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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1518 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.733636 (mmol/gDw/h)
  Minimum Production Rate : 0.466716 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.194027
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.325817
  EX_pi_e : 1.174385
  EX_so4_e : 0.184744
  EX_k_e : 0.143201
  EX_mg2_e : 0.006364
  EX_fe2_e : 0.006055
  EX_fe3_e : 0.005728
  EX_ca2_e : 0.003819
  EX_cl_e : 0.003819
  EX_cu2_e : 0.000520
  EX_mn2_e : 0.000507
  EX_zn2_e : 0.000250
  EX_ni2_e : 0.000237
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.469248
  EX_co2_e : 25.293102
  EX_h_e : 8.109676
  Auxiliary production reaction : 0.466716
  EX_ac_e : 0.427112
  EX_adn_e : 0.000494
  DM_mththf_c : 0.000329
  DM_5drib_c : 0.000165
  DM_4crsol_c : 0.000164

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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