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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b1238 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3821 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522448 (mmol/gDw/h)
  Minimum Production Rate : 0.521588 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.430031
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.293509
  EX_pi_e : 1.547133
  EX_so4_e : 0.653151
  EX_k_e : 0.101978
  EX_fe2_e : 0.008391
  EX_mg2_e : 0.004532
  EX_ca2_e : 0.002719
  EX_cl_e : 0.002719
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.251522
  EX_co2_e : 22.066534
  EX_h_e : 9.132655
  EX_ac_e : 2.767432
  Auxiliary production reaction : 0.521588
  DM_mththf_c : 0.000234
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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