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 : udpLa4o_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b3831 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4161 b4138 b4123 b0621 b2913 b4381 b2406 b3453 b2197 b3918 b1912 b2240 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.696579 (mmol/gDw/h)
  Minimum Production Rate : 0.367895 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.649810
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.510951
  EX_pi_e : 1.407714
  EX_so4_e : 0.175413
  EX_k_e : 0.135967
  EX_fe2_e : 0.011188
  EX_mg2_e : 0.006043
  EX_ca2_e : 0.003626
  EX_cl_e : 0.003626
  EX_cu2_e : 0.000494
  EX_mn2_e : 0.000481
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000225
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.278697
  EX_co2_e : 22.848217
  EX_h_e : 8.105388
  EX_succ_e : 0.726387
  Auxiliary production reaction : 0.367895
  EX_ura_e : 0.126083
  DM_5drib_c : 0.000157
  DM_4crsol_c : 0.000155

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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