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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2066 b0238 b0125 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3236 b2883 b3962 b0477 b2498 b3616 b3589 b2210 b4267 b2361 b2291 b0261 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b0325 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435963 (mmol/gDw/h)
  Minimum Production Rate : 0.321951 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.536092
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.730706
  EX_pi_e : 0.420533
  EX_so4_e : 0.109784
  EX_k_e : 0.085097
  EX_fe2_e : 0.007002
  EX_mg2_e : 0.003782
  EX_cl_e : 0.002269
  EX_ca2_e : 0.002269
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.379073
  EX_co2_e : 32.794301
  EX_h_e : 8.309465
  EX_ac_e : 1.281321
  EX_thym_e : 0.705558
  Auxiliary production reaction : 0.321951
  EX_ade_e : 0.000293
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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