Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
BACKGROUND
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.


BACKGROUND
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/
van Bakel
Harm
H
Complex Genetics Group, Department of Biomedical Genetics, Stratenum 2.117, University Medical Center Utrecht, PO Box 80030, 3508 TA Utrecht, The Netherlands.
Huynen
Martijn
M
Wijmenga
Cisca
C
D000465:Algorithms; D002352:Carrier Proteins / Q000235:genetics* / Q000378:metabolism*; D003300:Copper / Q000378:metabolism*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology; D014644:Genetic Variation / Q000235:genetics; D020407:Internet; D009876:Operon / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
C093341:ATX1 protein, S cerevisiae; D002352:Carrier Proteins; D029701:Saccharomyces cerevisiae Proteins; D003300:Copper