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 : cdpdhdec9eg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1855 b3831 b2744 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b1701 b1805 b4138 b4123 b0621 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.566072 (mmol/gDw/h)
  Minimum Production Rate : 0.298968 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.492907
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.215360
  EX_pi_e : 1.143973
  EX_so4_e : 0.142548
  EX_k_e : 0.110493
  EX_fe2_e : 0.009092
  EX_mg2_e : 0.004911
  EX_cl_e : 0.002946
  EX_ca2_e : 0.002946
  EX_cu2_e : 0.000401
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.777292
  EX_co2_e : 20.839697
  EX_h_e : 6.885780
  EX_succ_e : 0.590296
  Auxiliary production reaction : 0.298968
  EX_ura_e : 0.102461
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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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