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 : pe140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3831 b3614 b0910 b4152 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b2440 b4138 b4123 b0621 b2913 b4381 b2406 b0452 b2197 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454767 (mmol/gDw/h)
  Minimum Production Rate : 0.234120 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 999.886768
  EX_h_e : 994.341550
  EX_o2_e : 277.082574
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.796626
  EX_pi_e : 0.672791
  EX_so4_e : 0.114520
  EX_k_e : 0.088767
  EX_mg2_e : 0.003945
  EX_ca2_e : 0.002367
  EX_cl_e : 0.002367
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.879464
  EX_h2o_e : 545.146870
  EX_co2_e : 30.408918
  EX_succ_e : 0.474228
  EX_ura_e : 0.322497
  Auxiliary production reaction : 0.234120
  EX_etha_e : 0.006063
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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