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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b4382 b0474 b2518 b3831 b4384 b1278 b3752 b4152 b2779 b2781 b1612 b1611 b4122 b0907 b1759 b4161 b4138 b4123 b0621 b2406 b0114 b2492 b0904 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441420 (mmol/gDw/h)
  Minimum Production Rate : 0.233098 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.623378
  EX_o2_e : 285.980200
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.626466
  EX_pi_e : 1.125092
  EX_so4_e : 0.111158
  EX_k_e : 0.086162
  EX_mg2_e : 0.003829
  EX_cl_e : 0.002298
  EX_ca2_e : 0.002298
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992910
  EX_h2o_e : 551.301479
  EX_co2_e : 36.457368
  EX_succ_e : 0.460310
  Auxiliary production reaction : 0.233098
  EX_ura_e : 0.079934
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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