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 : nicrnt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b0474 b2518 b1241 b0351 b3831 b3752 b4152 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b2781 b3617 b1232 b1612 b1611 b4122 b2690 b1759 b4161 b4015 b0614 b3945 b4138 b4123 b0621 b2406 b0452 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482402 (mmol/gDw/h)
  Minimum Production Rate : 0.254778 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.345394
  EX_o2_e : 281.330905
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.639307
  EX_pi_e : 0.720106
  EX_so4_e : 0.121478
  EX_k_e : 0.094161
  EX_mg2_e : 0.004185
  EX_ca2_e : 0.002511
  EX_cl_e : 0.002511
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992252
  EX_h2o_e : 547.685005
  EX_co2_e : 31.477908
  EX_succ_e : 1.252051
  EX_ac_e : 0.280847
  Auxiliary production reaction : 0.254778
  EX_ura_e : 0.087316
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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.

Last updated: 21-Sep-2023
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