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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2925 b2097 b2883 b0907 b2690 b1982 b3616 b3589 b0411 b3945 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408181 (mmol/gDw/h)
  Minimum Production Rate : 0.435362 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.831679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.510627
  EX_pi_e : 0.829095
  EX_so4_e : 0.102788
  EX_k_e : 0.079674
  EX_fe2_e : 0.006556
  EX_mg2_e : 0.003541
  EX_ca2_e : 0.002125
  EX_cl_e : 0.002125
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.451545
  EX_co2_e : 25.586365
  EX_h_e : 8.982345
  EX_pyr_e : 2.129508
  EX_acald_e : 1.445096
  EX_gsn_e : 0.446042
  Auxiliary production reaction : 0.435362
  EX_ade_e : 0.000275
  DM_mththf_c : 0.000183
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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