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 : iasp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 9: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b2836 b2242 b3553 b4382 b1241 b0351 b4069 b3708 b3752 b3115 b1849 b2296 b2407 b1612 b1611 b2883 b4122 b1779 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b1415 b1014 b0261 b0411 b0822 b4138 b4123 b0621 b4381 b2406 b0112 b2868 b0114 b1539 b2492 b0904 b1533 b3028 b1380 b0325 b4042 b0494 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369346 (mmol/gDw/h)
  Minimum Production Rate : 0.495030 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.623335
  EX_o2_e : 285.339020
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.696029
  EX_pi_e : 0.356273
  EX_so4_e : 0.093009
  EX_k_e : 0.072094
  EX_mg2_e : 0.003204
  EX_ca2_e : 0.001922
  EX_cl_e : 0.001922
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994068
  EX_h2o_e : 550.685292
  EX_co2_e : 33.534376
  EX_ac_e : 1.403253
  EX_succ_e : 0.938175
  EX_hxan_e : 0.553024
  Auxiliary production reaction : 0.495030
  EX_dxylnt_e : 0.000247
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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.

Last updated: 21-Sep-2023
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