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 : uamr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 39: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b3831 b2744 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b2197 b3918 b4042 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.682122 (mmol/gDw/h)
  Minimum Production Rate : 0.360259 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.331365
  EX_o2_e : 271.080588
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.694566
  EX_pi_e : 1.378497
  EX_so4_e : 0.171772
  EX_k_e : 0.133145
  EX_mg2_e : 0.005917
  EX_cl_e : 0.003550
  EX_ca2_e : 0.003550
  EX_cu2_e : 0.000484
  EX_mn2_e : 0.000471
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989044
  EX_h2o_e : 545.116967
  EX_co2_e : 21.457745
  EX_succ_e : 0.711311
  Auxiliary production reaction : 0.360259
  EX_ura_e : 0.123466
  DM_5drib_c : 0.000153
  DM_4crsol_c : 0.000152

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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