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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b0261 b1602 b0153 b4381 b0590 b2406 b1727 b0114 b0529 b1539 b2492 b0904 b2954 b3029 b1380 b2660 b1771 b3662 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.451488 (mmol/gDw/h)
  Minimum Production Rate : 0.208358 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.955870
  EX_o2_e : 286.915189
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.917819
  EX_pi_e : 1.268941
  EX_so4_e : 0.113694
  EX_k_e : 0.088127
  EX_mg2_e : 0.003917
  EX_ca2_e : 0.002350
  EX_cl_e : 0.002350
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992749
  EX_h2o_e : 552.612085
  EX_co2_e : 37.473433
  EX_ac_e : 0.262850
  Auxiliary production reaction : 0.208358
  EX_12ppd__S_e : 0.113994
  EX_glyclt_e : 0.000505
  DM_5drib_c : 0.000303
  DM_4crsol_c : 0.000101

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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