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 : udpLa4fn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3846 b2341 b3831 b3614 b0910 b4152 b2779 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b4381 b2406 b0452 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.659905 (mmol/gDw/h)
  Minimum Production Rate : 0.348526 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.962226
  EX_o2_e : 274.265072
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.411387
  EX_pi_e : 1.333600
  EX_so4_e : 0.166177
  EX_k_e : 0.128809
  EX_mg2_e : 0.005725
  EX_cl_e : 0.003435
  EX_ca2_e : 0.003435
  EX_cu2_e : 0.000468
  EX_mn2_e : 0.000456
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989401
  EX_h2o_e : 546.995806
  EX_co2_e : 24.455683
  EX_succ_e : 0.688144
  Auxiliary production reaction : 0.348526
  EX_ura_e : 0.119445
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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