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 : h2o2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b3426 b2242 b3942 b1732 b1779 b3962 b4139 b3946 b0825 b4267 b1415 b3551 b4015 b1014 b2799 b4219 b1832 b1778 b1539 b3028 b1710 b2480 b0508 b4266 b1813 b2285 b1378 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.603276 (mmol/gDw/h)
  Minimum Production Rate : 0.732282 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.323966
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.515325
  EX_pi_e : 0.581923
  EX_so4_e : 0.151917
  EX_k_e : 0.117755
  EX_mg2_e : 0.005233
  EX_fe2_e : 0.004979
  EX_fe3_e : 0.004710
  EX_ca2_e : 0.003140
  EX_cl_e : 0.003140
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.418321
  EX_co2_e : 35.238310
  EX_h_e : 5.547847
  Auxiliary production reaction : 0.748473
  DM_5drib_c : 0.000136
  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.

Last updated: 21-Sep-2023
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