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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2779 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b0411 b4381 b2406 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.694725 (mmol/gDw/h)
  Minimum Production Rate : 0.159877 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.800387
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.144813
  EX_pi_e : 0.670135
  EX_so4_e : 0.174946
  EX_k_e : 0.135605
  EX_fe2_e : 0.011158
  EX_mg2_e : 0.006027
  EX_ca2_e : 0.003616
  EX_cl_e : 0.003616
  EX_cu2_e : 0.000493
  EX_mn2_e : 0.000480
  EX_zn2_e : 0.000237
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.831285
  EX_co2_e : 29.882081
  EX_h_e : 7.025254
  Auxiliary production reaction : 0.159877
  EX_ade_e : 0.000468
  DM_mththf_c : 0.000311
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155

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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