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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b3844 b1238 b0583 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3709 b4381 b3161 b0112 b2868 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b3447 b4141 b1798 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.702420 (mmol/gDw/h)
  Minimum Production Rate : 0.193770 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.519655
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.946399
  EX_pi_e : 1.258870
  EX_so4_e : 0.370654
  EX_k_e : 0.137107
  EX_fe2_e : 0.011282
  EX_mg2_e : 0.006093
  EX_cl_e : 0.003656
  EX_ca2_e : 0.003656
  EX_cu2_e : 0.000498
  EX_mn2_e : 0.000485
  EX_zn2_e : 0.000240
  EX_ni2_e : 0.000227
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.739719
  EX_co2_e : 25.113710
  EX_h_e : 7.835836
  EX_ac_e : 0.602709
  Auxiliary production reaction : 0.193770
  EX_ade_e : 0.000786
  DM_5drib_c : 0.000471
  DM_4crsol_c : 0.000157

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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