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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b1479 b2925 b2097 b3617 b3844 b3236 b0907 b1779 b2463 b3962 b1525 b0104 b3946 b2210 b0825 b4267 b1033 b1415 b3551 b1014 b2799 b0726 b3945 b4138 b4123 b0621 b4219 b1832 b1778 b0114 b1539 b1380 b1710 b2480 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504979 (mmol/gDw/h)
  Minimum Production Rate : 0.086957 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.747318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.453735
  EX_pi_e : 0.487106
  EX_so4_e : 0.127164
  EX_k_e : 0.098568
  EX_fe2_e : 0.008110
  EX_mg2_e : 0.004381
  EX_cl_e : 0.002628
  EX_ca2_e : 0.002628
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.159953
  EX_co2_e : 31.737885
  EX_h_e : 8.407129
  EX_ac_e : 3.593036
  EX_mal__L_e : 0.086957
  EX_dxylnt_e : 0.000225
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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