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 : dtdp4d6dg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3831 b3614 b0910 b4152 b2925 b2097 b2781 b1850 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1779 b1759 b1200 b4138 b4123 b0621 b4381 b2406 b0452 b2835 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610533 (mmol/gDw/h)
  Minimum Production Rate : 0.046024 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.056814
  EX_o2_e : 276.939293
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.275365
  EX_pi_e : 0.680971
  EX_so4_e : 0.153744
  EX_k_e : 0.119172
  EX_mg2_e : 0.005296
  EX_ca2_e : 0.003178
  EX_cl_e : 0.003178
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.898069
  EX_h2o_e : 547.923012
  EX_co2_e : 28.082928
  EX_succ_e : 0.636659
  EX_ura_e : 0.110557
  EX_pheme_e : 0.092126
  Auxiliary production reaction : 0.046024
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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