Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins.
BACKGROUND
Assessing the false positive rate of function prediction methods is difficult, as it is hard to establish that a protein does not have a certain function. To determine to what extent proteins with similar sequences have a common function, we focused on photosynthesis-related proteins. A protein that comes from a non-photosynthetic organism is, undoubtedly, not involved in photosynthesis.


RESULTS
We show that function diverges very rapidly: 70% of the close homologs of photosynthetic proteins come from non-photosynthetic organisms. Therefore, high sequence similarity, in most cases, is not tantamount to similar function. However, we found that many functionally similar proteins often share short sequence elements, which may correspond to a functional site and could reveal functional similarities more accurately than sequence similarity.


CONCLUSIONS
These results shed light on the way biological function is conserved in evolution and may help improve large-scale analysis of protein function.
The Goodman faculty of life sciences, Bar Ilan University, Ramat Gan 52900, Israel.
Shaul
S
Ashkenazi
Rotem
R
Snir
Yanay
Y
Ofran
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D058977:Molecular Sequence Annotation; D010788:Photosynthesis; D011506:Proteins / Q000737:chemistry / Q000502:physiology; D017386:Sequence Homology, Amino Acid
D011506:Proteins