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 : 4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b0474 b2518 b2744 b4152 b2781 b1851 b1612 b1611 b4122 b1779 b1759 b4374 b4161 b0675 b4388 b4138 b4123 b0621 b4381 b0529 b2197 b3821 b1380 b3918 b1912 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597366 (mmol/gDw/h)
  Minimum Production Rate : 0.074463 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.482928
  EX_o2_e : 278.458039
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.373210
  EX_pi_e : 0.725148
  EX_so4_e : 0.150429
  EX_k_e : 0.116602
  EX_mg2_e : 0.005182
  EX_ca2_e : 0.003109
  EX_cl_e : 0.003109
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990406
  EX_h2o_e : 548.153744
  EX_co2_e : 29.103830
  EX_succ_e : 0.622929
  EX_thymd_e : 0.241033
  EX_ura_e : 0.108125
  Auxiliary production reaction : 0.074463
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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