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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2799 b1602 b2913 b4381 b2406 b3915 b2366 b2492 b0904 b1781 b3001 b1533 b1380 b0325 b1771 b1517 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400811 (mmol/gDw/h)
  Minimum Production Rate : 0.192723 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.694626
  EX_o2_e : 283.380318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.486370
  EX_pi_e : 0.579341
  EX_so4_e : 0.100933
  EX_k_e : 0.078236
  EX_mg2_e : 0.003477
  EX_ca2_e : 0.002086
  EX_cl_e : 0.002086
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993561
  EX_h2o_e : 544.634982
  EX_co2_e : 31.353167
  EX_glyclt_e : 4.610562
  EX_ac_e : 0.233348
  Auxiliary production reaction : 0.192716
  EX_ade_e : 0.000270
  DM_mththf_c : 0.000180
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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