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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0871 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b1602 b0755 b3612 b2492 b0904 b1380 b2660 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.432608 (mmol/gDw/h)
  Minimum Production Rate : 2.508969 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.538831
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.672132
  EX_pi_e : 0.417297
  EX_so4_e : 0.108939
  EX_k_e : 0.084442
  EX_fe2_e : 0.006948
  EX_mg2_e : 0.003753
  EX_ca2_e : 0.002252
  EX_cl_e : 0.002252
  EX_cu2_e : 0.000307
  EX_mn2_e : 0.000299
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.140499
  EX_co2_e : 34.716511
  EX_h_e : 3.974977
  Auxiliary production reaction : 2.508969
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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