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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1238 b2920 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b2342 b3845 b3709 b4381 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0728 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b3447 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.659492 (mmol/gDw/h)
  Minimum Production Rate : 0.394761 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.450572
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.886518
  EX_pi_e : 1.425671
  EX_so4_e : 0.166073
  EX_k_e : 0.128728
  EX_fe2_e : 0.010592
  EX_mg2_e : 0.005721
  EX_ca2_e : 0.003433
  EX_cl_e : 0.003433
  EX_cu2_e : 0.000468
  EX_mn2_e : 0.000456
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 48.787362
  EX_co2_e : 23.870079
  EX_h_e : 8.418899
  Auxiliary production reaction : 0.394761
  EX_ac_e : 0.383947
  DM_oxam_c : 0.000738
  DM_5drib_c : 0.000443
  DM_4crsol_c : 0.000147

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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