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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4384 b3708 b3008 b0871 b2926 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505612 (mmol/gDw/h)
  Minimum Production Rate : 0.020480 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.572781
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.767776
  EX_pi_e : 0.549158
  EX_so4_e : 0.209245
  EX_k_e : 0.098692
  EX_tungs_e : 0.020480
  EX_fe2_e : 0.008121
  EX_mg2_e : 0.004386
  EX_ca2_e : 0.002632
  EX_cl_e : 0.002632
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.884361
  EX_co2_e : 38.631400
  EX_h_e : 4.707208
  Auxiliary production reaction : 0.020480
  DM_5drib_c : 0.000339
  DM_4crsol_c : 0.000113

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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