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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b0411 b4138 b4123 b0621 b2197 b2835 b3918 b0789 b1249 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.599174 (mmol/gDw/h)
  Minimum Production Rate : 0.316451 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.701947
  EX_o2_e : 267.902033
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.320832
  EX_pi_e : 0.894417
  EX_so4_e : 0.150884
  EX_k_e : 0.116955
  EX_mg2_e : 0.005198
  EX_ca2_e : 0.003119
  EX_cl_e : 0.003119
  EX_cu2_e : 0.000425
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990377
  EX_h2o_e : 540.914224
  EX_co2_e : 21.714284
  EX_succ_e : 0.624814
  EX_ura_e : 0.424903
  Auxiliary production reaction : 0.316451
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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