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 (62 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4069 b4384 b2744 b3708 b3115 b1849 b2296 b0030 b2407 b2388 b1982 b2797 b3117 b1814 b4471 b3565 b0411 b4381 b2868 b0837 b0124 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.725046 (mmol/gDw/h)
  Minimum Production Rate : 0.307559 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.539154
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.370675
  EX_pi_e : 1.314503
  EX_so4_e : 0.182581
  EX_k_e : 0.141524
  EX_fe2_e : 0.011645
  EX_mg2_e : 0.006290
  EX_ca2_e : 0.003774
  EX_cl_e : 0.003774
  EX_cu2_e : 0.000514
  EX_mn2_e : 0.000501
  EX_zn2_e : 0.000247
  EX_ni2_e : 0.000234
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 49.465918
  EX_co2_e : 26.316300
  EX_h_e : 8.316804
  EX_ac_e : 0.422112
  Auxiliary production reaction : 0.307559
  EX_ade_e : 0.000488
  DM_mththf_c : 0.000325
  DM_5drib_c : 0.000163
  DM_4crsol_c : 0.000162

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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