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 : gdptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b1539 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447982 (mmol/gDw/h)
  Minimum Production Rate : 0.670266 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.559167
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.189995
  EX_pi_e : 3.783455
  EX_so4_e : 0.112811
  EX_k_e : 0.087443
  EX_fe2_e : 0.007195
  EX_mg2_e : 0.003886
  EX_ca2_e : 0.002332
  EX_cl_e : 0.002332
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.058933
  EX_co2_e : 31.503720
  EX_h_e : 7.159784
  EX_ac_e : 1.702015
  Auxiliary production reaction : 0.670266
  DM_oxam_c : 0.000501
  DM_5drib_c : 0.000301
  DM_4crsol_c : 0.000100

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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