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 (70 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b4152 b2779 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b0411 b4138 b4123 b0621 b2913 b0452 b0529 b3918 b0789 b1249 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445751 (mmol/gDw/h)
  Minimum Production Rate : 0.055492 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.521642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.501776
  EX_pi_e : 0.540958
  EX_so4_e : 0.112249
  EX_k_e : 0.087008
  EX_fe2_e : 0.007159
  EX_mg2_e : 0.003867
  EX_ca2_e : 0.002320
  EX_cl_e : 0.002320
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.219894
  EX_co2_e : 36.946174
  EX_h_e : 5.546617
  EX_succ_e : 0.464826
  EX_thymd_e : 0.179858
  EX_ura_e : 0.080754
  Auxiliary production reaction : 0.055492
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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