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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b0586 b4069 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b0160 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0822 b1727 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1912   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.728309 (mmol/gDw/h)
  Minimum Production Rate : 0.014899 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.390222
  EX_o2_e : 273.903710
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.785125
  EX_pi_e : 0.702532
  EX_so4_e : 0.635676
  EX_k_e : 0.142161
  EX_mg2_e : 0.006318
  EX_ca2_e : 0.003791
  EX_cl_e : 0.003791
  EX_cu2_e : 0.000516
  EX_mn2_e : 0.000503
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988303
  EX_h2o_e : 547.004017
  EX_co2_e : 25.932253
  EX_ac_e : 0.876284
  EX_cgly_e : 0.452273
  Auxiliary production reaction : 0.014899
  DM_5drib_c : 0.002517
  DM_4crsol_c : 0.002191

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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