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 : pgp180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 69: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b2242 b4382 b4384 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b0675 b4138 b4123 b0621 b2406 b0306 b3605 b2197 b3028 b3821 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455574 (mmol/gDw/h)
  Minimum Production Rate : 0.240609 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.451021
  EX_o2_e : 273.660402
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.566298
  EX_pi_e : 0.920667
  EX_so4_e : 0.114723
  EX_k_e : 0.088925
  EX_mg2_e : 0.003952
  EX_ca2_e : 0.002371
  EX_cl_e : 0.002371
  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 : 999.992683
  EX_h2o_e : 542.841682
  EX_co2_e : 28.002651
  EX_succ_e : 0.475069
  EX_ura_e : 0.323069
  Auxiliary production reaction : 0.240609
  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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