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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2779 b2926 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466676 (mmol/gDw/h)
  Minimum Production Rate : 0.349265 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.304299
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.738799
  EX_pi_e : 0.450158
  EX_so4_e : 0.117518
  EX_k_e : 0.091092
  EX_fe2_e : 0.007495
  EX_mg2_e : 0.004048
  EX_ca2_e : 0.002429
  EX_cl_e : 0.002429
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 42.289741
  EX_co2_e : 26.473992
  EX_h_e : 7.807843
  EX_ac_e : 1.773096
  DM_oxam_c : 0.698739
  DM_5drib_c : 0.698530
  DM_4crsol_c : 0.698321
  EX_glyc__R_e : 0.349265

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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