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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1241 b0351 b4384 b2744 b0871 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b0937 b0411 b2799 b3945 b1602 b4381 b0452 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b2975 b3603 b0529 b2492 b0904 b3927 b1380 b2660 b1518 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368188 (mmol/gDw/h)
  Minimum Production Rate : 0.099087 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.323792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.174578
  EX_pi_e : 0.454244
  EX_so4_e : 0.092717
  EX_k_e : 0.071868
  EX_fe2_e : 0.005913
  EX_mg2_e : 0.003194
  EX_ca2_e : 0.001916
  EX_cl_e : 0.001916
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.023778
  EX_co2_e : 28.413522
  EX_h_e : 8.874132
  EX_pyr_e : 5.292896
  Auxiliary production reaction : 0.099087
  DM_mththf_c : 0.000165
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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