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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b0945 b4382 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b2388 b1982 b0394 b2688 b2797 b3117 b1814 b4471 b2440 b0595 b0261 b2406 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0723 b3662 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.697806 (mmol/gDw/h)
  Minimum Production Rate : 0.090688 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.012828
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.387728
  EX_pi_e : 0.945173
  EX_so4_e : 0.483016
  EX_k_e : 0.136207
  EX_fe2_e : 0.011207
  EX_mg2_e : 0.006053
  EX_ca2_e : 0.003632
  EX_cl_e : 0.003632
  EX_cu2_e : 0.000495
  EX_mn2_e : 0.000482
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000225
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.923839
  EX_co2_e : 26.018966
  EX_h_e : 7.551564
  EX_ac_e : 0.713547
  EX_met__L_e : 0.216606
  EX_succ_e : 0.140074
  Auxiliary production reaction : 0.090688
  DM_5drib_c : 0.000468
  DM_4crsol_c : 0.000156
  EX_etha_e : 0.000056

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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