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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4161 b1852 b4138 b4123 b0621 b2406 b0452 b0529 b2197 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453223 (mmol/gDw/h)
  Minimum Production Rate : 0.239294 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.515368
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.537575
  EX_pi_e : 0.437182
  EX_so4_e : 0.114131
  EX_k_e : 0.088466
  EX_fe2_e : 0.007279
  EX_mg2_e : 0.003932
  EX_ca2_e : 0.002359
  EX_cl_e : 0.002359
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 33.606847
  EX_co2_e : 19.319557
  EX_h_e : 13.528193
  EX_ac_e : 7.536465
  EX_succ_e : 0.472617
  EX_ura_e : 0.321402
  Auxiliary production reaction : 0.239294
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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