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 : pgp161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 68: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b4381 b2406 b2197 b2835 b3918 b0789 b1249 b0494 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488137 (mmol/gDw/h)
  Minimum Production Rate : 0.257807 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.869529
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.964166
  EX_pi_e : 0.986475
  EX_so4_e : 0.122923
  EX_k_e : 0.095281
  EX_fe2_e : 0.007840
  EX_mg2_e : 0.004235
  EX_ca2_e : 0.002541
  EX_cl_e : 0.002541
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.166003
  EX_co2_e : 26.746772
  EX_h_e : 5.937769
  EX_succ_e : 0.509026
  EX_ura_e : 0.346162
  Auxiliary production reaction : 0.257807
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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