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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b3617 b3124 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4014 b0261 b2976 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b1539 b2492 b0904 b0591 b1533 b3821 b1473 b1600 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.303642 (mmol/gDw/h)
  Minimum Production Rate : 0.051139 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.689167
  EX_nh4_e : 11.219795
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.129475
  EX_so4_e : 0.127602
  EX_k_e : 0.059269
  EX_fe2_e : 0.004877
  EX_mg2_e : 0.002634
  EX_ca2_e : 0.001580
  EX_cl_e : 0.001580
  EX_cu2_e : 0.000215
  EX_mn2_e : 0.000210
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_h2o_e : 50.261915
  EX_co2_e : 18.430389
  EX_h_e : 11.395084
  EX_ac_e : 2.544047
  EX_fad_e : 0.841581
  Auxiliary production reaction : 0.051139
  DM_oxam_c : 0.008285
  DM_5drib_c : 0.000204
  DM_4crsol_c : 0.000068

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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