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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b0160 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b0675 b2361 b0261 b1701 b1805 b3709 b4381 b2406 b3161 b0112 b2868 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392000 (mmol/gDw/h)
  Minimum Production Rate : 0.576249 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.750823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.310534
  EX_pi_e : 2.106874
  EX_so4_e : 0.674963
  EX_k_e : 0.076516
  EX_fe2_e : 0.006296
  EX_mg2_e : 0.003401
  EX_ca2_e : 0.002040
  EX_cl_e : 0.002040
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 45.562518
  EX_co2_e : 20.131697
  EX_h_e : 8.592156
  EX_ac_e : 2.641822
  Auxiliary production reaction : 0.576249
  EX_xan_e : 0.010257
  EX_ade_e : 0.000439
  DM_5drib_c : 0.000263
  EX_glyclt_e : 0.000262
  DM_4crsol_c : 0.000087

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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