Bioinformatics Advance Access originally published online on May 14, 2004
Bioinformatics 2004 20(16):2644-2655; doi:10.1093/bioinformatics/bth298
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway
1 Complex Genetics Group, Department of Biomedical Genetics, Stratenum 2.117, University Medical Center Utrecht, PO Box 80030, 3508 TA Utrecht, The Netherlands and 2 Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
Received on March 3, 2004; accepted on April 26, 2004
Advance Access Publication May 14, 2004
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be conserved between eukaryotes and prokaryotes. However, the degree to which these genes share their functional context as members of the same pathway in the prokaryotic domain is less clear.
Results: The co-occurrence of gene families involved in Atx1p-mediated copper transport in the genomes and operon structures of 80 non-redundant prokaryotes was investigated. For this purpose, we developed a Web tool (SHOPS) to display the operon context for a given set of proteins. In total, a set of 43 putative operons was identified. These were found to be involved in a variety of pathways and indicate a large diversity in the functional context of the individual gene family members.
Availability: The SHOPS tool can be found at http://www.bioinformatics.med.uu.nl/shops. Supplemental data are available at http://humgen.med.uu.nl/publications/vanbakel/pathway/
Supplementary information: For additional information on our datasets and for the supplemental figures referred to in the text, please see http://humgen.med.uu.nl/publications/vanbakel/pathway/. The Web-based tool, SHOPS, can be found at http://www.bioinformatics.med.uu.nl/shops/
Contact: t.n.wijmenga{at}med.uu.nl
* To whom correspondence should be addressed.
NMCLS, University Medical Center Street, Radboud, Nijmegen, The Netherlands.
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