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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b0160 b3236 b1982 b2210 b0675 b2361 b4388 b4381 b0112 b2868 b0114 b0755 b3612 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523409 (mmol/gDw/h)
  Minimum Production Rate : 0.989755 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.263496
  EX_nh4_e : 10.658089
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.463902
  EX_so4_e : 0.131805
  EX_k_e : 0.102166
  EX_fe2_e : 0.008406
  EX_mg2_e : 0.004541
  EX_ca2_e : 0.002724
  EX_cl_e : 0.002724
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.164117
  EX_co2_e : 23.369231
  EX_h_e : 10.424236
  EX_ac_e : 2.589139
  Auxiliary production reaction : 0.989755
  EX_xan_e : 0.013696
  EX_ade_e : 0.000352
  DM_mththf_c : 0.000234
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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