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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b2297 b2458 b2779 b2925 b2097 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4374 b2361 b2291 b3945 b2868 b0114 b1539 b2492 b0904 b1533 b3821 b1511 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364456 (mmol/gDw/h)
  Minimum Production Rate : 0.062965 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.058933
  EX_o2_e : 280.265566
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.252150
  EX_pi_e : 0.540453
  EX_so4_e : 0.091777
  EX_k_e : 0.071139
  EX_mg2_e : 0.003162
  EX_ca2_e : 0.001897
  EX_cl_e : 0.001897
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994146
  EX_h2o_e : 544.121606
  EX_co2_e : 28.220082
  EX_pyr_e : 5.396199
  Auxiliary production reaction : 0.062965
  EX_ade_e : 0.000245
  DM_mththf_c : 0.000163
  EX_glyc__R_e : 0.000122
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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