Table 6. Extract of reconstructions and their key properties that were constructed in accordance with this protocol.
For a complete list of reconstructions, constructed in part or in full in accordance with this protocol can be found at http://gcrg.ucsd.edu/In_Silico_Organisms/Other_Organisms. This website is continuously updated. GR – genes in reconstruction. Mets – metabolites, Rnxs – reactions, Comp – compartments, Ref – reference. Please refer to Table S1 for compartment abbreviations.
| Organism | Strain | Genes | Version | GR | Mets | Rxns | Comp | Ref |
|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | 4,225 | model_v3 | 844 | 988 | 1,020 | 2 (c,e) | 75 | |
| Escherichia coli | K12 MG1655 | 4,405 | iAF1260 | 1,260 | 1,039 | 2,077 | 3 (c,e,p) | 65 |
| Helicobacter pylori | 26695 | 1,632 | iIT341 | 341 | 485 | 476 | 2 (c,e) | 76 |
| Pseudomonas putida | KT2440 | 5,350 | iNJ746 | 746 | 911 | 950 | 3 (c,p,e) | 57 |
| Pseudomonas putida | KT2440 | 5,350 | iJP815 | 815 | 886 | 877 | 2 (c,e) | 96 |
| Pseudomonas aeruginosa | PA01 | 5,640 | iMO1056 | 1,056 | 760 | 883 | 2 (c,e) | 97 |
| Mycoplasma genitalium | G-37 | 521 | iPS189 | 189 | 274 | 262 | 2 (c,e) | 98 |
| Lactobacillus plantarum | WCFS1 | 3,009 | 721 | 531 | 643 | 2 (c,e) | 73 | |
| Streptomyces coelicolor | A3(2) | 8,042 | 700 | 500 | 700 | 2 (c,e) | 99 | |
| Leishmania major | Friedlin | 8,370 | iAC560 | 560 | 1,101 | 1,112 | 8 (a,f,y,c,e,m,r,n) | 100 |
| Saccharomyces cerevisiae | Sc288 | 6,183 | iMM904 | 904 | 713 | 1,412 | 8(c,e,m,x,n,r,v,g) | 101 |
| Homo sapiens | 28,783 | Recon 1 | 1,496 | 2,766 | 3,311 | 8 (c,e,m,x,n,r,v,g) | 15 |