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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b0512 b2297 b2458 b2779 b0160 b2407 b1779 b1982 b3616 b3589 b0675 b2361 b0261 b2913 b4381 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418644 (mmol/gDw/h)
  Minimum Production Rate : 1.602307 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.942347
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.334776
  EX_pi_e : 2.006133
  EX_so4_e : 0.105423
  EX_k_e : 0.081716
  EX_fe2_e : 0.006724
  EX_mg2_e : 0.003632
  EX_ca2_e : 0.002179
  EX_cl_e : 0.002179
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.516906
  EX_co2_e : 24.230595
  EX_h_e : 11.532805
  EX_ac_e : 2.871958
  Auxiliary production reaction : 1.602307
  EX_alltn_e : 0.001634
  DM_5drib_c : 0.001447
  DM_4crsol_c : 0.001259
  EX_glyc__R_e : 0.000723

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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