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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b0474 b2518 b1241 b0351 b2744 b4152 b0871 b2297 b2458 b2925 b2097 b3617 b1612 b1611 b4122 b0907 b1779 b3946 b0825 b4374 b4161 b0675 b4015 b0614 b4138 b4123 b0621 b0452 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448534 (mmol/gDw/h)
  Minimum Production Rate : 0.236891 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.350982
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.243392
  EX_pi_e : 0.432659
  EX_so4_e : 0.112950
  EX_k_e : 0.087551
  EX_fe2_e : 0.007204
  EX_mg2_e : 0.003891
  EX_ca2_e : 0.002335
  EX_cl_e : 0.002335
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.325932
  EX_co2_e : 31.244872
  EX_h_e : 9.056853
  EX_succ_e : 1.646133
  EX_ac_e : 1.007123
  Auxiliary production reaction : 0.236891
  EX_ura_e : 0.081186
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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