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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b4382 b4384 b2744 b3708 b3008 b0871 b0160 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b2291 b0261 b2406 b0114 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b1600 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.760863 (mmol/gDw/h)
  Minimum Production Rate : 0.104762 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.577614
  EX_o2_e : 274.626982
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.950658
  EX_pi_e : 1.048221
  EX_so4_e : 0.296363
  EX_k_e : 0.148515
  EX_mg2_e : 0.006600
  EX_ca2_e : 0.003960
  EX_cl_e : 0.003960
  EX_cu2_e : 0.000539
  EX_mn2_e : 0.000526
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000246
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987780
  EX_h2o_e : 548.540135
  EX_co2_e : 26.253935
  Auxiliary production reaction : 0.104762
  DM_5drib_c : 0.000511
  DM_4crsol_c : 0.000170
  EX_etha_e : 0.000061

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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