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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2925 b2097 b3617 b0160 b1238 b2690 b1982 b0675 b2361 b3945 b4381 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448813 (mmol/gDw/h)
  Minimum Production Rate : 0.122920 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.378009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.216200
  EX_pi_e : 0.432927
  EX_so4_e : 0.113020
  EX_k_e : 0.087605
  EX_fe2_e : 0.007208
  EX_mg2_e : 0.003893
  EX_ca2_e : 0.002336
  EX_cl_e : 0.002336
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.875429
  EX_co2_e : 30.810368
  EX_h_e : 5.942963
  EX_ac_e : 1.080971
  DM_oxam_c : 0.369061
  DM_mththf_c : 0.368960
  Auxiliary production reaction : 0.122920
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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