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 (9 of 15: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b3426 b2242 b4384 b0910 b3114 b3952 b0903 b2407 b1638 b1779 b3962 b4139 b4267 b1014 b4014 b2976 b2799 b3945 b0507 b0529 b0306 b1539 b3605 b3028 b0508 b4266 b1813 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458854 (mmol/gDw/h)
  Minimum Production Rate : 0.014455 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.962518
  EX_o2_e : 282.921962
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.769563
  EX_pi_e : 0.896108
  EX_so4_e : 0.115549
  EX_k_e : 0.089565
  EX_mg2_e : 0.003981
  EX_cl_e : 0.002388
  EX_ca2_e : 0.002388
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992630
  EX_h2o_e : 551.904592
  EX_co2_e : 33.456742
  EX_fmn_e : 0.439039
  Auxiliary production reaction : 0.014455
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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