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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b1478 b3399 b3846 b2341 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b1623 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2913 b4381 b3915 b2975 b3603 b0755 b3612 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393814 (mmol/gDw/h)
  Minimum Production Rate : 0.294567 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.492577
  EX_o2_e : 287.525505
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.317329
  EX_pi_e : 0.379875
  EX_so4_e : 0.099170
  EX_k_e : 0.076870
  EX_mg2_e : 0.003416
  EX_ca2_e : 0.002050
  EX_cl_e : 0.002050
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993675
  EX_h2o_e : 553.480332
  EX_co2_e : 37.482780
  Auxiliary production reaction : 0.294567
  EX_ac_e : 0.229273
  EX_ade_e : 0.000441
  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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