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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b2836 b4384 b2744 b3708 b3008 b3752 b3926 b0871 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b1602 b4381 b2868 b4064 b4464 b0114 b0886 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477829 (mmol/gDw/h)
  Minimum Production Rate : 0.109691 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.213496
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.711574
  EX_pi_e : 0.570595
  EX_so4_e : 0.120328
  EX_k_e : 0.093269
  EX_fe2_e : 0.007676
  EX_mg2_e : 0.004145
  EX_ca2_e : 0.002487
  EX_cl_e : 0.002487
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.007068
  EX_co2_e : 38.848091
  EX_h_e : 5.160901
  Auxiliary production reaction : 0.109678
  EX_ade_e : 0.000535
  DM_5drib_c : 0.000321
  DM_4crsol_c : 0.000107

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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