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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b0512 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b0494 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.754254 (mmol/gDw/h)
  Minimum Production Rate : 0.317512 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.313939
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.427706
  EX_pi_e : 1.045070
  EX_so4_e : 0.189936
  EX_k_e : 0.147225
  EX_fe2_e : 0.012114
  EX_mg2_e : 0.006543
  EX_ca2_e : 0.003926
  EX_cl_e : 0.003926
  EX_cu2_e : 0.000535
  EX_mn2_e : 0.000521
  EX_zn2_e : 0.000257
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.393339
  EX_co2_e : 24.962331
  EX_h_e : 8.651330
  EX_ac_e : 0.439116
  Auxiliary production reaction : 0.317512
  EX_alltn_e : 0.002945
  DM_mththf_c : 0.002439
  DM_5drib_c : 0.000506
  DM_4crsol_c : 0.000168

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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