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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0160 b1779 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b3654 b3714 b3664 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.641244 (mmol/gDw/h)
  Minimum Production Rate : 0.408586 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.681439
  EX_o2_e : 278.904978
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.968314
  EX_pi_e : 1.027134
  EX_so4_e : 0.161478
  EX_k_e : 0.125166
  EX_mg2_e : 0.005563
  EX_ca2_e : 0.003338
  EX_cl_e : 0.003338
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000443
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989701
  EX_h2o_e : 550.677299
  EX_co2_e : 29.254514
  Auxiliary production reaction : 0.408586
  EX_ac_e : 0.373323
  EX_mththf_e : 0.000287
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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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