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 (105 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b2925 b2097 b0030 b1238 b2883 b1779 b2920 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b0261 b0507 b4381 b2406 b0112 b0452 b2868 b4064 b4464 b2975 b0114 b3603 b0728 b0886 b0529 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588403 (mmol/gDw/h)
  Minimum Production Rate : 0.237990 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.665128
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.023969
  EX_pi_e : 1.043557
  EX_so4_e : 0.148172
  EX_k_e : 0.114852
  EX_fe2_e : 0.009450
  EX_mg2_e : 0.005104
  EX_ca2_e : 0.003063
  EX_cl_e : 0.003063
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.095200
  EX_co2_e : 26.619935
  EX_h_e : 8.008503
  EX_pyr_e : 1.408782
  Auxiliary production reaction : 0.237990
  EX_ade_e : 0.000658
  DM_5drib_c : 0.000395
  DM_4crsol_c : 0.000131
  EX_etha_e : 0.000047

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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