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Bioinformatics Advance Access published online on October 4, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl506
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© 2006 The Author(s)
Received July 27, 2006
Revised August 28, 2006
Accepted September 24, 2006

Discovery note

Predicted function of the vaccinia virus G5R protein

Melissa Da Silva 1, Ling Shen 1, Vasily Tcherepanov 1, Cristalle Watson 1, and Chris Upton 1 *

1 Department of Biochemistry and Microbiology, University of Victoria, Petch Building 207, Ring Road, Victoria, BC, V8P 5C2, Canada

* To whom correspondence should be addressed.
Chris Upton, E-mail: cupton{at}uvic.ca


  Abstract

Motivation: Of the approximately 200 proteins that have been identified for the vaccinia virus genome, many are currently listed as having an unknown function, and 7 of these are also found in all other poxvirus genomes that have been sequenced. The G5R protein of vaccinia virus is included in this list, and to date, very little is known about this essential and highly conserved protein. Conventional similarity searches of protein databases do not identify significantly similar proteins, and experimental approaches have been unsuccessful at determining protein function.

Results: Using HHsearch, a Hidden Markov Model (HMM) comparison search tool, the G5R protein was found to be similar to both human and archaeal flap endonucleases (FEN-1) with 96% probability. The G5R protein structure was subsequently successfully modeled using the Robetta protein structure prediction server with an archaeal FEN-1 as the template. The G5R model was then compared to the human FEN-1 crystal structure and was found to be structurally similar to human FEN-1 in both active site residues and DNA substrate binding regions.

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman
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