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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b0910 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b0160 b1238 b3236 b2690 b1982 b2210 b0675 b2361 b0822 b4388 b4381 b0112 b2868 b1727 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.275207 (mmol/gDw/h)
  Minimum Production Rate : 1.055223 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.977873
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.138624
  EX_pi_e : 2.375913
  EX_so4_e : 0.069303
  EX_k_e : 0.053719
  EX_fe2_e : 0.004420
  EX_mg2_e : 0.002387
  EX_ca2_e : 0.001432
  EX_cl_e : 0.001432
  EX_cu2_e : 0.000195
  EX_mn2_e : 0.000190
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_h2o_e : 47.081314
  EX_co2_e : 26.703790
  EX_h_e : 9.085041
  EX_pyr_e : 3.611390
  Auxiliary production reaction : 1.055223
  EX_ac_e : 0.833751
  EX_hxan_e : 0.000185
  DM_mththf_c : 0.000123
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000061

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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