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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523327 (mmol/gDw/h)
  Minimum Production Rate : 0.391663 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.235936
  EX_o2_e : 271.090390
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.435448
  EX_pi_e : 0.504804
  EX_so4_e : 0.131784
  EX_k_e : 0.102150
  EX_mg2_e : 0.004540
  EX_cl_e : 0.002724
  EX_ca2_e : 0.002724
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991595
  EX_h2o_e : 540.135640
  EX_co2_e : 22.404176
  EX_ac_e : 1.988337
  DM_oxam_c : 0.783561
  DM_5drib_c : 0.783327
  DM_4crsol_c : 0.783092
  EX_glyc__R_e : 0.391663

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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