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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b4382 b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2779 b2926 b3844 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b1033 b2440 b0261 b3709 b2406 b3161 b0112 b2789 b3127 b0452 b2868 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.623880 (mmol/gDw/h)
  Minimum Production Rate : 0.264240 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.575054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.591077
  EX_pi_e : 1.394520
  EX_so4_e : 0.157106
  EX_k_e : 0.121777
  EX_fe2_e : 0.010020
  EX_mg2_e : 0.005412
  EX_ca2_e : 0.003247
  EX_cl_e : 0.003247
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000431
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.407346
  EX_co2_e : 28.112124
  EX_h_e : 7.156127
  EX_ac_e : 0.363214
  Auxiliary production reaction : 0.264240
  EX_ade_e : 0.000698
  DM_5drib_c : 0.000419
  DM_4crsol_c : 0.000139
  EX_etha_e : 0.000050

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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