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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2797 b3117 b1814 b4471 b3616 b3589 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.520740 (mmol/gDw/h)
  Minimum Production Rate : 0.510786 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.786694
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.199446
  EX_pi_e : 2.034666
  EX_so4_e : 0.641918
  EX_k_e : 0.101645
  EX_fe2_e : 0.008364
  EX_mg2_e : 0.004517
  EX_ca2_e : 0.002710
  EX_cl_e : 0.002710
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.864978
  EX_co2_e : 22.408749
  EX_h_e : 9.061925
  EX_ac_e : 2.744803
  Auxiliary production reaction : 0.510786
  EX_mththf_e : 0.000233
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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