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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b2797 b3117 b1814 b4471 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.658014 (mmol/gDw/h)
  Minimum Production Rate : 0.985398 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.122086
  EX_nh4_e : 12.033485
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.634724
  EX_so4_e : 0.165701
  EX_k_e : 0.128440
  EX_fe2_e : 0.010568
  EX_mg2_e : 0.005708
  EX_ca2_e : 0.003425
  EX_cl_e : 0.003425
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000224
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.293118
  EX_co2_e : 23.062807
  EX_h_e : 13.473222
  EX_ac_e : 2.500137
  Auxiliary production reaction : 0.985398
  DM_mththf_c : 0.000295
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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