Protein Science, Vol 1, Issue 12 1677-1690, Copyright © 1992 by Cold Spring Harbor Laboratory Press

ARTICLE

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III

P. BORK, C. OUZOUNIS, C. SANDER, M. SCHARF, R. SCHNEIDER and E. SONNHAMMER
European Molecular Biology Laboratory, Heidelberg, Germany

With the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S.G., et al., 1992, Nature 357, 38-46). We have tested the predictive power of computer sequence analysis on the 176 probable protein products of this chromosome, after exclusion of six problem cases. When the results of database similarity searches are pooled with prior knowledge, a likely function can be assigned to 42% of the proteins, and a predicted three-dimensional structure to a third of these (14% of the total). The function of the remaining 58% remains to be determined. Of these, about one-third have one or more probable transmembrane segments. Among the most interesting proteins with predicted functions are a new member of the type X polymerase family, a transcription factor with an N-terminal DNA-binding domain related to GAL4, a ``fork head'' DNA-binding domain previously known only in Drosophila and in mammals, and a putative methyltransferase. Our analysis increased the number of known significant sequence similarities on chromosome III by 13, to now 67. Although the near 40% success rate of identifying unknown protein function by sequence analysis is surprisingly high, the information gap between known protein sequences and unknown function is expected to widen and become a major bottleneck of genome projects in the near future. Based on the experience gained in this test study, we suggest that the development of an automated computer workbench for protein sequence analysis must be an important item in genome projects.
CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				C. H. Sterling and J. B. Sweasy DNA Polymerase 4 of Saccharomyces cerevisiae Is Important for Accurate Repair of Methyl-Methanesulfonate-Induced DNA Damage Genetics, January 1, 2006; 172(1): 89 - 98. [Abstract] [Full Text] [PDF]

				L. Pintard, D. Kressler, and B. Lapeyre Spb1p Is a Yeast Nucleolar Protein Associated with Nop1p and Nop58p That Is Able To Bind S-Adenosyl-L-Methionine In Vitro Mol. Cell. Biol., February 15, 2000; 20(4): 1370 - 1381. [Abstract] [Full Text]

				S. M. Laidlaw, M. A. Anwar, W. Thomas, P. Green, K. Shaw, and M. A. Skinner Fowlpox Virus Encodes Nonessential Homologs of Cellular Alpha-SNAP, PC-1, and an Orphan Human Homolog of a Secreted Nematode Protein J. Virol., August 1, 1998; 72(8): 6742 - 6751. [Abstract] [Full Text] [PDF]

				C. A. Clairmont and J. B. Sweasy The Pol beta -14 Dominant Negative Rat DNA Polymerase beta  Mutator Mutant Commits Errors during the Gap-Filling Step of Base Excision Repair in Saccharomyces cerevisiae J. Bacteriol., May 1, 1998; 180(9): 2292 - 2297. [Abstract] [Full Text]

				M. Oliveros, R. J. Yanez, M. L. Salas, J. Salas, E. Vinuela, and L. Blanco Characterization of an African Swine Fever Virus 20-kDa DNA Polymerase Involved in DNA Repair J. Biol. Chem., December 5, 1997; 272(49): 30899 - 30910. [Abstract] [Full Text] [PDF]

				S. Ernstsson, S. Pierrou, M. Hulander, A. Cederberg, M. Hellqvist, P. Carlsson, and S. Enerback Characterization of the Human Forkhead Gene FREAC-4. EVIDENCE FOR REGULATION BY WILMS' TUMOR SUPPRESSOR GENE (WT-1) AND p53 J. Biol. Chem., August 30, 1996; 271(35): 21094 - 21099. [Abstract] [Full Text] [PDF]

				M. Hellqvist, M. Mahlapuu, L. Samuelsson, S. Enerbäck, and P. Carlsson Differential Activation of Lung-specific Genes by Two Forkhead Proteins, FREAC-1 and FREAC-2 J. Biol. Chem., February 23, 1996; 271(8): 4482 - 4490. [Abstract] [Full Text] [PDF]

				M. Sawaya, H Pelletier, A Kumar, S. Wilson, and J Kraut Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism Science, June 24, 1994; 264(5167): 1930 - 1935. [Abstract] [PDF]

				B. Dujon Mapping and Sequencing the Nuclear Genome of the Yeast Saccharomyces cerevisiae: Strategies and Results of the European Enterprise Cold Spring Harb Symp Quant Biol, January 1, 1993; 58(0): 357 - 366. [Abstract] [PDF]

				A. Nyyssola, J. Kerovuo, P. Kaukinen, N. von Weymarn, and T. Reinikainen Extreme Halophiles Synthesize Betaine from Glycine by Methylation J. Biol. Chem., July 14, 2000; 275(29): 22196 - 22201. [Abstract] [Full Text] [PDF]