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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b2836 b1478 b3399 b4382 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b2799 b3945 b1602 b2913 b2406 b1539 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409135 (mmol/gDw/h)
  Minimum Production Rate : 0.227970 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.453967
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.016695
  EX_pi_e : 0.850593
  EX_so4_e : 0.330998
  EX_k_e : 0.079860
  EX_fe2_e : 0.006571
  EX_mg2_e : 0.003549
  EX_cl_e : 0.002130
  EX_ca2_e : 0.002130
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.156118
  EX_co2_e : 36.243974
  EX_h_e : 5.531674
  EX_glyclt_e : 0.620022
  EX_ac_e : 0.466162
  Auxiliary production reaction : 0.227970
  EX_ade_e : 0.000458
  DM_5drib_c : 0.000275
  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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