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 : pg180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b2744 b1278 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b4381 b2406 b3915 b2197 b3918 b1695 b1206 b3546   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.540864 (mmol/gDw/h)
  Minimum Production Rate : 0.284858 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.409779
  EX_o2_e : 266.891330
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.608393
  EX_pi_e : 0.806579
  EX_so4_e : 0.136200
  EX_k_e : 0.105573
  EX_mg2_e : 0.004692
  EX_ca2_e : 0.002815
  EX_cl_e : 0.002815
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991313
  EX_h2o_e : 539.366034
  EX_co2_e : 22.036159
  EX_succ_e : 0.564009
  EX_ura_e : 0.383553
  Auxiliary production reaction : 0.284858
  EX_hxa_e : 0.001593
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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