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 : pg160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 68: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b3831 b4384 b1278 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b1701 b1805 b4138 b4123 b0621 b2406 b0529 b2197 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.419513 (mmol/gDw/h)
  Minimum Production Rate : 0.070486 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.588095
  EX_o2_e : 278.596459
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.276775
  EX_pi_e : 0.626228
  EX_so4_e : 0.105642
  EX_k_e : 0.081886
  EX_mg2_e : 0.003639
  EX_ca2_e : 0.002184
  EX_cl_e : 0.002184
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993262
  EX_h2o_e : 545.519213
  EX_co2_e : 31.522378
  EX_succ_e : 0.437465
  EX_ura_e : 0.297497
  Auxiliary production reaction : 0.070486
  EX_enlipa_e : 0.050359
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000094

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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