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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b1701 b1805 b2406 b2943 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b0516 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.757510 (mmol/gDw/h)
  Minimum Production Rate : 0.174326 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.153864
  EX_o2_e : 276.065642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.054708
  EX_pi_e : 0.905024
  EX_so4_e : 0.190756
  EX_k_e : 0.147861
  EX_mg2_e : 0.006571
  EX_ca2_e : 0.003943
  EX_cl_e : 0.003943
  EX_cu2_e : 0.000537
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987834
  EX_h2o_e : 549.253848
  EX_co2_e : 27.160717
  Auxiliary production reaction : 0.174326
  EX_alltn_e : 0.000510
  DM_mththf_c : 0.000339
  DM_5drib_c : 0.000170
  DM_4crsol_c : 0.000169

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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