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 (63 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b2744 b3708 b3008 b0871 b2883 b2797 b3117 b1814 b4471 b0261 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.764879 (mmol/gDw/h)
  Minimum Production Rate : 0.102075 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.370027
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.975159
  EX_pi_e : 1.044033
  EX_so4_e : 0.294687
  EX_k_e : 0.149299
  EX_fe2_e : 0.012285
  EX_mg2_e : 0.006635
  EX_ca2_e : 0.003981
  EX_cl_e : 0.003981
  EX_cu2_e : 0.000542
  EX_mn2_e : 0.000529
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.395264
  EX_co2_e : 26.053333
  EX_h_e : 7.436318
  Auxiliary production reaction : 0.102075
  DM_5drib_c : 0.000172
  DM_4crsol_c : 0.000171

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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