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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b2925 b2097 b3617 b1238 b3236 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b0261 b4381 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459122 (mmol/gDw/h)
  Minimum Production Rate : 1.107601 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.705694
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.066081
  EX_pi_e : 1.550473
  EX_so4_e : 0.115616
  EX_k_e : 0.089617
  EX_fe2_e : 0.007374
  EX_mg2_e : 0.003983
  EX_ca2_e : 0.002390
  EX_cl_e : 0.002390
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.718754
  EX_co2_e : 29.103937
  EX_h_e : 6.601667
  Auxiliary production reaction : 1.107601
  EX_acald_e : 0.789598
  EX_pyr_e : 0.167867
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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