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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b0512 b2297 b2458 b3617 b0160 b3236 b1982 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0511 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352634 (mmol/gDw/h)
  Minimum Production Rate : 1.351628 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.789628
  EX_nh4_e : 11.919762
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.340153
  EX_so4_e : 0.088800
  EX_k_e : 0.068832
  EX_fe2_e : 0.005664
  EX_mg2_e : 0.003059
  EX_ca2_e : 0.001835
  EX_cl_e : 0.001835
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 51.103666
  EX_co2_e : 20.161982
  EX_h_e : 15.922346
  EX_ac_e : 3.219232
  Auxiliary production reaction : 1.351628
  EX_xan_e : 0.000395
  DM_5drib_c : 0.000237
  DM_4crsol_c : 0.000079

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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