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 (2 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b1478 b1241 b0351 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1033 b1602 b4381 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 : 0.462221 (mmol/gDw/h)
  Minimum Production Rate : 1.953973 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.745506
  EX_o2_e : 283.200804
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.991946
  EX_pi_e : 0.445861
  EX_so4_e : 0.116396
  EX_k_e : 0.090222
  EX_mg2_e : 0.004010
  EX_ca2_e : 0.002406
  EX_cl_e : 0.002406
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992576
  EX_h2o_e : 547.368300
  EX_co2_e : 35.166036
  Auxiliary production reaction : 1.953973
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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