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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b1241 b0351 b0871 b2925 b2097 b0517 b2388 b3962 b4139 b3616 b3589 b3946 b0825 b4267 b1033 b1493 b3565 b3517 b2799 b0726 b4381 b0837 b0124 b0114 b2492 b0904 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.552156 (mmol/gDw/h)
  Minimum Production Rate : 0.438746 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.553366
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.963233
  EX_pi_e : 0.532613
  EX_so4_e : 0.139044
  EX_k_e : 0.107777
  EX_fe2_e : 0.008868
  EX_mg2_e : 0.004790
  EX_ca2_e : 0.002874
  EX_cl_e : 0.002874
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 44.858054
  EX_co2_e : 28.063692
  EX_h_e : 7.725633
  EX_pyr_e : 2.213461
  Auxiliary production reaction : 0.438746
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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