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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b2744 b0871 b2925 b2097 b3236 b2883 b1779 b2690 b0477 b3616 b3589 b2210 b4374 b2361 b2291 b0261 b3945 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.312518 (mmol/gDw/h)
  Minimum Production Rate : 0.127078 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.019868
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.756400
  EX_pi_e : 0.555612
  EX_so4_e : 0.078698
  EX_k_e : 0.061001
  EX_fe2_e : 0.005019
  EX_mg2_e : 0.002711
  EX_cl_e : 0.001627
  EX_ca2_e : 0.001627
  EX_cu2_e : 0.000222
  EX_mn2_e : 0.000216
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 43.610296
  EX_co2_e : 30.550835
  EX_h_e : 5.136714
  EX_pyr_e : 2.011019
  EX_acald_e : 0.274776
  Auxiliary production reaction : 0.127078
  DM_5drib_c : 0.000070
  DM_4crsol_c : 0.000070

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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