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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b2407 b0907 b1779 b1982 b3616 b3589 b0261 b2406 b0112 b0114 b0529 b2492 b0904 b3662 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.440923 (mmol/gDw/h)
  Minimum Production Rate : 0.370420 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.929607
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.503068
  EX_pi_e : 0.425317
  EX_so4_e : 0.111033
  EX_k_e : 0.086065
  EX_fe2_e : 0.007082
  EX_mg2_e : 0.003825
  EX_cl_e : 0.002295
  EX_ca2_e : 0.002295
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 42.498007
  EX_co2_e : 26.779823
  EX_h_e : 5.904072
  EX_acald_e : 1.820034
  DM_oxam_c : 0.741137
  DM_5drib_c : 0.740940
  DM_4crsol_c : 0.740742
  Auxiliary production reaction : 0.370420

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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