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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.606006 (mmol/gDw/h)
  Minimum Production Rate : 0.906700 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.426492
  EX_nh4_e : 10.171611
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.584557
  EX_so4_e : 0.152604
  EX_k_e : 0.118288
  EX_fe2_e : 0.009733
  EX_mg2_e : 0.005257
  EX_ca2_e : 0.003154
  EX_cl_e : 0.003154
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.523042
  EX_co2_e : 21.453106
  EX_h_e : 11.497417
  EX_ac_e : 2.302395
  Auxiliary production reaction : 0.906700
  DM_5drib_c : 0.000407
  DM_4crsol_c : 0.000135

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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