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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b2925 b2097 b2926 b3617 b3844 b1004 b3713 b1109 b0046 b2463 b3946 b2210 b0825 b1033 b3551 b3945 b1602 b4219 b1832 b1778 b0452 b1727 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536755 (mmol/gDw/h)
  Minimum Production Rate : 0.741815 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.930838
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.796912
  EX_pi_e : 0.517757
  EX_so4_e : 0.135166
  EX_k_e : 0.104771
  EX_fe2_e : 0.008621
  EX_mg2_e : 0.004656
  EX_ca2_e : 0.002794
  EX_cl_e : 0.002794
  EX_cu2_e : 0.000381
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.621418
  EX_co2_e : 32.447193
  EX_h_e : 6.579932
  EX_ac_e : 1.648010
  Auxiliary production reaction : 0.741815
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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