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 (34 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b0160 b3124 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2440 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b0494 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527699 (mmol/gDw/h)
  Minimum Production Rate : 0.388042 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.169625
  EX_o2_e : 270.975652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.489239
  EX_pi_e : 0.509022
  EX_so4_e : 0.132885
  EX_k_e : 0.103003
  EX_mg2_e : 0.004578
  EX_ca2_e : 0.002747
  EX_cl_e : 0.002747
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000365
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991525
  EX_h2o_e : 540.114555
  EX_co2_e : 22.276257
  EX_ac_e : 2.004886
  DM_oxam_c : 0.790129
  DM_5drib_c : 0.776085
  DM_4crsol_c : 0.775849
  EX_glyc__R_e : 0.388042

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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