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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b3617 b2797 b3117 b1814 b4471 b4381 b2868 b0114 b2366 b0755 b3612 b2492 b0904 b1518 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434416 (mmol/gDw/h)
  Minimum Production Rate : 0.341625 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.904536
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.446716
  EX_pi_e : 1.102291
  EX_so4_e : 0.109395
  EX_k_e : 0.084795
  EX_fe2_e : 0.006977
  EX_mg2_e : 0.003769
  EX_cl_e : 0.002261
  EX_ca2_e : 0.002261
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.510983
  EX_co2_e : 36.492892
  EX_h_e : 5.405022
  EX_acald_e : 1.100394
  Auxiliary production reaction : 0.341625
  EX_xan_e : 0.011367
  EX_ade_e : 0.000292
  DM_mththf_c : 0.000195
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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