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 : nadphx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4382 b4069 b4384 b2744 b3708 b3008 b3752 b0871 b2297 b2458 b2925 b2097 b2926 b2883 b2690 b1982 b2688 b2797 b3117 b1814 b4471 b0261 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b1473 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.586459 (mmol/gDw/h)
  Minimum Production Rate : 0.248422 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.998469
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.075947
  EX_pi_e : 1.310969
  EX_so4_e : 0.147682
  EX_k_e : 0.114473
  EX_fe2_e : 0.009419
  EX_mg2_e : 0.005088
  EX_ca2_e : 0.003053
  EX_cl_e : 0.003053
  EX_cu2_e : 0.000416
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.768555
  EX_co2_e : 25.948055
  EX_h_e : 8.334167
  EX_pyr_e : 1.358726
  EX_ac_e : 0.341428
  Auxiliary production reaction : 0.248422
  EX_ade_e : 0.000656
  DM_5drib_c : 0.000394
  DM_4crsol_c : 0.000131

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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