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 : uri_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b0474 b2518 b1241 b0351 b3831 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b0871 b2297 b2458 b2926 b3617 b1612 b1611 b4122 b2690 b1302 b2662 b4015 b0614 b0726 b3945 b4388 b4138 b4123 b0621 b0452 b2197 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365531 (mmol/gDw/h)
  Minimum Production Rate : 0.193053 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.763152
  EX_o2_e : 280.198331
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.466134
  EX_pi_e : 0.352593
  EX_so4_e : 0.092048
  EX_k_e : 0.071349
  EX_mg2_e : 0.003171
  EX_ca2_e : 0.001903
  EX_cl_e : 0.001903
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994129
  EX_h2o_e : 543.805913
  EX_co2_e : 28.514996
  EX_pyr_e : 3.770887
  EX_ac_e : 0.820669
  EX_succ_e : 0.381173
  EX_uri_e : 0.193053
  EX_ura_e : 0.066162
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000082

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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