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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b3617 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0112 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.587541 (mmol/gDw/h)
  Minimum Production Rate : 0.084435 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.019831
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.014686
  EX_so4_e : 1.310641
  EX_pi_e : 0.820051
  EX_k_e : 0.114684
  EX_fe2_e : 0.009436
  EX_mg2_e : 0.005097
  EX_ca2_e : 0.003058
  EX_cl_e : 0.003058
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000406
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.549772
  EX_co2_e : 26.104807
  EX_h_e : 4.573612
  EX_acald_e : 2.258421
  EX_cys__L_e : 1.078251
  Auxiliary production reaction : 0.084435
  DM_5drib_c : 0.000394
  DM_4crsol_c : 0.000131

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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