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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1238 b0517 b0121 b1982 b2797 b3117 b1814 b4471 b2440 b0595 b0675 b2361 b0261 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.553019 (mmol/gDw/h)
  Minimum Production Rate : 0.380723 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.073090
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.117246
  EX_pi_e : 1.294891
  EX_so4_e : 0.139261
  EX_k_e : 0.107945
  EX_fe2_e : 0.008882
  EX_mg2_e : 0.004797
  EX_ca2_e : 0.002878
  EX_cl_e : 0.002878
  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 : 51.905349
  EX_co2_e : 33.870810
  EX_h_e : 5.845280
  Auxiliary production reaction : 0.380723
  EX_alltn_e : 0.000619
  DM_5drib_c : 0.000371
  DM_4crsol_c : 0.000123
  EX_etha_e : 0.000045

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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