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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b0474 b2518 b3831 b4069 b3752 b4152 b2297 b2458 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4161 b0675 b0822 b4138 b4123 b0621 b4381 b0452 b1727 b0114 b0529 b2492 b0904 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.576370 (mmol/gDw/h)
  Minimum Production Rate : 0.304314 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.563223
  EX_o2_e : 277.021951
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.042207
  EX_pi_e : 1.164597
  EX_so4_e : 0.145141
  EX_k_e : 0.112503
  EX_mg2_e : 0.005000
  EX_ca2_e : 0.003000
  EX_cl_e : 0.003000
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990743
  EX_h2o_e : 546.418284
  EX_co2_e : 27.949264
  EX_ac_e : 1.416389
  EX_succ_e : 0.601034
  EX_ura_e : 0.408731
  Auxiliary production reaction : 0.304314
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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