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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b4069 b4384 b3752 b0512 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b3945 b1602 b4381 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458844 (mmol/gDw/h)
  Minimum Production Rate : 0.159020 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.895720
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.752120
  EX_fe3_e : 1.933738
  EX_pi_e : 0.919663
  EX_so4_e : 0.115546
  EX_k_e : 0.089563
  EX_mg2_e : 0.003980
  EX_ca2_e : 0.002388
  EX_cl_e : 0.002388
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.418823
  EX_co2_e : 39.039525
  EX_h_e : 6.895516
  EX_fe2_e : 1.926368
  EX_ac_e : 0.267133
  Auxiliary production reaction : 0.159020
  EX_ade_e : 0.000309
  DM_mththf_c : 0.000206
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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