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 : ins_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3942 b1732 b0474 b2518 b4069 b3708 b3008 b1479 b3115 b1849 b2296 b0030 b2407 b3844 b3236 b2883 b1779 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b4219 b1832 b1778 b4381 b2406 b0452 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1710 b2480 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453427 (mmol/gDw/h)
  Minimum Production Rate : 0.192267 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.457731
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.667568
  EX_pi_e : 0.437378
  EX_so4_e : 0.114182
  EX_k_e : 0.088506
  EX_fe2_e : 0.007282
  EX_mg2_e : 0.003933
  EX_ca2_e : 0.002360
  EX_cl_e : 0.002360
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.507336
  EX_co2_e : 36.279985
  EX_h_e : 6.528716
  EX_fum_e : 0.663937
  EX_ac_e : 0.263979
  Auxiliary production reaction : 0.192267
  EX_ade_e : 0.000305
  DM_mththf_c : 0.000203
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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