MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b1478 b3399 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b1479 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b3844 b3236 b1779 b2690 b2463 b3962 b1982 b2210 b4267 b0675 b2361 b1415 b3551 b1014 b3945 b4219 b1832 b1778 b4381 b2406 b0112 b2868 b0114 b0509 b3125 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b4266 b1813 b1517 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.272977 (mmol/gDw/h)
  Minimum Production Rate : 0.051091 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.000537
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.093304
  EX_pi_e : 0.365498
  EX_so4_e : 0.068741
  EX_k_e : 0.053283
  EX_fe2_e : 0.004384
  EX_mg2_e : 0.002368
  EX_ca2_e : 0.001421
  EX_cl_e : 0.001421
  EX_cu2_e : 0.000194
  EX_mn2_e : 0.000189
  EX_zn2_e : 0.000093
  EX_ni2_e : 0.000088

Product: (mmol/gDw/h)
  EX_h2o_e : 43.860613
  EX_co2_e : 26.805356
  EX_h_e : 10.353394
  EX_pyr_e : 4.879543
  EX_ac_e : 0.922454
  EX_hxan_e : 0.465286
  EX_mththf_e : 0.465103
  Auxiliary production reaction : 0.051091
  EX_xan_e : 0.007143
  DM_5drib_c : 0.000183
  EX_dxylnt_e : 0.000183
  DM_4crsol_c : 0.000061

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

---

Last updated: 21-Sep-2023
Contact