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 : cdpdhdecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b4382 b3831 b4384 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b2406 b0452 b2197 b3918 b1912 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.552428 (mmol/gDw/h)
  Minimum Production Rate : 0.291762 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.249827
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.041443
  EX_pi_e : 1.116399
  EX_so4_e : 0.139112
  EX_k_e : 0.107830
  EX_fe2_e : 0.008873
  EX_mg2_e : 0.004792
  EX_ca2_e : 0.002875
  EX_cl_e : 0.002875
  EX_cu2_e : 0.000392
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.657106
  EX_co2_e : 21.783606
  EX_h_e : 6.719808
  EX_succ_e : 0.576067
  Auxiliary production reaction : 0.291762
  EX_ura_e : 0.099991
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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