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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b4384 b2744 b3752 b0871 b2779 b3617 b2883 b0907 b1982 b0477 b0261 b0411 b0507 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.326150 (mmol/gDw/h)
  Minimum Production Rate : 0.530118 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.051596
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.704932
  EX_pi_e : 1.374844
  EX_so4_e : 0.082131
  EX_k_e : 0.063662
  EX_fe2_e : 0.005238
  EX_mg2_e : 0.002829
  EX_ca2_e : 0.001698
  EX_cl_e : 0.001698
  EX_cu2_e : 0.000231
  EX_mn2_e : 0.000225
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_h2o_e : 52.039359
  EX_co2_e : 32.820611
  EX_h_e : 5.119244
  EX_acald_e : 1.328542
  Auxiliary production reaction : 0.530118
  EX_ade_e : 0.000365
  DM_5drib_c : 0.000219
  EX_glyclt_e : 0.000145
  DM_4crsol_c : 0.000073

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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