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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4384 b3708 b3008 b0512 b0871 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b2239 b2406 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.576573 (mmol/gDw/h)
  Minimum Production Rate : 0.066172 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.447567
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.692720
  EX_pi_e : 0.754681
  EX_so4_e : 0.211364
  EX_k_e : 0.112543
  EX_fe2_e : 0.009260
  EX_mg2_e : 0.005002
  EX_ca2_e : 0.003001
  EX_cl_e : 0.003001
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.362165
  EX_co2_e : 34.742350
  EX_h_e : 5.498876
  Auxiliary production reaction : 0.066172
  EX_alltn_e : 0.000645
  DM_5drib_c : 0.000387
  DM_4crsol_c : 0.000129

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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