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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b0261 b2239 b2406 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3447 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.643984 (mmol/gDw/h)
  Minimum Production Rate : 0.272755 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.031963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.318803
  EX_pi_e : 1.166754
  EX_so4_e : 0.162168
  EX_k_e : 0.125701
  EX_fe2_e : 0.010343
  EX_mg2_e : 0.005587
  EX_ca2_e : 0.003352
  EX_cl_e : 0.003352
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.549014
  EX_co2_e : 28.724545
  EX_h_e : 7.110316
  EX_ac_e : 0.374919
  Auxiliary production reaction : 0.272755
  DM_5drib_c : 0.000432
  DM_4crsol_c : 0.000144
  EX_g3pe_e : 0.000052

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.

Last updated: 21-Sep-2023
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