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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b2930 b4232 b3697 b3925 b0871 b3617 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b0477 b4139 b0675 b2361 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277173 (mmol/gDw/h)
  Minimum Production Rate : 0.203410 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.860391
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.480469
  EX_pi_e : 0.674182
  EX_so4_e : 0.069798
  EX_k_e : 0.054102
  EX_mg2_e : 0.002404
  EX_fe2_e : 0.002288
  EX_fe3_e : 0.002164
  EX_ca2_e : 0.001443
  EX_cl_e : 0.001443
  EX_cu2_e : 0.000197
  EX_mn2_e : 0.000192
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 44.478849
  EX_co2_e : 26.407032
  EX_h_e : 9.384321
  EX_pyr_e : 4.755177
  EX_acald_e : 0.889002
  EX_his__L_e : 0.480321
  Auxiliary production reaction : 0.203410
  EX_xan_e : 0.007253
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000062

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