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 (13 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3426 b2242 b3553 b3942 b1732 b2926 b3962 b4139 b4267 b1033 b3551 b4015 b1014 b3945 b4219 b1832 b1778 b0306 b1539 b3605 b3028 b0325 b1710 b2480 b4266 b2285 b1378 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.603287 (mmol/gDw/h)
  Minimum Production Rate : 0.731390 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.323043
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.515444
  EX_pi_e : 0.581934
  EX_so4_e : 0.151920
  EX_k_e : 0.117757
  EX_mg2_e : 0.005234
  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 : 50.419050
  EX_co2_e : 35.237855
  EX_h_e : 5.547949
  Auxiliary production reaction : 0.747581
  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.

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Last updated: 21-Sep-2023
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