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 : u3hga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b2781 b3844 b1612 b1611 b4122 b2690 b1759 b3945 b4138 b4123 b0621 b4381 b2406 b0529 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.644890 (mmol/gDw/h)
  Minimum Production Rate : 0.032653 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 993.852544
  EX_h_e : 985.722365
  EX_o2_e : 276.121631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.912058
  EX_pi_e : 0.687371
  EX_so4_e : 0.162396
  EX_k_e : 0.125878
  EX_mg2_e : 0.005594
  EX_ca2_e : 0.003357
  EX_cl_e : 0.003357
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000446
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 993.842187
  EX_h2o_e : 545.300537
  EX_co2_e : 28.194657
  EX_succ_e : 0.672486
  EX_ura_e : 0.424670
  Auxiliary production reaction : 0.032653
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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.

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Last updated: 21-Sep-2023
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