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 : ser__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b0474 b2518 b3831 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b2926 b3617 b3236 b3962 b0477 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4267 b1033 b2361 b2291 b0726 b0114 b2366 b2492 b0904 b1533 b0325 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445672 (mmol/gDw/h)
  Minimum Production Rate : 2.378260 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.519572
  EX_o2_e : 284.808709
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.191477
  EX_pi_e : 0.429898
  EX_so4_e : 0.112229
  EX_k_e : 0.086992
  EX_mg2_e : 0.003866
  EX_ca2_e : 0.002320
  EX_cl_e : 0.002320
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992842
  EX_h2o_e : 548.716082
  EX_co2_e : 34.572441
  Auxiliary production reaction : 2.378260
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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