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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b0261 b0411 b1602 b2913 b4381 b3915 b0114 b0755 b3612 b0529 b2492 b0904 b3029 b1380 b1771 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359971 (mmol/gDw/h)
  Minimum Production Rate : 0.149547 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.353150
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.248651
  EX_pi_e : 0.646324
  EX_so4_e : 0.090648
  EX_k_e : 0.070264
  EX_fe3_e : 0.005781
  EX_mg2_e : 0.003123
  EX_ca2_e : 0.001874
  EX_cl_e : 0.001874
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 52.216496
  EX_co2_e : 35.393371
  EX_h_e : 6.375239
  EX_acald_e : 1.030925
  EX_his__L_e : 0.871086
  Auxiliary production reaction : 0.149547
  DM_5drib_c : 0.000242
  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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