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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0595 b0261 b0507 b3709 b2239 b2406 b3161 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435569 (mmol/gDw/h)
  Minimum Production Rate : 0.651677 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 19.633560
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.266372
  EX_pi_e : 2.375219
  EX_so4_e : 0.761362
  EX_k_e : 0.085020
  EX_fe2_e : 0.006996
  EX_mg2_e : 0.003779
  EX_ca2_e : 0.002267
  EX_cl_e : 0.002267
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.750881
  EX_co2_e : 20.562475
  EX_h_e : 9.568351
  EX_ac_e : 2.958519
  Auxiliary production reaction : 0.651677
  DM_oxam_c : 0.000487
  DM_5drib_c : 0.000292
  DM_4crsol_c : 0.000097
  EX_g3pe_e : 0.000035

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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