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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b2407 b0120 b1982 b0675 b2361 b4014 b0261 b2976 b0507 b2406 b0112 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.337653 (mmol/gDw/h)
  Minimum Production Rate : 1.097629 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.527797
  EX_nh4_e : 11.330401
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.325702
  EX_so4_e : 0.085028
  EX_k_e : 0.065907
  EX_fe2_e : 0.005423
  EX_mg2_e : 0.002929
  EX_ca2_e : 0.001757
  EX_cl_e : 0.001757
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000233
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 48.973525
  EX_co2_e : 19.201346
  EX_h_e : 12.981903
  EX_acald_e : 2.492737
  Auxiliary production reaction : 1.097629
  DM_oxam_c : 0.000378
  DM_5drib_c : 0.000227
  DM_4crsol_c : 0.000075

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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