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 : nicrnt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2781 b1612 b1611 b4122 b2388 b1759 b0394 b4161 b0411 b4138 b4123 b0621 b4381 b0452 b0837 b0124 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.592889 (mmol/gDw/h)
  Minimum Production Rate : 0.313036 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.680091
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.931005
  EX_pi_e : 0.884940
  EX_so4_e : 0.149301
  EX_k_e : 0.115728
  EX_fe2_e : 0.009522
  EX_mg2_e : 0.005143
  EX_cl_e : 0.003086
  EX_ca2_e : 0.003086
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000410
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.321680
  EX_co2_e : 29.318565
  EX_h_e : 7.212075
  EX_succ_e : 0.618260
  Auxiliary production reaction : 0.313036
  EX_ura_e : 0.107410
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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