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 (64 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0121 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b1701 b1805 b2799 b3945 b1602 b0507 b3709 b2913 b2406 b3161 b0112 b2366 b2492 b0904 b1533 b1380 b1473 b4141 b1798 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392835 (mmol/gDw/h)
  Minimum Production Rate : 0.009845 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.640398
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.203250
  EX_pi_e : 0.408465
  EX_so4_e : 0.108769
  EX_k_e : 0.076679
  EX_fe2_e : 0.006309
  EX_mg2_e : 0.003408
  EX_cl_e : 0.002045
  EX_ca2_e : 0.002045
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.744882
  EX_co2_e : 34.753817
  EX_h_e : 8.053104
  EX_ac_e : 1.512448
  EX_gsn_e : 0.577911
  Auxiliary production reaction : 0.009845
  EX_ade_e : 0.000440
  DM_5drib_c : 0.000264
  DM_4crsol_c : 0.000088

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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