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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3399 b0586 b3831 b4069 b4384 b2744 b1278 b3708 b3008 b3614 b0910 b3752 b2297 b2458 b2781 b2883 b1759 b1982 b2797 b3117 b1814 b4471 b1623 b4014 b0261 b2976 b0411 b0507 b3709 b4381 b2406 b3161 b0112 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b3918 b1473 b0494 b1600 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.691460 (mmol/gDw/h)
  Minimum Production Rate : 0.143472 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.303262
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.991947
  EX_pi_e : 1.097402
  EX_so4_e : 0.317595
  EX_k_e : 0.134968
  EX_fe2_e : 0.011106
  EX_mg2_e : 0.005998
  EX_ca2_e : 0.003599
  EX_cl_e : 0.003599
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000478
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.923861
  EX_co2_e : 24.643642
  EX_h_e : 8.012129
  EX_ac_e : 0.546030
  EX_thym_e : 0.250535
  Auxiliary production reaction : 0.143472
  DM_oxam_c : 0.018866
  DM_5drib_c : 0.000464
  DM_4crsol_c : 0.000154

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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