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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b4384 b2744 b3708 b3008 b3752 b0871 b1238 b3236 b2883 b0121 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b3709 b4381 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0515 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.754289 (mmol/gDw/h)
  Minimum Production Rate : 0.008899 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.817169
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.836240
  EX_pi_e : 0.727591
  EX_so4_e : 0.189945
  EX_k_e : 0.147232
  EX_fe2_e : 0.012115
  EX_mg2_e : 0.006543
  EX_cl_e : 0.003926
  EX_ca2_e : 0.003926
  EX_cu2_e : 0.000535
  EX_mn2_e : 0.000521
  EX_zn2_e : 0.000257
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.929528
  EX_co2_e : 26.261719
  EX_h_e : 7.620692
  EX_alltn_e : 0.168047
  DM_5drib_c : 0.167709
  DM_4crsol_c : 0.167371
  Auxiliary production reaction : 0.008899

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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