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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3831 b4069 b3614 b0910 b3752 b4152 b3115 b1849 b2296 b2779 b2925 b2097 b1612 b1611 b4122 b3946 b0825 b4388 b4138 b4123 b0621 b4381 b0114 b0529 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372508 (mmol/gDw/h)
  Minimum Production Rate : 0.196738 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.617016
  EX_o2_e : 279.297646
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.551387
  EX_pi_e : 0.556062
  EX_so4_e : 0.093805
  EX_k_e : 0.072711
  EX_mg2_e : 0.003232
  EX_ca2_e : 0.001939
  EX_cl_e : 0.001939
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994017
  EX_h2o_e : 539.125839
  EX_co2_e : 27.385906
  EX_glyc__R_e : 4.432150
  EX_succ_e : 0.388449
  EX_ura_e : 0.264164
  EX_ac_e : 0.216869
  Auxiliary production reaction : 0.196738
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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