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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b2291 b0261 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544491 (mmol/gDw/h)
  Minimum Production Rate : 0.814663 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.475580
  EX_o2_e : 271.350342
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.953773
  EX_pi_e : 2.154545
  EX_so4_e : 0.137114
  EX_k_e : 0.106281
  EX_mg2_e : 0.004723
  EX_ca2_e : 0.002834
  EX_cl_e : 0.002834
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991255
  EX_h2o_e : 546.257364
  EX_co2_e : 20.477949
  EX_ac_e : 2.068683
  Auxiliary production reaction : 0.814663
  DM_5drib_c : 0.000365
  DM_4crsol_c : 0.000121

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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