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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0512 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.571027 (mmol/gDw/h)
  Minimum Production Rate : 0.065512 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.544908
  EX_o2_e : 283.668463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.628191
  EX_pi_e : 0.747354
  EX_so4_e : 0.209309
  EX_k_e : 0.111461
  EX_mg2_e : 0.004954
  EX_ca2_e : 0.002972
  EX_cl_e : 0.002972
  EX_cu2_e : 0.000405
  EX_mn2_e : 0.000395
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990829
  EX_h2o_e : 551.375211
  EX_co2_e : 34.985819
  Auxiliary production reaction : 0.065512
  EX_alltn_e : 0.000639
  DM_5drib_c : 0.000383
  DM_4crsol_c : 0.000127

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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