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 : amp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b4374 b2361 b2291 b0411 b2799 b1602 b0153 b2913 b0529 b2492 b0904 b1781 b3001 b0591 b1380 b0325 b1771 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403893 (mmol/gDw/h)
  Minimum Production Rate : 0.635502 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.868643
  EX_o2_e : 287.320371
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.540610
  EX_pi_e : 1.025100
  EX_so4_e : 0.101708
  EX_k_e : 0.078837
  EX_mg2_e : 0.003504
  EX_ca2_e : 0.002102
  EX_cl_e : 0.002102
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993513
  EX_h2o_e : 554.885404
  EX_co2_e : 36.594474
  Auxiliary production reaction : 0.635502
  EX_ac_e : 0.235141
  EX_hxan_e : 0.000272
  DM_mththf_c : 0.000181
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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