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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (117 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b2836 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b2366 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413315 (mmol/gDw/h)
  Minimum Production Rate : 0.098482 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.884225
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.942845
  EX_pi_e : 0.694132
  EX_so4_e : 0.498009
  EX_mobd_e : 0.098485
  EX_k_e : 0.080676
  EX_fe2_e : 0.006638
  EX_mg2_e : 0.003586
  EX_ca2_e : 0.002151
  EX_cl_e : 0.002151
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.537966
  EX_co2_e : 37.286093
  EX_h_e : 5.490767
  EX_glyclt_e : 0.761216
  EX_ac_e : 0.634554
  Auxiliary production reaction : 0.098482
  EX_hxan_e : 0.000462
  DM_5drib_c : 0.000277
  DM_4crsol_c : 0.000092

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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