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 : fmnh2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 15: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b3426 b2242 b3399 b2744 b3114 b3952 b0903 b2925 b2097 b1850 b3124 b1638 b3962 b4139 b4267 b2361 b2291 b1415 b4015 b1014 b4388 b0509 b3125 b0755 b3612 b0529 b1539 b3028 b0325 b0514 b4266 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362744 (mmol/gDw/h)
  Minimum Production Rate : 0.358507 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.227113
  EX_o2_e : 288.420114
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.351629
  EX_pi_e : 0.708411
  EX_so4_e : 0.091346
  EX_k_e : 0.070805
  EX_mg2_e : 0.003147
  EX_ca2_e : 0.001888
  EX_cl_e : 0.001888
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994174
  EX_h2o_e : 553.253154
  EX_co2_e : 39.016420
  Auxiliary production reaction : 0.358507
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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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