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 : pg180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b0474 b2518 b3831 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4161 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455964 (mmol/gDw/h)
  Minimum Production Rate : 0.240510 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.446571
  EX_o2_e : 273.648019
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.570458
  EX_pi_e : 0.680336
  EX_so4_e : 0.114821
  EX_k_e : 0.089001
  EX_mg2_e : 0.003955
  EX_ca2_e : 0.002373
  EX_cl_e : 0.002373
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992677
  EX_h2o_e : 542.598059
  EX_co2_e : 27.989261
  EX_succ_e : 0.475476
  EX_ura_e : 0.323041
  Auxiliary production reaction : 0.240510
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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