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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b0910 b3752 b3115 b1849 b2296 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b4381 b0112 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b2835 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577677 (mmol/gDw/h)
  Minimum Production Rate : 1.728628 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.020547
  EX_nh4_e : 11.427976
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.557230
  EX_so4_e : 0.145471
  EX_k_e : 0.112758
  EX_fe2_e : 0.009278
  EX_mg2_e : 0.005011
  EX_cl_e : 0.003007
  EX_ca2_e : 0.003007
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.156285
  EX_co2_e : 23.251834
  EX_h_e : 10.098863
  Auxiliary production reaction : 1.728628
  EX_ac_e : 1.330450
  EX_ade_e : 0.000646
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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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