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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2779 b2925 b2097 b3617 b0030 b2407 b3236 b1982 b3946 b2210 b0825 b0261 b0411 b2913 b4381 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478959 (mmol/gDw/h)
  Minimum Production Rate : 1.276162 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.842792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.427629
  EX_pi_e : 3.014330
  EX_so4_e : 0.120612
  EX_k_e : 0.093489
  EX_fe2_e : 0.007693
  EX_mg2_e : 0.004155
  EX_cl_e : 0.002493
  EX_ca2_e : 0.002493
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.226000
  EX_co2_e : 24.823135
  EX_h_e : 6.380313
  EX_acald_e : 1.312807
  Auxiliary production reaction : 1.276162
  EX_gsn_e : 0.140410
  DM_oxam_c : 0.000536
  DM_5drib_c : 0.000321
  EX_glyc__R_e : 0.000160
  DM_4crsol_c : 0.000107

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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