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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1238 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3825 b2413 b0494 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.727316 (mmol/gDw/h)
  Minimum Production Rate : 0.231759 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.155803
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.245499
  EX_pi_e : 0.701573
  EX_so4_e : 0.414911
  EX_k_e : 0.141967
  EX_fe2_e : 0.011681
  EX_mg2_e : 0.006309
  EX_cl_e : 0.003786
  EX_ca2_e : 0.003786
  EX_cu2_e : 0.000516
  EX_mn2_e : 0.000503
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.043046
  EX_co2_e : 25.592031
  EX_h_e : 8.265092
  EX_ac_e : 0.655192
  Auxiliary production reaction : 0.231759
  DM_5drib_c : 0.000164
  DM_4crsol_c : 0.000162

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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