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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0474 b2518 b2744 b2930 b4232 b3697 b3925 b4152 b2297 b2458 b2779 b2781 b3236 b1612 b1611 b4122 b2690 b1759 b2210 b4374 b4161 b0675 b3945 b4138 b4123 b0621 b2913 b4381 b0529 b2197 b3918 b1912 b1206 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379011 (mmol/gDw/h)
  Minimum Production Rate : 0.200173 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.193628
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.831008
  EX_pi_e : 0.765942
  EX_so4_e : 0.095443
  EX_k_e : 0.073980
  EX_fe2_e : 0.006087
  EX_mg2_e : 0.003288
  EX_ca2_e : 0.001973
  EX_cl_e : 0.001973
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 44.351051
  EX_co2_e : 31.200882
  EX_h_e : 8.802611
  EX_ac_e : 3.989647
  EX_succ_e : 0.396456
  Auxiliary production reaction : 0.200173
  EX_ura_e : 0.068602
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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