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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4384 b3708 b3008 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b0030 b2407 b3844 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b0507 b2913 b4381 b2406 b0452 b0114 b0886 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610845 (mmol/gDw/h)
  Minimum Production Rate : 0.138411 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.597391
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.298668
  EX_pi_e : 1.142868
  EX_so4_e : 0.153823
  EX_k_e : 0.119233
  EX_fe2_e : 0.009811
  EX_mg2_e : 0.005299
  EX_ca2_e : 0.003179
  EX_cl_e : 0.003179
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.970810
  EX_co2_e : 26.497197
  EX_h_e : 8.145674
  EX_pyr_e : 2.106513
  Auxiliary production reaction : 0.138411
  EX_alltn_e : 0.002385
  DM_5drib_c : 0.002111
  DM_4crsol_c : 0.001837
  EX_glyclt_e : 0.001701

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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