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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b0512 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536665 (mmol/gDw/h)
  Minimum Production Rate : 0.788911 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.294035
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.799065
  EX_pi_e : 2.095492
  EX_so4_e : 0.135143
  EX_k_e : 0.104753
  EX_fe2_e : 0.008619
  EX_mg2_e : 0.004656
  EX_ca2_e : 0.002793
  EX_cl_e : 0.002793
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.742302
  EX_co2_e : 20.423203
  EX_h_e : 9.395349
  EX_ac_e : 2.038950
  Auxiliary production reaction : 0.788911
  EX_alltn_e : 0.014643
  DM_5drib_c : 0.000360
  DM_4crsol_c : 0.000120

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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