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 : aconm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2239 b3453 b0114 b1539 b2492 b0904 b1533 b3927 b3825   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.766181 (mmol/gDw/h)
  Minimum Production Rate : 0.228634 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.652829
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.274687
  EX_pi_e : 0.739063
  EX_so4_e : 0.192940
  EX_k_e : 0.149553
  EX_fe2_e : 0.012306
  EX_mg2_e : 0.006647
  EX_cl_e : 0.003988
  EX_ca2_e : 0.003988
  EX_cu2_e : 0.000543
  EX_mn2_e : 0.000529
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 46.977858
  EX_co2_e : 26.059240
  EX_h_e : 7.943303
  EX_ac_e : 0.446060
  Auxiliary production reaction : 0.228634
  DM_5drib_c : 0.000172
  DM_4crsol_c : 0.000171

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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