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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b0871 b0160 b2797 b3117 b1814 b4471 b3665 b0675 b2361 b0261 b1701 b1805 b4381 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775847 (mmol/gDw/h)
  Minimum Production Rate : 0.089476 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.590316
  EX_o2_e : 274.527769
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.005418
  EX_pi_e : 1.016816
  EX_so4_e : 0.284850
  EX_k_e : 0.151440
  EX_mg2_e : 0.006730
  EX_ca2_e : 0.004038
  EX_cl_e : 0.004038
  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_fe3_e : 999.987539
  EX_h2o_e : 548.457833
  EX_co2_e : 26.276034
  Auxiliary production reaction : 0.089476
  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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