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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2925 b2097 b3617 b1612 b1611 b4122 b1779 b3946 b0825 b4138 b4123 b0621 b4381 b0114 b2492 b0904 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.552621 (mmol/gDw/h)
  Minimum Production Rate : 0.109064 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.752253
  EX_o2_e : 274.881901
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.970419
  EX_pi_e : 0.533062
  EX_so4_e : 0.139161
  EX_k_e : 0.107868
  EX_mg2_e : 0.004794
  EX_cl_e : 0.002876
  EX_ca2_e : 0.002876
  EX_cu2_e : 0.000392
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991124
  EX_h2o_e : 544.402317
  EX_co2_e : 28.031109
  EX_acald_e : 0.921143
  EX_succ_e : 0.578426
  Auxiliary production reaction : 0.109064
  DM_oxam_c : 0.002157
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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