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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b2502 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b3665 b0675 b2361 b0822 b4381 b2406 b1727 b0114 b1539 b2492 b0904 b1533 b3927 b1912 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.640994 (mmol/gDw/h)
  Minimum Production Rate : 0.130740 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.622258
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.595312
  EX_pi_e : 0.879787
  EX_so4_e : 0.161415
  EX_k_e : 0.125118
  EX_fe2_e : 0.010295
  EX_mg2_e : 0.005561
  EX_ca2_e : 0.003336
  EX_cl_e : 0.003336
  EX_cu2_e : 0.000454
  EX_mn2_e : 0.000443
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.243135
  EX_co2_e : 26.695359
  EX_h_e : 8.331785
  EX_pyr_e : 1.883413
  Auxiliary production reaction : 0.130740
  DM_oxam_c : 0.016772
  EX_ade_e : 0.000431
  DM_mththf_c : 0.000287
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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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