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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2883 b0120 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b4381 b3161 b0112 b4064 b4464 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.749907 (mmol/gDw/h)
  Minimum Production Rate : 0.172130 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.518863
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.304677
  EX_pi_e : 0.723364
  EX_so4_e : 0.188841
  EX_k_e : 0.146377
  EX_fe2_e : 0.012044
  EX_mg2_e : 0.006505
  EX_ca2_e : 0.003903
  EX_cl_e : 0.003903
  EX_cu2_e : 0.000532
  EX_mn2_e : 0.000518
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000242
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.676807
  EX_co2_e : 25.773827
  EX_h_e : 8.269160
  Auxiliary production reaction : 0.172130
  DM_oxam_c : 0.000839
  DM_5drib_c : 0.000503
  DM_4crsol_c : 0.000167

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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