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 (58 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3708 b0512 b2297 b2458 b3617 b0160 b3844 b1004 b3713 b1109 b0046 b1982 b2797 b3117 b1814 b4471 b2210 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b3161 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b3035 b1533 b3825 b1380 b1473 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.302289 (mmol/gDw/h)
  Minimum Production Rate : 0.451848 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.352641
  EX_o2_e : 277.915751
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.432351
  EX_pi_e : 1.647134
  EX_so4_e : 0.527971
  EX_k_e : 0.059005
  EX_mg2_e : 0.002622
  EX_cl_e : 0.001573
  EX_ca2_e : 0.001573
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000209
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995145
  EX_h2o_e : 548.751137
  EX_co2_e : 29.012114
  EX_ac_e : 2.052840
  Auxiliary production reaction : 0.451848
  EX_alltn_e : 0.001180
  DM_5drib_c : 0.001045
  DM_4crsol_c : 0.000909

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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