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 (8 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b0586 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b3617 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b3709 b3161 b0112 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3821 b1473 b4141 b1798 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391625 (mmol/gDw/h)
  Minimum Production Rate : 0.586471 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.974965
  EX_o2_e : 268.412019
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.334811
  EX_pi_e : 2.137177
  EX_so4_e : 0.685090
  EX_k_e : 0.076442
  EX_mg2_e : 0.003397
  EX_ca2_e : 0.002038
  EX_cl_e : 0.002038
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993710
  EX_h2o_e : 546.009097
  EX_co2_e : 19.835797
  EX_ac_e : 2.660928
  Auxiliary production reaction : 0.586471
  EX_mththf_e : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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