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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2965 b0693 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.691282 (mmol/gDw/h)
  Minimum Production Rate : 0.070293 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.356701
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.957831
  EX_pi_e : 0.877692
  EX_so4_e : 0.244371
  EX_k_e : 0.134933
  EX_fe2_e : 0.011103
  EX_mg2_e : 0.005997
  EX_ca2_e : 0.003598
  EX_cl_e : 0.003598
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000478
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.598191
  EX_co2_e : 29.937503
  EX_h_e : 6.562648
  Auxiliary production reaction : 0.070293
  DM_5drib_c : 0.000464
  DM_4crsol_c : 0.000154

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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