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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b1278 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b1852 b4388 b4138 b4123 b0621 b2223 b4381 b2406 b2197 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408410 (mmol/gDw/h)
  Minimum Production Rate : 0.431333 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 16.378010
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.990037
  EX_pi_e : 0.393955
  EX_so4_e : 0.102846
  EX_k_e : 0.079719
  EX_fe2_e : 0.006559
  EX_mg2_e : 0.003543
  EX_ca2_e : 0.002126
  EX_cl_e : 0.002126
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 32.496163
  EX_co2_e : 19.405854
  EX_h_e : 12.648698
  EX_ac_e : 7.033714
  Auxiliary production reaction : 0.431333
  EX_succ_e : 0.425886
  EX_ura_e : 0.289623
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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