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 (42 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4382 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2883 b1982 b2688 b2797 b3117 b1814 b4471 b1033 b0261 b0507 b3709 b4381 b2406 b3161 b0112 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.697747 (mmol/gDw/h)
  Minimum Production Rate : 0.221673 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.292117
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.091215
  EX_pi_e : 1.338068
  EX_so4_e : 0.397379
  EX_k_e : 0.136195
  EX_fe2_e : 0.011207
  EX_mg2_e : 0.006053
  EX_ca2_e : 0.003632
  EX_cl_e : 0.003632
  EX_cu2_e : 0.000495
  EX_mn2_e : 0.000482
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000225
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.867815
  EX_co2_e : 24.779326
  EX_h_e : 7.929659
  EX_ac_e : 0.627891
  Auxiliary production reaction : 0.221673
  EX_ade_e : 0.000781
  DM_5drib_c : 0.000468
  DM_4crsol_c : 0.000156

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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