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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b2836 b3553 b3399 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b3945 b1602 b0507 b2913 b4381 b2406 b1727 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359045 (mmol/gDw/h)
  Minimum Production Rate : 0.214044 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.347081
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.773014
  EX_pi_e : 0.346337
  EX_so4_e : 0.090415
  EX_k_e : 0.070083
  EX_fe2_e : 0.005767
  EX_mg2_e : 0.003115
  EX_cl_e : 0.001869
  EX_ca2_e : 0.001869
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 43.728648
  EX_co2_e : 32.660792
  EX_h_e : 9.507353
  EX_ac_e : 5.312945
  Auxiliary production reaction : 0.214044
  EX_hxan_e : 0.009797
  DM_5drib_c : 0.000241
  DM_4crsol_c : 0.000080

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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