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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b0871 b2926 b1612 b1611 b4122 b2690 b3945 b4138 b4123 b0621 b4381 b2406 b0114 b2492 b0904 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357052 (mmol/gDw/h)
  Minimum Production Rate : 0.143949 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.700383
  EX_o2_e : 279.732272
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.362531
  EX_pi_e : 0.488363
  EX_so4_e : 0.089913
  EX_k_e : 0.069694
  EX_mg2_e : 0.003097
  EX_ca2_e : 0.001858
  EX_cl_e : 0.001858
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994265
  EX_h2o_e : 543.662851
  EX_co2_e : 27.692598
  EX_pyr_e : 4.762084
  EX_succ_e : 0.372331
  Auxiliary production reaction : 0.143949
  EX_thym_e : 0.143949
  EX_ura_e : 0.109254
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000080

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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