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Open Access Highly Accessed Research article

An in silico platform for the design of heterologous pathways in nonnative metabolite production

Sunisa Chatsurachai1, Chikara Furusawa23* and Hiroshi Shimizu3*

Author Affiliations

1 Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

2 Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan

3 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan

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BMC Bioinformatics 2012, 13:93  doi:10.1186/1471-2105-13-93

Published: 11 May 2012

Additional files

Additional file 1 :

List of reactions used in this study. The sheet “kegg_reaction_information” contains the metabolic reactions from the KEGG ligand database.

Format: XLS Size: 5.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2 :

List of connectable nonnative metabolites whenCorynebacterium glutamicumwas used as the host. The sheet “C.glutamicum_connectable” contains all of the connected metabolites, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 12MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3 :

List of connectable nonnative metabolites whenEscherichia coliwas used as the host. The sheet “E.coli_connectable” contains all of the connected metabolites, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 1.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4 :

List of connectable nonnative metabolites whenSaccharomyces cerevisiaewas used as the host. The sheet “S.cerevisiae_connectable” contains all of the connected metabolites, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 5.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5 :

List of producible nonnative metabolites whenCorynebacterium glutamicumwas used as the host.The sheet “C.glutamicum_maxTarget” contains all of the producible metabolites under the target maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database. The sheet “C.glutamicum_maxBiomass” contains the producible metabolites under the biomass maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 9.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6 :

List of producible nonnative metabolites whenEscherichia coliwas used as the host.The sheet “E.coli_maxTarget” contains all of the producible metabolites under the target maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database (nonstandard format). The sheet “E.coli_maxBiomass” contains the producible metabolites under the biomass maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7 :

List of producible nonnative metabolite whenSaccharomyces cerevisiaewas used as the host. The sheet “S.cerevisiae_maxTarget” contains all of the producible metabolites under the target maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database. The sheet “S.cerevisiae_maxBiomass” contains the producible metabolites under the biomass maximization condition, including heterologous reaction(s), information about gene(s) from the KEGG database and the minimum Km value from the BRENDA database.

Format: XLS Size: 1.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data