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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3399 b4382 b4384 b2744 b3708 b3008 b0871 b0160 b2407 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b2239 b2406 b3453 b0114 b0886 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b1600 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.763597 (mmol/gDw/h)
  Minimum Production Rate : 0.262847 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.183022
  EX_o2_e : 275.314502
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.561081
  EX_pi_e : 1.525173
  EX_so4_e : 0.192289
  EX_k_e : 0.149049
  EX_mg2_e : 0.006624
  EX_ca2_e : 0.003975
  EX_cl_e : 0.003975
  EX_cu2_e : 0.000541
  EX_mn2_e : 0.000528
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987736
  EX_h2o_e : 549.865644
  EX_co2_e : 26.290214
  Auxiliary production reaction : 0.262847
  DM_5drib_c : 0.000512
  DM_4crsol_c : 0.000170
  EX_g3pe_e : 0.000062

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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