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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b0474 b2518 b1241 b0351 b3831 b0910 b2930 b4232 b3697 b3925 b4152 b0871 b2297 b2458 b0030 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b1779 b3946 b0825 b0411 b1602 b4138 b4123 b0621 b2492 b0904 b1380 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.395046 (mmol/gDw/h)
  Minimum Production Rate : 0.208642 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.614758
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.826761
  EX_pi_e : 0.381064
  EX_so4_e : 0.099481
  EX_k_e : 0.077110
  EX_fe2_e : 0.006345
  EX_mg2_e : 0.003427
  EX_cl_e : 0.002056
  EX_ca2_e : 0.002056
  EX_cu2_e : 0.000280
  EX_mn2_e : 0.000273
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 47.096720
  EX_co2_e : 33.019889
  EX_h_e : 8.490875
  EX_succ_e : 2.035374
  EX_ac_e : 0.229990
  Auxiliary production reaction : 0.208642
  EX_ura_e : 0.071505
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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