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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b3617 b0030 b2407 b1982 b0261 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.471642 (mmol/gDw/h)
  Minimum Production Rate : 1.807779 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.983114
  EX_nh4_e : 12.325338
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.262728
  EX_so4_e : 0.118769
  EX_k_e : 0.092061
  EX_fe2_e : 0.007575
  EX_mg2_e : 0.004091
  EX_ca2_e : 0.002455
  EX_cl_e : 0.002455
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000326
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.099193
  EX_co2_e : 19.373363
  EX_h_e : 14.063696
  EX_ac_e : 2.497889
  Auxiliary production reaction : 1.807779
  DM_oxam_c : 0.000528
  DM_5drib_c : 0.000316
  DM_4crsol_c : 0.000105

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