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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b2744 b0871 b0160 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0477 b4139 b0675 b2361 b4015 b0411 b2799 b3945 b1602 b0153 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0584 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b2660 b1985 b1518 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410122 (mmol/gDw/h)
  Minimum Production Rate : 0.623875 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.234283
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.548652
  EX_pi_e : 0.395606
  EX_so4_e : 0.103277
  EX_k_e : 0.080053
  EX_mg2_e : 0.003558
  EX_fe2_e : 0.003385
  EX_fe3_e : 0.003202
  EX_ca2_e : 0.002135
  EX_cl_e : 0.002135
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.617926
  EX_co2_e : 37.550604
  EX_h_e : 6.890936
  Auxiliary production reaction : 0.623875
  EX_mththf_e : 0.000184
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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