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 : acald_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b4384 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b4139 b3665 b1493 b3517 b4015 b1602 b2913 b3915 b0755 b3612 b0529 b2954 b3029 b1380 b1301 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.566916 (mmol/gDw/h)
  Minimum Production Rate : 0.487884 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.298911
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.122643
  EX_pi_e : 0.546850
  EX_so4_e : 0.142761
  EX_k_e : 0.110658
  EX_fe3_e : 0.009105
  EX_mg2_e : 0.004918
  EX_ca2_e : 0.002951
  EX_cl_e : 0.002951
  EX_cu2_e : 0.000402
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.721068
  EX_co2_e : 35.754940
  EX_h_e : 5.218154
  EX_acald_e : 0.487884
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000126

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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