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 : cdg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2781 b0099 b3617 b0160 b2883 b1982 b1623 b0261 b0507 b2406 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463929 (mmol/gDw/h)
  Minimum Production Rate : 1.778217 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.381973
  EX_nh4_e : 12.125862
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.447509
  EX_so4_e : 0.116827
  EX_k_e : 0.090556
  EX_fe2_e : 0.007451
  EX_mg2_e : 0.004025
  EX_ca2_e : 0.002415
  EX_cl_e : 0.002415
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.074616
  EX_co2_e : 20.036162
  EX_h_e : 17.391708
  EX_ac_e : 4.235259
  Auxiliary production reaction : 1.778217
  EX_ade_e : 0.000519
  DM_5drib_c : 0.000311
  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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