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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b3617 b0030 b2407 b3844 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2406 b0112 b0452 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.508846 (mmol/gDw/h)
  Minimum Production Rate : 0.507526 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.202533
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.048750
  EX_pi_e : 2.013415
  EX_so4_e : 0.635664
  EX_k_e : 0.099323
  EX_fe2_e : 0.008173
  EX_mg2_e : 0.004414
  EX_ca2_e : 0.002649
  EX_cl_e : 0.002649
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.130162
  EX_co2_e : 21.541273
  EX_h_e : 9.401736
  EX_ac_e : 3.202196
  Auxiliary production reaction : 0.507526
  DM_oxam_c : 0.000569
  DM_5drib_c : 0.000341
  EX_glyclt_e : 0.000340
  DM_4crsol_c : 0.000113

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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