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 (23 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b3942 b1732 b1241 b0351 b2744 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b2690 b2463 b2210 b4374 b0675 b3551 b2799 b3945 b1602 b0507 b2223 b4219 b1832 b1778 b3915 b1727 b0529 b1539 b1380 b1710 b2480 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527369 (mmol/gDw/h)
  Minimum Production Rate : 0.213546 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.574932
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.695542
  EX_pi_e : 0.508703
  EX_so4_e : 0.132802
  EX_k_e : 0.102939
  EX_fe3_e : 0.008470
  EX_mg2_e : 0.004575
  EX_ca2_e : 0.002745
  EX_cl_e : 0.002745
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.624592
  EX_co2_e : 31.952953
  EX_h_e : 7.590598
  EX_ac_e : 2.309358
  EX_etoh_e : 0.464033
  Auxiliary production reaction : 0.213546
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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