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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b2210 b4381 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b0516 b1813 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419243 (mmol/gDw/h)
  Minimum Production Rate : 0.528520 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.615893
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.215396
  EX_pi_e : 0.932924
  EX_so4_e : 0.105574
  EX_k_e : 0.081833
  EX_fe2_e : 0.006733
  EX_mg2_e : 0.003637
  EX_ca2_e : 0.002182
  EX_cl_e : 0.002182
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.647420
  EX_co2_e : 35.155371
  EX_h_e : 7.692521
  EX_ac_e : 1.152461
  Auxiliary production reaction : 0.528520
  EX_alltn_e : 0.011252
  EX_glyclt_e : 0.000280
  EX_mththf_e : 0.000188
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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