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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b3553 b3399 b4382 b3846 b2341 b2744 b3708 b3008 b0871 b0160 b3124 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2868 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.740001 (mmol/gDw/h)
  Minimum Production Rate : 0.451481 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.392702
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.427159
  EX_pi_e : 2.068252
  EX_so4_e : 0.186347
  EX_k_e : 0.144443
  EX_fe2_e : 0.011885
  EX_mg2_e : 0.006420
  EX_ca2_e : 0.003852
  EX_cl_e : 0.003852
  EX_cu2_e : 0.000525
  EX_mn2_e : 0.000511
  EX_zn2_e : 0.000252
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.698326
  EX_co2_e : 25.460406
  EX_h_e : 7.331674
  Auxiliary production reaction : 0.451481
  EX_xan_e : 0.019363
  EX_hxan_e : 0.000828
  DM_5drib_c : 0.000497
  DM_4crsol_c : 0.000165

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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