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

Gene deletion strategy (104 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 63
  Gene deletion: b2242 b3553 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3614 b0910 b2297 b2458 b2926 b2781 b2407 b3844 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b4374 b0675 b1415 b1014 b0822 b2799 b4388 b1907 b4138 b4123 b0621 b2406 b0112 b3915 b0452 b2868 b0114 b1539 b2492 b0904 b1533 b3028 b1380 b3918 b1912 b1473 b4266 b3662 b2842 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339024 (mmol/gDw/h)
  Minimum Production Rate : 0.388608 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.040138
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.592165
  EX_pi_e : 1.104240
  EX_so4_e : 0.085373
  EX_k_e : 0.066175
  EX_fe3_e : 0.005445
  EX_mg2_e : 0.002941
  EX_ca2_e : 0.001765
  EX_cl_e : 0.001765
  EX_cu2_e : 0.000240
  EX_mn2_e : 0.000234
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 51.186204
  EX_co2_e : 33.778656
  EX_h_e : 8.285165
  EX_ac_e : 1.289025
  EX_succ_e : 0.860930
  EX_hxan_e : 0.507399
  EX_ura_e : 0.450571
  Auxiliary production reaction : 0.388608
  EX_dxylnt_e : 0.000227
  DM_mththf_c : 0.000152
  DM_5drib_c : 0.000076
  DM_4crsol_c : 0.000076

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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