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 (52 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1478 b2066 b0474 b2518 b1241 b0351 b4384 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2498 b1033 b1602 b2913 b0529 b2492 b0904 b1380 b1771 b1511 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505999 (mmol/gDw/h)
  Minimum Production Rate : 0.060058 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.939907
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.464749
  EX_pi_e : 0.488090
  EX_so4_e : 0.127421
  EX_k_e : 0.098768
  EX_fe2_e : 0.008127
  EX_mg2_e : 0.004390
  EX_ca2_e : 0.002634
  EX_cl_e : 0.002634
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.411789
  EX_co2_e : 39.049749
  EX_h_e : 4.649323
  Auxiliary production reaction : 0.060058
  DM_mththf_c : 0.000227
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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