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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0160 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b4374 b0675 b2361 b2291 b0112 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.547534 (mmol/gDw/h)
  Minimum Production Rate : 1.639813 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.716872
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.192949
  EX_pi_e : 2.167968
  EX_so4_e : 0.137880
  EX_k_e : 0.106875
  EX_fe2_e : 0.008794
  EX_mg2_e : 0.004750
  EX_ca2_e : 0.002850
  EX_cl_e : 0.002850
  EX_cu2_e : 0.000388
  EX_mn2_e : 0.000378
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.183063
  EX_co2_e : 20.245508
  EX_h_e : 9.571181
  Auxiliary production reaction : 1.639813
  EX_ac_e : 1.260593
  DM_mththf_c : 0.000245
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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