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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3926 b3115 b1849 b2296 b2926 b3617 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0675 b2361 b0261 b3945 b1602 b4381 b2406 b3915 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339666 (mmol/gDw/h)
  Minimum Production Rate : 0.674646 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.194158
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.232524
  EX_pi_e : 1.002290
  EX_so4_e : 0.085535
  EX_k_e : 0.066300
  EX_fe3_e : 0.005455
  EX_mg2_e : 0.002947
  EX_ca2_e : 0.001768
  EX_cl_e : 0.001768
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 51.717637
  EX_co2_e : 33.921276
  EX_h_e : 7.888351
  EX_etoh_e : 0.982787
  Auxiliary production reaction : 0.674646
  EX_his__L_e : 0.609501
  EX_ac_e : 0.197749
  EX_hxan_e : 0.009268
  DM_5drib_c : 0.000228
  DM_4crsol_c : 0.000076

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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