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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b3115 b1849 b2296 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b4138 b4123 b0621 b2913 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.466482 (mmol/gDw/h)
  Minimum Production Rate : 0.246370 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.973499
  EX_o2_e : 280.390450
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.699574
  EX_pi_e : 0.449971
  EX_so4_e : 0.117469
  EX_k_e : 0.091054
  EX_mg2_e : 0.004047
  EX_cl_e : 0.002428
  EX_ca2_e : 0.002428
  EX_cu2_e : 0.000331
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992508
  EX_h2o_e : 545.596335
  EX_co2_e : 30.894746
  EX_ac_e : 3.098291
  EX_succ_e : 0.486444
  Auxiliary production reaction : 0.246370
  EX_ura_e : 0.084435
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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