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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b3617 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b1602 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446726 (mmol/gDw/h)
  Minimum Production Rate : 0.001153 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.398496
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.042102
  EX_pi_e : 0.436637
  EX_so4_e : 0.113640
  EX_k_e : 0.087198
  EX_fe2_e : 0.007177
  EX_mg2_e : 0.003875
  EX_ca2_e : 0.002325
  EX_cl_e : 0.002325
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.910147
  EX_co2_e : 33.669193
  EX_h_e : 7.315627
  EX_his__L_e : 1.069829
  EX_acald_e : 0.772214
  Auxiliary production reaction : 0.001145
  DM_5drib_c : 0.000300
  EX_glyclt_e : 0.000299
  DM_4crsol_c : 0.000100

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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