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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3500 b4382 b4384 b2744 b3614 b0910 b4152 b2781 b2235 b1612 b1611 b4122 b1779 b1759 b4374 b0675 b4388 b4138 b4123 b0621 b2197 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459933 (mmol/gDw/h)
  Minimum Production Rate : 0.057331 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.773914
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.676894
  EX_pi_e : 0.558317
  EX_so4_e : 0.115820
  EX_k_e : 0.089776
  EX_fe2_e : 0.007387
  EX_mg2_e : 0.003990
  EX_ca2_e : 0.002394
  EX_cl_e : 0.002394
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.940176
  EX_co2_e : 36.211953
  EX_h_e : 5.722939
  EX_succ_e : 0.479615
  EX_thymd_e : 0.185580
  EX_ura_e : 0.083249
  Auxiliary production reaction : 0.057331
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000103

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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