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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b2744 b4152 b0871 b2925 b2097 b1612 b1611 b4122 b1779 b2690 b4374 b4161 b0675 b3945 b4138 b4123 b0621 b4381 b0114 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401437 (mmol/gDw/h)
  Minimum Production Rate : 0.212017 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 986.453165
  EX_o2_e : 280.573014
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.692830
  EX_pi_e : 0.387229
  EX_so4_e : 0.101090
  EX_k_e : 0.078358
  EX_mg2_e : 0.003482
  EX_ca2_e : 0.002089
  EX_cl_e : 0.002089
  EX_cu2_e : 0.000285
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993553
  EX_h2o_e : 540.909354
  EX_co2_e : 28.469716
  EX_for_e : 5.074554
  EX_ac_e : 3.370677
  EX_succ_e : 0.418616
  Auxiliary production reaction : 0.212017
  EX_ura_e : 0.072661
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000090

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.

Last updated: 21-Sep-2023
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