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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3942 b1732 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b3236 b2883 b1779 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2440 b4381 b2406 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372229 (mmol/gDw/h)
  Minimum Production Rate : 0.056941 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.181944
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.297762
  EX_pi_e : 0.415996
  EX_so4_e : 0.093735
  EX_k_e : 0.072657
  EX_fe2_e : 0.005978
  EX_mg2_e : 0.003229
  EX_cl_e : 0.001937
  EX_ca2_e : 0.001937
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.046049
  EX_co2_e : 28.184617
  EX_h_e : 9.003535
  EX_pyr_e : 5.305627
  Auxiliary production reaction : 0.056941
  EX_ade_e : 0.009990
  DM_mththf_c : 0.000167
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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