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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b2502 b2744 b3708 b3008 b0871 b3124 b0120 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0114 b0886 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.766484 (mmol/gDw/h)
  Minimum Production Rate : 0.155879 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.435468
  EX_o2_e : 274.472138
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.454750
  EX_pi_e : 0.739355
  EX_so4_e : 0.193016
  EX_k_e : 0.149612
  EX_mg2_e : 0.006649
  EX_ca2_e : 0.003990
  EX_cl_e : 0.003990
  EX_cu2_e : 0.000543
  EX_mn2_e : 0.000530
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987690
  EX_h2o_e : 547.213426
  EX_co2_e : 26.001768
  DM_oxam_c : 0.176793
  DM_5drib_c : 0.156394
  DM_4crsol_c : 0.156050
  Auxiliary production reaction : 0.155879

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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