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 : udpLa4fn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2779 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b1701 b1805 b4138 b4123 b0621 b2406 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.659195 (mmol/gDw/h)
  Minimum Production Rate : 0.348151 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.970875
  EX_o2_e : 274.303526
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.402335
  EX_pi_e : 1.332165
  EX_so4_e : 0.165999
  EX_k_e : 0.128670
  EX_mg2_e : 0.005719
  EX_ca2_e : 0.003431
  EX_cl_e : 0.003431
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000456
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989413
  EX_h2o_e : 547.009799
  EX_co2_e : 24.493932
  EX_succ_e : 0.687403
  Auxiliary production reaction : 0.348151
  EX_ura_e : 0.119316
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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.

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Last updated: 21-Sep-2023
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