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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2744 b3708 b3008 b0871 b2883 b2797 b3117 b1814 b4471 b3449 b0411 b4381 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b2947 b1533 b3927 b3662 b1813 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690293 (mmol/gDw/h)
  Minimum Production Rate : 0.018527 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.764703
  EX_o2_e : 279.100291
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.758847
  EX_pi_e : 0.665861
  EX_so4_e : 0.384939
  EX_k_e : 0.134740
  EX_mg2_e : 0.005988
  EX_ca2_e : 0.003593
  EX_cl_e : 0.003593
  EX_cu2_e : 0.000489
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988913
  EX_h2o_e : 549.695703
  EX_co2_e : 30.846509
  EX_cys__L_e : 0.211110
  Auxiliary production reaction : 0.018527
  DM_mththf_c : 0.000309
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000154

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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