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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0512 b0871 b0030 b2883 b1982 b2688 b2797 b3117 b1814 b4471 b1623 b0411 b4381 b0452 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b3927 b2835 b1511 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.700421 (mmol/gDw/h)
  Minimum Production Rate : 0.142805 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.021830
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.353706
  EX_pi_e : 0.675630
  EX_so4_e : 0.176380
  EX_k_e : 0.136717
  EX_fe2_e : 0.011249
  EX_mg2_e : 0.006076
  EX_cl_e : 0.003646
  EX_ca2_e : 0.003646
  EX_cu2_e : 0.000497
  EX_mn2_e : 0.000484
  EX_zn2_e : 0.000239
  EX_ni2_e : 0.000226
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 50.230358
  EX_co2_e : 30.174537
  EX_h_e : 7.082161
  Auxiliary production reaction : 0.142805
  EX_alltn_e : 0.018799
  DM_mththf_c : 0.000314
  DM_5drib_c : 0.000158
  DM_4crsol_c : 0.000156

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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