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 : urdglyc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b0238 b0125 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b0521 b0477 b2797 b3117 b1814 b4471 b3616 b3589 b0507 b0511 b0114 b1539 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690532 (mmol/gDw/h)
  Minimum Production Rate : 0.256718 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.771129
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.403807
  EX_pi_e : 0.666092
  EX_so4_e : 0.173890
  EX_k_e : 0.134787
  EX_fe2_e : 0.011091
  EX_mg2_e : 0.005990
  EX_cl_e : 0.003594
  EX_ca2_e : 0.003594
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 43.952618
  EX_co2_e : 24.082054
  EX_h_e : 10.949251
  EX_ac_e : 2.968390
  DM_oxam_c : 0.432679
  Auxiliary production reaction : 0.256718
  EX_glyclt_e : 0.000462
  DM_mththf_c : 0.000309
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000154

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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