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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b1054 b3553 b1478 b1241 b0351 b4069 b3708 b3115 b1849 b2296 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b1701 b1805 b2799 b3945 b1602 b3709 b0153 b2913 b4381 b0590 b2406 b3161 b0112 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b1473 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.422249 (mmol/gDw/h)
  Minimum Production Rate : 0.011054 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.907088
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.122365
  EX_pi_e : 0.440467
  EX_so4_e : 0.117385
  EX_k_e : 0.082420
  EX_fe2_e : 0.006782
  EX_mg2_e : 0.003663
  EX_ca2_e : 0.002198
  EX_cl_e : 0.002198
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.995226
  EX_co2_e : 35.955683
  EX_h_e : 8.024326
  EX_ac_e : 1.626640
  EX_xan_e : 0.621183
  Auxiliary production reaction : 0.011054
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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