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 (21 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3752 b0512 b2297 b2458 b2925 b2097 b3617 b2407 b1851 b1982 b3946 b0825 b0261 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445883 (mmol/gDw/h)
  Minimum Production Rate : 1.709045 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.992658
  EX_nh4_e : 13.362718
  EX_glc__D_e : 10.000000
  EX_pi_e : 5.557237
  EX_so4_e : 0.573112
  EX_k_e : 0.087033
  EX_fe2_e : 0.007161
  EX_mg2_e : 0.003868
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 55.587443
  EX_co2_e : 21.591831
  EX_h_e : 10.665586
  EX_ac_e : 2.361166
  Auxiliary production reaction : 1.709045
  EX_h2s_e : 0.460830
  EX_alltn_e : 0.000499
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000099

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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