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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2066 b4384 b3708 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b2498 b2210 b3945 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381084 (mmol/gDw/h)
  Minimum Production Rate : 0.263951 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.503813
  EX_o2_e : 279.884414
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.115675
  EX_pi_e : 0.367596
  EX_so4_e : 0.095965
  EX_k_e : 0.074385
  EX_mg2_e : 0.003306
  EX_ca2_e : 0.001984
  EX_cl_e : 0.001984
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993879
  EX_h2o_e : 543.385733
  EX_co2_e : 28.600854
  EX_pyr_e : 4.724564
  Auxiliary production reaction : 0.263951
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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