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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (98 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b2242 b2930 b4232 b3697 b3925 b2297 b2458 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b2690 b2210 b3945 b4138 b4123 b0621 b0306 b3605 b2492 b0904 b3028 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439509 (mmol/gDw/h)
  Minimum Production Rate : 0.311677 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.980839
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.058341
  EX_pi_e : 0.423953
  EX_so4_e : 0.110677
  EX_k_e : 0.085789
  EX_fe2_e : 0.007059
  EX_mg2_e : 0.003813
  EX_ca2_e : 0.002288
  EX_cl_e : 0.002288
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.758101
  EX_co2_e : 32.620387
  EX_h_e : 8.552434
  EX_succ_e : 1.661422
  Auxiliary production reaction : 0.311677
  EX_ac_e : 0.255876
  EX_glyclt_e : 0.000294
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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