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 : ttdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b2029 b1759 b4138 b4123 b0621 b4381 b2406 b0529 b2197 b3918 b0789 b1249 b1695 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377122 (mmol/gDw/h)
  Minimum Production Rate : 0.397730 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 983.866692
  EX_o2_e : 261.424122
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.607760
  EX_pi_e : 0.363774
  EX_so4_e : 0.094967
  EX_k_e : 0.073612
  EX_mg2_e : 0.003272
  EX_ca2_e : 0.001963
  EX_cl_e : 0.001963
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993943
  EX_h2o_e : 525.840146
  EX_co2_e : 14.153980
  EX_ac_e : 10.942359
  Auxiliary production reaction : 0.397730
  EX_succ_e : 0.393260
  EX_thym_e : 0.267436
  EX_hxa_e : 0.000620
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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