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Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

Jorge Valdés1, Inti Pedroso1, Raquel Quatrini1, Robert J Dodson2, Herve Tettelin23, Robert Blake6, Jonathan A Eisen245 and David S Holmes1*

Author Affiliations

1 Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago Chile

2 J. Craig Venter Institute, Rockville, MD, USA

3 The Institute for Genomic Sciences, University of Maryland, Baltimore, MD, USA

4 University of California Davis Genome Center, Section of Evolution and Ecology, U.C. Davis, Davis, CA, USA

5 University of California Davis Genome Center, Dept of Medical Microbiology and Immunology, U.C. Davis, Davis, CA, USA

6 Division of Basic Pharmaceutical Sciences, Xavier University, New Orleans, LA, USA

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BMC Genomics 2008, 9:597  doi:10.1186/1471-2164-9-597

Published: 11 December 2008

Additional files

Additional file 1:

Gene lists for amino acid metabolism, cofactor biosynthesis and purine and pyrimidine metabolism. A list of genes in the A. ferrooxidans ATCC 23270 genome is provided that are predicted to be involved in amino acid metabolism, cofactor biosynthesis and purine and pyrimidine metabolism.

Format: XLS Size: 81KB Download file

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Additional file 2:

Phylogram of four different Rubisco enzymes in various bacteria. Phylogenetic tree of forms I (CbbL1, CbbL2), II (CbbM), and IV (RLP, Rubisco-like protein) of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) from various organisms. The multiple sequence alignments and trees were produced with ClustalW and visualized with MEGA. Bootstrap values indicated at the nodes are based on 1,000 trials. The RubisCOs from A. ferrooxidans are highlighted by blue boxes. Species names are as follows: Archaeoglobus fulgidus, Bacillus subtilis, Chlorobium limicola, Chlorobium tepidum, Hydrogenovibrio marinus, Ralstonia eutropha, Rhodobacter capsulatus, Rhodobacter sphaeroides, Rhodopseudomonas palustris, Rhodospirilum rubrum, Synechococcus sp. PCC6301, Thiobacillus intermedius, and Thiobacillus neapolitanus.

Format: PNG Size: 153KB Download file

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Additional file 3:

Gene lists and predicted properties for several metabolic and cellular processes. This data provides a list of genes and predicted properties for transposase families, hydrogenase systems, nutrient transport systems, osmotic balance, heavy metal resistance systems and toxic organic compounds extrusion systems deduced from the A. ferrooxidans ATCC 23270 genome sequence.

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Additional file 4:

Gene clusters predicted to be involved in nitrogen metabolism. This data provides a schematic representation of some of the gene clusters and genes predicted to be involved in nitrogen fixation.

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Additional file 5:

Genes predicted to be involved type IV pilus formation. This data provides a list of genes predicted to be involved type IV pilus formation.

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