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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b3708 b3008 b0871 b3617 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b0494 b1600 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.573664 (mmol/gDw/h)
  Minimum Production Rate : 1.382642 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.698905
  EX_nh4_e : 10.343447
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.701284
  EX_so4_e : 0.144460
  EX_k_e : 0.111975
  EX_fe2_e : 0.009214
  EX_mg2_e : 0.004977
  EX_ca2_e : 0.002986
  EX_cl_e : 0.002986
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.009512
  EX_co2_e : 22.034216
  EX_h_e : 6.653695
  Auxiliary production reaction : 1.382642
  EX_acald_e : 0.987229
  DM_5drib_c : 0.000385
  DM_4crsol_c : 0.000128

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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