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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.541195 (mmol/gDw/h)
  Minimum Production Rate : 0.809731 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.396215
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.893517
  EX_pi_e : 2.141502
  EX_so4_e : 0.136284
  EX_k_e : 0.105638
  EX_fe2_e : 0.008692
  EX_mg2_e : 0.004695
  EX_ca2_e : 0.002817
  EX_cl_e : 0.002817
  EX_cu2_e : 0.000384
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.154633
  EX_co2_e : 21.526931
  EX_h_e : 9.458071
  EX_ac_e : 2.056160
  Auxiliary production reaction : 0.809731
  DM_5drib_c : 0.000363
  DM_4crsol_c : 0.000121

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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