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 : u3hga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2836 b2242 b3831 b2744 b1278 b3614 b0910 b3752 b2781 b3844 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b2361 b2291 b1415 b0411 b4138 b4123 b0621 b2197 b3028 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.500471 (mmol/gDw/h)
  Minimum Production Rate : 0.264281 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.168403
  EX_o2_e : 277.613478
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.379145
  EX_pi_e : 1.011320
  EX_so4_e : 0.126029
  EX_k_e : 0.097688
  EX_mg2_e : 0.004342
  EX_cl_e : 0.002605
  EX_ca2_e : 0.002605
  EX_cu2_e : 0.000355
  EX_mn2_e : 0.000346
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991962
  EX_h2o_e : 546.437902
  EX_co2_e : 29.343743
  EX_succ_e : 0.521887
  Auxiliary production reaction : 0.264281
  EX_ura_e : 0.090627
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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