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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2407 b3962 b1982 b4139 b3616 b3589 b4267 b0675 b2361 b0261 b4381 b0112 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 : 0.479276 (mmol/gDw/h)
  Minimum Production Rate : 1.837041 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.716552
  EX_nh4_e : 10.687803
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.462313
  EX_so4_e : 0.120691
  EX_k_e : 0.093551
  EX_fe2_e : 0.007698
  EX_mg2_e : 0.004158
  EX_ca2_e : 0.002495
  EX_cl_e : 0.002495
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.581282
  EX_co2_e : 27.901599
  EX_h_e : 10.616938
  Auxiliary production reaction : 1.837041
  EX_ac_e : 0.700960
  DM_oxam_c : 0.000536
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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