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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b3399 b2744 b3926 b0871 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2690 b3945 b1602 b2913 b4381 b0114 b0529 b2492 b0904 b1380 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390248 (mmol/gDw/h)
  Minimum Production Rate : 0.070745 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.943412
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.610264
  EX_pi_e : 0.517926
  EX_so4_e : 0.098272
  EX_k_e : 0.076174
  EX_fe2_e : 0.006268
  EX_mg2_e : 0.003385
  EX_cl_e : 0.002031
  EX_ca2_e : 0.002031
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 44.450605
  EX_co2_e : 28.085781
  EX_h_e : 8.956135
  EX_pyr_e : 5.045507
  Auxiliary production reaction : 0.070745
  EX_hxan_e : 0.010474
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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.

Last updated: 21-Sep-2023
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