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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b3617 b0160 b0517 b1982 b4374 b0675 b2361 b2291 b0505 b4388 b0112 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370030 (mmol/gDw/h)
  Minimum Production Rate : 1.416409 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.687521
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.251294
  EX_pi_e : 0.356933
  EX_so4_e : 0.093181
  EX_k_e : 0.072227
  EX_fe2_e : 0.005943
  EX_mg2_e : 0.003210
  EX_ca2_e : 0.001926
  EX_cl_e : 0.001926
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 52.336539
  EX_co2_e : 34.056512
  EX_h_e : 8.777201
  Auxiliary production reaction : 1.416409
  EX_ac_e : 1.122215
  EX_alltn_e : 0.001445
  DM_mththf_c : 0.001196
  DM_5drib_c : 0.000248
  DM_4crsol_c : 0.000083

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