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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0910 b2930 b4232 b3697 b3925 b0871 b2690 b3616 b3589 b0675 b0822 b4381 b2868 b1727 b4064 b4464 b0114 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.689415 (mmol/gDw/h)
  Minimum Production Rate : 0.207133 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.083657
  EX_o2_e : 274.158238
  EX_nh4_e : 10.016273
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.665014
  EX_so4_e : 0.173608
  EX_k_e : 0.134569
  EX_mg2_e : 0.005981
  EX_ca2_e : 0.003588
  EX_cl_e : 0.003588
  EX_cu2_e : 0.000489
  EX_mn2_e : 0.000476
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988927
  EX_h2o_e : 548.895087
  EX_co2_e : 24.911118
  EX_acald_e : 1.789130
  Auxiliary production reaction : 0.624624
  EX_xan_e : 0.018039
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000154

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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