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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2781 b0099 b0160 b2883 b1982 b3616 b3589 b2361 b2291 b0411 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.581073 (mmol/gDw/h)
  Minimum Production Rate : 1.114000 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.625162
  EX_nh4_e : 11.847493
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.560506
  EX_so4_e : 0.146326
  EX_k_e : 0.113421
  EX_fe2_e : 0.009333
  EX_mg2_e : 0.005041
  EX_cl_e : 0.003024
  EX_ca2_e : 0.003024
  EX_cu2_e : 0.000412
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.681646
  EX_co2_e : 21.079206
  EX_h_e : 12.874667
  EX_ac_e : 1.963582
  Auxiliary production reaction : 1.114000
  EX_ade_e : 0.000391
  DM_mththf_c : 0.000260
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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