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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b2297 b2458 b2407 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610992 (mmol/gDw/h)
  Minimum Production Rate : 0.388222 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.898347
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.764010
  EX_pi_e : 0.977588
  EX_so4_e : 0.153860
  EX_k_e : 0.119261
  EX_fe2_e : 0.009813
  EX_mg2_e : 0.005300
  EX_cl_e : 0.003180
  EX_ca2_e : 0.003180
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.278411
  EX_co2_e : 27.813105
  EX_h_e : 8.391838
  EX_ac_e : 1.999989
  Auxiliary production reaction : 0.388222
  DM_oxam_c : 0.000684
  DM_5drib_c : 0.000410
  DM_4crsol_c : 0.000136

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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