technology Place, Rockland, MA 02370, USA. Jadwiga.Bienkowska@serono.com
Hartman
Hyman
H
Smith
Temple F
TF
D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000378:metabolism*; D016415:Sequence Alignment; D017385:Sequence Homology; D013466:Sulfurtransferases / Q000235:genetics / Q000378:metabolism; D025801:Ubiquitin / Q000235:genetics* / Q000378:metabolism
D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D025801:Ubiquitin; C411655:thiS protein, E coli; D013466:Sulfurtransferases; C085585:molybdopterin synthase