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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b4384 b2744 b1278 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4388 b4138 b4123 b0621 b2406 b0452 b2197 b3918 b0418 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.671314 (mmol/gDw/h)
  Minimum Production Rate : 0.075084 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 997.217196
  EX_h_e : 988.610823
  EX_o2_e : 275.397908
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.202259
  EX_pi_e : 0.647554
  EX_so4_e : 0.169050
  EX_k_e : 0.131036
  EX_mg2_e : 0.005824
  EX_ca2_e : 0.003494
  EX_cl_e : 0.003494
  EX_cu2_e : 0.000476
  EX_mn2_e : 0.000464
  EX_zn2_e : 0.000229
  EX_ni2_e : 0.000217
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 997.206414
  EX_h2o_e : 546.251319
  EX_co2_e : 26.840212
  EX_succ_e : 0.700041
  EX_ura_e : 0.476061
  Auxiliary production reaction : 0.075084
  DM_5drib_c : 0.000151
  DM_4crsol_c : 0.000150

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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