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 : 4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b1478 b1241 b3831 b3614 b0910 b3752 b3926 b4152 b0871 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b0907 b2690 b1759 b3945 b4138 b4123 b0621 b4381 b2406 b0114 b2492 b0904 b2835 b1380 b3918 b4042 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.553414 (mmol/gDw/h)
  Minimum Production Rate : 0.143499 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.967438
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.905228
  EX_pi_e : 0.820825
  EX_so4_e : 0.139361
  EX_k_e : 0.108023
  EX_fe2_e : 0.008888
  EX_mg2_e : 0.004801
  EX_ca2_e : 0.002881
  EX_cl_e : 0.002881
  EX_cu2_e : 0.000392
  EX_mn2_e : 0.000382
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.053597
  EX_co2_e : 26.503307
  EX_h_e : 8.703388
  EX_pyr_e : 1.822802
  EX_succ_e : 0.577096
  EX_ura_e : 0.248953
  Auxiliary production reaction : 0.143499
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000123

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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