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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3399 b4384 b2744 b3708 b3008 b3752 b0871 b2925 b2097 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b1623 b3665 b3945 b4381 b2406 b4064 b4464 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.776317 (mmol/gDw/h)
  Minimum Production Rate : 0.067834 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.797221
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.881925
  EX_pi_e : 0.952342
  EX_so4_e : 0.263326
  EX_k_e : 0.151532
  EX_fe2_e : 0.012468
  EX_mg2_e : 0.006735
  EX_ca2_e : 0.004041
  EX_cl_e : 0.004041
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000265
  EX_ni2_e : 0.000251
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.387438
  EX_co2_e : 26.427564
  EX_h_e : 7.436804
  Auxiliary production reaction : 0.067834
  EX_pyr_e : 0.056950
  DM_oxam_c : 0.020313
  EX_ade_e : 0.000522
  DM_mththf_c : 0.000348
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000173

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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