Research article
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
1 Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
2 Department of Bioengineering, University of California, San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
3 PhD program in Bioinformatics, University of California, San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
BMC Systems Biology 2008, 2:79 doi:10.1186/1752-0509-2-79
Published: 16 September 2008Additional files
Additional file 1:
Table S1. Carbon, nitrogen, and sulfur sources, which enabled growth of iJN746.
Format: DOC Size: 174KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 2:
Table S2. Essentials genes predicted correctly in iJN746 compared with experimental data of P. aeruginosa.
Format: DOC Size: 82KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 3:
Figure S1. Schematic representation of in silico gene essentiality in iJN746 (iLB medium) compared experimental data of gene essentiality in P. aeruginosa [83].
Format: DOC Size: 34KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 4:
Table S3. False-positive essential genes in iJN746 when compared with P. aeruginosa's experimental data [83].
Format: DOC Size: 80KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 5:
Table S4. False-negative essential genes in iJN746. Genes that were not predicted to be essential in iJN746 but were reported as essential genes in P. aeruginosa [83].
Format: DOC Size: 73KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 6:
Table S5. Predicted essential genes in Glucose-iM9 minimal medium. Not shown are genes that were also predicted to be essential in iLB rich medium.
Format: DOC Size: 70KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 7:
Table S6. PHA polymer composition found in different Pseudomonas strains sorted by carbon sources.
Format: DOC Size: 52KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 8:
Table S7. List of metabolites in iJN746. The file contains a detail list of metabolites present in the metabolic reconstruction. The molecular formulae, the charge as well as the KeggID are shown.
Format: XLS Size: 183KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 9:
Table S8. List of the reactions contain in iJN746. The file details the reactions account in the metabolic reconstruction. The official name, the equation of the reaction, the subsystem, the EC number and de GPR association is shown.
Format: XLS Size: 277KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 10:
Table S9. List of biomass components in iJN746. This file contains the complete list of compounds which are part of Pseudomonas putida biomass.
Format: DOC Size: 49KB Download file
This file can be viewed with: Microsoft Word Viewer
