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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b0238 b0125 b1241 b0351 b4069 b2744 b3614 b0910 b4152 b2297 b2458 b3617 b1612 b1611 b4122 b0477 b4374 b0675 b2361 b2291 b0261 b4138 b4123 b0621 b2868 b0114 b0529 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.560410 (mmol/gDw/h)
  Minimum Production Rate : 0.086777 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.182771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.236657
  EX_pi_e : 0.540575
  EX_so4_e : 0.141122
  EX_k_e : 0.109388
  EX_fe2_e : 0.009001
  EX_mg2_e : 0.004862
  EX_ca2_e : 0.002917
  EX_cl_e : 0.002917
  EX_cu2_e : 0.000397
  EX_mn2_e : 0.000387
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 45.316292
  EX_co2_e : 20.931001
  EX_h_e : 11.653958
  EX_ac_e : 1.355145
  EX_succ_e : 0.982633
  EX_ura_e : 0.795655
  EX_xan_e : 0.398242
  Auxiliary production reaction : 0.086777
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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.

Last updated: 21-Sep-2023
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