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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4384 b3708 b3008 b0512 b0871 b2925 b2097 b2926 b0030 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b3945 b4381 b2406 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369894 (mmol/gDw/h)
  Minimum Production Rate : 0.012089 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.300889
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.020000
  EX_pi_e : 0.368891
  EX_so4_e : 0.093147
  EX_k_e : 0.072201
  EX_fe2_e : 0.005941
  EX_mg2_e : 0.003209
  EX_ca2_e : 0.001925
  EX_cl_e : 0.001925
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 43.647894
  EX_co2_e : 28.361186
  EX_h_e : 8.868456
  EX_pyr_e : 5.444546
  Auxiliary production reaction : 0.012089
  EX_thym_e : 0.012089
  EX_alltn_e : 0.000249
  DM_mththf_c : 0.000166
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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