Bioinformatics Vol. 17 no. 6 2001
Pages 560-563
© 2001 Oxford University Press
Discovery Note |
Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana
Department of Plant Biology, University of Minnesota, 220 Bioscience Center, 1445 Gortner Ave, St Paul, MN, USA
Received on November 1, 2000
; revised on February 26, 2001
; accepted on March 7, 2001
Motivation: The completion of the Arabidopsis genome
offers the first opportunity to analyze all of the membrane protein
sequences of a plant. The majority of integral membrane proteins
including transporters, channels, and pumps contain hydrophobic
-helices and can be selected based on TransMembrane
Spanning (TMS) domain prediction. By clustering the predicted
membrane proteins based on sequence, it is possible to sort the
membrane proteins into families of known function, based on
experimental evidence or homology, or unknown function. This
provides a way to identify target sequences for future functional
analysis.
Results: An automated approach was used to select potential membrane protein sequences from the set of all predicted proteins and cluster the sequences into related families. The recently completed sequence of Arabidopsis thaliana , a model plant, was analyzed. Of the 25470 predicted protein sequences 4589 (18%) were identified as containing two or more membrane spanning domains. The membrane protein sequences clustered into 628 distinct families containing 3208 sequences. Of these, 211 families (1764 sequences) either contained proteins of known function or showed homology to proteins of known function in other species. However, 417 families (1444 sequences) contained only sequences with no known function and no homology to proteins of known function. In addition, 1381 sequences did not cluster with any family and no function could be assigned to 1337 of these.
Availability: Results from the analysis of all proteins of A.thaliana , source code for the programs, and links to primary data are available at the following WWW site: http://www.cbs.umn.edu/arabidopsis
Contact: jward{at}tc.umn.edu
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