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 (66 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b3831 b4384 b3614 b0910 b3926 b4152 b2781 b0030 b1612 b1611 b4122 b0907 b0651 b2162 b1759 b3945 b4138 b4123 b0621 b2406 b3825 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.600025 (mmol/gDw/h)
  Minimum Production Rate : 0.316900 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.691579
  EX_o2_e : 278.299937
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.014331
  EX_pi_e : 0.895688
  EX_so4_e : 0.151098
  EX_k_e : 0.117121
  EX_mg2_e : 0.005205
  EX_ca2_e : 0.003123
  EX_cl_e : 0.003123
  EX_cu2_e : 0.000425
  EX_mn2_e : 0.000415
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990363
  EX_h2o_e : 548.175816
  EX_co2_e : 28.948601
  EX_succ_e : 0.625701
  Auxiliary production reaction : 0.316900
  EX_ura_e : 0.108606
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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