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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b2407 b1623 b3665 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.517618 (mmol/gDw/h)
  Minimum Production Rate : 0.992696 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.245049
  EX_nh4_e : 10.553708
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.484689
  EX_so4_e : 0.130347
  EX_k_e : 0.101035
  EX_fe2_e : 0.008313
  EX_mg2_e : 0.004490
  EX_ca2_e : 0.002694
  EX_cl_e : 0.002694
  EX_cu2_e : 0.000367
  EX_mn2_e : 0.000358
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.930862
  EX_co2_e : 19.371568
  EX_h_e : 9.483319
  EX_ac_e : 1.749152
  Auxiliary production reaction : 0.992696
  DM_mththf_c : 0.000232
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000115

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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