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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b1982 b3946 b0825 b1623 b3665 b4374 b0675 b2361 b2913 b4381 b0112 b0511 b0114 b0529 b2492 b0904 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.308173 (mmol/gDw/h)
  Minimum Production Rate : 1.165498 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.727892
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.692532
  EX_pi_e : 2.628261
  EX_so4_e : 0.077604
  EX_k_e : 0.060153
  EX_fe2_e : 0.004950
  EX_mg2_e : 0.002673
  EX_cl_e : 0.001604
  EX_ca2_e : 0.001604
  EX_cu2_e : 0.000218
  EX_mn2_e : 0.000213
  EX_zn2_e : 0.000105
  EX_ni2_e : 0.000100

Product: (mmol/gDw/h)
  EX_h2o_e : 46.731914
  EX_co2_e : 29.195281
  EX_h_e : 7.842405
  EX_ac_e : 3.811894
  Auxiliary production reaction : 1.165498
  EX_xan_e : 0.008064
  EX_ade_e : 0.000207
  EX_mththf_e : 0.000138
  EX_glyc__R_e : 0.000103
  DM_5drib_c : 0.000069
  DM_4crsol_c : 0.000069

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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