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 : 2agpg141_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 53: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b4138 b4123 b0621 b4381 b2406 b2197 b2835 b3918 b0789 b1249 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.642223 (mmol/gDw/h)
  Minimum Production Rate : 0.339187 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.177601
  EX_o2_e : 269.795617
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.846813
  EX_pi_e : 0.958679
  EX_so4_e : 0.161725
  EX_k_e : 0.125357
  EX_mg2_e : 0.005571
  EX_ca2_e : 0.003343
  EX_cl_e : 0.003343
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000444
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989685
  EX_h2o_e : 542.934831
  EX_co2_e : 22.355427
  EX_succ_e : 0.669705
  EX_ura_e : 0.455431
  Auxiliary production reaction : 0.339187
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000143

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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