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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b4069 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b2463 b2210 b1033 b3551 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b0584 b2492 b0904 b1380 b1710 b2480 b1518 b1206 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478405 (mmol/gDw/h)
  Minimum Production Rate : 0.921288 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.020767
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.166734
  EX_pi_e : 0.461472
  EX_so4_e : 0.120472
  EX_k_e : 0.093381
  EX_fe2_e : 0.007684
  EX_mg2_e : 0.004150
  EX_ca2_e : 0.002490
  EX_cl_e : 0.002490
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.675047
  EX_co2_e : 36.120404
  EX_h_e : 6.516874
  Auxiliary production reaction : 0.921288
  EX_ac_e : 0.278521
  EX_mththf_e : 0.000214
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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