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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b3945 b2943 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.716435 (mmol/gDw/h)
  Minimum Production Rate : 0.303422 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.244475
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.255344
  EX_pi_e : 1.297921
  EX_so4_e : 0.483835
  EX_k_e : 0.139843
  EX_fe2_e : 0.011507
  EX_mg2_e : 0.006215
  EX_cl_e : 0.003729
  EX_ca2_e : 0.003729
  EX_cu2_e : 0.000508
  EX_mn2_e : 0.000495
  EX_zn2_e : 0.000244
  EX_ni2_e : 0.000231
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.182332
  EX_co2_e : 26.013763
  EX_h_e : 8.265990
  EX_ac_e : 0.771233
  Auxiliary production reaction : 0.303422
  DM_oxam_c : 0.000802
  DM_5drib_c : 0.000481
  DM_4crsol_c : 0.000160

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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