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 : fum_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 7: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3942 b1732 b0474 b2518 b1241 b0351 b1479 b0871 b2925 b2097 b3236 b2463 b3962 b3946 b2210 b0825 b4267 b3551 b4219 b1832 b1778 b0114 b2492 b0904 b0325 b1710 b2480 b0508 b4266 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583059 (mmol/gDw/h)
  Minimum Production Rate : 2.161460 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.338312
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.296992
  EX_pi_e : 0.562423
  EX_so4_e : 0.146826
  EX_k_e : 0.113809
  EX_mg2_e : 0.005058
  EX_fe2_e : 0.004812
  EX_fe3_e : 0.004553
  EX_ca2_e : 0.003035
  EX_cl_e : 0.003035
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.139881
  EX_co2_e : 27.422251
  EX_h_e : 9.684854
  Auxiliary production reaction : 2.161460
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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