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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3942 b1732 b0238 b0125 b2744 b2930 b4232 b3697 b3925 b0871 b2779 b1612 b1611 b2883 b4122 b2690 b0477 b4374 b2361 b2291 b0411 b3945 b4388 b0114 b0529 b2492 b0904 b1380 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.582584 (mmol/gDw/h)
  Minimum Production Rate : 0.462925 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.071271
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.294129
  EX_pi_e : 1.487813
  EX_so4_e : 0.146706
  EX_k_e : 0.113716
  EX_fe2_e : 0.009357
  EX_mg2_e : 0.005054
  EX_cl_e : 0.003032
  EX_ca2_e : 0.003032
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.516625
  EX_co2_e : 27.808986
  EX_h_e : 7.287647
  EX_pyr_e : 1.173240
  EX_fum_e : 0.609788
  Auxiliary production reaction : 0.462925
  DM_oxam_c : 0.002274
  EX_glyc__R_e : 0.000195
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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