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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2925 b2097 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0595 b0261 b2406 b0112 b0511 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b0515 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355026 (mmol/gDw/h)
  Minimum Production Rate : 0.056396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.109155
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.005028
  EX_pi_e : 0.455251
  EX_so4_e : 0.089403
  EX_k_e : 0.069299
  EX_fe2_e : 0.005702
  EX_mg2_e : 0.003080
  EX_ca2_e : 0.001848
  EX_cl_e : 0.001848
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.593359
  EX_co2_e : 29.182535
  EX_h_e : 7.374481
  EX_pyr_e : 3.791288
  EX_ac_e : 0.206691
  Auxiliary production reaction : 0.056396
  EX_xan_e : 0.000397
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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