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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b3399 b4069 b2744 b3115 b1849 b2296 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b0261 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447900 (mmol/gDw/h)
  Minimum Production Rate : 0.329830 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.582511
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.217711
  EX_pi_e : 0.761877
  EX_so4_e : 0.112790
  EX_k_e : 0.087427
  EX_fe3_e : 0.007194
  EX_mg2_e : 0.003886
  EX_ca2_e : 0.002331
  EX_cl_e : 0.002331
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.094751
  EX_co2_e : 36.594907
  EX_h_e : 6.423528
  Auxiliary production reaction : 0.329830
  EX_ac_e : 0.260761
  EX_etoh_e : 0.074711
  EX_ade_e : 0.012221
  DM_5drib_c : 0.000301
  DM_4crsol_c : 0.000100

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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