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 : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b3617 b2883 b2687 b1982 b0477 b2797 b3117 b1814 b4471 b3449 b2406 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b0509 b3125 b1539 b2492 b0904 b1533 b0508 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.500230 (mmol/gDw/h)
  Minimum Production Rate : 0.748775 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.000364
  EX_o2_e : 271.490810
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.896763
  EX_so4_e : 0.874742
  EX_pi_e : 0.482524
  EX_k_e : 0.097641
  EX_mg2_e : 0.004339
  EX_ca2_e : 0.002604
  EX_cl_e : 0.002604
  EX_cu2_e : 0.000355
  EX_mn2_e : 0.000346
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991966
  EX_h2o_e : 545.128294
  EX_co2_e : 22.185204
  EX_ac_e : 3.398516
  EX_ade_e : 0.749110
  Auxiliary production reaction : 0.748775
  DM_5drib_c : 0.000336
  DM_4crsol_c : 0.000112

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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